Cron CI failure: timeout in micromamba list

[orbeckst]

The latest CI cron failed https://github.com/Becksteinlab/GromacsWrapper/actions/runs/11081172277

The job running on runner GitHub Actions xxx has exceeded the maximum execution time of 360 minutes.

It seems to be the

micromamba list

step.

Need to investigate.

[orbeckst]

Possibly mamba-org/setup-micromamba#225

[orbeckst]

There's some chatter that GH actions uses its own micromamba and ignores the installed one. In our logs, eg https://github.com/Becksteinlab/GromacsWrapper/actions/runs/11081172277/job/30886588889 , it looks as if we are installing in the right place:

1. Install to /home/runner/micromamba-bin/micromamba

Run mamba-org/setup-micromamba@v1
  with:
    environment-file: ci/conda-envs/test_env.yaml
    condarc: channels:
     - conda-forge
     - bioconda
  channel_priority: flexible         
  
    cache-downloads: true
    cache-environment: true
    create-args: python=3.11.*=*_cpython gromacs==2018.6
  env:
    MPLBACKEND: agg
Will download micromamba to /home/runner/micromamba-bin/micromamba
Install micromamba

We do get 2.0.1

 micromamba version : 2.0.1

which is the problematic version.
2. run list

/home/runner/micromamba-bin/micromamba list -r /home/runner/micromamba -n gromacs_wrapper

fails (inside the setup-micromamba action).

[orbeckst]

I just deleted all caches for GH actions and now trying to rerun.

[orbeckst]

Deleting caches did not help.