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: 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: 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 origin
          # in case of conflict, commit this next line, and follow instructions in the next comment two lines below
          git merge origin/r-daily
          git fetch upstream
          # in case of conflict, uncomment the next 5 lines and comment the last
          #git checkout upstream/master -- pkgs/development/r-modules/default.nix
          #git checkout upstream/master -- pkgs/development/r-modules/cran-packages.nix
          #git checkout upstream/master -- pkgs/development/r-modules/bioc-packages.nix
          #git checkout upstream/master -- pkgs/development/r-modules/bioc-annotation-packages.nix
          #git checkout upstream/master -- pkgs/development/r-modules/bioc-experiment-packages.nix
          git merge upstream/master

      - 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