From 797122da98837a90ece06560dfdebd3f08847349 Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Thu, 22 May 2025 15:04:24 -0400
Subject: [PATCH 01/19] Update dependencies and configs

---
 .make/.bumpversion.toml   |   2 +-
 .make/CHANGES_MAKEFILE.md |   5 +
 .make/Makefile            |   2 +-
 .make/base.make           | 416 +++++++++++++++++++++++++-------------
 Makefile.private.example  |   9 +
 noxfile.py                |  60 +++++-
 poetry.lock               |  59 +++++-
 pyproject.toml            |  74 +++++++
 8 files changed, 473 insertions(+), 154 deletions(-)

diff --git a/.make/.bumpversion.toml b/.make/.bumpversion.toml
index 79b246b..b65116a 100644
--- a/.make/.bumpversion.toml
+++ b/.make/.bumpversion.toml
@@ -1,6 +1,6 @@
 
 [tool.bumpversion]
-current_version = "0.4.0"
+current_version = "0.5.0"
 commit = true
 message = "Makefile version {new_version} released."
 tag = true
diff --git a/.make/CHANGES_MAKEFILE.md b/.make/CHANGES_MAKEFILE.md
index 20bccc5..9770eb8 100644
--- a/.make/CHANGES_MAKEFILE.md
+++ b/.make/CHANGES_MAKEFILE.md
@@ -5,6 +5,11 @@
 
 [//]: # (New changes here in list form)
 
+[0.5.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.5.0) (2025-03-11)
+-------------------------------------------------------------------------------------
+* Add venv support
+* Update and fix `poetry-install-auto` target
+
 [0.4.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.4.0) (2024-10-30)
 -------------------------------------------------------------------------------------
 
diff --git a/.make/Makefile b/.make/Makefile
index 08d0974..d4eb4f2 100644
--- a/.make/Makefile
+++ b/.make/Makefile
@@ -10,7 +10,7 @@
 # files to include.
 ########################################################################################
 PROJECT_PATH := $(dir $(abspath $(firstword $(MAKEFILE_LIST))))
-MAKEFILE_VERSION := 0.4.0
+MAKEFILE_VERSION := 0.5.0
 BUMP_TOOL := bump-my-version
 BUMP_CONFIG_FILE := $(PROJECT_PATH).bumpversion.toml
 
diff --git a/.make/base.make b/.make/base.make
index cd6622d..3f38651 100644
--- a/.make/base.make
+++ b/.make/base.make
@@ -3,7 +3,7 @@
 # If necessary, override the corresponding variable and/or target, or create new ones
 # in one of the following files, depending on the nature of the override :
 #
-# Makefile.variables, Makefile.targets or Makefile.private`,
+# Makefile.variables, Makefile.targets or Makefile.private,
 #
 # The only valid reason to modify this file is to fix a bug or to add new
 # files to include.
@@ -16,7 +16,7 @@ PROJECT_PATH := $(dir $(abspath $(firstword $(MAKEFILE_LIST))))
 MAKEFILE_NAME := $(word $(words $(MAKEFILE_LIST)),$(MAKEFILE_LIST))
 SHELL := /usr/bin/env bash
 BUMP_TOOL := bump-my-version
-MAKEFILE_VERSION := 0.4.0
+MAKEFILE_VERSION := 0.5.0
 DOCKER_COMPOSE ?= docker compose
 AUTO_INSTALL ?=
 
@@ -26,12 +26,22 @@ CONDA_TOOL := conda
 CONDA_ENVIRONMENT ?=
 CONDA_YES_OPTION ?=
 
+# Default environment to install package
+# Can be overridden in Makefile.private file
+DEFAULT_INSTALL_ENV ?=
+DEFAULT_POETRY_INSTALL_ENV ?=
+
 # Colors
 _SECTION := \033[1m\033[34m
 _TARGET  := \033[36m
 _NORMAL  := \033[0m
 
 .DEFAULT_GOAL := help
+
+# Project and Private variables and targets import to override variables for local
+# This is to make sure, sometimes the Makefile includes don't work.
+-include Makefile.variables
+-include Makefile.private
 ## -- Informative targets ------------------------------------------------------------------------------------------- ##
 
 .PHONY: all
@@ -70,150 +80,63 @@ targets: help
 version: ## display current version
 	@echo "version: $(APP_VERSION)"
 
-## -- Conda targets ------------------------------------------------------------------------------------------------- ##
+## -- Virtualenv targets -------------------------------------------------------------------------------------------- ##
 
-.PHONY: conda-install
-conda-install: ## Install Conda on your local machine
-	@echo "Looking for [$(CONDA_TOOL)]..."; \
-	$(CONDA_TOOL) --version; \
-	if [ $$? != "0" ]; then \
-		echo " "; \
-		echo "Your defined Conda tool [$(CONDA_TOOL)] has not been found."; \
-		echo " "; \
-		echo "If you know you already have [$(CONDA_TOOL)] or some other Conda tool installed,"; \
-		echo "Check your [CONDA_TOOL] variable in the Makefile.private for typos."; \
-		echo " "; \
-		echo "If your conda tool has not been initiated through your .bashrc file,"; \
-		echo "consider using the full path to its executable instead when"; \
-		echo "defining your [CONDA_TOOL] variable"; \
-		echo " "; \
-		echo "If in doubt, don't install Conda and manually create and activate"; \
-		echo "your own Python environment."; \
-		echo " "; \
-		echo -n "Would you like to install Miniconda ? [y/N]: "; \
-		read ans; \
-		case $$ans in \
-			[Yy]*) \
-				echo "Fetching and installing miniconda"; \
-				echo " "; \
-				wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh; \
-    			bash ~/miniconda.sh -b -p $${HOME}/.conda; \
-    			export PATH=$${HOME}/.conda/bin:$$PATH; \
-    			conda init; \
-				/usr/bin/rm ~/miniconda.sh; \
-				;; \
-			*) \
-				echo "Skipping installation."; \
-				echo " "; \
-				;; \
-		esac; \
-	else \
-		echo "Conda tool [$(CONDA_TOOL)] has been found, skipping installation"; \
-	fi;
+VENV_PATH := $(PROJECT_PATH).venv
+VENV_ACTIVATE := $(VENV_PATH)/bin/activate
 
-.PHONY: conda-create-env
-conda-create-env: conda-install ## Create a local Conda environment based on `environment.yml` file
-	@$(CONDA_TOOL) env create $(CONDA_YES_OPTION) -f environment.yml
+.PHONY: venv-create
+venv-create: ## Create a virtualenv '.venv' at the root of the project folder
+	@virtualenv $(VENV_PATH)
+	@make -s venv-activate
 
-.PHONY: conda-env-info
-conda-env-info: ## Print information about active Conda environment using <CONDA_TOOL>
-	@$(CONDA_TOOL) info
+.PHONY: venv-activate
+venv-activate: ## Print out the shell command to activate the project's virtualenv.
+	@echo "source $(VENV_ACTIVATE)"
 
-.PHONY: _conda-poetry-install
-_conda-poetry-install:
-	@$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) python --version;  \
-	if [ $$? != "0" ]; then \
-		echo "Target environment doesn't seem to exist..."; \
-		if [ "$(AUTO_INSTALL)" = "true" ]; then \
-				ans="y";\
-		else \
-			echo ""; \
-			echo -n "Do you want to create it? [y/N] "; \
-			read ans; \
-		fi; \
-		case $$ans in \
-			[Yy]*) \
-				echo "Creating conda environment : [$(CONDA_ENVIRONMENT)]"; \
-				make -s conda-create-env; \
-				;; \
-			*) \
-				echo "Exiting..."; \
-				exit 1;\
-				;; \
-		esac;\
-	fi;
-	$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) $(CONDA_TOOL) install $(CONDA_YES_OPTION) -c conda-forge poetry; \
-	CURRENT_VERSION=$$($(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) poetry --version | awk '{print $$NF}' | tr -d ')'); \
-	REQUIRED_VERSION="1.6.0"; \
-	if [ "$$(printf '%s\n' "$$REQUIRED_VERSION" "$$CURRENT_VERSION" | sort -V | head -n1)" != "$$REQUIRED_VERSION" ]; then \
-		echo "Poetry installed version $$CURRENT_VERSION is less than minimal version $$REQUIRED_VERSION, fixing urllib3 version to prevent problems"; \
-		$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT)  poetry add "urllib3<2.0.0"; \
-	fi;
+## -- Poetry targets ------------------------------------------------------------------------------------------------ ##
 
-.PHONY:conda-poetry-install
-conda-poetry-install: ## Install Poetry in the project's Conda environment. Will fail if Conda is not found
+.PHONY: poetry-install-auto
+poetry-install-auto: ## Install Poetry in Conda environment, or with pipx in a virtualenv if Conda not found
 	@poetry --version; \
     	if [ $$? != "0" ]; then \
 			echo "Poetry not found, proceeding to install Poetry..."; \
-			echo "Looking for [$(CONDA_TOOL)]...";\
-			$(CONDA_TOOL) --version; \
-			if [ $$? != "0" ]; then \
-				echo "$(CONDA_TOOL) not found; Poetry will not be installed"; \
-			else \
-				echo "Installing Poetry with Conda in [$(CONDA_ENVIRONMENT)] environment"; \
-				make -s _conda-poetry-install; \
-			fi; \
-		else \
-			echo ""; \
-			echo "Poetry has been found on this system :"; \
-			echo "    Install location: $$(which poetry)"; \
-			echo ""; \
-			if [ "$(AUTO_INSTALL)" = "true" ]; then \
-				ans="y";\
-			else \
-				echo -n "Would you like to install poetry in the project's conda environment anyway ? [y/N]: "; \
-				read ans; \
+			if [ "$(DEFAULT_POETRY_INSTALL_ENV)" == "conda" ]; then \
+				ans_where="conda"; \
+			elif [ "$(DEFAULT_POETRY_INSTALL_ENV)" == "venv" ]; then \
+				ans_where="venv"; \
+			else\
+				echo -n "Where would you like to install Poetry, in a dedicated virtualenv (venv), or a conda environment? [venv/conda]: "; \
+				read ans_where; \
 			fi; \
-			case $$ans in \
-				[Yy]*) \
-					echo "Installing Poetry with Conda in [$(CONDA_ENVIRONMENT)] environment"; \
-					make -s _conda-poetry-install; \
+			case $$ans_where in \
+				"venv" | "Venv" |"VENV") \
+					make AUTO_INSTALL=true -s poetry-install-venv; \
 					;; \
-				*) \
-					echo "Skipping installation."; \
-					echo " "; \
+				"conda" | "Conda" | "CONDA") \
+					echo "Installing poetry with Conda"; \
+					make AUTO_INSTALL=true -s conda-poetry-install; \
 					;; \
+				*) \
+					echo ""; \
+					echo -e "\e[1;39;41m-- WARNING --\e[0m Option $$ans_how not found, exiting process."; \
+					echo ""; \
+					exit 1; \
 			esac; \
 		fi;
 
-.PHONY: conda-poetry-uninstall
-conda-poetry-uninstall: ## Uninstall Poetry located in currently active Conda environment
-	$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) $(CONDA_TOOL) remove $(CONDA_YES_OPTION) poetry
-
-.PHONY: conda-clean-env
-conda-clean-env: ## Completely removes local project's Conda environment
-	$(CONDA_TOOL) env remove $(CONDA_YES_OPTION) -n $(CONDA_ENVIRONMENT)
+.PHONY: _pipx_install_poetry
+_pipx_install_poetry:
+	@output="$$(pip install poetry --dry-run)"; \
+	if echo "$$output" | grep -q computecanada ; then \
+		echo ""; \
+		echo -e "\e[1;39;41m-- WARNING --\e[0m Compute Canada (DRAC) environment detected: Installing Poetry < 2.0.0"; \
+		echo ""; \
+		pipx install 'poetry<2.0.0' ; \
+	else \
+		pipx install poetry ; \
+	fi;
 
-## -- Poetry targets ------------------------------------------------------------------------------------------------ ##
-
-.PHONY: poetry-install-auto
-poetry-install-auto: ## Install Poetry in Conda environment, or with pipx in a virtualenv if Conda not found
-	@poetry --version; \
-    	if [ $$? != "0" ]; then \
-			echo "Poetry not found, proceeding to install Poetry..."; \
-			echo "Looking for [$(CONDA_TOOL)]...";\
-			$(CONDA_TOOL) --version; \
-            if [ $$? != "0" ]; then \
-				echo "$(CONDA_TOOL) not found, trying with pipx"; \
-				pipx --version; \
-				if [ $$? != "0" ]; then \
-					make AUTO_INSTALL=true -s poetry-install-venv; \
-				fi; \
-			else \
-				echo "Installing poetry with Conda"; \
-				make AUTO_INSTALL=true -s conda-poetry-install; \
-			fi; \
-		fi;
 
 .PHONY: poetry-install
 poetry-install: ## Install standalone Poetry using pipx. Will ask where to install pipx.
@@ -267,7 +190,7 @@ poetry-install: ## Install standalone Poetry using pipx. Will ask where to insta
 					esac; \
 				else \
 					echo "Installing Poetry"; \
-					pipx install poetry; \
+					make -s _pipx_install_poetry; \
 				fi; \
 				;; \
 			*) \
@@ -288,8 +211,10 @@ poetry-install-venv: ## Install standalone Poetry. Will install pipx in $HOME/.p
 		source $(PIPX_VENV_PATH)/bin/activate; \
 		pip3 install pipx; \
 		pipx ensurepath; \
+		source $(PIPX_VENV_PATH)/bin/activate && make -s _pipx_install_poetry ; \
+	else \
+		make -s _pipx_install_poetry ; \
 	fi;
-	source $(PIPX_VENV_PATH)/bin/activate && pipx install poetry
 
 .PHONY: poetry-install-local
 poetry-install-local: ## Install standalone Poetry. Will install pipx with locally available pip.
@@ -300,7 +225,7 @@ poetry-install-local: ## Install standalone Poetry. Will install pipx with local
 		pipx ensurepath; \
 	fi;
 	@echo "Installing Poetry"
-	@pipx install poetry
+	@make -s _pipx_install_poetry
 
 
 .PHONY: poetry-env-info
@@ -319,6 +244,10 @@ poetry-create-env: ## Create a Poetry managed environment for the project (Outsi
 	@echo "Use <poetry --help> and <poetry list> for more information"
 	@echo""
 
+.PHONY: poetry-activate
+poetry-activate: ## Print the shell command to activate the project's poetry env.
+	poetry env activate
+
 .PHONY: poetry-remove-env
 poetry-remove-env: ## Remove current project's Poetry managed environment.
 	@if [ "$(AUTO_INSTALL)" = "true" ]; then \
@@ -339,6 +268,10 @@ poetry-remove-env: ## Remove current project's Poetry managed environment.
 			echo "If the active environment listed above is a Conda environment,"; \
 			echo "Choosing to delete it will have no effect; use the target <make conda-clean-env>"; \
 			echo""; \
+			echo""; \
+			echo "If the active environment listed above is a venv environment,"; \
+			echo "Choosing to delete it will have no effect; use the bash command $ rm -rf <PATH_TO_VENV>"; \
+			echo""; \
 			echo -n "Would you like delete the environment listed above? [y/N]: "; \
 			read ans_env; \
 		else \
@@ -370,7 +303,15 @@ poetry-uninstall: poetry-remove-env ## Uninstall pipx-installed Poetry and the c
 	fi; \
 	case $$ans in \
 		[Yy]*) \
-			pipx uninstall poetry; \
+			pipx --version ; \
+			if [ $$? != "0" ]; then \
+				echo "" ; \
+				echo "Pipx not found globally, trying with $(PIPX_VENV_PATH) env" ;\
+				echo "" ; \
+				source $(PIPX_VENV_PATH)/bin/activate && pipx uninstall poetry ; \
+			else \
+				pipx uninstall poetry ; \
+				fi; \
 			;; \
 		*) \
 			echo "Skipping uninstallation."; \
@@ -435,32 +376,217 @@ poetry-uninstall-venv: poetry-remove-env ## Uninstall pipx-installed Poetry, the
 			;; \
 	esac; \
 
-## -- Install targets (All install targets will install Poetry if not found using `make poetry-install-auto`)-------- ##
+## -- Conda targets ------------------------------------------------------------------------------------------------- ##
+
+.PHONY: conda-install
+conda-install: ## Install Conda on your local machine
+	@echo "Looking for [$(CONDA_TOOL)]..."; \
+	$(CONDA_TOOL) --version; \
+	if [ $$? != "0" ]; then \
+		echo " "; \
+		echo "Your defined Conda tool [$(CONDA_TOOL)] has not been found."; \
+		echo " "; \
+		echo "If you know you already have [$(CONDA_TOOL)] or some other Conda tool installed,"; \
+		echo "Check your [CONDA_TOOL] variable in the Makefile.private for typos."; \
+		echo " "; \
+		echo "If your conda tool has not been initiated through your .bashrc file,"; \
+		echo "consider using the full path to its executable instead when"; \
+		echo "defining your [CONDA_TOOL] variable"; \
+		echo " "; \
+		echo "If in doubt, don't install Conda and manually create and activate"; \
+		echo "your own Python environment."; \
+		echo " "; \
+		echo -n "Would you like to install Miniconda ? [y/N]: "; \
+		read ans; \
+		case $$ans in \
+			[Yy]*) \
+				echo "Fetching and installing miniconda"; \
+				echo " "; \
+				wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh; \
+    			bash ~/miniconda.sh -b -p $${HOME}/.conda; \
+    			export PATH=$${HOME}/.conda/bin:$$PATH; \
+    			conda init; \
+				/usr/bin/rm ~/miniconda.sh; \
+				;; \
+			*) \
+				echo "Skipping installation."; \
+				echo " "; \
+				;; \
+		esac; \
+	else \
+		echo "Conda tool [$(CONDA_TOOL)] has been found, skipping installation"; \
+	fi;
+
+.PHONY: conda-create-env
+conda-create-env: conda-install ## Create a local Conda environment based on 'environment.yml' file
+	@$(CONDA_TOOL) env create $(CONDA_YES_OPTION) -f environment.yml
+
+.PHONY: conda-env-info
+conda-env-info: ## Print information about active Conda environment using <CONDA_TOOL>
+	@$(CONDA_TOOL) info
+
+.PHONY: conda-activate
+conda-activate: ## Print the shell command to activate the project's Conda env.
+	@echo "$(CONDA_TOOL) activate $(CONDA_ENVIRONMENT)"
+
+.PHONY: _conda-poetry-install
+_conda-poetry-install:
+	@$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) python --version;  \
+	if [ $$? != "0" ]; then \
+		echo "Target environment doesn't seem to exist..."; \
+		if [ "$(AUTO_INSTALL)" = "true" ]; then \
+				ans="y";\
+		else \
+			echo ""; \
+			echo -n "Do you want to create it? [y/N] "; \
+			read ans; \
+		fi; \
+		case $$ans in \
+			[Yy]*) \
+				echo "Creating conda environment : [$(CONDA_ENVIRONMENT)]"; \
+				make -s conda-create-env; \
+				;; \
+			*) \
+				echo "Exiting..."; \
+				exit 1;\
+				;; \
+		esac;\
+	fi;
+	$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) $(CONDA_TOOL) install $(CONDA_YES_OPTION) -c conda-forge poetry; \
+	CURRENT_VERSION=$$($(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) poetry --version | awk '{print $$NF}' | tr -d ')'); \
+	REQUIRED_VERSION="1.6.0"; \
+	if [ "$$(printf '%s\n' "$$REQUIRED_VERSION" "$$CURRENT_VERSION" | sort -V | head -n1)" != "$$REQUIRED_VERSION" ]; then \
+		echo "Poetry installed version $$CURRENT_VERSION is less than minimal version $$REQUIRED_VERSION, fixing urllib3 version to prevent problems"; \
+		$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT)  poetry add "urllib3<2.0.0"; \
+	fi;
+
+.PHONY:conda-poetry-install
+conda-poetry-install: ## Install Poetry in the project's Conda environment. Will fail if Conda is not found
+	@poetry --version; \
+    	if [ $$? != "0" ]; then \
+			echo "Poetry not found, proceeding to install Poetry..."; \
+			echo "Looking for [$(CONDA_TOOL)]...";\
+			$(CONDA_TOOL) --version; \
+			if [ $$? != "0" ]; then \
+				echo "$(CONDA_TOOL) not found; Poetry will not be installed"; \
+			else \
+				echo "Installing Poetry with Conda in [$(CONDA_ENVIRONMENT)] environment"; \
+				make -s _conda-poetry-install; \
+			fi; \
+		else \
+			echo ""; \
+			echo "Poetry has been found on this system :"; \
+			echo "    Install location: $$(which poetry)"; \
+			echo ""; \
+			if [ "$(AUTO_INSTALL)" = "true" ]; then \
+				ans="y";\
+			else \
+				echo -n "Would you like to install poetry in the project's conda environment anyway ? [y/N]: "; \
+				read ans; \
+			fi; \
+			case $$ans in \
+				[Yy]*) \
+					echo "Installing Poetry with Conda in [$(CONDA_ENVIRONMENT)] environment"; \
+					make -s _conda-poetry-install; \
+					;; \
+				*) \
+					echo "Skipping installation."; \
+					echo " "; \
+					;; \
+			esac; \
+		fi;
+
+.PHONY: conda-poetry-uninstall
+conda-poetry-uninstall: ## Uninstall Poetry located in currently active Conda environment
+	$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) $(CONDA_TOOL) remove $(CONDA_YES_OPTION) poetry
+
+.PHONY: conda-clean-env
+conda-clean-env: ## Completely removes local project's Conda environment
+	$(CONDA_TOOL) env remove $(CONDA_YES_OPTION) -n $(CONDA_ENVIRONMENT)
+
+## -- Install targets (All install targets will install Poetry if not found using 'make poetry-install-auto')-------- ##
+
+POETRY_COMMAND := poetry
+
+ifeq ($(DEFAULT_INSTALL_ENV),venv)
+POETRY_COMMAND := source $(VENV_ACTIVATE) && poetry
+else ifeq ($(DEFAULT_INSTALL_ENV),poetry)
+POETRY_COMMAND := poetry
+else ifeq ($(DEFAULT_INSTALL_ENV),conda)
+POETRY_COMMAND := $(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) poetry
+endif
+
+.PHONY: _check-env
+_check-env:
+	@if ! [ $(DEFAULT_INSTALL_ENV) ]; then \
+		echo -e "\e[1;39;41m-- WARNING --\e[0m No installation environment have been defined." ; \
+		echo "" ; \
+		echo "Defaulting to Poetry managed environment - Poetry will either use activated environment, or '.venv'," ; \
+		echo "if found, or create and manage it's own environment if not." ; \
+	elif [ $(DEFAULT_INSTALL_ENV) = "venv" ]; then \
+		if [ ! -f $(VENV_ACTIVATE) ]; then \
+			make -s venv-create ;\
+		fi; \
+	elif [ $(DEFAULT_INSTALL_ENV) = "conda" ]; then \
+		if ! $(CONDA_TOOL) env list | grep -q $(CONDA_ENVIRONMENT) ; then \
+			make -s conda-create-env ; \
+		fi; \
+	fi;
+
+.PHONY: _remind-env-activate
+_remind-env-activate:
+	@echo ""
+	@echo "Activate your environment using the following command:"
+	@echo ""
+	@if ! [ $(DEFAULT_INSTALL_ENV) ] || [ $(DEFAULT_INSTALL_ENV) = "poetry" ]; then \
+		make -s poetry-env-activate ; \
+		echo "" ; \
+		echo "You can also use the eval bash command : eval \$$(make poetry-activate)"; \
+		echo "" ; \
+		echo "The environment can also be used through the 'poetry run <command>' command."; \
+		echo "" ; \
+		echo "    Ex: poetry run python <path_to_script>"; \
+	elif [ $(DEFAULT_INSTALL_ENV) = "venv" ]; then \
+		make -s venv-activate ; \
+		echo "" ; \
+		echo "You can also use the eval bash command : eval \$$(make venv-activate)"; \
+	elif [ $(DEFAULT_INSTALL_ENV) = "conda" ]; then \
+		make -s conda-activate ; \
+		echo "" ; \
+		echo "You can also use the eval bash command : eval \$$(make conda-activate)"; \
+	fi;
+	@echo ""
+
+test-echo:
+	@echo "use the eval bash command : eval \$$(make poetry-activate)"
 
 .PHONY: install
 install: install-precommit ## Install the application package, developer dependencies and pre-commit hook
 
 .PHONY: install-precommit
-install-precommit: install-dev## Install the pre-commit hooks (also installs developer dependencies)
+install-precommit: install-dev ## Install the pre-commit hooks (also installs developer dependencies)
 	@if [ -f .git/hooks/pre-commit ]; then \
 		echo "Pre-commit hook found"; \
 	else \
 	  	echo "Pre-commit hook not found, proceeding to configure it"; \
-		poetry run pre-commit install; \
+		$(POETRY_COMMAND) run pre-commit install; \
 	fi;
 
 .PHONY: install-dev
-install-dev: poetry-install-auto ## Install the application along with developer dependencies
-	@poetry install --with dev
+install-dev: poetry-install-auto _check-env ## Install the application along with developer dependencies
+	@$(POETRY_COMMAND) install --with dev
+	@make -s _remind-env-activate
 
 .PHONY: install-with-lab
-install-with-lab: poetry-install-auto ## Install the application and it's dev dependencies, including Jupyter Lab
-	@poetry install --with dev --with lab
+install-with-lab: poetry-install-auto _check-env ## Install the application and it's dev dependencies, including Jupyter Lab
+	@$(POETRY_COMMAND) install --with dev --with lab
+	@make -s _remind-env-activate
 
 
 .PHONY: install-package
-install-package: poetry-install-auto ## Install the application package only
-	@poetry install
+install-package: poetry-install-auto _check-env ## Install the application package only
+	@$(POETRY_COMMAND) install
+	@make -s _remind-env-activate
 
 ## -- Versioning targets -------------------------------------------------------------------------------------------- ##
 
@@ -472,7 +598,7 @@ ifeq ($(filter dry, $(MAKECMDGOALS)), dry)
 endif
 
 .PHONY: dry
-dry: ## Add the dry target for a preview of changes; ex. `make bump-major dry`
+dry: ## Add the dry target for a preview of changes; ex. 'make bump-major dry'
 	@-echo > /dev/null
 
 .PHONY: bump-major
diff --git a/Makefile.private.example b/Makefile.private.example
index be83cd0..278f083 100644
--- a/Makefile.private.example
+++ b/Makefile.private.example
@@ -24,5 +24,14 @@ DOCKER_COMPOSE := docker compose
 # a 'true' value will automatically install/remove without asking beforehand.
 AUTO_INSTALL := false
 
+# The default environment to use. The choices are as follow: [venv, poetry, conda]
+# If this is not set, the makefile will use the `poetry` command without activating
+# an environment before hand.
+DEFAULT_INSTALL_ENV := conda
+
+# The default environment where Poetry will be installed. The choices are as follow: [venv, conda]
+# If this is not set, the makefile will ask the user where they want to install Poetry
+DEFAULT_POETRY_INSTALL_ENV := venv
+
 ## -- Private targets ------------------------------------------------------------------------------------------------##
 
diff --git a/noxfile.py b/noxfile.py
index f5dee8f..035337a 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -1,22 +1,28 @@
+import re
 from pathlib import Path
 
 import nox
 
+ARG_RE = re.compile(r"^-[-\w=]+$")  # e.g. "-k", "--maxfail=1", "tests/foo.py"
+
 nox.options.reuse_existing_virtualenvs = True  # Reuse virtual environments
 nox.options.sessions = ["precommit"]
 
 
 def get_paths(session):
     package_path = Path(session.bin).parent.parent.parent
+    main_package = package_path / "geospatial_tools"
+    tests = package_path / "tests"
+    scripts = package_path / "scripts"
     return {
         "all": [
-            package_path / "geospatial_tools",
-            package_path / "tests",
-            package_path / "scripts",
+            main_package,
+            tests,
+            scripts,
         ],
         "module": [
-            package_path / "geospatial_tools",
-            package_path / "scripts",
+            main_package,
+            scripts,
         ],
     }
 
@@ -80,6 +86,8 @@ def check(session):
 @nox.session()
 def fix(session):
     paths = get_paths(session)
+    session.run("poetry", "run", "autoflake", "-v", *paths["all"], external=True)
+    session.run("poetry", "run", "autopep8", *paths["all"], external=True)
     session.run("poetry", "run", "black", *paths["all"], external=True)
     session.run("poetry", "run", "isort", *paths["all"], external=True)
     session.run("poetry", "run", "flynt", *paths["all"], external=True)
@@ -100,12 +108,30 @@ def precommit(session):
     session.run("poetry", "run", "pre-commit", "run", "--all-files", external=True)
 
 
+@nox.session()
+def autoflake(session):
+    paths = get_paths(session)
+    session.run("poetry", "run", "autoflake", "-v", *paths["all"], external=True)
+
+
+@nox.session()
+def autopep(session):
+    paths = get_paths(session)
+    session.run("poetry", "run", "autopep8", *paths["all"], external=True)
+
+
 @nox.session()
 def black(session):
     paths = get_paths(session)
     session.run("poetry", "run", "black", "--check", *paths["all"], external=True)
 
 
+@nox.session(name="black-fix")
+def black_fix(session):
+    paths = get_paths(session)
+    session.run("poetry", "run", "black", *paths["all"], external=True)
+
+
 @nox.session()
 def isort(session):
     paths = get_paths(session)
@@ -118,6 +144,24 @@ def flynt(session):
     session.run("poetry", "run", "flynt", *paths["all"], external=True)
 
 
+@nox.session(name="ruff-lint")
+def ruff_lint(session):
+    paths = get_paths(session)
+    session.run("poetry", "run", "ruff", "check", *paths["all"], external=True)
+
+
+@nox.session(name="ruff-fix")
+def ruff_fix(session):
+    paths = get_paths(session)
+    session.run("poetry", "run", "ruff", "check", "--fix", *paths["all"], external=True)
+
+
+@nox.session(name="ruff-format")
+def ruff_format(session):
+    paths = get_paths(session)
+    session.run("poetry", "run", "ruff", "format", *paths["all"], external=True)
+
+
 @nox.session()
 def test(session):
     session.run("poetry", "run", "pytest", external=True)
@@ -125,8 +169,12 @@ def test(session):
 
 @nox.session()
 def test_custom(session):
+    for a in session.posargs:
+        if not ARG_RE.match(a):
+            session.error(f"unsafe pytest argument detected: {a!r}")
+
     session.run(
-        "poetry", "run", "pytest", external=True, *session.posargs
+        "poetry", "run", "python", "-m", "pytest", external=True, *session.posargs
     )  # Pass additional arguments directly to pytest
 
 
diff --git a/poetry.lock b/poetry.lock
index 0ddd3da..5c0cbdc 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -225,6 +225,36 @@ docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphi
 tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
 tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
 
+[[package]]
+name = "autoflake"
+version = "2.3.1"
+description = "Removes unused imports and unused variables"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "autoflake-2.3.1-py3-none-any.whl", hash = "sha256:3ae7495db9084b7b32818b4140e6dc4fc280b712fb414f5b8fe57b0a8e85a840"},
+    {file = "autoflake-2.3.1.tar.gz", hash = "sha256:c98b75dc5b0a86459c4f01a1d32ac7eb4338ec4317a4469515ff1e687ecd909e"},
+]
+
+[package.dependencies]
+pyflakes = ">=3.0.0"
+tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
+
+[[package]]
+name = "autopep8"
+version = "2.3.2"
+description = "A tool that automatically formats Python code to conform to the PEP 8 style guide"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "autopep8-2.3.2-py2.py3-none-any.whl", hash = "sha256:ce8ad498672c845a0c3de2629c15b635ec2b05ef8177a6e7c91c74f3e9b51128"},
+    {file = "autopep8-2.3.2.tar.gz", hash = "sha256:89440a4f969197b69a995e4ce0661b031f455a9f776d2c5ba3dbd83466931758"},
+]
+
+[package.dependencies]
+pycodestyle = ">=2.12.0"
+tomli = {version = "*", markers = "python_version < \"3.11\""}
+
 [[package]]
 name = "babel"
 version = "2.16.0"
@@ -4269,6 +4299,33 @@ files = [
     {file = "rpds_py-0.20.0.tar.gz", hash = "sha256:d72a210824facfdaf8768cf2d7ca25a042c30320b3020de2fa04640920d4e121"},
 ]
 
+[[package]]
+name = "ruff"
+version = "0.11.10"
+description = "An extremely fast Python linter and code formatter, written in Rust."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "ruff-0.11.10-py3-none-linux_armv6l.whl", hash = "sha256:859a7bfa7bc8888abbea31ef8a2b411714e6a80f0d173c2a82f9041ed6b50f58"},
+    {file = "ruff-0.11.10-py3-none-macosx_10_12_x86_64.whl", hash = "sha256:968220a57e09ea5e4fd48ed1c646419961a0570727c7e069842edd018ee8afed"},
+    {file = "ruff-0.11.10-py3-none-macosx_11_0_arm64.whl", hash = "sha256:1067245bad978e7aa7b22f67113ecc6eb241dca0d9b696144256c3a879663bca"},
+    {file = "ruff-0.11.10-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f4854fd09c7aed5b1590e996a81aeff0c9ff51378b084eb5a0b9cd9518e6cff2"},
+    {file = "ruff-0.11.10-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:8b4564e9f99168c0f9195a0fd5fa5928004b33b377137f978055e40008a082c5"},
+    {file = "ruff-0.11.10-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:5b6a9cc5b62c03cc1fea0044ed8576379dbaf751d5503d718c973d5418483641"},
+    {file = "ruff-0.11.10-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:607ecbb6f03e44c9e0a93aedacb17b4eb4f3563d00e8b474298a201622677947"},
+    {file = "ruff-0.11.10-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:7b3a522fa389402cd2137df9ddefe848f727250535c70dafa840badffb56b7a4"},
+    {file = "ruff-0.11.10-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:2f071b0deed7e9245d5820dac235cbdd4ef99d7b12ff04c330a241ad3534319f"},
+    {file = "ruff-0.11.10-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:4a60e3a0a617eafba1f2e4186d827759d65348fa53708ca547e384db28406a0b"},
+    {file = "ruff-0.11.10-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:da8ec977eaa4b7bf75470fb575bea2cb41a0e07c7ea9d5a0a97d13dbca697bf2"},
+    {file = "ruff-0.11.10-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:ddf8967e08227d1bd95cc0851ef80d2ad9c7c0c5aab1eba31db49cf0a7b99523"},
+    {file = "ruff-0.11.10-py3-none-musllinux_1_2_i686.whl", hash = "sha256:5a94acf798a82db188f6f36575d80609072b032105d114b0f98661e1679c9125"},
+    {file = "ruff-0.11.10-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:3afead355f1d16d95630df28d4ba17fb2cb9c8dfac8d21ced14984121f639bad"},
+    {file = "ruff-0.11.10-py3-none-win32.whl", hash = "sha256:dc061a98d32a97211af7e7f3fa1d4ca2fcf919fb96c28f39551f35fc55bdbc19"},
+    {file = "ruff-0.11.10-py3-none-win_amd64.whl", hash = "sha256:5cc725fbb4d25b0f185cb42df07ab6b76c4489b4bfb740a175f3a59c70e8a224"},
+    {file = "ruff-0.11.10-py3-none-win_arm64.whl", hash = "sha256:ef69637b35fb8b210743926778d0e45e1bffa850a7c61e428c6b971549b5f5d1"},
+    {file = "ruff-0.11.10.tar.gz", hash = "sha256:d522fb204b4959909ecac47da02830daec102eeb100fb50ea9554818d47a5fa6"},
+]
+
 [[package]]
 name = "scooby"
 version = "0.10.0"
@@ -4913,4 +4970,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.10,<3.12"
-content-hash = "d1e1443c0d29d8cf6c156197f7c1f7991d093beaf1a8e88e9a9d7036f081184f"
+content-hash = "956680935c77616946350cc66cac1d94dac69e8e9745a9471e882f48d8004aca"
diff --git a/pyproject.toml b/pyproject.toml
index afd6154..4836852 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,6 +42,9 @@ docformatter = {extras = ["tomli"], version = "^1.7.5"}
 nbval = "^0.11.0"
 black = "^24.8.0"
 nox = "^2024.4.15"
+autoflake = "^2.3.1"
+autopep8 = "^2.3.2"
+ruff = "^0.11.10"
 
 [tool.poetry.group.lab.dependencies]
 jupyterlab = "^4.0.10"
@@ -118,6 +121,20 @@ exclude = [
     "__pycache__"
 ]
 
+[tool.autoflake]
+remove-all-unused-imports = true
+in-place = true
+ignore-init-module-imports = true
+remove-unused-variables = true
+recursive = true
+
+[tool.autopep8]
+max_line_length = 120
+in-place = true
+aggressive = 2
+ignore = ["W503", "E203", "E501"]
+recursive = true
+
 [tool.black]
 line-length = 120
 target-version = ["py311"]
@@ -138,3 +155,60 @@ wrap-summaries = 120
 blank = false
 exclude = []
 recursive = true
+
+[tool.ruff]
+line-length = 120
+
+target-version = "py311"
+
+exclude = [
+  ".git",
+  "migrations",
+  "__pycache__",
+]
+
+[tool.ruff.lint]
+select = [
+    "A",   # Flake8 Built ins
+    "E",   # Error (Flake8)
+    "F",   # Pyflakes (Flake8)
+    "W",   # Warning (Flake8)
+    "I",   # isort (import sorting)
+    "N",   # Naming conventions (Pylint, etc.)
+    "C90", # mccabe complexity (replaces flake8 --max-complexity and mccabe)
+    "B",   # Bugbear (common linting issues)
+    "UP",  # pyupgrade (suggests modern Python syntax)
+    "PLR", # Pylint refactor
+    "PLE", # Pylint error (specific Pylint error rules)
+    "PLW", # Pylint warning (specific Pylint warning rules)
+    "PLC", # Pylint convention (specific Pylint convention rules)
+    "R",   # Refactor (Pylint refactoring suggestions)
+    "TID", # TODO comments
+    "FAST",# FastAPI
+    "C4",  # List and dict comprehensions
+    "DJ",  # Django
+    "PIE", # Returns and unecessary returns
+    "Q",   # Double quotes
+    "RET", # Fix return statements
+    "PTH", # Enforce pathlib
+    "ARG", # Unused argument
+    "FLY", # Flynt
+    "NPY", # Numpy specific
+    "PD",  # Pandas specific
+    "RUF", # Ruff specific
+]
+
+ignore = [
+  "E203",  # whitespace before ':', Black already handles this
+  "E266",  # too many leading '#' for comments
+  "E501",  # line too long (we enforce via line-length instead)
+  "RET504",
+  "RUF013"
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy" # Corresponds to flake8's docstring-convention and docformatter style.
+
+[tool.ruff.lint.mccabe]
+# cyclomatic complexity
+max-complexity = 18

From 3a6e1200e7dc937b362c98a9cc9ec068f60ee63e Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Thu, 22 May 2025 15:05:24 -0400
Subject: [PATCH 02/19] Update dependencies and configs

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4836852..ca56900 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -183,7 +183,7 @@ select = [
     "PLW", # Pylint warning (specific Pylint warning rules)
     "PLC", # Pylint convention (specific Pylint convention rules)
     "R",   # Refactor (Pylint refactoring suggestions)
-    "TID", # TODO comments
+    "TID", # TO DO comments
     "FAST",# FastAPI
     "C4",  # List and dict comprehensions
     "DJ",  # Django

From d861194c88e8fba5982b8962585f2aaf84f0039e Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Thu, 22 May 2025 15:14:21 -0400
Subject: [PATCH 03/19] Ruff fix lint

---
 .pre-commit-config.yaml                       |   2 +-
 geospatial_tools/geotools_types.py            |   4 +-
 .../planetary_computer/sentinel_2.py          |  21 +-
 geospatial_tools/raster.py                    |  41 +-
 geospatial_tools/stac.py                      |  93 ++-
 geospatial_tools/utils.py                     |  15 +-
 geospatial_tools/vector.py                    |  13 +-
 poetry.lock                                   |  65 ++-
 pyproject.toml                                |   2 +-
 .../download_and_process.py                   |   4 +-
 .../test_planetary_computer_sentinel2.ipynb   | 545 +++++++++---------
 .../test_notebooks/test_stac_api_tools.ipynb  | 115 ++--
 tests/test_utils.py                           |   4 +-
 tests/test_vector.py                          |   2 +-
 14 files changed, 464 insertions(+), 462 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 3971ae8..eafade3 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -19,7 +19,7 @@ repos:
         files: '^(?!data/usa_polygon_5070\.gpkg$)(?!data/s2_grid_usa_polygon_5070\.gpkg$).*$'
 
   - repo: https://github.com/psf/black
-    rev: 23.12.1
+    rev: 24.8.0
     hooks:
       - id: black
 
diff --git a/geospatial_tools/geotools_types.py b/geospatial_tools/geotools_types.py
index 5ea9d0e..0c8c303 100644
--- a/geospatial_tools/geotools_types.py
+++ b/geospatial_tools/geotools_types.py
@@ -1,6 +1,6 @@
 """This module contains constants and functions pertaining to data types."""
 
-from typing import Tuple, Union
+from typing import Union
 
 from shapely.geometry import (
     GeometryCollection,
@@ -12,5 +12,5 @@
     Polygon,
 )
 
-BBoxLike = Tuple[float, float, float, float]
+BBoxLike = tuple[float, float, float, float]
 IntersectsLike = Union[Point, Polygon, LineString, MultiPolygon, MultiPoint, MultiLineString, GeometryCollection]
diff --git a/geospatial_tools/planetary_computer/sentinel_2.py b/geospatial_tools/planetary_computer/sentinel_2.py
index 46ebffb..9fef5f7 100644
--- a/geospatial_tools/planetary_computer/sentinel_2.py
+++ b/geospatial_tools/planetary_computer/sentinel_2.py
@@ -2,7 +2,6 @@
 import logging
 import pathlib
 from concurrent.futures import ThreadPoolExecutor, as_completed
-from typing import Optional, Union
 
 from geopandas import GeoDataFrame
 
@@ -35,7 +34,7 @@ def __init__(
         sentinel2_tiling_grid_column: str,
         vector_features: GeoDataFrame,
         vector_features_column: str,
-        date_ranges: Optional[list[str]] = None,
+        date_ranges: list[str] | None = None,
         max_cloud_cover: int = 5,
         max_no_data_value: int = 5,
         logger: logging.Logger = LOGGER,
@@ -127,7 +126,7 @@ def create_date_ranges(self, start_year: int, end_year: int, start_month: int, e
         )
         return self.date_ranges
 
-    def find_best_complete_products(self, max_cloud_cover: Optional[int] = None, max_no_data_value: int = 5) -> dict:
+    def find_best_complete_products(self, max_cloud_cover: int | None = None, max_no_data_value: int = 5) -> dict:
         """
         Finds the best complete products for each Sentinel 2 tiles. This function will filter out all products that have
         more than 5% of nodata values.
@@ -193,7 +192,7 @@ def select_best_products_per_feature(self) -> GeoDataFrame:
         self.vector_features_with_products = spatial_join_results
         return self.vector_features_with_products
 
-    def to_file(self, output_dir: Union[str, pathlib.Path]) -> None:
+    def to_file(self, output_dir: str | pathlib.Path) -> None:
         write_results_to_file(
             cloud_cover=self.max_cloud_cover,
             successful_results=self.successful_results,
@@ -208,7 +207,7 @@ def sentinel_2_complete_tile_search(
     date_ranges: list[str],
     max_cloud_cover: int,
     max_no_data_value: int = 5,
-) -> Optional[tuple[int, str, Optional[float], Optional[float]]]:
+) -> tuple[int, str, float | None, float | None] | None:
     client = StacSearch(PLANETARY_COMPUTER)
     collection = "sentinel-2-l2a"
     tile_ids = [tile_id]
@@ -280,7 +279,7 @@ def find_best_product_per_s2_tile(
 
 def _get_best_product_id_for_each_grid_tile(
     s2_tile_search_results: dict, feature_s2_tiles: GeoDataFrame, logger: logging.Logger = LOGGER
-) -> Optional[str]:
+) -> str | None:
     search_result_keys = s2_tile_search_results.keys()
     all_keys_present = all(item in search_result_keys for item in feature_s2_tiles)
     if not all_keys_present:
@@ -321,9 +320,9 @@ def write_best_product_ids_to_dataframe(
 def write_results_to_file(
     cloud_cover: int,
     successful_results: dict,
-    incomplete_results: Optional[list] = None,
-    error_results: Optional[list] = None,
-    output_dir: Union[str, pathlib.Path] = DATA_DIR,
+    incomplete_results: list | None = None,
+    error_results: list | None = None,
+    output_dir: str | pathlib.Path = DATA_DIR,
     logger: logging.Logger = LOGGER,
 ) -> dict:
     tile_filename = output_dir / f"data_lt{cloud_cover}cc.json"
@@ -358,8 +357,8 @@ def download_and_process_sentinel2_asset(
     product_id: str,
     product_bands: list[str],
     collections: str = "sentinel-2-l2a",
-    target_projection: Optional[Union[int, str]] = None,
-    base_directory: Union[str, pathlib.Path] = DATA_DIR,
+    target_projection: int | str | None = None,
+    base_directory: str | pathlib.Path = DATA_DIR,
     delete_intermediate_files: bool = False,
     logger: logging.Logger = LOGGER,
 ) -> Asset:
diff --git a/geospatial_tools/raster.py b/geospatial_tools/raster.py
index f7b44c7..9f4cd12 100644
--- a/geospatial_tools/raster.py
+++ b/geospatial_tools/raster.py
@@ -6,7 +6,6 @@
 import time
 from concurrent.futures import ProcessPoolExecutor
 from multiprocessing import cpu_count
-from typing import Optional, Union
 
 import geopandas as gpd
 import rasterio
@@ -21,11 +20,11 @@
 
 
 def reproject_raster(
-    dataset_path: Union[str, pathlib.Path],
-    target_crs: Union[str, int],
-    target_path: Union[str, pathlib.Path],
+    dataset_path: str | pathlib.Path,
+    target_crs: str | int,
+    target_path: str | pathlib.Path,
     logger: logging.Logger = LOGGER,
-) -> Union[pathlib.Path, None]:
+) -> pathlib.Path | None:
     """
 
     Parameters
@@ -76,12 +75,12 @@ def reproject_raster(
 
 
 def _clip_process(
-    raster_image: Union[pathlib.Path, str],
+    raster_image: pathlib.Path | str,
     id_polygon: tuple[int, GeoDataFrame],
-    base_output_filename: Optional[str],
-    output_dir: Union[pathlib.Path, str],
+    base_output_filename: str | None,
+    output_dir: pathlib.Path | str,
     logger: logging.Logger = LOGGER,
-) -> Union[tuple[int, GeoDataFrame, pathlib.Path], None]:
+) -> tuple[int, GeoDataFrame, pathlib.Path] | None:
     """
 
     Parameters
@@ -132,17 +131,17 @@ def _clip_process(
             else:
                 logger.warning(
                     f"There was an error writing the file :[Polygon ID: {polygon_id}"
-                    f"\nPolygon: {polygon}\nError message: {str(e)}]"
+                    f"\nPolygon: {polygon}\nError message: {e!s}]"
                 )
     return None
 
 
 def clip_raster_with_polygon(
-    raster_image: Union[pathlib.Path, str],
-    polygon_layer: Union[pathlib.Path, str, GeoDataFrame],
-    base_output_filename: Optional[str] = None,
-    output_dir: Union[str, pathlib.Path] = DATA_DIR,
-    num_of_workers: Optional[int] = None,
+    raster_image: pathlib.Path | str,
+    polygon_layer: pathlib.Path | str | GeoDataFrame,
+    base_output_filename: str | None = None,
+    output_dir: str | pathlib.Path = DATA_DIR,
+    num_of_workers: int | None = None,
     logger: logging.Logger = LOGGER,
 ) -> list[pathlib.Path]:
     """
@@ -195,7 +194,7 @@ def clip_raster_with_polygon(
     polygons = gdf["geometry"]
     ids = gdf.index
 
-    id_polygon_list = zip(ids, polygons)
+    id_polygon_list = zip(ids, polygons, strict=False)
     logger.info(f"Clipping raster image with {len(polygons)} polygons")
     with ProcessPoolExecutor(max_workers=workers) as executor:
         futures = [
@@ -219,7 +218,7 @@ def clip_raster_with_polygon(
     return path_list
 
 
-def get_total_band_count(raster_file_list: list[Union[pathlib.Path, str]], logger: logging.Logger = LOGGER) -> int:
+def get_total_band_count(raster_file_list: list[pathlib.Path | str], logger: logging.Logger = LOGGER) -> int:
     """
 
     Parameters
@@ -244,7 +243,7 @@ def get_total_band_count(raster_file_list: list[Union[pathlib.Path, str]], logge
 
 
 def create_merged_raster_bands_metadata(
-    raster_file_list: list[Union[pathlib.Path, str]], logger: logging.Logger = LOGGER
+    raster_file_list: list[pathlib.Path | str], logger: logging.Logger = LOGGER
 ) -> dict:
     """
 
@@ -266,12 +265,12 @@ def create_merged_raster_bands_metadata(
 
 
 def merge_raster_bands(
-    raster_file_list: list[Union[pathlib.Path, str]],
-    merged_filename: Union[pathlib.Path, str],
+    raster_file_list: list[pathlib.Path | str],
+    merged_filename: pathlib.Path | str,
     merged_band_names: list[str] = None,
     merged_metadata: dict = None,
     logger: logging.Logger = LOGGER,
-) -> Optional[pathlib.Path]:
+) -> pathlib.Path | None:
     """
     This function aims to combine multiple overlapping raster bands into a single raster image.
 
diff --git a/geospatial_tools/stac.py b/geospatial_tools/stac.py
index 3a820cc..75c77c3 100644
--- a/geospatial_tools/stac.py
+++ b/geospatial_tools/stac.py
@@ -3,7 +3,6 @@
 import logging
 import pathlib
 import time
-from typing import Optional, Union
 
 import pystac
 import pystac_client
@@ -30,7 +29,7 @@
 PLANETARY_COMPUTER_API = "https://planetarycomputer.microsoft.com/api/stac/v1"
 
 
-def create_planetary_computer_catalog(max_retries=3, delay=5, logger=LOGGER) -> Union[pystac_client.Client, None]:
+def create_planetary_computer_catalog(max_retries=3, delay=5, logger=LOGGER) -> pystac_client.Client | None:
     """
     Creates a Planetary Computer Catalog Client.
 
@@ -53,7 +52,7 @@ def create_planetary_computer_catalog(max_retries=3, delay=5, logger=LOGGER) ->
     return None
 
 
-def catalog_generator(catalog_name, logger=LOGGER) -> Optional[pystac_client.Client]:
+def catalog_generator(catalog_name, logger=LOGGER) -> pystac_client.Client | None:
     catalog_dict = {PLANETARY_COMPUTER: create_planetary_computer_catalog}
     if catalog_name not in catalog_dict:
         logger.error(f"Unsupported catalog name: {catalog_name}")
@@ -70,7 +69,7 @@ def list_available_catalogs(logger: logging.Logger = LOGGER) -> frozenset[str]:
 
 
 class AssetSubItem:
-    def __init__(self, asset, item_id: str, band: str, filename: Union[str, pathlib.Path]):
+    def __init__(self, asset, item_id: str, band: str, filename: str | pathlib.Path):
         if isinstance(filename, str):
             filename = pathlib.Path(filename)
         self.asset = asset
@@ -83,10 +82,10 @@ class Asset:
     def __init__(
         self,
         asset_id: str,
-        bands: Optional[list[str]] = None,
-        asset_item_list: Optional[list[AssetSubItem]] = None,
-        merged_asset_path: Optional[Union[str, pathlib.Path]] = None,
-        reprojected_asset: Optional[Union[str, pathlib.Path]] = None,
+        bands: list[str] | None = None,
+        asset_item_list: list[AssetSubItem] | None = None,
+        merged_asset_path: str | pathlib.Path | None = None,
+        reprojected_asset: str | pathlib.Path | None = None,
         logger: logging.Logger = LOGGER,
     ):
         self.asset_id = asset_id
@@ -110,8 +109,8 @@ def show_asset_items(self):
         self.logger.info(f"Asset list for asset [{self.asset_id}] : \n\t{asset_list}")
 
     def merge_asset(
-        self, base_directory: Optional[Union[str, pathlib.Path]] = None, delete_sub_items: bool = False
-    ) -> Union[pathlib.Path, None]:
+        self, base_directory: str | pathlib.Path | None = None, delete_sub_items: bool = False
+    ) -> pathlib.Path | None:
         if not base_directory:
             base_directory = ""
         if isinstance(base_directory, str):
@@ -142,8 +141,8 @@ def merge_asset(
 
     def reproject_merged_asset(
         self,
-        target_projection: Union[str, int],
-        base_directory: Union[str, pathlib.Path] = None,
+        target_projection: str | int,
+        base_directory: str | pathlib.Path = None,
         delete_merged_asset: bool = False,
     ):
         if not base_directory:
@@ -199,25 +198,25 @@ class StacSearch:
 
     def __init__(self, catalog_name, logger=LOGGER):
         self.catalog: pystac_client.Client = catalog_generator(catalog_name=catalog_name)
-        self.search_results: Optional[list[pystac.Item]] = None
-        self.cloud_cover_sorted_results: Optional[list[pystac.Item]] = None
-        self.filtered_results: Optional[list[pystac.Item]] = None
-        self.downloaded_search_assets: Optional[list[Asset]] = None
-        self.downloaded_cloud_cover_sorted_assets: Optional[list[Asset]] = None
+        self.search_results: list[pystac.Item] | None = None
+        self.cloud_cover_sorted_results: list[pystac.Item] | None = None
+        self.filtered_results: list[pystac.Item] | None = None
+        self.downloaded_search_assets: list[Asset] | None = None
+        self.downloaded_cloud_cover_sorted_assets: list[Asset] | None = None
         self.downloaded_best_sorted_asset = None
         self.logger = logger
 
     def search(
         self,
         date_range=None,
-        max_items: Optional[int] = None,
-        limit: Optional[int] = None,
-        ids: Optional[list] = None,
-        collections: Optional[Union[str, list]] = None,
-        bbox: Optional[geotools_types.BBoxLike] = None,
-        intersects: Optional[geotools_types.IntersectsLike] = None,
-        query: Optional[dict] = None,
-        sortby: Optional[Union[list, dict]] = None,
+        max_items: int | None = None,
+        limit: int | None = None,
+        ids: list | None = None,
+        collections: str | list | None = None,
+        bbox: geotools_types.BBoxLike | None = None,
+        intersects: geotools_types.IntersectsLike | None = None,
+        query: dict | None = None,
+        sortby: list | dict | None = None,
         max_retries=3,
         delay=5,
     ) -> list:
@@ -312,13 +311,13 @@ def search(
     def search_for_date_ranges(
         self,
         date_ranges: list[str],
-        max_items: Optional[int] = None,
-        limit: Optional[int] = None,
-        collections: Optional[Union[str, list]] = None,
-        bbox: Optional[geotools_types.BBoxLike] = None,
-        intersects: Optional[geotools_types.IntersectsLike] = None,
-        query: Optional[dict] = None,
-        sortby: Optional[Union[list, dict]] = None,
+        max_items: int | None = None,
+        limit: int | None = None,
+        collections: str | list | None = None,
+        bbox: geotools_types.BBoxLike | None = None,
+        intersects: geotools_types.IntersectsLike | None = None,
+        query: dict | None = None,
+        sortby: list | dict | None = None,
         max_retries=3,
         delay=5,
     ) -> list:
@@ -401,14 +400,14 @@ def search_for_date_ranges(
     def _base_catalog_search(
         self,
         date_range: str,
-        max_items: Optional[int] = None,
-        limit: Optional[int] = None,
-        ids: Optional[list] = None,
-        collections: Optional[Union[str, list]] = None,
-        bbox: Optional[geotools_types.BBoxLike] = None,
-        intersects: Optional[geotools_types.IntersectsLike] = None,
-        query: Optional[dict] = None,
-        sortby: Optional[Union[list, dict]] = None,
+        max_items: int | None = None,
+        limit: int | None = None,
+        ids: list | None = None,
+        collections: str | list | None = None,
+        bbox: geotools_types.BBoxLike | None = None,
+        intersects: geotools_types.IntersectsLike | None = None,
+        query: dict | None = None,
+        sortby: list | dict | None = None,
     ):
         search = self.catalog.search(
             datetime=date_range,
@@ -431,7 +430,7 @@ def _base_catalog_search(
         log_state(log_msg)
         return list(items)
 
-    def sort_results_by_cloud_coverage(self) -> Optional[list]:
+    def sort_results_by_cloud_coverage(self) -> list | None:
         """
         Sort results by cloud coverage.
 
@@ -449,7 +448,7 @@ def sort_results_by_cloud_coverage(self) -> Optional[list]:
         self.logger.warning("No results found: please run a search before trying to sort results")
         return None
 
-    def filter_no_data(self, property_name: str, max_no_data_value: int = 5) -> Optional[list[pystac.Item]]:
+    def filter_no_data(self, property_name: str, max_no_data_value: int = 5) -> list[pystac.Item] | None:
         """
         Filter results and sorted results that are above a nodata value threshold.
 
@@ -511,7 +510,7 @@ def _download_assets(self, item: pystac.Item, bands: list, base_directory: pathl
         return downloaded_files
 
     def _download_results(
-        self, results: Optional[list[pystac.Item]], bands: list, base_directory: Union[str, pathlib.Path]
+        self, results: list[pystac.Item] | None, bands: list, base_directory: str | pathlib.Path
     ) -> list[Asset]:
         if not results:
             return []
@@ -527,7 +526,7 @@ def _download_results(
             downloaded_search_results.append(downloaded_item)
         return downloaded_search_results
 
-    def download_search_results(self, bands: list, base_directory: Union[str, pathlib.Path]) -> list[Asset]:
+    def download_search_results(self, bands: list, base_directory: str | pathlib.Path) -> list[Asset]:
         """
 
         Parameters
@@ -561,7 +560,7 @@ def _generate_best_results(self):
         return results
 
     def download_sorted_by_cloud_cover_search_results(
-        self, bands: list, base_directory: Union[str, pathlib.Path], first_x_num_of_items: Optional[int] = None
+        self, bands: list, base_directory: str | pathlib.Path, first_x_num_of_items: int | None = None
     ) -> list[Asset]:
         """
 
@@ -589,9 +588,7 @@ def download_sorted_by_cloud_cover_search_results(
         self.downloaded_cloud_cover_sorted_assets = downloaded_search_results
         return downloaded_search_results
 
-    def download_best_cloud_cover_result(
-        self, bands: list, base_directory: Union[str, pathlib.Path]
-    ) -> Optional[Asset]:
+    def download_best_cloud_cover_result(self, bands: list, base_directory: str | pathlib.Path) -> Asset | None:
         """
 
         Parameters
diff --git a/geospatial_tools/utils.py b/geospatial_tools/utils.py
index ac7b2a8..1b95200 100644
--- a/geospatial_tools/utils.py
+++ b/geospatial_tools/utils.py
@@ -8,7 +8,6 @@
 import pathlib
 import sys
 import zipfile
-from typing import Optional, Union
 
 import requests
 import yaml
@@ -90,7 +89,7 @@ def get_yaml_config(yaml_config_file: str, logger: logging.Logger = LOGGER) -> d
     for path in potential_paths:
         if path.exists():
             config_filepath = path
-            logger.info(f"Yaml config file [{str(path)}] found.")
+            logger.info(f"Yaml config file [{path!s}] found.")
             break
 
     params = {}
@@ -137,7 +136,7 @@ def get_json_config(json_config_file: str, logger=LOGGER) -> dict:
     for path in potential_paths:
         if path.exists():
             config_filepath = path
-            logger.info(f"JSON config file [{str(path)}] found.")
+            logger.info(f"JSON config file [{path!s}] found.")
             break
 
     if not config_filepath:
@@ -153,7 +152,7 @@ def get_json_config(json_config_file: str, logger=LOGGER) -> dict:
         return {}
 
 
-def create_crs(dataset_crs: Union[str, int], logger=LOGGER):
+def create_crs(dataset_crs: str | int, logger=LOGGER):
     """
 
     Parameters
@@ -185,9 +184,7 @@ def create_crs(dataset_crs: Union[str, int], logger=LOGGER):
     logger.error(f"Encountered problem while trying to format EPSG code from input : [{dataset_crs}]")
 
 
-def download_url(
-    url: str, filename: Union[str, pathlib.Path], overwrite: bool = False, logger=LOGGER
-) -> Optional[pathlib.Path]:
+def download_url(url: str, filename: str | pathlib.Path, overwrite: bool = False, logger=LOGGER) -> pathlib.Path | None:
     """
     This function downloads a file from a given URL.
 
@@ -223,9 +220,7 @@ def download_url(
     return None
 
 
-def unzip_file(
-    zip_path: Union[str, pathlib.Path], extract_to: Union[str, pathlib.Path], logger: logging.Logger = LOGGER
-):
+def unzip_file(zip_path: str | pathlib.Path, extract_to: str | pathlib.Path, logger: logging.Logger = LOGGER):
     """
     This function unzips an archive to a specific directory.
 
diff --git a/geospatial_tools/vector.py b/geospatial_tools/vector.py
index f2083d9..a386bc0 100644
--- a/geospatial_tools/vector.py
+++ b/geospatial_tools/vector.py
@@ -6,7 +6,6 @@
 from concurrent.futures import ProcessPoolExecutor
 from multiprocessing import cpu_count
 from pathlib import Path
-from typing import Union
 
 import dask_geopandas as dgpd
 import geopandas as gpd
@@ -22,7 +21,7 @@
 
 
 def create_grid_coordinates(
-    bounding_box: Union[list, tuple], grid_size: float, logger: logging.Logger = LOGGER
+    bounding_box: list | tuple, grid_size: float, logger: logging.Logger = LOGGER
 ) -> tuple[ndarray, ndarray]:
     """
     Create grid coordinates based on input bounding box and grid size.
@@ -90,7 +89,7 @@ def _create_polygons_from_coords_chunk(chunk: tuple[ndarray, ndarray, float]) ->
     """
     lon_coords, lat_coords, grid_size = chunk
     polygons = []
-    for lon, lat in zip(lon_coords, lat_coords):
+    for lon, lat in zip(lon_coords, lat_coords, strict=False):
         polygons.append(
             Polygon([(lon, lat), (lon + grid_size, lat), (lon + grid_size, lat + grid_size), (lon, lat + grid_size)])
         )
@@ -98,7 +97,7 @@ def _create_polygons_from_coords_chunk(chunk: tuple[ndarray, ndarray, float]) ->
 
 
 def create_vector_grid(
-    bounding_box: Union[list, tuple], grid_size: float, crs: str = None, logger: logging.Logger = LOGGER
+    bounding_box: list | tuple, grid_size: float, crs: str = None, logger: logging.Logger = LOGGER
 ) -> GeoDataFrame:
     """
     Create a grid of polygons within the specified bounds and cell size. This function uses NumPy vectorized arrays for
@@ -142,9 +141,9 @@ def create_vector_grid(
 
 
 def create_vector_grid_parallel(
-    bounding_box: Union[list, tuple],
+    bounding_box: list | tuple,
     grid_size: float,
-    crs: Union[str, int] = None,
+    crs: str | int = None,
     num_of_workers: int = None,
     logger: logging.Logger = LOGGER,
 ) -> GeoDataFrame:
@@ -338,7 +337,7 @@ def select_polygons_by_location(
     return filtered_result_gdf
 
 
-def to_geopackage(gdf: GeoDataFrame, filename: Union[str, Path], logger=LOGGER) -> str:
+def to_geopackage(gdf: GeoDataFrame, filename: str | Path, logger=LOGGER) -> str:
     """
     Save GeoDataFrame to a Geopackage file.
 
diff --git a/poetry.lock b/poetry.lock
index 5c0cbdc..eea98d5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -292,47 +292,49 @@ lxml = ["lxml"]
 
 [[package]]
 name = "black"
-version = "24.8.0"
+version = "25.1.0"
 description = "The uncompromising code formatter."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "black-24.8.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:09cdeb74d494ec023ded657f7092ba518e8cf78fa8386155e4a03fdcc44679e6"},
-    {file = "black-24.8.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:81c6742da39f33b08e791da38410f32e27d632260e599df7245cccee2064afeb"},
-    {file = "black-24.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:707a1ca89221bc8a1a64fb5e15ef39cd755633daa672a9db7498d1c19de66a42"},
-    {file = "black-24.8.0-cp310-cp310-win_amd64.whl", hash = "sha256:d6417535d99c37cee4091a2f24eb2b6d5ec42b144d50f1f2e436d9fe1916fe1a"},
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-    {file = "black-24.8.0.tar.gz", hash = "sha256:2500945420b6784c38b9ee885af039f5e7471ef284ab03fa35ecdde4688cd83f"},
+    {file = "black-25.1.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:759e7ec1e050a15f89b770cefbf91ebee8917aac5c20483bc2d80a6c3a04df32"},
+    {file = "black-25.1.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:0e519ecf93120f34243e6b0054db49c00a35f84f195d5bce7e9f5cfc578fc2da"},
+    {file = "black-25.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:055e59b198df7ac0b7efca5ad7ff2516bca343276c466be72eb04a3bcc1f82d7"},
+    {file = "black-25.1.0-cp310-cp310-win_amd64.whl", hash = "sha256:db8ea9917d6f8fc62abd90d944920d95e73c83a5ee3383493e35d271aca872e9"},
+    {file = "black-25.1.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:a39337598244de4bae26475f77dda852ea00a93bd4c728e09eacd827ec929df0"},
+    {file = "black-25.1.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:96c1c7cd856bba8e20094e36e0f948718dc688dba4a9d78c3adde52b9e6c2299"},
+    {file = "black-25.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:bce2e264d59c91e52d8000d507eb20a9aca4a778731a08cfff7e5ac4a4bb7096"},
+    {file = "black-25.1.0-cp311-cp311-win_amd64.whl", hash = "sha256:172b1dbff09f86ce6f4eb8edf9dede08b1fce58ba194c87d7a4f1a5aa2f5b3c2"},
+    {file = "black-25.1.0-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:4b60580e829091e6f9238c848ea6750efed72140b91b048770b64e74fe04908b"},
+    {file = "black-25.1.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:1e2978f6df243b155ef5fa7e558a43037c3079093ed5d10fd84c43900f2d8ecc"},
+    {file = "black-25.1.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:3b48735872ec535027d979e8dcb20bf4f70b5ac75a8ea99f127c106a7d7aba9f"},
+    {file = "black-25.1.0-cp312-cp312-win_amd64.whl", hash = "sha256:ea0213189960bda9cf99be5b8c8ce66bb054af5e9e861249cd23471bd7b0b3ba"},
+    {file = "black-25.1.0-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:8f0b18a02996a836cc9c9c78e5babec10930862827b1b724ddfe98ccf2f2fe4f"},
+    {file = "black-25.1.0-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:afebb7098bfbc70037a053b91ae8437c3857482d3a690fefc03e9ff7aa9a5fd3"},
+    {file = "black-25.1.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:030b9759066a4ee5e5aca28c3c77f9c64789cdd4de8ac1df642c40b708be6171"},
+    {file = "black-25.1.0-cp313-cp313-win_amd64.whl", hash = "sha256:a22f402b410566e2d1c950708c77ebf5ebd5d0d88a6a2e87c86d9fb48afa0d18"},
+    {file = "black-25.1.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:a1ee0a0c330f7b5130ce0caed9936a904793576ef4d2b98c40835d6a65afa6a0"},
+    {file = "black-25.1.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:f3df5f1bf91d36002b0a75389ca8663510cf0531cca8aa5c1ef695b46d98655f"},
+    {file = "black-25.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:d9e6827d563a2c820772b32ce8a42828dc6790f095f441beef18f96aa6f8294e"},
+    {file = "black-25.1.0-cp39-cp39-win_amd64.whl", hash = "sha256:bacabb307dca5ebaf9c118d2d2f6903da0d62c9faa82bd21a33eecc319559355"},
+    {file = "black-25.1.0-py3-none-any.whl", hash = "sha256:95e8176dae143ba9097f351d174fdaf0ccd29efb414b362ae3fd72bf0f710717"},
+    {file = "black-25.1.0.tar.gz", hash = "sha256:33496d5cd1222ad73391352b4ae8da15253c5de89b93a80b3e2c8d9a19ec2666"},
 ]
 
 [package.dependencies]
 click = ">=8.0.0"
+ipython = {version = ">=7.8.0", optional = true, markers = "extra == \"jupyter\""}
 mypy-extensions = ">=0.4.3"
 packaging = ">=22.0"
 pathspec = ">=0.9.0"
 platformdirs = ">=2"
+tokenize-rt = {version = ">=3.2.0", optional = true, markers = "extra == \"jupyter\""}
 tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
 typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
-d = ["aiohttp (>=3.7.4)", "aiohttp (>=3.7.4,!=3.9.0)"]
+d = ["aiohttp (>=3.10)"]
 jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
@@ -4591,6 +4593,17 @@ webencodings = ">=0.4"
 doc = ["sphinx", "sphinx_rtd_theme"]
 test = ["pytest", "ruff"]
 
+[[package]]
+name = "tokenize-rt"
+version = "6.1.0"
+description = "A wrapper around the stdlib `tokenize` which roundtrips."
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "tokenize_rt-6.1.0-py2.py3-none-any.whl", hash = "sha256:d706141cdec4aa5f358945abe36b911b8cbdc844545da99e811250c0cee9b6fc"},
+    {file = "tokenize_rt-6.1.0.tar.gz", hash = "sha256:e8ee836616c0877ab7c7b54776d2fefcc3bde714449a206762425ae114b53c86"},
+]
+
 [[package]]
 name = "tomli"
 version = "2.0.1"
@@ -4970,4 +4983,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.10,<3.12"
-content-hash = "956680935c77616946350cc66cac1d94dac69e8e9745a9471e882f48d8004aca"
+content-hash = "74f183b89189fcd2a6eb408d828ee795ca2546fb311ad460ffbc3863c37786e0"
diff --git a/pyproject.toml b/pyproject.toml
index ca56900..b9c03f7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,7 +40,7 @@ pre-commit = "^3.7.0"
 flake8-pyproject = "^1.2.3"
 docformatter = {extras = ["tomli"], version = "^1.7.5"}
 nbval = "^0.11.0"
-black = "^24.8.0"
+black = {extras = ["jupyter"], version = "^25.1.0"}
 nox = "^2024.4.15"
 autoflake = "^2.3.1"
 autopep8 = "^2.3.2"
diff --git a/scripts/sentinel_2_search_and_process/download_and_process.py b/scripts/sentinel_2_search_and_process/download_and_process.py
index 5bbd757..448f1a2 100644
--- a/scripts/sentinel_2_search_and_process/download_and_process.py
+++ b/scripts/sentinel_2_search_and_process/download_and_process.py
@@ -29,7 +29,7 @@
 def _handle_product_list(product_list: str) -> list:
     parsed_product_list = []
     if product_list.endswith(".txt") and pathlib.Path(product_list).exists():
-        with open(product_list, "r", encoding="utf-8") as f:
+        with open(product_list, encoding="utf-8") as f:
             for line in f:
                 parsed_product_list.append(line.strip())
     if not product_list.endswith(".txt"):
@@ -87,7 +87,7 @@ def download_and_process(
     LOGGER.info(f"Will download and process the following products: {parsed_product_list}")
     if not parsed_product_list:
         LOGGER.error("Error - Product list not found!")
-        return None
+        return
 
     LOGGER.info(f"Loading best results file {best_products_file}")
     best_results = gpd.read_file(best_products_file)
diff --git a/tests/test_notebooks/test_planetary_computer_sentinel2.ipynb b/tests/test_notebooks/test_planetary_computer_sentinel2.ipynb
index b113487..1242506 100644
--- a/tests/test_notebooks/test_planetary_computer_sentinel2.ipynb
+++ b/tests/test_notebooks/test_planetary_computer_sentinel2.ipynb
@@ -2,6 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
+   "execution_count": 1,
    "id": "26590ffa",
    "metadata": {
     "ExecuteTime": {
@@ -9,22 +10,23 @@
      "start_time": "2025-05-22T18:12:04.226800Z"
     }
    },
+   "outputs": [],
    "source": [
     "import shutil\n",
     "\n",
-    "import leafmap\n",
     "import geopandas as gpd\n",
+    "import leafmap\n",
+    "\n",
     "from geospatial_tools import DATA_DIR, TESTS_DIR\n",
+    "from geospatial_tools.planetary_computer.sentinel_2 import BestProductsForFeatures, download_and_process_sentinel2_asset\n",
     "from geospatial_tools.raster import clip_raster_with_polygon\n",
     "from geospatial_tools.stac import Asset\n",
-    "from geospatial_tools.planetary_computer.sentinel_2 import BestProductsForFeatures, download_and_process_sentinel2_asset\n",
-    "from geospatial_tools.vector import create_vector_grid_parallel, to_geopackage, select_polygons_by_location"
-   ],
-   "outputs": [],
-   "execution_count": 1
+    "from geospatial_tools.vector import create_vector_grid_parallel, select_polygons_by_location, to_geopackage"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 2,
    "id": "bbf8d1aede2a4fd2",
    "metadata": {
     "ExecuteTime": {
@@ -32,12 +34,11 @@
      "start_time": "2025-05-22T18:12:05.677670Z"
     }
    },
+   "outputs": [],
    "source": [
     "TEST_TMP_DIR = TESTS_DIR / \"test_notebooks/tmp_sentinel2\"\n",
     "TEST_TMP_DIR.mkdir(exist_ok=True)"
-   ],
-   "outputs": [],
-   "execution_count": 2
+   ]
   },
   {
    "cell_type": "markdown",
@@ -62,6 +63,7 @@
   },
   {
    "cell_type": "code",
+   "execution_count": 3,
    "id": "fcb67d1eb21aafc1",
    "metadata": {
     "ExecuteTime": {
@@ -69,17 +71,17 @@
      "start_time": "2025-05-22T18:12:05.727177Z"
     }
    },
+   "outputs": [],
    "source": [
     "USA_POLYGON_FILE = DATA_DIR / \"usa_polygon_5070.gpkg\"\n",
     "S2_USA_GRID_FILE = DATA_DIR / \"s2_grid_usa_polygon_5070.gpkg\"\n",
     "usa_polygon = gpd.read_file(USA_POLYGON_FILE)\n",
     "s2_grid = gpd.read_file(S2_USA_GRID_FILE)"
-   ],
-   "outputs": [],
-   "execution_count": 3
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 4,
    "id": "314e7c068786ad4d",
    "metadata": {
     "ExecuteTime": {
@@ -87,19 +89,9 @@
      "start_time": "2025-05-22T18:12:05.780131Z"
     }
    },
-   "source": [
-    "usa_polygon"
-   ],
    "outputs": [
     {
      "data": {
-      "text/plain": [
-       "    AFFGEOID GEOID           NAME  \\\n",
-       "0  0100000US    US  United States   \n",
-       "\n",
-       "                                            geometry  \n",
-       "0  MULTIPOLYGON (((-2116048.733 3142966.552, -211...  "
-      ],
       "text/html": [
        "<div>\n",
        "<style scoped>\n",
@@ -136,6 +128,13 @@
        "  </tbody>\n",
        "</table>\n",
        "</div>"
+      ],
+      "text/plain": [
+       "    AFFGEOID GEOID           NAME  \\\n",
+       "0  0100000US    US  United States   \n",
+       "\n",
+       "                                            geometry  \n",
+       "0  MULTIPOLYGON (((-2116048.733 3142966.552, -211...  "
       ]
      },
      "execution_count": 4,
@@ -143,10 +142,13 @@
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 4
+   "source": [
+    "usa_polygon"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 5,
    "id": "3e9461ed5b602319",
    "metadata": {
     "ExecuteTime": {
@@ -154,41 +156,9 @@
      "start_time": "2025-05-22T18:12:05.865062Z"
     }
    },
-   "source": [
-    "s2_grid"
-   ],
    "outputs": [
     {
      "data": {
-      "text/plain": [
-       "      name   folders                                        description  \\\n",
-       "0    12TUP  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "1    12TYQ  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "2    12TYR  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "3    12TYN  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "4    12TYP  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "..     ...       ...                                                ...   \n",
-       "977  12TTM  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "978  12TUK  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "979  12TUQ  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "980  12TUR  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "981  12TUN  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "\n",
-       "                                              geometry  \n",
-       "0    MULTIPOLYGON Z (((-1386334.944 2487548.77 0, -...  \n",
-       "1    MULTIPOLYGON Z (((-976300.478 2523767.452 0, -...  \n",
-       "2    MULTIPOLYGON Z (((-960099.705 2622374.255 0, -...  \n",
-       "3    MULTIPOLYGON Z (((-1008622.024 2325748.358 0, ...  \n",
-       "4    MULTIPOLYGON Z (((-992478.385 2424861.34 0, -8...  \n",
-       "..                                                 ...  \n",
-       "977  MULTIPOLYGON Z (((-1515431.586 2304192.826 0, ...  \n",
-       "978  MULTIPOLYGON Z (((-1448525.813 2089886.667 0, ...  \n",
-       "979  MULTIPOLYGON Z (((-1371006.917 2586590.133 0, ...  \n",
-       "980  MULTIPOLYGON Z (((-1355793.563 2685354.08 0, -...  \n",
-       "981  MULTIPOLYGON Z (((-1401759.785 2388321.4 0, -1...  \n",
-       "\n",
-       "[982 rows x 4 columns]"
-      ],
       "text/html": [
        "<div>\n",
        "<style scoped>\n",
@@ -296,6 +266,35 @@
        "</table>\n",
        "<p>982 rows × 4 columns</p>\n",
        "</div>"
+      ],
+      "text/plain": [
+       "      name   folders                                        description  \\\n",
+       "0    12TUP  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "1    12TYQ  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "2    12TYR  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "3    12TYN  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "4    12TYP  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "..     ...       ...                                                ...   \n",
+       "977  12TTM  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "978  12TUK  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "979  12TUQ  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "980  12TUR  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "981  12TUN  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "\n",
+       "                                              geometry  \n",
+       "0    MULTIPOLYGON Z (((-1386334.944 2487548.77 0, -...  \n",
+       "1    MULTIPOLYGON Z (((-976300.478 2523767.452 0, -...  \n",
+       "2    MULTIPOLYGON Z (((-960099.705 2622374.255 0, -...  \n",
+       "3    MULTIPOLYGON Z (((-1008622.024 2325748.358 0, ...  \n",
+       "4    MULTIPOLYGON Z (((-992478.385 2424861.34 0, -8...  \n",
+       "..                                                 ...  \n",
+       "977  MULTIPOLYGON Z (((-1515431.586 2304192.826 0, ...  \n",
+       "978  MULTIPOLYGON Z (((-1448525.813 2089886.667 0, ...  \n",
+       "979  MULTIPOLYGON Z (((-1371006.917 2586590.133 0, ...  \n",
+       "980  MULTIPOLYGON Z (((-1355793.563 2685354.08 0, -...  \n",
+       "981  MULTIPOLYGON Z (((-1401759.785 2388321.4 0, -1...  \n",
+       "\n",
+       "[982 rows x 4 columns]"
       ]
      },
      "execution_count": 5,
@@ -303,7 +302,9 @@
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 5
+   "source": [
+    "s2_grid"
+   ]
   },
   {
    "cell_type": "markdown",
@@ -322,6 +323,7 @@
   },
   {
    "cell_type": "code",
+   "execution_count": 6,
    "id": "d4546352d604eaf",
    "metadata": {
     "ExecuteTime": {
@@ -329,15 +331,6 @@
      "start_time": "2025-05-22T18:12:05.982972Z"
     }
    },
-   "source": [
-    "grid_size = 10000\n",
-    "bbox = usa_polygon.total_bounds\n",
-    "grid_10km_filename = TEST_TMP_DIR / \"polygon_grid_10km.gpkg\"\n",
-    "print(\"Starting processing for [create_vector_grid_parallel]\")\n",
-    "grid_10km = create_vector_grid_parallel(bounding_box=bbox, grid_size=grid_size, crs=\"EPSG:5070\")\n",
-    "print(f\"Printing len(grid_parallel) to check if grid contains same amount of polygons : {len(grid_10km)}\")\n",
-    "to_geopackage(gdf=grid_10km, filename=grid_10km_filename)"
-   ],
    "outputs": [
     {
      "name": "stdout",
@@ -369,7 +362,15 @@
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 6
+   "source": [
+    "grid_size = 10000\n",
+    "bbox = usa_polygon.total_bounds\n",
+    "grid_10km_filename = TEST_TMP_DIR / \"polygon_grid_10km.gpkg\"\n",
+    "print(\"Starting processing for [create_vector_grid_parallel]\")\n",
+    "grid_10km = create_vector_grid_parallel(bounding_box=bbox, grid_size=grid_size, crs=\"EPSG:5070\")\n",
+    "print(f\"Printing len(grid_parallel) to check if grid contains same amount of polygons : {len(grid_10km)}\")\n",
+    "to_geopackage(gdf=grid_10km, filename=grid_10km_filename)"
+   ]
   },
   {
    "cell_type": "markdown",
@@ -388,6 +389,7 @@
   },
   {
    "cell_type": "code",
+   "execution_count": 7,
    "id": "7fb328be7527d9cb",
    "metadata": {
     "ExecuteTime": {
@@ -395,14 +397,6 @@
      "start_time": "2025-05-22T18:12:08.833455Z"
     }
    },
-   "source": [
-    "intersecting_polygons_filename = TEST_TMP_DIR / \"intersecting_polygon_grid_10km.gpkg\"\n",
-    "print(\"Starting intersect selection\")\n",
-    "intersecting_polygons = select_polygons_by_location(grid_10km, usa_polygon, num_of_workers=4)\n",
-    "\n",
-    "# Optionally save to a new file\n",
-    "to_geopackage(intersecting_polygons, intersecting_polygons_filename)"
-   ],
    "outputs": [
     {
      "name": "stdout",
@@ -428,7 +422,14 @@
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 7
+   "source": [
+    "intersecting_polygons_filename = TEST_TMP_DIR / \"intersecting_polygon_grid_10km.gpkg\"\n",
+    "print(\"Starting intersect selection\")\n",
+    "intersecting_polygons = select_polygons_by_location(grid_10km, usa_polygon, num_of_workers=4)\n",
+    "\n",
+    "# Optionally save to a new file\n",
+    "to_geopackage(intersecting_polygons, intersecting_polygons_filename)"
+   ]
   },
   {
    "cell_type": "markdown",
@@ -448,6 +449,7 @@
   },
   {
    "cell_type": "code",
+   "execution_count": 8,
    "id": "89c0d198-d672-4815-904b-7a7c4be6cb03",
    "metadata": {
     "ExecuteTime": {
@@ -455,11 +457,6 @@
      "start_time": "2025-05-22T18:12:13.945810Z"
     }
    },
-   "source": [
-    "# This is the full list of S2 grids\n",
-    "s2_tile_grid_list = s2_grid[\"name\"].to_list()\n",
-    "s2_tile_grid_list"
-   ],
    "outputs": [
     {
      "data": {
@@ -1453,10 +1450,15 @@
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 8
+   "source": [
+    "# This is the full list of S2 grids\n",
+    "s2_tile_grid_list = s2_grid[\"name\"].to_list()\n",
+    "s2_tile_grid_list"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 9,
    "id": "16a81d07b4c374f2",
    "metadata": {
     "ExecuteTime": {
@@ -1464,12 +1466,11 @@
      "start_time": "2025-05-22T18:12:14.006986Z"
     }
    },
+   "outputs": [],
    "source": [
     "# The list is a bit long, so we'll be continuing this notebook with the following subset\n",
     "s2_tile_grid_subset_list = [\"10TDK\", \"10TEK\", \"10SDJ\"]"
-   ],
-   "outputs": [],
-   "execution_count": 9
+   ]
   },
   {
    "cell_type": "markdown",
@@ -1483,6 +1484,7 @@
   },
   {
    "cell_type": "code",
+   "execution_count": 10,
    "id": "a28a39a8",
    "metadata": {
     "ExecuteTime": {
@@ -1490,43 +1492,9 @@
      "start_time": "2025-05-22T18:12:14.061969Z"
     }
    },
-   "source": [
-    "S2_USA_GRID_FILE = DATA_DIR / \"s2_grid_usa_polygon_5070.gpkg\"\n",
-    "s2_grid = gpd.read_file(S2_USA_GRID_FILE)\n",
-    "s2_grid"
-   ],
    "outputs": [
     {
      "data": {
-      "text/plain": [
-       "      name   folders                                        description  \\\n",
-       "0    12TUP  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "1    12TYQ  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "2    12TYR  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "3    12TYN  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "4    12TYP  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "..     ...       ...                                                ...   \n",
-       "977  12TTM  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "978  12TUK  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "979  12TUQ  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "980  12TUR  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "981  12TUN  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "\n",
-       "                                              geometry  \n",
-       "0    MULTIPOLYGON Z (((-1386334.944 2487548.77 0, -...  \n",
-       "1    MULTIPOLYGON Z (((-976300.478 2523767.452 0, -...  \n",
-       "2    MULTIPOLYGON Z (((-960099.705 2622374.255 0, -...  \n",
-       "3    MULTIPOLYGON Z (((-1008622.024 2325748.358 0, ...  \n",
-       "4    MULTIPOLYGON Z (((-992478.385 2424861.34 0, -8...  \n",
-       "..                                                 ...  \n",
-       "977  MULTIPOLYGON Z (((-1515431.586 2304192.826 0, ...  \n",
-       "978  MULTIPOLYGON Z (((-1448525.813 2089886.667 0, ...  \n",
-       "979  MULTIPOLYGON Z (((-1371006.917 2586590.133 0, ...  \n",
-       "980  MULTIPOLYGON Z (((-1355793.563 2685354.08 0, -...  \n",
-       "981  MULTIPOLYGON Z (((-1401759.785 2388321.4 0, -1...  \n",
-       "\n",
-       "[982 rows x 4 columns]"
-      ],
       "text/html": [
        "<div>\n",
        "<style scoped>\n",
@@ -1634,6 +1602,35 @@
        "</table>\n",
        "<p>982 rows × 4 columns</p>\n",
        "</div>"
+      ],
+      "text/plain": [
+       "      name   folders                                        description  \\\n",
+       "0    12TUP  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "1    12TYQ  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "2    12TYR  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "3    12TYN  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "4    12TYP  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "..     ...       ...                                                ...   \n",
+       "977  12TTM  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "978  12TUK  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "979  12TUQ  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "980  12TUR  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "981  12TUN  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "\n",
+       "                                              geometry  \n",
+       "0    MULTIPOLYGON Z (((-1386334.944 2487548.77 0, -...  \n",
+       "1    MULTIPOLYGON Z (((-976300.478 2523767.452 0, -...  \n",
+       "2    MULTIPOLYGON Z (((-960099.705 2622374.255 0, -...  \n",
+       "3    MULTIPOLYGON Z (((-1008622.024 2325748.358 0, ...  \n",
+       "4    MULTIPOLYGON Z (((-992478.385 2424861.34 0, -8...  \n",
+       "..                                                 ...  \n",
+       "977  MULTIPOLYGON Z (((-1515431.586 2304192.826 0, ...  \n",
+       "978  MULTIPOLYGON Z (((-1448525.813 2089886.667 0, ...  \n",
+       "979  MULTIPOLYGON Z (((-1371006.917 2586590.133 0, ...  \n",
+       "980  MULTIPOLYGON Z (((-1355793.563 2685354.08 0, -...  \n",
+       "981  MULTIPOLYGON Z (((-1401759.785 2388321.4 0, -1...  \n",
+       "\n",
+       "[982 rows x 4 columns]"
       ]
      },
      "execution_count": 10,
@@ -1641,10 +1638,15 @@
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 10
+   "source": [
+    "S2_USA_GRID_FILE = DATA_DIR / \"s2_grid_usa_polygon_5070.gpkg\"\n",
+    "s2_grid = gpd.read_file(S2_USA_GRID_FILE)\n",
+    "s2_grid"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 11,
    "id": "ba455cf71d209878",
    "metadata": {
     "ExecuteTime": {
@@ -1652,15 +1654,6 @@
      "start_time": "2025-05-22T18:12:14.147937Z"
     }
    },
-   "source": [
-    "# Creating our S2 grid tile subset\n",
-    "\n",
-    "S2_USA_GRID_SUBSET_FILE = TEST_TMP_DIR / \"s2_grid_usa_polygon_5070_subset.gpkg\"\n",
-    "s2_grid_subset = s2_grid[s2_grid[\"name\"].isin(s2_tile_grid_subset_list)]\n",
-    "\n",
-    "# Optionally save to geopackage\n",
-    "to_geopackage(gdf=s2_grid_subset, filename=S2_USA_GRID_SUBSET_FILE)"
-   ],
    "outputs": [
     {
      "name": "stdout",
@@ -1681,10 +1674,19 @@
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 11
+   "source": [
+    "# Creating our S2 grid tile subset\n",
+    "\n",
+    "S2_USA_GRID_SUBSET_FILE = TEST_TMP_DIR / \"s2_grid_usa_polygon_5070_subset.gpkg\"\n",
+    "s2_grid_subset = s2_grid[s2_grid[\"name\"].isin(s2_tile_grid_subset_list)]\n",
+    "\n",
+    "# Optionally save to geopackage\n",
+    "to_geopackage(gdf=s2_grid_subset, filename=S2_USA_GRID_SUBSET_FILE)"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 12,
    "id": "1768b409e3462310",
    "metadata": {
     "ExecuteTime": {
@@ -1692,23 +1694,9 @@
      "start_time": "2025-05-22T18:12:14.237600Z"
     }
    },
-   "source": [
-    "s2_grid_subset"
-   ],
    "outputs": [
     {
      "data": {
-      "text/plain": [
-       "      name   folders                                        description  \\\n",
-       "841  10SDJ  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "846  10TDK  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "857  10TEK  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
-       "\n",
-       "                                              geometry  \n",
-       "841  MULTIPOLYGON Z (((-2357236.175 2210256.163 0, ...  \n",
-       "846  MULTIPOLYGON Z (((-2329019.777 2307113.875 0, ...  \n",
-       "857  MULTIPOLYGON Z (((-2233778.019 2279366.081 0, ...  "
-      ],
       "text/html": [
        "<div>\n",
        "<style scoped>\n",
@@ -1759,6 +1747,17 @@
        "  </tbody>\n",
        "</table>\n",
        "</div>"
+      ],
+      "text/plain": [
+       "      name   folders                                        description  \\\n",
+       "841  10SDJ  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "846  10TDK  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "857  10TEK  Features  TILE PROPERTIES<br><table border=0 cellpadding...   \n",
+       "\n",
+       "                                              geometry  \n",
+       "841  MULTIPOLYGON Z (((-2357236.175 2210256.163 0, ...  \n",
+       "846  MULTIPOLYGON Z (((-2329019.777 2307113.875 0, ...  \n",
+       "857  MULTIPOLYGON Z (((-2233778.019 2279366.081 0, ...  "
       ]
      },
      "execution_count": 12,
@@ -1766,10 +1765,13 @@
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 12
+   "source": [
+    "s2_grid_subset"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 13,
    "id": "142cc83267ef999",
    "metadata": {
     "ExecuteTime": {
@@ -1777,18 +1779,6 @@
      "start_time": "2025-05-22T18:12:14.524824Z"
     }
    },
-   "source": [
-    "# Creating our polygon grid subset\n",
-    "\n",
-    "intersect_polygons_subset_filename = TEST_TMP_DIR / \"intersecting_polygon_grid_10km_subset.gpkg\"\n",
-    "print(\"Starting intersect selection\")\n",
-    "intersect_polygons_subset = select_polygons_by_location(intersecting_polygons, s2_grid_subset, predicate=\"within\",\n",
-    "                                                        num_of_workers=4)\n",
-    "# intersect_polygons_subset = gpd.read_file(intersect_polygons_subset_filename)\n",
-    "\n",
-    "# Optionally save to a new file\n",
-    "to_geopackage(intersect_polygons_subset, intersect_polygons_subset_filename)"
-   ],
    "outputs": [
     {
      "name": "stdout",
@@ -1815,7 +1805,18 @@
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 13
+   "source": [
+    "# Creating our polygon grid subset\n",
+    "\n",
+    "intersect_polygons_subset_filename = TEST_TMP_DIR / \"intersecting_polygon_grid_10km_subset.gpkg\"\n",
+    "print(\"Starting intersect selection\")\n",
+    "intersect_polygons_subset = select_polygons_by_location(intersecting_polygons, s2_grid_subset, predicate=\"within\",\n",
+    "                                                        num_of_workers=4)\n",
+    "# intersect_polygons_subset = gpd.read_file(intersect_polygons_subset_filename)\n",
+    "\n",
+    "# Optionally save to a new file\n",
+    "to_geopackage(intersect_polygons_subset, intersect_polygons_subset_filename)"
+   ]
   },
   {
    "cell_type": "markdown",
@@ -1827,6 +1828,7 @@
   },
   {
    "cell_type": "code",
+   "execution_count": 14,
    "id": "e6ccf064d6ac84c4",
    "metadata": {
     "ExecuteTime": {
@@ -1834,6 +1836,7 @@
      "start_time": "2025-05-22T18:12:14.975761Z"
     }
    },
+   "outputs": [],
    "source": [
     "s2_feature_name_columns = \"name\"\n",
     "vector_column_name = \"s2_tiles\"\n",
@@ -1844,36 +1847,19 @@
     "                                               vector_features=intersect_polygons_subset,\n",
     "                                               vector_features_column=vector_column_name,\n",
     "                                               max_cloud_cover=15)"
-   ],
-   "outputs": [],
-   "execution_count": 14
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 15,
    "id": "252557658101af43",
    "metadata": {
-    "scrolled": true,
     "ExecuteTime": {
      "end_time": "2025-05-22T18:12:16.895518Z",
      "start_time": "2025-05-22T18:12:15.030061Z"
-    }
+    },
+    "scrolled": true
    },
-   "source": [
-    "# NBVAL_IGNORE_OUTPUT\n",
-    "\n",
-    "# Executing the search\n",
-    "#\n",
-    "# This search look only for complete products, meaning products with less than\n",
-    "# 5 percent of nodata.\n",
-    "\n",
-    "start_year = 2024\n",
-    "end_year = 2024\n",
-    "start_month = 6\n",
-    "end_month = 7\n",
-    "\n",
-    "best_products_client.create_date_ranges(start_year, end_year, start_month, end_month)\n",
-    "products = best_products_client.find_best_complete_products()"
-   ],
    "outputs": [
     {
      "name": "stdout",
@@ -1893,10 +1879,26 @@
      ]
     }
    ],
-   "execution_count": 15
+   "source": [
+    "# NBVAL_IGNORE_OUTPUT\n",
+    "\n",
+    "# Executing the search\n",
+    "#\n",
+    "# This search look only for complete products, meaning products with less than\n",
+    "# 5 percent of nodata.\n",
+    "\n",
+    "start_year = 2024\n",
+    "end_year = 2024\n",
+    "start_month = 6\n",
+    "end_month = 7\n",
+    "\n",
+    "best_products_client.create_date_ranges(start_year, end_year, start_month, end_month)\n",
+    "products = best_products_client.find_best_complete_products()"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 16,
    "id": "3dfc816677db50aa",
    "metadata": {
     "ExecuteTime": {
@@ -1904,9 +1906,6 @@
      "start_time": "2025-05-22T18:12:16.911803Z"
     }
    },
-   "source": [
-    "products"
-   ],
    "outputs": [
     {
      "data": {
@@ -1924,10 +1923,13 @@
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 16
+   "source": [
+    "products"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 17,
    "id": "6a0a1885db3cd559",
    "metadata": {
     "ExecuteTime": {
@@ -1935,15 +1937,6 @@
      "start_time": "2025-05-22T18:12:16.969725Z"
     }
    },
-   "source": [
-    "# Selecting the best products for each vector tile\n",
-    "# This step is necessary as some of our vector polygons can be withing multiple S2 tiles.\n",
-    "# The best available S2 tile is therefore selected for each vector polygon.\n",
-    "\n",
-    "best_results_path = TEST_TMP_DIR / \"vector_tiles_with_s2tiles_subset.gpkg\"\n",
-    "best_results = best_products_client.select_best_products_per_feature()\n",
-    "to_geopackage(best_results, best_results_path)\n"
-   ],
    "outputs": [
     {
      "name": "stdout",
@@ -1970,7 +1963,15 @@
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 17
+   "source": [
+    "# Selecting the best products for each vector tile\n",
+    "# This step is necessary as some of our vector polygons can be withing multiple S2 tiles.\n",
+    "# The best available S2 tile is therefore selected for each vector polygon.\n",
+    "\n",
+    "best_results_path = TEST_TMP_DIR / \"vector_tiles_with_s2tiles_subset.gpkg\"\n",
+    "best_results = best_products_client.select_best_products_per_feature()\n",
+    "to_geopackage(best_results, best_results_path)\n"
+   ]
   },
   {
    "cell_type": "markdown",
@@ -1982,6 +1983,7 @@
   },
   {
    "cell_type": "code",
+   "execution_count": 19,
    "id": "48d5dd0759bc2a51",
    "metadata": {
     "ExecuteTime": {
@@ -1989,9 +1991,6 @@
      "start_time": "2025-05-22T18:12:17.101510Z"
     }
    },
-   "source": [
-    "best_products_client.successful_results"
-   ],
    "outputs": [
     {
      "data": {
@@ -2009,10 +2008,13 @@
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 19
+   "source": [
+    "best_products_client.successful_results"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 20,
    "id": "289caace-c963-4fe5-9a9e-b61a3f25473b",
    "metadata": {
     "ExecuteTime": {
@@ -2020,9 +2022,6 @@
      "start_time": "2025-05-22T18:12:17.161333Z"
     }
    },
-   "source": [
-    "best_products_client.incomplete_results"
-   ],
    "outputs": [
     {
      "data": {
@@ -2035,10 +2034,13 @@
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 20
+   "source": [
+    "best_products_client.incomplete_results"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 21,
    "id": "37ee4600ae353b9c",
    "metadata": {
     "ExecuteTime": {
@@ -2046,33 +2048,33 @@
      "start_time": "2025-05-22T18:12:17.227522Z"
     }
    },
-   "source": [
-    "m_best_results = leafmap.Map(center=[39.7, -123], zoom=8)\n",
-    "m_best_results.add_gdf(s2_grid_subset, layer_name='s2_tiles', style={\"color\": \"red\"})\n",
-    "m_best_results.add_gdf(best_results, layer_name='vector_tiles_s2_grid', style={\"color\": \"green\"})\n",
-    "m_best_results"
-   ],
    "outputs": [
     {
      "data": {
-      "text/plain": [
-       "Map(center=[39.7, -123], controls=(ZoomControl(options=['position', 'zoom_in_text', 'zoom_in_title', 'zoom_out…"
-      ],
       "application/vnd.jupyter.widget-view+json": {
+       "model_id": "662e526f758448dfb5e884177b3ca024",
        "version_major": 2,
-       "version_minor": 0,
-       "model_id": "662e526f758448dfb5e884177b3ca024"
-      }
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Map(center=[39.7, -123], controls=(ZoomControl(options=['position', 'zoom_in_text', 'zoom_in_title', 'zoom_out…"
+      ]
      },
      "execution_count": 21,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 21
+   "source": [
+    "m_best_results = leafmap.Map(center=[39.7, -123], zoom=8)\n",
+    "m_best_results.add_gdf(s2_grid_subset, layer_name=\"s2_tiles\", style={\"color\": \"red\"})\n",
+    "m_best_results.add_gdf(best_results, layer_name=\"vector_tiles_s2_grid\", style={\"color\": \"green\"})\n",
+    "m_best_results"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 22,
    "id": "4483f48422d09481",
    "metadata": {
     "ExecuteTime": {
@@ -2080,15 +2082,15 @@
      "start_time": "2025-05-22T18:12:17.415852Z"
     }
    },
+   "outputs": [],
    "source": [
     "# NBVAL_IGNORE_OUTPUT\n",
     "group_by_product = best_results.groupby(\"best_s2_product_id\")[\"feature_id\"].agg(list).reset_index()"
-   ],
-   "outputs": [],
-   "execution_count": 22
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 23,
    "id": "33797d5a6fdc1e59",
    "metadata": {
     "ExecuteTime": {
@@ -2096,10 +2098,6 @@
      "start_time": "2025-05-22T18:12:17.470155Z"
     }
    },
-   "source": [
-    "product_list = group_by_product[\"best_s2_product_id\"].tolist()\n",
-    "sorted(product_list)"
-   ],
    "outputs": [
     {
      "data": {
@@ -2113,7 +2111,10 @@
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 23
+   "source": [
+    "product_list = group_by_product[\"best_s2_product_id\"].tolist()\n",
+    "sorted(product_list)"
+   ]
   },
   {
    "cell_type": "markdown",
@@ -2133,6 +2134,7 @@
   },
   {
    "cell_type": "code",
+   "execution_count": 24,
    "id": "da281a638f42c0dc",
    "metadata": {
     "ExecuteTime": {
@@ -2140,20 +2142,6 @@
      "start_time": "2025-05-22T18:12:17.535342Z"
     }
    },
-   "source": [
-    "# NBVAL_IGNORE_OUTPUT\n",
-    "product_asset_list = []\n",
-    "bands = [\"B04\", \"B08\"]\n",
-    "download_directory = TEST_TMP_DIR / \"example_s2_download_and_processing\"\n",
-    "\n",
-    "for p in product_list:\n",
-    "    processed_product = download_and_process_sentinel2_asset(product_id=p,\n",
-    "                                                             product_bands=bands,\n",
-    "                                                             base_directory=download_directory,\n",
-    "                                                             target_projection=5070)\n",
-    "\n",
-    "    product_asset_list.append(processed_product)"
-   ],
    "outputs": [
     {
      "name": "stdout",
@@ -2206,10 +2194,24 @@
      ]
     }
    ],
-   "execution_count": 24
+   "source": [
+    "# NBVAL_IGNORE_OUTPUT\n",
+    "product_asset_list = []\n",
+    "bands = [\"B04\", \"B08\"]\n",
+    "download_directory = TEST_TMP_DIR / \"example_s2_download_and_processing\"\n",
+    "\n",
+    "for p in product_list:\n",
+    "    processed_product = download_and_process_sentinel2_asset(product_id=p,\n",
+    "                                                             product_bands=bands,\n",
+    "                                                             base_directory=download_directory,\n",
+    "                                                             target_projection=5070)\n",
+    "\n",
+    "    product_asset_list.append(processed_product)"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 25,
    "id": "99d6fe45792cd970",
    "metadata": {
     "ExecuteTime": {
@@ -2217,11 +2219,6 @@
      "start_time": "2025-05-22T18:14:00.552939Z"
     }
    },
-   "source": [
-    "for p in product_asset_list:\n",
-    "    print(f\"Asset ID : [{p.asset_id}]\")\n",
-    "    print(f\"Reprojected ID path : \\n[{p.reprojected_asset_path}]\\n\")\n"
-   ],
    "outputs": [
     {
      "name": "stdout",
@@ -2238,10 +2235,15 @@
      ]
     }
    ],
-   "execution_count": 25
+   "source": [
+    "for p in product_asset_list:\n",
+    "    print(f\"Asset ID : [{p.asset_id}]\")\n",
+    "    print(f\"Reprojected ID path : \\n[{p.reprojected_asset_path}]\\n\")\n"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 26,
    "id": "715945b328c8ef71",
    "metadata": {
     "ExecuteTime": {
@@ -2249,14 +2251,13 @@
      "start_time": "2025-05-22T18:14:00.617720Z"
     }
    },
+   "outputs": [],
    "source": [
     "# Here, we are creating a new Asset object simply for convenience, from the printed outputs above\n",
     "\n",
     "product = Asset(asset_id=\"S2A_MSIL2A_20240705T185921_R013_T10SDJ_20240706T050346\",\n",
     "                reprojected_asset=download_directory / \"S2A_MSIL2A_20240705T185921_R013_T10SDJ_20240706T050346_reprojected.tif\", )"
-   ],
-   "outputs": [],
-   "execution_count": 26
+   ]
   },
   {
    "cell_type": "markdown",
@@ -2268,6 +2269,7 @@
   },
   {
    "cell_type": "code",
+   "execution_count": 27,
    "id": "77a04eaa79969a9c",
    "metadata": {
     "ExecuteTime": {
@@ -2275,17 +2277,6 @@
      "start_time": "2025-05-22T18:14:00.678421Z"
     }
    },
-   "source": [
-    "\n",
-    "s2_product_id = product.asset_id\n",
-    "product_path = product.reprojected_asset_path\n",
-    "product_id_series = group_by_product[group_by_product[\"best_s2_product_id\"] == s2_product_id]\n",
-    "# Since it's grouped by product id, there should always be only one row in the series\n",
-    "feature_ids = product_id_series[\"feature_id\"].iloc[0]\n",
-    "vector_features = best_results[best_results[\"feature_id\"].isin(feature_ids)]\n",
-    "vector_features_path = TEST_TMP_DIR / \"vector_features.gpkg\"\n",
-    "to_geopackage(vector_features, TEST_TMP_DIR / \"vector_features.gpkg\")"
-   ],
    "outputs": [
     {
      "name": "stdout",
@@ -2306,7 +2297,17 @@
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 27
+   "source": [
+    "\n",
+    "s2_product_id = product.asset_id\n",
+    "product_path = product.reprojected_asset_path\n",
+    "product_id_series = group_by_product[group_by_product[\"best_s2_product_id\"] == s2_product_id]\n",
+    "# Since it's grouped by product id, there should always be only one row in the series\n",
+    "feature_ids = product_id_series[\"feature_id\"].iloc[0]\n",
+    "vector_features = best_results[best_results[\"feature_id\"].isin(feature_ids)]\n",
+    "vector_features_path = TEST_TMP_DIR / \"vector_features.gpkg\"\n",
+    "to_geopackage(vector_features, TEST_TMP_DIR / \"vector_features.gpkg\")"
+   ]
   },
   {
    "cell_type": "markdown",
@@ -2318,6 +2319,7 @@
   },
   {
    "cell_type": "code",
+   "execution_count": 28,
    "id": "398c4fe713929a94",
    "metadata": {
     "ExecuteTime": {
@@ -2325,12 +2327,6 @@
      "start_time": "2025-05-22T18:14:00.745973Z"
     }
    },
-   "source": [
-    "clip_list = clip_raster_with_polygon(raster_image=product_path,\n",
-    "                                     polygon_layer=vector_features_path,\n",
-    "                                     base_output_filename=s2_product_id,\n",
-    "                                     output_dir=download_directory / \"test_sentinel2_clip\")"
-   ],
    "outputs": [
     {
      "name": "stdout",
@@ -2343,10 +2339,16 @@
      ]
     }
    ],
-   "execution_count": 28
+   "source": [
+    "clip_list = clip_raster_with_polygon(raster_image=product_path,\n",
+    "                                     polygon_layer=vector_features_path,\n",
+    "                                     base_output_filename=s2_product_id,\n",
+    "                                     output_dir=download_directory / \"test_sentinel2_clip\")"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 29,
    "id": "2d24fa3dad57032c",
    "metadata": {
     "ExecuteTime": {
@@ -2354,9 +2356,6 @@
      "start_time": "2025-05-22T18:14:02.111120Z"
     }
    },
-   "source": [
-    "sorted(clip_list)"
-   ],
    "outputs": [
     {
      "data": {
@@ -2441,10 +2440,13 @@
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 29
+   "source": [
+    "sorted(clip_list)"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 30,
    "id": "43a5f61e33592e0b",
    "metadata": {
     "ExecuteTime": {
@@ -2452,11 +2454,10 @@
      "start_time": "2025-05-22T18:14:02.180315Z"
     }
    },
+   "outputs": [],
    "source": [
     "shutil.rmtree(TEST_TMP_DIR)"
-   ],
-   "outputs": [],
-   "execution_count": 30
+   ]
   }
  ],
  "metadata": {
diff --git a/tests/test_notebooks/test_stac_api_tools.ipynb b/tests/test_notebooks/test_stac_api_tools.ipynb
index 47b3c40..95e520a 100644
--- a/tests/test_notebooks/test_stac_api_tools.ipynb
+++ b/tests/test_notebooks/test_stac_api_tools.ipynb
@@ -10,6 +10,7 @@
   },
   {
    "cell_type": "code",
+   "execution_count": 1,
    "id": "d9905141ab1e36a5",
    "metadata": {
     "ExecuteTime": {
@@ -17,20 +18,21 @@
      "start_time": "2025-05-22T18:17:07.194864Z"
     }
    },
+   "outputs": [],
    "source": [
     "import shutil\n",
+    "from pathlib import Path\n",
+    "\n",
     "import geopandas as gpd\n",
     "\n",
-    "from pathlib import Path\n",
     "from geospatial_tools import DATA_DIR, TESTS_DIR\n",
-    "from geospatial_tools.stac import StacSearch, PLANETARY_COMPUTER\n",
+    "from geospatial_tools.stac import PLANETARY_COMPUTER, StacSearch\n",
     "from geospatial_tools.utils import create_date_range_for_specific_period"
-   ],
-   "outputs": [],
-   "execution_count": 1
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 2,
    "id": "bc3faf4a613adec0",
    "metadata": {
     "ExecuteTime": {
@@ -38,15 +40,15 @@
      "start_time": "2025-05-22T18:17:07.875690Z"
     }
    },
+   "outputs": [],
    "source": [
     "TEST_TMP_DIR = TESTS_DIR / \"tmp_stac_api_tools\"\n",
     "TEST_TMP_DIR.mkdir(exist_ok=True)"
-   ],
-   "outputs": [],
-   "execution_count": 2
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 3,
    "id": "e93f22661d7785fa",
    "metadata": {
     "ExecuteTime": {
@@ -54,12 +56,11 @@
      "start_time": "2025-05-22T18:17:07.923669Z"
     }
    },
+   "outputs": [],
    "source": [
     "S2_USA_GRID_FILE = DATA_DIR / \"s2_grid_usa_polygon_5070.gpkg\"\n",
     "s2_grid = gpd.read_file(S2_USA_GRID_FILE)"
-   ],
-   "outputs": [],
-   "execution_count": 3
+   ]
   },
   {
    "cell_type": "markdown",
@@ -81,6 +82,7 @@
   },
   {
    "cell_type": "code",
+   "execution_count": 4,
    "id": "ee10a895c05db253",
    "metadata": {
     "ExecuteTime": {
@@ -88,6 +90,17 @@
      "start_time": "2025-05-22T18:17:07.972574Z"
     }
    },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[2025-05-22 14:17:08] INFO       [MainThread][geospatial_tools.stac] Running STAC API search for the following parameters: \n",
+      "\tDate ranges : ['2024-06-01T00:00:00Z/2024-07-31T23:59:59Z'] \n",
+      "\tQuery : {'eo:cloud_cover': {'lt': 1}, 's2:mgrs_tile': {'in': ['10SDJ']}}\n"
+     ]
+    }
+   ],
    "source": [
     "# Date ranges\n",
     "start_year = 2024\n",
@@ -120,22 +133,11 @@
     "\n",
     "filtered_items = search_client.filtered_results\n",
     "optimal_result = filtered_items[0]"
-   ],
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "[2025-05-22 14:17:08] INFO       [MainThread][geospatial_tools.stac] Running STAC API search for the following parameters: \n",
-      "\tDate ranges : ['2024-06-01T00:00:00Z/2024-07-31T23:59:59Z'] \n",
-      "\tQuery : {'eo:cloud_cover': {'lt': 1}, 's2:mgrs_tile': {'in': ['10SDJ']}}\n"
-     ]
-    }
-   ],
-   "execution_count": 4
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 5,
    "id": "a847c23f04916c18",
    "metadata": {
     "ExecuteTime": {
@@ -143,17 +145,6 @@
      "start_time": "2025-05-22T18:17:09.946550Z"
     }
    },
-   "source": [
-    "print(\"\\nSorted results\")\n",
-    "for item in filtered_items:\n",
-    "    print(f\"Item: {item.id}, {item.datetime}, \"\n",
-    "          f\"Cloud cover: {item.properties['eo:cloud_cover']}, \"\n",
-    "          f\"Nodata: {item.properties['s2:nodata_pixel_percentage']}\")\n",
-    "\n",
-    "print(f\"\\nOptimal result: {optimal_result.id}, {optimal_result.datetime}, \"\n",
-    "      f\"Cloud cover: {optimal_result.properties['eo:cloud_cover']}, \"\n",
-    "      f\"Nodata: {optimal_result.properties['s2:nodata_pixel_percentage']}\")"
-   ],
    "outputs": [
     {
      "name": "stdout",
@@ -172,10 +163,21 @@
      ]
     }
    ],
-   "execution_count": 5
+   "source": [
+    "print(\"\\nSorted results\")\n",
+    "for item in filtered_items:\n",
+    "    print(f\"Item: {item.id}, {item.datetime}, \"\n",
+    "          f\"Cloud cover: {item.properties['eo:cloud_cover']}, \"\n",
+    "          f\"Nodata: {item.properties['s2:nodata_pixel_percentage']}\")\n",
+    "\n",
+    "print(f\"\\nOptimal result: {optimal_result.id}, {optimal_result.datetime}, \"\n",
+    "      f\"Cloud cover: {optimal_result.properties['eo:cloud_cover']}, \"\n",
+    "      f\"Nodata: {optimal_result.properties['s2:nodata_pixel_percentage']}\")"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 6,
    "id": "f4ec68848b408098",
    "metadata": {
     "ExecuteTime": {
@@ -183,12 +185,6 @@
      "start_time": "2025-05-22T18:17:09.997517Z"
     }
    },
-   "source": [
-    "# NBVAL_IGNORE_OUTPUT\n",
-    "bands = [\"visual\"]\n",
-    "file_base_path = Path(f\"{TEST_TMP_DIR}/sentinel-2/\")\n",
-    "best_result = search_client.download_best_cloud_cover_result(bands=bands, base_directory=file_base_path)"
-   ],
    "outputs": [
     {
      "name": "stdout",
@@ -200,10 +196,16 @@
      ]
     }
    ],
-   "execution_count": 6
+   "source": [
+    "# NBVAL_IGNORE_OUTPUT\n",
+    "bands = [\"visual\"]\n",
+    "file_base_path = Path(f\"{TEST_TMP_DIR}/sentinel-2/\")\n",
+    "best_result = search_client.download_best_cloud_cover_result(bands=bands, base_directory=file_base_path)"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 7,
    "id": "d39afa9f75ed355f",
    "metadata": {
     "ExecuteTime": {
@@ -211,9 +213,6 @@
      "start_time": "2025-05-22T18:17:45.519522Z"
     }
    },
-   "source": [
-    "best_result.asset_id"
-   ],
    "outputs": [
     {
      "data": {
@@ -226,10 +225,13 @@
      "output_type": "execute_result"
     }
    ],
-   "execution_count": 7
+   "source": [
+    "best_result.asset_id"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 8,
    "id": "553190ac13f3f758",
    "metadata": {
     "ExecuteTime": {
@@ -237,12 +239,6 @@
      "start_time": "2025-05-22T18:17:45.584293Z"
     }
    },
-   "source": [
-    "merged = best_result.merge_asset(base_directory=file_base_path, delete_sub_items=True)\n",
-    "reprojected = best_result.reproject_merged_asset(target_projection=5070, \n",
-    "                                                 base_directory=file_base_path,\n",
-    "                                                 delete_merged_asset=True)"
-   ],
    "outputs": [
     {
      "name": "stdout",
@@ -268,10 +264,16 @@
      ]
     }
    ],
-   "execution_count": 8
+   "source": [
+    "merged = best_result.merge_asset(base_directory=file_base_path, delete_sub_items=True)\n",
+    "reprojected = best_result.reproject_merged_asset(target_projection=5070,\n",
+    "                                                 base_directory=file_base_path,\n",
+    "                                                 delete_merged_asset=True)"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 9,
    "id": "5be37e4e719010a5",
    "metadata": {
     "ExecuteTime": {
@@ -279,11 +281,10 @@
      "start_time": "2025-05-22T18:17:54.661901Z"
     }
    },
+   "outputs": [],
    "source": [
     "shutil.rmtree(TEST_TMP_DIR)"
-   ],
-   "outputs": [],
-   "execution_count": 9
+   ]
   }
  ],
  "metadata": {
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 1251aa6..028330f 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -1,5 +1,3 @@
-from typing import Union
-
 import pytest
 
 from geospatial_tools.utils import create_crs, create_date_range_for_specific_period
@@ -17,7 +15,7 @@
         pytest.param("ESPGG:5070", "EPSG:5070", id="From full code but with typo in EPSG"),
     ],
 )
-def test_create_crs(code: Union[str, int], expected: str):
+def test_create_crs(code: str | int, expected: str):
     crs = create_crs(code)
     assert crs == expected
 
diff --git a/tests/test_vector.py b/tests/test_vector.py
index 9642e2c..334fe83 100644
--- a/tests/test_vector.py
+++ b/tests/test_vector.py
@@ -70,5 +70,5 @@ def test_spatial_join_within():
         check_dtype=False,  # Ignore dtype differences if necessary
     )
 
-    for result_geom, expected_geom in zip(result_sorted.geometry, expected_sorted.geometry):
+    for result_geom, expected_geom in zip(result_sorted.geometry, expected_sorted.geometry, strict=False):
         assert result_geom.equals_exact(expected_geom, tolerance=1e-6)

From edd63dc027a38ef953cb4fb4831b6a112dddc035 Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Thu, 22 May 2025 16:02:01 -0400
Subject: [PATCH 04/19] Fix using Ruff

---
 geospatial_tools/geotools_types.py            |  4 +-
 geospatial_tools/utils.py                     |  1 +
 geospatial_tools/vector.py                    |  8 ++--
 pyproject.toml                                |  6 ++-
 .../test_planetary_computer_sentinel2.ipynb   | 45 ++++++++++---------
 .../test_notebooks/test_stac_api_tools.ipynb  | 36 ++++++++-------
 6 files changed, 56 insertions(+), 44 deletions(-)

diff --git a/geospatial_tools/geotools_types.py b/geospatial_tools/geotools_types.py
index 0c8c303..b13de62 100644
--- a/geospatial_tools/geotools_types.py
+++ b/geospatial_tools/geotools_types.py
@@ -1,7 +1,5 @@
 """This module contains constants and functions pertaining to data types."""
 
-from typing import Union
-
 from shapely.geometry import (
     GeometryCollection,
     LineString,
@@ -13,4 +11,4 @@
 )
 
 BBoxLike = tuple[float, float, float, float]
-IntersectsLike = Union[Point, Polygon, LineString, MultiPolygon, MultiPoint, MultiLineString, GeometryCollection]
+IntersectsLike = Point | Polygon | LineString | MultiPolygon | MultiPoint | MultiLineString | GeometryCollection
diff --git a/geospatial_tools/utils.py b/geospatial_tools/utils.py
index 1b95200..683d29a 100644
--- a/geospatial_tools/utils.py
+++ b/geospatial_tools/utils.py
@@ -182,6 +182,7 @@ def create_crs(dataset_crs: str | int, logger=LOGGER):
             return CRS.from_epsg(recovered_code)
 
     logger.error(f"Encountered problem while trying to format EPSG code from input : [{dataset_crs}]")
+    return None
 
 
 def download_url(url: str, filename: str | pathlib.Path, overwrite: bool = False, logger=LOGGER) -> pathlib.Path | None:
diff --git a/geospatial_tools/vector.py b/geospatial_tools/vector.py
index a386bc0..e6852c2 100644
--- a/geospatial_tools/vector.py
+++ b/geospatial_tools/vector.py
@@ -458,11 +458,13 @@ def add_and_fill_contained_column(
     logger.info(f"Selecting all vector features that are within {feature_name}")
     selected_features = select_all_within_feature(polygon_feature=polygon_feature, vector_features=vector_features)
     logger.info(f"Writing [{feature_name}] to selected vector features")
-    [  # pylint: disable=W0106
-        vector_features.at[idx, vector_column_name].add(feature_name) for idx in selected_features.index
-    ]
+
+    vector_features.loc[selected_features.index, vector_column_name] = vector_features.loc[
+        selected_features.index, vector_column_name
+    ].apply(lambda s: s | {feature_name})
 
 
+# Potential outdated function
 def find_and_write_all_contained_features(
     polygon_features: gpd.GeoDataFrame,
     polygon_column: str,
diff --git a/pyproject.toml b/pyproject.toml
index b9c03f7..4568253 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -203,12 +203,16 @@ ignore = [
   "E266",  # too many leading '#' for comments
   "E501",  # line too long (we enforce via line-length instead)
   "RET504",
-  "RUF013"
+  "RUF013",
+  "PTH123"
 ]
 
 [tool.ruff.lint.pydocstyle]
 convention = "numpy" # Corresponds to flake8's docstring-convention and docformatter style.
 
+[tool.ruff.lint.pylint]
+max-args = 16
+
 [tool.ruff.lint.mccabe]
 # cyclomatic complexity
 max-complexity = 18
diff --git a/tests/test_notebooks/test_planetary_computer_sentinel2.ipynb b/tests/test_notebooks/test_planetary_computer_sentinel2.ipynb
index 1242506..85647d0 100644
--- a/tests/test_notebooks/test_planetary_computer_sentinel2.ipynb
+++ b/tests/test_notebooks/test_planetary_computer_sentinel2.ipynb
@@ -1810,8 +1810,9 @@
     "\n",
     "intersect_polygons_subset_filename = TEST_TMP_DIR / \"intersecting_polygon_grid_10km_subset.gpkg\"\n",
     "print(\"Starting intersect selection\")\n",
-    "intersect_polygons_subset = select_polygons_by_location(intersecting_polygons, s2_grid_subset, predicate=\"within\",\n",
-    "                                                        num_of_workers=4)\n",
+    "intersect_polygons_subset = select_polygons_by_location(\n",
+    "    intersecting_polygons, s2_grid_subset, predicate=\"within\", num_of_workers=4\n",
+    ")\n",
     "# intersect_polygons_subset = gpd.read_file(intersect_polygons_subset_filename)\n",
     "\n",
     "# Optionally save to a new file\n",
@@ -1842,11 +1843,13 @@
     "vector_column_name = \"s2_tiles\"\n",
     "\n",
     "# Initiating our client\n",
-    "best_products_client = BestProductsForFeatures(sentinel2_tiling_grid=s2_grid_subset,\n",
-    "                                               sentinel2_tiling_grid_column=s2_feature_name_columns,\n",
-    "                                               vector_features=intersect_polygons_subset,\n",
-    "                                               vector_features_column=vector_column_name,\n",
-    "                                               max_cloud_cover=15)"
+    "best_products_client = BestProductsForFeatures(\n",
+    "    sentinel2_tiling_grid=s2_grid_subset,\n",
+    "    sentinel2_tiling_grid_column=s2_feature_name_columns,\n",
+    "    vector_features=intersect_polygons_subset,\n",
+    "    vector_features_column=vector_column_name,\n",
+    "    max_cloud_cover=15,\n",
+    ")"
    ]
   },
   {
@@ -1970,7 +1973,7 @@
     "\n",
     "best_results_path = TEST_TMP_DIR / \"vector_tiles_with_s2tiles_subset.gpkg\"\n",
     "best_results = best_products_client.select_best_products_per_feature()\n",
-    "to_geopackage(best_results, best_results_path)\n"
+    "to_geopackage(best_results, best_results_path)"
    ]
   },
   {
@@ -2201,10 +2204,9 @@
     "download_directory = TEST_TMP_DIR / \"example_s2_download_and_processing\"\n",
     "\n",
     "for p in product_list:\n",
-    "    processed_product = download_and_process_sentinel2_asset(product_id=p,\n",
-    "                                                             product_bands=bands,\n",
-    "                                                             base_directory=download_directory,\n",
-    "                                                             target_projection=5070)\n",
+    "    processed_product = download_and_process_sentinel2_asset(\n",
+    "        product_id=p, product_bands=bands, base_directory=download_directory, target_projection=5070\n",
+    "    )\n",
     "\n",
     "    product_asset_list.append(processed_product)"
    ]
@@ -2238,7 +2240,7 @@
    "source": [
     "for p in product_asset_list:\n",
     "    print(f\"Asset ID : [{p.asset_id}]\")\n",
-    "    print(f\"Reprojected ID path : \\n[{p.reprojected_asset_path}]\\n\")\n"
+    "    print(f\"Reprojected ID path : \\n[{p.reprojected_asset_path}]\\n\")"
    ]
   },
   {
@@ -2255,8 +2257,10 @@
    "source": [
     "# Here, we are creating a new Asset object simply for convenience, from the printed outputs above\n",
     "\n",
-    "product = Asset(asset_id=\"S2A_MSIL2A_20240705T185921_R013_T10SDJ_20240706T050346\",\n",
-    "                reprojected_asset=download_directory / \"S2A_MSIL2A_20240705T185921_R013_T10SDJ_20240706T050346_reprojected.tif\", )"
+    "product = Asset(\n",
+    "    asset_id=\"S2A_MSIL2A_20240705T185921_R013_T10SDJ_20240706T050346\",\n",
+    "    reprojected_asset=download_directory / \"S2A_MSIL2A_20240705T185921_R013_T10SDJ_20240706T050346_reprojected.tif\",\n",
+    ")"
    ]
   },
   {
@@ -2298,7 +2302,6 @@
     }
    ],
    "source": [
-    "\n",
     "s2_product_id = product.asset_id\n",
     "product_path = product.reprojected_asset_path\n",
     "product_id_series = group_by_product[group_by_product[\"best_s2_product_id\"] == s2_product_id]\n",
@@ -2340,10 +2343,12 @@
     }
    ],
    "source": [
-    "clip_list = clip_raster_with_polygon(raster_image=product_path,\n",
-    "                                     polygon_layer=vector_features_path,\n",
-    "                                     base_output_filename=s2_product_id,\n",
-    "                                     output_dir=download_directory / \"test_sentinel2_clip\")"
+    "clip_list = clip_raster_with_polygon(\n",
+    "    raster_image=product_path,\n",
+    "    polygon_layer=vector_features_path,\n",
+    "    base_output_filename=s2_product_id,\n",
+    "    output_dir=download_directory / \"test_sentinel2_clip\",\n",
+    ")"
    ]
   },
   {
diff --git a/tests/test_notebooks/test_stac_api_tools.ipynb b/tests/test_notebooks/test_stac_api_tools.ipynb
index 95e520a..e6fd2f0 100644
--- a/tests/test_notebooks/test_stac_api_tools.ipynb
+++ b/tests/test_notebooks/test_stac_api_tools.ipynb
@@ -107,10 +107,9 @@
     "end_year = 2024\n",
     "start_month = 6\n",
     "end_month = 7\n",
-    "date_ranges = create_date_range_for_specific_period(start_year=start_year,\n",
-    "                                                    end_year=end_year,\n",
-    "                                                    start_month_range=start_month,\n",
-    "                                                    end_month_range=end_month)\n",
+    "date_ranges = create_date_range_for_specific_period(\n",
+    "    start_year=start_year, end_year=end_year, start_month_range=start_month, end_month_range=end_month\n",
+    ")\n",
     "\n",
     "# Search arguments\n",
     "collection = \"sentinel-2-l2a\"\n",
@@ -122,10 +121,9 @@
     "\n",
     "# Searching for results\n",
     "search_client = StacSearch(PLANETARY_COMPUTER)\n",
-    "search_client.search_for_date_ranges(date_ranges=date_ranges,\n",
-    "                                     collections=collection,\n",
-    "                                     query=query,\n",
-    "                                     sortby=sortby, limit=100)\n",
+    "search_client.search_for_date_ranges(\n",
+    "    date_ranges=date_ranges, collections=collection, query=query, sortby=sortby, limit=100\n",
+    ")\n",
     "\n",
     "# Selecting optimal result\n",
     "search_client.sort_results_by_cloud_coverage()\n",
@@ -166,13 +164,17 @@
    "source": [
     "print(\"\\nSorted results\")\n",
     "for item in filtered_items:\n",
-    "    print(f\"Item: {item.id}, {item.datetime}, \"\n",
-    "          f\"Cloud cover: {item.properties['eo:cloud_cover']}, \"\n",
-    "          f\"Nodata: {item.properties['s2:nodata_pixel_percentage']}\")\n",
+    "    print(\n",
+    "        f\"Item: {item.id}, {item.datetime}, \"\n",
+    "        f\"Cloud cover: {item.properties['eo:cloud_cover']}, \"\n",
+    "        f\"Nodata: {item.properties['s2:nodata_pixel_percentage']}\"\n",
+    "    )\n",
     "\n",
-    "print(f\"\\nOptimal result: {optimal_result.id}, {optimal_result.datetime}, \"\n",
-    "      f\"Cloud cover: {optimal_result.properties['eo:cloud_cover']}, \"\n",
-    "      f\"Nodata: {optimal_result.properties['s2:nodata_pixel_percentage']}\")"
+    "print(\n",
+    "    f\"\\nOptimal result: {optimal_result.id}, {optimal_result.datetime}, \"\n",
+    "    f\"Cloud cover: {optimal_result.properties['eo:cloud_cover']}, \"\n",
+    "    f\"Nodata: {optimal_result.properties['s2:nodata_pixel_percentage']}\"\n",
+    ")"
    ]
   },
   {
@@ -266,9 +268,9 @@
    ],
    "source": [
     "merged = best_result.merge_asset(base_directory=file_base_path, delete_sub_items=True)\n",
-    "reprojected = best_result.reproject_merged_asset(target_projection=5070,\n",
-    "                                                 base_directory=file_base_path,\n",
-    "                                                 delete_merged_asset=True)"
+    "reprojected = best_result.reproject_merged_asset(\n",
+    "    target_projection=5070, base_directory=file_base_path, delete_merged_asset=True\n",
+    ")"
    ]
   },
   {

From 049e05a1d7f5c99cc132c9183be48e68a5400b41 Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Thu, 22 May 2025 16:03:30 -0400
Subject: [PATCH 05/19] Remove less useful target

---
 noxfile.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/noxfile.py b/noxfile.py
index 035337a..420bd9e 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -126,12 +126,6 @@ def black(session):
     session.run("poetry", "run", "black", "--check", *paths["all"], external=True)
 
 
-@nox.session(name="black-fix")
-def black_fix(session):
-    paths = get_paths(session)
-    session.run("poetry", "run", "black", *paths["all"], external=True)
-
-
 @nox.session()
 def isort(session):
     paths = get_paths(session)

From 820d6f5f1b134b958dd4055ca2c8aab32331abeb Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Sat, 24 May 2025 11:37:12 -0400
Subject: [PATCH 06/19] Update CI with caching

---
 .github/workflows/lint.yml       | 14 ++++++++++----
 .github/workflows/pre-commit.yml | 16 +++++++++++-----
 .github/workflows/test.yml       | 14 ++++++++++----
 3 files changed, 31 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 0c184e0..7bc4e28 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -23,9 +23,15 @@ jobs:
         run: |
           pip install poetry
 
-      - name: Configure Poetry
-        run: |
-          poetry config virtualenvs.create false
+      - name: Cache Poetry virtualenv and dependencies
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cache/pypoetry
+            ~/.cache/pip
+          key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+          restore-keys: |
+            poetry-${{ runner.os }}-
 
       - name: Install dependencies
         run: |
@@ -33,4 +39,4 @@ jobs:
 
       - name: Run linting checks
         run: |
-          make check-pylint
\ No newline at end of file
+          make check-pylint
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
index 611645d..068370f 100644
--- a/.github/workflows/pre-commit.yml
+++ b/.github/workflows/pre-commit.yml
@@ -23,14 +23,20 @@ jobs:
         run: |
           pip install poetry
 
-      - name: Configure Poetry
-        run: |
-          poetry config virtualenvs.create false
-
+      - name: Cache Poetry virtualenv and dependencies
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cache/pypoetry
+            ~/.cache/pip
+          key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+          restore-keys: |
+            poetry-${{ runner.os }}-
+      
       - name: Install dependencies
         run: |
           make install
 
       - name: Run Pre-commit checks
         run: |
-          make precommit
\ No newline at end of file
+          make precommit
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index c342052..3021ba2 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -23,9 +23,15 @@ jobs:
         run: |
           pip install poetry
 
-      - name: Configure Poetry
-        run: |
-          poetry config virtualenvs.create false
+      - name: Cache Poetry virtualenv and dependencies
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cache/pypoetry
+            ~/.cache/pip
+          key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+          restore-keys: |
+            poetry-${{ runner.os }}-
 
       - name: Install dependencies
         run: |
@@ -33,4 +39,4 @@ jobs:
 
       - name: Run tests
         run: |
-          make test
\ No newline at end of file
+          make test

From 101551e745691723cf1bf985ec139810704320fb Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Mon, 26 May 2025 10:16:15 -0400
Subject: [PATCH 07/19] Add autoflake and autopep8 to pre-commit

---
 .pre-commit-config.yaml | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index eafade3..6276f5a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -18,6 +18,16 @@ repos:
         args: ["--maxkb=5000"]
         files: '^(?!data/usa_polygon_5070\.gpkg$)(?!data/s2_grid_usa_polygon_5070\.gpkg$).*$'
 
+  - repo: https://github.com/PyCQA/autoflake
+    rev: v2.3.1
+    hooks:
+      - id: autoflake
+
+  -   repo: https://github.com/hhatto/autopep8
+      rev: v2.3.2
+      hooks:
+      -   id: autopep8
+  
   - repo: https://github.com/psf/black
     rev: 24.8.0
     hooks:

From defb29cde79bc24dd1a4c427f345ef695f12e902 Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Mon, 26 May 2025 13:50:29 -0400
Subject: [PATCH 08/19] Fix typo

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4568253..770bee2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -187,7 +187,7 @@ select = [
     "FAST",# FastAPI
     "C4",  # List and dict comprehensions
     "DJ",  # Django
-    "PIE", # Returns and unecessary returns
+    "PIE", # Returns and unnecessary returns
     "Q",   # Double quotes
     "RET", # Fix return statements
     "PTH", # Enforce pathlib

From aa00a82d3ee057eb7cc8686081c50f2b019834e5 Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Fri, 30 May 2025 16:34:33 -0400
Subject: [PATCH 09/19] Update documentation

---
 .make/.bumpversion.toml              |  39 --------
 .make/CHANGES_MAKEFILE.md            |  23 -----
 .make/Makefile                       |  84 ----------------
 .make/README.md                      |  17 ----
 .make/base.make                      | 126 +++++++++++++++++++++---
 Makefile.private.example             |   2 +-
 docs/conda_environment_creation.md   |  49 +++++++++-
 docs/environment_creation_drac.md    |  82 ++++++++--------
 docs/environment_creation_mila.md    |  43 ++++++--
 docs/makefile_environment_targets.md | 141 +++++++++++++++++++++------
 docs/migrating_to_drac.md            |  27 ++---
 11 files changed, 364 insertions(+), 269 deletions(-)
 delete mode 100644 .make/.bumpversion.toml
 delete mode 100644 .make/CHANGES_MAKEFILE.md
 delete mode 100644 .make/Makefile
 delete mode 100644 .make/README.md

diff --git a/.make/.bumpversion.toml b/.make/.bumpversion.toml
deleted file mode 100644
index b65116a..0000000
--- a/.make/.bumpversion.toml
+++ /dev/null
@@ -1,39 +0,0 @@
-
-[tool.bumpversion]
-current_version = "0.5.0"
-commit = true
-message = "Makefile version {new_version} released."
-tag = true
-tag_name = "makefile-{new_version}"
-parse = '(?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+) (?P<releaseTime>.*)?'
-serialize = [
-    "{major}.{minor}.{patch}",
-    "{utcnow:%Y-%m-%dT%H:%M:%SZ}"
-]
-
-[[tool.bumpversion.files]]
-filename = "CHANGES_MAKEFILE.md"
-search = '''
-[Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest)
--------------------------------------------------------------------------------------
-'''
-replace = '''
-[Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest)
--------------------------------------------------------------------------------------
-
-[//]: # (New changes here in list form)
-
-[{new_version}](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-{new_version}) ({utcnow:%Y-%m-%d})
--------------------------------------------------------------------------------------
-'''
-
-[[tool.bumpversion.files]]
-filename = "base.make"
-search = 'MAKEFILE_VERSION := {current_version}'
-replace = 'MAKEFILE_VERSION := {new_version}'
-
-
-[[tool.bumpversion.files]]
-filename = "Makefile"
-search = 'MAKEFILE_VERSION := {current_version}'
-replace = 'MAKEFILE_VERSION := {new_version}'
diff --git a/.make/CHANGES_MAKEFILE.md b/.make/CHANGES_MAKEFILE.md
deleted file mode 100644
index 9770eb8..0000000
--- a/.make/CHANGES_MAKEFILE.md
+++ /dev/null
@@ -1,23 +0,0 @@
-# CHANGES.md
-
-[Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest)
--------------------------------------------------------------------------------------
-
-[//]: # (New changes here in list form)
-
-[0.5.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.5.0) (2025-03-11)
--------------------------------------------------------------------------------------
-* Add venv support
-* Update and fix `poetry-install-auto` target
-
-[0.4.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.4.0) (2024-10-30)
--------------------------------------------------------------------------------------
-
-* Add cyclomatic complexity check target
-
-[0.3.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.3.0) (2024-10-30)
--------------------------------------------------------------------------------------
-
-* Add utilities to track makefile versions
-* Fix many of the targets relating to standalone `poetry` installation
-
diff --git a/.make/Makefile b/.make/Makefile
deleted file mode 100644
index d4eb4f2..0000000
--- a/.make/Makefile
+++ /dev/null
@@ -1,84 +0,0 @@
-########################################################################################
-#
-# DO NOT MODIFY!!!
-# If necessary, override the corresponding variable and/or target, or create new ones
-# in one of the following files, depending on the nature of the override :
-#
-# `Makefile.variables`, `Makefile.targets` or `Makefile.private`,
-#
-# The only valid reason to modify this file is to fix a bug or to add new
-# files to include.
-########################################################################################
-PROJECT_PATH := $(dir $(abspath $(firstword $(MAKEFILE_LIST))))
-MAKEFILE_VERSION := 0.5.0
-BUMP_TOOL := bump-my-version
-BUMP_CONFIG_FILE := $(PROJECT_PATH).bumpversion.toml
-
-# Colors
-_SECTION := \033[1m\033[34m
-_TARGET  := \033[36m
-_NORMAL  := \033[0m
-
-.DEFAULT_GOAL := help
-## -- Informative targets ------------------------------------------------------------------------------------------- ##
-
-.PHONY: all
-all: help
-
-# Auto documented help targets & sections from comments
-#	detects lines marked by double #, then applies the corresponding target/section markup
-#   target comments must be defined after their dependencies (if any)
-#	section comments must have at least a double dash (-)
-#
-# 	Original Reference:
-#		https://marmelab.com/blog/2016/02/29/auto-documented-makefile.html
-# 	Formats:
-#		https://misc.flogisoft.com/bash/tip_colors_and_formatting
-#
-#	As well as influenced by it's implementation in the Weaver Project
-#		https://github.com/crim-ca/weaver/tree/master
-
-.PHONY: help
-# note: use "\#\#" to escape results that would self-match in this target's search definition
-help: ## print this help message (default)
-	@echo ""
-	@echo "Please use 'make <target>' where <target> is one of below options."
-	@echo ""
-	@for makefile in $(MAKEFILE_LIST); do \
-        grep -E '\#\#.*$$' "$(PROJECT_PATH)/$${makefile}" | \
-            awk 'BEGIN {FS = "(:|\-\-\-)+.*\#\# "}; \
-            	/\--/ {printf "$(_SECTION)%s$(_NORMAL)\n", $$1;} \
-				/:/  {printf "    $(_TARGET)%-24s$(_NORMAL) %s\n", $$1, $$2} ' 2>/dev/null ; \
-    done
-
-.PHONY: targets
-targets: help
-
-.PHONY: version
-version: ## display current version of makefile
-	@echo "version: $(MAKEFILE_VERSION)"
-
-## -- Makefile versioning targets --------------------------------------------------- ##
-
-# Use the "dry" target for a dry-run version bump, ex.
-# make bump-major dry
-BUMP_ARGS ?= --verbose
-ifeq ($(filter dry, $(MAKECMDGOALS)), dry)
-	BUMP_ARGS := $(BUMP_ARGS) --dry-run --allow-dirty
-endif
-
-.PHONY: dry
-dry: ## Add the dry target for a preview of changes; ex. `make bump-major dry`
-	@-echo > /dev/null
-
-.PHONY: bump-major
-bump-major: ## Bump makefile major version  <X.0.0>
-	$(BUMP_TOOL) $(BUMP_ARGS) bump major --config-file $(BUMP_CONFIG_FILE)
-
-.PHONY: bump-minor
-bump-minor: ## Bump makefile minor version  <0.X.0>
-	$(BUMP_TOOL) $(BUMP_ARGS) bump minor --config-file $(BUMP_CONFIG_FILE)
-
-.PHONY: bump-patch
-bump-patch: ## Bump makefile patch version  <0.0.X>
-	$(BUMP_TOOL) $(BUMP_ARGS) bump patch --config-file $(BUMP_CONFIG_FILE)
diff --git a/.make/README.md b/.make/README.md
deleted file mode 100644
index 0135556..0000000
--- a/.make/README.md
+++ /dev/null
@@ -1,17 +0,0 @@
-# Makefile documentation
-
-This folder contains the base makefile targets.
-
-It should not be modified outside of the [Template's repository](https://github.com/RolnickLab/lab-advanced-template).
-
-If there is a problem with the contents of these targets, please open an issue [here](https://github.com/RolnickLab/lab-advanced-template/issues).
-
-If you know how to fix the problem, please also consider opening a pull request with 
-your proposed solution.
-
-You can always override the faulty targets located here by creating new targets
-with the same names inside [Makefile.targets](../Makefile.targets).
-
-The Makefile and `bump-my-version` related files in this directory are to help with
-change tracking for the makefile itself. If you are using this makefile as part of a 
-template in another repository
\ No newline at end of file
diff --git a/.make/base.make b/.make/base.make
index 3f38651..20c9a01 100644
--- a/.make/base.make
+++ b/.make/base.make
@@ -16,7 +16,7 @@ PROJECT_PATH := $(dir $(abspath $(firstword $(MAKEFILE_LIST))))
 MAKEFILE_NAME := $(word $(words $(MAKEFILE_LIST)),$(MAKEFILE_LIST))
 SHELL := /usr/bin/env bash
 BUMP_TOOL := bump-my-version
-MAKEFILE_VERSION := 0.5.0
+MAKEFILE_VERSION := 0.6.0
 DOCKER_COMPOSE ?= docker compose
 AUTO_INSTALL ?=
 
@@ -94,20 +94,57 @@ venv-create: ## Create a virtualenv '.venv' at the root of the project folder
 venv-activate: ## Print out the shell command to activate the project's virtualenv.
 	@echo "source $(VENV_ACTIVATE)"
 
+.PHONY: venv-remove
+venv-remove: ## Delete the virtualenv '.venv' at the root of the project folder.
+	@if [ -d $(VENV_PATH) ]; then \
+  	  echo "Current venv folder is [$(VENV_PATH)]"; \
+  	  if [ "$(AUTO_INSTALL)" = "true" ]; then \
+			ans="y";\
+	  else \
+	    echo ""; \
+		echo -n "Would you like to completely delete this virtual environment? [y/N]: "; \
+		read ans; \
+	  fi; \
+	  case $$ans in \
+			[Yy]*) \
+				echo ""; \
+				echo "Starting deletion process for [$(VENV_PATH)]"; \
+				rm -rf $(VENV_PATH); \
+				echo ""; \
+				echo "-- Deletion complete --"; \
+				;; \
+			*) \
+	    		echo ""; \
+				echo "Skipping virtual environment deletion."; \
+				echo " "; \
+				;; \
+		esac; \
+  	else \
+  	  echo "Venv [$(VENV_PATH)] does not exist, nothing to do"; \
+  	fi;
+
 ## -- Poetry targets ------------------------------------------------------------------------------------------------ ##
 
 .PHONY: poetry-install-auto
-poetry-install-auto: ## Install Poetry in Conda environment, or with pipx in a virtualenv if Conda not found
+poetry-install-auto: ## Install Poetry automatically using DEFAULT_POETRY_INSTALL_ENV. Defaults to venv install
 	@poetry --version; \
     	if [ $$? != "0" ]; then \
 			echo "Poetry not found, proceeding to install Poetry..."; \
 			if [ "$(DEFAULT_POETRY_INSTALL_ENV)" == "conda" ]; then \
+			    echo ""; \
+			    echo "[DEFAULT_POETRY_INSTALL_ENV] is defined as 'conda', installing poetry with the 'poetry-install-conda' target"; \
+			    echo ""; \
 				ans_where="conda"; \
 			elif [ "$(DEFAULT_POETRY_INSTALL_ENV)" == "venv" ]; then \
+				echo ""; \
+				echo "[DEFAULT_POETRY_INSTALL_ENV] is defined as 'venv', installing poetry with the 'poetry-install-venv' target"; \
+				echo ""; \
 				ans_where="venv"; \
 			else\
-				echo -n "Where would you like to install Poetry, in a dedicated virtualenv (venv), or a conda environment? [venv/conda]: "; \
-				read ans_where; \
+				echo ""; \
+				echo "[DEFAULT_POETRY_INSTALL_ENV] is not defined, defaulting to installing poetry with the 'poetry-install-venv' target"; \
+				echo ""; \
+				ans_where="venv"; \
 			fi; \
 			case $$ans_where in \
 				"venv" | "Venv" |"VENV") \
@@ -119,7 +156,7 @@ poetry-install-auto: ## Install Poetry in Conda environment, or with pipx in a v
 					;; \
 				*) \
 					echo ""; \
-					echo -e "\e[1;39;41m-- WARNING --\e[0m Option $$ans_how not found, exiting process."; \
+					echo -e "\e[1;39;41m-- WARNING --\e[0m There was an unexpected error. Option $$ans_how not found, exiting process."; \
 					echo ""; \
 					exit 1; \
 			esac; \
@@ -139,7 +176,7 @@ _pipx_install_poetry:
 
 
 .PHONY: poetry-install
-poetry-install: ## Install standalone Poetry using pipx. Will ask where to install pipx.
+poetry-install: ## Install Poetry interactively.
 	@echo "Looking for Poetry version...";\
 	poetry --version; \
 	if [ $$? != "0" ]; then \
@@ -379,7 +416,7 @@ poetry-uninstall-venv: poetry-remove-env ## Uninstall pipx-installed Poetry, the
 ## -- Conda targets ------------------------------------------------------------------------------------------------- ##
 
 .PHONY: conda-install
-conda-install: ## Install Conda on your local machine
+conda-install: ## Install Miniconda on your local machine
 	@echo "Looking for [$(CONDA_TOOL)]..."; \
 	$(CONDA_TOOL) --version; \
 	if [ $$? != "0" ]; then \
@@ -396,7 +433,11 @@ conda-install: ## Install Conda on your local machine
 		echo "If in doubt, don't install Conda and manually create and activate"; \
 		echo "your own Python environment."; \
 		echo " "; \
-		echo -n "Would you like to install Miniconda ? [y/N]: "; \
+		echo "It is strongly NOT advisable to execute this command if you are on a"; \
+		echo "Compute Cluster (ie. Mila/DRAC), as they either have modules available (Mila),"; \
+		echo "or even prohibit the installation and use of Conda (DRAC) based environments."; \
+		echo " "; \
+		echo -n "Would you like to install and initialize Miniconda ? [y/N]: "; \
 		read ans; \
 		case $$ans in \
 			[Yy]*) \
@@ -417,6 +458,48 @@ conda-install: ## Install Conda on your local machine
 		echo "Conda tool [$(CONDA_TOOL)] has been found, skipping installation"; \
 	fi;
 
+.PHONY: mamba-install
+mamba-install: ## Install Micromamba on you local machine
+	@echo "Looking for [micromamba]..."; \
+	micromamba --version; \
+	if [ $$? != "0" ]; then \
+	  	echo ""; \
+	  	echo "[micromamba] has not been found."; \
+	  	echo ""; \
+	  	echo "If you know you already have installed [micromamba] installed, it might not have"; \
+	  	echo "been properly activated (which can also be on purpose)."; \
+	  	echo ""; \
+	  	echo "If your Conda/Micromamba tool has not been initiated through your .bashrc file,"; \
+		echo "consider using the full path to its executable instead when"; \
+		echo "defining your [CONDA_TOOL] variable"; \
+		echo " "; \
+		echo "If you do decide to install Micromamba, please take care to define the [CONDA_TOOL]"; \
+		echo "variable in you personal 'Makefile.private' file as CONDA_TOOL := micromamba."; \
+		echo " "; \
+		echo "If in doubt, don't install Micromamba and manually create and activate"; \
+		echo "your own Python environment."; \
+	  	echo ""; \
+	  	echo "It is strongly NOT advisable to execute this command if you are on a"; \
+		echo "Compute Cluster (ie. Mila/DRAC), as they either have modules available (Mila),"; \
+		echo "or even prohibit the installation and use of Conda based environments (DRAC)."; \
+	  	echo ""; \
+		echo -n "Would you like to install and initialize [micromamba] ? [y/N]: "; \
+		read ans; \
+		case $$ans in \
+			[Yy]*) \
+				echo 'Installing Micromamba'
+				wget -qO- https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba;\
+				mv bin/micromamba ~/.local/bin/micromamba;\
+				rm -rf bin/;\
+				~/.local/bin/micromamba shell init -s bash ~/.micromamba;\
+				;; \
+			*) \
+				echo "Skipping installation."; \
+				echo " "; \
+				;; \
+		esac; \
+
+
 .PHONY: conda-create-env
 conda-create-env: conda-install ## Create a local Conda environment based on 'environment.yml' file
 	@$(CONDA_TOOL) env create $(CONDA_YES_OPTION) -f environment.yml
@@ -521,8 +604,9 @@ _check-env:
 	@if ! [ $(DEFAULT_INSTALL_ENV) ]; then \
 		echo -e "\e[1;39;41m-- WARNING --\e[0m No installation environment have been defined." ; \
 		echo "" ; \
-		echo "Defaulting to Poetry managed environment - Poetry will either use activated environment, or '.venv'," ; \
-		echo "if found, or create and manage it's own environment if not." ; \
+		echo "[DEFAULT_INSTALL_ENV] is not defined - Poetry will use the currently activated environment." ; \
+		echo "If there is no currently active environment (ie. conda or venv)," ; \
+		echo "Poetry will create and manage it's own environment." ; \
 	elif [ $(DEFAULT_INSTALL_ENV) = "venv" ]; then \
 		if [ ! -f $(VENV_ACTIVATE) ]; then \
 			make -s venv-create ;\
@@ -539,7 +623,7 @@ _remind-env-activate:
 	@echo "Activate your environment using the following command:"
 	@echo ""
 	@if ! [ $(DEFAULT_INSTALL_ENV) ] || [ $(DEFAULT_INSTALL_ENV) = "poetry" ]; then \
-		make -s poetry-env-activate ; \
+		make -s poetry-activate ; \
 		echo "" ; \
 		echo "You can also use the eval bash command : eval \$$(make poetry-activate)"; \
 		echo "" ; \
@@ -603,15 +687,15 @@ dry: ## Add the dry target for a preview of changes; ex. 'make bump-major dry'
 
 .PHONY: bump-major
 bump-major: ## Bump application major version  <X.0.0>
-	$(BUMP_TOOL) $(BUMP_ARGS) bump major
+	$(BUMP_TOOL) bump $(BUMP_ARGS) major
 
 .PHONY: bump-minor
 bump-minor: ## Bump application minor version  <0.X.0>
-	$(BUMP_TOOL) $(BUMP_ARGS) bump minor
+	$(BUMP_TOOL) bump $(BUMP_ARGS) minor
 
 .PHONY: bump-patch
 bump-patch: ## Bump application patch version  <0.0.X>
-	$(BUMP_TOOL) $(BUMP_ARGS) bump patch
+	$(BUMP_TOOL) bump $(BUMP_ARGS) patch
 
 ## -- Docker targets ------------------------------------------------------------------------------------------------ ##
 
@@ -632,13 +716,25 @@ check-complexity: ## Check code cyclomatic complexity with Flake8-McCabe
 	poetry run nox -s complexity
 
 .PHONY: fix-lint
-fix-lint: ## Fix code linting (black, isort, flynt, docformatter)
+fix-lint: ## Fix code linting (autoflake, autopep8, black, isort, flynt, docformatter)
 	poetry run nox -s fix
 
 .PHONY: precommit
 precommit: ## Run Pre-commit on all files manually
 	poetry run nox -s precommit
 
+.PHONY: ruff
+ruff: ## Run the ruff linter
+	poetry run nox -s ruff-lint
+
+.PHONY: ruff-fix
+ruff-fix: ## Run the ruff linter and fix automatically fixable errors
+	poetry run nox -s ruff-fix
+
+.PHONY: ruff-format
+ruff-format: ## Run the ruff code formatter
+	poetry run nox -s ruff-format
+
 ## -- Tests targets ------------------------------------------------------------------------------------------------- ##
 
 .PHONY: test
diff --git a/Makefile.private.example b/Makefile.private.example
index 278f083..4deb9d7 100644
--- a/Makefile.private.example
+++ b/Makefile.private.example
@@ -27,7 +27,7 @@ AUTO_INSTALL := false
 # The default environment to use. The choices are as follow: [venv, poetry, conda]
 # If this is not set, the makefile will use the `poetry` command without activating
 # an environment before hand.
-DEFAULT_INSTALL_ENV := conda
+DEFAULT_INSTALL_ENV := venv
 
 # The default environment where Poetry will be installed. The choices are as follow: [venv, conda]
 # If this is not set, the makefile will ask the user where they want to install Poetry
diff --git a/docs/conda_environment_creation.md b/docs/conda_environment_creation.md
index 982222d..d6479d4 100644
--- a/docs/conda_environment_creation.md
+++ b/docs/conda_environment_creation.md
@@ -1,23 +1,49 @@
 # Creating a Conda Environment
 
-First, read the [Conda section](https://docs.mila.quebec/Userguide.html#conda) 
+First, read the [Conda section](https://docs.mila.quebec/Userguide.html#conda)
 in Mila's documentation.
 
+To make full use of the Conda makefile target, make sure to define the variables found
+in [Makefile.variables](../Makefile.variables) appropriately, and ensure that
+the `CONDA_ENVIRONMENT` variable lines up with the name defined in the
+[environment.yml](../environment.yml) file.
+
 ## Install Conda
-If you still need to install a newer version of Conda, or if you want to install 
-it on your personal computer:
+
+**Warning!!!**
+
+**Unless absolutely necessary, it is not recommended to install a local
+version of Conda when using a compute cluster like Mila or DRAC. You should only
+install Conda if you will be working directly on your local machine.**
+
+If you need to install a newer version of Miniconda, or if you want to install
+it for the first time on your personal computer:
 
 ```shell
 make conda-install
 ```
 
+### Alternative : Mamba
+
+You can also choose to install [micromamba](https://mamba.readthedocs.io/en/latest/index.html)
+as an alternative or a complement to miniconda.
+
+If you do install mamba, make sure to create a renamed copy of
+[Makefile.private.example](../Makefile.private.example) -> `Makefile.private` and set
+the `CONDA_TOOL` variable to `CONDA_TOOL := micromamba` so the Makefile can use it.
+
+```shell
+make mamba-install
+```
+
 ## Environment Creation
 
 Creating a Conda Environment is relatively straightforward with the makefile.
 
-First, make sure the name of the environment has been updated in the 
+First, make sure the name of the environment has been updated in the
 [environment.yml file](../environment.yml) before running the following command:
-```
+
+```shell
 make conda-create-env
 ```
 
@@ -26,5 +52,18 @@ make conda-create-env
 Once created, the environment must be activated:
 
 ```
+# If using micromamba, replace 'conda' with 'micromamba'
 conda activate <name_of_environment>
+```
+
+You can use this command to see the command as configured for the project:
+
+```shell
+make conda-activate
+```
+
+You can also use the eval command to activate the environment:
+
+```shell
+eval $(make conda-activate)
 ```
\ No newline at end of file
diff --git a/docs/environment_creation_drac.md b/docs/environment_creation_drac.md
index c3b0802..03d7b8a 100644
--- a/docs/environment_creation_drac.md
+++ b/docs/environment_creation_drac.md
@@ -1,109 +1,115 @@
-
 # Environment Creation and Management for DRAC
 
 First things first, read the amazing [DRAC Python documentation](https://docs.alliancecan.ca/wiki/Python).
 
-If you are also new to using Slurm clusters, please read 
-[Getting started with DRAC](https://docs.alliancecan.ca/wiki/Getting_started) and 
+If you are also new to using Slurm clusters, please read
+[Getting started with DRAC](https://docs.alliancecan.ca/wiki/Getting_started) and
 [How to run jobs on the DRAC cluster](https://docs.alliancecan.ca/wiki/Running_jobs)
 
-Below are simplified steps on how to create and manage a virtual environment on the 
+Below are simplified steps on how to create and manage a virtual environment on the
 DRAC cluster.
 
 ## Pre-built Python wheels and available modules
 
-DRAC offers pre-build Python wheels for commonly used libraries. You can [consult them 
+DRAC offers pre-build Python wheels for commonly used libraries. You can [consult them
 here](https://docs.alliancecan.ca/wiki/Available_Python_wheels).
 
-However, many libraries, or newer versions of those libraries, are not available through 
+However, many libraries, or newer versions of those libraries, are not available through
 those wheels.
 
-For some libraries, like Pytorch or scientific libraries like Numpy, it can be 
+For some libraries, like Pytorch or scientific libraries like Numpy, it can be
 better/simpler to use the pre-built versions.
 
-For secondary or simple utility libraries, like `pytest`, `flake8` or `requests`, using 
-versions from the pre-built wheels might not be critical or even preferred, as using 
+For secondary or simple utility libraries, like `pytest`, `flake8` or `requests`, using
+versions from the pre-built wheels might not be critical or even preferred, as using
 the latest versions might be better overall.
 
-While there are generally no problems with building your virtual environment with 
-Pypi versions of the libraries on DRAC, sometimes this can lead to poorer performance and/or 
-runtime errors. What's more, you also won't be available to build your environment 
-inside your job ([like recommended here](https://docs.alliancecan.ca/wiki/Python#Creating_virtual_environments_inside_of_your_jobs)), 
+While there are generally no problems with building your virtual environment with
+Pypi versions of the libraries on DRAC, sometimes this can lead to poorer performance and/or
+runtime errors. What's more, you also won't be available to build your environment
+inside your
+job ([like recommended here](https://docs.alliancecan.ca/wiki/Python#Creating_virtual_environments_inside_of_your_jobs)),
 unless you are working on Cedar, since its nodes have access to internet.
 
-Do note that building your environment inside your job can help with some performance 
+Do note that building your environment inside your job can help with some performance
 issues, but it is not required.
 
-See [Managing Dependencies](#managing-dependencies-on-drac) below for more information 
+See [Managing Dependencies](#managing-dependencies-on-drac) below for more information
 on how to install dependencies from the local pre-built wheels.
 
 **Important note**
-While working on DRAC with pre-built Python wheels, the use of the `poetry.lock` file is not recommended; 
-use [Tilde requirements](https://python-poetry.org/docs/dependency-specification/#tilde-requirements) 
+While working on DRAC with pre-built Python wheels, the use of the `poetry.lock` file is not recommended;
+use [Tilde requirements](https://python-poetry.org/docs/dependency-specification/#tilde-requirements)
 instead to ensure reproducibility across different environments.
 
 ## Creating an environment on the DRAC cluster
 
-The preferred method of creating a virtual environment for the DRAC cluster is 
+The preferred method of creating a virtual environment for the DRAC cluster is
 with `virtualenv`
 
 First, a python module is loaded by default on DRAC.
 
 To see the available modules:
+
 ```
 module avail python
 ```
+
 To load a particular model (assuming 3.11.5 is available):
+
 ```
 module load python/3.11.5
 ```
 
 Then create the environment:
+
 ```
 virtualenv <PATH_TO_ENV>
 ```
 
 ## Managing dependencies on DRAC
 
-### The 3 choices
+### The three choices
 
-* Limit your self exclusively to DRAC's pre-built wheels, and code anything that's 
+* Limit yourself exclusively to DRAC's pre-built wheels, and code anything that's
   missing yourself.
 * Don't use pre-build wheels at all
 * Use a mix of the 2.
 
-The first 2 are pretty straight forward, but using a mix of dependency sources will 
+The first 2 are pretty straight forward, but using a mix of dependency sources will
 require careful tracking and documentation.
 
-Dependencies intended to be installed from pre-built wheels should go in the 
-`[tool.poetry.dependencies]` section of the `pyproject.toml` file, while other 
-dependencies should be added to an optional dependency group, which can then be installed 
+Dependencies intended to be installed from pre-built wheels should go in the
+`[tool.poetry.dependencies]` section of the `pyproject.toml` file, while other
+dependencies should be added to an optional dependency group, which can then be installed
 with `poetry` ([See Adding Dependencies](../CONTRIBUTING.md#adding-dependencies))
 
-For example, dependencies intended to be installed from DRAC's pre-build wheels should 
-be added manually in the `[tool.poetry.dependencies]` section of the `pyproject.toml` file 
-and installed using the `pip install -e . --no-index` command from the root of your 
-repository root. 
+For example, dependencies intended to be installed from DRAC's pre-build wheels should
+be added manually in the `[tool.poetry.dependencies]` section of the `pyproject.toml` file
+and installed using the `pip install -e . --no-index` command from the root of your
+repository root.
 
-For the other dependencies, an optional dependency group should be created in the 
-`pyproject.toml` file. Make sure to [make the group optional](https://python-poetry.org/docs/managing-dependencies/#optional-groups).
-Dependencies can be added to this group using the `poetry add --group <group_name> <dependency_name>` 
+For the other dependencies, an optional dependency group should be created in the
+`pyproject.toml` file. Make sure
+to [make the group optional](https://python-poetry.org/docs/managing-dependencies/#optional-groups).
+Dependencies can be added to this group using the `poetry add --group <group_name> <dependency_name>`
 and can be installed with the command `poetry install --with <group_name>`
 
 ### Reproducibility
 
-If using any dependencies from the DRAC pre-built wheels, you will still need to 
-document the versions in a way that users outside DRAC can still use your code. 
+If using any dependencies from the DRAC pre-built wheels, you will still need to
+document the versions in a way that users outside DRAC can still use your code.
 
-For example : the requests library
+For example, the requests library
 *as of July 24th, 2024*
 
 * Version available on DRAC : `2.31.0`
 * Full version (what we see with `pip list`) : `requests==2.31.0+computecanada`
-  * This version is obviously not available outside DRAC
+    * This version is not available outside DRAC
 * How to add it to the pyproject.toml:
-  * If not on DRAC, you can use poetry to add it using `poetry add requests~2.31.0`
-  * If on DRAC, add it manually to the pyproject.toml file under the `[tool.poetry.dependencies]` section : `requests = "~2.31.0"`
+    * If not on DRAC, you can use poetry to add it using `poetry add requests~2.31.0`
+    * If on DRAC, add it manually to the pyproject.toml file under the `[tool.poetry.dependencies]` section :
+      `requests = "~2.31.0"`
 
-This will help ensure reproducibility between environments even when using pre-built 
+This will help ensure reproducibility between environments even when using pre-built
 wheel versions of Python dependencies.
diff --git a/docs/environment_creation_mila.md b/docs/environment_creation_mila.md
index c79b6d7..4ed0936 100644
--- a/docs/environment_creation_mila.md
+++ b/docs/environment_creation_mila.md
@@ -1,26 +1,44 @@
 # Creating a Virtual Environment on the Mila Cluster
 
-On the Mila cluster, both `venv` and `virtualenv` can be used to create a virtual 
+On the Mila cluster, both `venv` and `virtualenv` can be used to create a virtual
 environment.
 
 First, load the python module:
+
 ```
-module load python/3.11
+module load python/3.10
 ```
 
 Then, for `venv`:
+
 ```
 python3 -m venv <PATH_TO_ENV>
 ```
 
 or for `virtualenv`:
+
 ```
 virtualenv <PATH_TO_ENV>
 ```
 
-where `<PATH_TO_ENV>` is the path where the environment will be created. It normally 
-should be inside your project's folder (but ignored by git), and commonly named `.env`, 
-`.venv`.
+where `<PATH_TO_ENV>` is the path where the environment will be created. It normally
+should be inside your project's folder (but ignored by git), and commonly named `
+`.venv`. 
+
+* _On a side note, `.env` is generally reserved for a text file listing 
+  environment variables, used by various tools like `python-dotenv` and `docker compose`_
+
+You can also make use of the following makefile targets:
+
+```shell
+# To create a .venv environment
+make venv-create
+```
+
+```shell
+# To remove the .venv environment
+make venv-remove
+```
 
 You can then activate your environment using the following commandline:
 
@@ -28,4 +46,17 @@ You can then activate your environment using the following commandline:
 source <PATH_TO_ENV>/bin/activate
 ```
 
-After the environment is created and activated, follow the [Poetry Instructions](../README.md#poetry)
\ No newline at end of file
+If you used the `make venv-create` target, or create it at `<REPOSITORY_ROOT>/.venv`,
+you can also use:
+
+```shell
+# To get the path for activation
+make venv-activate
+```
+
+```shell
+# To activate it
+eval $(make venv-activate)
+```
+
+After the environment is created and activated, follow the [Poetry Instructions](../README.md#poetry)
diff --git a/docs/makefile_environment_targets.md b/docs/makefile_environment_targets.md
index 8b6adc8..7a90ba7 100644
--- a/docs/makefile_environment_targets.md
+++ b/docs/makefile_environment_targets.md
@@ -1,90 +1,175 @@
 # Environment and Installation Related Makefile Targets
 
-## Poetry targets
+## Venv targets
 
-There are 2 possibilities available in how to manage `Poetry` if it is not already
+There are three targets in the makefile to help with streamling classic python virtual
+environments.
+
+```shell
+# Create a virtual environment at <REPOSITORY_ROOT>/.venv/
+make venv-create
+```
+
+```shell
+# Get the path to activate the virtual environment created at <REPOSITORY_ROOT>/.venv/
+make venv-activate
+```
+
+```shell
+# Activate the virtual environment using the path returned by 'make venv-activate'
+eval $(make venv-activate)
+```
+
+```shell
+# Remove a virtual environment at <REPOSITORY_ROOT>/.venv/
+make venv-remove
+```
+
+## Poetry install targets
+
+### Installing poetry
+
+There are two possibilities available to manage `poetry` if it is not already
 configured on your system.
 
-**It is not recommended to install `Poetry` in the same environment that will be managed
-by `Poetry`; It should be installed by `Conda` (as in, `conda install poetry`) or 
-on the system using `pipx`, in order to minimize dependency conflicts.**
+**It is generally not recommended to install `poetry` in the same environment that will
+be managed by `poetry`; It is preferable to install it on the system using `pipx`,
+to minimize dependency conflicts.**
+
+That being said, having `poetry` installed in a `conda` environment, and using `poetry`
+to manage that same `conda` environment is not the end of the world and is an acceptable
+workaround for some projects.
+
+See the [official documentation on how to install poetry](https://python-poetry.org/docs/#installation)
+for more details if you prefer to install `poetry` manually.
+
+The following target will install `poetry` interactively, asking questions along the way:
+
+```shell
+make poetry-install
+```
 
-The following target will first try to install `Poetry` in the active `Conda` 
-environment; if it can't find `Conda`, it will proceed to install via `pipx`
+To install `poetry` in a non-interactive way, you can instead use this target:
 
 ```shell
 make poetry-install-auto
 ```
 
-To install `Poetry` using `Conda`:
+The above target will try to install `poetry` according to the `DEFAULT_POETRY_INSTALL_ENV`
+Makefile variable; if it's not defined, installation of `poetry` will proceed via `pipx`.
+
+The `DEFAULT_POETRY_INSTALL_ENV` variable can be set in your local `Makefile.private` file.
+If you don't have one, this file can be created by copying from the
+[Makefile.private.example](../Makefile.private.example) file.
+
+If you know exactly how you want to install `poetry`, you have three options:
+
+```shell
+# This will install poetry using pipx. If pipx needs to be installed, it will be installed
+# using the locally available pip. This does not work on the different compute clusters.
+make poetry-install-local
+```
 
 ```shell
+# This will install poetry with pipx. If pipx needs to be install, it will be installed
+# in a newly created virtual environment in $HOME/.pipx_venv.
+make poetry-install-venv
+```
+
+```shell
+# This will install poetry in the projects conda environment, along side all other python
+# dependencies.
 make conda-poetry-install
 ```
 
-Using `pipx` will instead allow environment management directly with `Poetry`. The
-following target will also make `Poetry` use a Python 3.11 environment for this
-project.
+Both install methods have their respective cleanup targets:
 
 ```shell
-make poetry-install-venv
+make poetry-uninstall
 ```
 
-This will also create a virtual environment managed by `Poetry`.
+```shell
+make conda-poetry-uninstall
+```
 
-A standalone environment can also be created later using the `make poetry-create-env`
-command, and removed with the `make poetry-remove-env` command.
+You can also use `make poetry-uninstall-pipx` or `make poetry-uninstall-venv` to also
+remove the `pipx` library and the `pipx` virtualenv, respectively, depending on how you
+chose to install `pipx` and `poetry`.
 
-Information about the currently active environment used by Poetry, 
-whether Conda or Poetry, can be seen using the `make poetry-env-info` command.
+### Environment creation with Poetry
 
-Both install methods can also be cleaned up:
+Using `poetry` to create a virtual environment is different from creating one using `venv`
+or `virtualenv`, as they are centralized and managed by `poetry`.
+
+A `poetry` virtual environment can be created using the following target:
 
 ```shell
-make conda-poetry-uninstall
+make poetry-create-env
 ```
-or
+
+and be removed with:
+
 ```shell
-make poetry-uninstall-pipx
+make poetry-remove-env
 ```
 
-**Important note!**
+Information about the currently active environment used by Poetry,
+whether Conda or Poetry, can be seen using:
 
-If you have an active `Conda` environment  and install `Poetry` using `pipx`,
-you will have to use `poetry run python <your_command_or_script_path>` instead of 
-`python <your_command_or_script_path>`, (which is normal when using Poetry) as 
-`python` will use Conda's active environment.
+```shell 
+poetry-env-info
+```
 
 ## Conda Targets
 
+### Installing Conda
+
 If you need or want to install Conda:
+
 ```shell
 make conda-install 
 ```
 
+```shell
+# Alternatively, you can also install micromamba.
+make mamba-install 
+```
+
+On the Mila cluster, it is preferable to use the available `anaconda` module instead:
+
+```shell
+module load anaconda/3
+```
+
+### Environment creation
+
 To create the conda environment:
+
 ```shell
 make conda-create-env
 ```
 
 To remove the conda environment:
+
 ```shell
 make conda-clean-env
 ```
 
-Make sure to activate the configured environment before installing.
+Make sure to activate the configured environment before using the install targets.
 
 ## Install targets
 
 **All `install` targets will first check if `Poetry` is available and try to install
 it with the `make poetry-install-auto` target.**
 
-To install the package, development dependencies and CLI tools (if available):
+To install the package, development dependencies, and CLI tools (if available):
+
 ```shell
 make install
 ```
 
 To install only the package, without development tools:
+
 ```shell
 make install-package
 ```
diff --git a/docs/migrating_to_drac.md b/docs/migrating_to_drac.md
index 5e3f091..dbb0924 100644
--- a/docs/migrating_to_drac.md
+++ b/docs/migrating_to_drac.md
@@ -2,28 +2,29 @@
 
 DISCLAIMER
 
-Working across multiple clusters (ex. Mila and DRAC) at the same time can quickly 
-become quite complex, as you will have to manage your project dependencies very 
-attentively. Different versions of the same libraries can have different secondary 
+Working across multiple clusters (ex. Mila and DRAC) at the same time can quickly
+become quite complex, as you will have to manage your project dependencies very
+attentively. Different versions of the same libraries can have different secondary
 dependencies and their behavior can change.
 
-While usually only true for major version changes (i.e. version X.2.1, where "X" is the number that changes), 
-sometimes minor version changes (i.e. 2.X.0) can also introduce breaking changes, like 
-function names changing, functions not working the same way or even being removed.
+While usually only true for major version changes (i.e. version X.2.1, where "X" is the
+number that changes), sometimes minor version changes (i.e. 2.X.0) can also introduce
+breaking changes, like function names changing, functions not working the same way or
+even being removed.
 
 ## Things to consider when migrating to DRAC
 
-If your project has been initiated somewhere else, either on your own workstation 
-or on the Mila cluster, chances are you are using the most recent (at the time of your 
+If your project has been initiated somewhere else, either on your own workstation
+or on the Mila cluster, chances are you are using the most recent (at the time of your
 project's creation) versions of your Python libraries.
 
-The first things to consider are therefore : Are those versions available in DRAC's 
+The first things to consider are therefore: Are those versions available in DRAC's
 pre-built wheels, and do I need to use these pre-built versions?
 
-Version differences also need to take into account. If downgrading a 
-library to match the version available on DRAC requires drastic changes to your code 
-because of breaking changes between those versions, it might be better off not 
-using the DRAC version if you don't have the time to make these changes (or don't 
+Version differences also need to take into account. If downgrading a
+library to match the version available on DRAC requires drastic changes to your code
+because of breaking changes between those versions. It might be better off not
+using the DRAC version if you don't have the time to make these changes (or don't
 want to break your code in other environments outside DRAC)
 
 [See the Environment Creation and Management for DRAC document](environment_creation_drac.md)

From 9f61a9aeb6901e28f8f731df1773fe1fd668489a Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Fri, 30 May 2025 16:34:56 -0400
Subject: [PATCH 10/19] Update documentation

---
 docs/nox_session_descriptions.md | 37 +++++++++++++++
 docs/poetry_documentation.md     | 80 ++++++++++++++++++++++++++++++++
 2 files changed, 117 insertions(+)
 create mode 100644 docs/nox_session_descriptions.md
 create mode 100644 docs/poetry_documentation.md

diff --git a/docs/nox_session_descriptions.md b/docs/nox_session_descriptions.md
new file mode 100644
index 0000000..7c4eb96
--- /dev/null
+++ b/docs/nox_session_descriptions.md
@@ -0,0 +1,37 @@
+# Nox sessions
+
+The configurations can be found in the [noxfile.py](../noxfile.py) file.
+
+Feel free to modify the contents of existing sessions, as well as add new ones for your
+project.
+
+However, it would be best to avoid renaming existing ones as the Makefile expects the
+current session names unless you also plan to override the existing Makefile targets
+that use them.
+
+With the `nox` tool, individual _commands_ are called sessions, and can be executed using
+the following syntax:
+
+```shell
+nox -s <session_name>
+```
+
+* Main `nox` sessions:
+    * No session specified; executing `nox` : Runs the pre-commit configuration
+    * `check` Runs all checks on the code base without modifying the code
+    * `fix` : Runs the autoflake, autopep8, black, isort, docformatter and flynt tools on the code base
+    * `flake8` : Runs the `flake8` linter
+    * `autoflake` : Run the `autoflake` lint fixer to remove unused imports and variables
+    * `autopep8` : Run the `autopep8` lint fixer to automatically fix most other `flake8` warnings
+    * `black` : Runs the code formatter
+    * `isort` : Runs the import sorter
+    * `flynt` : Runs the `f-string formatter
+    * `docformatter` : Runs the docstring formatter
+    * `test` : Runs tests found in the `tests/` folder with `pytest`
+
+* `ruff` - Experimental sessions:
+    * `ruff-lint` : Check lint using the `ruff` linter. This linter is stricter
+      than `flake8`, but less than `pylint`
+    * `ruff-fix` : Check lint using the `ruff` linter and automatically fix the
+      warnings that can be fixed by `ruff`
+    * `ruff-format` : Format the code using the `ruff` formatter
\ No newline at end of file
diff --git a/docs/poetry_documentation.md b/docs/poetry_documentation.md
new file mode 100644
index 0000000..dcc7273
--- /dev/null
+++ b/docs/poetry_documentation.md
@@ -0,0 +1,80 @@
+# Poetry Documentation
+
+## Considerations when using Poetry in a Compute Cluster environment
+
+### Version concerns on DRAC
+
+As of this writing (February 2025), the newest available version on DRAC for `poetry` is
+`2.0.1+computecanada`, and is the version causing problems.
+
+Newer versions of `poetry`, `>=2.0.0` are raising errors when trying to
+resolve dependencies when installing projects and adding new dependencies.
+
+If you encounter such issues, please try reinstalling `poetry` at a lesser version:
+`pipx install 'poetry<2.0.0', or newer, non-computecanada versions if available.
+
+### Poetry Cache Management
+
+Whether installing `poetry` as a standalone tool or in a conda environment, cache
+management is an important consideration in a shared compute cluster.
+
+If you maintain the default configuration, `poetry`'s cache is located
+somewhere in your `$HOME` folder, ex. `$HOME/.cache/pypoetry`.
+
+The cache can get big quite fast. It is also something that can change a lot
+over time, which is not ideal for drive that are backed up regularly, like `/projects/`.
+
+Since a cache is supposed to be temporary by nature, and easy to recreate
+(most of the time), it can make sense to move the cache to `$SCRATCH`,
+as there are very few and limited consequences if it ends up being deleted by the
+`purge` policies.
+
+To see current configs and current `cache-dir` path :
+
+```bash
+poetry config --list
+```
+
+There are a few options available in managing `poetry`'s cache in a cluster environment
+
+### Option 1: move the cache
+
+To set a new cache path:
+
+```bash
+poetry config cache-dir /PATH/TO/SCRATCH/.cache/pypoetry
+```
+
+### Option 2: clean your caches periodically, or disable them
+
+You can view the existing caches (typically `PyPI` and `_default_cache`) :
+
+```bash
+poetry cache list
+```
+
+You can clean your caches directly:
+
+```bash
+poetry cache clear <CACHE_NAME> --all
+```
+
+Or disable them altogether:
+
+```bash
+poetry cache clear <CACHE_NAME> --no-cache
+```
+
+### Option 3: manually skip cache when installing dependencies
+
+When adding dependencies :
+
+```bash
+poetry add <DEPENDENCY_NAME> --no-cache
+```
+
+When installing a project:
+
+```bash
+poetry install --no-cache
+```
\ No newline at end of file

From dc4709f01cd074af6b907d59308e6594e0fd91c3 Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Fri, 30 May 2025 16:35:08 -0400
Subject: [PATCH 11/19] Update CHANGES.md

---
 CHANGES.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/CHANGES.md b/CHANGES.md
index 655d322..d348ac1 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -3,7 +3,10 @@
 [Unreleased](https://github.com/RolnickLab/geospatial-tools/tree/main) (latest)
 -------------------------------------------------------------------------------------
 
-[//]: # (New changes here in list form)
+* Refactor the stac.py module to extract logic that belongs more in raster.py
+* Update the makefile
+* Update the project dependencies
+* Add new QA tools : `autoflake`, `autopep8` and `ruff`
 
 [0.1.3](https://github.com/RolnickLab/geospatial-tools/tree/0.1.3) (2024-09-23)
 -------------------------------------------------------------------------------------

From 915ca6e79308575d1c568db9571e0841f7133657 Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Fri, 30 May 2025 16:36:11 -0400
Subject: [PATCH 12/19] Update README.md

---
 README.md | 263 ++++++++++++++++++++++++++++++++++++++++--------------
 1 file changed, 198 insertions(+), 65 deletions(-)

diff --git a/README.md b/README.md
index 9a4fb48..0892907 100644
--- a/README.md
+++ b/README.md
@@ -1,11 +1,15 @@
 # Geospatial-Tools
 
+## Description
+
+This repository is a collection of tools and scripts for geospatial use cases.
+
 ## Requirements
 
 This project has only been tested in a Linux (Debian based) environment and assumes
 some basic tools for development are already installed.
 
-The project uses a Makefile to automate most operations. If `make` is available on your 
+The project uses a Makefile to automate most operations. If `make` is available on your
 machine there's a good chance this will work.
 
 The following Makefile files should not be modified, but can be consulted:
@@ -18,6 +22,10 @@ The following Makefile files are project or user specific:
 * [Makefile.variables](Makefile.variables) : Shared project variables.
 * [Makefile.targets](Makefile.targets) : Shared project targets.
 * [Makefile.private](Makefile.private.example) : User specific variables and targets.
+    * This file is ignored by git and should never be committed, as it can also contain
+      secrets.
+    * You can create your own version locally by copying from
+      [Makefile.private.example](Makefile.private.example)
 
 ## Basic Information
 
@@ -32,136 +40,261 @@ This project uses Python version 3.11
 
 ## Build Tool
 
-This project uses Poetry as a build tool. Using a build tool has the advantage of 
+This project uses `poetry` as a build tool. Using a build tool has the advantage of
 streamlining script use as well as fix path issues related to imports.
 
-## Installation
+## First Time User Quick Setup
 
-This project assumes environment management will be done with `Conda` or directly through
-`Poetry`. 
-
-* [Poetry](https://python-poetry.org/docs/basic-usage/)
-* [Conda](https://conda.io/projects/conda/en/latest/user-guide/getting-started.html)
-
-While it is possible to manage the environment with, for example, pyenv or virtualenv, 
-those specific use cases are not supported by the Makefile and require users to set up 
-their own environments beforehand.
+### Installing poetry
 
-For detailed information about `Poetry` and `Conda`:
-
-If you want to use something else than `Conda` or `Poetry` to manage environment isolation, 
-it is recommended to follow 
-[Poetry's guidelines on managing environments](https://python-poetry.org/docs/managing-environments/)
-
-Poetry is not included in the [environment.yml](environment.yml), due to some possible problems
-in compute cluster environments, but will be installed automatically if needed
-by most `install` targets.
-
-### Environment Management
-
-You will need to create a virtual environment for your dependencies.
+If on a compute cluster, first load the appropriate python module:
 
 * [How to create a virtual environment for the Mila cluster](docs/environment_creation_mila.md)
 * [How to create an environment for the DRAC cluster](docs/environment_creation_drac.md)
-* [How to create a Conda environment](docs/conda_environment_creation.md)
-* [Migrating to DRAC from another environment](docs/migrating_to_drac.md)
 
-Do note that Conda is not available on the DRAC cluster, and there are some extra steps
-to use Conda on the Mila cluster compared to a workstation.
+Installing `pipx` and `poetry`:
 
-####  Environment management choices
+```shell
+make poetry-install
+```
 
-Environment management can become quite complicated. Using Conda allows a certain
-ease of management since the Poetry installation is contained inside the created Conda 
-environment.
+Next, let's choose how to manage our development environment
 
-However, some computing environments do not permit the use of Conda (like certain SLURM
-clusters). This is why the `pipx` option for Poetry is also enabled. To 
-install `pipx`, a user needs to have write access for the current environment, which is 
-why, for compatibility reasons, we install it in a lightweight, standalone virtual environment.
+### Environment management choice
 
-*Disclaimer for those that already know a lot about Poetry...*
+Choose between managing your development with either `virtualenv`, `poetry` or `conda`.
 
-Yes, `Poetry` can manage environments directly, and there are a lot of other more advanced 
-uses that are not explored in this repository. This is done on purpose, as an introduction 
-to this tool in a context that is familiar for most users (i.e. creating virtual environments
-with venv/virtualenv/conda). If you are comfortable with `Poetry` and especially its use 
-on compute clusters, feel free to disregard the recommendations below. Just don't forget 
-to document its use for the project!
+#### Virtualenv (or Venv)
 
-### First Time User Quick Setup
+This is the simplest way and what most people in the lab are already used to.
 
-#### Poetry
+Make sure that `python 3.10 or 3.11` is available either locally, through loaded cluster
+modules (ex. `module load python/<PYTHON_VERSION>`) or `pyenv` before executing the
+following command:
 
-The easiest and quickest way to get up and running with Poetry.
+```shell
+make venv-create
+```
 
-Install pipx and Poetry and activate project environment :
+You can see the shell command to activate the environment with the following target:
 
 ```shell
-make poetry-install-venv
+make venv-activate
 ```
 
-**Or, if Poetry is already available:**
+#### Poetry
+
+Make sure that `python 3.10 or 3.11` is available either locally, through loaded cluster
+modules (ex. `module load python/<PYTHON_VERSION>`) or `pyenv` before executing the
+following command:
 
 ```shell
 make poetry-create-env
 ```
 
-Install package:
+Make sure to read up
+on [how to use your poetry virtual environment](https://python-poetry.org/docs/basic-usage/#using-your-virtual-environment)
 
-```shell
-make install
-```
+You can:
+
+* Use the `poetry run` command to access your executables
+    * ex. `poetry run python your_script.py`, or `poetry run pylint src/`
+* Use the `poetry shell` command to activate and step in your project environment
 
 #### Conda
-The easiest and quickest way to get up and running with Conda.
 
-Create Conda environment (will check for Conda and install it if not found):
+Reminder: `conda` is not available on DRAC.
+
+If working on the Mila cluster, first load the appropriate module :
+`module load anaconda/3`
+
+1. Create `conda` environment (will check for `conda` and install it if not found):
 
 ```shell
 make conda-create-env
 ```
 
-Activate Conda environment (substitute with your <CONDA_TOOL> if something else 
-than `conda`:
+2. Activate `conda` environment (substitute with your <CONDA_TOOL> if something else
+   than `conda`:
 
 ```
-conda activate geospatial-tools
+conda activate <environment_name>
 ```
 
-Install package:
+### Install
+
+Once the environment is taken care of, you can verify everything with the following
+command before continuing:
+
+```shell
+make poetry-env-info
+```
+
+or
+
+```shell
+poetry env info
+```
+
+To install the package and its dependencies:
 
 ```shell
 make install
 ```
 
-### In depth Environment and Install Targets
+This also installs and configures the `pre-commit` hook. See ...
+
+### Development
+
+1. [Add required dependencies](./CONTRIBUTING.md#adding-dependencies)
+2. Create some new modules in the [src](./src) folder!
+
+## Detailed documentation
+
+This project assumes environment management will be done with `conda`, a classic
+python virtual environment, or directly through `poetry`.
+
+* [Poetry](https://python-poetry.org/docs/basic-usage/)
+* [Conda](https://conda.io/projects/conda/en/latest/user-guide/getting-started.html)
+
+While it is possible to manage the environment with, for example, pyenv or virtualenv,
+those specific use cases are not supported by the Makefile and require users to set up
+their own environments beforehand.
+
+If you want to use something else than `conda` or `poetry` to manage environment isolation,
+it is recommended to follow
+[Poetry's guidelines on managing environments](https://python-poetry.org/docs/managing-environments/)
+
+`poetry` is not included in the [environment.yml](environment.yml), due to some possible problems
+in compute cluster environments, but will be installed automatically if needed
+by most `install` targets.
+
+See [Environment and Install targets](docs/makefile_environment_targets.md) for more
+information.
+
+### Environment Management
+
+Your project will need a virtual environment for your dependencies.
+
+* [How to create a virtual environment for the Mila cluster](docs/environment_creation_mila.md)
+* [How to create an environment for the DRAC cluster](docs/environment_creation_drac.md)
+* [How to create a Conda environment](docs/conda_environment_creation.md)
+* [Migrating to DRAC from another environment](docs/migrating_to_drac.md)
+
+There are different ways of managing your python version in these environments. On the
+clusters, you have access to different python modules, and through `conda` you have access
+to practically all the versions that are available.
+
+However, on your own system, if you do not wish to use `conda`, you will have to either
+manually install different versions of python manually for them to be usable by `poetry`
+or use a tool like [pyenv](https://github.com/pyenv/pyenv).
+
+Do note that `conda` is not available on the DRAC cluster, and there are some extra steps
+to use `conda` on the Mila cluster compared to a workstation.
+
+#### How to use conda with poetry
+
+When using `conda`, it is important to understand that it is both an environment management
+tool AND a dependency management tool... and so is `poetry`. The difference is that with `conda`
+you can install different versions of python, as well as have access to non
+python applications and binary packages.
+
+To use them together, it is recommended to use `conda` as the environment and python
+version manager, for non-python dependencies, and use `poetry` as the python
+dependency manager.
+
+Using both `conda` and `poetry` (and `pip` directly, for that matter), to install and
+manage python dependencies is a great recipe for breaking your environment.
+
+If you do need to install python dependencies in both (ex. pytorch through `conda`, and
+others using `poetry`), you need to be cautious as one dependency manager can and will
+interfere with the dependencies managed by the other one and will make dependency
+conflicts challenging to fix.
+
+If there are no ways around it, you could also manage and use two environments at the same time
+(one via conda and one via poetry). This, however, requires an enormous amount of discipline
+to work and is strongly discouraged.
+
+#### Environment management choices
+
+The choice of which environment manager to use between `conda` and `poetry` is ultimately
+determined by either project requirements or personal preference. Both are allowed and
+supported by this project.
+
+### Installation
+
+There are a few installation targets available.
 
-See [Environment and Install targets](docs/makefile_environment_targets.md)
+![](img/install_targets.png)
 
-## Useful targets for development
+Generally, `make install` is the most useful, but the others can have their uses.
+For example, using `make install-package` is great for an environment where
+you will only be executing your code and do no development.
+
+### Useful Makefile targets for development
+
+To run linting checks with `flake8`, `pylint`, `black`, `isort` and `docformatter`:
 
-To run linting checks with `flake8`, `pylint`, `black` and `isort`:
 ```shell
 make check-lint
 ```
 
-To fix linting with `black`, `flynt` and `isort`:
+To fix linting with `autoflake`,`autopep8`,`black`, `isort`, `flynt` and `docformatter`:
+
 ```shell
 make fix-lint
 ```
 
 To run a `pre-commit` check before actually committing:
+
 ```shell
 make precommit
 ```
 
 To run tests:
+
 ```shell
 make test
 ```
 
+#### The use of Nox
+
+Behind the scenes, the targets in this section make use of the
+[Nox automation tool](https://nox.thea.codes/en/stable/).
+
+The configurations can be found in the [noxfile.py](noxfile.py) file.
+
+For more information about how `nox` is used in this project, see
+[Nox session descriptions](docs/nox_session_descriptions.md).
+
+#### Experimental targets
+
+The `ruff` tool is now also available in the makefile. This tool is not yet integrated
+into the `pre-commit` configuration and should be used, optionally, as a complement to
+the other code quality tools.
+
+To run linting using `ruff`:
+
+```shell
+make ruff
+```
+
+To run linting using `ruff` and fix automatically fixable warnings:
+
+```shell
+make ruff-fix
+```
+
+To run code formatting using `ruff`
+
+```shell
+make ruff-format
+```
+
+For more information of `ruff`, see it's [official documentation here](https://docs.astral.sh/ruff/).
+
 ## Configurations
+
 Configurations are in the [config/](configs) folder.
 
 ## Data

From 32337fcba9091e63cde3daaa7dd79825de7a2bc5 Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Fri, 30 May 2025 16:36:38 -0400
Subject: [PATCH 13/19] Update project dependencies

---
 poetry.lock    | 3587 +++++++++++++++++++++++-------------------------
 pyproject.toml |    3 +-
 2 files changed, 1727 insertions(+), 1863 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index eea98d5..f1e2289 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -28,25 +28,25 @@ files = [
 
 [[package]]
 name = "anyio"
-version = "4.4.0"
+version = "4.9.0"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "anyio-4.4.0-py3-none-any.whl", hash = "sha256:c1b2d8f46a8a812513012e1107cb0e68c17159a7a594208005a57dc776e1bdc7"},
-    {file = "anyio-4.4.0.tar.gz", hash = "sha256:5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94"},
+    {file = "anyio-4.9.0-py3-none-any.whl", hash = "sha256:9f76d541cad6e36af7beb62e978876f3b41e3e04f2c1fbf0884604c0a9c4d93c"},
+    {file = "anyio-4.9.0.tar.gz", hash = "sha256:673c0c244e15788651a4ff38710fea9675823028a6f08a5eda409e0c9840a028"},
 ]
 
 [package.dependencies]
 exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""}
 idna = ">=2.8"
 sniffio = ">=1.1"
-typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""}
+typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""}
 
 [package.extras]
-doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
-test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"]
-trio = ["trio (>=0.23)"]
+doc = ["Sphinx (>=8.2,<9.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx_rtd_theme"]
+test = ["anyio[trio]", "blockbuster (>=1.5.23)", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "trustme", "truststore (>=0.9.1)", "uvloop (>=0.21)"]
+trio = ["trio (>=0.26.1)"]
 
 [[package]]
 name = "appnope"
@@ -61,13 +61,13 @@ files = [
 
 [[package]]
 name = "argcomplete"
-version = "3.5.0"
+version = "3.6.2"
 description = "Bash tab completion for argparse"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "argcomplete-3.5.0-py3-none-any.whl", hash = "sha256:d4bcf3ff544f51e16e54228a7ac7f486ed70ebf2ecfe49a63a91171c76bf029b"},
-    {file = "argcomplete-3.5.0.tar.gz", hash = "sha256:4349400469dccfb7950bb60334a680c58d88699bff6159df61251878dc6bf74b"},
+    {file = "argcomplete-3.6.2-py3-none-any.whl", hash = "sha256:65b3133a29ad53fb42c48cf5114752c7ab66c1c38544fdf6460f450c09b42591"},
+    {file = "argcomplete-3.6.2.tar.gz", hash = "sha256:d0519b1bc867f5f4f4713c41ad0aba73a4a5f007449716b16f385f2166dc6adf"},
 ]
 
 [package.extras]
@@ -162,66 +162,63 @@ files = [
 
 [[package]]
 name = "astroid"
-version = "3.2.4"
+version = "3.3.10"
 description = "An abstract syntax tree for Python with inference support."
 optional = false
-python-versions = ">=3.8.0"
+python-versions = ">=3.9.0"
 files = [
-    {file = "astroid-3.2.4-py3-none-any.whl", hash = "sha256:413658a61eeca6202a59231abb473f932038fbcbf1666587f66d482083413a25"},
-    {file = "astroid-3.2.4.tar.gz", hash = "sha256:0e14202810b30da1b735827f78f5157be2bbd4a7a59b7707ca0bfc2fb4c0063a"},
+    {file = "astroid-3.3.10-py3-none-any.whl", hash = "sha256:104fb9cb9b27ea95e847a94c003be03a9e039334a8ebca5ee27dafaf5c5711eb"},
+    {file = "astroid-3.3.10.tar.gz", hash = "sha256:c332157953060c6deb9caa57303ae0d20b0fbdb2e59b4a4f2a6ba49d0a7961ce"},
 ]
 
 [package.dependencies]
-typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
+typing-extensions = {version = ">=4", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "asttokens"
-version = "2.4.1"
+version = "3.0.0"
 description = "Annotate AST trees with source code positions"
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
 files = [
-    {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
-    {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
+    {file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"},
+    {file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"},
 ]
 
-[package.dependencies]
-six = ">=1.12.0"
-
 [package.extras]
-astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
-test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
+astroid = ["astroid (>=2,<4)"]
+test = ["astroid (>=2,<4)", "pytest", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "async-lru"
-version = "2.0.4"
+version = "2.0.5"
 description = "Simple LRU cache for asyncio"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "async-lru-2.0.4.tar.gz", hash = "sha256:b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627"},
-    {file = "async_lru-2.0.4-py3-none-any.whl", hash = "sha256:ff02944ce3c288c5be660c42dbcca0742b32c3b279d6dceda655190240b99224"},
+    {file = "async_lru-2.0.5-py3-none-any.whl", hash = "sha256:ab95404d8d2605310d345932697371a5f40def0487c03d6d0ad9138de52c9943"},
+    {file = "async_lru-2.0.5.tar.gz", hash = "sha256:481d52ccdd27275f42c43a928b4a50c3bfb2d67af4e78b170e3e0bb39c66e5bb"},
 ]
 
 [package.dependencies]
-typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
+typing_extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "attrs"
-version = "24.2.0"
+version = "25.3.0"
 description = "Classes Without Boilerplate"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"},
-    {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"},
+    {file = "attrs-25.3.0-py3-none-any.whl", hash = "sha256:427318ce031701fea540783410126f03899a97ffc6f61596ad581ac2e40e3bc3"},
+    {file = "attrs-25.3.0.tar.gz", hash = "sha256:75d7cefc7fb576747b2c81b4442d4d4a1ce0900973527c011d1030fd3bf4af1b"},
 ]
 
 [package.extras]
 benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
 cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
+dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier"]
 tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
 tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
 
@@ -257,31 +254,32 @@ tomli = {version = "*", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "babel"
-version = "2.16.0"
+version = "2.17.0"
 description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"},
-    {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"},
+    {file = "babel-2.17.0-py3-none-any.whl", hash = "sha256:4d0b53093fdfb4b21c92b5213dba5a1b23885afa8383709427046b21c366e5f2"},
+    {file = "babel-2.17.0.tar.gz", hash = "sha256:0c54cffb19f690cdcc52a3b50bcbf71e07a808d1c80d549f2459b9d2cf0afb9d"},
 ]
 
 [package.extras]
-dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+dev = ["backports.zoneinfo", "freezegun (>=1.0,<2.0)", "jinja2 (>=3.0)", "pytest (>=6.0)", "pytest-cov", "pytz", "setuptools", "tzdata"]
 
 [[package]]
 name = "beautifulsoup4"
-version = "4.12.3"
+version = "4.13.4"
 description = "Screen-scraping library"
 optional = false
-python-versions = ">=3.6.0"
+python-versions = ">=3.7.0"
 files = [
-    {file = "beautifulsoup4-4.12.3-py3-none-any.whl", hash = "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"},
-    {file = "beautifulsoup4-4.12.3.tar.gz", hash = "sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051"},
+    {file = "beautifulsoup4-4.13.4-py3-none-any.whl", hash = "sha256:9bbbb14bfde9d79f38b8cd5f8c7c85f4b8f2523190ebed90e950a8dea4cb1c4b"},
+    {file = "beautifulsoup4-4.13.4.tar.gz", hash = "sha256:dbb3c4e1ceae6aefebdaf2423247260cd062430a410e38c66f2baa50a8437195"},
 ]
 
 [package.dependencies]
 soupsieve = ">1.2"
+typing-extensions = ">=4.0.0"
 
 [package.extras]
 cchardet = ["cchardet"]
@@ -340,31 +338,31 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "bleach"
-version = "6.1.0"
+version = "6.2.0"
 description = "An easy safelist-based HTML-sanitizing tool."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "bleach-6.1.0-py3-none-any.whl", hash = "sha256:3225f354cfc436b9789c66c4ee030194bee0568fbf9cbdad3bc8b5c26c5f12b6"},
-    {file = "bleach-6.1.0.tar.gz", hash = "sha256:0a31f1837963c41d46bbf1331b8778e1308ea0791db03cc4e7357b97cf42a8fe"},
+    {file = "bleach-6.2.0-py3-none-any.whl", hash = "sha256:117d9c6097a7c3d22fd578fcd8d35ff1e125df6736f554da4e432fdd63f31e5e"},
+    {file = "bleach-6.2.0.tar.gz", hash = "sha256:123e894118b8a599fd80d3ec1a6d4cc7ce4e5882b1317a7e1ba69b56e95f991f"},
 ]
 
 [package.dependencies]
-six = ">=1.9.0"
+tinycss2 = {version = ">=1.1.0,<1.5", optional = true, markers = "extra == \"css\""}
 webencodings = "*"
 
 [package.extras]
-css = ["tinycss2 (>=1.1.0,<1.3)"]
+css = ["tinycss2 (>=1.1.0,<1.5)"]
 
 [[package]]
 name = "bqplot"
-version = "0.12.43"
+version = "0.12.45"
 description = "Interactive plotting for the Jupyter notebook, using d3.js and ipywidgets."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "bqplot-0.12.43-py2.py3-none-any.whl", hash = "sha256:65aa2f10bf2e4b500e628d5c1b876e6d2cdc2b82883200e4b1bb65edc17d111b"},
-    {file = "bqplot-0.12.43.tar.gz", hash = "sha256:f2b469d1f03df4f51873cb0406a24b56cdf4a835fc5aa9560776fc636b8b3449"},
+    {file = "bqplot-0.12.45-py2.py3-none-any.whl", hash = "sha256:cf2e046adb401670902ab53a18d9f63540091279bc45c4ef281bfdadf6e7e92c"},
+    {file = "bqplot-0.12.45.tar.gz", hash = "sha256:ede00e9fdf7d92e43cc2d1b9691c7da176b6216fdd187c8e92f19d7beaca5e2a"},
 ]
 
 [package.dependencies]
@@ -376,13 +374,13 @@ traittypes = ">=0.0.6"
 
 [[package]]
 name = "branca"
-version = "0.7.2"
+version = "0.8.1"
 description = "Generate complex HTML+JS pages with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "branca-0.7.2-py3-none-any.whl", hash = "sha256:853a359c34d08fd06498be762d8be9932750db4049cac11e25dd6f23562e25c2"},
-    {file = "branca-0.7.2.tar.gz", hash = "sha256:ca4c94643ef31b819987ca5bd19c6009ea17b440baa3aac04628545f7a4da023"},
+    {file = "branca-0.8.1-py3-none-any.whl", hash = "sha256:d29c5fab31f7c21a92e34bf3f854234e29fecdcf5d2df306b616f20d816be425"},
+    {file = "branca-0.8.1.tar.gz", hash = "sha256:ac397c2d79bd13af0d04193b26d5ed17031d27609a7f1fab50c438b8ae712390"},
 ]
 
 [package.dependencies]
@@ -414,13 +412,13 @@ test = ["coverage", "pre-commit", "pytest", "pytest-cov", "pytest-mock"]
 
 [[package]]
 name = "certifi"
-version = "2024.8.30"
+version = "2025.4.26"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
-    {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
+    {file = "certifi-2025.4.26-py3-none-any.whl", hash = "sha256:30350364dfe371162649852c63336a15c70c6510c2ad5015b21c2345311805f3"},
+    {file = "certifi-2025.4.26.tar.gz", hash = "sha256:0a816057ea3cdefcef70270d2c515e4506bbc954f417fa5ade2021213bb8f0c6"},
 ]
 
 [[package]]
@@ -515,112 +513,114 @@ files = [
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.2"
+version = "3.4.2"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
-python-versions = ">=3.7.0"
+python-versions = ">=3.7"
 files = [
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 [[package]]
 name = "click"
-version = "8.1.7"
+version = "8.2.1"
 description = "Composable command line interface toolkit"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.10"
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 ]
 
 [package.dependencies]
@@ -662,13 +662,13 @@ test = ["pytest-cov"]
 
 [[package]]
 name = "cloudpickle"
-version = "3.0.0"
+version = "3.1.1"
 description = "Pickler class to extend the standard pickle.Pickler functionality"
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [[package]]
@@ -684,13 +684,13 @@ files = [
 
 [[package]]
 name = "colorlog"
-version = "6.8.2"
+version = "6.9.0"
 description = "Add colours to the output of Python's logging module."
 optional = false
 python-versions = ">=3.6"
 files = [
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 ]
 
 [package.dependencies]
@@ -732,76 +732,68 @@ test = ["pytest"]
 
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-version = "1.3.0"
+version = "1.3.2"
 description = "Python library for calculating contours of 2D quadrilateral grids"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
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 [package.dependencies]
@@ -810,89 +802,84 @@ numpy = ">=1.23"
 [package.extras]
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 docs = ["furo", "sphinx (>=7.2)", "sphinx-copybutton"]
-mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.11.1)", "types-Pillow"]
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 test = ["Pillow", "contourpy[test-no-images]", "matplotlib"]
 test-no-images = ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-xdist", "wurlitzer"]
 
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 [package.extras]
@@ -915,70 +902,50 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "dask"
-version = "2024.9.0"
+version = "2025.5.1"
 description = "Parallel PyData with Task Scheduling"
 optional = false
 python-versions = ">=3.10"
 files = [
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 [package.dependencies]
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 fsspec = ">=2021.09.0"
-importlib-metadata = {version = ">=4.13.0", markers = "python_version < \"3.12\""}
+importlib_metadata = {version = ">=4.13.0", markers = "python_version < \"3.12\""}
 numpy = {version = ">=1.24", optional = true, markers = "extra == \"array\""}
 packaging = ">=20.0"
 pandas = {version = ">=2.0", optional = true, markers = "extra == \"dataframe\""}
 partd = ">=1.4.0"
+pyarrow = {version = ">=14.0.1", optional = true, markers = "extra == \"dataframe\""}
 pyyaml = ">=5.3.1"
 toolz = ">=0.10.0"
 
 [package.extras]
 array = ["numpy (>=1.24)"]
 complete = ["dask[array,dataframe,diagnostics,distributed]", "lz4 (>=4.3.2)", "pyarrow (>=14.0.1)"]
-dataframe = ["dask-expr (>=1.1,<1.2)", "dask[array]", "pandas (>=2.0)"]
+dataframe = ["dask[array]", "pandas (>=2.0)", "pyarrow (>=14.0.1)"]
 diagnostics = ["bokeh (>=3.1.0)", "jinja2 (>=2.10.3)"]
-distributed = ["distributed (==2024.9.0)"]
-test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-rerunfailures", "pytest-timeout", "pytest-xdist"]
-
-[[package]]
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-
-[package.dependencies]
-dask = "2024.9.0"
-pandas = ">=2"
-pyarrow = ">=14.0.1"
-
-[package.extras]
-analyze = ["crick", "distributed"]
+distributed = ["distributed (==2025.5.1)"]
+test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytest-rerunfailures", "pytest-timeout", "pytest-xdist"]
 
 [[package]]
 name = "dask-geopandas"
-version = "0.4.1"
+version = "0.4.3"
 description = "Parallel GeoPandas with Dask"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 files = [
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 ]
 
 [package.dependencies]
-dask = {version = ">=2022.06.0", extras = ["dataframe"]}
-distributed = ">=2022.06.0"
-geopandas = ">=0.12"
+dask = {version = ">=2025.1.0", extras = ["dataframe"]}
+geopandas = ">=0.14.3"
 packaging = "*"
 shapely = ">=2.0"
 
@@ -987,44 +954,48 @@ test = ["pytest"]
 
 [[package]]
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 ]
 
 [[package]]
 name = "decorator"
-version = "5.1.1"
+version = "5.2.1"
 description = "Decorators for Humans"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
@@ -1040,13 +1011,13 @@ files = [
 
 [[package]]
 name = "dill"
-version = "0.3.8"
+version = "0.4.0"
 description = "serialize all of Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -1055,52 +1026,24 @@ profile = ["gprof2dot (>=2022.7.29)"]
 
 [[package]]
 name = "distlib"
-version = "0.3.8"
+version = "0.3.9"
 description = "Distribution utilities"
 optional = false
 python-versions = "*"
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-
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-locket = ">=1.0.0"
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-toolz = ">=0.11.2"
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-urllib3 = ">=1.26.5"
-zict = ">=3.0.0"
-
 [[package]]
 name = "docformatter"
-version = "1.7.5"
+version = "1.7.7"
 description = "Formats docstrings to follow PEP 257"
 optional = false
-python-versions = ">=3.7,<4.0"
+python-versions = "<4.0,>=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -1113,82 +1056,75 @@ tomli = ["tomli (>=2.0.0,<3.0.0)"]
 
 [[package]]
 name = "duckdb"
-version = "1.1.0"
+version = "1.3.0"
 description = "DuckDB in-process database"
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 python-versions = ">=3.7.0"
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 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
+[package.dependencies]
+typing-extensions = {version = ">=4.6.0", markers = "python_version < \"3.13\""}
+
 [package.extras]
 test = ["pytest (>=6)"]
 
 [[package]]
 name = "executing"
-version = "2.1.0"
+version = "2.2.0"
 description = "Get the currently executing AST node of a frame, and other information"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -1196,13 +1132,13 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth
 
 [[package]]
 name = "fastjsonschema"
-version = "2.20.0"
+version = "2.21.1"
 description = "Fastest Python implementation of JSON schema"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [package.extras]
@@ -1210,35 +1146,35 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
 
 [[package]]
 name = "filelock"
-version = "3.16.1"
+version = "3.18.0"
 description = "A platform independent file lock."
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-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.extras]
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+docs = ["furo (>=2024.8.6)", "sphinx (>=8.1.3)", "sphinx-autodoc-typehints (>=3)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.6.10)", "diff-cover (>=9.2.1)", "pytest (>=8.3.4)", "pytest-asyncio (>=0.25.2)", "pytest-cov (>=6)", "pytest-mock (>=3.14)", "pytest-timeout (>=2.3.1)", "virtualenv (>=20.28.1)"]
 typing = ["typing-extensions (>=4.12.2)"]
 
 [[package]]
 name = "flake8"
-version = "7.1.1"
+version = "7.2.0"
 description = "the modular source code checker: pep8 pyflakes and co"
 optional = false
-python-versions = ">=3.8.1"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
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-pycodestyle = ">=2.12.0,<2.13.0"
-pyflakes = ">=3.2.0,<3.3.0"
+pycodestyle = ">=2.13.0,<2.14.0"
+pyflakes = ">=3.3.0,<3.4.0"
 
 [[package]]
 name = "flake8-pyproject"
@@ -1259,13 +1195,13 @@ dev = ["pyTest", "pyTest-cov"]
 
 [[package]]
 name = "flynt"
-version = "1.0.1"
+version = "1.0.2"
 description = "CLI tool to convert a python project's %-formatted strings to f-strings."
 optional = false
 python-versions = ">=3.7"
 files = [
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@@ -1277,13 +1213,13 @@ dev = ["build", "pre-commit", "pytest", "pytest-cov", "twine"]
 
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 ]
 
 [package.extras]
@@ -1407,7 +1343,7 @@ sftp = ["paramiko"]
 smb = ["smbprotocol"]
 ssh = ["paramiko"]
 test = ["aiohttp (!=4.0.0a0,!=4.0.0a1)", "numpy", "pytest", "pytest-asyncio (!=0.22.0)", "pytest-benchmark", "pytest-cov", "pytest-mock", "pytest-recording", "pytest-rerunfailures", "requests"]
-test-downstream = ["aiobotocore (>=2.5.4,<3.0.0)", "dask-expr", "dask[dataframe,test]", "moto[server] (>4,<5)", "pytest-timeout", "xarray"]
+test-downstream = ["aiobotocore (>=2.5.4,<3.0.0)", "dask[dataframe,test]", "moto[server] (>4,<5)", "pytest-timeout", "xarray"]
 test-full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "cloudpickle", "dask", "distributed", "dropbox", "dropboxdrivefs", "fastparquet", "fusepy", "gcsfs", "jinja2", "kerchunk", "libarchive-c", "lz4", "notebook", "numpy", "ocifs", "pandas", "panel", "paramiko", "pyarrow", "pyarrow (>=1)", "pyftpdlib", "pygit2", "pytest", "pytest-asyncio (!=0.22.0)", "pytest-benchmark", "pytest-cov", "pytest-mock", "pytest-recording", "pytest-rerunfailures", "python-snappy", "requests", "smbprotocol", "tqdm", "urllib3", "zarr", "zstandard"]
 tqdm = ["tqdm"]
 
@@ -1433,13 +1369,13 @@ test = ["build", "mypy", "pytest", "pytest-xdist", "ruff", "twine", "types-reque
 
 [[package]]
 name = "geojson"
-version = "3.1.0"
+version = "3.2.0"
 description = "Python bindings and utilities for GeoJSON"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "geojson-3.1.0-py3-none-any.whl", hash = "sha256:68a9771827237adb8c0c71f8527509c8f5bef61733aa434cefc9c9d4f0ebe8f3"},
-    {file = "geojson-3.1.0.tar.gz", hash = "sha256:58a7fa40727ea058efc28b0e9ff0099eadf6d0965e04690830208d3ef571adac"},
+    {file = "geojson-3.2.0-py3-none-any.whl", hash = "sha256:69d14156469e13c79479672eafae7b37e2dcd19bdfd77b53f74fa8fe29910b52"},
+    {file = "geojson-3.2.0.tar.gz", hash = "sha256:b860baba1e8c6f71f8f5f6e3949a694daccf40820fa8f138b3f712bd85804903"},
 ]
 
 [[package]]
@@ -1467,45 +1403,45 @@ dev = ["black", "codecov", "pre-commit", "pytest (>=3.1.0)", "pytest-cov", "pyte
 
 [[package]]
 name = "h11"
-version = "0.14.0"
+version = "0.16.0"
 description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "h11-0.14.0-py3-none-any.whl", hash = "sha256:e3fe4ac4b851c468cc8363d500db52c2ead036020723024a109d37346efaa761"},
-    {file = "h11-0.14.0.tar.gz", hash = "sha256:8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d"},
+    {file = "h11-0.16.0-py3-none-any.whl", hash = "sha256:63cf8bbe7522de3bf65932fda1d9c2772064ffb3dae62d55932da54b31cb6c86"},
+    {file = "h11-0.16.0.tar.gz", hash = "sha256:4e35b956cf45792e4caa5885e69fba00bdbc6ffafbfa020300e549b208ee5ff1"},
 ]
 
 [[package]]
 name = "httpcore"
-version = "1.0.5"
+version = "1.0.9"
 description = "A minimal low-level HTTP client."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "httpcore-1.0.5-py3-none-any.whl", hash = "sha256:421f18bac248b25d310f3cacd198d55b8e6125c107797b609ff9b7a6ba7991b5"},
-    {file = "httpcore-1.0.5.tar.gz", hash = "sha256:34a38e2f9291467ee3b44e89dd52615370e152954ba21721378a87b2960f7a61"},
+    {file = "httpcore-1.0.9-py3-none-any.whl", hash = "sha256:2d400746a40668fc9dec9810239072b40b4484b640a8c38fd654a024c7a1bf55"},
+    {file = "httpcore-1.0.9.tar.gz", hash = "sha256:6e34463af53fd2ab5d807f399a9b45ea31c3dfa2276f15a2c3f00afff6e176e8"},
 ]
 
 [package.dependencies]
 certifi = "*"
-h11 = ">=0.13,<0.15"
+h11 = ">=0.16"
 
 [package.extras]
 asyncio = ["anyio (>=4.0,<5.0)"]
 http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
-trio = ["trio (>=0.22.0,<0.26.0)"]
+trio = ["trio (>=0.22.0,<1.0)"]
 
 [[package]]
 name = "httpx"
-version = "0.27.2"
+version = "0.28.1"
 description = "The next generation HTTP client."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "httpx-0.27.2-py3-none-any.whl", hash = "sha256:7bb2708e112d8fdd7829cd4243970f0c223274051cb35ee80c03301ee29a3df0"},
-    {file = "httpx-0.27.2.tar.gz", hash = "sha256:f7c2be1d2f3c3c3160d441802406b206c2b76f5947b11115e6df10c6c65e66c2"},
+    {file = "httpx-0.28.1-py3-none-any.whl", hash = "sha256:d909fcccc110f8c7faf814ca82a9a4d816bc5a6dbfea25d6591d6985b8ba59ad"},
+    {file = "httpx-0.28.1.tar.gz", hash = "sha256:75e98c5f16b0f35b567856f597f06ff2270a374470a5c2392242528e3e3e42fc"},
 ]
 
 [package.dependencies]
@@ -1513,7 +1449,6 @@ anyio = "*"
 certifi = "*"
 httpcore = "==1.*"
 idna = "*"
-sniffio = "*"
 
 [package.extras]
 brotli = ["brotli", "brotlicffi"]
@@ -1524,13 +1459,13 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "identify"
-version = "2.6.1"
+version = "2.6.12"
 description = "File identification library for Python"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "identify-2.6.1-py2.py3-none-any.whl", hash = "sha256:53863bcac7caf8d2ed85bd20312ea5dcfc22226800f6d6881f232d861db5a8f0"},
-    {file = "identify-2.6.1.tar.gz", hash = "sha256:91478c5fb7c3aac5ff7bf9b4344f803843dc586832d5f110d672b19aa1984c98"},
+    {file = "identify-2.6.12-py2.py3-none-any.whl", hash = "sha256:ad9672d5a72e0d2ff7c5c8809b62dfa60458626352fb0eb7b55e69bdc45334a2"},
+    {file = "identify-2.6.12.tar.gz", hash = "sha256:d8de45749f1efb108badef65ee8386f0f7bb19a7f26185f74de6367bffbaf0e6"},
 ]
 
 [package.extras]
@@ -1552,13 +1487,13 @@ all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2
 
 [[package]]
 name = "importlib-metadata"
-version = "8.5.0"
+version = "8.7.0"
 description = "Read metadata from Python packages"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "importlib_metadata-8.5.0-py3-none-any.whl", hash = "sha256:45e54197d28b7a7f1559e60b95e7c567032b602131fbd588f1497f47880aa68b"},
-    {file = "importlib_metadata-8.5.0.tar.gz", hash = "sha256:71522656f0abace1d072b9e5481a48f07c138e00f079c38c8f883823f9c26bd7"},
+    {file = "importlib_metadata-8.7.0-py3-none-any.whl", hash = "sha256:e5dd1551894c77868a30651cef00984d50e1002d06942a7101d34870c5f02afd"},
+    {file = "importlib_metadata-8.7.0.tar.gz", hash = "sha256:d13b81ad223b890aa16c5471f2ac3056cf76c5f10f82d6f9292f0b415f389000"},
 ]
 
 [package.dependencies]
@@ -1570,18 +1505,18 @@ cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 enabler = ["pytest-enabler (>=2.2)"]
 perf = ["ipython"]
-test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
+test = ["flufl.flake8", "importlib_resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
 type = ["pytest-mypy"]
 
 [[package]]
 name = "iniconfig"
-version = "2.0.0"
+version = "2.1.0"
 description = "brain-dead simple config-ini parsing"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
-    {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
+    {file = "iniconfig-2.1.0-py3-none-any.whl", hash = "sha256:9deba5723312380e77435581c6bf4935c94cbfab9b1ed33ef8d238ea168eb760"},
+    {file = "iniconfig-2.1.0.tar.gz", hash = "sha256:3abbd2e30b36733fee78f9c7f7308f2d0050e88f0087fd25c2645f63c773e1c7"},
 ]
 
 [[package]]
@@ -1669,13 +1604,13 @@ xyzservices = ">=2021.8.1"
 
 [[package]]
 name = "ipython"
-version = "8.27.0"
+version = "8.36.0"
 description = "IPython: Productive Interactive Computing"
 optional = false
 python-versions = ">=3.10"
 files = [
-    {file = "ipython-8.27.0-py3-none-any.whl", hash = "sha256:f68b3cb8bde357a5d7adc9598d57e22a45dfbea19eb6b98286fa3b288c9cd55c"},
-    {file = "ipython-8.27.0.tar.gz", hash = "sha256:0b99a2dc9f15fd68692e898e5568725c6d49c527d36a9fb5960ffbdeaa82ff7e"},
+    {file = "ipython-8.36.0-py3-none-any.whl", hash = "sha256:12b913914d010dcffa2711505ec8be4bf0180742d97f1e5175e51f22086428c1"},
+    {file = "ipython-8.36.0.tar.gz", hash = "sha256:24658e9fe5c5c819455043235ba59cfffded4a35936eefceceab6b192f7092ff"},
 ]
 
 [package.dependencies]
@@ -1685,16 +1620,16 @@ exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
 jedi = ">=0.16"
 matplotlib-inline = "*"
 pexpect = {version = ">4.3", markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""}
-prompt-toolkit = ">=3.0.41,<3.1.0"
+prompt_toolkit = ">=3.0.41,<3.1.0"
 pygments = ">=2.4.0"
-stack-data = "*"
+stack_data = "*"
 traitlets = ">=5.13.0"
-typing-extensions = {version = ">=4.6", markers = "python_version < \"3.12\""}
+typing_extensions = {version = ">=4.6", markers = "python_version < \"3.12\""}
 
 [package.extras]
 all = ["ipython[black,doc,kernel,matplotlib,nbconvert,nbformat,notebook,parallel,qtconsole]", "ipython[test,test-extra]"]
 black = ["black"]
-doc = ["docrepr", "exceptiongroup", "intersphinx-registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli", "typing-extensions"]
+doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli", "typing_extensions"]
 kernel = ["ipykernel"]
 matplotlib = ["matplotlib"]
 nbconvert = ["nbconvert"]
@@ -1703,7 +1638,7 @@ notebook = ["ipywidgets", "notebook"]
 parallel = ["ipyparallel"]
 qtconsole = ["qtconsole"]
 test = ["packaging", "pickleshare", "pytest", "pytest-asyncio (<0.22)", "testpath"]
-test-extra = ["curio", "ipython[test]", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.23)", "pandas", "trio"]
+test-extra = ["curio", "ipython[test]", "jupyter_ai", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.23)", "pandas", "trio"]
 
 [[package]]
 name = "ipytree"
@@ -1721,21 +1656,21 @@ ipywidgets = ">=7.5.0,<9"
 
 [[package]]
 name = "ipywidgets"
-version = "8.1.5"
+version = "8.1.7"
 description = "Jupyter interactive widgets"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "ipywidgets-8.1.5-py3-none-any.whl", hash = "sha256:3290f526f87ae6e77655555baba4f36681c555b8bdbbff430b70e52c34c86245"},
-    {file = "ipywidgets-8.1.5.tar.gz", hash = "sha256:870e43b1a35656a80c18c9503bbf2d16802db1cb487eec6fab27d683381dde17"},
+    {file = "ipywidgets-8.1.7-py3-none-any.whl", hash = "sha256:764f2602d25471c213919b8a1997df04bef869251db4ca8efba1b76b1bd9f7bb"},
+    {file = "ipywidgets-8.1.7.tar.gz", hash = "sha256:15f1ac050b9ccbefd45dccfbb2ef6bed0029d8278682d569d71b8dd96bee0376"},
 ]
 
 [package.dependencies]
 comm = ">=0.1.3"
 ipython = ">=6.1.0"
-jupyterlab-widgets = ">=3.0.12,<3.1.0"
+jupyterlab_widgets = ">=3.0.15,<3.1.0"
 traitlets = ">=4.3.1"
-widgetsnbextension = ">=4.0.12,<4.1.0"
+widgetsnbextension = ">=4.0.14,<4.1.0"
 
 [package.extras]
 test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
@@ -1770,32 +1705,32 @@ colors = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "jedi"
-version = "0.19.1"
+version = "0.19.2"
 description = "An autocompletion tool for Python that can be used for text editors."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "jedi-0.19.1-py2.py3-none-any.whl", hash = "sha256:e983c654fe5c02867aef4cdfce5a2fbb4a50adc0af145f70504238f18ef5e7e0"},
-    {file = "jedi-0.19.1.tar.gz", hash = "sha256:cf0496f3651bc65d7174ac1b7d043eff454892c708a87d1b683e57b569927ffd"},
+    {file = "jedi-0.19.2-py2.py3-none-any.whl", hash = "sha256:a8ef22bde8490f57fe5c7681a3c83cb58874daf72b4784de3cce5b6ef6edb5b9"},
+    {file = "jedi-0.19.2.tar.gz", hash = "sha256:4770dc3de41bde3966b02eb84fbcf557fb33cce26ad23da12c742fb50ecb11f0"},
 ]
 
 [package.dependencies]
-parso = ">=0.8.3,<0.9.0"
+parso = ">=0.8.4,<0.9.0"
 
 [package.extras]
 docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"]
 qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
-testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
+testing = ["Django", "attrs", "colorama", "docopt", "pytest (<9.0.0)"]
 
 [[package]]
 name = "jinja2"
-version = "3.1.4"
+version = "3.1.6"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"},
-    {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"},
+    {file = "jinja2-3.1.6-py3-none-any.whl", hash = "sha256:85ece4451f492d0c13c5dd7c13a64681a86afae63a5f347908daf103ce6d2f67"},
+    {file = "jinja2-3.1.6.tar.gz", hash = "sha256:0137fb05990d35f1275a587e9aee6d56da821fc83491a0fb838183be43f66d6d"},
 ]
 
 [package.dependencies]
@@ -1806,15 +1741,18 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "json5"
-version = "0.9.25"
+version = "0.12.0"
 description = "A Python implementation of the JSON5 data format."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.8.0"
 files = [
-    {file = "json5-0.9.25-py3-none-any.whl", hash = "sha256:34ed7d834b1341a86987ed52f3f76cd8ee184394906b6e22a1e0deb9ab294e8f"},
-    {file = "json5-0.9.25.tar.gz", hash = "sha256:548e41b9be043f9426776f05df8635a00fe06104ea51ed24b67f908856e151ae"},
+    {file = "json5-0.12.0-py3-none-any.whl", hash = "sha256:6d37aa6c08b0609f16e1ec5ff94697e2cbbfbad5ac112afa05794da9ab7810db"},
+    {file = "json5-0.12.0.tar.gz", hash = "sha256:0b4b6ff56801a1c7dc817b0241bca4ce474a0e6a163bfef3fc594d3fd263ff3a"},
 ]
 
+[package.extras]
+dev = ["build (==1.2.2.post1)", "coverage (==7.5.4)", "coverage (==7.8.0)", "mypy (==1.14.1)", "mypy (==1.15.0)", "pip (==25.0.1)", "pylint (==3.2.7)", "pylint (==3.3.6)", "ruff (==0.11.2)", "twine (==6.1.0)", "uv (==0.6.11)"]
+
 [[package]]
 name = "jsonpointer"
 version = "3.0.0"
@@ -1828,13 +1766,13 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.23.0"
+version = "4.24.0"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "jsonschema-4.23.0-py3-none-any.whl", hash = "sha256:fbadb6f8b144a8f8cf9f0b89ba94501d143e50411a1278633f56a7acf7fd5566"},
-    {file = "jsonschema-4.23.0.tar.gz", hash = "sha256:d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"},
+    {file = "jsonschema-4.24.0-py3-none-any.whl", hash = "sha256:a462455f19f5faf404a7902952b6f0e3ce868f3ee09a359b05eca6673bd8412d"},
+    {file = "jsonschema-4.24.0.tar.gz", hash = "sha256:0b4e8069eb12aedfa881333004bccaec24ecef5a8a6a4b6df142b2cc9599d196"},
 ]
 
 [package.dependencies]
@@ -1857,13 +1795,13 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
 name = "jsonschema-specifications"
-version = "2023.12.1"
+version = "2025.4.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "jsonschema_specifications-2023.12.1-py3-none-any.whl", hash = "sha256:87e4fdf3a94858b8a2ba2778d9ba57d8a9cafca7c7489c46ba0d30a8bc6a9c3c"},
-    {file = "jsonschema_specifications-2023.12.1.tar.gz", hash = "sha256:48a76787b3e70f5ed53f1160d2b81f586e4ca6d1548c5de7085d1682674764cc"},
+    {file = "jsonschema_specifications-2025.4.1-py3-none-any.whl", hash = "sha256:4653bffbd6584f7de83a67e0d620ef16900b390ddc7939d56684d6c81e33f1af"},
+    {file = "jsonschema_specifications-2025.4.1.tar.gz", hash = "sha256:630159c9f4dbea161a6a2205c3011cc4f18ff381b189fff48bb39b9bf26ae608"},
 ]
 
 [package.dependencies]
@@ -1893,13 +1831,13 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt
 
 [[package]]
 name = "jupyter-core"
-version = "5.7.2"
+version = "5.8.1"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1908,22 +1846,23 @@ pywin32 = {version = ">=300", markers = "sys_platform == \"win32\" and platform_
 traitlets = ">=5.3"
 
 [package.extras]
-docs = ["myst-parser", "pydata-sphinx-theme", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
-test = ["ipykernel", "pre-commit", "pytest (<8)", "pytest-cov", "pytest-timeout"]
+docs = ["intersphinx-registry", "myst-parser", "pydata-sphinx-theme", "sphinx-autodoc-typehints", "sphinxcontrib-spelling", "traitlets"]
+test = ["ipykernel", "pre-commit", "pytest (<9)", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "jupyter-events"
-version = "0.10.0"
+version = "0.12.0"
 description = "Jupyter Event System library"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
 jsonschema = {version = ">=4.18.0", extras = ["format-nongpl"]}
+packaging = "*"
 python-json-logger = ">=2.0.4"
 pyyaml = ">=5.3"
 referencing = "*"
@@ -1933,7 +1872,7 @@ traitlets = ">=5.3"
 
 [package.extras]
 cli = ["click", "rich"]
-docs = ["jupyterlite-sphinx", "myst-parser", "pydata-sphinx-theme", "sphinxcontrib-spelling"]
+docs = ["jupyterlite-sphinx", "myst-parser", "pydata-sphinx-theme (>=0.16)", "sphinx (>=8)", "sphinxcontrib-spelling"]
 test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "pytest-console-scripts", "rich"]
 
 [[package]]
@@ -1963,13 +1902,13 @@ jupyter-server = ">=1.1.2"
 
 [[package]]
 name = "jupyter-server"
-version = "2.14.2"
+version = "2.16.0"
 description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -1978,7 +1917,7 @@ argon2-cffi = ">=21.1"
 jinja2 = ">=3.0.3"
 jupyter-client = ">=7.4.4"
 jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
-jupyter-events = ">=0.9.0"
+jupyter-events = ">=0.11.0"
 jupyter-server-terminals = ">=0.4.4"
 nbconvert = ">=6.4.4"
 nbformat = ">=5.3.0"
@@ -2018,13 +1957,13 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (>
 
 [[package]]
 name = "jupyterlab"
-version = "4.2.5"
+version = "4.4.3"
 description = "JupyterLab computational environment"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -2038,31 +1977,31 @@ jupyter-server = ">=2.4.0,<3"
 jupyterlab-server = ">=2.27.1,<3"
 notebook-shim = ">=0.2"
 packaging = "*"
-setuptools = ">=40.1.0"
+setuptools = ">=41.1.0"
 tomli = {version = ">=1.2.2", markers = "python_version < \"3.11\""}
 tornado = ">=6.2.0"
 traitlets = "*"
 
 [package.extras]
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+dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.11.4)"]
+docs = ["jsx-lexer", "myst-parser", "pydata-sphinx-theme (>=0.13.0)", "pytest", "pytest-check-links", "pytest-jupyter", "sphinx (>=1.8,<8.2.0)", "sphinx-copybutton"]
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 upgrade-extension = ["copier (>=9,<10)", "jinja2-time (<0.3)", "pydantic (<3.0)", "pyyaml-include (<3.0)", "tomli-w (<2.0)"]
 
 [[package]]
 name = "jupyterlab-lsp"
-version = "5.1.0"
+version = "5.1.1"
 description = "Coding assistance for JupyterLab with Language Server Protocol"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
-jupyter-lsp = ">=2.0.0"
+jupyter_lsp = ">=2.0.0"
 jupyterlab = ">=4.1.0,<5.0.0a0"
 
 [[package]]
@@ -2103,136 +2042,102 @@ test = ["hatch", "ipykernel", "openapi-core (>=0.18.0,<0.19.0)", "openapi-spec-v
 
 [[package]]
 name = "jupyterlab-widgets"
-version = "3.0.13"
+version = "3.0.15"
 description = "Jupyter interactive widgets for JupyterLab"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
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 description = "A fast implementation of the Cassowary constraint solver"
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-python-versions = ">=3.8"
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 [package.dependencies]
@@ -2444,7 +2344,7 @@ pyparsing = ">=2.3.1"
 python-dateutil = ">=2.7"
 
 [package.extras]
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 [[package]]
 name = "matplotlib-inline"
@@ -2484,108 +2384,62 @@ files = [
 
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+python-versions = ">=3.8"
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 ]
 
+[package.dependencies]
+typing-extensions = {version = "*", markers = "python_version < \"3.11\""}
+
 [[package]]
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 version = "1.1.0"
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 python-versions = ">=3.8"
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-description = "Type system extensions for programs checked with the mypy type checker."
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+description = "Extremely lightweight compatibility layer between dataframe libraries"
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-python-versions = ">=3.5"
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 files = [
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+dask = ["dask[dataframe] (>=2024.8)"]
+duckdb = ["duckdb (>=1.0)"]
+ibis = ["ibis-framework (>=6.0.0)", "packaging", "pyarrow-hotfix", "rich"]
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+polars = ["polars (>=0.20.3)"]
+pyarrow = ["pyarrow (>=11.0.0)"]
+pyspark = ["pyspark (>=3.5.0)"]
+pyspark-connect = ["pyspark[connect] (>=3.5.0)"]
+sqlframe = ["sqlframe (>=3.22.0)"]
+
 [[package]]
 name = "nbclient"
-version = "0.10.0"
+version = "0.10.2"
 description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
 optional = false
-python-versions = ">=3.8.0"
+python-versions = ">=3.9.0"
 files = [
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 [package.dependencies]
@@ -2596,23 +2450,23 @@ traitlets = ">=5.4"
 
 [package.extras]
 dev = ["pre-commit"]
-docs = ["autodoc-traits", "mock", "moto", "myst-parser", "nbclient[test]", "sphinx (>=1.7)", "sphinx-book-theme", "sphinxcontrib-spelling"]
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+docs = ["autodoc-traits", "flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "mock", "moto", "myst-parser", "nbconvert (>=7.1.0)", "pytest (>=7.0,<8)", "pytest-asyncio", "pytest-cov (>=4.0)", "sphinx (>=1.7)", "sphinx-book-theme", "sphinxcontrib-spelling", "testpath", "xmltodict"]
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 name = "nbconvert"
-version = "7.16.4"
+version = "7.16.6"
 description = "Converting Jupyter Notebooks (.ipynb files) to other formats.  Output formats include asciidoc, html, latex, markdown, pdf, py, rst, script.  nbconvert can be used both as a Python library (`import nbconvert`) or as a command line tool (invoked as `jupyter nbconvert ...`)."
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 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 beautifulsoup4 = "*"
-bleach = "!=5.0.0"
+bleach = {version = "!=5.0.0", extras = ["css"]}
 defusedxml = "*"
 jinja2 = ">=3.0"
 jupyter-core = ">=4.7"
@@ -2624,7 +2478,6 @@ nbformat = ">=5.7"
 packaging = "*"
 pandocfilters = ">=1.4.1"
 pygments = ">=2.4.1"
-tinycss2 = "*"
 traitlets = ">=5.1"
 
 [package.extras]
@@ -2699,18 +2552,18 @@ files = [
 
 [[package]]
 name = "notebook"
-version = "7.2.2"
+version = "7.4.3"
 description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 jupyter-server = ">=2.4.0,<3"
-jupyterlab = ">=4.2.0,<4.3"
+jupyterlab = ">=4.4.3,<4.5"
 jupyterlab-server = ">=2.27.1,<3"
 notebook-shim = ">=0.2,<0.3"
 tornado = ">=6.2.0"
@@ -2739,18 +2592,18 @@ test = ["pytest", "pytest-console-scripts", "pytest-jupyter", "pytest-tornasync"
 
 [[package]]
 name = "nox"
-version = "2024.4.15"
+version = "2024.10.9"
 description = "Flexible test automation."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 python-dateutil = ">=2.8.2"
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 ]
 
 [package.extras]
-docs = ["furo", "olefile", "sphinx (>=7.3)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinxext-opengraph"]
+docs = ["furo", "olefile", "sphinx (>=8.2)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinxext-opengraph"]
 fpx = ["olefile"]
 mic = ["olefile"]
-tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
+test-arrow = ["pyarrow"]
+tests = ["check-manifest", "coverage (>=7.4.2)", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout", "trove-classifiers (>=2024.10.12)"]
 typing = ["typing-extensions"]
 xmp = ["defusedxml"]
 
@@ -3109,49 +2980,54 @@ dev = ["black", "flake8", "mypy", "pytest", "responses", "setuptools", "types-re
 
 [[package]]
 name = "platformdirs"
-version = "4.3.6"
+version = "4.3.8"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=8.3.2)", "pytest-cov (>=5)", "pytest-mock (>=3.14)"]
-type = ["mypy (>=1.11.2)"]
+docs = ["furo (>=2024.8.6)", "proselint (>=0.14)", "sphinx (>=8.1.3)", "sphinx-autodoc-typehints (>=3)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=8.3.4)", "pytest-cov (>=6)", "pytest-mock (>=3.14)"]
+type = ["mypy (>=1.14.1)"]
 
 [[package]]
 name = "plotly"
-version = "5.24.1"
-description = "An open-source, interactive data visualization library for Python"
+version = "6.1.2"
+description = "An open-source interactive data visualization library for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
+narwhals = ">=1.15.1"
 packaging = "*"
-tenacity = ">=6.2.0"
+
+[package.extras]
+dev = ["black (==25.1.0)"]
+express = ["numpy"]
+kaleido = ["kaleido (==1.0.0rc13)"]
 
 [[package]]
 name = "pluggy"
-version = "1.5.0"
+version = "1.6.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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+    {file = "pluggy-1.6.0-py3-none-any.whl", hash = "sha256:e920276dd6813095e9377c0bc5566d94c932c33b27a3e3945d8389c374dd4746"},
+    {file = "pluggy-1.6.0.tar.gz", hash = "sha256:7dcc130b76258d33b90f61b658791dede3486c3e6bfb003ee5c9bfb396dd22f3"},
 ]
 
 [package.extras]
 dev = ["pre-commit", "tox"]
-testing = ["pytest", "pytest-benchmark"]
+testing = ["coverage", "pytest", "pytest-benchmark"]
 
 [[package]]
 name = "pre-commit"
@@ -3173,13 +3049,13 @@ virtualenv = ">=20.10.0"
 
 [[package]]
 name = "prometheus-client"
-version = "0.20.0"
+version = "0.22.0"
 description = "Python client for the Prometheus monitoring system."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.extras]
@@ -3187,13 +3063,13 @@ twisted = ["twisted"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.47"
+version = "3.0.51"
 description = "Library for building powerful interactive command lines in Python"
 optional = false
-python-versions = ">=3.7.0"
+python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -3201,32 +3077,26 @@ wcwidth = "*"
 
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 name = "psutil"
-version = "6.0.0"
-description = "Cross-platform lib for process and system monitoring in Python."
+version = "7.0.0"
+description = "Cross-platform lib for process and system monitoring in Python.  NOTE: the syntax of this script MUST be kept compatible with Python 2.7."
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
+python-versions = ">=3.6"
 files = [
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 ]
 
 [package.extras]
-test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"]
+dev = ["abi3audit", "black (==24.10.0)", "check-manifest", "coverage", "packaging", "pylint", "pyperf", "pypinfo", "pytest", "pytest-cov", "pytest-xdist", "requests", "rstcheck", "ruff", "setuptools", "sphinx", "sphinx_rtd_theme", "toml-sort", "twine", "virtualenv", "vulture", "wheel"]
+test = ["pytest", "pytest-xdist", "setuptools"]
 
 [[package]]
 name = "ptyprocess"
@@ -3306,13 +3176,13 @@ test = ["cffi", "hypothesis", "pandas", "pytest", "pytz"]
 
 [[package]]
 name = "pycodestyle"
-version = "2.12.1"
+version = "2.13.0"
 description = "Python style guide checker"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [[package]]
@@ -3328,19 +3198,20 @@ files = [
 
 [[package]]
 name = "pydantic"
-version = "2.9.2"
+version = "2.11.5"
 description = "Data validation using Python type hints"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 [package.dependencies]
 annotated-types = ">=0.6.0"
-pydantic-core = "2.23.4"
-typing-extensions = {version = ">=4.6.1", markers = "python_version < \"3.13\""}
+pydantic-core = "2.33.2"
+typing-extensions = ">=4.12.2"
+typing-inspection = ">=0.4.0"
 
 [package.extras]
 email = ["email-validator (>=2.0.0)"]
@@ -3348,100 +3219,110 @@ timezone = ["tzdata"]
 
 [[package]]
 name = "pydantic-core"
-version = "2.23.4"
+version = "2.33.2"
 description = "Core functionality for Pydantic validation and serialization"
 optional = false
-python-versions = ">=3.8"
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 [package.dependencies]
@@ -3449,44 +3330,47 @@ typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
 
 [[package]]
 name = "pydantic-settings"
-version = "2.5.2"
+version = "2.9.1"
 description = "Settings management using Pydantic"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
 pydantic = ">=2.7.0"
 python-dotenv = ">=0.21.0"
+typing-inspection = ">=0.4.0"
 
 [package.extras]
+aws-secrets-manager = ["boto3 (>=1.35.0)", "boto3-stubs[secretsmanager]"]
 azure-key-vault = ["azure-identity (>=1.16.0)", "azure-keyvault-secrets (>=4.8.0)"]
+gcp-secret-manager = ["google-cloud-secret-manager (>=2.23.1)"]
 toml = ["tomli (>=2.0.1)"]
 yaml = ["pyyaml (>=6.0.1)"]
 
 [[package]]
 name = "pyflakes"
-version = "3.2.0"
+version = "3.3.2"
 description = "passive checker of Python programs"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [[package]]
 name = "pygments"
-version = "2.18.0"
+version = "2.19.1"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -3494,26 +3378,27 @@ windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "pylint"
-version = "3.2.7"
+version = "3.3.7"
 description = "python code static checker"
 optional = false
-python-versions = ">=3.8.0"
+python-versions = ">=3.9.0"
 files = [
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 ]
 
 [package.dependencies]
-astroid = ">=3.2.4,<=3.3.0-dev0"
+astroid = ">=3.3.8,<=3.4.0.dev0"
 colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
 dill = [
     {version = ">=0.2", markers = "python_version < \"3.11\""},
-    {version = ">=0.3.6", markers = "python_version >= \"3.11\""},
+    {version = ">=0.3.7", markers = "python_version >= \"3.12\""},
+    {version = ">=0.3.6", markers = "python_version >= \"3.11\" and python_version < \"3.12\""},
 ]
-isort = ">=4.2.5,<5.13.0 || >5.13.0,<6"
+isort = ">=4.2.5,<5.13 || >5.13,<7"
 mccabe = ">=0.6,<0.8"
-platformdirs = ">=2.2.0"
-tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
+platformdirs = ">=2.2"
+tomli = {version = ">=1.1", markers = "python_version < \"3.11\""}
 tomlkit = ">=0.10.1"
 
 [package.extras]
@@ -3568,13 +3453,13 @@ test = ["pytest", "pytest-cov"]
 
 [[package]]
 name = "pyparsing"
-version = "3.1.4"
+version = "3.2.3"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = false
-python-versions = ">=3.6.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.extras]
@@ -3582,38 +3467,44 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pyproj"
-version = "3.6.1"
+version = "3.7.1"
 description = "Python interface to PROJ (cartographic projections and coordinate transformations library)"
 optional = false
-python-versions = ">=3.9"
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@@ -3644,13 +3535,13 @@ files = [
 
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@@ -4016,36 +3894,32 @@ cffi = {version = "*", markers = "implementation_name == \"pypy\""}
 
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@@ -4055,32 +3929,32 @@ certifi = "*"
 click = ">=4.0"
 click-plugins = "*"
 cligj = ">=0.5"
-numpy = "*"
-setuptools = "*"
-snuggs = ">=1.4.1"
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 [package.dependencies]
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 rpds-py = ">=0.7.0"
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 [[package]]
 name = "requests"
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 [package.extras]
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 [package.dependencies]
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 rich = ">=10.7"
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 [package.extras]
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 [[package]]
 name = "rioxarray"
@@ -4191,152 +4066,166 @@ interp = ["scipy"]
 
 [[package]]
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+version = "0.10.1"
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@@ -4360,81 +4249,80 @@ win32 = ["pywin32"]
 
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 [package.dependencies]
-numpy = ">=1.14,<3"
+numpy = ">=1.21"
 
 [package.extras]
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-test = ["pytest", "pytest-cov"]
+test = ["pytest", "pytest-cov", "scipy-doctest"]
 
 [[package]]
 name = "shellingham"
@@ -4449,13 +4337,13 @@ files = [
 
 [[package]]
 name = "six"
-version = "1.16.0"
+version = "1.17.0"
 description = "Python 2 and 3 compatibility utilities"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
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 ]
 
 [[package]]
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-
-[package.dependencies]
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-
-[package.extras]
-test = ["hypothesis", "pytest"]
-
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-
 [[package]]
 name = "soupsieve"
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 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
@@ -4528,32 +4387,6 @@ pure-eval = "*"
 [package.extras]
 tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 
-[[package]]
-name = "tblib"
-version = "3.0.0"
-description = "Traceback serialization library."
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-python-versions = ">=3.8"
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-test = ["pytest", "tornado (>=4.5)", "typeguard"]
-
 [[package]]
 name = "terminado"
 version = "0.18.1"
@@ -4577,13 +4410,13 @@ typing = ["mypy (>=1.6,<2.0)", "traitlets (>=5.11.1)"]
 
 [[package]]
 name = "tinycss2"
-version = "1.3.0"
+version = "1.4.0"
 description = "A tiny CSS parser"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -4595,24 +4428,54 @@ test = ["pytest", "ruff"]
 
 [[package]]
 name = "tokenize-rt"
-version = "6.1.0"
+version = "6.2.0"
 description = "A wrapper around the stdlib `tokenize` which roundtrips."
 optional = false
 python-versions = ">=3.9"
 files = [
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 ]
 
 [[package]]
 name = "tomli"
-version = "2.0.1"
+version = "2.2.1"
 description = "A lil' TOML parser"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
@@ -4628,51 +4491,53 @@ files = [
 
 [[package]]
 name = "toolz"
-version = "0.12.1"
+version = "1.0.0"
 description = "List processing tools and functional utilities"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "tornado"
-version = "6.4.1"
+version = "6.5.1"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [[package]]
 name = "tqdm"
-version = "4.66.5"
+version = "4.67.1"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "tqdm-4.66.5-py3-none-any.whl", hash = "sha256:90279a3770753eafc9194a0364852159802111925aa30eb3f9d85b0e805ac7cd"},
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 ]
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [package.extras]
-dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"]
+dev = ["nbval", "pytest (>=6)", "pytest-asyncio (>=0.24)", "pytest-cov", "pytest-timeout"]
+discord = ["requests"]
 notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
@@ -4728,35 +4593,49 @@ typing-extensions = ">=3.7.4.3"
 
 [[package]]
 name = "types-python-dateutil"
-version = "2.9.0.20240906"
+version = "2.9.0.20250516"
 description = "Typing stubs for python-dateutil"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [[package]]
 name = "typing-extensions"
-version = "4.12.2"
+version = "4.13.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "typing_extensions-4.13.2-py3-none-any.whl", hash = "sha256:a439e7c04b49fec3e5d3e2beaa21755cadbbdc391694e28ccdd36ca4a1408f8c"},
+    {file = "typing_extensions-4.13.2.tar.gz", hash = "sha256:e6c81219bd689f51865d9e372991c540bda33a0379d5573cddb9a3a23f7caaef"},
 ]
 
+[[package]]
+name = "typing-inspection"
+version = "0.4.1"
+description = "Runtime typing introspection tools"
+optional = false
+python-versions = ">=3.9"
+files = [
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+]
+
+[package.dependencies]
+typing-extensions = ">=4.12.0"
+
 [[package]]
 name = "tzdata"
-version = "2024.1"
+version = "2025.2"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
 files = [
-    {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"},
-    {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"},
+    {file = "tzdata-2025.2-py2.py3-none-any.whl", hash = "sha256:1a403fada01ff9221ca8044d701868fa132215d84beb92242d9acd2147f667a8"},
+    {file = "tzdata-2025.2.tar.gz", hash = "sha256:b60a638fcc0daffadf82fe0f57e53d06bdec2f36c4df66280ae79bce6bd6f2b9"},
 ]
 
 [[package]]
@@ -4785,13 +4664,13 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake
 
 [[package]]
 name = "urllib3"
-version = "2.2.3"
+version = "2.4.0"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "urllib3-2.2.3-py3-none-any.whl", hash = "sha256:ca899ca043dcb1bafa3e262d73aa25c465bfb49e0bd9dd5d59f1d0acba2f8fac"},
-    {file = "urllib3-2.2.3.tar.gz", hash = "sha256:e7d814a81dad81e6caf2ec9fdedb284ecc9c73076b62654547cc64ccdcae26e9"},
+    {file = "urllib3-2.4.0-py3-none-any.whl", hash = "sha256:4e16665048960a0900c702d4a66415956a584919c03361cac9f1df5c5dd7e813"},
+    {file = "urllib3-2.4.0.tar.gz", hash = "sha256:414bc6535b787febd7567804cc015fee39daab8ad86268f1310a9250697de466"},
 ]
 
 [package.extras]
@@ -4802,13 +4681,13 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.26.5"
+version = "20.31.2"
 description = "Virtual Python Environment builder"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "virtualenv-20.26.5-py3-none-any.whl", hash = "sha256:4f3ac17b81fba3ce3bd6f4ead2749a72da5929c01774948e243db9ba41df4ff6"},
-    {file = "virtualenv-20.26.5.tar.gz", hash = "sha256:ce489cac131aa58f4b25e321d6d186171f78e6cb13fafbf32a840cee67733ff4"},
+    {file = "virtualenv-20.31.2-py3-none-any.whl", hash = "sha256:36efd0d9650ee985f0cad72065001e66d49a6f24eb44d98980f630686243cf11"},
+    {file = "virtualenv-20.31.2.tar.gz", hash = "sha256:e10c0a9d02835e592521be48b332b6caee6887f332c111aa79a09b9e79efc2af"},
 ]
 
 [package.dependencies]
@@ -4833,19 +4712,15 @@ files = [
 
 [[package]]
 name = "webcolors"
-version = "24.8.0"
+version = "24.11.1"
 description = "A library for working with the color formats defined by HTML and CSS."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "webcolors-24.8.0-py3-none-any.whl", hash = "sha256:fc4c3b59358ada164552084a8ebee637c221e4059267d0f8325b3b560f6c7f0a"},
-    {file = "webcolors-24.8.0.tar.gz", hash = "sha256:08b07af286a01bcd30d583a7acadf629583d1f79bfef27dd2c2c5c263817277d"},
+    {file = "webcolors-24.11.1-py3-none-any.whl", hash = "sha256:515291393b4cdf0eb19c155749a096f779f7d909f7cceea072791cb9095b92e9"},
+    {file = "webcolors-24.11.1.tar.gz", hash = "sha256:ecb3d768f32202af770477b8b65f318fa4f566c22948673a977b00d589dd80f6"},
 ]
 
-[package.extras]
-docs = ["furo", "sphinx", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-notfound-page", "sphinxext-opengraph"]
-tests = ["coverage[toml]"]
-
 [[package]]
 name = "webencodings"
 version = "0.5.1"
@@ -4875,13 +4750,13 @@ test = ["websockets"]
 
 [[package]]
 name = "whitebox"
-version = "2.3.5"
-description = "An advanced geospatial data analysis platform"
+version = "2.3.6"
+description = "An advanced geospatial data analysis platform "
 optional = false
 python-versions = "*"
 files = [
-    {file = "whitebox-2.3.5-py2.py3-none-any.whl", hash = "sha256:dd9db85bbb687356741afe935dd25286a2b31e7bf87b74c60b655cdf84a9d922"},
-    {file = "whitebox-2.3.5.tar.gz", hash = "sha256:4a9fb6da799dc0f99daf139d6dbe573ca12af3785c48708e56728b8372c6a2a7"},
+    {file = "whitebox-2.3.6-py2.py3-none-any.whl", hash = "sha256:16b780134cabb9b9d067078f42265da692963d466747cbe655f573fab0f3f60e"},
+    {file = "whitebox-2.3.6.tar.gz", hash = "sha256:69571640a778253e27a05c63b08aed670457803798a0b8f233761eabcd39188b"},
 ]
 
 [package.dependencies]
@@ -4906,70 +4781,60 @@ whitebox = "*"
 
 [[package]]
 name = "widgetsnbextension"
-version = "4.0.13"
+version = "4.0.14"
 description = "Jupyter interactive widgets for Jupyter Notebook"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "widgetsnbextension-4.0.13-py3-none-any.whl", hash = "sha256:74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71"},
-    {file = "widgetsnbextension-4.0.13.tar.gz", hash = "sha256:ffcb67bc9febd10234a362795f643927f4e0c05d9342c727b65d2384f8feacb6"},
+    {file = "widgetsnbextension-4.0.14-py3-none-any.whl", hash = "sha256:4875a9eaf72fbf5079dc372a51a9f268fc38d46f767cbf85c43a36da5cb9b575"},
+    {file = "widgetsnbextension-4.0.14.tar.gz", hash = "sha256:a3629b04e3edb893212df862038c7232f62973373869db5084aed739b437b5af"},
 ]
 
 [[package]]
 name = "xarray"
-version = "2024.9.0"
+version = "2025.4.0"
 description = "N-D labeled arrays and datasets in Python"
 optional = false
 python-versions = ">=3.10"
 files = [
-    {file = "xarray-2024.9.0-py3-none-any.whl", hash = "sha256:4fd534abdf12d5fa75dd566c56483d5081f77864462cf3d6ad53e13f9db48222"},
-    {file = "xarray-2024.9.0.tar.gz", hash = "sha256:e796a6b3eaec11da24f33e4bb14af41897011660a0516fa4037d3ae4bbd1d378"},
+    {file = "xarray-2025.4.0-py3-none-any.whl", hash = "sha256:b27defd082c5cb85d32c695708de6bb05c2838fb7caaf3f952982e602a35b9b8"},
+    {file = "xarray-2025.4.0.tar.gz", hash = "sha256:2a89cd6a1dfd589aa90ac45f4e483246f31fc641836db45dd2790bb78bd333dc"},
 ]
 
 [package.dependencies]
 numpy = ">=1.24"
-packaging = ">=23.1"
+packaging = ">=23.2"
 pandas = ">=2.1"
 
 [package.extras]
-accel = ["bottleneck", "flox", "numbagg", "opt-einsum", "scipy"]
-complete = ["xarray[accel,dev,io,parallel,viz]"]
-dev = ["hypothesis", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-env", "pytest-timeout", "pytest-xdist", "ruff", "xarray[complete]"]
+accel = ["bottleneck", "flox", "numba (>=0.54)", "numbagg", "opt_einsum", "scipy"]
+complete = ["xarray[accel,etc,io,parallel,viz]"]
+etc = ["sparse"]
 io = ["cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap", "scipy", "zarr"]
 parallel = ["dask[complete]"]
-viz = ["matplotlib", "nc-time-axis", "seaborn"]
+types = ["pandas-stubs", "scipy-stubs", "types-PyYAML", "types-Pygments", "types-colorama", "types-decorator", "types-defusedxml", "types-docutils", "types-networkx", "types-openpyxl", "types-pexpect", "types-psutil", "types-pycurl", "types-python-dateutil", "types-pytz", "types-setuptools"]
+viz = ["cartopy", "matplotlib", "nc-time-axis", "seaborn"]
 
 [[package]]
 name = "xyzservices"
-version = "2024.9.0"
+version = "2025.4.0"
 description = "Source of XYZ tiles providers"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "xyzservices-2024.9.0-py3-none-any.whl", hash = "sha256:776ae82b78d6e5ca63dd6a94abb054df8130887a4a308473b54a6bd364de8644"},
-    {file = "xyzservices-2024.9.0.tar.gz", hash = "sha256:68fb8353c9dbba4f1ff6c0f2e5e4e596bb9e1db7f94f4f7dfbcb26e25aa66fde"},
-]
-
-[[package]]
-name = "zict"
-version = "3.0.0"
-description = "Mutable mapping tools"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "zict-3.0.0-py2.py3-none-any.whl", hash = "sha256:5796e36bd0e0cc8cf0fbc1ace6a68912611c1dbd74750a3f3026b9b9d6a327ae"},
-    {file = "zict-3.0.0.tar.gz", hash = "sha256:e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5"},
+    {file = "xyzservices-2025.4.0-py3-none-any.whl", hash = "sha256:8d4db9a59213ccb4ce1cf70210584f30b10795bff47627cdfb862b39ff6e10c9"},
+    {file = "xyzservices-2025.4.0.tar.gz", hash = "sha256:6fe764713648fac53450fbc61a3c366cb6ae5335a1b2ae0c3796b495de3709d8"},
 ]
 
 [[package]]
 name = "zipp"
-version = "3.20.2"
+version = "3.22.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"},
-    {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"},
+    {file = "zipp-3.22.0-py3-none-any.whl", hash = "sha256:fe208f65f2aca48b81f9e6fd8cf7b8b32c26375266b009b413d45306b6148343"},
+    {file = "zipp-3.22.0.tar.gz", hash = "sha256:dd2f28c3ce4bc67507bfd3781d21b7bb2be31103b51a4553ad7d90b84e57ace5"},
 ]
 
 [package.extras]
@@ -4977,10 +4842,10 @@ check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
 cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 enabler = ["pytest-enabler (>=2.2)"]
-test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+test = ["big-O", "importlib_resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
 type = ["pytest-mypy"]
 
 [metadata]
 lock-version = "2.0"
-python-versions = ">=3.10,<3.12"
-content-hash = "74f183b89189fcd2a6eb408d828ee795ca2546fb311ad460ffbc3863c37786e0"
+python-versions = ">=3.10,<3.13"
+content-hash = "e3601ca1b1f2b6d6a9f268da4403a9c2f87840fd2f0c8626a834cb121b11bb8b"
diff --git a/pyproject.toml b/pyproject.toml
index 770bee2..ed762bb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,7 @@ optional = true
 optional = true
 
 [tool.poetry.dependencies]
-python = ">=3.10,<3.12"
+python = ">=3.10,<3.13"
 rasterio = "^1.3.10"
 geopandas = "^1.0.1"
 leafmap = "^0.31.9"
@@ -73,7 +73,6 @@ tag_name = "{new_version}"
 parse = '(?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+) (?P<releaseTime>.*)?'
 serialize = [
     "{major}.{minor}.{patch}",
-    "{utcnow:%Y-%m-%dT%H:%M:%SZ}"
 ]
 
 [[tool.bumpversion.files]]

From a6a97726658e7e5809b785b03241a48853217ad8 Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Fri, 30 May 2025 17:07:02 -0400
Subject: [PATCH 14/19] Update project dependencies

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index ed762bb..6380592 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -107,6 +107,7 @@ max-line-length = 120
 max-locals = 20
 max-args = 16
 max-attributes = 20
+max-positional-arguments = 16
 
 [tool.flake8]
 max-line-length = 120

From 10f29b65e0f31f5bb016007cd51fce78402e21ad Mon Sep 17 00:00:00 2001
From: Francis Pelletier <32526367+f-PLT@users.noreply.github.com>
Date: Sun, 1 Jun 2025 12:18:15 -0400
Subject: [PATCH 15/19] Update .pre-commit-config.yaml

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6276f5a..e8a83ae 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,4 +1,4 @@
-exclude: "^docs/|/migrations/"
+exclude: ^docs/|/migrations/|Makefile*
 default_stages: [ commit ]
 
 repos:

From 8ac823c3192b9840378555fa7132448a24138b08 Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Thu, 14 Aug 2025 19:15:55 -0400
Subject: [PATCH 16/19] Run mdformat and generalize noxfile.py

---
 .mdformat.toml                                |  2 +
 .pre-commit-config.yaml                       | 17 +++++-
 CHANGES.md                                    | 28 ++++++----
 CONTRIBUTING.md                               | 21 +++----
 README.md                                     | 42 +++++++-------
 data/README.md                                | 14 ++---
 notebooks/README.md                           |  2 +-
 noxfile.py                                    | 56 ++++++++-----------
 pyproject.toml                                | 11 ++--
 scripts/README.md                             |  8 +--
 .../sentinel_2_search_and_process/README.md   |  8 +--
 11 files changed, 112 insertions(+), 97 deletions(-)
 create mode 100644 .mdformat.toml

diff --git a/.mdformat.toml b/.mdformat.toml
new file mode 100644
index 0000000..802e359
--- /dev/null
+++ b/.mdformat.toml
@@ -0,0 +1,2 @@
+number = true
+extensions = ["gfm", "gfm_alerts"]
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e8a83ae..5057701 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,4 +1,4 @@
-exclude: ^docs/|/migrations/|Makefile*
+exclude: "^docs/|/migrations/|Makefile*"
 default_stages: [ commit ]
 
 repos:
@@ -56,6 +56,21 @@ repos:
     hooks:
       - id: flynt
 
+  - repo: https://github.com/tcort/markdown-link-check
+    rev: v3.13.7
+    hooks:
+      - id: markdown-link-check
+        args: [ -q ]
+
+  - repo: https://github.com/hukkin/mdformat
+    rev: 0.7.22
+    hooks:
+      - id: mdformat
+        additional_dependencies:
+          - mdformat-gfm
+          - mdformat-gfm-alerts
+
+
 # sets up .pre-commit-ci.yaml to ensure pre-commit dependencies stay up to date
 ci:
   autoupdate_schedule: weekly
diff --git a/CHANGES.md b/CHANGES.md
index d348ac1..413146e 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,32 +1,36 @@
 # CHANGES.md
 
 [Unreleased](https://github.com/RolnickLab/geospatial-tools/tree/main) (latest)
--------------------------------------------------------------------------------------
 
-* Refactor the stac.py module to extract logic that belongs more in raster.py
-* Update the makefile
-* Update the project dependencies
-* Add new QA tools : `autoflake`, `autopep8` and `ruff`
+______________________________________________________________________
+
+- Refactor the stac.py module to extract logic that belongs more in raster.py
+- Update the makefile
+- Update the project dependencies
+- Add new QA tools : `autoflake`, `autopep8` and `ruff`
 
 [0.1.3](https://github.com/RolnickLab/geospatial-tools/tree/0.1.3) (2024-09-23)
--------------------------------------------------------------------------------------
+
+______________________________________________________________________
 
 - Convert project to use `nox` instead of `tox` for cluster storage optimization.
 
 [0.1.2](https://github.com/RolnickLab/geospatial-tools/tree/0.1.2) (2024-09-23)
--------------------------------------------------------------------------------------
 
-- Fix `docformatter` with missing extra dependency for use with `pyproject.toml`
+______________________________________________________________________
 
+- Fix `docformatter` with missing extra dependency for use with `pyproject.toml`
 
 [0.1.1](https://github.com/RolnickLab/geospatial-tools/tree/0.1.1) (2024-09-20)
--------------------------------------------------------------------------------------
+
+______________________________________________________________________
 
 - Fix `black` dependency that was not correctly setup in dev dependency group
 
 [0.1.0](https://github.com/RolnickLab/geospatial-tools/tree/0.1.0) (2024-09-20)
--------------------------------------------------------------------------------------
-	
+
+______________________________________________________________________
+
 - Add `resample_tiff_raster.py` script
 - Implement functions for clipping and reprojecting raster images
 - Implement vector functions for grid creation
@@ -35,4 +39,4 @@
 - Implement functions and scripts to search for and process Sentinel 2 products from
   Microsoft's Planetary Computer
 - Add examples of the above in Jupyter notebook formats
-- Add tests and notebook tests
\ No newline at end of file
+- Add tests and notebook tests
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 81f0991..e439538 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -17,7 +17,7 @@ To add a new dependency with a specific version:
 poetry add "<dependency_name>==<x.x.x>"
 ```
 
-To add a new dependency to a specific group of dependencies 
+To add a new dependency to a specific group of dependencies
 (for example, the development dependencies):
 
 ```
@@ -25,36 +25,37 @@ poetry add --group dev <dependency_name>
 ```
 
 ## Design patterns
+
 Two main considerations should be made when contributing to this package.
 
 First, a polymorphic approach, using abstract classes and their concrete implementation,
 should be prioritized in order to increase maintainability and extensibility.
 
 Therefore, new additions should try to follow this design pattern and either implement
-new concrete classes or create new abstract classes and their implementations for 
+new concrete classes or create new abstract classes and their implementations for
 completely new behavior or needs.
 
-Avoid multiple levels of inheritance; the approach should be _AbstractClass -> 
-[ConcreteClass1, ConcreteClass2, ...]_ and not 
+Avoid multiple levels of inheritance; the approach should be _AbstractClass ->
+[ConcreteClass1, ConcreteClass2, ...]_ and not
 _AbstractClass -> ChildClass -> GrandChildClass -> ..._
 
-Next, a dependency-injection approach is to be preferred, as well as a composition 
+Next, a dependency-injection approach is to be preferred, as well as a composition
 approach when creating new modules or extending existing ones.
 
 Functional approaches are also acceptable when appropriate, but classes should still
-be used for data management/representation. This can be done with either regular 
+be used for data management/representation. This can be done with either regular
 classes, `dataclasses`, or `pydantic` models.
 
 ## Tests
 
-New contributions should include appropriate tests. Pytest is the preferred library to 
+New contributions should include appropriate tests. Pytest is the preferred library to
 use for testing in this project.
 
 To get started and to learn more about testing in Python:
 
-* [Getting started with testing](https://realpython.com/python-testing/)
-* [Testing in the contest of Machine Learning](https://fullstackdeeplearning.com/course/2022/lecture-3-troubleshooting-and-testing/)
-* [Pytest Documentation](https://docs.pytest.org/en/stable/how-to/index.html)
+- [Getting started with testing](https://realpython.com/python-testing/)
+- [Testing in the contest of Machine Learning](https://fullstackdeeplearning.com/course/2022/lecture-3-troubleshooting-and-testing/)
+- [Pytest Documentation](https://docs.pytest.org/en/stable/how-to/index.html)
 
 ## Docstring and type hinting
 
diff --git a/README.md b/README.md
index 0892907..1d303af 100644
--- a/README.md
+++ b/README.md
@@ -14,18 +14,18 @@ machine there's a good chance this will work.
 
 The following Makefile files should not be modified, but can be consulted:
 
-* [Makefile](Makefile) : Orchestration of the different files
-* [base.make](.make/base.make) : Shared utilities, project agnostic.
+- [Makefile](Makefile) : Orchestration of the different files
+- [base.make](.make/base.make) : Shared utilities, project agnostic.
 
 The following Makefile files are project or user specific:
 
-* [Makefile.variables](Makefile.variables) : Shared project variables.
-* [Makefile.targets](Makefile.targets) : Shared project targets.
-* [Makefile.private](Makefile.private.example) : User specific variables and targets.
-    * This file is ignored by git and should never be committed, as it can also contain
-      secrets.
-    * You can create your own version locally by copying from
-      [Makefile.private.example](Makefile.private.example)
+- [Makefile.variables](Makefile.variables) : Shared project variables.
+- [Makefile.targets](Makefile.targets) : Shared project targets.
+- [Makefile.private](Makefile.private.example) : User specific variables and targets.
+  - This file is ignored by git and should never be committed, as it can also contain
+    secrets.
+  - You can create your own version locally by copying from
+    [Makefile.private.example](Makefile.private.example)
 
 ## Basic Information
 
@@ -49,8 +49,8 @@ streamlining script use as well as fix path issues related to imports.
 
 If on a compute cluster, first load the appropriate python module:
 
-* [How to create a virtual environment for the Mila cluster](docs/environment_creation_mila.md)
-* [How to create an environment for the DRAC cluster](docs/environment_creation_drac.md)
+- [How to create a virtual environment for the Mila cluster](docs/environment_creation_mila.md)
+- [How to create an environment for the DRAC cluster](docs/environment_creation_drac.md)
 
 Installing `pipx` and `poetry`:
 
@@ -97,9 +97,9 @@ on [how to use your poetry virtual environment](https://python-poetry.org/docs/b
 
 You can:
 
-* Use the `poetry run` command to access your executables
-    * ex. `poetry run python your_script.py`, or `poetry run pylint src/`
-* Use the `poetry shell` command to activate and step in your project environment
+- Use the `poetry run` command to access your executables
+  - ex. `poetry run python your_script.py`, or `poetry run pylint src/`
+- Use the `poetry shell` command to activate and step in your project environment
 
 #### Conda
 
@@ -114,7 +114,7 @@ If working on the Mila cluster, first load the appropriate module :
 make conda-create-env
 ```
 
-2. Activate `conda` environment (substitute with your <CONDA_TOOL> if something else
+2. Activate `conda` environment (substitute with your \<CONDA_TOOL> if something else
    than `conda`:
 
 ```
@@ -154,8 +154,8 @@ This also installs and configures the `pre-commit` hook. See ...
 This project assumes environment management will be done with `conda`, a classic
 python virtual environment, or directly through `poetry`.
 
-* [Poetry](https://python-poetry.org/docs/basic-usage/)
-* [Conda](https://conda.io/projects/conda/en/latest/user-guide/getting-started.html)
+- [Poetry](https://python-poetry.org/docs/basic-usage/)
+- [Conda](https://conda.io/projects/conda/en/latest/user-guide/getting-started.html)
 
 While it is possible to manage the environment with, for example, pyenv or virtualenv,
 those specific use cases are not supported by the Makefile and require users to set up
@@ -176,10 +176,10 @@ information.
 
 Your project will need a virtual environment for your dependencies.
 
-* [How to create a virtual environment for the Mila cluster](docs/environment_creation_mila.md)
-* [How to create an environment for the DRAC cluster](docs/environment_creation_drac.md)
-* [How to create a Conda environment](docs/conda_environment_creation.md)
-* [Migrating to DRAC from another environment](docs/migrating_to_drac.md)
+- [How to create a virtual environment for the Mila cluster](docs/environment_creation_mila.md)
+- [How to create an environment for the DRAC cluster](docs/environment_creation_drac.md)
+- [How to create a Conda environment](docs/conda_environment_creation.md)
+- [Migrating to DRAC from another environment](docs/migrating_to_drac.md)
 
 There are different ways of managing your python version in these environments. On the
 clusters, you have access to different python modules, and through `conda` you have access
diff --git a/data/README.md b/data/README.md
index ce6b693..f52f328 100644
--- a/data/README.md
+++ b/data/README.md
@@ -4,10 +4,10 @@
 
 ### International
 
-* [NASA's EarthData](https://www.earthdata.nasa.gov/)
-* [USGS Earth Explorer](https://earthexplorer.usgs.gov/)
-* [Copernicus Open Access Hub](https://scihub.copernicus.eu/)
-* [Climate Data Store](https://cds.climate.copernicus.eu/cdsapp#!/home)
+- [NASA's EarthData](https://www.earthdata.nasa.gov/)
+- [USGS Earth Explorer](https://earthexplorer.usgs.gov/)
+- [Copernicus Open Access Hub](https://scihub.copernicus.eu/)
+- [Climate Data Store](https://cds.climate.copernicus.eu/cdsapp#!/home)
 
 ## Satellite data
 
@@ -25,9 +25,9 @@ The tiling grid can be found here in KML format : [](https://sentiwiki.copernicu
 
 ### Canada
 
-* [GEO.ca](https://geo.ca/) : Canada's geographic information portal
-* [Données Québec](https://www.donneesquebec.ca/) : Quebec's open data portal
+- [GEO.ca](https://geo.ca/) : Canada's geographic information portal
+- [Données Québec](https://www.donneesquebec.ca/) : Quebec's open data portal
 
 ### USA
 
-* [Cartographic Boundaries, Census Office](https://www.census.gov/geographies/mapping-files/time-series/geo/carto-boundary-file.html)
+- [Cartographic Boundaries, Census Office](https://www.census.gov/geographies/mapping-files/time-series/geo/carto-boundary-file.html)
diff --git a/notebooks/README.md b/notebooks/README.md
index 260fe6c..09a7493 100644
--- a/notebooks/README.md
+++ b/notebooks/README.md
@@ -1,3 +1,3 @@
 # Notebooks
 
-Place to store all the project's notebooks
\ No newline at end of file
+Place to store all the project's notebooks
diff --git a/noxfile.py b/noxfile.py
index 420bd9e..21a8f7c 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -35,27 +35,25 @@ def get_paths(session):
 @nox.session()
 def pylint(session):
     paths = get_paths(session)
-    session.run("poetry", "run", "pylint", *paths["module"], external=True)
+    session.run("pylint", *paths["module"], external=True)
 
 
 @nox.session()
 def flake8(session):
     paths = get_paths(session)
-    session.run("poetry", "run", "flake8", *paths["all"], external=True)
+    session.run("flake8", *paths["all"], external=True)
 
 
 @nox.session()
 def complexity(session):
     paths = get_paths(session)
-    session.run("poetry", "run", "flake8", "--max-complexity", "7", *paths["all"], external=True)
+    session.run("flake8", "--max-complexity", "7", *paths["all"], external=True)
 
 
 @nox.session()
 def docformatter(session):
     paths = get_paths(session)
     session.run(
-        "poetry",
-        "run",
         "docformatter",
         "--config",
         f"{paths['all'][0].parent}/pyproject.toml",
@@ -67,33 +65,29 @@ def docformatter(session):
 @nox.session()
 def check(session):
     paths = get_paths(session)
-    session.run("poetry", "run", "black", "--check", *paths["all"], external=True)
-    session.run("poetry", "run", "isort", *paths["all"], "--check", external=True)
-    session.run("poetry", "run", "flynt", *paths["all"], external=True)
+    session.run("black", "--check", *paths["all"], external=True)
+    session.run("isort", *paths["all"], "--check", external=True)
+    session.run("flynt", *paths["all"], external=True)
     session.run(
-        "poetry",
-        "run",
         "docformatter",
         "--config",
         f"{paths['all'][0].parent}/pyproject.toml",
         *paths["all"],
         external=True,
     )
-    session.run("poetry", "run", "flake8", *paths["all"], external=True)
-    session.run("poetry", "run", "pylint", *paths["module"], external=True)
+    session.run("flake8", *paths["all"], external=True)
+    session.run("pylint", *paths["module"], external=True)
 
 
 @nox.session()
 def fix(session):
     paths = get_paths(session)
-    session.run("poetry", "run", "autoflake", "-v", *paths["all"], external=True)
-    session.run("poetry", "run", "autopep8", *paths["all"], external=True)
-    session.run("poetry", "run", "black", *paths["all"], external=True)
-    session.run("poetry", "run", "isort", *paths["all"], external=True)
-    session.run("poetry", "run", "flynt", *paths["all"], external=True)
+    session.run("autoflake", "-v", *paths["all"], external=True)
+    session.run("autopep8", *paths["all"], external=True)
+    session.run("black", *paths["all"], external=True)
+    session.run("isort", *paths["all"], external=True)
+    session.run("flynt", *paths["all"], external=True)
     session.run(
-        "poetry",
-        "run",
         "docformatter",
         "--in-place",
         "--config",
@@ -105,60 +99,60 @@ def fix(session):
 
 @nox.session()
 def precommit(session):
-    session.run("poetry", "run", "pre-commit", "run", "--all-files", external=True)
+    session.run("pre-commit", "run", "--all-files", external=True)
 
 
 @nox.session()
 def autoflake(session):
     paths = get_paths(session)
-    session.run("poetry", "run", "autoflake", "-v", *paths["all"], external=True)
+    session.run("autoflake", "-v", *paths["all"], external=True)
 
 
 @nox.session()
 def autopep(session):
     paths = get_paths(session)
-    session.run("poetry", "run", "autopep8", *paths["all"], external=True)
+    session.run("autopep8", *paths["all"], external=True)
 
 
 @nox.session()
 def black(session):
     paths = get_paths(session)
-    session.run("poetry", "run", "black", "--check", *paths["all"], external=True)
+    session.run("black", "--check", *paths["all"], external=True)
 
 
 @nox.session()
 def isort(session):
     paths = get_paths(session)
-    session.run("poetry", "run", "isort", *paths["all"], "--check", external=True)
+    session.run("isort", *paths["all"], "--check", external=True)
 
 
 @nox.session()
 def flynt(session):
     paths = get_paths(session)
-    session.run("poetry", "run", "flynt", *paths["all"], external=True)
+    session.run("flynt", *paths["all"], external=True)
 
 
 @nox.session(name="ruff-lint")
 def ruff_lint(session):
     paths = get_paths(session)
-    session.run("poetry", "run", "ruff", "check", *paths["all"], external=True)
+    session.run("ruff", "check", *paths["all"], external=True)
 
 
 @nox.session(name="ruff-fix")
 def ruff_fix(session):
     paths = get_paths(session)
-    session.run("poetry", "run", "ruff", "check", "--fix", *paths["all"], external=True)
+    session.run("ruff", "check", "--fix", *paths["all"], external=True)
 
 
 @nox.session(name="ruff-format")
 def ruff_format(session):
     paths = get_paths(session)
-    session.run("poetry", "run", "ruff", "format", *paths["all"], external=True)
+    session.run("ruff", "format", *paths["all"], external=True)
 
 
 @nox.session()
 def test(session):
-    session.run("poetry", "run", "pytest", external=True)
+    session.run("pytest", external=True)
 
 
 @nox.session()
@@ -168,15 +162,13 @@ def test_custom(session):
             session.error(f"unsafe pytest argument detected: {a!r}")
 
     session.run(
-        "poetry", "run", "python", "-m", "pytest", external=True, *session.posargs
+        "python", "-m", "pytest", external=True, *session.posargs
     )  # Pass additional arguments directly to pytest
 
 
 @nox.session()
 def test_nb(session):
     session.run(
-        "poetry",
-        "run",
         "pytest",
         "--nbval",
         "tests/test_notebooks/",
diff --git a/pyproject.toml b/pyproject.toml
index 6380592..549913e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -79,17 +79,18 @@ serialize = [
 filename = "CHANGES.md"
 search = '''
 [Unreleased](https://github.com/RolnickLab/geospatial-tools/tree/main) (latest)
--------------------------------------------------------------------------------------
-'''
+
+______________________________________________________________________'''
 replace = '''
 [Unreleased](https://github.com/RolnickLab/geospatial-tools/tree/main) (latest)
--------------------------------------------------------------------------------------
+
+______________________________________________________________________
 
 [//]: # (New changes here in list form)
 
 [{new_version}](https://github.com/RolnickLab/geospatial-tools/tree/{new_version}) ({utcnow:%Y-%m-%d})
--------------------------------------------------------------------------------------
-'''
+
+______________________________________________________________________'''
 
 [[tool.bumpversion.files]]
 filename = "pyproject.toml"
diff --git a/scripts/README.md b/scripts/README.md
index b8bd76c..f09de6e 100644
--- a/scripts/README.md
+++ b/scripts/README.md
@@ -1,13 +1,13 @@
 # Scripts
 
-----
+______________________________________________________________________
 
 **Important note for SLURM scripts**
 
-All Slurm scripts need to be run from the [scripts/](.) folder, as they use the 
+All Slurm scripts need to be run from the [scripts/](.) folder, as they use the
 [config.sh](config.sh.example) that also needs to be configured by each user.
 
-----
+______________________________________________________________________
 
 This folder is dedicated to scripts, whether python, bash or sbatch.
 
@@ -18,4 +18,4 @@ itself.
 
 ## Scripts
 
-* [resample_tiff_raster.py](resample_tiff_raster.py) : Script to resample a target tiff image, so it matches a source image's grid size and area. Resampling strategy is using a Nearest Neighbor algorythm to keep original values. Use the scripts CLI for more information : `python3 resample_tiff_raster.py --help` 
+- [resample_tiff_raster.py](resample_tiff_raster.py) : Script to resample a target tiff image, so it matches a source image's grid size and area. Resampling strategy is using a Nearest Neighbor algorythm to keep original values. Use the scripts CLI for more information : `python3 resample_tiff_raster.py --help`
diff --git a/scripts/sentinel_2_search_and_process/README.md b/scripts/sentinel_2_search_and_process/README.md
index cff67c7..40378a0 100644
--- a/scripts/sentinel_2_search_and_process/README.md
+++ b/scripts/sentinel_2_search_and_process/README.md
@@ -2,8 +2,8 @@
 
 Scripts to run in order:
 
-* [product_search.py](product_search.py) : Execute the search for products for a given region of interest
-* [download_and_process.py](download_and_process.py) : Process the products found in previous scripts
+- [product_search.py](product_search.py) : Execute the search for products for a given region of interest
+- [download_and_process.py](download_and_process.py) : Process the products found in previous scripts
 
 Both scripts can be used with the `--help` option to have more information.
 
@@ -19,5 +19,5 @@ python download_and_process.py --help
 
 The above scripts have their Slurm equivalent:
 
-* [search.py](search.sh) : Execute the search for products for a given region of interest
-* [process.py](process.sh) : Process the products found in previous scripts
+- [search.py](search.sh) : Execute the search for products for a given region of interest
+- [process.py](process.sh) : Process the products found in previous scripts

From 3f155b501307191a8be6744cd0a265db5b01b7e2 Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Thu, 14 Aug 2025 19:19:25 -0400
Subject: [PATCH 17/19] Add pre-commit cache to CI

---
 .github/workflows/pre-commit.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
index 068370f..0fc99f7 100644
--- a/.github/workflows/pre-commit.yml
+++ b/.github/workflows/pre-commit.yml
@@ -32,6 +32,13 @@ jobs:
           key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
           restore-keys: |
             poetry-${{ runner.os }}-
+
+      - name: Cache pre-commit
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cache/pre-commit
+          key: pre-commit-3|${{ env.pythonLocation }}|${{ hashFiles('.pre-commit-config.yaml') }}
       
       - name: Install dependencies
         run: |

From c8ec11939ff6f849e29a6b5e81605c4b2f3cfc25 Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Wed, 17 Sep 2025 15:18:20 -0400
Subject: [PATCH 18/19] Update from makefile project

---
 .github/workflows/lint.yml           |   2 +-
 .github/workflows/pre-commit.yml     |   2 +-
 .github/workflows/test.yml           |   2 +-
 .make/.bumpversion.toml              |  40 ++
 .make/CHANGES_MAKEFILE.md            |  46 ++
 .make/Makefile                       |  84 ++++
 .make/README.md                      |  29 ++
 .make/base.make                      | 634 +--------------------------
 .make/conda.make                     | 176 ++++++++
 .make/lint.make                      |  37 ++
 .make/poetry.make                    | 387 ++++++++++++++++
 .make/test.make                      |  45 ++
 .make/tests/test-script.sh           | 244 +++++++++++
 .make/tests/test_environment.yml     |   6 +
 .make/uv.make                        | 312 +++++++++++++
 CHANGES.md                           |  10 +-
 Makefile                             |  41 +-
 docs/conda_environment_creation.md   |   2 +-
 docs/environment_creation_drac.md    |  20 +-
 docs/environment_creation_mila.md    |   5 +-
 docs/makefile_environment_targets.md |   2 +-
 docs/nox_session_descriptions.md     |  41 +-
 docs/poetry_documentation.md         |   4 +-
 docs/uv_documentation.md             | 291 ++++++++++++
 noxfile.py                           |   7 +
 pyproject.toml                       |  14 +-
 26 files changed, 1795 insertions(+), 688 deletions(-)
 create mode 100644 .make/.bumpversion.toml
 create mode 100644 .make/CHANGES_MAKEFILE.md
 create mode 100644 .make/Makefile
 create mode 100644 .make/README.md
 create mode 100644 .make/conda.make
 create mode 100644 .make/lint.make
 create mode 100644 .make/poetry.make
 create mode 100644 .make/test.make
 create mode 100755 .make/tests/test-script.sh
 create mode 100644 .make/tests/test_environment.yml
 create mode 100644 .make/uv.make
 create mode 100644 docs/uv_documentation.md

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 7bc4e28..01a0710 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -35,7 +35,7 @@ jobs:
 
       - name: Install dependencies
         run: |
-          make install
+          make install-dev
 
       - name: Run linting checks
         run: |
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
index 0fc99f7..5036281 100644
--- a/.github/workflows/pre-commit.yml
+++ b/.github/workflows/pre-commit.yml
@@ -42,7 +42,7 @@ jobs:
       
       - name: Install dependencies
         run: |
-          make install
+          make install-dev
 
       - name: Run Pre-commit checks
         run: |
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 3021ba2..4f0820f 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -35,7 +35,7 @@ jobs:
 
       - name: Install dependencies
         run: |
-          make install
+          make install-dev
 
       - name: Run tests
         run: |
diff --git a/.make/.bumpversion.toml b/.make/.bumpversion.toml
new file mode 100644
index 0000000..4be7e96
--- /dev/null
+++ b/.make/.bumpversion.toml
@@ -0,0 +1,40 @@
+[tool.bumpversion]
+current_version = "0.7.0"
+commit = true
+message = "Makefile version {new_version} released."
+tag = true
+tag_name = "makefile-{new_version}"
+parse = '(?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+) (?P<releaseTime>.*)?'
+serialize = [
+    "{major}.{minor}.{patch}"
+]
+
+[[tool.bumpversion.files]]
+filename = "CHANGES_MAKEFILE.md"
+search = '''
+[Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest)
+
+______________________________________________________________________
+'''
+replace = '''
+[Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest)
+
+______________________________________________________________________
+
+<!-- (New changes here in list form) -->
+
+[{new_version}](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-{new_version}) ({utcnow:%Y-%m-%d})
+
+______________________________________________________________________
+'''
+
+[[tool.bumpversion.files]]
+filename = "base.make"
+search = 'MAKEFILE_VERSION := {current_version}'
+replace = 'MAKEFILE_VERSION := {new_version}'
+
+
+[[tool.bumpversion.files]]
+filename = "Makefile"
+search = 'MAKEFILE_VERSION := {current_version}'
+replace = 'MAKEFILE_VERSION := {new_version}'
diff --git a/.make/CHANGES_MAKEFILE.md b/.make/CHANGES_MAKEFILE.md
new file mode 100644
index 0000000..2e18b06
--- /dev/null
+++ b/.make/CHANGES_MAKEFILE.md
@@ -0,0 +1,46 @@
+# CHANGES.md
+
+## [Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest)
+
+______________________________________________________________________
+
+<!-- (New changes here in list form) -->
+
+## [0.7.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.7.0) (2025-09-10)
+
+______________________________________________________________________
+
+- Add `mdformat` tool for markdown linting
+- Modularize the Makefile structure, allowing to choose which tools are available
+- Add tests for the Makefile
+
+## [0.6.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.6.0) (2025-05-29)
+
+______________________________________________________________________
+
+- Improve venv support
+- Add venv remove target
+- Refactor `poetry-install-auto` to really be automatic
+- Add `mamba-install` target as an alternative/complement to conda for local dev
+- Add `autoflake`, `autopep8` and `ruff` targets
+- Fix some typos that caused targets to fail
+
+## [0.5.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.5.0) (2025-03-11)
+
+______________________________________________________________________
+
+- Add venv support
+- Update and fix `poetry-install-auto` target
+
+## [0.4.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.4.0) (2024-10-30)
+
+______________________________________________________________________
+
+- Add cyclomatic complexity check target
+
+## [0.3.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.3.0) (2024-10-30)
+
+______________________________________________________________________
+
+- Add utilities to track makefile versions
+- Fix many of the targets relating to standalone `poetry` installation
diff --git a/.make/Makefile b/.make/Makefile
new file mode 100644
index 0000000..fe5e88e
--- /dev/null
+++ b/.make/Makefile
@@ -0,0 +1,84 @@
+########################################################################################
+#
+# DO NOT MODIFY!!!
+# If necessary, override the corresponding variable and/or target, or create new ones
+# in one of the following files, depending on the nature of the override :
+#
+# `Makefile.variables`, `Makefile.targets` or `Makefile.private`,
+#
+# The only valid reason to modify this file is to fix a bug or to add new
+# files to include.
+########################################################################################
+PROJECT_PATH := $(dir $(abspath $(firstword $(MAKEFILE_LIST))))
+MAKEFILE_VERSION := 0.7.0
+BUMP_TOOL := bump-my-version
+BUMP_CONFIG_FILE := $(PROJECT_PATH).bumpversion.toml
+
+# Colors
+_SECTION := \033[1m\033[34m
+_TARGET  := \033[36m
+_NORMAL  := \033[0m
+
+.DEFAULT_GOAL := help
+## -- Informative targets ------------------------------------------------------------------------------------------- ##
+
+.PHONY: all
+all: help
+
+# Auto documented help targets & sections from comments
+#	detects lines marked by double #, then applies the corresponding target/section markup
+#   target comments must be defined after their dependencies (if any)
+#	section comments must have at least a double dash (-)
+#
+# 	Original Reference:
+#		https://marmelab.com/blog/2016/02/29/auto-documented-makefile.html
+# 	Formats:
+#		https://misc.flogisoft.com/bash/tip_colors_and_formatting
+#
+#	As well as influenced by it's implementation in the Weaver Project
+#		https://github.com/crim-ca/weaver/tree/master
+
+.PHONY: help
+# note: use "\#\#" to escape results that would self-match in this target's search definition
+help: ## print this help message (default)
+	@echo ""
+	@echo "Please use 'make <target>' where <target> is one of below options."
+	@echo ""
+	@for makefile in $(MAKEFILE_LIST); do \
+        grep -E '\#\#.*$$' "$(PROJECT_PATH)/$${makefile}" | \
+            awk 'BEGIN {FS = "(:|\-\-\-)+.*\#\# "}; \
+            	/\--/ {printf "$(_SECTION)%s$(_NORMAL)\n", $$1;} \
+				/:/  {printf "    $(_TARGET)%-24s$(_NORMAL) %s\n", $$1, $$2} ' 2>/dev/null ; \
+    done
+
+.PHONY: targets
+targets: help
+
+.PHONY: version
+version: ## display current version of makefile
+	@echo "version: $(MAKEFILE_VERSION)"
+
+## -- Makefile versioning targets --------------------------------------------------- ##
+
+# Use the "dry" target for a dry-run version bump, ex.
+# make bump-major dry
+BUMP_ARGS ?= --verbose
+ifeq ($(filter dry, $(MAKECMDGOALS)), dry)
+	BUMP_ARGS := $(BUMP_ARGS) --dry-run --allow-dirty
+endif
+
+.PHONY: dry
+dry: ## Add the dry target for a preview of changes; ex. `make bump-major dry`
+	@-echo > /dev/null
+
+.PHONY: bump-major
+bump-major: ## Bump makefile major version  <X.0.0>
+	$(BUMP_TOOL) bump $(BUMP_ARGS) major --config-file $(BUMP_CONFIG_FILE)
+
+.PHONY: bump-minor
+bump-minor: ## Bump makefile minor version  <0.X.0>
+	$(BUMP_TOOL) bump $(BUMP_ARGS) minor --config-file $(BUMP_CONFIG_FILE)
+
+.PHONY: bump-patch
+bump-patch: ## Bump makefile patch version  <0.0.X>
+	$(BUMP_TOOL) bump $(BUMP_ARGS) patch --config-file $(BUMP_CONFIG_FILE)
diff --git a/.make/README.md b/.make/README.md
new file mode 100644
index 0000000..eb26919
--- /dev/null
+++ b/.make/README.md
@@ -0,0 +1,29 @@
+# Makefile documentation
+
+This folder contains the base makefile targets.
+
+It should not be modified outside the [Template's repository](https://github.com/RolnickLab/lab-advanced-template).
+
+If there is a problem with the contents of these targets, please open an
+issue [here](https://github.com/RolnickLab/lab-advanced-template/issues).
+
+If you know how to fix the problem, please also consider opening a pull request with
+your proposed solution.
+
+You can always override the faulty targets located here by creating new targets
+with the same names inside [Makefile.targets](../Makefile.targets).
+
+The Makefile and `bump-my-version` related files in this directory are to help with
+change tracking for the makefile itself. If you are using this makefile as part of a
+template in another repository, you won't have to interact with them.
+
+## Tests
+
+Makefile tests can be found in the [.make/tests/](tests) folder. Current tests are
+essentially bash scripts to test the different makefile targets.
+
+These should only be run when modifying the makefiles inside the
+[Template's repository](https://github.com/RolnickLab/lab-advanced-template).
+
+They should never be run in a project implemented from the template, as they could cause
+side effects to your project.
diff --git a/.make/base.make b/.make/base.make
index 20c9a01..7362c6c 100644
--- a/.make/base.make
+++ b/.make/base.make
@@ -16,7 +16,7 @@ PROJECT_PATH := $(dir $(abspath $(firstword $(MAKEFILE_LIST))))
 MAKEFILE_NAME := $(word $(words $(MAKEFILE_LIST)),$(MAKEFILE_LIST))
 SHELL := /usr/bin/env bash
 BUMP_TOOL := bump-my-version
-MAKEFILE_VERSION := 0.6.0
+MAKEFILE_VERSION := 0.7.0
 DOCKER_COMPOSE ?= docker compose
 AUTO_INSTALL ?=
 
@@ -86,7 +86,7 @@ VENV_PATH := $(PROJECT_PATH).venv
 VENV_ACTIVATE := $(VENV_PATH)/bin/activate
 
 .PHONY: venv-create
-venv-create: ## Create a virtualenv '.venv' at the root of the project folder
+venv-create: ## Create a virtualenv '.venv' at the root of the project folder 
 	@virtualenv $(VENV_PATH)
 	@make -s venv-activate
 
@@ -123,555 +123,6 @@ venv-remove: ## Delete the virtualenv '.venv' at the root of the project folder.
   	  echo "Venv [$(VENV_PATH)] does not exist, nothing to do"; \
   	fi;
 
-## -- Poetry targets ------------------------------------------------------------------------------------------------ ##
-
-.PHONY: poetry-install-auto
-poetry-install-auto: ## Install Poetry automatically using DEFAULT_POETRY_INSTALL_ENV. Defaults to venv install
-	@poetry --version; \
-    	if [ $$? != "0" ]; then \
-			echo "Poetry not found, proceeding to install Poetry..."; \
-			if [ "$(DEFAULT_POETRY_INSTALL_ENV)" == "conda" ]; then \
-			    echo ""; \
-			    echo "[DEFAULT_POETRY_INSTALL_ENV] is defined as 'conda', installing poetry with the 'poetry-install-conda' target"; \
-			    echo ""; \
-				ans_where="conda"; \
-			elif [ "$(DEFAULT_POETRY_INSTALL_ENV)" == "venv" ]; then \
-				echo ""; \
-				echo "[DEFAULT_POETRY_INSTALL_ENV] is defined as 'venv', installing poetry with the 'poetry-install-venv' target"; \
-				echo ""; \
-				ans_where="venv"; \
-			else\
-				echo ""; \
-				echo "[DEFAULT_POETRY_INSTALL_ENV] is not defined, defaulting to installing poetry with the 'poetry-install-venv' target"; \
-				echo ""; \
-				ans_where="venv"; \
-			fi; \
-			case $$ans_where in \
-				"venv" | "Venv" |"VENV") \
-					make AUTO_INSTALL=true -s poetry-install-venv; \
-					;; \
-				"conda" | "Conda" | "CONDA") \
-					echo "Installing poetry with Conda"; \
-					make AUTO_INSTALL=true -s conda-poetry-install; \
-					;; \
-				*) \
-					echo ""; \
-					echo -e "\e[1;39;41m-- WARNING --\e[0m There was an unexpected error. Option $$ans_how not found, exiting process."; \
-					echo ""; \
-					exit 1; \
-			esac; \
-		fi;
-
-.PHONY: _pipx_install_poetry
-_pipx_install_poetry:
-	@output="$$(pip install poetry --dry-run)"; \
-	if echo "$$output" | grep -q computecanada ; then \
-		echo ""; \
-		echo -e "\e[1;39;41m-- WARNING --\e[0m Compute Canada (DRAC) environment detected: Installing Poetry < 2.0.0"; \
-		echo ""; \
-		pipx install 'poetry<2.0.0' ; \
-	else \
-		pipx install poetry ; \
-	fi;
-
-
-.PHONY: poetry-install
-poetry-install: ## Install Poetry interactively.
-	@echo "Looking for Poetry version...";\
-	poetry --version; \
-	if [ $$? != "0" ]; then \
-		if [ "$(AUTO_INSTALL)" = "true" ]; then \
-			ans="y";\
-		else \
-			echo "Poetry not found..."; \
-			echo "Looking for pipx version...";\
-			pipx_found=0; \
-			pipx --version; \
-				if [ $$? != "0" ]; then \
-					pipx_found=1; \
-					echo "pipx not found..."; \
-					echo""; \
-					echo -n "Would you like to install pipx and Poetry? [y/N]: "; \
-				else \
-					echo""; \
-					echo -n "Would you like to install Poetry using pipx? [y/N]: "; \
-				fi; \
-			read ans; \
-		fi; \
-		case $$ans in \
-			[Yy]*) \
-				if [ $$pipx_found == "1" ]; then \
-					echo""; \
-					echo -e "\e[1;39;41m-- WARNING --\e[0m The following pip has been found and will be used to install pipx: "; \
-					echo "    -> "$$(which pip); \
-					echo""; \
-					echo "If you do not have write permission to that environment, using it to install pipx will fail."; \
-					echo "If this is the case, you should install pipx using a virtual one."; \
-					echo""; \
-					echo "See documentation for more information."; \
-					echo""; \
-					echo -n "Would you like to use the local available pip above, or create virtual environment to install pipx? [local/virtual]: "; \
-					read ans_how; \
-					case $$ans_how in \
-						"LOCAL" | "Local" |"local") \
-							make -s poetry-install-local; \
-							;; \
-						"VIRTUAL" | "Virtual" | "virtual") \
-							make -s poetry-install-venv; \
-							;; \
-						*) \
-							echo ""; \
-							echo -e "\e[1;39;41m-- WARNING --\e[0m Option $$ans_how not found, exiting process."; \
-							echo ""; \
-							exit 1; \
-					esac; \
-				else \
-					echo "Installing Poetry"; \
-					make -s _pipx_install_poetry; \
-				fi; \
-				;; \
-			*) \
-				echo "Skipping installation."; \
-				echo " "; \
-				;; \
-		esac; \
-	fi;
-
-PIPX_VENV_PATH := $$HOME/.pipx_venv
-.PHONY: poetry-install-venv
-poetry-install-venv: ## Install standalone Poetry. Will install pipx in $HOME/.pipx_venv
-	@pipx --version; \
-	if [ $$? != "0" ]; then \
-		echo "Creating virtual environment using venv here : [$(PIPX_VENV_PATH)]"; \
-		python3 -m venv $(PIPX_VENV_PATH); \
-		echo "Activating virtual environment [$(PIPX_VENV_PATH)]"; \
-		source $(PIPX_VENV_PATH)/bin/activate; \
-		pip3 install pipx; \
-		pipx ensurepath; \
-		source $(PIPX_VENV_PATH)/bin/activate && make -s _pipx_install_poetry ; \
-	else \
-		make -s _pipx_install_poetry ; \
-	fi;
-
-.PHONY: poetry-install-local
-poetry-install-local: ## Install standalone Poetry. Will install pipx with locally available pip.
-	@pipx --version; \
-	if [ $$? != "0" ]; then \
-		echo "pipx not found; installing pipx"; \
-		pip3 install pipx; \
-		pipx ensurepath; \
-	fi;
-	@echo "Installing Poetry"
-	@make -s _pipx_install_poetry
-
-
-.PHONY: poetry-env-info
-poetry-env-info: ## Information about the currently active environment used by Poetry
-	@poetry env info
-
-.PHONY: poetry-create-env
-poetry-create-env: ## Create a Poetry managed environment for the project (Outside of Conda environment).
-	@echo "Creating Poetry environment that will use Python $(PYTHON_VERSION)"; \
-	poetry env use $(PYTHON_VERSION); \
-	poetry env info
-	@echo""
-	@echo "This environment can be accessed either by using the <poetry run YOUR COMMAND>"
-	@echo "command, or activated with the <poetry shell> command."
-	@echo""
-	@echo "Use <poetry --help> and <poetry list> for more information"
-	@echo""
-
-.PHONY: poetry-activate
-poetry-activate: ## Print the shell command to activate the project's poetry env.
-	poetry env activate
-
-.PHONY: poetry-remove-env
-poetry-remove-env: ## Remove current project's Poetry managed environment.
-	@if [ "$(AUTO_INSTALL)" = "true" ]; then \
-		ans_env="y";\
-		env_path=$$(poetry env info -p); \
-		env_name=$$(basename $$env_path); \
-	else \
-		echo""; \
-		echo "Looking for poetry environments..."; \
-		env_path=$$(poetry env info -p); \
-		if [[ "$$env_path" != "" ]]; then \
-			echo "The following environment has been found for this project: "; \
-			env_name=$$(basename $$env_path); \
-			echo""; \
-			echo "Env name : $$env_name"; \
-			echo "PATH     : $$env_path"; \
-			echo""; \
-			echo "If the active environment listed above is a Conda environment,"; \
-			echo "Choosing to delete it will have no effect; use the target <make conda-clean-env>"; \
-			echo""; \
-			echo""; \
-			echo "If the active environment listed above is a venv environment,"; \
-			echo "Choosing to delete it will have no effect; use the bash command $ rm -rf <PATH_TO_VENV>"; \
-			echo""; \
-			echo -n "Would you like delete the environment listed above? [y/N]: "; \
-			read ans_env; \
-		else \
-			env_name="None"; \
-			env_path="None"; \
-  		fi; \
-	fi; \
-	if [[ $$env_name != "None" ]]; then \
-		case $$ans_env in \
-			[Yy]*) \
-				poetry env remove $$env_name || echo "No environment was removed"; \
-				;; \
-			*) \
-				echo "No environment was found/provided - skipping environment deletion"; \
-				;;\
-		esac; \
-	else \
-		echo "No environments were found... skipping environment deletion"; \
-	fi; \
-
-.PHONY: poetry-uninstall
-poetry-uninstall: poetry-remove-env ## Uninstall pipx-installed Poetry and the created environment
-	@if [ "$(AUTO_INSTALL)" = "true" ]; then \
-		ans="y";\
-	else \
-		echo""; \
-		echo -n "Would you like to uninstall pipx-installed Poetry? [y/N]: "; \
-		read ans; \
-	fi; \
-	case $$ans in \
-		[Yy]*) \
-			pipx --version ; \
-			if [ $$? != "0" ]; then \
-				echo "" ; \
-				echo "Pipx not found globally, trying with $(PIPX_VENV_PATH) env" ;\
-				echo "" ; \
-				source $(PIPX_VENV_PATH)/bin/activate && pipx uninstall poetry ; \
-			else \
-				pipx uninstall poetry ; \
-				fi; \
-			;; \
-		*) \
-			echo "Skipping uninstallation."; \
-			echo " "; \
-			;; \
-	esac; \
-
-.PHONY: poetry-uninstall-pipx
-poetry-uninstall-pipx: poetry-remove-env ## Uninstall pipx-installed Poetry, the created Poetry environment and pipx
-	@if [ "$(AUTO_INSTALL)" = "true" ]; then \
-		ans="y";\
-	else \
-		echo""; \
-		echo -n "Would you like to uninstall pipx-installed Poetry and pipx? [y/N]: "; \
-		read ans; \
-	fi; \
-	case $$ans in \
-		[Yy]*) \
-			pipx uninstall poetry; \
-			pip uninstall -y pipx; \
-			;; \
-		*) \
-			echo "Skipping uninstallation."; \
-			echo " "; \
-			;; \
-	esac; \
-
-.PHONY: poetry-uninstall-venv
-poetry-uninstall-venv: poetry-remove-env ## Uninstall pipx-installed Poetry, the created Poetry environment, pipx and $HOME/.pipx_venv
-	@if [ "$(AUTO_INSTALL)" = "true" ]; then \
-		ans="y";\
-	else \
-		echo""; \
-		echo -n "Would you like to uninstall pipx-installed Poetry and pipx? [y/N]: "; \
-		read ans; \
-	fi; \
-	case $$ans in \
-		[Yy]*) \
-			(source $(PIPX_VENV_PATH)/bin/activate && pipx uninstall poetry); \
-			(source $(PIPX_VENV_PATH)/bin/activate && pip uninstall -y pipx); \
-			;; \
-		*) \
-			echo "Skipping uninstallation."; \
-			echo " "; \
-			;; \
-	esac; \
-
-	@if [ "$(AUTO_INSTALL)" = "true" ]; then \
-		ans="y";\
-	else \
-		echo""; \
-		echo -n "Would you like to remove the virtual environment located here : [$(PIPX_VENV_PATH)] ? [y/N]: "; \
-		read ans; \
-	fi; \
-	case $$ans in \
-		[Yy]*) \
-			rm -r $(PIPX_VENV_PATH); \
-			;; \
-		*) \
-			echo "Skipping [$(PIPX_VENV_PATH)] virtual environment removal."; \
-			echo ""; \
-			;; \
-	esac; \
-
-## -- Conda targets ------------------------------------------------------------------------------------------------- ##
-
-.PHONY: conda-install
-conda-install: ## Install Miniconda on your local machine
-	@echo "Looking for [$(CONDA_TOOL)]..."; \
-	$(CONDA_TOOL) --version; \
-	if [ $$? != "0" ]; then \
-		echo " "; \
-		echo "Your defined Conda tool [$(CONDA_TOOL)] has not been found."; \
-		echo " "; \
-		echo "If you know you already have [$(CONDA_TOOL)] or some other Conda tool installed,"; \
-		echo "Check your [CONDA_TOOL] variable in the Makefile.private for typos."; \
-		echo " "; \
-		echo "If your conda tool has not been initiated through your .bashrc file,"; \
-		echo "consider using the full path to its executable instead when"; \
-		echo "defining your [CONDA_TOOL] variable"; \
-		echo " "; \
-		echo "If in doubt, don't install Conda and manually create and activate"; \
-		echo "your own Python environment."; \
-		echo " "; \
-		echo "It is strongly NOT advisable to execute this command if you are on a"; \
-		echo "Compute Cluster (ie. Mila/DRAC), as they either have modules available (Mila),"; \
-		echo "or even prohibit the installation and use of Conda (DRAC) based environments."; \
-		echo " "; \
-		echo -n "Would you like to install and initialize Miniconda ? [y/N]: "; \
-		read ans; \
-		case $$ans in \
-			[Yy]*) \
-				echo "Fetching and installing miniconda"; \
-				echo " "; \
-				wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh; \
-    			bash ~/miniconda.sh -b -p $${HOME}/.conda; \
-    			export PATH=$${HOME}/.conda/bin:$$PATH; \
-    			conda init; \
-				/usr/bin/rm ~/miniconda.sh; \
-				;; \
-			*) \
-				echo "Skipping installation."; \
-				echo " "; \
-				;; \
-		esac; \
-	else \
-		echo "Conda tool [$(CONDA_TOOL)] has been found, skipping installation"; \
-	fi;
-
-.PHONY: mamba-install
-mamba-install: ## Install Micromamba on you local machine
-	@echo "Looking for [micromamba]..."; \
-	micromamba --version; \
-	if [ $$? != "0" ]; then \
-	  	echo ""; \
-	  	echo "[micromamba] has not been found."; \
-	  	echo ""; \
-	  	echo "If you know you already have installed [micromamba] installed, it might not have"; \
-	  	echo "been properly activated (which can also be on purpose)."; \
-	  	echo ""; \
-	  	echo "If your Conda/Micromamba tool has not been initiated through your .bashrc file,"; \
-		echo "consider using the full path to its executable instead when"; \
-		echo "defining your [CONDA_TOOL] variable"; \
-		echo " "; \
-		echo "If you do decide to install Micromamba, please take care to define the [CONDA_TOOL]"; \
-		echo "variable in you personal 'Makefile.private' file as CONDA_TOOL := micromamba."; \
-		echo " "; \
-		echo "If in doubt, don't install Micromamba and manually create and activate"; \
-		echo "your own Python environment."; \
-	  	echo ""; \
-	  	echo "It is strongly NOT advisable to execute this command if you are on a"; \
-		echo "Compute Cluster (ie. Mila/DRAC), as they either have modules available (Mila),"; \
-		echo "or even prohibit the installation and use of Conda based environments (DRAC)."; \
-	  	echo ""; \
-		echo -n "Would you like to install and initialize [micromamba] ? [y/N]: "; \
-		read ans; \
-		case $$ans in \
-			[Yy]*) \
-				echo 'Installing Micromamba'
-				wget -qO- https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba;\
-				mv bin/micromamba ~/.local/bin/micromamba;\
-				rm -rf bin/;\
-				~/.local/bin/micromamba shell init -s bash ~/.micromamba;\
-				;; \
-			*) \
-				echo "Skipping installation."; \
-				echo " "; \
-				;; \
-		esac; \
-
-
-.PHONY: conda-create-env
-conda-create-env: conda-install ## Create a local Conda environment based on 'environment.yml' file
-	@$(CONDA_TOOL) env create $(CONDA_YES_OPTION) -f environment.yml
-
-.PHONY: conda-env-info
-conda-env-info: ## Print information about active Conda environment using <CONDA_TOOL>
-	@$(CONDA_TOOL) info
-
-.PHONY: conda-activate
-conda-activate: ## Print the shell command to activate the project's Conda env.
-	@echo "$(CONDA_TOOL) activate $(CONDA_ENVIRONMENT)"
-
-.PHONY: _conda-poetry-install
-_conda-poetry-install:
-	@$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) python --version;  \
-	if [ $$? != "0" ]; then \
-		echo "Target environment doesn't seem to exist..."; \
-		if [ "$(AUTO_INSTALL)" = "true" ]; then \
-				ans="y";\
-		else \
-			echo ""; \
-			echo -n "Do you want to create it? [y/N] "; \
-			read ans; \
-		fi; \
-		case $$ans in \
-			[Yy]*) \
-				echo "Creating conda environment : [$(CONDA_ENVIRONMENT)]"; \
-				make -s conda-create-env; \
-				;; \
-			*) \
-				echo "Exiting..."; \
-				exit 1;\
-				;; \
-		esac;\
-	fi;
-	$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) $(CONDA_TOOL) install $(CONDA_YES_OPTION) -c conda-forge poetry; \
-	CURRENT_VERSION=$$($(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) poetry --version | awk '{print $$NF}' | tr -d ')'); \
-	REQUIRED_VERSION="1.6.0"; \
-	if [ "$$(printf '%s\n' "$$REQUIRED_VERSION" "$$CURRENT_VERSION" | sort -V | head -n1)" != "$$REQUIRED_VERSION" ]; then \
-		echo "Poetry installed version $$CURRENT_VERSION is less than minimal version $$REQUIRED_VERSION, fixing urllib3 version to prevent problems"; \
-		$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT)  poetry add "urllib3<2.0.0"; \
-	fi;
-
-.PHONY:conda-poetry-install
-conda-poetry-install: ## Install Poetry in the project's Conda environment. Will fail if Conda is not found
-	@poetry --version; \
-    	if [ $$? != "0" ]; then \
-			echo "Poetry not found, proceeding to install Poetry..."; \
-			echo "Looking for [$(CONDA_TOOL)]...";\
-			$(CONDA_TOOL) --version; \
-			if [ $$? != "0" ]; then \
-				echo "$(CONDA_TOOL) not found; Poetry will not be installed"; \
-			else \
-				echo "Installing Poetry with Conda in [$(CONDA_ENVIRONMENT)] environment"; \
-				make -s _conda-poetry-install; \
-			fi; \
-		else \
-			echo ""; \
-			echo "Poetry has been found on this system :"; \
-			echo "    Install location: $$(which poetry)"; \
-			echo ""; \
-			if [ "$(AUTO_INSTALL)" = "true" ]; then \
-				ans="y";\
-			else \
-				echo -n "Would you like to install poetry in the project's conda environment anyway ? [y/N]: "; \
-				read ans; \
-			fi; \
-			case $$ans in \
-				[Yy]*) \
-					echo "Installing Poetry with Conda in [$(CONDA_ENVIRONMENT)] environment"; \
-					make -s _conda-poetry-install; \
-					;; \
-				*) \
-					echo "Skipping installation."; \
-					echo " "; \
-					;; \
-			esac; \
-		fi;
-
-.PHONY: conda-poetry-uninstall
-conda-poetry-uninstall: ## Uninstall Poetry located in currently active Conda environment
-	$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) $(CONDA_TOOL) remove $(CONDA_YES_OPTION) poetry
-
-.PHONY: conda-clean-env
-conda-clean-env: ## Completely removes local project's Conda environment
-	$(CONDA_TOOL) env remove $(CONDA_YES_OPTION) -n $(CONDA_ENVIRONMENT)
-
-## -- Install targets (All install targets will install Poetry if not found using 'make poetry-install-auto')-------- ##
-
-POETRY_COMMAND := poetry
-
-ifeq ($(DEFAULT_INSTALL_ENV),venv)
-POETRY_COMMAND := source $(VENV_ACTIVATE) && poetry
-else ifeq ($(DEFAULT_INSTALL_ENV),poetry)
-POETRY_COMMAND := poetry
-else ifeq ($(DEFAULT_INSTALL_ENV),conda)
-POETRY_COMMAND := $(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) poetry
-endif
-
-.PHONY: _check-env
-_check-env:
-	@if ! [ $(DEFAULT_INSTALL_ENV) ]; then \
-		echo -e "\e[1;39;41m-- WARNING --\e[0m No installation environment have been defined." ; \
-		echo "" ; \
-		echo "[DEFAULT_INSTALL_ENV] is not defined - Poetry will use the currently activated environment." ; \
-		echo "If there is no currently active environment (ie. conda or venv)," ; \
-		echo "Poetry will create and manage it's own environment." ; \
-	elif [ $(DEFAULT_INSTALL_ENV) = "venv" ]; then \
-		if [ ! -f $(VENV_ACTIVATE) ]; then \
-			make -s venv-create ;\
-		fi; \
-	elif [ $(DEFAULT_INSTALL_ENV) = "conda" ]; then \
-		if ! $(CONDA_TOOL) env list | grep -q $(CONDA_ENVIRONMENT) ; then \
-			make -s conda-create-env ; \
-		fi; \
-	fi;
-
-.PHONY: _remind-env-activate
-_remind-env-activate:
-	@echo ""
-	@echo "Activate your environment using the following command:"
-	@echo ""
-	@if ! [ $(DEFAULT_INSTALL_ENV) ] || [ $(DEFAULT_INSTALL_ENV) = "poetry" ]; then \
-		make -s poetry-activate ; \
-		echo "" ; \
-		echo "You can also use the eval bash command : eval \$$(make poetry-activate)"; \
-		echo "" ; \
-		echo "The environment can also be used through the 'poetry run <command>' command."; \
-		echo "" ; \
-		echo "    Ex: poetry run python <path_to_script>"; \
-	elif [ $(DEFAULT_INSTALL_ENV) = "venv" ]; then \
-		make -s venv-activate ; \
-		echo "" ; \
-		echo "You can also use the eval bash command : eval \$$(make venv-activate)"; \
-	elif [ $(DEFAULT_INSTALL_ENV) = "conda" ]; then \
-		make -s conda-activate ; \
-		echo "" ; \
-		echo "You can also use the eval bash command : eval \$$(make conda-activate)"; \
-	fi;
-	@echo ""
-
-test-echo:
-	@echo "use the eval bash command : eval \$$(make poetry-activate)"
-
-.PHONY: install
-install: install-precommit ## Install the application package, developer dependencies and pre-commit hook
-
-.PHONY: install-precommit
-install-precommit: install-dev ## Install the pre-commit hooks (also installs developer dependencies)
-	@if [ -f .git/hooks/pre-commit ]; then \
-		echo "Pre-commit hook found"; \
-	else \
-	  	echo "Pre-commit hook not found, proceeding to configure it"; \
-		$(POETRY_COMMAND) run pre-commit install; \
-	fi;
-
-.PHONY: install-dev
-install-dev: poetry-install-auto _check-env ## Install the application along with developer dependencies
-	@$(POETRY_COMMAND) install --with dev
-	@make -s _remind-env-activate
-
-.PHONY: install-with-lab
-install-with-lab: poetry-install-auto _check-env ## Install the application and it's dev dependencies, including Jupyter Lab
-	@$(POETRY_COMMAND) install --with dev --with lab
-	@make -s _remind-env-activate
-
-
-.PHONY: install-package
-install-package: poetry-install-auto _check-env ## Install the application package only
-	@$(POETRY_COMMAND) install
-	@make -s _remind-env-activate
-
 ## -- Versioning targets -------------------------------------------------------------------------------------------- ##
 
 # Use the "dry" target for a dry-run version bump, ex.
@@ -697,86 +148,5 @@ bump-minor: ## Bump application minor version  <0.X.0>
 bump-patch: ## Bump application patch version  <0.0.X>
 	$(BUMP_TOOL) bump $(BUMP_ARGS) patch
 
-## -- Docker targets ------------------------------------------------------------------------------------------------ ##
-
-## -- Apptainer/Singularity targets --------------------------------------------------------------------------------- ##
-
-## -- Linting targets ----------------------------------------------------------------------------------------------- ##
-
-.PHONY: check-lint
-check-lint: ## Check code linting (black, isort, flake8, docformatter and pylint)
-	poetry run nox -s check
-
-.PHONY: check-pylint
-check-pylint: ## Check code with pylint
-	poetry run nox -s pylint
-
-.PHONY: check-complexity
-check-complexity: ## Check code cyclomatic complexity with Flake8-McCabe
-	poetry run nox -s complexity
-
-.PHONY: fix-lint
-fix-lint: ## Fix code linting (autoflake, autopep8, black, isort, flynt, docformatter)
-	poetry run nox -s fix
-
-.PHONY: precommit
-precommit: ## Run Pre-commit on all files manually
-	poetry run nox -s precommit
-
-.PHONY: ruff
-ruff: ## Run the ruff linter
-	poetry run nox -s ruff-lint
-
-.PHONY: ruff-fix
-ruff-fix: ## Run the ruff linter and fix automatically fixable errors
-	poetry run nox -s ruff-fix
-
-.PHONY: ruff-format
-ruff-format: ## Run the ruff code formatter
-	poetry run nox -s ruff-format
-
-## -- Tests targets ------------------------------------------------------------------------------------------------- ##
-
-.PHONY: test
-test: ## Run all tests
-	poetry run nox -s test
-
-TEST_ARGS ?=
-MARKER_TEST_ARGS = -m "$(TEST_ARGS)"
-SPECIFIC_TEST_ARGS = -k "$(TEST_ARGS)"
-CUSTOM_TEST_ARGS = "$(TEST_ARGS)"
 
-.PHONY: test-marker
-test-marker: ## Run tests using pytest markers. Ex. make test-marker TEST_ARGS="<marker>"
-	@if [ -n "$(TEST_ARGS)" ]; then \
-		poetry run nox -s test_custom -- -- $(MARKER_TEST_ARGS); \
-	else \
-		echo "" ; \
-    	echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \
-	  	echo "" ; \
-    	echo '            make test-marker TEST_ARGS="<marker>"' ; \
-	  	echo "" ; \
-    fi
-.PHONY: test-specific
-test-specific: ## Run specific tests using the -k option. Ex. make test-specific TEST_ARGS="<name-of-test>"
-	@if [ -n "$(TEST_ARGS)" ]; then \
-  		poetry run nox -s test_custom -- -- $(SPECIFIC_TEST_ARGS); \
-	else \
-		echo "" ; \
-    	echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \
-	  	echo "" ; \
-    	echo '            make test-specific TEST_ARGS="<name-of-the-test>"' ; \
-	  	echo "" ; \
-    fi
 
-.PHONY: test-custom
-test-custom: ## Run tests with custom args. Ex. make test-custom TEST_ARGS="-m 'not offline'"
-	@if [ -n "$(TEST_ARGS)" ]; then \
-  		poetry run nox -s test_custom -- -- $(CUSTOM_TEST_ARGS); \
-	else \
-	  	echo "" ; \
-    	echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \
-	  	echo "" ; \
-    	echo '            make test-custom TEST_ARGS="<custom-args>"' ; \
-	  	echo "" ; \
-    fi
\ No newline at end of file
diff --git a/.make/conda.make b/.make/conda.make
new file mode 100644
index 0000000..855f80e
--- /dev/null
+++ b/.make/conda.make
@@ -0,0 +1,176 @@
+
+
+## -- Conda targets ------------------------------------------------------------------------------------------------- ##
+
+CONDA_ENVIRONMENT_FILE := environment.yml
+.PHONY: conda-install
+conda-install: ## Install Miniconda on your local machine
+	@echo "Looking for [$(CONDA_TOOL)]..."; \
+	$(CONDA_TOOL) --version; \
+	if [ $$? != "0" ]; then \
+		echo " "; \
+		echo "Your defined Conda tool [$(CONDA_TOOL)] has not been found."; \
+		echo " "; \
+		echo "If you know you already have [$(CONDA_TOOL)] or some other Conda tool installed,"; \
+		echo "Check your [CONDA_TOOL] variable in the Makefile.private for typos."; \
+		echo " "; \
+		echo "If your conda tool has not been initiated through your .bashrc file,"; \
+		echo "consider using the full path to its executable instead when"; \
+		echo "defining your [CONDA_TOOL] variable"; \
+		echo " "; \
+		echo "If in doubt, don't install Conda and manually create and activate"; \
+		echo "your own Python environment."; \
+		echo " "; \
+		echo "It is strongly NOT advisable to execute this command if you are on a"; \
+		echo "Compute Cluster (ie. Mila/DRAC), as they either have modules available (Mila),"; \
+		echo "or even prohibit the installation and use of Conda (DRAC) based environments."; \
+		echo " "; \
+		echo -n "Would you like to install and initialize Miniconda ? [y/N]: "; \
+		read ans; \
+		case $$ans in \
+			[Yy]*) \
+				echo "Fetching and installing miniconda"; \
+				echo " "; \
+				wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh; \
+    			bash ~/miniconda.sh -b -p $${HOME}/.conda; \
+    			export PATH=$${HOME}/.conda/bin:$$PATH; \
+    			conda init; \
+				/usr/bin/rm ~/miniconda.sh; \
+				;; \
+			*) \
+				echo "Skipping installation."; \
+				echo " "; \
+				;; \
+		esac; \
+	else \
+		echo "Conda tool [$(CONDA_TOOL)] has been found, skipping installation"; \
+	fi;
+
+.PHONY: mamba-install
+mamba-install: ## Install Micromamba on you local machine
+	@echo "Looking for [micromamba]..."; \
+	micromamba --version; \
+	if [ $$? != "0" ]; then \
+	  	echo ""; \
+	  	echo "[micromamba] has not been found."; \
+	  	echo ""; \
+	  	echo "If you know you already have installed [micromamba] installed, it might not have"; \
+	  	echo "been properly activated (which can also be on purpose)."; \
+	  	echo ""; \
+	  	echo "If your Conda/Micromamba tool has not been initiated through your .bashrc file,"; \
+		echo "consider using the full path to its executable instead when"; \
+		echo "defining your [CONDA_TOOL] variable"; \
+		echo " "; \
+		echo "If you do decide to install Micromamba, please take care to define the [CONDA_TOOL]"; \
+		echo "variable in you personal 'Makefile.private' file as CONDA_TOOL := micromamba."; \
+		echo " "; \
+		echo "If in doubt, don't install Micromamba and manually create and activate"; \
+		echo "your own Python environment."; \
+	  	echo ""; \
+	  	echo "It is strongly NOT advisable to execute this command if you are on a"; \
+		echo "Compute Cluster (ie. Mila/DRAC), as they either have modules available (Mila),"; \
+		echo "or even prohibit the installation and use of Conda based environments (DRAC)."; \
+	  	echo ""; \
+		echo -n "Would you like to install and initialize [micromamba] ? [y/N]: "; \
+		read ans; \
+		case $$ans in \
+			[Yy]*) \
+				echo 'Installing Micromamba'
+				wget -qO- https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba;\
+				mv bin/micromamba ~/.local/bin/micromamba;\
+				rm -rf bin/;\
+				~/.local/bin/micromamba shell init -s bash ~/.micromamba;\
+				;; \
+			*) \
+				echo "Skipping installation."; \
+				echo " "; \
+				;; \
+		esac; \
+
+
+.PHONY: conda-create-env
+conda-create-env: conda-install ## Create a local Conda environment based on 'environment.yml' file
+	@$(CONDA_TOOL) env create $(CONDA_YES_OPTION) -f $(CONDA_ENVIRONMENT_FILE)
+
+.PHONY: conda-env-info
+conda-env-info: ## Print information about active Conda environment using <CONDA_TOOL>
+	@$(CONDA_TOOL) info
+
+.PHONY: conda-activate
+conda-activate: ## Print the shell command to activate the project's Conda env.
+	@echo "$(CONDA_TOOL) activate $(CONDA_ENVIRONMENT)"
+
+.PHONY: _conda-poetry-install
+_conda-poetry-install:
+	@$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) python --version;  \
+	if [ $$? != "0" ]; then \
+		echo "Target environment doesn't seem to exist..."; \
+		if [ "$(AUTO_INSTALL)" = "true" ]; then \
+				ans="y";\
+		else \
+			echo ""; \
+			echo -n "Do you want to create it? [y/N] "; \
+			read ans; \
+		fi; \
+		case $$ans in \
+			[Yy]*) \
+				echo "Creating conda environment : [$(CONDA_ENVIRONMENT)]"; \
+				make -s conda-create-env; \
+				;; \
+			*) \
+				echo "Exiting..."; \
+				exit 1;\
+				;; \
+		esac;\
+	fi;
+	$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) $(CONDA_TOOL) install $(CONDA_YES_OPTION) -c conda-forge poetry; \
+	CURRENT_VERSION=$$($(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) poetry --version | awk '{print $$NF}' | tr -d ')'); \
+	REQUIRED_VERSION="1.6.0"; \
+	if [ "$$(printf '%s\n' "$$REQUIRED_VERSION" "$$CURRENT_VERSION" | sort -V | head -n1)" != "$$REQUIRED_VERSION" ]; then \
+		echo "Poetry installed version $$CURRENT_VERSION is less than minimal version $$REQUIRED_VERSION, fixing urllib3 version to prevent problems"; \
+		$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT)  poetry add "urllib3<2.0.0"; \
+	fi;
+
+.PHONY:conda-poetry-install
+conda-poetry-install: ## Install Poetry in the project's Conda environment. Will fail if Conda is not found
+	@poetry --version; \
+    	if [ $$? != "0" ]; then \
+			echo "Poetry not found, proceeding to install Poetry..."; \
+			echo "Looking for [$(CONDA_TOOL)]...";\
+			$(CONDA_TOOL) --version; \
+			if [ $$? != "0" ]; then \
+				echo "$(CONDA_TOOL) not found; Poetry will not be installed"; \
+			else \
+				echo "Installing Poetry with Conda in [$(CONDA_ENVIRONMENT)] environment"; \
+				make -s _conda-poetry-install; \
+			fi; \
+		else \
+			echo ""; \
+			echo "Poetry has been found on this system :"; \
+			echo "    Install location: $$(which poetry)"; \
+			echo ""; \
+			if [ "$(AUTO_INSTALL)" = "true" ]; then \
+				ans="y";\
+			else \
+				echo -n "Would you like to install poetry in the project's conda environment anyway ? [y/N]: "; \
+				read ans; \
+			fi; \
+			case $$ans in \
+				[Yy]*) \
+					echo "Installing Poetry with Conda in [$(CONDA_ENVIRONMENT)] environment"; \
+					make -s _conda-poetry-install; \
+					;; \
+				*) \
+					echo "Skipping installation."; \
+					echo " "; \
+					;; \
+			esac; \
+		fi;
+
+.PHONY: conda-poetry-uninstall
+conda-poetry-uninstall: ## Uninstall Poetry located in currently active Conda environment
+	$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) $(CONDA_TOOL) remove $(CONDA_YES_OPTION) poetry
+
+.PHONY: conda-clean-env
+conda-clean-env: ## Completely removes local project's Conda environment
+	$(CONDA_TOOL) env remove $(CONDA_YES_OPTION) -n $(CONDA_ENVIRONMENT)
diff --git a/.make/lint.make b/.make/lint.make
new file mode 100644
index 0000000..cd79c88
--- /dev/null
+++ b/.make/lint.make
@@ -0,0 +1,37 @@
+## -- Linting targets ----------------------------------------------------------------------------------------------- ##
+
+.PHONY: check-lint
+check-lint: ## Check code linting (black, isort, flake8, docformatter and pylint)
+	$(ENV_COMMAND_TOOL) run nox -s check
+
+.PHONY: check-pylint
+check-pylint: ## Check code with pylint
+	$(ENV_COMMAND_TOOL) run nox -s pylint
+
+.PHONY: check-complexity
+check-complexity: ## Check code cyclomatic complexity with Flake8-McCabe
+	$(ENV_COMMAND_TOOL) run nox -s complexity
+
+.PHONY: fix-lint
+fix-lint: ## Fix code linting (autoflake, autopep8, black, isort, flynt, docformatter)
+	$(ENV_COMMAND_TOOL) run nox -s fix
+
+.PHONY: markdown-lint
+markdown-lint: ## Fix markdown linting using mdformat
+	$(ENV_COMMAND_TOOL) run nox -s mdformat
+
+.PHONY: precommit
+precommit: ## Run Pre-commit on all files manually
+	$(ENV_COMMAND_TOOL) run nox -s precommit
+
+.PHONY: ruff
+ruff: ## Run the ruff linter
+	$(ENV_COMMAND_TOOL) run nox -s ruff-lint
+
+.PHONY: ruff-fix
+ruff-fix: ## Run the ruff linter and fix automatically fixable errors
+	$(ENV_COMMAND_TOOL) run nox -s ruff-fix
+
+.PHONY: ruff-format
+ruff-format: ## Run the ruff code formatter
+	$(ENV_COMMAND_TOOL) run nox -s ruff-format
diff --git a/.make/poetry.make b/.make/poetry.make
new file mode 100644
index 0000000..2b39348
--- /dev/null
+++ b/.make/poetry.make
@@ -0,0 +1,387 @@
+# Project and Private variables and targets import to override variables for local
+# This is to make sure, sometimes the Makefile includes don't work.
+-include Makefile.variables
+-include Makefile.private
+
+ENV_COMMAND_TOOL := poetry
+
+## -- Poetry targets ------------------------------------------------------------------------------------------------ ##
+
+.PHONY: poetry-install-auto
+poetry-install-auto: ## Install Poetry automatically using DEFAULT_POETRY_INSTALL_ENV. Defaults to venv install
+	@poetry --version; \
+    	if [ $$? != "0" ]; then \
+			echo "Poetry not found, proceeding to install Poetry..."; \
+			if [ "$(DEFAULT_POETRY_INSTALL_ENV)" == "conda" ]; then \
+			    echo ""; \
+			    echo "[DEFAULT_POETRY_INSTALL_ENV] is defined as 'conda', installing poetry with the 'poetry-install-conda' target"; \
+			    echo ""; \
+				ans_where="conda"; \
+			elif [ "$(DEFAULT_POETRY_INSTALL_ENV)" == "venv" ]; then \
+				echo ""; \
+				echo "[DEFAULT_POETRY_INSTALL_ENV] is defined as 'venv', installing poetry with the 'poetry-install-venv' target"; \
+				echo ""; \
+				ans_where="venv"; \
+			else\
+				echo ""; \
+				echo "[DEFAULT_POETRY_INSTALL_ENV] is not defined, defaulting to installing poetry with the 'poetry-install-venv' target"; \
+				echo ""; \
+				ans_where="venv"; \
+			fi; \
+			case $$ans_where in \
+				"venv" | "Venv" |"VENV") \
+					make AUTO_INSTALL=true -s poetry-install-venv; \
+					;; \
+				"conda" | "Conda" | "CONDA") \
+					echo "Installing poetry with Conda"; \
+					make AUTO_INSTALL=true -s conda-poetry-install; \
+					;; \
+				*) \
+					echo ""; \
+					echo -e "\e[1;39;41m-- WARNING --\e[0m There was an unexpected error. Option $$ans_how not found, exiting process."; \
+					echo ""; \
+					exit 1; \
+			esac; \
+		fi;
+
+.PHONY: _pipx_install_poetry
+_pipx_install_poetry:
+	@output="$$(pip install poetry --dry-run)"; \
+	if echo "$$output" | grep -q computecanada ; then \
+		echo ""; \
+		echo -e "\e[1;39;41m-- WARNING --\e[0m Compute Canada (DRAC) environment detected: Installing Poetry < 2.0.0"; \
+		echo ""; \
+		pipx install 'poetry<2.0.0' ; \
+	else \
+		pipx install poetry ; \
+	fi;
+
+
+.PHONY: poetry-install
+poetry-install: ## Install Poetry interactively.
+	@echo "Looking for Poetry version...";\
+	poetry --version; \
+	if [ $$? != "0" ]; then \
+		if [ "$(AUTO_INSTALL)" = "true" ]; then \
+			ans="y";\
+		else \
+			echo "Poetry not found..."; \
+			echo "Looking for pipx version...";\
+			pipx_found=0; \
+			pipx --version; \
+				if [ $$? != "0" ]; then \
+					pipx_found=1; \
+					echo "pipx not found..."; \
+					echo""; \
+					echo -n "Would you like to install pipx and Poetry? [y/N]: "; \
+				else \
+					echo""; \
+					echo -n "Would you like to install Poetry using pipx? [y/N]: "; \
+				fi; \
+			read ans; \
+		fi; \
+		case $$ans in \
+			[Yy]*) \
+				if [ $$pipx_found == "1" ]; then \
+					echo""; \
+					echo -e "\e[1;39;41m-- WARNING --\e[0m The following pip has been found and will be used to install pipx: "; \
+					echo "    -> "$$(which pip); \
+					echo""; \
+					echo "If you do not have write permission to that environment, using it to install pipx will fail."; \
+					echo "If this is the case, you should install pipx using a virtual one."; \
+					echo""; \
+					echo "See documentation for more information."; \
+					echo""; \
+					echo -n "Would you like to use the local available pip above, or create virtual environment to install pipx? [local/virtual]: "; \
+					read ans_how; \
+					case $$ans_how in \
+						"LOCAL" | "Local" |"local") \
+							make -s poetry-install-local; \
+							;; \
+						"VIRTUAL" | "Virtual" | "virtual") \
+							make -s poetry-install-venv; \
+							;; \
+						*) \
+							echo ""; \
+							echo -e "\e[1;39;41m-- WARNING --\e[0m Option $$ans_how not found, exiting process."; \
+							echo ""; \
+							exit 1; \
+					esac; \
+				else \
+					echo "Installing Poetry"; \
+					make -s _pipx_install_poetry; \
+				fi; \
+				;; \
+			*) \
+				echo "Skipping installation."; \
+				echo " "; \
+				;; \
+		esac; \
+	fi;
+
+PIPX_VENV_PATH := $$HOME/.pipx_venv
+.PHONY: poetry-install-venv
+poetry-install-venv: ## Install standalone Poetry. Will install pipx in $HOME/.pipx_venv
+	@pipx --version; \
+	if [ $$? != "0" ]; then \
+		echo "Creating virtual environment using venv here : [$(PIPX_VENV_PATH)]"; \
+		python3 -m venv $(PIPX_VENV_PATH); \
+		echo "Activating virtual environment [$(PIPX_VENV_PATH)]"; \
+		source $(PIPX_VENV_PATH)/bin/activate; \
+		pip3 install pipx; \
+		pipx ensurepath; \
+		source $(PIPX_VENV_PATH)/bin/activate && make -s _pipx_install_poetry ; \
+	else \
+		make -s _pipx_install_poetry ; \
+	fi;
+
+.PHONY: poetry-install-local
+poetry-install-local: ## Install standalone Poetry. Will install pipx with locally available pip.
+	@pipx --version; \
+	if [ $$? != "0" ]; then \
+		echo "pipx not found; installing pipx"; \
+		pip3 install pipx; \
+		pipx ensurepath; \
+	fi;
+	@echo "Installing Poetry"
+	@make -s _pipx_install_poetry
+
+
+.PHONY: poetry-env-info
+poetry-env-info: ## Information about the currently active environment used by Poetry
+	@poetry env info
+
+.PHONY: poetry-create-env
+poetry-create-env: ## Create a Poetry managed environment for the project (Outside of Conda environment).
+	@echo "Creating Poetry environment that will use Python $(PYTHON_VERSION)"; \
+	poetry env use $(PYTHON_VERSION); \
+	poetry env info
+	@echo""
+	@echo "This environment can be accessed either by using the <poetry run YOUR COMMAND>"
+	@echo "command, or activated with the <poetry shell> command."
+	@echo""
+	@echo "Use <poetry --help> and <poetry list> for more information"
+	@echo""
+
+.PHONY: poetry-activate
+poetry-activate: ## Print the shell command to activate the project's poetry env.
+	poetry env activate
+
+.PHONY: poetry-remove-env
+poetry-remove-env: ## Remove current project's Poetry managed environment.
+	@if [ "$(AUTO_INSTALL)" = "true" ]; then \
+		ans_env="y";\
+		env_path=$$(poetry env info -p); \
+		env_name=$$(basename $$env_path); \
+	else \
+		echo""; \
+		echo "Looking for poetry environments..."; \
+		env_path=$$(poetry env info -p); \
+		if [[ "$$env_path" != "" ]]; then \
+			echo "The following environment has been found for this project: "; \
+			env_name=$$(basename $$env_path); \
+			echo""; \
+			echo "Env name : $$env_name"; \
+			echo "PATH     : $$env_path"; \
+			echo""; \
+			echo "If the active environment listed above is a Conda environment,"; \
+			echo "Choosing to delete it will have no effect; use the target <make conda-clean-env>"; \
+			echo""; \
+			echo""; \
+			echo "If the active environment listed above is a venv environment,"; \
+			echo "Choosing to delete it will have no effect; use the bash command $ rm -rf <PATH_TO_VENV>"; \
+			echo""; \
+			echo -n "Would you like delete the environment listed above? [y/N]: "; \
+			read ans_env; \
+		else \
+			env_name="None"; \
+			env_path="None"; \
+  		fi; \
+	fi; \
+	if [[ $$env_name != "None" ]]; then \
+		case $$ans_env in \
+			[Yy]*) \
+				poetry env remove $$env_name || echo "No environment was removed"; \
+				;; \
+			*) \
+				echo "No environment was found/provided - skipping environment deletion"; \
+				;;\
+		esac; \
+	else \
+		echo "No environments were found... skipping environment deletion"; \
+	fi; \
+
+.PHONY: poetry-uninstall
+poetry-uninstall: poetry-remove-env ## Uninstall pipx-installed Poetry and the created environment
+	@if [ "$(AUTO_INSTALL)" = "true" ]; then \
+		ans="y";\
+	else \
+		echo""; \
+		echo -n "Would you like to uninstall pipx-installed Poetry? [y/N]: "; \
+		read ans; \
+	fi; \
+	case $$ans in \
+		[Yy]*) \
+			pipx --version ; \
+			if [ $$? != "0" ]; then \
+				echo "" ; \
+				echo "Pipx not found globally, trying with $(PIPX_VENV_PATH) env" ;\
+				echo "" ; \
+				source $(PIPX_VENV_PATH)/bin/activate && pipx uninstall poetry ; \
+			else \
+				pipx uninstall poetry ; \
+				fi; \
+			;; \
+		*) \
+			echo "Skipping uninstallation."; \
+			echo " "; \
+			;; \
+	esac; \
+
+.PHONY: poetry-uninstall-pipx
+poetry-uninstall-pipx: poetry-remove-env ## Uninstall pipx-installed Poetry, the created Poetry environment and pipx
+	@if [ "$(AUTO_INSTALL)" = "true" ]; then \
+		ans="y";\
+	else \
+		echo""; \
+		echo -n "Would you like to uninstall pipx-installed Poetry and pipx? [y/N]: "; \
+		read ans; \
+	fi; \
+	case $$ans in \
+		[Yy]*) \
+			pipx --version ; \
+			if [ $$? != "0" ]; then \
+				echo "" ; \
+				echo "Pipx not found globally, trying with $(PIPX_VENV_PATH) env" ;\
+				echo "" ; \
+				source $(PIPX_VENV_PATH)/bin/activate && pipx uninstall poetry && pip uninstall -y pipx; \
+			else \
+				pipx uninstall poetry ; \
+				pip uninstall -y pipx ;\
+				fi; \
+			;; \
+		*) \
+			echo "Skipping uninstallation."; \
+			echo " "; \
+			;; \
+	esac; \
+
+.PHONY: poetry-uninstall-venv
+poetry-uninstall-venv: poetry-remove-env ## Uninstall pipx-installed Poetry, the created Poetry environment, pipx and $HOME/.pipx_venv
+	@if [ "$(AUTO_INSTALL)" = "true" ]; then \
+		ans="y";\
+	else \
+		echo""; \
+		echo -n "Would you like to uninstall pipx-installed Poetry and pipx? [y/N]: "; \
+		read ans; \
+	fi; \
+	case $$ans in \
+		[Yy]*) \
+			(source $(PIPX_VENV_PATH)/bin/activate && pipx uninstall poetry); \
+			(source $(PIPX_VENV_PATH)/bin/activate && pip uninstall -y pipx); \
+			;; \
+		*) \
+			echo "Skipping uninstallation."; \
+			echo " "; \
+			;; \
+	esac; \
+
+	@if [ "$(AUTO_INSTALL)" = "true" ]; then \
+		ans="y";\
+	else \
+		echo""; \
+		echo -n "Would you like to remove the virtual environment located here : [$(PIPX_VENV_PATH)] ? [y/N]: "; \
+		read ans; \
+	fi; \
+	case $$ans in \
+		[Yy]*) \
+			rm -r $(PIPX_VENV_PATH); \
+			;; \
+		*) \
+			echo "Skipping [$(PIPX_VENV_PATH)] virtual environment removal."; \
+			echo ""; \
+			;; \
+	esac; \
+
+## -- Install targets (All install targets will install Poetry if not found using 'make poetry-install-auto')-------- ##
+
+
+POETRY_COMMAND := poetry
+
+ifeq ($(DEFAULT_INSTALL_ENV),venv)
+POETRY_COMMAND := source $(VENV_ACTIVATE) && poetry
+else ifeq ($(DEFAULT_INSTALL_ENV),poetry)
+POETRY_COMMAND := poetry
+else ifeq ($(DEFAULT_INSTALL_ENV),conda)
+POETRY_COMMAND := $(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) poetry
+endif
+
+.PHONY: _check-env
+_check-env:
+	@if ! [ $(DEFAULT_INSTALL_ENV) ]; then \
+		echo -e "\e[1;39;41m-- WARNING --\e[0m No installation environment have been defined." ; \
+		echo "" ; \
+		echo "[DEFAULT_INSTALL_ENV] is not defined - Poetry will use the currently activated environment." ; \
+		echo "If there is no currently active environment (ie. conda or venv)," ; \
+		echo "Poetry will create and manage it's own environment." ; \
+	elif [ $(DEFAULT_INSTALL_ENV) = "venv" ]; then \
+		if [ ! -f $(VENV_ACTIVATE) ]; then \
+			make -s venv-create ;\
+		fi; \
+	elif [ $(DEFAULT_INSTALL_ENV) = "conda" ]; then \
+		if ! $(CONDA_TOOL) env list | grep -q $(CONDA_ENVIRONMENT) ; then \
+			make -s conda-create-env ; \
+		fi; \
+	fi;
+
+.PHONY: _remind-env-activate
+_remind-env-activate:
+	@echo ""
+	@echo "Activate your environment using the following command:"
+	@echo ""
+	@if ! [ $(DEFAULT_INSTALL_ENV) ] || [ $(DEFAULT_INSTALL_ENV) = "poetry" ]; then \
+		make -s poetry-activate ; \
+		echo "" ; \
+		echo "You can also use the eval bash command : eval \$$(make poetry-activate)"; \
+		echo "" ; \
+		echo "The environment can also be used through the 'poetry run <command>' command."; \
+		echo "" ; \
+		echo "    Ex: poetry run python <path_to_script>"; \
+	elif [ $(DEFAULT_INSTALL_ENV) = "venv" ]; then \
+		make -s venv-activate ; \
+		echo "" ; \
+		echo "You can also use the eval bash command : eval \$$(make venv-activate)"; \
+	elif [ $(DEFAULT_INSTALL_ENV) = "conda" ]; then \
+		make -s conda-activate ; \
+		echo "" ; \
+		echo "You can also use the eval bash command : eval \$$(make conda-activate)"; \
+	fi;
+	@echo ""
+
+.PHONY: install
+install: install-precommit ## Install the application package, developer dependencies and pre-commit hook
+
+.PHONY: install-precommit
+install-precommit: install-dev ## Install the pre-commit hooks (also installs developer dependencies)
+	@if [ -f .git/hooks/pre-commit ]; then \
+		echo "Pre-commit hook found"; \
+	else \
+	  	echo "Pre-commit hook not found, proceeding to configure it"; \
+		$(POETRY_COMMAND) run pre-commit install; \
+	fi;
+
+.PHONY: install-dev
+install-dev: poetry-install-auto _check-env ## Install the application along with developer dependencies
+	@$(POETRY_COMMAND) install --with dev
+	@make -s _remind-env-activate
+
+.PHONY: install-with-lab
+install-with-lab: poetry-install-auto _check-env ## Install the application and it's dev dependencies, including Jupyter Lab
+	@$(POETRY_COMMAND) install --with dev --with lab
+	@make -s _remind-env-activate
+
+
+.PHONY: install-package
+install-package: poetry-install-auto _check-env ## Install the application package only
+	@$(POETRY_COMMAND) install
+	@make -s _remind-env-activate
diff --git a/.make/test.make b/.make/test.make
new file mode 100644
index 0000000..86b78de
--- /dev/null
+++ b/.make/test.make
@@ -0,0 +1,45 @@
+## -- Tests targets ------------------------------------------------------------------------------------------------- ##
+
+.PHONY: test
+test: ## Run all tests
+	$(ENV_COMMAND_TOOL) run nox -s test
+
+TEST_ARGS ?=
+MARKER_TEST_ARGS = -m "$(TEST_ARGS)"
+SPECIFIC_TEST_ARGS = -k "$(TEST_ARGS)"
+CUSTOM_TEST_ARGS = "$(TEST_ARGS)"
+
+.PHONY: test-marker
+test-marker: ## Run tests using pytest markers. Ex. make test-marker TEST_ARGS="<marker>"
+	@if [ -n "$(TEST_ARGS)" ]; then \
+		$(ENV_COMMAND_TOOL) run nox -s test_custom -- -- $(MARKER_TEST_ARGS); \
+	else \
+		echo "" ; \
+    	echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \
+	  	echo "" ; \
+    	echo '            make test-marker TEST_ARGS="<marker>"' ; \
+	  	echo "" ; \
+    fi
+.PHONY: test-specific
+test-specific: ## Run specific tests using the -k option. Ex. make test-specific TEST_ARGS="<name-of-test>"
+	@if [ -n "$(TEST_ARGS)" ]; then \
+  		$(ENV_COMMAND_TOOL) run nox -s test_custom -- -- $(SPECIFIC_TEST_ARGS); \
+	else \
+		echo "" ; \
+    	echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \
+	  	echo "" ; \
+    	echo '            make test-specific TEST_ARGS="<name-of-the-test>"' ; \
+	  	echo "" ; \
+    fi
+
+.PHONY: test-custom
+test-custom: ## Run tests with custom args. Ex. make test-custom TEST_ARGS="-m 'not offline'"
+	@if [ -n "$(TEST_ARGS)" ]; then \
+  		$(ENV_COMMAND_TOOL) run nox -s test_custom -- -- $(CUSTOM_TEST_ARGS); \
+	else \
+	  	echo "" ; \
+    	echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \
+	  	echo "" ; \
+    	echo '            make test-custom TEST_ARGS="<custom-args>"' ; \
+	  	echo "" ; \
+    fi
\ No newline at end of file
diff --git a/.make/tests/test-script.sh b/.make/tests/test-script.sh
new file mode 100755
index 0000000..4536f5b
--- /dev/null
+++ b/.make/tests/test-script.sh
@@ -0,0 +1,244 @@
+#!/usr/bin/env bash
+
+SCRIPT_PATH="$(readlink -f "$0")"
+
+# Get the directory of the script
+SCRIPT_DIR="$(dirname "$SCRIPT_PATH")"
+MAKE_DIR="$(dirname "$SCRIPT_DIR")"
+PROJECT_DIR="$(dirname "$MAKE_DIR")"
+
+TEST_ENV="$PROJECT_DIR/.testvenv"
+PIPX_TEST_ENV="$PROJECT_DIR/.testvenvpipx"
+
+# Test base.make
+
+base() {
+  echo ""
+  echo "###"
+  echo "### Test base targets"
+  echo "###"
+  echo ""
+  echo "### Running 'make targets': ###"
+  echo ""
+  cd "$PROJECT_DIR" && make targets
+
+  echo "### Running 'make version': ###"
+  echo ""
+  cd "$PROJECT_DIR" && make version
+
+  # Test venv
+
+  echo ""
+  echo "### Running 'make venv-create' and 'make venv-remove: ###"
+  echo ""
+  (
+    cd "$PROJECT_DIR" && \
+    make VENV_PATH="$PROJECT_PATH.testvenv" venv-create && \
+    make VENV_PATH="$PROJECT_PATH.testvenv" AUTO_INSTALL=true venv-remove
+  )
+  # Versioning
+
+  echo ""
+  echo "### Running 'make bump' targets ###"
+  echo ""
+  (
+    cd "$PROJECT_DIR" && \
+    make bump-major dry && \
+    make bump-minor dry && \
+    make bump-patch dry
+  )
+}
+
+TEST_CONDA_ENV="lab-advanced-template-testing"
+MAKEFILE_ARGS_CONDA_OVERRIDE="-f $PROJECT_DIR/Makefile -f $PROJECT_DIR/.make/conda.make"
+conda(){
+  echo ""
+  echo "###"
+  echo "### Test conda targets"
+  echo "###"
+  echo ""
+  (
+    cd "$PROJECT_DIR" &&
+    make $MAKEFILE_ARGS_CONDA_OVERRIDE CONDA_ENVIRONMENT_FILE="$SCRIPT_DIR/test_environment.yml" CONDA_YES_OPTION="-y" conda-create-env && \
+    make $MAKEFILE_ARGS_CONDA_OVERRIDE conda-env-info && \
+    make $MAKEFILE_ARGS_CONDA_OVERRIDE CONDA_ENVIRONMENT="$TEST_CONDA_ENV" conda-activate && \
+    make $MAKEFILE_ARGS_CONDA_OVERRIDE CONDA_ENVIRONMENT="$TEST_CONDA_ENV" AUTO_INSTALL=true conda-poetry-install && \
+    make $MAKEFILE_ARGS_CONDA_OVERRIDE CONDA_ENVIRONMENT="$TEST_CONDA_ENV" AUTO_INSTALL=true conda-poetry-uninstall && \
+    make $MAKEFILE_ARGS_CONDA_OVERRIDE CONDA_ENVIRONMENT="$TEST_CONDA_ENV" AUTO_INSTALL=true conda-clean-env
+  )
+}
+
+MAKEFILE_ARGS_POETRY_OVERRIDE="-f $PROJECT_DIR/Makefile -f $PROJECT_DIR/.make/conda.make -f $PROJECT_DIR/.make/poetry.make"
+lint() {
+  echo ""
+  echo "###"
+  echo "### Test pipx poetry targets"
+  echo "###"
+  echo ""
+  (
+    cd "$PROJECT_DIR"  && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry poetry-create-env && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry install && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry check-lint && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry check-pylint && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry check-complexity && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry fix-lint && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry precommit && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry ruff && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry ruff-fix && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry ruff-format
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry AUTO_INSTALL=true poetry-remove-env
+  )
+}
+
+poetry(){
+  echo ""
+  echo "###"
+  echo "### Test Poetry managed and venv managed installs"
+  echo "###"
+  echo ""
+  (
+    cd "$PROJECT_DIR"  && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry poetry-create-env && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry install && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry AUTO_INSTALL=true poetry-remove-env && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=venv VENV_PATH="$TEST_ENV" install && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=venv VENV_PATH="$TEST_ENV" AUTO_INSTALL=true venv-remove
+  )
+  echo ""
+  echo "### Test conda managed installs"
+  echo ""
+  (
+    cd "$PROJECT_DIR" && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE CONDA_ENVIRONMENT_FILE="$SCRIPT_DIR/test_environment.yml" CONDA_YES_OPTION="-y" conda-create-env && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=conda CONDA_ENVIRONMENT="$TEST_CONDA_ENV" install && \
+    make $MAKEFILE_ARGS_POETRY_OVERRIDE CONDA_ENVIRONMENT="$TEST_CONDA_ENV" AUTO_INSTALL=true conda-clean-env
+  )
+
+}
+
+poetry-pipx(){
+  echo ""
+  echo "###"
+  echo "### Test pipx poetry targets"
+  echo "###"
+  echo ""
+  (
+    cd "$PROJECT_DIR" && \
+    make PIPX_VENV_PATH="$PIPX_TEST_ENV" poetry-install-venv && \
+    make PIPX_VENV_PATH="$PIPX_TEST_ENV" AUTO_INSTALL=true poetry-uninstall-venv && \
+    make poetry-install-venv
+  )
+}
+
+MAKEFILE_ARGS_UV_OVERRIDE="-f $PROJECT_DIR/Makefile -f $PROJECT_DIR/.make/uv.make"
+
+uv(){
+  echo ""
+  echo "###"
+  echo "### Test uv managed managed installs"
+  echo "###"
+  echo ""
+  (
+    cd "$PROJECT_DIR" && \
+    make $MAKEFILE_ARGS_UV_OVERRIDE AUTO_INSTALL=true uv-migrate-from-poetry && \
+    make $MAKEFILE_ARGS_UV_OVERRIDE uv-create-env && \
+    make $MAKEFILE_ARGS_UV_OVERRIDE AUTO_INSTALL=true install && \
+    make $MAKEFILE_ARGS_UV_OVERRIDE AUTO_INSTALL=true uv-remove-env && \
+    make $MAKEFILE_ARGS_UV_OVERRIDE AUTO_INSTALL=true uv-migrate-undo && \
+    rm -rf pyproject.toml.uv.backup
+  )
+}
+
+uv-pipx(){
+  echo ""
+  echo "###"
+  echo "### Test pipx uv pipx targets"
+  echo "###"
+  echo ""
+  (
+    cd "$PROJECT_DIR" && \
+    make $MAKEFILE_ARGS_UV_OVERRIDE PIPX_VENV_PATH="$PIPX_TEST_ENV" uv-install-venv && \
+    make $MAKEFILE_ARGS_UV_OVERRIDE PIPX_VENV_PATH="$PIPX_TEST_ENV" AUTO_INSTALL=true uv-uninstall-venv && \
+    make $MAKEFILE_ARGS_UV_OVERRIDE uv-install-venv
+  )
+}
+
+all() {
+  base
+  conda
+  lint
+  poetry
+}
+
+list () {
+    echo
+    echo "!!! Do not run this script outside of the 'lab-advanced-template' repository."
+    echo "This script exists only to test the makefiles for integrity when adding or"
+    echo "modifying targets !!!"
+    echo
+    echo " List of available tests:"
+    echo
+    echo "    - base   : Test 'base' targets"
+    echo "    - conda  : Test 'conda' targets"
+    echo "    - lint   : Test 'linting' targets"
+    echo "    - poetry : Test 'poetry' targets"
+    echo "    - poetry-pipx : Test 'poetry' targets related to pipx"
+    echo "    - uv : Test 'uv' targets"
+    echo "    - uv-pipx : Test 'uv' targets related to pipx"
+    echo "    - test   : Test 'test' targets"
+
+    echo
+    echo " Full test suite"
+    echo
+    echo "    - all    : Run most tests, except 'poetry-pipx'"
+    echo
+
+}
+
+if [[ "$#" -eq 0 ]]; then
+    list
+fi
+
+for var in "$@"
+do
+    # Order is set according to use, not alphabetical order
+    case "$var" in
+        "list")
+            list
+            ;;
+        "base")
+            base
+            ;;
+        "conda")
+            conda
+            ;;
+        "lint")
+            lint
+            ;;
+        "poetry")
+            poetry
+            ;;
+        "poetry-pipx")
+            poetry-pipx
+            ;;
+        "uv")
+            uv
+            ;;
+        "uv-pipx")
+            uv-pipx
+            ;;
+        "all")
+            all
+            ;;
+        *)
+            echo "* * * * * * * * * * * * * * * * * * * * * * * * * "
+            echo "* ""$var"" is not a valid input "
+            echo "* Use the list command to see available inputs"
+            echo "* * * * * * * * * * * * * * * * * * * * * * * * *"
+            echo
+            list
+            echo
+            exit 1
+    esac
+done
\ No newline at end of file
diff --git a/.make/tests/test_environment.yml b/.make/tests/test_environment.yml
new file mode 100644
index 0000000..3cd99a6
--- /dev/null
+++ b/.make/tests/test_environment.yml
@@ -0,0 +1,6 @@
+name: lab-advanced-template-testing
+channels:
+  - conda-forge
+dependencies:
+  - python=3.11
+
diff --git a/.make/uv.make b/.make/uv.make
new file mode 100644
index 0000000..43eae1c
--- /dev/null
+++ b/.make/uv.make
@@ -0,0 +1,312 @@
+# Project and Private variables and targets import to override variables for local
+# This is to make sure, sometimes the Makefile includes don't work.
+
+## -- UV targets ------------------------------------------------------------------------------------------------ ##
+ENV_COMMAND_TOOL := uv
+
+.PHONY: uv-install-auto
+uv-install-auto:
+	uv --version; \
+	if [ $$? != "0" ]; then \
+		@make -s uv-install-venv; \
+	fi;
+
+.PHONY: uv-install
+uv-install: ## Install uv interactively.
+	@echo "Looking for uv version...";\
+	uv --version; \
+	if [ $$? != "0" ]; then \
+		if [ "$(AUTO_INSTALL)" = "true" ]; then \
+			ans="y";\
+		else \
+			echo "uv not found..."; \
+			echo "Looking for pipx version...";\
+			pipx_found=0; \
+			pipx --version; \
+				if [ $$? != "0" ]; then \
+					pipx_found=1; \
+					echo "pipx not found..."; \
+					echo""; \
+					echo -n "Would you like to install pipx and uv? [y/N]: "; \
+				else \
+					echo""; \
+					echo -n "Would you like to install uv using pipx? [y/N]: "; \
+				fi; \
+			read ans; \
+		fi; \
+		case $$ans in \
+			[Yy]*) \
+				if [ $$pipx_found == "1" ]; then \
+					echo""; \
+					echo -e "\e[1;39;41m-- WARNING --\e[0m The following pip has been found and will be used to install pipx: "; \
+					echo "    -> "$$(which pip); \
+					echo""; \
+					echo "If you do not have write permission to that environment, using it to install pipx will fail."; \
+					echo "If this is the case, you should install pipx using a virtual one."; \
+					echo""; \
+					echo "See documentation for more information."; \
+					echo""; \
+					echo -n "Would you like to use the local available pip above, or create virtual environment to install pipx? [local/virtual]: "; \
+					read ans_how; \
+					case $$ans_how in \
+						"LOCAL" | "Local" |"local") \
+							make -s uv-install-local; \
+							;; \
+						"VIRTUAL" | "Virtual" | "virtual") \
+							make -s uv-install-venv; \
+							;; \
+						*) \
+							echo ""; \
+							echo -e "\e[1;39;41m-- WARNING --\e[0m Option $$ans_how not found, exiting process."; \
+							echo ""; \
+							exit 1; \
+					esac; \
+				else \
+					echo "Installing uv"; \
+					make -s _pipx_install_uv; \
+				fi; \
+				;; \
+			*) \
+				echo "Skipping installation."; \
+				echo " "; \
+				;; \
+		esac; \
+	fi;
+
+.PHONY: _pipx_install_uv
+_pipx_install_uv:
+	@pipx install uv
+
+
+PIPX_VENV_PATH := $$HOME/.pipx_venv
+.PHONY: uv-install-venv
+uv-install-venv: ## Install standalone uv. Will install pipx in $HOME/.pipx_venv
+	@pipx --version; \
+	if [ $$? != "0" ]; then \
+		echo "Creating virtual environment using venv here : [$(PIPX_VENV_PATH)]"; \
+		python3 -m venv $(PIPX_VENV_PATH); \
+		echo "Activating virtual environment [$(PIPX_VENV_PATH)]"; \
+		source $(PIPX_VENV_PATH)/bin/activate; \
+		pip3 install pipx; \
+		pipx ensurepath; \
+		source $(PIPX_VENV_PATH)/bin/activate && make -s _pipx_install_uv ; \
+	else \
+		make -s _pipx_install_uv ; \
+	fi;
+
+.PHONY: uv-install-local
+uv-install-local: ## Install standalone uv. Will install pipx with locally available pip.
+	@pipx --version; \
+	if [ $$? != "0" ]; then \
+		echo "pipx not found; installing pipx"; \
+		pip3 install pipx; \
+		pipx ensurepath; \
+	fi;
+	@echo "Installing UV"
+	@make -s _pipx_install_uv
+
+.PHONY: uv-create-env
+uv-create-env: ## Create a virtual environment for uv, using the project's python version.
+	@uv python install $(PYTHON_VERSION)
+	@uv venv --python $(PYTHON_VERSION)
+
+.PHONY: uv-activate
+uv-activate: ## Print out the shell command to activate the project's uv environment.
+	@make -s venv-activate
+
+.PHONY: uv-remove-env
+uv-remove-env: ## Remove current project's uv managed environment.
+	@make -s venv-remove
+
+.PHONY: uv-uninstall
+uv-uninstall: uv-remove-env ## Uninstall pipx-installed uv and the created environment
+	@if [ "$(AUTO_INSTALL)" = "true" ]; then \
+		ans="y";\
+	else \
+		echo""; \
+		echo -n "Would you like to uninstall pipx-installed uv? [y/N]: "; \
+		read ans; \
+	fi; \
+	case $$ans in \
+		[Yy]*) \
+			pipx --version ; \
+			if [ $$? != "0" ]; then \
+				echo "" ; \
+				echo "Pipx not found globally, trying with $(PIPX_VENV_PATH) env" ;\
+				echo "" ; \
+				source $(PIPX_VENV_PATH)/bin/activate && pipx uninstall uv ; \
+			else \
+				pipx uninstall uv ; \
+				fi; \
+			;; \
+		*) \
+			echo "Skipping uninstallation."; \
+			echo " "; \
+			;; \
+	esac; \
+
+.PHONY: uv-uninstall-pipx
+uv-uninstall-pipx: uv-remove-env ## Uninstall pipx-installed uv, the created uv environment and pipx
+	@if [ "$(AUTO_INSTALL)" = "true" ]; then \
+		ans="y";\
+	else \
+		echo""; \
+		echo -n "Would you like to uninstall pipx-installed uv and pipx? [y/N]: "; \
+		read ans; \
+	fi; \
+	case $$ans in \
+		[Yy]*) \
+			pipx --version ; \
+			if [ $$? != "0" ]; then \
+				echo "" ; \
+				echo "Pipx not found globally, trying with $(PIPX_VENV_PATH) env" ;\
+				echo "" ; \
+				source $(PIPX_VENV_PATH)/bin/activate && pipx uninstall uv && pip uninstall -y pipx; \
+			else \
+				pipx uninstall uv ; \
+				pip uninstall -y pipx ;\
+				fi; \
+			;; \
+		*) \
+			echo "Skipping uninstallation."; \
+			echo " "; \
+			;; \
+	esac; \
+
+.PHONY: uv-uninstall-venv
+uv-uninstall-venv: uv-remove-env ## Uninstall pipx-installed uv, the created uv environment, pipx and $HOME/.pipx_venv
+	@if [ "$(AUTO_INSTALL)" = "true" ]; then \
+		ans="y";\
+	else \
+		echo""; \
+		echo -n "Would you like to uninstall pipx-installed uv and pipx? [y/N]: "; \
+		read ans; \
+	fi; \
+	case $$ans in \
+		[Yy]*) \
+			(source $(PIPX_VENV_PATH)/bin/activate && pipx uninstall uv); \
+			(source $(PIPX_VENV_PATH)/bin/activate && pip uninstall -y pipx); \
+			;; \
+		*) \
+			echo "Skipping uninstallation."; \
+			echo " "; \
+			;; \
+	esac; \
+
+	@if [ "$(AUTO_INSTALL)" = "true" ]; then \
+		ans="y";\
+	else \
+		echo""; \
+		echo -n "Would you like to remove the virtual environment located here : [$(PIPX_VENV_PATH)] ? [y/N]: "; \
+		read ans; \
+	fi; \
+	case $$ans in \
+		[Yy]*) \
+			rm -r $(PIPX_VENV_PATH); \
+			;; \
+		*) \
+			echo "Skipping [$(PIPX_VENV_PATH)] virtual environment removal."; \
+			echo ""; \
+			;; \
+	esac; \
+
+PHONY: uv-migrate-from-poetry
+uv-migrate-from-poetry: ## Migrate the project's default poetry 'pyproject.toml' to uv.
+	@if [ "$(AUTO_INSTALL)" = "true" ]; then \
+		ans="y";\
+	else \
+		echo""; \
+		echo -n "Would you like to convert your current pyproject.toml file to use uv instead of poetry ? [y/N]: "; \
+		read ans; \
+	fi; \
+	case $$ans in \
+		[Yy]*) \
+		  	echo "Creating backup copy of current pyproject.toml file"; \
+		  	cp pyproject.toml pyproject.toml.poetry.backup ; \
+		  	echo "Migrating pyproject.toml file to use uv"; \
+			uvx migrate-to-uv --dependency-groups-strategy keep-existing; \
+			if [ -e pyproject.toml.uv.backup ]; then \
+				echo "pyproject.toml.uv.backup file found. Proceeding to delete it."; \
+			  	rm pyproject.toml.uv.backup ; \
+			fi; \
+			;; \
+		*) \
+			echo "Skipping pyproject.toml migration."; \
+			echo ""; \
+			;; \
+	esac; \
+
+PHONY: uv-migrate-undo
+uv-migrate-undo: ## Undo previous migration of the project's default poetry 'pyproject.toml' to uv.
+	@if [ "$(AUTO_INSTALL)" = "true" ]; then \
+		ans="y";\
+	else \
+		echo""; \
+		echo -n "Would you like to revert your current pyproject.toml file to use the previous backup of the file ? [y/N]: "; \
+		read ans; \
+	fi; \
+	case $$ans in \
+		[Yy]*) \
+		  	echo "Checking if backup pyproject.toml file exists"; \
+		  	if [ -e "$(PROJECT_PATH)/pyproject.toml.poetry.backup" ]; then \
+		  	  	echo "Backup file found"; \
+		  	  	echo "Making backup of current uv pyproject.toml"; \
+				cp "$(PROJECT_PATH)/pyproject.toml" "$(PROJECT_PATH)/pyproject.toml.uv.backup"  ; \
+		  	  	echo "Reverting pyproject.toml file to previous poetry backup."; \
+				cp "$(PROJECT_PATH)pyproject.toml.poetry.backup" "$(PROJECT_PATH)/pyproject.toml"  ; \
+		  	  	echo "Removing previous poetry backup."; \
+				rm "$(PROJECT_PATH)/pyproject.toml.poetry.backup" ; \
+		  	  	echo "Removing uv.lock file."; \
+				rm "$(PROJECT_PATH)/uv.lock" ; \
+			else \
+				echo ""; \
+				echo "Backup file not found. Skipping migration undo"; \
+			fi; \
+			;; \
+		*) \
+			echo "Skipping pyproject.toml migration."; \
+			echo ""; \
+			;; \
+	esac; \
+
+
+## -- Install targets (All install targets will install uv if not found using 'make uv-install-auto')---------------- ##
+.PHONY: _remind-env-activate
+_remind-env-activate:
+	@echo ""
+	@echo "Activate your environment using the following command:"
+	@echo ""
+	@make -s uv-activate
+	@echo ""
+	@echo "You can also use the following command line to interact with the environment"
+	@echo ""
+	@echo "  $$ uv run <command>"
+	@echo ""
+
+.PHONY: install
+install: install-precommit ## Install the application package, developer dependencies and pre-commit hook
+
+.PHONY: install-precommit
+install-precommit: install-dev ## Install the pre-commit hooks (also installs developer dependencies)
+	@if [ -f .git/hooks/pre-commit ]; then \
+		echo "Pre-commit hook found"; \
+	else \
+	  	echo "Pre-commit hook not found, proceeding to configure it"; \
+		$(ENV_COMMAND_TOOL) run pre-commit install; \
+	fi;
+
+.PHONY: install-dev
+install-dev: uv-install-auto ## Install the application along with developer dependencies
+	@uv sync --group dev
+	@make -s _remind-env-activate
+
+.PHONY: install-with-lab
+install-with-lab: uv-install-auto ## Install the application and it's dev dependencies, including Jupyter Lab
+	@uv --group dev --group lab
+	@make -s _remind-env-activate
+
+
+.PHONY: install-package
+install-package: uv-install-auto ## Install the application package only
+	@uv sync
+	@make -s _remind-env-activate
diff --git a/CHANGES.md b/CHANGES.md
index 413146e..f09b30e 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,6 +1,6 @@
 # CHANGES.md
 
-[Unreleased](https://github.com/RolnickLab/geospatial-tools/tree/main) (latest)
+## [Unreleased](https://github.com/RolnickLab/geospatial-tools/tree/main) (latest)
 
 ______________________________________________________________________
 
@@ -9,25 +9,25 @@ ______________________________________________________________________
 - Update the project dependencies
 - Add new QA tools : `autoflake`, `autopep8` and `ruff`
 
-[0.1.3](https://github.com/RolnickLab/geospatial-tools/tree/0.1.3) (2024-09-23)
+## [0.1.3](https://github.com/RolnickLab/geospatial-tools/tree/0.1.3) (2024-09-23)
 
 ______________________________________________________________________
 
 - Convert project to use `nox` instead of `tox` for cluster storage optimization.
 
-[0.1.2](https://github.com/RolnickLab/geospatial-tools/tree/0.1.2) (2024-09-23)
+## [0.1.2](https://github.com/RolnickLab/geospatial-tools/tree/0.1.2) (2024-09-23)
 
 ______________________________________________________________________
 
 - Fix `docformatter` with missing extra dependency for use with `pyproject.toml`
 
-[0.1.1](https://github.com/RolnickLab/geospatial-tools/tree/0.1.1) (2024-09-20)
+## [0.1.1](https://github.com/RolnickLab/geospatial-tools/tree/0.1.1) (2024-09-20)
 
 ______________________________________________________________________
 
 - Fix `black` dependency that was not correctly setup in dev dependency group
 
-[0.1.0](https://github.com/RolnickLab/geospatial-tools/tree/0.1.0) (2024-09-20)
+## [0.1.0](https://github.com/RolnickLab/geospatial-tools/tree/0.1.0) (2024-09-20)
 
 ______________________________________________________________________
 
diff --git a/Makefile b/Makefile
index 1bc3994..7ca3c48 100644
--- a/Makefile
+++ b/Makefile
@@ -1,19 +1,48 @@
 ########################################################################################
 #
-# DO NOT MODIFY!!!
+# MODIFY WITH CARE!!!
 # If necessary, override the corresponding variable and/or target, or create new ones
 # in one of the following files, depending on the nature of the override :
 #
 # `Makefile.variables`, `Makefile.targets` or `Makefile.private`,
 #
-# The only valid reason to modify this file is to fix a bug or to add new
+# The only valid reason to modify this file is to fix a bug or to add/remove
 # files to include.
+#
+# REMEMBER!!!
+# This is a project level config, any changes here will affect all other users
+#
 ########################################################################################
-
-#Include base makefile
+#
+# Necessary make files
+#
 include .make/base.make
-# Include custom targets and variables
+
+#
+# Optional makefiles - Comment/uncomment the targets you want for the project
+#
+## Conda targets
+include .make/conda.make
+
+## Poetry targets - !!! If using Poetry, you should comment out the UV file below and consider
+## if you need the conda file above !!!
+include .make/poetry.make
+
+## UV targets - !!! If using UV, you should comment out the poetry file above, and possibly the conda file too !!!
+#include .make/uv.make
+
+## Linting targets
+include .make/lint.make
+
+## Test related targets
+include .make/test.make
+
+#
+# Project related makefiles
+#
+## Custom targets and variables
 -include Makefile.targets
 -include Makefile.variables
-# Private variables and targets import to override variables for local
+
+## Private variables and targets import to override variables for local
 -include Makefile.private
diff --git a/docs/conda_environment_creation.md b/docs/conda_environment_creation.md
index d6479d4..9ce51ef 100644
--- a/docs/conda_environment_creation.md
+++ b/docs/conda_environment_creation.md
@@ -66,4 +66,4 @@ You can also use the eval command to activate the environment:
 
 ```shell
 eval $(make conda-activate)
-```
\ No newline at end of file
+```
diff --git a/docs/environment_creation_drac.md b/docs/environment_creation_drac.md
index 03d7b8a..6b2956d 100644
--- a/docs/environment_creation_drac.md
+++ b/docs/environment_creation_drac.md
@@ -71,10 +71,10 @@ virtualenv <PATH_TO_ENV>
 
 ### The three choices
 
-* Limit yourself exclusively to DRAC's pre-built wheels, and code anything that's
+- Limit yourself exclusively to DRAC's pre-built wheels, and code anything that's
   missing yourself.
-* Don't use pre-build wheels at all
-* Use a mix of the 2.
+- Don't use pre-build wheels at all
+- Use a mix of the 2.
 
 The first 2 are pretty straight forward, but using a mix of dependency sources will
 require careful tracking and documentation.
@@ -103,13 +103,13 @@ document the versions in a way that users outside DRAC can still use your code.
 For example, the requests library
 *as of July 24th, 2024*
 
-* Version available on DRAC : `2.31.0`
-* Full version (what we see with `pip list`) : `requests==2.31.0+computecanada`
-    * This version is not available outside DRAC
-* How to add it to the pyproject.toml:
-    * If not on DRAC, you can use poetry to add it using `poetry add requests~2.31.0`
-    * If on DRAC, add it manually to the pyproject.toml file under the `[tool.poetry.dependencies]` section :
-      `requests = "~2.31.0"`
+- Version available on DRAC : `2.31.0`
+- Full version (what we see with `pip list`) : `requests==2.31.0+computecanada`
+  - This version is not available outside DRAC
+- How to add it to the pyproject.toml:
+  - If not on DRAC, you can use poetry to add it using `poetry add requests~2.31.0`
+  - If on DRAC, add it manually to the pyproject.toml file under the `[tool.poetry.dependencies]` section :
+    `requests = "~2.31.0"`
 
 This will help ensure reproducibility between environments even when using pre-built
 wheel versions of Python dependencies.
diff --git a/docs/environment_creation_mila.md b/docs/environment_creation_mila.md
index 4ed0936..bbc6e37 100644
--- a/docs/environment_creation_mila.md
+++ b/docs/environment_creation_mila.md
@@ -22,10 +22,9 @@ virtualenv <PATH_TO_ENV>
 ```
 
 where `<PATH_TO_ENV>` is the path where the environment will be created. It normally
-should be inside your project's folder (but ignored by git), and commonly named `
-`.venv`. 
+should be inside your project's folder (but ignored by git), and commonly named ` `.venv\`.
 
-* _On a side note, `.env` is generally reserved for a text file listing 
+- _On a side note, `.env` is generally reserved for a text file listing
   environment variables, used by various tools like `python-dotenv` and `docker compose`_
 
 You can also make use of the following makefile targets:
diff --git a/docs/makefile_environment_targets.md b/docs/makefile_environment_targets.md
index 7a90ba7..aefaedf 100644
--- a/docs/makefile_environment_targets.md
+++ b/docs/makefile_environment_targets.md
@@ -116,7 +116,7 @@ make poetry-remove-env
 Information about the currently active environment used by Poetry,
 whether Conda or Poetry, can be seen using:
 
-```shell 
+```shell
 poetry-env-info
 ```
 
diff --git a/docs/nox_session_descriptions.md b/docs/nox_session_descriptions.md
index 7c4eb96..6dc10eb 100644
--- a/docs/nox_session_descriptions.md
+++ b/docs/nox_session_descriptions.md
@@ -16,22 +16,25 @@ the following syntax:
 nox -s <session_name>
 ```
 
-* Main `nox` sessions:
-    * No session specified; executing `nox` : Runs the pre-commit configuration
-    * `check` Runs all checks on the code base without modifying the code
-    * `fix` : Runs the autoflake, autopep8, black, isort, docformatter and flynt tools on the code base
-    * `flake8` : Runs the `flake8` linter
-    * `autoflake` : Run the `autoflake` lint fixer to remove unused imports and variables
-    * `autopep8` : Run the `autopep8` lint fixer to automatically fix most other `flake8` warnings
-    * `black` : Runs the code formatter
-    * `isort` : Runs the import sorter
-    * `flynt` : Runs the `f-string formatter
-    * `docformatter` : Runs the docstring formatter
-    * `test` : Runs tests found in the `tests/` folder with `pytest`
-
-* `ruff` - Experimental sessions:
-    * `ruff-lint` : Check lint using the `ruff` linter. This linter is stricter
-      than `flake8`, but less than `pylint`
-    * `ruff-fix` : Check lint using the `ruff` linter and automatically fix the
-      warnings that can be fixed by `ruff`
-    * `ruff-format` : Format the code using the `ruff` formatter
\ No newline at end of file
+- Main `nox` sessions:
+
+  - No session specified; executing `nox` : Runs the pre-commit configuration
+  - `check` Runs all checks on the code base without modifying the code
+  - `fix` : Runs the autoflake, autopep8, black, isort, docformatter and flynt tools on the code base
+  - `flake8` : Runs the `flake8` linter
+  - `autoflake` : Run the `autoflake` lint fixer to remove unused imports and variables
+  - `autopep8` : Run the `autopep8` lint fixer to automatically fix most other `flake8` warnings
+  - `black` : Runs the code formatter
+  - `isort` : Runs the import sorter
+  - `flynt` : Runs the `f-string` formatter
+  - `mdformat` : Runs the markdown formatter
+  - `docformatter` : Runs the docstring formatter
+  - `test` : Runs tests found in the `tests/` folder with `pytest`
+
+- `ruff` - Experimental sessions:
+
+  - `ruff-lint` : Check lint using the `ruff` linter. This linter is stricter
+    than `flake8`, but less than `pylint`
+  - `ruff-fix` : Check lint using the `ruff` linter and automatically fix the
+    warnings that can be fixed by `ruff`
+  - `ruff-format` : Format the code using the `ruff` formatter
diff --git a/docs/poetry_documentation.md b/docs/poetry_documentation.md
index dcc7273..1ed2612 100644
--- a/docs/poetry_documentation.md
+++ b/docs/poetry_documentation.md
@@ -11,7 +11,7 @@ Newer versions of `poetry`, `>=2.0.0` are raising errors when trying to
 resolve dependencies when installing projects and adding new dependencies.
 
 If you encounter such issues, please try reinstalling `poetry` at a lesser version:
-`pipx install 'poetry<2.0.0', or newer, non-computecanada versions if available.
+`pipx install 'poetry<2.0.0'`, or newer, non-computecanada versions if available.
 
 ### Poetry Cache Management
 
@@ -77,4 +77,4 @@ When installing a project:
 
 ```bash
 poetry install --no-cache
-```
\ No newline at end of file
+```
diff --git a/docs/uv_documentation.md b/docs/uv_documentation.md
new file mode 100644
index 0000000..083e647
--- /dev/null
+++ b/docs/uv_documentation.md
@@ -0,0 +1,291 @@
+# UV
+
+`uv` is an alternative tool for dependency management, like `poetry` and `conda`.
+It is blazingly fast and also comes with the possibility of easily getting access to
+other versions of Python without tools like `pyenv`.
+
+However, using `conda` together with `uv` can be very cumbersome and is not really recommended,
+as the most useful dependency management features of `uv` will not work. If you really
+want to use `uv` together with `conda`, see [using uv-pip](#note-about-using-pip-with-uv)
+
+Therefore, if you require binary dependencies from `conda` (non-python dependencies likes
+`cdo`, for example), it is recommended to use the classic `poetry` version of this
+template, unless you have other ways of installing those dependencies.
+
+This README is a quick and concise guide to get you started. Reading the
+[official documentation](https://docs.astral.sh/uv/) is wholeheartedly recommended, as
+you'll find yourself rapidly limited in what you can do.
+
+## Getting started.
+
+The only thing you have to do is start your project off from the template, like
+[described here](https://github.com/RolnickLab/lab-basic-template/blob/main/README.md#initialization),
+and then replace the contents of the
+`pyproject.toml` file with the one present in this branch.
+
+## Install UV
+
+`uv` first needs to be installed.
+
+The recommended way to install `uv` is with `pipx`.
+
+On your personal computer, you can do the following:
+
+```shell
+pip install pipx
+pipx ensurepath
+pipx install uv
+```
+
+On compute clusters, like Mila and DRAC, you won't be able to use the default pip
+available after loading a python module.
+
+You will first need to create and activate a base virtual environment in which you have
+write access.
+
+For example, on the Mila cluster:
+
+```
+module load python/3.10
+python3 -m venv ~/.pipx_env
+source ~/.base_env/bin/activate
+```
+
+Next, `pipx` and `uv` can be installed using this new virtual environment's `pip`:
+
+```
+pip install pipx
+pipx ensurepath
+pipx install uv
+```
+
+The `pipx` way is pretty straightforward, but you can also install `uv`
+many other ways, which are documented here:
+[uv installation methods](https://docs.astral.sh/uv/getting-started/installation/#installation-methods)
+
+## Setting up your environment
+
+First download the version of python you want for your environment with `uv`:
+
+```shell
+# As an example, here is for python 3.12
+uv python install 3.12
+```
+
+Then create your environment:
+
+```shell
+uv venv --python 3.12
+```
+
+### DRAC problems with uv venv
+
+Creating an environment using `uv` on DRAC can create problems, most probably because
+of the custom indexing and python wheels (exact reason has not been confirmed yet).
+
+On the DRAC cluster, it is therefore preferred to load the python module and then create the environment
+manually:
+
+```shell
+module load python/3.12
+virtualenv --no-download .venv
+source .venv/bin/activate
+```
+
+## Using uv with the makefile
+
+First, make sure that the `uv` targets are activated, and that the `poetry` targets
+are commented out in the [Makefile](../Makefile) main file.
+
+To install `uv` on your system:
+
+```shell
+make uv-install
+```
+
+To create a new virtual environment:
+
+```shell
+make uv-create-env
+```
+
+To see the required command to activate your new environment:
+
+```shell
+make uv-activate
+```
+
+To migrate a `poetry` `pyproject.toml` file to uv:
+
+```shell
+make uv-migrate-from-poetry
+```
+
+For more information, see the `uv` target description with the following command:
+
+```shell
+make targets
+```
+
+To install the application:
+
+```shell
+make install
+```
+
+## Installing and managing dependencies manually
+
+To first install the dependencies, after creating and activating the environment:
+
+```shell
+uv sync
+```
+
+To install the dev dependencies:
+
+```shell
+uv sync --group dev
+```
+
+To add a dependency:
+
+```shell
+uv add <dependency-name>
+```
+
+To add a dependency to the dev group:
+
+```shell
+uv add --group dev <dependency-name>
+```
+
+For more information about managing dependencies with `uv`, see the following
+documentation [Managing dependencies with uv](https://docs.astral.sh/uv/guides/projects/#managing-dependencies)
+
+### Installing DRAC custom wheels
+
+To install dependencies like described in the
+[DRAC documentation](https://docs.alliancecan.ca/wiki/Python#Creating_and_using_a_virtual_environment),
+you can use the `--offline` flag, with either `sync` or `add`.
+
+Ex:
+
+```shell
+uv sync --offline
+```
+
+You should also consider updating your `pyproject.toml` file with the following:
+
+```toml
+[tool.uv]
+python-preference = "system"
+
+## From https://docs.astral.sh/uv/reference/settings/#index-strategy:
+## "Only use results from the first index that returns a match for a given package name."
+## In other words: only get the package from PyPI if there isn't a version of it in the DRAC wheelhouse.
+# index-strategy = "first-index"
+
+## "Search for every package name across all indexes, exhausting the versions from the first index before
+##  moving on to the next"
+## In other words: Only get the package from PyPI if the requested version is higher than the version
+## in the DRAC wheelhouse.
+# index-strategy = "unsafe-first-match"
+
+## "Search for every package name across all indexes, preferring the "best" version found.
+##  If a package version is in multiple indexes, only look at the entry for the first index."
+## In other words: Consider all versions of the package DRAC + PyPI, and use the version that best matches
+## the requested version. In a tie, choose the DRAC wheel.
+index-strategy = "unsafe-best-match"
+
+[[tool.uv.index]]
+name = "drac-gentoo2023-x86-64-v3"
+url = "/cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo2023/x86-64-v3"
+format = "flat"
+
+[[tool.uv.index]]
+name = "drac-gentoo2023-generic"
+url = "/cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo2023/generic"
+format = "flat"
+
+[[tool.uv.index]]
+name = "drac-generic"
+url = "/cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic"
+format = "flat"
+```
+
+### Note about using pip with uv
+
+While it is possible to use `pip`, you should try to avoid it when possible, for two reasons:
+
+- If you do have to use `pip`, you should always use `uv pip`, as you will benefit
+  from `uv`'s speed. Moreover, you could have another active `pip`, even if your `.venv` has
+  been sourced; which will cause your use of `pip` to interact with another environment.
+- Using `uv pip` does not update the `pyproject.toml` file, and does not update OR use
+  the `uv.lock` file, which means you have to set your dependencies manually.
+
+This last point is not necessarily a dealbreaker, and in some situations it might even
+be necessary, like if you want to use `uv` with existing repositories that use
+`requirements.txt` files.
+
+You will, however, lose one of the most powerful features of `uv` that ensures your
+environment is easily reproducible.
+
+One more thing that is **very important** to note:
+
+`uv pip` will always interact with the **active**
+**environment**. This means that if you have your `.venv` environment in your repository,
+but you also have, say, the base `conda` environment active, `uv pip` will interact
+with the `conda` environment.
+
+This is one way of working with both `conda` and `uv`,
+but like mentioned above, you lose the ability to automatically manage your
+`pyproject.toml` file and won't be able to use `uv.lock` file.
+
+Consult the documentation to learn more about [uv's pip interfare](https://docs.astral.sh/uv/pip/).
+
+## Using uv
+
+To list the installed dependencies:
+
+```shell
+uv pip list
+```
+
+If you have sourced your `.venv`, you can use `python` and other tools through the
+command line like you are used to.
+
+You can also use the `uv run` command instead. Without the need to
+manually source your `.venv` folder, this command allows access to your environment and
+the installed dependencies - This is already taken into account in the Makefile targets:
+
+```shell
+# Execute a python script
+uv run python scripts/my_python_script.py
+```
+
+```shell
+# Execute the pre-commit check
+uv run pre-commit run --all-files
+```
+
+For the development tool `nox`, you still have to be at the root of the repository, as
+the command requires the presence of the `noxfile.py`:
+
+```shell
+# Don't forget to install the dev dependencies first with
+# uv sync --group dev
+
+uv run nox -s ruff-lint
+```
+
+## Converting to UV from poetry manually
+
+You can easily convert your current `poetry` pyproject.toml file to `uv` with the following commands:
+
+```shell
+echo "Creating backup copy of current pyproject.toml file"
+cp pyproject.toml pyproject.toml.poetry.backup 
+
+echo "Migrating pyproject.toml file to use uv"
+uvx migrate-to-uv --dependency-groups-strategy keep-existing
+```
diff --git a/noxfile.py b/noxfile.py
index 21a8f7c..d89ca63 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -95,6 +95,7 @@ def fix(session):
         *paths["all"],
         external=True,
     )
+    session.run("mdformat", *paths["root"], external=True)
 
 
 @nox.session()
@@ -132,6 +133,12 @@ def flynt(session):
     session.run("flynt", *paths["all"], external=True)
 
 
+@nox.session()
+def mdformat(session):
+    paths = get_paths(session)
+    session.run("mdformat", *paths["root"], external=True)
+
+
 @nox.session(name="ruff-lint")
 def ruff_lint(session):
     paths = get_paths(session)
diff --git a/pyproject.toml b/pyproject.toml
index 549913e..0f600f4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -78,19 +78,21 @@ serialize = [
 [[tool.bumpversion.files]]
 filename = "CHANGES.md"
 search = '''
-[Unreleased](https://github.com/RolnickLab/geospatial-tools/tree/main) (latest)
+## [Unreleased](https://github.com/RolnickLab/geospatial-tools/tree/main) (latest)
 
-______________________________________________________________________'''
+______________________________________________________________________
+'''
 replace = '''
-[Unreleased](https://github.com/RolnickLab/geospatial-tools/tree/main) (latest)
+## [Unreleased](https://github.com/RolnickLab/geospatial-tools/tree/main) (latest)
 
 ______________________________________________________________________
 
-[//]: # (New changes here in list form)
+<!-- (New changes here in list form) -->
 
-[{new_version}](https://github.com/RolnickLab/geospatial-tools/tree/{new_version}) ({utcnow:%Y-%m-%d})
+## [{new_version}](https://github.com/RolnickLab/geospatial-tools/tree/{new_version}) ({utcnow:%Y-%m-%d})
 
-______________________________________________________________________'''
+______________________________________________________________________
+'''
 
 [[tool.bumpversion.files]]
 filename = "pyproject.toml"

From 37cac8a6c7370a853d9372712e3ba4b3d080713d Mon Sep 17 00:00:00 2001
From: f-PLT <fplt.softwaredeveloper@gmail.com>
Date: Wed, 17 Sep 2025 16:16:37 -0400
Subject: [PATCH 19/19] Update from makefile project

---
 .make/.bumpversion.toml   |  8 ++++----
 .make/CHANGES_MAKEFILE.md |  6 ++++++
 .make/Makefile            |  2 +-
 .make/base.make           |  2 +-
 .make/lint.make           | 18 +++++++++---------
 .make/poetry.make         |  2 +-
 .make/test.make           |  8 ++++----
 .make/uv.make             |  4 ++--
 Makefile.private.example  | 20 +++++++++++++-------
 Makefile.targets          |  2 +-
 10 files changed, 42 insertions(+), 30 deletions(-)

diff --git a/.make/.bumpversion.toml b/.make/.bumpversion.toml
index 4be7e96..dbfd1e4 100644
--- a/.make/.bumpversion.toml
+++ b/.make/.bumpversion.toml
@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.7.0"
+current_version = "0.7.1"
 commit = true
 message = "Makefile version {new_version} released."
 tag = true
@@ -12,18 +12,18 @@ serialize = [
 [[tool.bumpversion.files]]
 filename = "CHANGES_MAKEFILE.md"
 search = '''
-[Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest)
+## [Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest)
 
 ______________________________________________________________________
 '''
 replace = '''
-[Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest)
+## [Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest)
 
 ______________________________________________________________________
 
 <!-- (New changes here in list form) -->
 
-[{new_version}](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-{new_version}) ({utcnow:%Y-%m-%d})
+## [{new_version}](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-{new_version}) ({utcnow:%Y-%m-%d})
 
 ______________________________________________________________________
 '''
diff --git a/.make/CHANGES_MAKEFILE.md b/.make/CHANGES_MAKEFILE.md
index 2e18b06..c20049d 100644
--- a/.make/CHANGES_MAKEFILE.md
+++ b/.make/CHANGES_MAKEFILE.md
@@ -6,6 +6,12 @@ ______________________________________________________________________
 
 <!-- (New changes here in list form) -->
 
+## [0.7.1](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.7.1) (2025-09-17)
+
+______________________________________________________________________
+
+<!-- (New changes here in list form) -->
+
 ## [0.7.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.7.0) (2025-09-10)
 
 ______________________________________________________________________
diff --git a/.make/Makefile b/.make/Makefile
index fe5e88e..293b7f5 100644
--- a/.make/Makefile
+++ b/.make/Makefile
@@ -10,7 +10,7 @@
 # files to include.
 ########################################################################################
 PROJECT_PATH := $(dir $(abspath $(firstword $(MAKEFILE_LIST))))
-MAKEFILE_VERSION := 0.7.0
+MAKEFILE_VERSION := 0.7.1
 BUMP_TOOL := bump-my-version
 BUMP_CONFIG_FILE := $(PROJECT_PATH).bumpversion.toml
 
diff --git a/.make/base.make b/.make/base.make
index 7362c6c..5f40e6c 100644
--- a/.make/base.make
+++ b/.make/base.make
@@ -16,7 +16,7 @@ PROJECT_PATH := $(dir $(abspath $(firstword $(MAKEFILE_LIST))))
 MAKEFILE_NAME := $(word $(words $(MAKEFILE_LIST)),$(MAKEFILE_LIST))
 SHELL := /usr/bin/env bash
 BUMP_TOOL := bump-my-version
-MAKEFILE_VERSION := 0.7.0
+MAKEFILE_VERSION := 0.7.1
 DOCKER_COMPOSE ?= docker compose
 AUTO_INSTALL ?=
 
diff --git a/.make/lint.make b/.make/lint.make
index cd79c88..022edf3 100644
--- a/.make/lint.make
+++ b/.make/lint.make
@@ -2,36 +2,36 @@
 
 .PHONY: check-lint
 check-lint: ## Check code linting (black, isort, flake8, docformatter and pylint)
-	$(ENV_COMMAND_TOOL) run nox -s check
+	$(ENV_COMMAND_TOOL) nox -s check
 
 .PHONY: check-pylint
 check-pylint: ## Check code with pylint
-	$(ENV_COMMAND_TOOL) run nox -s pylint
+	$(ENV_COMMAND_TOOL) nox -s pylint
 
 .PHONY: check-complexity
 check-complexity: ## Check code cyclomatic complexity with Flake8-McCabe
-	$(ENV_COMMAND_TOOL) run nox -s complexity
+	$(ENV_COMMAND_TOOL) nox -s complexity
 
 .PHONY: fix-lint
 fix-lint: ## Fix code linting (autoflake, autopep8, black, isort, flynt, docformatter)
-	$(ENV_COMMAND_TOOL) run nox -s fix
+	$(ENV_COMMAND_TOOL) nox -s fix
 
 .PHONY: markdown-lint
 markdown-lint: ## Fix markdown linting using mdformat
-	$(ENV_COMMAND_TOOL) run nox -s mdformat
+	$(ENV_COMMAND_TOOL) nox -s mdformat
 
 .PHONY: precommit
 precommit: ## Run Pre-commit on all files manually
-	$(ENV_COMMAND_TOOL) run nox -s precommit
+	$(ENV_COMMAND_TOOL) nox -s precommit
 
 .PHONY: ruff
 ruff: ## Run the ruff linter
-	$(ENV_COMMAND_TOOL) run nox -s ruff-lint
+	$(ENV_COMMAND_TOOL) nox -s ruff-lint
 
 .PHONY: ruff-fix
 ruff-fix: ## Run the ruff linter and fix automatically fixable errors
-	$(ENV_COMMAND_TOOL) run nox -s ruff-fix
+	$(ENV_COMMAND_TOOL) nox -s ruff-fix
 
 .PHONY: ruff-format
 ruff-format: ## Run the ruff code formatter
-	$(ENV_COMMAND_TOOL) run nox -s ruff-format
+	$(ENV_COMMAND_TOOL) nox -s ruff-format
diff --git a/.make/poetry.make b/.make/poetry.make
index 2b39348..92af1ad 100644
--- a/.make/poetry.make
+++ b/.make/poetry.make
@@ -3,7 +3,7 @@
 -include Makefile.variables
 -include Makefile.private
 
-ENV_COMMAND_TOOL := poetry
+ENV_COMMAND_TOOL := poetry run
 
 ## -- Poetry targets ------------------------------------------------------------------------------------------------ ##
 
diff --git a/.make/test.make b/.make/test.make
index 86b78de..6c31024 100644
--- a/.make/test.make
+++ b/.make/test.make
@@ -2,7 +2,7 @@
 
 .PHONY: test
 test: ## Run all tests
-	$(ENV_COMMAND_TOOL) run nox -s test
+	$(ENV_COMMAND_TOOL) nox -s test
 
 TEST_ARGS ?=
 MARKER_TEST_ARGS = -m "$(TEST_ARGS)"
@@ -12,7 +12,7 @@ CUSTOM_TEST_ARGS = "$(TEST_ARGS)"
 .PHONY: test-marker
 test-marker: ## Run tests using pytest markers. Ex. make test-marker TEST_ARGS="<marker>"
 	@if [ -n "$(TEST_ARGS)" ]; then \
-		$(ENV_COMMAND_TOOL) run nox -s test_custom -- -- $(MARKER_TEST_ARGS); \
+		$(ENV_COMMAND_TOOL) nox -s test_custom -- -- $(MARKER_TEST_ARGS); \
 	else \
 		echo "" ; \
     	echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \
@@ -23,7 +23,7 @@ test-marker: ## Run tests using pytest markers. Ex. make test-marker TEST_ARGS="
 .PHONY: test-specific
 test-specific: ## Run specific tests using the -k option. Ex. make test-specific TEST_ARGS="<name-of-test>"
 	@if [ -n "$(TEST_ARGS)" ]; then \
-  		$(ENV_COMMAND_TOOL) run nox -s test_custom -- -- $(SPECIFIC_TEST_ARGS); \
+  		$(ENV_COMMAND_TOOL) nox -s test_custom -- -- $(SPECIFIC_TEST_ARGS); \
 	else \
 		echo "" ; \
     	echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \
@@ -35,7 +35,7 @@ test-specific: ## Run specific tests using the -k option. Ex. make test-specific
 .PHONY: test-custom
 test-custom: ## Run tests with custom args. Ex. make test-custom TEST_ARGS="-m 'not offline'"
 	@if [ -n "$(TEST_ARGS)" ]; then \
-  		$(ENV_COMMAND_TOOL) run nox -s test_custom -- -- $(CUSTOM_TEST_ARGS); \
+  		$(ENV_COMMAND_TOOL) nox -s test_custom -- -- $(CUSTOM_TEST_ARGS); \
 	else \
 	  	echo "" ; \
     	echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \
diff --git a/.make/uv.make b/.make/uv.make
index 43eae1c..13c07dd 100644
--- a/.make/uv.make
+++ b/.make/uv.make
@@ -2,7 +2,7 @@
 # This is to make sure, sometimes the Makefile includes don't work.
 
 ## -- UV targets ------------------------------------------------------------------------------------------------ ##
-ENV_COMMAND_TOOL := uv
+ENV_COMMAND_TOOL := uv run
 
 .PHONY: uv-install-auto
 uv-install-auto:
@@ -292,7 +292,7 @@ install-precommit: install-dev ## Install the pre-commit hooks (also installs de
 		echo "Pre-commit hook found"; \
 	else \
 	  	echo "Pre-commit hook not found, proceeding to configure it"; \
-		$(ENV_COMMAND_TOOL) run pre-commit install; \
+		$(ENV_COMMAND_TOOL) pre-commit install; \
 	fi;
 
 .PHONY: install-dev
diff --git a/Makefile.private.example b/Makefile.private.example
index 4deb9d7..148bd0d 100644
--- a/Makefile.private.example
+++ b/Makefile.private.example
@@ -16,12 +16,9 @@
 
 ## Private variables
 
-# If you use a different Conda tool, say `micromamba`, or if you use a different alias
-# CONDA_TOOL := <YOU_CONDA_TOOL_IF_DIFFERENT_FROM_CONDA>
-DOCKER_COMPOSE := docker compose
-
-# Some targets use this variable. A 'false' value will ask user to confirm some steps.
-# a 'true' value will automatically install/remove without asking beforehand.
+# Most, but not all install/remove targets use this variable. A 'false' value will ask
+# users to confirm some steps. A 'true' value will automatically install/remove without
+# asking beforehand.
 AUTO_INSTALL := false
 
 # The default environment to use. The choices are as follow: [venv, poetry, conda]
@@ -31,7 +28,16 @@ DEFAULT_INSTALL_ENV := venv
 
 # The default environment where Poetry will be installed. The choices are as follow: [venv, conda]
 # If this is not set, the makefile will ask the user where they want to install Poetry
-DEFAULT_POETRY_INSTALL_ENV := venv
+#DEFAULT_POETRY_INSTALL_ENV := venv
+
+
+# This variable is to enable the '-y' flag when newer version of conda is available.
+# The default Mila conda module does not allow this flag; leave blanks or commented out
+#CONDA_YES_OPTION := -y
+
+# If you use a different Conda tool, say `micromamba`, or if you use a different alias
+# CONDA_TOOL := <YOU_CONDA_TOOL_IF_DIFFERENT_FROM_CONDA>
+DOCKER_COMPOSE := docker compose
 
 ## -- Private targets ------------------------------------------------------------------------------------------------##
 
diff --git a/Makefile.targets b/Makefile.targets
index 078a1eb..e4f8a33 100644
--- a/Makefile.targets
+++ b/Makefile.targets
@@ -5,4 +5,4 @@
 
 .PHONY: test-notebooks
 test-notebooks: ## Execute test notebooks using pytest and nbval
-	nox -s test_nb
\ No newline at end of file
+	$(ENV_COMMAND_TOOL) nox -s test_nb
\ No newline at end of file