Merge pull request #104 from karel-brinda/tests #188
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| Testing: | |
| runs-on: ${{ matrix.os }} | |
| continue-on-error: true | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-latest, macos-latest ] | |
| python-version: [ "3.11" ] | |
| snakemake-version: [ 6, 7, 8 ] | |
| exclude: | |
| - python-version: "3.11" #package dep conflict | |
| snakemake-version: 6 | |
| include: | |
| - os: ubuntu-latest | |
| python-version: "3.8" | |
| snakemake-version: 7 | |
| - os: ubuntu-latest | |
| python-version: "3.9" | |
| snakemake-version: 7 | |
| - os: ubuntu-latest | |
| python-version: "3.10" | |
| snakemake-version: 7 | |
| #- os: ubuntu-latest ###### problem: snakemake bug; TypeError: SpawnedJobArgsFactory.general_args() | |
| # python-version: "3.11" | |
| # snakemake-version: "8.1" | |
| - os: ubuntu-latest | |
| python-version: "3.11" | |
| snakemake-version: "8.2" | |
| - os: ubuntu-latest | |
| python-version: "3.11" | |
| snakemake-version: "8.3" | |
| - os: ubuntu-latest | |
| python-version: "3.11" | |
| snakemake-version: "8.4" | |
| - os: ubuntu-latest | |
| python-version: "3.11" | |
| snakemake-version: "8.5" | |
| - os: ubuntu-latest | |
| python-version: "3.8" | |
| snakemake-version: 7 | |
| ############################################################ | |
| - os: macos-latest | |
| python-version: "3.9" | |
| snakemake-version: 7 | |
| - os: macos-latest | |
| python-version: "3.10" | |
| snakemake-version: 7 | |
| #- os: ubuntu-latest ###### problem: snakemake bug; TypeError: SpawnedJobArgsFactory.general_args() | |
| # python-version: "3.11" | |
| # snakemake-version: "8.1" | |
| - os: macos-latest | |
| python-version: "3.11" | |
| snakemake-version: "8.2" | |
| - os: macos-latest | |
| python-version: "3.11" | |
| snakemake-version: "8.3" | |
| - os: macos-latest | |
| python-version: "3.11" | |
| snakemake-version: "8.4" | |
| - os: macos-latest | |
| python-version: "3.11" | |
| snakemake-version: "8.5" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| micromamba-version: "1.5.6-0" | |
| environment-name: test-env | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| - defaults | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| snakemake-minimal=${{ matrix.snakemake-version }} | |
| mamba | |
| make | |
| init-shell: bash | |
| cache-environment: true | |
| post-cleanup: all | |
| - name: Versions | |
| shell: bash -el {0} | |
| run: | | |
| micromamba activate test-env | |
| python -v | |
| snakemake -v | |
| - name: Make test | |
| shell: bash -el {0} | |
| run: | | |
| micromamba activate test-env | |
| make test | |
| # - name: Make bigtest | |
| # shell: bash -el {0} | |
| # run: | | |
| # make cleanall | |
| # micromamba activate test-env | |
| # make bigtest |