python-package.yml

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
name: Mikado
on:
  [ push, pull_request ]
jobs:
  build:
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash -l {0}
    strategy:
      matrix:
        python-version: [ "3.7", "3.8", "3.9" ]
        solver: ["classic", "libmamba"]
        # os: [ubuntu-latest, macos-latest]
        os: [ubuntu-latest]
    steps:
    - name: Install system development tools
      if: startsWith(runner.os, 'Linux')
      run: |
        export DEBIAN_FRONTEND=noninteractive
        sudo apt update
        sudo apt install -y build-essential zlib1g-dev zlib1g
    - uses: actions/checkout@v2
    - uses: actions/cache@v2
      if: startsWith(runner.os, 'Linux')
      with:
        path: ~/.cache/pip
        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
        restore-keys: |
          ${{ runner.os }}-pip-
    - uses: actions/cache@v2
      if: startsWith(runner.os, 'macOS')
      with:
        path: ~/Library/Caches/pip
        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
        restore-keys: |
          ${{ runner.os }}-pip-
    - name: Cache conda
      id: cache-miniconda
      uses: actions/cache@v2
      env:
        CACHE_NUMBER: 1
      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@v3
      id: setup-miniconda
      continue-on-error: true
      with:
        auto-update-conda: true
        conda-solver: ${{ matrix.solver }}
        python-version: ${{ matrix.python-version }}
        miniconda-version: "latest"
        mamba-version: "*"
        use-mamba: true
        channels: conda-forge, defaults, bioconda, anaconda
        channel-priority: true
        use-only-tar-bz2: true  # IMPORTANT: This needs to be set for caching to work properly!
        activate-environment: "mikado2"
        environment-file: ./environment.yml
        # auto-activate-base: false
    - name: Install dependencies
      run: |
        gcc --help
        pip install -r requirements.txt
        python -c "import pysam; print(pysam.__version__)"
        pip install Cython pytest-cov
        python setup.py develop
    - name: Test light
      run: |
        pytest -m slow Mikado/tests/test_light.py::LightTest::test_subprocess_multi_empty_orfs
    - name: Test full with coverage
      if: startsWith(runner.os, 'Linux')
      run: |
        pytest --cov=Mikado --cov-report=xml --cov-config=.coveragerc -m 'not triage';
    - name: Test full without coverage
      if: startsWith(runner.os, 'macOS')
      run: |
        pytest -m 'not triage';
    - 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 fast
      run: |
        python -c "import Mikado; Mikado.test(label='fast')";
    - name: Test seed
      run: |
        # Check that the seed is set properly
        mikado serialise --junctions sample_data/junctions.bed --genome Mikado/tests/chr5.fas.gz \
          --transcripts Mikado/tests/check_seed.fa --configuration Mikado/tests/check_seed.yaml;
        mikado pick --log $(pwd)/pick.20a.log --procs 2 --seed 20 --genome Mikado/tests/chr5.fas.gz  \
          --configuration Mikado/tests/check_seed.yaml -od 20a Mikado/tests/check_seed.gtf;
        mikado pick --log $(pwd)/pick.20b.log --procs 2 --seed 20 --genome Mikado/tests/chr5.fas.gz  \
          --configuration Mikado/tests/check_seed.yaml -od 20b Mikado/tests/check_seed.gtf;
        mikado pick --log $(pwd)/pick.20c.log --procs 2 --seed 20 --genome Mikado/tests/chr5.fas.gz  \
          --json-conf Mikado/tests/check_seed.yaml -od 20c Mikado/tests/check_seed.gtf;
        mikado pick --log $(pwd)/pick.20d.log --procs 2 --seed 20 --genome Mikado/tests/chr5.fas.gz  \
          --json-conf Mikado/tests/check_seed.yaml -od 20d Mikado/tests/check_seed.gtf;
        mikado pick --log $(pwd)/pick.10.log --procs 2 --seed 1000 --genome Mikado/tests/chr5.fas.gz  \
          --json-conf Mikado/tests/check_seed.yaml -od 1000 Mikado/tests/check_seed.gtf;
        if [[ $(diff -q 20a 20b) || $(diff -q 20a 20c) || $(diff -q 20a 20d) ]]; then exit 1; fi
        if [[ ! $(diff -q 20a 1000) ]]; then exit 1; fi