barcode_validator/.github/workflows/python-package.yml at main · bge-barcoding/barcode_validator · GitHub

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name: Python package

on:
  push:
    branches: [ "main", "refactor", "schema", "batched", "in-place-record-trimming" ]
    tags:
      - 'v*'  # Trigger on any tag that starts with 'v'
  pull_request:
    branches: [ "main" ]

jobs:
  build:
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0  # Important for setuptools_scm to determine the version

    - name: Set up Conda
      uses: conda-incubator/setup-miniconda@v3
      with:
        channels: conda-forge,bioconda
        channel-priority: strict
        activate-environment: barcode_validator
        environment-file: environment.yml
        auto-activate-base: false

    - name: Install additional test dependencies
      shell: bash -l {0}
      run: |
        conda activate barcode_validator
        pip install pytest pytest-cov flake8
        pip install -e .

    - name: Test environment
      shell: bash -l {0}
      run: |
        conda activate barcode_validator
        conda list
        which python
        which blastn
        which hmmalign

    - name: Lint with flake8
      shell: bash -l {0}
      run: |
        conda activate barcode_validator
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics

    - name: Test with pytest
      shell: bash -l {0}
      env:
        GALAXY_DOMAIN: ${{ secrets.GALAXY_DOMAIN }}
        GALAXY_API_KEY: ${{ secrets.GALAXY_API_KEY }}
      run: |
        conda activate barcode_validator
        pytest --cov=barcode_validator --cov-report=xml

    - name: Upload coverage to Codecov
      uses: codecov/codecov-action@v3
      with:
        file: ./coverage.xml
        flags: unittests
        name: codecov-umbrella
        fail_ci_if_error: false

  publish:
    needs: build  # Only run if the build job passes
    if: startsWith(github.ref, 'refs/tags/v')  # Only run on tag pushes starting with 'v'
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0  # Important for setuptools_scm to determine the version

    - name: Set up Conda
      uses: conda-incubator/setup-miniconda@v3
      with:
        channels: conda-forge,bioconda
        channel-priority: strict
        activate-environment: barcode_validator
        environment-file: environment.yml
        auto-activate-base: false

    - name: Install build dependencies
      shell: bash -l {0}
      run: |
        conda activate barcode_validator
        pip install build twine

    - name: Build package
      shell: bash -l {0}
      run: |
        conda activate barcode_validator
        python -m build

    - name: Publish package
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        user: __token__
        password: ${{ secrets.PYPI_API_TOKEN }}