diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index ae06734e..a06fb747 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -8,11 +8,13 @@ jobs: runs-on: ${{ matrix.os }} defaults: run: - shell: bash -l {0} + shell: bash -el {0} strategy: matrix: - python-version: [ 3.7, 3.8, 3.9 ] - os: [ubuntu-latest, macos-latest] + # python-version: [ "3.8", "3.9" ] + python-version: [ "3.9" ] + # os: [ubuntu-latest, macos-latest] + os: [ubuntu-latest] steps: - name: Install system development tools if: startsWith(runner.os, 'Linux') @@ -39,30 +41,40 @@ jobs: id: cache-miniconda uses: actions/cache@v2 env: - CACHE_NUMBER: 1 + CACHE_NUMBER: 0 with: - repo-token: ${{ secrets.GITHUB_TOKEN }} path: ~/conda_pkgs_dir key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('./environment.yml') }} + - uses: actions/checkout@v4 - uses: conda-incubator/setup-miniconda@v2 + name: setup-Mambaforge with: python-version: ${{ matrix.python-version }} - repo-token: ${{ secrets.GITHUB_TOKEN }} - miniconda-version: "latest" + miniforge-variant: Mambaforge + miniforge-version: 4.9.2-4 + # mamba-version: "*" + # channels: conda-forge, defaults + channels: conda-forge, bioconda, defaults, anaconda + channel-priority: true + activate-environment: "mikado2" environment-file: ./environment.yml - mamba-version: "*" use-mamba: true - channels: conda-forge, defaults - use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! - # auto-update-conda: false - activate-environment: "mikado2" - # auto-activate-base: false + # use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! + - name: Verify conda environment + run: | + conda info --envs + conda env list + conda activate mikado2 + conda list - name: Install dependencies run: | - gcc --help + conda activate mikado2 + python --version + gcc --version + pip --version pip install -r requirements.txt - python -c "import pysam; print(pysam.__version__)" + python -c "import pysam; print(pysam.__version__)" pip install Cython pytest-cov python setup.py develop - name: Test light @@ -79,17 +91,17 @@ jobs: - name: Upload coverage to Codecov if: startsWith(runner.os, 'Linux') uses: codecov/codecov-action@v1 - - name: Test daijin - if: startsWith(runner.os, 'Linux') - run: | - mamba install -c bioconda -c conda-forge -y bioconda::portcullis stringtie scallop "gmap!=2021.02.22" \ - star hisat2 prodigal blast diamond transdecoder conda-forge::gnuplot kallisto samtools gffread; - cd sample_data; snakemake --latency-wait 60 --jobs 5 --cores 5 - - name: Test daijin mikado - if: startsWith(runner.os, 'macOS') - run: | - mamba install -c bioconda -c conda-forge -y prodigal blast diamond transdecoder kallisto samtools gffread; - cd sample_data; snakemake --latency-wait 60 --jobs 5 --cores 5 complete_no_assemble + # - name: Test daijin + # if: startsWith(runner.os, 'Linux') + # run: | + # mamba install -c bioconda -c conda-forge -y bioconda::portcullis stringtie scallop "gmap!=2021.02.22" \ + # star hisat2 prodigal blast diamond transdecoder conda-forge::gnuplot kallisto samtools gffread; + # cd sample_data; snakemake --latency-wait 60 --jobs 5 --cores 5 + # - name: Test daijin mikado + # if: startsWith(runner.os, 'macOS') + # run: | + # mamba install -c bioconda -c conda-forge -y prodigal blast diamond transdecoder kallisto samtools gffread; + # cd sample_data; snakemake --latency-wait 60 --jobs 5 --cores 5 complete_no_assemble - name: Test fast run: | python -c "import Mikado; Mikado.test(label='fast')";