python-app.yaml

name: MONSDA CI

on:
  push:
    branches: [main, develop]
    tags:
      - "v*"
  pull_request:
    types: [opened, synchronize, reopened, labeled, unlabeled]
  workflow_dispatch:
    inputs:
      run_full_pipeline:
        description: "Run full pipeline integration test"
        required: false
        default: false
        type: boolean

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

jobs:
  lint:
    name: Lint (flake8, isort)
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: "3.12"
          cache: "pip"
      - name: Install linting tools
        run: |
          python -m pip install --upgrade pip
          python -m pip install flake8 isort
      - name: Check import sorting with isort
        run: isort --check-only --diff MONSDA/ tests/
        continue-on-error: true
      - name: Lint with flake8
        run: flake8 MONSDA/ tests/ --count --statistics --show-source
        continue-on-error: true

  tests:
    name: Unit tests (pytest)
    runs-on: ubuntu-latest
    needs: lint
    defaults:
      run:
        shell: bash -el {0}
    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive
      - uses: conda-incubator/setup-miniconda@v3
        with:
          miniconda-version: "latest"
          activate-environment: monsda-test
          environment-file: environment.yml
          python-version: 3.12.2
          channels: conda-forge,bioconda
          allow-softlinks: true
          channel-priority: flexible
          show-channel-urls: true
          use-only-tar-bz2: false
          auto-activate-base: false
      - name: Install dependencies
        run: |
          cd ${{ github.workspace }}
          python -m pip install --upgrade pip
          python -m pip install -e .
          python -m pip install pytest pytest-cov
      - name: Run unit tests with coverage
        run: |          
          cd ${{ github.workspace }}
          pytest tests/ -v --cov=MONSDA --cov-report=xml --cov-report=html --cov-fail-under=25
      - name: Upload coverage reports
        uses: codecov/codecov-action@v4
        if: always()
        with:
          files: ./coverage.xml
          fail_ci_if_error: false
          verbose: true

  build:
    name: Build package
    runs-on: ubuntu-latest
    needs: tests
    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive
          fetch-depth: 0
      - uses: actions/setup-python@v5
        with:
          python-version: "3.12"
          cache: "pip"
      - name: Install build tools
        run: |
          python -m pip install --upgrade pip
          python -m pip install build wheel setuptools versioneer
      - name: Sync config versions
        run: |
          python scripts/update_config_versions.py configs/*.json tests/data/config_*.json
      - name: Build distribution
        run: |
          python -m build
      - name: Check build artifacts
        run: |
          ls -lh dist/
          python -m pip install twine
          twine check dist/*
      - name: Upload build artifacts
        uses: actions/upload-artifact@v4
        with:
          name: python-package-distributions
          path: dist/
          retention-days: 7

  full-pipeline:
    name: Full pipeline integration test
    runs-on: ubuntu-latest
    needs: tests
    if: >-
      (github.event_name == 'workflow_dispatch' && inputs.run_full_pipeline) ||
      (github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'full-pipeline'))
    defaults:
      run:
        shell: bash -el {0}
    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive
          fetch-depth: 0
      - uses: conda-incubator/setup-miniconda@v3
        with:
          miniconda-version: "latest"
          activate-environment: monsda-test
          environment-file: environment.yml
          python-version: 3.12.2
          channels: conda-forge,bioconda
          allow-softlinks: true
          channel-priority: flexible
          show-channel-urls: true
          use-only-tar-bz2: false
          auto-activate-base: false
      - name: Build and install MONSDA
        run: |
          cd ${{ github.workspace }}
          python -m pip install --upgrade pip
          python -m pip install -e .
      - name: Prepare integration test config
        run: |
          cd ${{ github.workspace }}
          python scripts/update_config_versions.py tests/data/config_Test.json
      - name: Run full pipeline test
        run: |
          cd ${{ github.workspace }}/tests
          ln -fs data/* .
          mkdir -p CONDALIB
          monsda -j 6 -c config_Test.json --directory ${PWD} --use-conda --conda-prefix CONDALIB --save
      - name: Upload test logs on failure
        if: failure()
        uses: actions/upload-artifact@v4
        with:
          name: full-pipeline-debug-artifacts
          path: |
            ${{ github.workspace }}/tests/LOGS
            ${{ github.workspace }}/tests/SUBSNAKES
            ${{ github.workspace }}/tests/FASTQ
            ${{ github.workspace }}/tests/MAPPED
            ${{ github.workspace }}/tests/QC
            ${{ github.workspace }}/tests/COUNTING
            ${{ github.workspace }}/tests/PEAKS
            ${{ github.workspace }}/tests/TRACKS

  publish:
    name: Publish to PyPI
    runs-on: ubuntu-latest
    needs: build
    if: startsWith(github.ref, 'refs/tags/')
    environment:
      name: pypi
      url: https://pypi.org/project/MONSDA
    permissions:
      id-token: write
    steps:
      - name: Download build artifacts
        uses: actions/download-artifact@v4
        with:
          name: python-package-distributions
          path: dist/
      - name: Publish to PyPI
        uses: pypa/gh-action-pypi-publish@release/v1
        with:
          repository-url: https://upload.pypi.org/legacy/