Render the website #623
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 $OSTYPE above | |
| shell: bash | |
| - name: Compile and install SLiM | |
| run: | | |
| # download SLiM into a separate directory to avoid CRAN errors | |
| mkdir -p ~/deps | |
| cd ~/deps | |
| # installation instructions copied from the SLiM manual: | |
| wget https://github.com/MesserLab/SLiM/releases/download/v4.1/SLiM.zip | |
| unzip SLiM.zip | |
| cd SLiM | |
| cmake . | |
| make slim | |
| - name: Populate PATH with compiled binaries | |
| run: | | |
| export PATH="$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", "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 |