tests.yml

name: tests

on:
  push:
    branches:
      - "**"
    tags:
      - "!**"
  workflow_call:

env:
  POETRY_VERSION: 1.8.2

jobs:
  Tests:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        PYTHON_VERSION: ["3.11", "3.12"]
    steps:
      - uses: actions/checkout@v4
      - name: Checkout fulcrumgenomics/bwa
        uses: actions/checkout@v4
        with:
          repository: fulcrumgenomics/bwa
          ref: interactive_aln
          path: bwa
          fetch-depth: 0

      - name: Set up Python ${{ matrix.PYTHON_VERSION }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.PYTHON_VERSION }}

      - name: Set up miniconda
        uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-variant: Mambaforge
          miniforge-version: latest
          channels: conda-forge,bioconda
          activate-environment: prymer
          environment-file: prymer.yml
          channel-priority: true
          auto-update-conda: true
          auto-activate-base: false
          python-version: ${{ matrix.PYTHON_VERSION }}

      - name: Install fulcrumgenomics/bwa
        shell: bash -l {0}
        run: |
          conda activate prymer
          pushd bwa
          make -j $(nproc)
          cp bwa ${CONDA_PREFIX}/bin
          popd

      - name: Configure poetry and check lock file
        shell: bash -l {0}
        run: |
          conda activate prymer
          poetry config virtualenvs.in-project false
          poetry check --lock

      - name: Poetry install
        shell: bash -l {0}
        run: |
          conda activate prymer
          poetry lock --no-update
          poetry install --with dev

      - name: Unit tests (with doctest and coverage)
        shell: bash -l {0}
        run: |
          conda activate prymer
          poetry run pytest --cov=prymer --cov-report=xml --cov-branch --doctest-plus --doctest-modules prymer tests

      - name: Upload coverage reports to Codecov
        uses: codecov/codecov-action@v4.5.0
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
      
      - name: Style checking
        shell: bash -l {0}
        run: |
          conda activate prymer
          poetry run ruff format --check

      - name: Run lint
        shell: bash -l {0}
        run: |
          conda activate prymer
          poetry run ruff check

      - name: Run mypy
        shell: bash -l {0}
        run: |
          conda activate prymer
          poetry run mypy

      - name: Run docs
        shell: bash -l {0}
        run: |
          conda activate prymer
          set -euo pipefail
          poetry run mkdocs build --strict