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: Cherry-pick R bump
      #  run: |
      #    set -e
      #    git fetch upstream
      #    if git cherry-pick --empty=drop -m 1 a65b87c485e1^..ad0a16337834; then
      #      echo "Cherry-pick successful"
      #    else
      #      echo "Cherry-pick failed — aborting"
      #      git cherry-pick --abort
      #      exit 1
      #    fi

      - name: Cherry-pick pypmml PR
        run: |
          set -e
          # Fetch the PR from upstream
          git fetch upstream pull/507209/head:pr-507209
          # Try cherry-pick
          if git cherry-pick pr-507209; then
            echo "Cherry-pick successful"
          else
            echo "Cherry-pick failed, aborting"
            git cherry-pick --abort
          fi

      - name: Cherry-pick fix skl2onnx PR
        run: |
          set -e
          git fetch upstream pull/505958/head
          if git cherry-pick 6a4cf18e0b7ba2ee3cf160c8446a95d154a080d0 d31cf4a3206f72382dd5bd5a53917274be56d4d5; then
            echo "Cherry-pick successful"
          else
            echo "Cherry-pick failed, aborting"
            git cherry-pick --abort
          fi
    
      - name: Cherry-pick skl2onnx PR
        run: |
          set -e
          # Fetch the PR from upstream
          git fetch upstream pull/505944/head:pr-505944
          # Try cherry-pick
          if git cherry-pick pr-505944; then
            echo "Cherry-pick successful"
          else
            echo "Cherry-pick failed, aborting"
            git cherry-pick --abort
          fi

      - name: Cherry-pick jpmml-statsmodels PR
        run: |
          set -e
          # Fetch the PR from upstream
          git fetch upstream pull/495154/head:pr-495154
          # Try cherry-pick
          if git cherry-pick pr-495154; then
            echo "Cherry-pick successful"
          else
            echo "Cherry-pick failed, aborting"
            git cherry-pick --abort
          fi

      - name: Cherry-pick jmmpl_evaluator
        run: |
          set -e
          # Fetch the PR from upstream
          git fetch upstream pull/507541/head:pr-507541
          # Try cherry-pick
          if git cherry-pick pr-507541; then
            echo "Cherry-pick successful"
          else
            echo "Cherry-pick failed, aborting"
            git cherry-pick --abort
          fi

      - name: Updating files
        run: |
          wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/.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.json
          #wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/pkgs/development/r-modules/cran-packages.json
          #wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/pkgs/development/r-modules/bioc-packages.json
          #wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/pkgs/development/r-modules/bioc-annotation-packages.json
          #wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/pkgs/development/r-modules/bioc-experiment-packages.json

      - name: Get ryxpress
        run: |      
          mkdir -p pkgs/development/python-modules/ryxpress
          cd pkgs/development/python-modules/ryxpress
          wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/refs/heads/add_rixpress/pkgs/development/python-modules/ryxpress/default.nix

      - name: Get talvez
        run: |      
          mkdir -p pkgs/development/python-modules/talvez
          cd pkgs/development/python-modules/talvez
          wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/refs/heads/add_talvez/pkgs/development/python-modules/talvez/default.nix

      - name: Insert ryxpress in python-packages.nix
        run: |
          FILE="pkgs/top-level/python-packages.nix"
          # Insert ryxpress after ryd-client
          sed -i '/ryd-client = callPackage .*;/a \
          \  ryxpress = callPackage ../development/python-modules/ryxpress { };' "$FILE"

      - name: Insert talvez in python-packages.nix
        run: |
          FILE="pkgs/top-level/python-packages.nix"
          # Insert talvez after takethetime
          sed -i '/takethetime = callPackage .*;/a \
          \  talvez = callPackage ../development/python-modules/talvez { };' "$FILE"
   
      - name: Get patches for Bioc devel
        run: |
          wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/bioc_devel.patch

      #- name: Update R to 4.5.3 until merged in master
      #  run: |
      #    sed -i 's|hash = "sha256-DXH/cQbsac18Z+HpXtGjzuNViAkx8ut4xTABSp43nyA=";|hash = "sha256-qlwe1Ck8cnGsUT1lRnA1asDopq1eQr4BQ2XREVC1uPI=";|' pkgs/applications/science/math/R/default.nix
      #    sed -i 's|version = "4.5.2";|version = "4.5.3";|' pkgs/applications/science/math/R/default.nix

      - name: Add libuv build input for fs
        run: |
          sed -i '/rsvg = \[ pkgs.pkg-config \];/a\    fs = [ pkgs.which pkgs.pkg-config pkgs.libuv.dev pkgs.cmake ];' pkgs/development/r-modules/default.nix

      - name: Install Nix
        uses: DeterminateSystems/nix-installer-action@main
        with:
          logger: pretty
          log-directives: nix_installer=trace
          backtrace: full

      # ───────────────────────────────────────────────────────────────────────────────
      #  ▼ NEW STEP: install nix-prefetch-git
      - name: Install nix-prefetch-git
        run: |
          nix profile install nixpkgs#nix-prefetch-git

      #  ▼ NEW STEP: fetch and patch registry.nix for CodeDownIO/General
      - name: Update Julia “General” registry to latest commit
        run: |
          # 1. Get the latest commit hash from the remote repo:
          LATEST_COMMIT=$(
            git ls-remote https://github.com/CodeDownIO/General.git HEAD \
            | cut -f1
          )
          echo "Latest commit is $LATEST_COMMIT"

          # 2. Prefetch that exact revision and parse JSON to extract just the base32 sha256:
          RAW_JSON=$(
            nix-prefetch-git https://github.com/CodeDownIO/General.git "$LATEST_COMMIT"
          )
          SHA=$(echo "$RAW_JSON" | jq -r .sha256)
          echo "Computed sha256 (base32) is $SHA"

          # 3. In-place replace rev = "…"  and sha256 = "…" in registry.nix:
          sed -i \
            "s|rev = \".*\";|rev = \"$LATEST_COMMIT\";|" \
            pkgs/development/julia-modules/registry.nix

          sed -i \
            "s|sha256 = \".*\";|sha256 = \"$SHA\";|" \
            pkgs/development/julia-modules/registry.nix

      - name: Bump BiocManager in cran-packages.json
        run: |
          FILE="pkgs/development/r-modules/cran-packages.json"

          sed -i '
            /"BiocManager": {/,/}/ {
              s|"version": "1\.30\.26"|"version": "1.30.27"|
              s|"sha256": ".*"|"sha256": "1dgv0gfa7ff3w96dax8p7jna1bf2652sav2mhn82gj02jvqdrgxc"|
            }
          ' "$FILE"


      - name: Check cran-packages.json
        run: grep -n -A6 -B1 '"BiocManager":' pkgs/development/r-modules/cran-packages.json

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

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

      - 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

      - name: Get current date
        id: date
        run: echo "::set-output name=date::$(date +'%Y-%m-%d')"

      - name: Pushing updates to dated branch
        run: |
          git checkout -b ${{ steps.date.outputs.date }}
          git add .
          git commit -m "R CRAN and Bioc update" || echo "no updated R packages in this period"
          git push --force origin ${{ steps.date.outputs.date }}

      # now update for bioc devel
      - name: Apply patch
        run: git apply bioc_devel.patch

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

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

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

      - name: Get sha of r-devel
        id: r-devel-sha
        run: echo "::set-output name=r-devel-sha::$(nix-prefetch-url https://cran.r-project.org/src/base-prerelease/R-devel.tar.gz)"


      - name: Patch for R-devel
        run: |
          sed -i 's|sha256 = ".*";|sha256 = "${{ steps.r-devel-sha.outputs.r-devel-sha }}";|' pkgs/applications/science/math/R/default.nix
          sed -i 's|url = "https://cran.r-project.org/src/base/R-.*";|url = "https://cran.r-project.org/src/base-prerelease/R-devel.tar.gz";|' pkgs/applications/science/math/R/default.nix

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

      - name: Pushing updates r-devel
        run: |
          git checkout r-daily
          sed -i 's|sha256 = ".*";|sha256 = "${{ steps.r-devel-sha.outputs.r-devel-sha }}";|' pkgs/applications/science/math/R/default.nix
          sed -i 's|url = "https://cran.r-project.org/src/base/R-.*";|url = "https://cran.r-project.org/src/base-prerelease/R-devel.tar.gz";|' pkgs/applications/science/math/R/default.nix
          git checkout -b r-devel
          git add .
          git commit -m "r-devel update" || echo "no updated R packages in this period"
          git push --force origin r-devel