feat: bring your own condarc

[jakevc]

Summary by CodeRabbit

• New Features
  • Added support for specifying a custom Conda configuration file when running the Snakemake GitHub Action.
• Documentation
  • Updated documentation to describe new input parameters and provide usage examples for custom Conda configuration.
• Tests
  • Introduced automated tests to verify functionality with a custom Conda configuration file.

[coderabbitai[bot]]

📝 Walkthrough

Walkthrough

The changes introduce a new optional condarc-file input to the Snakemake GitHub Action, allowing users to specify a custom Conda configuration file. Documentation and workflow examples are updated, and the action now validates and applies the custom Conda configuration during runs. A new test job verifies this functionality.

Changes

File(s)	Change Summary
README.md	Documents new inputs: snakemake-version, install-apptainer, condarc-file; updates usage examples.
action.yml	Adds condarc-file input, validates its existence, passes it to Conda setup, and updates Conda environment setup.
.github/workflows/main.yml	Renames "build" job to "test"; adds "test-condarc" job to test custom Conda config file usage.
.test/condarc.yaml	Adds sample Conda configuration file for testing the condarc-file input.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant GitHub Actions Runner
    participant Snakemake Action
    participant Conda Setup

    User->>GitHub Actions Runner: Push workflow with condarc-file input
    GitHub Actions Runner->>Snakemake Action: Start action with condarc-file
    Snakemake Action->>Snakemake Action: Validate condarc-file exists
    alt condarc-file found
        Snakemake Action->>Conda Setup: Setup Miniconda with condarc-file
        Conda Setup->>Snakemake Action: Conda environment configured
    else condarc-file missing
        Snakemake Action->>GitHub Actions Runner: Fail with error
    end
    Snakemake Action->>GitHub Actions Runner: Run workflow with custom Conda config

Possibly related PRs

• snakemake/snakemake-github-action#39: Adds and modifies composite action structure, including Conda-based setup and related input parameters, directly affecting the same files and logic as this PR.

Suggested reviewers

• johanneskoester

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[m-jahn]

Hi @jakevc Is this PR still active? If yes I can review if you like to invite me. I've gone through the changes and can not see how this extra feature would harm the action.

[johanneskoester]

I would like to wait with this. Reason: Snakemake will soon move away from conda to directly using rattler for conda package deployment. This would deprecate the desired option.