From 8a3e7b7daf2c732d0eed62c1fc30678cfd5e1147 Mon Sep 17 00:00:00 2001
From: Henri Casanova <henric@hawaii.edu>
Date: Wed, 28 Jan 2026 20:26:30 -1000
Subject: [PATCH 01/15] Updated Makeflow logger

---
 tests/test_helpers.py                         |   8 +-
 .../test_translators_loggers.py               |  23 ++--
 wfcommons/wfinstances/logs/makeflow.py        | 104 ++++++++++--------
 3 files changed, 75 insertions(+), 60 deletions(-)

diff --git a/tests/test_helpers.py b/tests/test_helpers.py
index af549278..3458ca80 100644
--- a/tests/test_helpers.py
+++ b/tests/test_helpers.py
@@ -123,16 +123,16 @@ def _get_total_size_of_directory(directory_path: str):
             total_size += os.path.getsize(filepath)
     return total_size
 
-def _compare_workflows(workflow1: Workflow, workflow_2: Workflow):
+def _compare_workflows(workflow_1: Workflow, workflow_2: Workflow):
     
     # Test the number of tasks
-    assert (len(workflow1.tasks) == len(workflow_2.tasks))
+    assert (len(workflow_1.tasks) == len(workflow_2.tasks))
     # Test the task graph topology
-    assert (networkx.is_isomorphic(workflow1, workflow_2))
+    assert (networkx.is_isomorphic(workflow_1, workflow_2))
     # Test the total file size sum
     workflow1_input_bytes, workflow2_input_bytes = 0, 0
     workflow1_output_bytes, workflow2_output_bytes = 0, 0
-    for workflow1_task, workflow2_task in zip(workflow1.tasks.values(), workflow_2.tasks.values()):
+    for workflow1_task, workflow2_task in zip(workflow_1.tasks.values(), workflow_2.tasks.values()):
         # sys.stderr.write(f"WORKFLOW1: {workflow1_task.task_id}  WORKFLOW2 TASK: {workflow2_task.task_id}\n")
         for input_file in workflow1_task.input_files:
             # sys.stderr.write(f"WORKFLOW1 INPUT FILE: {input_file.file_id} {input_file.size}\n")
diff --git a/tests/translators_loggers/test_translators_loggers.py b/tests/translators_loggers/test_translators_loggers.py
index 1be31b9a..74ae661e 100644
--- a/tests/translators_loggers/test_translators_loggers.py
+++ b/tests/translators_loggers/test_translators_loggers.py
@@ -38,6 +38,7 @@
 
 from wfcommons.wfinstances import PegasusLogsParser
 from wfcommons.wfinstances.logs import TaskVineLogsParser
+from wfcommons.wfinstances.logs import MakeflowLogsParser
 
 
 def _create_workflow_benchmark() -> (WorkflowBenchmark, int):
@@ -165,7 +166,7 @@ def run_workflow_taskvine(container, num_tasks, str_dirpath):
 
 def run_workflow_makeflow(container, num_tasks, str_dirpath):
     # Run the workflow (with full logging)
-    exit_code, output = container.exec_run(cmd=["bash", "-c", "source ~/conda/etc/profile.d/conda.sh && conda activate && makeflow --log-verbose ./workflow.makeflow"], stdout=True, stderr=True)
+    exit_code, output = container.exec_run(cmd=["bash", "-c", "source ~/conda/etc/profile.d/conda.sh && conda activate && makeflow --log-verbose  --monitor=./monitor_data/ ./workflow.makeflow"], stdout=True, stderr=True)
     # Check sanity
     assert (exit_code == 0)
     num_completed_jobs = len(re.findall(r'job \d+ completed', output.decode()))
@@ -229,16 +230,16 @@ class TestTranslators:
     @pytest.mark.parametrize(
         "backend",
         [
-           "swiftt",
-           "dask",
-           "parsl",
-           "nextflow",
-           "airflow",
-           "bash",
-           "taskvine",
+           # "swiftt",
+           # "dask",
+           # "parsl",
+           # "nextflow",
+           # "airflow",
+           # "bash",
+           # "taskvine",
            "makeflow",
-           "cwl",
-           "pegasus",
+           # "cwl",
+           # "pegasus",
         ])
     @pytest.mark.unit
     # @pytest.mark.skip(reason="tmp")
@@ -274,6 +275,8 @@ def test_translator(self, backend) -> None:
             parser = PegasusLogsParser(dirpath / "work/wfcommons/pegasus/Blast-Benchmark/run0001/")
         elif backend == "taskvine":
             parser = TaskVineLogsParser(dirpath / "vine-run-info/most-recent/vine-logs", filenames_to_ignore=["cpu-benchmark","stress-ng", "wfbench"])
+        elif backend == "makeflow":
+            parser = MakeflowLogsParser(execution_dir = dirpath, resource_monitor_logs_dir = dirpath / "monitor_data/")
         else:
             parser = None
 
diff --git a/wfcommons/wfinstances/logs/makeflow.py b/wfcommons/wfinstances/logs/makeflow.py
index 88f3b0dc..8306fc0d 100644
--- a/wfcommons/wfinstances/logs/makeflow.py
+++ b/wfcommons/wfinstances/logs/makeflow.py
@@ -28,9 +28,9 @@ class MakeflowLogsParser(LogsParser):
     """
     Parse Makeflow submit directory to generate workflow instance.
 
-    :param execution_dir: Makeflow workflow execution directory (contains .mf and .makeflowlog files).
+    :param execution_dir: Makeflow workflow execution directory (contains .mf/.makeflow and .makeflowlog files).
     :type execution_dir: pathlib.Path
-    :param resource_monitor_logs_dir: Resource Monitor log files directory.
+    :param resource_monitor_logs_dir: Resource Monitor log files directory (created with `makeflow ----monitor=... ...`)
     :type resource_monitor_logs_dir: pathlib.Path
     :param description: Workflow instance description.
     :type description: Optional[str]
@@ -46,28 +46,38 @@ def __init__(self,
         """Create an object of the makeflow log parser."""
         super().__init__('Makeflow', 'http://ccl.cse.nd.edu/software/makeflow/', description, logger)
 
-        # Sanity check
+        # Sanity checks
         if not execution_dir.is_dir():
             raise OSError(f'The provided path does not exist or is not a folder: {execution_dir}')
+        if not resource_monitor_logs_dir.is_dir():
+            raise OSError(f'The provided path does not exist or is not a folder: {resource_monitor_logs_dir}')
 
+        # Makeflow file
         files: List[pathlib.Path] = list(execution_dir.glob('*.mf'))
+        if len(files) > 1:
+            raise OSError(f'Multiple .mf files in: {execution_dir}')
         if len(files) == 0:
-            raise OSError(f'Unable to find .mf file in: {execution_dir}')
+            files: List[pathlib.Path] = list(execution_dir.glob('*.makeflow'))
+            if len(files) > 1:
+                raise OSError(f'Multiple .makeflow files in: {execution_dir}')
+            if len(files) == 0:
+                raise OSError(f'Unable to find a .mf or .makeflow file in: {execution_dir}')
         self.mf_file: pathlib.Path = files[0]
 
+        # Log file
         files = list(execution_dir.glob('*.makeflowlog'))
         if len(files) == 0:
             raise OSError(f'Unable to find .makeflowlog file in: {execution_dir}')
+        if len(files) > 1:
+            raise OSError(f'Multiple .makeflowlog files in: {execution_dir}')
         self.mf_log_file: pathlib.Path = files[0]
+        if self.mf_log_file.read_text().count("# NODE") == 0:
+            raise OSError(f'Not sufficiently verbose log file {self.mf_log_file}. Re-run the workflow with `makeflow --log-verbose ...`')
 
-        if not resource_monitor_logs_dir.is_dir():
-            raise OSError(f'The provided path does not exist or is not a folder: {resource_monitor_logs_dir}')
-
-        self.execution_dir: pathlib.Path = execution_dir
-
-        self.resource_monitor_logs_dir: pathlib.Path = resource_monitor_logs_dir
-        self.files_map = {}
-        self.args_map = {}
+        self._execution_dir: pathlib.Path = execution_dir
+        self._resource_monitor_logs_dir: pathlib.Path = resource_monitor_logs_dir
+        self._files_map = {}
+        self._args_map = {}
 
     def build_workflow(self, workflow_name: Optional[str] = None) -> Workflow:
         """
@@ -106,30 +116,31 @@ def _parse_workflow_file(self) -> None:
             outputs = []
             inputs = []
             for line in f:
-                if ':' in line:
+                # print(f"Processing line: {line}")
+                if line.lstrip().startswith('#'):
+                    continue
+                if ':' in line and '\t' not in line:
                     outputs = line.split(':')[0].split()
                     inputs = line.split(':')[1].split()
 
                     for file in itertools.chain(outputs, inputs):
-                        if file not in self.files_map:
-                            self.files_map[file] = {'task_name': None, 'children': [], 'file': []}
+                        if file not in self._files_map:
+                            self._files_map[file] = {'task_name': None, 'children': [], 'file': []}
 
-                elif len(line.strip()) > 0:
-                    # task execution command
-                    prefix = line.replace('./', '').replace('perl', '').strip().split()[1 if 'LOCAL' in line else 0]
-                    task_name = "{}_ID{:07d}".format(prefix, task_id_counter)
+                elif '\t' in line:
+                    # task execution command (likely olf here)
+                    prefix = line.replace('./', '').strip().split()[1 if 'LOCAL' in line else 0]
+                    task_name = "ID{:07d}".format(task_id_counter)
 
-                    # create list of task files
-                    list_files = []
+                    # create list of input and output files
                     output_files = self._create_files(outputs, "output", task_name)
                     input_files = self._create_files(inputs, "input", task_name)
 
                     # create task
-                    args = ' '.join(line.replace('LOCAL', '').replace('perl', '').strip().split())
+                    args = ' '.join(line.split())
                     task = Task(name=task_name,
-                                task_id="ID{:07d}".format(task_id_counter),
+                                task_id=task_name,
                                 category=prefix,
-                                task_type=TaskType.COMPUTE,
                                 runtime=0,
                                 program=prefix,
                                 args=args.split(),
@@ -137,15 +148,16 @@ def _parse_workflow_file(self) -> None:
                                 input_files=input_files,
                                 output_files=output_files,
                                 logger=self.logger)
-                    self.workflow.add_node(task_name, task=task)
-                    self.args_map[args] = task
+                    self.workflow.add_task(task)
+                    args = args.replace('\\\\', '\\')
+                    self._args_map[args] = task
                     task_id_counter += 1
 
         # adding edges
-        for file in self.files_map:
-            for child in self.files_map[file]['children']:
-                if self.files_map[file]['task_name']:
-                    self.workflow.add_edge(self.files_map[file]['task_name'], child)
+        for file in self._files_map:
+            for child in self._files_map[file]['children']:
+                if self._files_map[file]['task_name']:
+                    self.workflow.add_edge(self._files_map[file]['task_name'], child)
 
     def _create_files(self, files_list: List[str], input_or_output: str, task_name: str) -> List[File]:
         """
@@ -163,16 +175,16 @@ def _create_files(self, files_list: List[str], input_or_output: str, task_name:
         """
         list_files = []
         for file in files_list:
-            if self.files_map[file]['file']:
+            if self._files_map[file]['file']:
                 list_files.append(
-                    self.files_map[file]['file'][0] if input_or_output == "input" else self.files_map[file]['file'][1])
+                    self._files_map[file]['file'][0] if input_or_output == "input" else self._files_map[file]['file'][1])
             else:
                 size = 0
-                file_path = self.execution_dir.joinpath(file)
+                file_path = self._execution_dir.joinpath(file)
                 if file_path.is_dir():
-                    size = sum(math.ceil(f.stat().st_size / 1000) for f in file_path.glob("*") if f.is_file())
+                    size = sum(f.stat().st_size for f in file_path.glob("*") if f.is_file())
                 elif file_path.is_file():
-                    size = int(math.ceil(file_path.stat().st_size / 1000))  # B to KB
+                    size = int(file_path.stat().st_size)
 
                 file_obj_in = File(file_id=file,
                                    size=size,
@@ -181,13 +193,13 @@ def _create_files(self, files_list: List[str], input_or_output: str, task_name:
                                     size=size,
                                     logger=self.logger)
                 list_files.append(file_obj_in if input_or_output == "input" else file_obj_out)
-                self.files_map[file]['file'].extend([file_obj_in, file_obj_out])
+                self._files_map[file]['file'].extend([file_obj_in, file_obj_out])
 
             # files dependencies
             if input_or_output == "input":
-                self.files_map[file]['children'].append(task_name)
+                self._files_map[file]['children'].append(task_name)
             else:
-                self.files_map[file]['task_name'] = task_name
+                self._files_map[file]['task_name'] = task_name
 
         return list_files
 
@@ -208,24 +220,24 @@ def _parse_makeflow_log_file(self):
 
                 elif line.startswith('# FILE') and 'condorlog' not in line:
                     file_name = line.split()[3]
-                    if file_name in self.files_map:
-                        size = int(math.ceil(int(line.split()[5]) / 1000))  # B to KB
-                        for file_obj in self.files_map[file_name]['file']:
+                    if file_name in self._files_map:
+                        size = int(line.split()[5])
+                        for file_obj in self._files_map[file_name]['file']:
                             file_obj.size = size
 
     def _parse_resource_monitor_logs(self):
         """Parse the log files produced by resource monitor"""
-        for file in pathlib.Path.glob(f'{self.resource_monitor_logs_dir}/*.summary'):
+        for file in self._resource_monitor_logs_dir.glob("*.summary"):
             with open(file) as f:
                 data = json.load(f)
 
                 # task
-                task = self.args_map[data['command'].replace('perl', '').strip()]
+                task = self._args_map[data['command'].replace('perl', '').strip()]
                 task.runtime = float(data['wall_time'][0])
                 task.cores = float(data['cores'][0])
-                task.memory = int(data['memory'][0]) * 1000  # MB to KB
-                task.bytes_read = int(data['bytes_read'][0] * 1000)  # MB to KB
-                task.bytes_written = int(data['bytes_written'][0] * 1000)  # MB to KB
+                task.memory = int(data['memory'][0])
+                task.bytes_read = int(data['bytes_read'][0])
+                task.bytes_written = int(data['bytes_written'][0])
                 task.avg_cpu = float('%.4f' % (float(data['cpu_time'][0]) / float(data['wall_time'][0]) * 100))
                 task.machine = Machine(name=data['host'],
                                        cpu={'coreCount': int(data['machine_cpus'][0]), 'speedInMHz': 0, 'vendor': ''},

From 1fed32ceec4cd8a6f618537206874d51473124c0 Mon Sep 17 00:00:00 2001
From: Henri Casanova <henric@hawaii.edu>
Date: Wed, 28 Jan 2026 20:31:30 -1000
Subject: [PATCH 02/15] re-enabling all tests

---
 .../test_translators_loggers.py                | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/tests/translators_loggers/test_translators_loggers.py b/tests/translators_loggers/test_translators_loggers.py
index 74ae661e..c5c8b9bf 100644
--- a/tests/translators_loggers/test_translators_loggers.py
+++ b/tests/translators_loggers/test_translators_loggers.py
@@ -230,16 +230,16 @@ class TestTranslators:
     @pytest.mark.parametrize(
         "backend",
         [
-           # "swiftt",
-           # "dask",
-           # "parsl",
-           # "nextflow",
-           # "airflow",
-           # "bash",
-           # "taskvine",
+           "swiftt",
+           "dask",
+           "parsl",
+           "nextflow",
+           "airflow",
+           "bash",
+           "taskvine",
            "makeflow",
-           # "cwl",
-           # "pegasus",
+           "cwl",
+           "pegasus",
         ])
     @pytest.mark.unit
     # @pytest.mark.skip(reason="tmp")

From 3c2623aff1ffece404770e17adecd98f384b06bf Mon Sep 17 00:00:00 2001
From: Henri Casanova <henric@hawaii.edu>
Date: Thu, 29 Jan 2026 09:46:12 -1000
Subject: [PATCH 03/15] Updated test helpers to force a cpu-benchmark rebuild,
 via an ugly in-place rewrite of setup.py

---
 tests/test_helpers.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/test_helpers.py b/tests/test_helpers.py
index 3458ca80..d23d8596 100644
--- a/tests/test_helpers.py
+++ b/tests/test_helpers.py
@@ -42,13 +42,15 @@ def _install_WfCommons_on_container(container):
     # Cleanup files from the host
     exit_code, output = container.exec_run("sudo /bin/rm -rf /tmp/WfCommons/build/", stdout=True, stderr=True)
     exit_code, output = container.exec_run("sudo /bin/rm -rf /tmp/WfCommons/*.egg-info/", stdout=True, stderr=True)
+    # Clean up and force a rebuild of cpu-benchmark (because it may be compiled for the wrong architecture)
     exit_code, output = container.exec_run("sudo /bin/rm -rf /tmp/WfCommons/bin/cpu-benchmark.o", stdout=True,
                                            stderr=True)
     exit_code, output = container.exec_run("sudo /bin/rm -rf /tmp/WfCommons/bin/cpu-benchmark", stdout=True,
                                            stderr=True)
+    exit_code, output = container.exec_run(r"sudo sed -i 's|if os.path.exists(cpu_benchmark_path):|if True:|' /tmp/WfCommons/setup.py")
 
     # Install WfCommons on the container (to install wfbench and cpu-benchmark really)
-    exit_code, output = container.exec_run("sudo python3 -m pip install . --break-system-packages",
+    exit_code, output = container.exec_run("sudo python3 -m pip install -v . --break-system-packages",
                                            workdir="/tmp/WfCommons", stdout=True, stderr=True)
     if exit_code != 0:
         raise RuntimeError("Failed to install WfCommons on the container")
@@ -88,6 +90,7 @@ def _start_docker_container(backend, mounted_dir, working_dir, bin_dir, command=
                                                stdout=True, stderr=True)
         if exit_code != 0:
             raise RuntimeError("Failed to copy wfbench script to the bin directory")
+
         exit_code, output = container.exec_run(["sh", "-c", "sudo cp -f `which cpu-benchmark` " + bin_dir],
                                                stdout=True, stderr=True)
         if exit_code != 0:

From af18065f2b4d8cbf2aafed0a8f6c05063390eea1 Mon Sep 17 00:00:00 2001
From: Henri Casanova <henric@hawaii.edu>
Date: Thu, 29 Jan 2026 13:32:31 -1000
Subject: [PATCH 04/15] comment++

---
 tests/test_helpers.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/test_helpers.py b/tests/test_helpers.py
index d23d8596..eebe094e 100644
--- a/tests/test_helpers.py
+++ b/tests/test_helpers.py
@@ -39,7 +39,7 @@ def _install_WfCommons_on_container(container):
     target_path = '/tmp/'  # inside container
     tar_data = _make_tarfile_of_wfcommons()
     container.put_archive(target_path, tar_data)
-    # Cleanup files from the host
+    # Cleanup files that came from the host
     exit_code, output = container.exec_run("sudo /bin/rm -rf /tmp/WfCommons/build/", stdout=True, stderr=True)
     exit_code, output = container.exec_run("sudo /bin/rm -rf /tmp/WfCommons/*.egg-info/", stdout=True, stderr=True)
     # Clean up and force a rebuild of cpu-benchmark (because it may be compiled for the wrong architecture)
@@ -52,6 +52,7 @@ def _install_WfCommons_on_container(container):
     # Install WfCommons on the container (to install wfbench and cpu-benchmark really)
     exit_code, output = container.exec_run("sudo python3 -m pip install -v . --break-system-packages",
                                            workdir="/tmp/WfCommons", stdout=True, stderr=True)
+    # print(output.decode())
     if exit_code != 0:
         raise RuntimeError("Failed to install WfCommons on the container")
 

From bf8d74fa799321ec1b57341aa0e0e8f8558940fd Mon Sep 17 00:00:00 2001
From: Henri Casanova <henric@hawaii.edu>
Date: Thu, 29 Jan 2026 13:48:09 -1000
Subject: [PATCH 05/15] tweak

---
 tests/test_helpers.py                          |  2 +-
 .../test_translators_loggers.py                | 18 +++++++++---------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/tests/test_helpers.py b/tests/test_helpers.py
index eebe094e..d1c99a82 100644
--- a/tests/test_helpers.py
+++ b/tests/test_helpers.py
@@ -50,7 +50,7 @@ def _install_WfCommons_on_container(container):
     exit_code, output = container.exec_run(r"sudo sed -i 's|if os.path.exists(cpu_benchmark_path):|if True:|' /tmp/WfCommons/setup.py")
 
     # Install WfCommons on the container (to install wfbench and cpu-benchmark really)
-    exit_code, output = container.exec_run("sudo python3 -m pip install -v . --break-system-packages",
+    exit_code, output = container.exec_run("sudo python3 -m pip install . --break-system-packages",
                                            workdir="/tmp/WfCommons", stdout=True, stderr=True)
     # print(output.decode())
     if exit_code != 0:
diff --git a/tests/translators_loggers/test_translators_loggers.py b/tests/translators_loggers/test_translators_loggers.py
index c5c8b9bf..47ad7f33 100644
--- a/tests/translators_loggers/test_translators_loggers.py
+++ b/tests/translators_loggers/test_translators_loggers.py
@@ -230,16 +230,16 @@ class TestTranslators:
     @pytest.mark.parametrize(
         "backend",
         [
-           "swiftt",
-           "dask",
+           # "swiftt",
+           # "dask",
            "parsl",
-           "nextflow",
-           "airflow",
-           "bash",
-           "taskvine",
-           "makeflow",
-           "cwl",
-           "pegasus",
+           # "nextflow",
+           # "airflow",
+           # "bash",
+           # "taskvine",
+           # "makeflow",
+           # "cwl",
+           # "pegasus",
         ])
     @pytest.mark.unit
     # @pytest.mark.skip(reason="tmp")

From 4718b3265435593284cf6caf40b977af26c507f3 Mon Sep 17 00:00:00 2001
From: Henri Casanova <henric@hawaii.edu>
Date: Thu, 29 Jan 2026 14:28:49 -1000
Subject: [PATCH 06/15] temporarily disabling parsl testing

---
 .../test_translators_loggers.py               | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/tests/translators_loggers/test_translators_loggers.py b/tests/translators_loggers/test_translators_loggers.py
index 47ad7f33..3225068c 100644
--- a/tests/translators_loggers/test_translators_loggers.py
+++ b/tests/translators_loggers/test_translators_loggers.py
@@ -230,16 +230,16 @@ class TestTranslators:
     @pytest.mark.parametrize(
         "backend",
         [
-           # "swiftt",
-           # "dask",
-           "parsl",
-           # "nextflow",
-           # "airflow",
-           # "bash",
-           # "taskvine",
-           # "makeflow",
-           # "cwl",
-           # "pegasus",
+           "swiftt",
+           "dask",
+           # "parsl",
+           "nextflow",
+           "airflow",
+           "bash",
+           "taskvine",
+           "makeflow",
+           "cwl",
+           "pegasus",
         ])
     @pytest.mark.unit
     # @pytest.mark.skip(reason="tmp")

From 5dc466efb86719ea82f87f8745bbda03c3967559 Mon Sep 17 00:00:00 2001
From: Henri Casanova <henric@hawaii.edu>
Date: Thu, 29 Jan 2026 15:14:07 -1000
Subject: [PATCH 07/15] leaving only a couple of backends for testing

---
 .../test_translators_loggers.py                    | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/tests/translators_loggers/test_translators_loggers.py b/tests/translators_loggers/test_translators_loggers.py
index 3225068c..01e3c675 100644
--- a/tests/translators_loggers/test_translators_loggers.py
+++ b/tests/translators_loggers/test_translators_loggers.py
@@ -230,16 +230,16 @@ class TestTranslators:
     @pytest.mark.parametrize(
         "backend",
         [
-           "swiftt",
-           "dask",
+           # "swiftt",
+           # "dask",
            # "parsl",
-           "nextflow",
-           "airflow",
+           # "nextflow",
+           # "airflow",
            "bash",
-           "taskvine",
-           "makeflow",
+           # "taskvine",
+           # "makeflow",
            "cwl",
-           "pegasus",
+           # "pegasus",
         ])
     @pytest.mark.unit
     # @pytest.mark.skip(reason="tmp")

From 67cc4a1e67746ec67bb69dee86461412060e0100 Mon Sep 17 00:00:00 2001
From: Henri Casanova <henric@hawaii.edu>
Date: Thu, 29 Jan 2026 17:11:43 -1000
Subject: [PATCH 08/15] Disabling test backends that seem to, suddenly, suffer
 from permission errors. (in spite of making the translation directory
 world-writable).

---
 tests/test_helpers.py                                 |  5 +++++
 tests/translators_loggers/test_translators_loggers.py | 11 ++++++++---
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/tests/test_helpers.py b/tests/test_helpers.py
index d1c99a82..cf8d0d71 100644
--- a/tests/test_helpers.py
+++ b/tests/test_helpers.py
@@ -99,6 +99,11 @@ def _start_docker_container(backend, mounted_dir, working_dir, bin_dir, command=
     else:
         sys.stderr.write(f"[{backend}] Not Copying wfbench and cpu-benchmark...\n")
 
+    # Change file permissions
+    exit_code, output = container.exec_run(["sh", "-c", "sudo chown -R wfcommons:wfcommons "],
+                                           stdout=True, stderr=True)
+
+
     container.backend = backend
     return container
 
diff --git a/tests/translators_loggers/test_translators_loggers.py b/tests/translators_loggers/test_translators_loggers.py
index 01e3c675..abda09c7 100644
--- a/tests/translators_loggers/test_translators_loggers.py
+++ b/tests/translators_loggers/test_translators_loggers.py
@@ -15,6 +15,7 @@
 import json
 import time
 import re
+import os
 
 from tests.test_helpers import _create_fresh_local_dir
 from tests.test_helpers import _remove_local_dir_if_it_exists
@@ -230,11 +231,11 @@ class TestTranslators:
     @pytest.mark.parametrize(
         "backend",
         [
-           # "swiftt",
-           # "dask",
+           "swiftt",
+           "dask",
            # "parsl",
            # "nextflow",
-           # "airflow",
+           "airflow",
            "bash",
            # "taskvine",
            # "makeflow",
@@ -258,6 +259,10 @@ def test_translator(self, backend) -> None:
         translator = translator_classes[backend](benchmark.workflow)
         translator.translate(output_folder=dirpath)
 
+        # Make the directory that holds the translation world-writable,
+        # so that docker commands won't fail
+        os.chmod(dirpath, 0o777)
+
         # Start the Docker container
         container = _start_docker_container(backend, str_dirpath, str_dirpath, str_dirpath + "bin/")
 

From c19123f15ad2cb2714376da53ceb024d0b0b4bd9 Mon Sep 17 00:00:00 2001
From: Henri Casanova <henric@hawaii.edu>
Date: Thu, 29 Jan 2026 17:35:59 -1000
Subject: [PATCH 09/15] Remove all but one translator Added debug info to see
 what's wrong on the GitHub Runner It has to do with cpu-benchmark (again!)

---
 .github/workflows/build.yml                          |  4 ++--
 .../translators_loggers/test_translators_loggers.py  | 12 ++++++++----
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index e0618644..82e543ec 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.11", "3.12", "3.13", "3.14" ]
+        python-version: [ "3.14" ]
     steps:
       - uses: actions/checkout@v4
   
@@ -37,7 +37,7 @@ jobs:
           pip install .
 
       - name: Run tests
-        run: python3 -m pytest -s -v -m unit --cov=wfcommons tests/
+        run: python3 -m pytest -s -v -m unit --cov=wfcommons tests/translators_loggers
 
       - name: Upload coverage
         if: github.ref == 'refs/heads/main'
diff --git a/tests/translators_loggers/test_translators_loggers.py b/tests/translators_loggers/test_translators_loggers.py
index abda09c7..76081863 100644
--- a/tests/translators_loggers/test_translators_loggers.py
+++ b/tests/translators_loggers/test_translators_loggers.py
@@ -231,15 +231,15 @@ class TestTranslators:
     @pytest.mark.parametrize(
         "backend",
         [
-           "swiftt",
-           "dask",
+           # "swiftt",
+           # "dask",
            # "parsl",
            # "nextflow",
-           "airflow",
+           # "airflow",
            "bash",
            # "taskvine",
            # "makeflow",
-           "cwl",
+           # "cwl",
            # "pegasus",
         ])
     @pytest.mark.unit
@@ -257,6 +257,10 @@ def test_translator(self, backend) -> None:
         # Perform the translation
         sys.stderr.write(f"\n[{backend}] Translating workflow...\n")
         translator = translator_classes[backend](benchmark.workflow)
+        sys.stderr.write("Checking that cpu-benchmark is in the path")
+        sys.stderr.write(f"{shutil.which('cpu-benchmark')}")
+        for path in os.environ["PATH"].split(os.pathsep):
+            sys.stderr.write(f"In PATH: {path}...\n")
         translator.translate(output_folder=dirpath)
 
         # Make the directory that holds the translation world-writable,

From d9bbdc54258e8386c8beba74248706eb1139a2a0 Mon Sep 17 00:00:00 2001
From: Henri Casanova <henric@hawaii.edu>
Date: Thu, 29 Jan 2026 17:41:38 -1000
Subject: [PATCH 10/15] Just double-checking that the setup.py change is indeed
 the culprit again

---
 setup.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 876fd37e..ec71ab73 100644
--- a/setup.py
+++ b/setup.py
@@ -34,7 +34,8 @@ def run(self):
 # Conditionally include cpu-benchmark if it exists
 data_files = []
 cpu_benchmark_path = 'bin/cpu-benchmark'
-if os.path.exists(cpu_benchmark_path):
+if True:
+#if os.path.exists(cpu_benchmark_path):
     data_files.append(('bin', [cpu_benchmark_path]))
 
 setup(

From c364b2c0a7334cb5ec3f8043ef8102ca9ac39708 Mon Sep 17 00:00:00 2001
From: Henri Casanova <henric@hawaii.edu>
Date: Thu, 29 Jan 2026 17:47:35 -1000
Subject: [PATCH 11/15] Re-enabling all translator tests just to be sure

---
 .../test_translators_loggers.py                | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/tests/translators_loggers/test_translators_loggers.py b/tests/translators_loggers/test_translators_loggers.py
index 76081863..dcc4e22e 100644
--- a/tests/translators_loggers/test_translators_loggers.py
+++ b/tests/translators_loggers/test_translators_loggers.py
@@ -231,16 +231,16 @@ class TestTranslators:
     @pytest.mark.parametrize(
         "backend",
         [
-           # "swiftt",
-           # "dask",
-           # "parsl",
-           # "nextflow",
-           # "airflow",
+           "swiftt",
+           "dask",
+           "parsl",
+           "nextflow",
+           "airflow",
            "bash",
-           # "taskvine",
-           # "makeflow",
-           # "cwl",
-           # "pegasus",
+           "taskvine",
+           "makeflow",
+           "cwl",
+           "pegasus",
         ])
     @pytest.mark.unit
     # @pytest.mark.skip(reason="tmp")

From abfd5a9b5e27e5ce3d3f9d41cb11e292a8541e39 Mon Sep 17 00:00:00 2001
From: Henri Casanova <henric@hawaii.edu>
Date: Thu, 29 Jan 2026 19:10:58 -1000
Subject: [PATCH 12/15] Hacking the github workflow to work with the setup.py

---
 .github/workflows/build.yml | 1 +
 setup.py                    | 3 +--
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 82e543ec..14cdd91b 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -34,6 +34,7 @@ jobs:
 
       - name: Check package install
         run: |
+          sudo sed -i 's|if os.path.exists(cpu_benchmark_path):|if True:|' ./setup.py
           pip install .
 
       - name: Run tests
diff --git a/setup.py b/setup.py
index ec71ab73..876fd37e 100644
--- a/setup.py
+++ b/setup.py
@@ -34,8 +34,7 @@ def run(self):
 # Conditionally include cpu-benchmark if it exists
 data_files = []
 cpu_benchmark_path = 'bin/cpu-benchmark'
-if True:
-#if os.path.exists(cpu_benchmark_path):
+if os.path.exists(cpu_benchmark_path):
     data_files.append(('bin', [cpu_benchmark_path]))
 
 setup(

From 5ec72eea755d291b812b3ba260ab155fe444b849 Mon Sep 17 00:00:00 2001
From: Henri Casanova <henric@hawaii.edu>
Date: Thu, 29 Jan 2026 21:49:18 -1000
Subject: [PATCH 13/15] Re-established different python versions for testing

---
 .github/workflows/build.yml                           | 2 +-
 tests/translators_loggers/test_translators_loggers.py | 4 ----
 2 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 14cdd91b..07a6526c 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.14" ]
+        python-version: [ "3.11", "3.12", "3.13", "3.14" ]
     steps:
       - uses: actions/checkout@v4
   
diff --git a/tests/translators_loggers/test_translators_loggers.py b/tests/translators_loggers/test_translators_loggers.py
index dcc4e22e..3d6ae9fb 100644
--- a/tests/translators_loggers/test_translators_loggers.py
+++ b/tests/translators_loggers/test_translators_loggers.py
@@ -257,10 +257,6 @@ def test_translator(self, backend) -> None:
         # Perform the translation
         sys.stderr.write(f"\n[{backend}] Translating workflow...\n")
         translator = translator_classes[backend](benchmark.workflow)
-        sys.stderr.write("Checking that cpu-benchmark is in the path")
-        sys.stderr.write(f"{shutil.which('cpu-benchmark')}")
-        for path in os.environ["PATH"].split(os.pathsep):
-            sys.stderr.write(f"In PATH: {path}...\n")
         translator.translate(output_folder=dirpath)
 
         # Make the directory that holds the translation world-writable,

From 4c735dd6645f90a723fcdc96770e84acf681199e Mon Sep 17 00:00:00 2001
From: Henri Casanova <henric@hawaii.edu>
Date: Fri, 30 Jan 2026 10:16:38 -1000
Subject: [PATCH 14/15] Text fixes

---
 .github/workflows/build.yml                           | 1 -
 tests/test_helpers.py                                 | 1 -
 tests/translators_loggers/test_translators_loggers.py | 8 +++++---
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 07a6526c..49683a7e 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -34,7 +34,6 @@ jobs:
 
       - name: Check package install
         run: |
-          sudo sed -i 's|if os.path.exists(cpu_benchmark_path):|if True:|' ./setup.py
           pip install .
 
       - name: Run tests
diff --git a/tests/test_helpers.py b/tests/test_helpers.py
index cf8d0d71..943ae9c3 100644
--- a/tests/test_helpers.py
+++ b/tests/test_helpers.py
@@ -47,7 +47,6 @@ def _install_WfCommons_on_container(container):
                                            stderr=True)
     exit_code, output = container.exec_run("sudo /bin/rm -rf /tmp/WfCommons/bin/cpu-benchmark", stdout=True,
                                            stderr=True)
-    exit_code, output = container.exec_run(r"sudo sed -i 's|if os.path.exists(cpu_benchmark_path):|if True:|' /tmp/WfCommons/setup.py")
 
     # Install WfCommons on the container (to install wfbench and cpu-benchmark really)
     exit_code, output = container.exec_run("sudo python3 -m pip install . --break-system-packages",
diff --git a/tests/translators_loggers/test_translators_loggers.py b/tests/translators_loggers/test_translators_loggers.py
index 3d6ae9fb..400a45a8 100644
--- a/tests/translators_loggers/test_translators_loggers.py
+++ b/tests/translators_loggers/test_translators_loggers.py
@@ -259,9 +259,11 @@ def test_translator(self, backend) -> None:
         translator = translator_classes[backend](benchmark.workflow)
         translator.translate(output_folder=dirpath)
 
-        # Make the directory that holds the translation world-writable,
-        # so that docker commands won't fail
-        os.chmod(dirpath, 0o777)
+        # # Make the directory that holds the translation world-writable,
+        # # so that docker commands won't fail
+        # TODO: Explore whether this below makes tests runnable on Linux due to
+        #       different Docker permission schemes, etc.
+        # os.chmod(dirpath, 0o777)
 
         # Start the Docker container
         container = _start_docker_container(backend, str_dirpath, str_dirpath, str_dirpath + "bin/")

From dda0ab3e4668468891d9ea6f340da6e4758bfb4a Mon Sep 17 00:00:00 2001
From: Henri Casanova <henric@hawaii.edu>
Date: Fri, 30 Jan 2026 10:17:40 -1000
Subject: [PATCH 15/15] re-etablishing all tests

---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 49683a7e..0a4023b0 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -37,7 +37,7 @@ jobs:
           pip install .
 
       - name: Run tests
-        run: python3 -m pytest -s -v -m unit --cov=wfcommons tests/translators_loggers
+        run: python3 -m pytest -s -v -m unit --cov=wfcommons tests
 
       - name: Upload coverage
         if: github.ref == 'refs/heads/main'