diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 2e9db02f..7266a40b 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -13,20 +13,31 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.8", "3.9"] + python-version: ["3.12"] steps: - uses: actions/checkout@v2 - name: Setup mamba - uses: mamba-org/provision-with-micromamba@main + uses: mamba-org/setup-micromamba@v1 with: environment-file: test-env.yaml cache-downloads: true - channels: conda-forge, bioconda, defaults + condarc: | + channels: + - conda-forge + - bioconda + - defaults + channel_priority: flexible extra-specs: | python=${{ matrix.python-version }} + - name: Debug Micromamba + run: | + micromamba env list + micromamba info + micromamba env export -n test-env + - name: Run black manually run: | black --check --verbose ./ diff --git a/test-env.yaml b/test-env.yaml index 83b06361..23e47931 100644 --- a/test-env.yaml +++ b/test-env.yaml @@ -4,18 +4,18 @@ channels: - bioconda - defaults dependencies: - - scanpy=1.9.3 + - scanpy=1.10.3 - louvain - igraph - leidenalg - loompy - Click <8 - harmonypy>=0.0.5 - - bbknn>=1.5.0,<1.6.0 + - bbknn >=1.6.0 - mnnpy>=0.1.9.5 - # for mnnpy using n_jobs - - scipy <1.9.0 - - scikit-learn <1.3.0 + # Current Scipy installed requires certain numpy restrictions + - numpy >=1.17.3,<1.25.0 + - scipy - scrublet - fa2 # for testing