Remove aicsfiles from requirements.txt

[pgarrison]

Purpose

For non-AICS users, the requirements.txt files shouldn't include aicsfiles.

Changes

• Add the -d flag to the pdm requirements command to ignore aicsfiles in the internal dependency group
• Install python (3.9) from pyenv instead of using the default python on the github actions runner, which has now updated to 3.14. 3.14 is incompatible with the old pdm version we're on (2.12.2).
• Update the github actions dependencies (checkout, download-artifact, upload-artifact, and peter-evans/create-pull-request). The previous versions were too old to run on github anymore.
• Mention in the pdm docs that 2.12.2 is the version we test against, in case that helps someone debug.

Testing

• The make-requirements action is working, and its results are part of this PR.
• Tests are passing in CI
• Still in progress:
  • pdm run python run_all_manuscript_workflows.py with virtual env from requirements.txt

[jcass11]

Install python (3.9) from pyenv instead of using the default python on the github actions runner, which has now updated to 3.14. 3.14 is incompatible with the old pdm version we're on (2.12.2).

Sorry for my lack of knowledge here, but I'm not sure how things change for a user starting from scratch using Python 3.9 now that 3.9 has officially reached its end of life. If a user is following the instructions in the landing page readme we say to have python 3.9 downloaded first. In step 3 is there a change that we make to python -m venv venv for the user to specify that this virtual environment should be made using 3.9? For example python3.9 -m venv venv or is there a more accepted/better way of doing this?

I am currently testing this branch as an external user (no VPN) on my Mac by following the current installation instructions on this branch with just the change of using python3.9 -m venv venv instead of python -m venv venv to make sure my virtual environment is 3.9. Currently getting an error with pyshtools:

Collecting pyshtools==4.10
  Downloading pyshtools-4.10.tar.gz (37.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.7/37.7 MB 49.1 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [6 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/private/var/folders/wf/rs611gbs7p99s8lcxjnv7v2r0000gp/T/pip-install-z04135a6/pyshtools_7798a421b59143f0a454fa5047eeb8f3/setup.py", line 21, in <module>
          import numpy  # noqa: E402
      ModuleNotFoundError: No module named 'numpy'
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

@pgarrison wondering if you ran into any issues with this or if there is anything else I should change about how I follow the installation instructions?

[jcass11]

& following up on above

Or do you want this PR to just isolate fixing the aicsfiles issue and is not meant to address all current issues with installation and my issue/question above is out of scope for this PR and something to be addressed separately?

[pgarrison]

Or do you want this PR to just isolate fixing the aicsfiles issue and is not meant to address all current issues with installation and my issue/question above is out of scope for this PR and something to be addressed separately?

Yup, this one is just about removing AICS-specific dependencies from the requirements.txt files!

[jcass11]

Thank you! When I tested with the basic installation it no longer fails looking aicsfiles ✅ there are downstream issues that are unrelated to this specific change but discussed with @pgarrison that that is not intended to be addressed in the PR. So this looks good to go for me!