Stream: git

Topic: Failing github actions

view this post on Zulip Michael Levy (Dec 17 2024 at 16:13):

I have a repository that runs some Github Actions overnight, and now these tests are failing in the mamba-org/setup-micromamba@v2 stage while trying to install some dependencies with pip:

  Installing pip packages: sphinx-click, sphinxcontrib-autoyaml, git+https://github.com/dask/dask-mpi.git, --editable=..
    error: subprocess-exited-with-error

    × Getting requirements to build wheel did not run successfully.
    │ exit code: 1
    ╰─> [17 lines of output]
        Traceback (most recent call last):
          File "/home/runner/micromamba/envs/dev-feisty/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
            main()
          File "/home/runner/micromamba/envs/dev-feisty/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
            json_out['return_val'] = hook(**hook_input['kwargs'])
          File "/home/runner/micromamba/envs/dev-feisty/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
            return hook(config_settings)
          File "/tmp/pip-build-env-bly_n4i8/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 334, in get_requires_for_build_wheel
            return self._get_build_requires(config_settings, requirements=[])
          File "/tmp/pip-build-env-bly_n4i8/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 304, in _get_build_requires
            self.run_setup()
          File "/tmp/pip-build-env-bly_n4i8/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 522, in run_setup
            super().run_setup(setup_script=setup_script)
          File "/tmp/pip-build-env-bly_n4i8/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 320, in run_setup
            exec(code, locals())
          File "<string>", line 3, in <module>
        ModuleNotFoundError: No module named 'yaml'
        [end of output]

    note: This error originates from a subprocess, and is likely not a problem with pip.
  error: subprocess-exited-with-error

  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> See above for output.

  note: This error originates from a subprocess, and is likely not a problem with pip.
  critical libmamba pip failed to install packages

The last successful run was Sunday night, and then it started to fail. As far as I can tell, pyyaml is in the environment that mamba is trying to create, but I've tried:

  1. Explicitly adding pyyaml to the environment file
  2. Running pip install pyyaml before running micromamba (it was already installed with the system python)
  3. Pinning versions of the packages installed by pip

I don't see what else changed between those two runs... has anyone else seen something like this? Did you find a solution?

view this post on Zulip Katelyn FitzGerald (Dec 17 2024 at 16:52):

I'd have to look deeper to know exactly what's going on, but often the conda/mamba + pip installs are quite brittle and more things are on conda-forge these days. It might be worth seeing if you can install everything via conda-forge.

view this post on Zulip Michael Levy (Dec 17 2024 at 18:06):

Moving from pip to conda-forge seems to have done the trick -- thanks for the suggestion! I'm getting a sphinx build error in the build-docs test, but at least the environment is being created successfully :)

Last updated: May 16 2025 at 17:14 UTC