Add support for Python3.13

[Zeitsperre]

Pull Request Checklist:

• This PR addresses an already opened issue (for bug fixes / features)
  • This PR fixes issue #xyz
• Tests for the changes have been added (for bug fixes / features)
• Documentation has been added / updated (for bug fixes / features)
• HISTORY.rst has been updated (with summary of main changes)

What kind of change does this PR introduce?:

• First attempt at supporting Python3.13.
• Added a few security fixes to the GitHub Workflows and CI configurations.
• Reorganized the LICENSE to be more machine-parsable.
• Added coverage for Anaconda-based builds in CI.
• Adjust the README.rst to use a table of badges and added some relevant badges.
• READTHEDOCS build now reinstall the build environment Python3.12 with psy-maps (should be addressed in the future; see below).
• Adjusted all use_cftime calls to decode_times=xr.coders.CFDatetimeCoder(use_cftime=True), as is suggested by xarray.
  • This effectively silences 7800 warnings emitted in the testing suite!
• Lifted the pins on xarray and numpy (failures with specific types of data need to be fixed upstream).

Does this PR introduce a breaking change?:

Yes:

• psy-map is no longer installed via the conda environment, but is instead patched into the ReadTheDocs environment when building the docs. Ideally, we should remove the code-blocks using this (are there alternatives available?).
• CI dependencies are now in a new CI directory in the top-level. This makes it easier for Dependabot to perform updates on these libraries. They are installed via commit hashes for added security.
• All tests that fail due to cf-time/cf-xarray issues are now marked as xfail.

Other information:

The use_cftime keyword arg has been deprecated as of xarray v2025.01.1 (https://docs.xarray.dev/en/stable/generated/xarray.open_dataset.html).

It looks like the psy-maps library is no longer maintained and the package metadata only lists support for version until Python3.10! There is a need to remove this library if we want to build documentation on newer Python versions.

There's also a need to lift the pin on xarray. I know that we have some outstanding issues related to cf-time/cf-xarray that need to be dealt with for that to happen. Relevant issue/PR:

• TypeError for time_bnds variable when calling Dataset.to_netcdf pydata/xarray#7794
• Add small test exposing issue from #7794 and suggestion for _wrap_numpy_scalars fix pydata/xarray#8821

[coveralls]

Pull Request Test Coverage Report for Build 13585994050

Details

• 1 of 2 (50.0%) changed or added relevant lines in 2 files are covered.
• 1 unchanged line in 1 file lost coverage.
• Overall coverage increased (+10.1%) to 86.652%

---

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
clisops/project_utils.py	0	1	0.0%

Files with Coverage Reduction	New Missed Lines	%
clisops/project_utils.py	1	89.86%

Totals
Change from base Build 13525219205:	10.1%
Covered Lines:	3077
Relevant Lines:	3551

---

💛 - Coveralls

[Zeitsperre]

@cehbrecht I'm going to continue organizing this PR so that we can at least receive automated updates. This should make the management of the library a bit simpler. The next step will be to pull out clisops.core and all the tests for that specific module into strop.

[cehbrecht]

@Zeitsperre could we also add pytest-xdist to run tests in parallel?

[Zeitsperre]

@cehbrecht Possibly! If the tests are written to handle it, I think it shouldn't be an issue. I'll test it locally.

[Zeitsperre]

@cehbrecht This is ready to go. Should I wait for #397 before merging this?

Also, FYI, the finish step isn't reporting because I renamed it in the workflow. I'll adjust things in the repo once things are approved.

[cehbrecht]

do you have a link to the xarray docs for this?

[Zeitsperre]

https://docs.xarray.dev/en/stable/whats-new.html#v2025-01-1-jan-9-2025

[cehbrecht]

@cehbrecht This is ready to go. Should I wait for #397 before merging this?

Also, FYI, the finish step isn't reporting because I renamed it in the workflow. I'll adjust things in the repo once things are approved.

@Zeitsperre looks good. thanks :) you can merge this before the other PR #397