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@v3

      - name: Install rgdal dependencies (macOS)
        if: runner.os == 'macOS'
        run: brew install gdal

      - name: Install ADMIXTOOLS dependencies
        run: sudo apt-get install libopenblas-dev libgsl-dev liblapack-dev

      - 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

          # 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: Compile and install SLiM
        run: |
          # download SLiM into a separate directory to avoid CRAN errors
          mkdir -p ~/deps
          cd ~/deps

          # installation instructions copied from the SLiM manual:
          wget https://github.com/MesserLab/SLiM/releases/download/v4.2/SLiM.zip
          unzip SLiM.zip
          cd SLiM
          cmake .
          make slim

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

      - name: Set R_LIBS path on unix
        run: |
          mkdir ~/R_LIBS
          echo "R_LIBS_USER=~/R_LIBS" >> ~/.Renviron

      - name: Setup dedicated Python environment for slendr
        run: |
          install.packages("reticulate", repos = "http://cran.rstudio.com")
          reticulate::install_miniconda()
          deps <- c("msprime==1.3.1", "tskit==0.5.6", "pyslim==1.0.4")
          PYTHON_ENV <- paste0("Python-3.12_", paste(gsub("==", "-", c(deps, "tspop==0.0.2")), collapse = "_"))
          reticulate::conda_create(envname = PYTHON_ENV, python_version = '3.11')
          reticulate::use_condaenv(PYTHON_ENV, required = TRUE)
          pip <- Sys.info()["sysname"] != "Windows"
          reticulate::conda_install(envname = PYTHON_ENV, packages = deps, pip = pip)
          reticulate::conda_install(envname = PYTHON_ENV, packages = c("tspop==0.0.2", "pyarrow"), pip = TRUE)
        shell: Rscript {0}

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

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

      - name: Test coverage
        run: |
          covr::codecov(
            token = "${{secrets.CODECOV_TOKEN}}",
            quiet = FALSE,
            clean = FALSE,
            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"),
            type = c("tests", "vignettes"),
            function_exclusions = c("print\\.", "setup_env", "clear_env", "init_env", "check_env", "check_dependencies", "animate_model", "ts_draw")
          )
        shell: Rscript {0}

      - name: Show testthat output
        if: always()
        run: |
          ## --------------------------------------------------------------------
          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
        shell: bash

      - name: Upload test results
        if: failure()
        uses: actions/upload-artifact@v3
        with:
          name: coverage-test-failures
          path: ${{ runner.temp }}/package