ci: Update CI to include new packages, typing and tests

[mlemayTTE]

Closes #58

This PR add tests and type checking in the CI. The work done includes:

• add pytest in the CI and small corrections when possible or disable failing tests in geos-trame and geos-mesh packages
• add new github workflow typing-check to include packages that respect typing (geos-posp, geos-timehistory, geos-utils, geos-xml-tools, hdf5-wrapper)
• linting TTE packages with CI rules

Future work:

• update disabled tests and remove skip decorator
• add tests to packages that do not have any
• update packages where type checking fails (geos-ats, geos-mesh, geos-xml-viewer, geos-trame) and add them to the typing-check workflow
• add test coverage (need at least one test per package)

[mlemayTTE]

@CusiniM if you have a moment, can you check everything is ok at least in geos-ats, geos-mesh and the CI configuration?
@untereiner same for geos-mesh, geos-xml-tools, geos-xml-viewer, geos-trame and the CI configuration?
@alexbenedicto same for geos-mesh, geos-timehistory, TTE packages, and hdf5-wrapper?
@paloma-martinez same for TTE packages?
Thanks all!

[untereiner]

Is it possible to add this step in the CI. Adding conventional semantics checking will ease packaging. You'll be able to add automatic package numbering for deployment based on the work you are doing now.

[untereiner]

As a more modern approach I would recommend to keep the mypy section in the pyproject.toml. Mypy will look for it's configuration in this file

[mlemayTTE]

As a more modern approach I would recommend to keep the mypy section in the pyproject.toml. Mypy will look for it's configuration in this file

I choose to add a .mypy.ini file to ensure that all the packages follow the same typing rules (similarly to linting approach using the .style.yml file). @untereiner do you mean to define typing (and linting) rules in a pyproject.toml file in the root directory in addition to the pyproject.toml in each package directory?

[untereiner]

Ok you are right. Not sure it is possible to have a root pyproject only for mypy and linting.

[alexbenedicto]

After discussing the question of python version in the infrastructure meeting, @CusiniM told me that you could build GEOS with your own python version as long as your pygeos uses the same. So there is no limitation of a specific 3.9 version as I thought. So using 3.10 as a baseline is okay.

[alexbenedicto]

I noticed in the checks of the docs that some warnings appeared, are these problematic ?

[mlemayTTE]

@alexbenedicto The warning in the doc does not prevent building it but I agree it is a bit annoying. I tried to fix it by installing additional packages (from Google research) but it still appeared (this commit).
So I think we can keep working with it since it is not an error and we will try to solve it in the future.

[mlemayTTE]

@untereiner do you have any additional comments or are you ok with the PR?

[untereiner]

LGTM !