Extract mutation ancestral states in Python #787
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| # 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: R-CMD-check | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| # vignette rendering is switched off though because of: | |
| # - https://github.com/tidyverse/ggplot2/issues/2252#issuecomment-1006713187 | |
| # - https://github.com/lcolladotor/biocthis/issues/27 | |
| - {os: macOS-latest, r: 'release'} | |
| - {os: windows-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'devel'} | |
| - {os: ubuntu-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'oldrel-1'} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - uses: actions/checkout@v4 | |
| # - name: Set NOT_CRAN=false on Windows | |
| # if: runner.os == 'Windows' | |
| # run: | | |
| # echo "NOT_CRAN=false" >> $GITHUB_ENV | |
| # shell: bash | |
| - name: Install rgdal dependencies (macOS) | |
| if: runner.os == 'macOS' | |
| run: brew install gdal | |
| - name: Install ADMIXTOOLS dependencies (Linux) | |
| if: runner.os == 'Linux' | |
| run: sudo apt-get install libopenblas-dev libgsl-dev liblapack-dev | |
| - name: Install ADMIXTOOLS dependencies (macOS) | |
| if: runner.os == 'macOS' | |
| run: brew install openblas gsl lapack bedtools | |
| - name: Compile and install ADMIXTOOLS (Linux) # + macOS) | |
| # if: runner.os != 'Windows' | |
| if: runner.os == 'Linux' | |
| run: | | |
| # create a single directory for all external software | |
| mkdir -p ~/deps | |
| cd ~/deps | |
| # download and unpack the ADMIXTOOLS source code | |
| curl -LO https://github.com/DReichLab/AdmixTools/archive/v7.0.2.tar.gz | |
| tar xf v7.0.2.tar.gz | |
| cd AdmixTools-7.0.2 | |
| # set compiler flags (compilation on macOS was failing unable to find | |
| # openblas library files) | |
| export LDFLAGS="-L/usr/local/opt/openblas/lib" | |
| export CPPFLAGS="-I/usr/local/opt/openblas/include" | |
| # compile ADMIXTOOLS and move binaries under bin/ | |
| cd src | |
| make clobber | |
| make LDLIBS="-llapack" all | |
| make install | |
| # # download testing data for unit tests | |
| # cd ../ | |
| # curl -LO https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/AdmixTools_Example_Data.tar_.gz | |
| # tar xf AdmixTools_Example_Data.tar_.gz | |
| # | |
| # # run the Perl script with tests for the compiled binaries | |
| # cd examples | |
| # # fix unportable Perl shebang | |
| # if [[ "$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 $OSTYPE above | |
| shell: bash | |
| - name: Compile and install SLiM on Unix | |
| if: runner.os != 'Windows' | |
| run: | | |
| # download SLiM into a separate directory to avoid CRAN errors | |
| mkdir -p ~/deps | |
| cd ~/deps | |
| # installation instructions copied from the SLiM manual: | |
| wget https://github.com/MesserLab/SLiM/releases/download/v4.2/SLiM.zip | |
| unzip SLiM.zip | |
| cd SLiM | |
| cmake . | |
| make slim | |
| - name: Populate PATH with compiled binaries on Unix | |
| if: runner.os != 'Windows' | |
| run: | | |
| export PATH="$HOME/deps/SLiM:$HOME/deps/AdmixTools-7.0.2/bin:$PATH" | |
| echo "PATH=$PATH" >> ~/.Renviron | |
| - name: Install SLiM on Windows | |
| if: runner.os == 'Windows' | |
| uses: msys2/setup-msys2@v2 | |
| with: | |
| update: true | |
| install: >- | |
| mingw-w64-x86_64-slim-simulator | |
| bash | |
| - name: Install pandoc on Windows | |
| if: runner.os == 'Windows' | |
| run: | | |
| install.packages("gh", repos = "http://cran.rstudio.com") | |
| install.packages("pandoc", repos = "http://cran.rstudio.com") | |
| pandoc::pandoc_install() | |
| shell: Rscript {0} | |
| #- name: Check ming64/bin contents | |
| # if: runner.os == 'Windows' | |
| # run: | | |
| # dir ${{ runner.temp }}\msys64\mingw64\bin | |
| # shell: cmd | |
| #- name: Check usr/bin contents | |
| # if: runner.os == 'Windows' | |
| # run: dir ${{ runner.temp }}\msys64\usr\bin | |
| # shell: cmd | |
| - name: Populate PATH with compiled binaries on Windows | |
| if: runner.os == 'Windows' | |
| run: | | |
| writeLines( | |
| paste0( | |
| "PATH=D:/a/_temp/msys64/mingw64/bin", | |
| "\n", | |
| "RSTUDIO_PANDOC=", normalizePath(dirname(pandoc::pandoc_bin()), winslash = "/"), | |
| "\n", | |
| "GTIFF_SRS_SOURCE=EPSG # silence GDAL warning" | |
| ), | |
| con = paste0(normalizePath(path.expand("~"), winslash = "/"), "/.Renviron")) | |
| shell: Rscript {0} | |
| # The Windows GDAL GitHub Actions warning solved by setting 'GTIFF_SRS_SOURCE' above | |
| # is actually not the first time this happened, interesting: | |
| # https://github.com/bodkan/slendr/blob/3e02fa2ad7fb085ccbcc23df518bca6b72e782b1/R/compilation.R#L730 | |
| # - name: Check PATHs | |
| # if: runner.os == 'Windows' | |
| # run: | | |
| # cat(Sys.getenv("PATH"), "\n") | |
| # cat(Sys.getenv("RSTUDIO_PANDOC"), "\n") | |
| # shell: Rscript {0} | |
| - name: Set R_LIBS path on unix | |
| if: runner.os == 'Windows' | |
| run: | | |
| mkdir ~/R_LIBS | |
| echo "GTIFF_SRS_SOURCE='EPSG'" >> ~/.Renviron | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - name: Setup dedicated Python environment for slendr | |
| run: | | |
| install.packages("reticulate", repos = "http://cran.rstudio.com") | |
| reticulate::install_miniconda() | |
| deps <- c("msprime==1.3.3", "tskit==0.5.8", "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 = '3.12') | |
| reticulate::use_condaenv(PYTHON_ENV, required = TRUE) | |
| reticulate::conda_install(envname = PYTHON_ENV, packages = c("msprime==1.3.1", "tskit==0.5.6"), pip = FALSE) | |
| reticulate::conda_install(envname = PYTHON_ENV, packages = c("tspop==0.0.2", "pyslim==1.0.4", "pyarrow"), pip = TRUE) | |
| shell: Rscript {0} | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck | |
| needs: check | |
| - uses: r-lib/actions/check-r-package@v2 |