r-daily.yml

name: r-daily

on:
  push:
    branches:
      - r-daily-source

jobs:
  r-daily-update:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.MY_PAT }}
      GITHUB_TOKEN: ${{ secrets.MY_PAT }}
    steps:

      - name: Checkout repo
        uses: actions/checkout@v4
        with:
          #fetch-depth: 0
          token: ${{ secrets.MY_PAT }}

      - name: Configure git
        run: |
          git config --global user.name "Bruno Rodrigues"
          git config --global user.email "bruno@brodrigues.co"

      - name: Synching fork
        run: |
          git remote add upstream https://github.com/NixOS/nixpkgs
          git checkout r-daily-source
          git fetch upstream
          git reset --hard upstream/master

    #  - name: Change Bioconductor mirror
    #    run: sed -i 's|http://bioconductor\.statistik\.tu-dortmund\.de/packages/|http://bioconductor.org/packages/|g' pkgs/development/r-modules/generate-r-packages.R

      #- name: Remove escapeName
      #  run: sed -i 's|escapeName(name)|name|g' pkgs/development/r-modules/generate-r-packages.R


      - name: Update R
        run:  |
          sed -i 's|version = "4.3.3"|version = "4.4.0"|g' pkgs/applications/science/math/R/default.nix
          sed -i 's|sha256 = "sha256-gIUSMTk7hb84d+6eObKC51Dthkxexgy9aObhOfBSAzA="|sha256 = "sha256-rOQSX5uXbSxTvMX8owx14w1O3EAVhIWcutsIDnK18DA="|g' pkgs/applications/science/math/R/default.nix
         
      - name: Fix for rJava
        run: sed -i 's|rJava = with pkgs; \[ zlib bzip2\.dev icu xz\.dev pcre\.dev jdk libzip \];|rJava = with pkgs; \[ zlib bzip2\.dev icu xz\.dev pcre\.dev jdk libzip libdeflate \];|g' pkgs/development/r-modules/default.nix 
         
      - name: Fix for S4Vectors (https://github.com/Bioconductor/S4Vectors/commit/31853e4e97ff6bc3a8a2e0fdcc6dde72fb61c045) and sf, terra, vapour
        run: |
          sed -i '/flowClust = old/a \
            S4Vectors = old.S4Vectors.overrideAttrs (attrs: {\
                hardeningDisable = [ "format" ];\
            });\
            S4Arrays = old.S4Arrays.overrideAttrs (attrs: {\
                hardeningDisable = [ "format" ];\
            });\
            XVector = old.XVector.overrideAttrs (attrs: {\
                hardeningDisable = [ "format" ];\
            });\
            SparseArray = old.SparseArray.overrideAttrs (attrs: {\
                hardeningDisable = [ "format" ];\
            });\
            Rsamtools = old.Rsamtools.overrideAttrs (attrs: {\
                hardeningDisable = [ "format" ];\
            });\
           rtracklayer = old.rtracklayer.overrideAttrs (attrs: {\
                hardeningDisable = [ "format" ];\
            });\
            VariantAnnotation = old.VariantAnnotation.overrideAttrs (attrs: {\
                hardeningDisable = [ "format" ];\
            });\
              terra = old.terra.overrideAttrs (attrs: {\
                configureFlags = [\
                    "--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib"\
                    ];\
              });\
              sf = old.sf.overrideAttrs (attrs: {\
                configureFlags = [\
                    "--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib"\
                    ];\
              });\
              vapour = old.vapour.overrideAttrs (attrs: {\
                configureFlags = [\
                    "--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib"\
                    ];\
              });\
          ' pkgs/development/r-modules/default.nix

      - name: Updating files
        run: |
          wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily-source/.github/workflows/update-cachix.yml -P .github/workflows/
          # start with environments
          wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/r-daily.nix
          wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/cachix.nix
          # get updated files from r-daily branch
          #cd pkgs/development/r-modules/
          #rm *-packages.nix
          #wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/pkgs/development/r-modules/cran-packages.nix
          #wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/pkgs/development/r-modules/bioc-packages.nix
          #wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/pkgs/development/r-modules/bioc-annotation-packages.nix
          #wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/pkgs/development/r-modules/bioc-experiment-packages.nix
 
      - name: Install Nix
        uses: DeterminateSystems/nix-installer-action@main
        with:
          logger: pretty
          log-directives: nix_installer=trace
          backtrace: full

      - name: Nix cache
        uses: DeterminateSystems/magic-nix-cache-action@main

      - name: Build development environment
        run: |
          nix-build r-daily.nix

      - name: Update R packages
        run: |
          nix-shell r-daily.nix --run "cd pkgs/development/r-modules/ && Rscript generate-r-packages.R cran > cran-packages.nix.new"
          nix-shell r-daily.nix --run "cd pkgs/development/r-modules/ && Rscript generate-r-packages.R bioc > bioc-packages.nix.new"
          nix-shell r-daily.nix --run "cd pkgs/development/r-modules/ && Rscript generate-r-packages.R 'bioc-annotation' > bioc-annotation-packages.nix.new"
          nix-shell r-daily.nix --run "cd pkgs/development/r-modules/ && Rscript generate-r-packages.R 'bioc-experiment' > bioc-experiment-packages.nix.new"

      - name: Rename files
        run: |
          cd pkgs/development/r-modules/
          mv cran-packages.nix.new cran-packages.nix
          mv bioc-packages.nix.new bioc-packages.nix
          mv bioc-annotation-packages.nix.new bioc-annotation-packages.nix
          mv bioc-experiment-packages.nix.new bioc-experiment-packages.nix

      - name: Pushing updates
        run: |
          git checkout -b r-daily
          git add .
          git commit -m "daily update" || echo "no updated R packages in this period"
          git push --force origin r-daily