run-tests.yaml

on:
  push:
    branches:
      - master
  pull_request:

name: Build the tool

jobs:
  test:
    runs-on: ubuntu-latest

    steps:
    - name: Checkout repo
      uses: actions/checkout@v4

    - name: Cache installed
      id: installed
      uses: actions/cache@v4
      with:
        path: extern/installed
        key: deps-${{ hashFiles('extern/**/build.sh') }}

    - name: Build igraph
      if: steps.installed.outputs.cache-hit != 'true'
      run: |
        cd extern/igraph
        bash build.sh

    - name: Prepare the build
      run: |
        cmake \
            -S . \
            -B build \
            -DCMAKE_BUILD_TYPE=Release \
            -DCMAKE_INSTALL_PREFIX=extern/installed

    - name: Check all transitive dependencies are pinned
      run: |
        cat extern/CMakeLists.txt | \
            grep "FetchContent_MakeAvailable" | \
            sed "s/FetchContent_MakeAvailable(//" | \
            sed "s/)//" | \
            tr '[:upper:]' '[:lower:]' | \
            sort > requested.txt
        ls build/_deps/ | \
            grep "src$" | \
            sed "s/-src//" | \
            sort > observed.txt
        diffs=$(diff observed.txt requested.txt )
        if [[ $diffs != '' ]]
        then
            exit 1
        fi

    - name: Compile the tool
      run: cmake --build build

    - name: Download Zeisel
      uses: wei/wget@v1
      with:
        args: -O matrix.mtx.gz https://github.com/kanaverse/random-test-files/releases/download/zeisel-brain-v1.0.0/matrix.mtx.gz

    - name: Run the tool
      run: ./build/scran --mito-list 19972-20005 matrix.mtx.gz