ci.yaml

name: CI

on:
  push:
    # The docker branch tracks master, so it doesn't need testing separately
    branches-ignore:
      docker
  pull_request:

defaults:
  run:
    shell: bash

jobs:
  # Main TractoR tests, on Linux only
  integration-check:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        R: [ '3.6.2', '4.2.3', 'release' ]
    
    steps:
    - name: Check out code
      uses: actions/checkout@v4
      with:
        submodules: true
    
    - name: Install and set up R
      uses: r-lib/actions/setup-r@v2
      with:
        r-version: ${{ matrix.R }}
    
    # igraph depends on glpk in the 2.0.x series, so this is required for deep testing
    - name: Install upstream system dependencies
      run: sudo apt-get install -y libglpk-dev
    
    - name: Cache dependencies
      id: cache-deps
      uses: actions/cache@v4
      with:
        path: lib/R
        key: ${{ runner.os }}-deps-${{ matrix.R }}-${{ hashFiles('lib/*/DESCRIPTION') }}
    
    - name: Install dependencies
      if: ${{ steps.cache-deps.outputs.cache-hit != 'true' }}
      run: make install-libs
    
    - name: Install main packages
      run: make install-main
    
    - name: Run tests
      run: make deeptest
    
    - name: Generate debug test output
      if: failure()
      run: make dtest
  
  # Standard R CMD check on tractor.base package (Linux and Windows)
  base-check:
    strategy:
      fail-fast: false
      matrix:
        os: [ ubuntu-latest, windows-latest ]
        R: [ release, devel ]
    
    runs-on: ${{ matrix.os }}
    
    # No submodules needed in this case, as we'll install dependencies from CRAN
    steps:
    - name: Check out code
      uses: actions/checkout@v4
      with:
        submodules: false
    
    - name: Install and set up R
      uses: r-lib/actions/setup-r@v2
      with:
        r-version: ${{ matrix.R }}
    
    - name: Parse and install dependencies
      run: |
        deps <- read.dcf(file.path("tractor.base","DESCRIPTION"), c("Depends","Imports","LinkingTo","Suggests","Enhances"))
        deps <- na.omit(unlist(strsplit(deps, "\\s*,\\s*", perl=TRUE)))
        deps <- setdiff(unique(sub("\\s*\\([^\\)]+\\)\\s*$", "", deps, perl=TRUE)), c("R", rownames(installed.packages())))
        install.packages(deps)
      shell: Rscript {0}
    
    - name: Build package
      run: R CMD build tractor.base
    
    - name: Check package
      run: R CMD check --no-manual tractor.base*tar.gz
    
    # Upload the check directory as an artefact on failure
    - name: Upload check results
      if: failure()
      uses: actions/upload-artifact@v4
      with:
        name: ${{ matrix.os }}-R${{ matrix.R }}-check
        path: tractor.base.Rcheck