Python environment broken using uv/pip after setup-python

[flying-sheep]

Description

When installing Python modules into setup-python’s system environment for Python 3.12 on ubuntu-24.04, they can’t be imported for some reason.

See also:

• Fix Python 3.12 CI theislab/anndata2ri#211
• Fix CI scverse/pertpy#704

Platforms affected

• Azure DevOps
• GitHub Actions - Standard Runners
• GitHub Actions - Larger Runners

Runner images affected

• Ubuntu 20.04
• Ubuntu 22.04
• Ubuntu 24.04
• macOS 13
• macOS 13 Arm64
• macOS 14
• macOS 14 Arm64
• macOS 15
• macOS 15 Arm64
• Windows Server 2019
• Windows Server 2022
• Windows Server 2025

Image version and build link

20250126.1.0 and 20250209.1.0

• https://github.com/theislab/anndata2ri/actions/runs/13410556199/job/37459572518
• https://github.com/scverse/pertpy/actions/runs/13060568006/job/36442285406?pr=704

Is it regression?

Yes, it worked with ubuntu 22.04 and runners 20241215.1.0 and 20250105.1.0:

• https://github.com/theislab/anndata2ri/actions/runs/12647235334/job/35239243341
• https://github.com/scverse/pertpy/actions/runs/12718464229/job/35456949286

Expected behavior

installed Python packages are importable

Actual behavior

ModuleNotFoundError: No module named '…'

Repro steps

jobs:
  test:
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: '3.12'
      - run: pip install build
      - run: python -m build

[flying-sheep]

Update: We circumvented the problem in both CI workflows by using ubuntu-2022.04.

This is still quite a concerning issue.

[Prabhatkumar59]

Hi @flying-sheep - Thank you for bringing this issue to our attention. We will look into this issue and will update you after investigating.
Appreciate your patience! Thanks

[subir0071]

Hi @flying-sheep - Tried reproducing your issue, but was unable to do so.
Please see my sample workflow and the test run of the same.

Let me know in cae I missed something.
Thanks.

[flying-sheep]

It’s certainly a thing, see the linked logs. Try forking one of the repos above and reverting the change from ubuntu-latest to ubuntu-2022 to see it in action (unless it’s been fixed within the last 6 days)

[subir0071]

Unfortunately it is difficult to analyze individual user's repo to understand the anomaly.
Please help us with a workflow as provided above that helps reproduce the issue.

If the issue is with the runner image, it should be reproducible in any similar repository.

Thanks.