test.yml

name: test

# run unit and integration tests for the ProteinCartography package

on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main
    # 'synchronize' means the PR was updated with new commits
    types: [opened, reopened, labeled, synchronize]

jobs:
  test:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -el {0}
    steps:
      - uses: actions/checkout@v4

      - name: Setup conda
        uses: conda-incubator/setup-miniconda@v2
        with:
          miniforge-variant: Mambaforge
          miniforge-version: latest
          python-version: "3.9"
          use-mamba: true
          activate-environment: test-env
          auto-activate-base: false
          # note: the docs claim `use-only-tar-bz2` must be set to true
          # in order for package caching to work properly,
          # but this results in many package-not-found errors,
          # so we set it to false and do not use package caching
          use-only-tar-bz2: false

      - name: Cache the conda env
        uses: actions/cache@v2
        id: cache-conda-env
        with:
          path: ${{ env.CONDA }}/envs
          key:
            conda-${{ runner.os }}--${{ runner.arch }}--${{ hashFiles('envs/cartography_test.yml') }}

      - name: Create the conda env from which to run snakemake
        run: |
          mamba env update -n test-env -f envs/cartography_test.yml
        if: steps.cache-conda-env.outputs.cache-hit != 'true'

      - name: Cache the conda envs created by snakemake
        uses: actions/cache@v2
        id: cache-snakemake-conda-envs
        with:
          path: .snakemake/conda
          key:
            conda-${{ runner.os }}--${{ runner.arch }}--${{ hashFiles('envs/*.yml') }}

      - name: Create the snakemake conda envs
        run: |
          snakemake --configfile demo/search-mode/config_actin.yml --use-conda --conda-create-envs-only --cores 1
        if: steps.cache-snakemake-conda-envs.outputs.cache-hit != 'true'

      - name: Run the tests
        run: |
          make test

      - name: Run the tests without mocks
        if: contains(github.event.pull_request.labels.*.name, 'run-slow-tests')
        run: |
          make test-without-mocks