feat: allow to use custom snakemake branch instead of conda version

[johanneskoester]

Summary by CodeRabbit

• New Features

  • Added configurable Snakemake version selection from conda channels
  • Added support for installing Snakemake from a specific git branch, with precedence over version selection

• Documentation

  • Updated documentation with new input parameters and usage examples

• Chores

  • Enhanced CI testing with branch-targeted test execution
  • Updated conda environment configuration defaults

[coderabbitai]

📝 Walkthrough

Walkthrough

The PR adds support for installing Snakemake from a git branch via a new snakemake-branch input parameter. When specified, this input overrides snakemake-version and installs Snakemake directly from source. The changes include action input configuration, documentation updates, and a new CI test step demonstrating the feature.

Changes

Cohort / File(s)	Summary
Action Configuration action.yml	Added snakemake-branch input to support git-based Snakemake installation. When set, environment preparation installs python and pip instead of pinned snakemake, then executes conditional pip install step. Updated boolean input defaults from unquoted to string format ("false"); reformatted snakemake-version description; updated miniforge-version to latest.
Documentation README.md	Documented new inputs snakemake-version (conda version, default *) and snakemake-branch (git branch, optional). Specified precedence where snakemake-branch overrides snakemake-version. Added example workflow step demonstrating snakemake-branch: main usage.
CI Workflow .github/workflows/main.yml	Added "Test run branch" workflow step that executes the action against .test directory with snakemake-branch: "main" input before the existing "Test containerize" step.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The pull request title accurately describes the main change: adding the ability to use a custom Snakemake branch as an alternative to the conda version.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch feat/custom-branch

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[coderabbitai]

🧹 Nitpick comments (1)

action.yml (1)

102-106: Consider pinning Snakemake's dependencies or adding installation verification.

The pip install from git works, but a few observations:

1. If the branch name doesn't exist, pip will fail with an error message that may not be immediately clear to users.
2. Snakemake has many dependencies that will be resolved by pip rather than conda, which could lead to different behavior than the conda-installed version.

These are acceptable trade-offs for a feature explicitly designed for testing custom branches, but you might want to add a brief echo statement before the install to clarify what's happening.

💡 Optional: Add informative message before install

     - name: Install snakemake from git branch
       if: ${{ inputs.snakemake-branch != '' }}
       shell: bash -el {0}
       run: |
+        echo "Installing Snakemake from branch: ${{ inputs.snakemake-branch }}"
         python -m pip install "git+https://github.com/snakemake/snakemake@${{ inputs.snakemake-branch }}"

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@action.yml` around lines 102 - 106, The "Install snakemake from git branch"
step that installs via python -m pip install
"git+https://github.com/snakemake/snakemake@${{ inputs.snakemake-branch }}"
should be made more transparent and resilient: add an echo or printf before the
install indicating which branch is being installed (referencing the step name
and inputs.snakemake-branch), then after the pip install run a quick
verification such as checking the exit code and running python -m pip show
snakemake or snakemake --version to confirm installation succeeded; optionally,
if you want stricter reproducibility, consider adding pinned dependency
constraints or a requirements file reference to the pip install command to avoid
unexpected dependency resolution differences from the conda build.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Nitpick comments:
In `@action.yml`:
- Around line 102-106: The "Install snakemake from git branch" step that
installs via python -m pip install
"git+https://github.com/snakemake/snakemake@${{ inputs.snakemake-branch }}"
should be made more transparent and resilient: add an echo or printf before the
install indicating which branch is being installed (referencing the step name
and inputs.snakemake-branch), then after the pip install run a quick
verification such as checking the exit code and running python -m pip show
snakemake or snakemake --version to confirm installation succeeded; optionally,
if you want stricter reproducibility, consider adding pinned dependency
constraints or a requirements file reference to the pip install command to avoid
unexpected dependency resolution differences from the conda build.

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 3824ff98-159b-4367-8b0b-64a759f0cf60

📥 Commits

Reviewing files that changed from the base of the PR and between ae3c4be and 7712655.

📒 Files selected for processing (3)

• .github/workflows/main.yml
• README.md
• action.yml