mgatk/.github/workflows/ci.yml at master · caleblareau/mgatk · GitHub

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name: CI

on:
  push:
    branches: [master, main]
  pull_request:
    branches: [master, main]

jobs:
  # ---------------------------------------------------------------------------
  # Fast job: install the package on a Python matrix, confirm every console
  # script imports and reports its version, and run the pure-Python unit tests.
  # The R/snakemake-dependent end-to-end tests skip themselves here (see the
  # `requires_*` markers in tests/conftest.py).
  # ---------------------------------------------------------------------------
  unit:
    name: Unit tests (Python ${{ matrix.python-version }})
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.11", "3.12"]
    steps:
      - uses: actions/checkout@v4

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: pip
          cache-dependency-path: setup.py

      - name: Install mgatk + test dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -e ".[test]"

      - name: Console scripts resolve and report a version
        run: |
          mgatk --version
          mgatk-del --version
          mgatk-del-find --version

      - name: Run test suite (end-to-end tests auto-skip without R)
        run: pytest -v

  # ---------------------------------------------------------------------------
  # Full job: adds R + Bioconductor and runs the complete suite, including the
  # snakemake/R end-to-end pipeline tests against the bundled sample data.
  # snakemake is installed into the same environment as the package, so the
  # subprocess it launches can import mgatk.processing.
  # ---------------------------------------------------------------------------
  end-to-end:
    name: End-to-end (snakemake + R/Bioconductor)
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.12"
          cache: pip
          cache-dependency-path: setup.py

      - name: Set up R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: release
          use-public-rspm: true

      - name: Cache R packages
        uses: actions/cache@v4
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-rpkgs-${{ hashFiles('.github/workflows/ci.yml') }}
          restore-keys: ${{ runner.os }}-rpkgs-

      - name: Install R / Bioconductor packages
        run: |
          Rscript -e 'install.packages(c("data.table", "Matrix", "dplyr", "ggplot2", "ggrepel"), repos = "https://cloud.r-project.org")'
          Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager", repos = "https://cloud.r-project.org"); BiocManager::install(c("SummarizedExperiment", "GenomicRanges"), update = FALSE, ask = FALSE)'

      - name: Install mgatk + test dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -e ".[test]"

      - name: Confirm snakemake and R are visible to mgatk
        run: |
          mgatk --version
          snakemake --version
          Rscript -e 'stopifnot(all(sapply(c("data.table", "SummarizedExperiment", "GenomicRanges", "Matrix", "dplyr"), requireNamespace, quietly = TRUE)))'

      - name: Run full test suite
        run: pytest -v