BarcodeForge/.github/workflows/python-test.yml at main · andersen-lab/BarcodeForge · GitHub

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name: BarcodeForge CI

on:
  push:
    branches: [ main ]
  pull_request:

permissions:
  contents: read

jobs:
  testsuite:
    name: Test Package (Python ${{ matrix.python-version }} | ${{ matrix.os }})
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest]
        python-version: [ "3.10", "3.11", "3.12", "3.13" ]

    steps:
      # Downloads a copy of the code in your repository before running CI tests
      - name: Check out repository code
        uses: actions/checkout@v6

      - name: Setup for conda
        uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          channels: bioconda,conda-forge
          channel-priority: true
          python-version: ${{ matrix.python-version }}
          activate-environment: test

      - name: Install
        shell: bash -l {0}
        run: |
          conda install -n base conda-libmamba-solver
          conda config --set solver libmamba
          conda config --add channels bioconda
          conda config --add channels conda-forge
          conda install usher ucsc-fatovcf -y
          pip install '.[dev-requirements,test-requirements]'

      - name: Test
        shell: bash -l {0}
        run: |
          conda activate test
          pytest -vvv --tb=short

      - name: Run barcode generation test
        shell: bash -l {0}
        run: |
          barcodeforge --debug barcode barcodeforge/assets/reference.fasta barcodeforge/assets/aligned.fasta barcodeforge/assets/tree.nwk barcodeforge/assets/lineages.tsv --matutils-overlap 0.8 --threads 4 --prefix RSVa
          diff -q RSVa-barcode.csv barcodeforge/assets/RSVa-barcode.csv || (echo "Files are not identical!" && exit 1)

  lint:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v6
    - name: Set up Python
      uses: actions/setup-python@v6
      with:
        python-version: '3.10'
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install black
    - name: Lint with Black
      run: |
        black --check .