test-coverage.yaml

# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]

name: test-coverage

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

jobs:
  test-coverage:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - uses: actions/checkout@v2
 
      - name: Install ADMIXTOOLS/admixr dependencies
        run: sudo apt-get install libopenblas-dev libgsl-dev liblapack-dev bedtools

      - name: Compile and install ADMIXTOOLS
        run: |
          # create a single directory for all external software
          mkdir -p ~/deps
          cd ~/deps

          # download and unpack the ADMIXTOOLS source code
          curl -LO https://github.com/DReichLab/AdmixTools/archive/v7.0.2.tar.gz
          tar xf v7.0.2.tar.gz
          cd AdmixTools-7.0.2

          # set compiler flags (compilation on macOS was failing unable to find
          # openblas library files)
          export LDFLAGS="-L/usr/local/opt/openblas/lib"
          export CPPFLAGS="-I/usr/local/opt/openblas/include"

          # compile ADMIXTOOLS and move binaries under bin/
          cd src
          make clobber
          make LDLIBS="-llapack" all
          make install
          # for some reason, mergeit isn't built in 6.x and 5.x?
          # compile it and copy it
          make mergeit
          cp mergeit ../bin

          # download testing data for unit tests
          cd ../
          curl -LO https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/AdmixTools_Example_Data.tar_.gz
          tar xf AdmixTools_Example_Data.tar_.gz

          # run the Perl script with tests for the compiled binaries
          cd examples
          # fix unportable Perl shebang
          if [[ "$OSTYPE" == "darwin"* ]]; then
            sed -i '' "1s/.*/\#\!\/usr\/bin\/env perl -w/" mklog
          else
            sed -i "1s/.*/\#\!\/usr\/bin\/env perl/" mklog
          fi
          ./mklog
          cd ../

          # we need to do this in bash because of $OSTYPE above
        shell: bash

      - name: Populate PATH with compiled binaries
        run: |
          export PATH="$HOME/deps/AdmixTools-7.0.2/bin:$PATH"
          echo "PATH=$PATH" > ~/.Renviron

      - uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: covr

      - name: Test coverage
        run: covr::codecov(type = c("tests", "vignettes"))
        shell: Rscript {0}