Python 3.12 related fixes

[poshul]

Description

Checklist

• Make sure that you are listed in the AUTHORS file
• Add relevant changes and new features to the CHANGELOG file
• I have commented my code, particularly in hard-to-understand areas
• New and existing unit tests pass locally with my changes
• Updated or added python bindings for changed or new classes (Tick if no updates were necessary.)

How can I get additional information on failed tests during CI

Click to expand

If your PR is failing you can check out

• The details of the action statuses at the end of the PR or the "Checks" tab.
• http://cdash.openms.de/index.php?project=OpenMS and look for your PR. Use the "Show filters" capability on the top right to search for your PR number.
  If you click in the column that lists the failed tests you will get detailed error messages.

Advanced commands (admins / reviewer only)

Click to expand

• /reformat (experimental) applies the clang-format style changes as additional commit. Note: your branch must have a different name (e.g., yourrepo:feature/XYZ) than the receiving branch (e.g., OpenMS:develop). Otherwise, reformat fails to push.
• setting the label "NoJenkins" will skip tests for this PR on jenkins (saves resources e.g., on edits that do not affect tests)
• commenting with rebuild jenkins will retrigger Jenkins-based CI builds

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⚠️ Note: Once you opened a PR try to minimize the number of pushes to it as every push will trigger CI (automated builds and test) and is rather heavy on our infrastructure (e.g., if several pushes per day are performed).

[jpfeuffer]

Centos7 is not supported by GitHub Actions anymore. Node was upgraded to 20, which requires a newer glibc.

https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

[poshul]

Centos7 is not supported by GitHub Actions anymore. Node was upgraded to 20, which requires a newer glibc.

https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

Yeah. I noticed. Any suggestions on the best way to move forward is?

[jpfeuffer]

Only workaround is to update many Linux. Otherwise it will fail mid May.

[poshul]

Only workaround is to update many Linux. Otherwise it will fail mid May.

So this effectively means manylinux2014 is dead for GHA?

[jpfeuffer]

I am pretty sure, yes. If they require node 20 for security (even when downgrading actions versions) then yes, you won't be able to use actions that use nodejs anymore. Which are most of them I guess.

[poshul]

Okay. I can start taking a look at putting together a separate PR for upgrading which manylinux we are using. Tomorrow. It's past my bedtime already

[jpfeuffer]

Hm maybe they keep old action versions running/allowed?
actions/upload-artifact#479

[jpfeuffer]

But the linked PR feels more like a desperate attempt to evade the inevitable

[jpfeuffer]

OpenMS/contrib#142

Just try to update the base container in the Linux branch of the actions here.

[jpfeuffer]

I feel like you should ignore the system compat check in the test, not build step

[timosachsenberg]

maybe also say here that it is a workaround for mac neded for XYZ? above is kind of fine because there it specifies on which os it runs.

[ecederstrand]

@poshul Is there any chance this could reach a version on PyPI soon?