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fix: check if miniconda is present before installation, closes #47 #48

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fix: check if miniconda is present before installation, closes #47 #48

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2dd07a3
fix: check if miniconda is present before installation, closes #47
m-jahn Dec 4, 2025
c1be8a7
fix: change conda test file o executable
m-jahn Dec 4, 2025
17d67ca
fix: test more explicit check
m-jahn Dec 4, 2025
772c083
fix: use home env var
m-jahn Dec 4, 2025
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11 changes: 11 additions & 0 deletions action.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,18 @@ runs:
- snakemake ==${{ inputs.snakemake-version }}
EOF

- name: Check if miniconda is already installed
id: check-miniconda
shell: bash -el {0}
run: |
if [ -d "$HOME/miniconda3" ]; then
echo "installed=true" >> $GITHUB_OUTPUT
else
echo "installed=false" >> $GITHUB_OUTPUT
fi

- name: Setup conda
if: steps.check-miniconda.outputs.installed == 'false'
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@ezherman ezherman Dec 4, 2025

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If the setup step is skipped, conda won't be set up with .snakemake.environment.yaml as the default environment. Will snakemake then not be available as a consequence? If so, I imagine we need an additional step that installs snakemake into the base environment, or creates a snakemake conda environment, if conda is already available.

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@m-jahn m-jahn Dec 4, 2025

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the idea is that this check is specific for the miniconda setup step. when you run this step twice, as we do in the standard snakemake testing workflow, the env is already present and checked out from the first step, including snakemake. the test in this repo succeeded, meaning it works as expected. that's why I would also not test for any conda installation, as this could be the wrong one, only for the specific miniconda3 one.

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@ezherman ezherman Dec 4, 2025 •
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Gotcha yes, I see the containerize step would trigger a second setup miniconda step so there isn't a need for a second run step.

Regarding testing for miniconda3: if the workflow includes setup-miniconda upstream, then I believe the current implementation would not install snakemake. Or am I missing something? For example, if setup-miniconda is used to enable pytest:

  Testing:
    runs-on: ubuntu-latest
    needs:
      - Linting
      - Formatting
    steps:
      - uses: actions/checkout@v4

      - uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-version: latest
          use-mamba: true
          environment-file: .test/envs/test.yaml

      - name: Test workflow python functions with pytest
        shell: bash -el {0}
        run: |
          pytest workflow/tests/*.py

      - name: Test workflow
        uses: snakemake/[email protected]
        with:
          directory: .test
          snakefile: workflow/Snakefile
          args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache"

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@m-jahn m-jahn Dec 4, 2025

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Right. This is an edge case. A custom workflow with another setup-miniconda@v3 step would skip installing snakemake and fail. Is this a risk we can take (honest question)? In the end, the github action needs to work mainly for the test workflows, and it does so by wrapping several steps into a single one. In the example you posted, one would need to work around this by replacing the snakemake action with some selected steps.

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@ezherman ezherman Dec 5, 2025

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It's actually an important use-case, in my opinion. An extension is of this is to follow the snakemake-github-action with integration tests, which would not be possible if the action needs to be run in a separate job. Why limit the action to only operate in jobs that only use the snakemake github action?

What could go wrong by checking for a conda installation more generally, and updating/installing the snakemake environment if i conda exists?

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@m-jahn m-jahn Dec 5, 2025

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An extension of this is to follow the snakemake-github-action with integration tests, which would not be possible if the action needs to be run in a separate job

You can do this if you first run the snakemake action that installs miniconda, then the tests. The other way around as the example above won't work.

What could go wrong by checking for a conda installation more generally, and updating/installing the snakemake environment if i conda exists?

Possible, but then the action steps will change quite a lot. One would need different checks, like A) is any conda available? If not install miniconda + snakemake env as before. If yes, is snakemake available? If not create only env and activate, not using the setup-miniconda action. And checking for conda does not make sure that mamba is available (don't know what consequences that would have). At least current conda should also use the libmamba solver so should be equally fast.
If you have a good solution in mind don't hesitate to make a commit!

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@ezherman ezherman Dec 7, 2025

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Perhaps I'm biased as I believe the current implementation would require us to change a few of our github actions workflows, in which we run the snakemake github action as part of a collection of tests in the same job.

I'm heading into a busy week ahead of a few weeks off - I'll do my best to give this some thought and get back to you regarding the checks! Are you aware of anyone else who's opinion we could ask for?

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@m-jahn m-jahn Dec 8, 2025

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Hi Ezra, no rush I think this is probably going to be fixed upstream in miniconda, see David's other PR here. I've converted this PR to draft and we might close it without merging.

uses: conda-incubator/setup-miniconda@v3
with:
channels: conda-forge,bioconda
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