release.yml

name: Build and Release

on:
  push:
    tags:
      - 'v*'

concurrency:
  group: release-${{ github.ref_name }}
  cancel-in-progress: true

jobs:
  # ── CLI executables (PyInstaller --onedir, for command-line users) ──────────
  build:
    name: Build CLI on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        include:
          - os: ubuntu-latest
            artifact: yleaf-linux.tar.gz
          - os: macos-latest
            artifact: yleaf-macos.tar.gz
          - os: windows-latest
            artifact: yleaf-windows.zip

    steps:
      - uses: actions/checkout@v4

      # ── Linux / macOS ─────────────────────────────────────────────────────
      - name: Set up Miniconda (Linux/macOS)
        if: runner.os != 'Windows'
        uses: conda-incubator/setup-miniconda@v3
        with:
          channels: conda-forge,bioconda,defaults
          auto-activate: true
          activate-environment: base
          miniforge-version: latest

      - name: Install tools (Linux/macOS)
        if: runner.os != 'Windows'
        shell: bash -el {0}
        run: mamba install -y --strict-channel-priority samtools minimap2 bcftools

      - name: Install Yleaf + PyInstaller (Linux/macOS)
        if: runner.os != 'Windows'
        shell: bash -el {0}
        run: pip install -e . && pip install pyinstaller

      - name: Build (Linux/macOS)
        if: runner.os != 'Windows'
        shell: bash -el {0}
        run: python -m PyInstaller --distpath dist --workpath build --noconfirm pyinstaller_yleaf.spec

      - name: Package (Linux/macOS)
        if: runner.os != 'Windows'
        shell: bash
        run: tar czf ${{ matrix.artifact }} -C dist yleaf

      # ── Windows ───────────────────────────────────────────────────────────
      - name: Install MSYS2 packages (Windows)
        if: runner.os == 'Windows'
        uses: msys2/setup-msys2@v2
        with:
          msystem: MINGW64
          update: false
          install: >-
            mingw-w64-x86_64-samtools
            mingw-w64-x86_64-bcftools
            mingw-w64-x86_64-gcc
            mingw-w64-x86_64-zlib
            make
            git

      - name: Build minimap2 from source (Windows)
        if: runner.os == 'Windows'
        shell: msys2 {0}
        run: |
          git clone --depth 1 --branch v2.28 https://github.com/lh3/minimap2.git /tmp/minimap2
          cd /tmp/minimap2
          make
          # MinGW may or may not append .exe — normalise to minimap2.exe
          if [ ! -f minimap2.exe ] && [ -f minimap2 ]; then mv minimap2 minimap2.exe; fi
          ls -la minimap2.exe

      - name: Stage tools and DLLs (Windows)
        if: runner.os == 'Windows'
        shell: msys2 {0}
        run: |
          set +e  # don't let a single missing dep kill the whole step
          mkdir -p /c/yleaf-tools
          cp /mingw64/bin/samtools.exe /c/yleaf-tools/
          cp /mingw64/bin/bcftools.exe /c/yleaf-tools/
          cp /tmp/minimap2/minimap2.exe /c/yleaf-tools/
          for exe in /c/yleaf-tools/samtools.exe /c/yleaf-tools/bcftools.exe /c/yleaf-tools/minimap2.exe; do
            for f in $(ldd "$exe" 2>/dev/null | grep '/mingw64' | awk '{print $3}'); do
              cp "$f" /c/yleaf-tools/ 2>/dev/null
            done
          done
          echo "Staged $(ls /c/yleaf-tools | wc -l) files:"
          ls /c/yleaf-tools

      - name: Install Graphviz and stage binaries (Windows)
        if: runner.os == 'Windows'
        shell: pwsh
        run: |
          choco install graphviz -y --no-progress
          $gv_bin = "C:\Program Files\Graphviz\bin"
          Get-ChildItem "$gv_bin" | Copy-Item -Destination "C:\yleaf-tools\"
          Write-Host "Graphviz staged. Total files in C:\yleaf-tools: $((Get-ChildItem C:\yleaf-tools).Count)"

      - name: Verify bundled tools (Windows)
        if: runner.os == 'Windows'
        shell: pwsh
        run: |
          $required = @('samtools.exe', 'bcftools.exe', 'minimap2.exe', 'dot.exe')
          $missing = @()
          foreach ($exe in $required) {
            if (-not (Test-Path "C:\yleaf-tools\$exe")) { $missing += $exe }
          }
          if ($missing.Count -gt 0) {
            Write-Error "Missing required tools in C:\yleaf-tools: $($missing -join ', ')"
            exit 1
          }
          Write-Host "All required tools staged."

      - name: Set YLEAF_BUNDLED_TOOLS (Windows)
        if: runner.os == 'Windows'
        shell: pwsh
        run: echo "YLEAF_BUNDLED_TOOLS=C:/yleaf-tools" >> $env:GITHUB_ENV

      - name: Set up Python (Windows)
        if: runner.os == 'Windows'
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"

      - name: Install Yleaf + PyInstaller (Windows)
        if: runner.os == 'Windows'
        run: pip install -e . && pip install pyinstaller

      - name: Build (Windows)
        if: runner.os == 'Windows'
        run: python -m PyInstaller --distpath dist --workpath build --noconfirm pyinstaller_yleaf.spec

      - name: Package (Windows)
        if: runner.os == 'Windows'
        shell: pwsh
        run: Compress-Archive -Path dist\yleaf -DestinationPath ${{ matrix.artifact }}

      - name: Upload artifact
        uses: actions/upload-artifact@v4
        with:
          name: ${{ matrix.artifact }}
          path: ${{ matrix.artifact }}

  # ── Dashboard (Tauri GUI, the default interface for end users) ──────────────
  tauri-build:
    name: Build Dashboard on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        include:
          - os: ubuntu-latest
            tauri_target: x86_64-unknown-linux-gnu
          - os: macos-latest
            tauri_target: aarch64-apple-darwin
          - os: windows-latest
            tauri_target: x86_64-pc-windows-msvc

    steps:
      - uses: actions/checkout@v4

      # ── Linux system deps (required by Tauri / WebKitGTK) ─────────────────
      - name: Install Linux system dependencies
        if: runner.os == 'Linux'
        run: |
          sudo apt-get update
          sudo apt-get install -y \
            libwebkit2gtk-4.1-dev \
            libayatana-appindicator3-dev \
            librsvg2-dev \
            patchelf

      # ── Install bioinformatics tools ─────────────────────────────────────
      - name: Set up Miniconda (Linux/macOS)
        if: runner.os != 'Windows'
        uses: conda-incubator/setup-miniconda@v3
        with:
          channels: conda-forge,bioconda,defaults
          auto-activate: true
          activate-environment: base
          miniforge-version: latest

      - name: Install tools (Linux/macOS)
        if: runner.os != 'Windows'
        shell: bash -el {0}
        run: mamba install -y --strict-channel-priority samtools minimap2 bcftools

      - name: Install Yleaf + PyInstaller (Linux/macOS)
        if: runner.os != 'Windows'
        shell: bash -el {0}
        run: pip install -e . && pip install pyinstaller

      - name: Install MSYS2 packages (Windows)
        if: runner.os == 'Windows'
        uses: msys2/setup-msys2@v2
        with:
          msystem: MINGW64
          update: false
          install: >-
            mingw-w64-x86_64-samtools
            mingw-w64-x86_64-bcftools
            mingw-w64-x86_64-gcc
            mingw-w64-x86_64-zlib
            make
            git

      - name: Build minimap2 from source (Windows)
        if: runner.os == 'Windows'
        shell: msys2 {0}
        run: |
          git clone --depth 1 --branch v2.28 https://github.com/lh3/minimap2.git /tmp/minimap2
          cd /tmp/minimap2
          make
          # MinGW may or may not append .exe — normalise to minimap2.exe
          if [ ! -f minimap2.exe ] && [ -f minimap2 ]; then mv minimap2 minimap2.exe; fi
          ls -la minimap2.exe

      - name: Stage tools and DLLs (Windows)
        if: runner.os == 'Windows'
        shell: msys2 {0}
        run: |
          set +e  # don't let a single missing dep kill the whole step
          mkdir -p /c/yleaf-tools
          cp /mingw64/bin/samtools.exe /c/yleaf-tools/
          cp /mingw64/bin/bcftools.exe /c/yleaf-tools/
          cp /tmp/minimap2/minimap2.exe /c/yleaf-tools/
          for exe in /c/yleaf-tools/samtools.exe /c/yleaf-tools/bcftools.exe /c/yleaf-tools/minimap2.exe; do
            for f in $(ldd "$exe" 2>/dev/null | grep '/mingw64' | awk '{print $3}'); do
              cp "$f" /c/yleaf-tools/ 2>/dev/null
            done
          done
          echo "Staged $(ls /c/yleaf-tools | wc -l) files:"
          ls /c/yleaf-tools

      - name: Install Graphviz and stage binaries (Windows)
        if: runner.os == 'Windows'
        shell: pwsh
        run: |
          choco install graphviz -y --no-progress
          $gv_bin = "C:\Program Files\Graphviz\bin"
          Get-ChildItem "$gv_bin" | Copy-Item -Destination "C:\yleaf-tools\"
          Write-Host "Graphviz staged. Total files in C:\yleaf-tools: $((Get-ChildItem C:\yleaf-tools).Count)"

      - name: Verify bundled tools (Windows)
        if: runner.os == 'Windows'
        shell: pwsh
        run: |
          $required = @('samtools.exe', 'bcftools.exe', 'minimap2.exe', 'dot.exe')
          $missing = @()
          foreach ($exe in $required) {
            if (-not (Test-Path "C:\yleaf-tools\$exe")) { $missing += $exe }
          }
          if ($missing.Count -gt 0) {
            Write-Error "Missing required tools in C:\yleaf-tools: $($missing -join ', ')"
            exit 1
          }
          Write-Host "All required tools staged."

      - name: Set YLEAF_BUNDLED_TOOLS (Windows)
        if: runner.os == 'Windows'
        shell: pwsh
        run: echo "YLEAF_BUNDLED_TOOLS=C:/yleaf-tools" >> $env:GITHUB_ENV

      - name: Set up Python (Windows)
        if: runner.os == 'Windows'
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"

      - name: Install Yleaf + PyInstaller (Windows)
        if: runner.os == 'Windows'
        run: pip install -e . && pip install pyinstaller

      # ── Build the PyInstaller sidecar ─────────────────────────────────────
      - name: Build sidecar (Linux/macOS)
        if: runner.os != 'Windows'
        shell: bash -el {0}
        run: |
          python -m PyInstaller \
            --distpath /tmp/sidecar-dist \
            --workpath /tmp/sidecar-build \
            --noconfirm \
            dashboard/pyinstaller_yleaf.spec
          mkdir -p dashboard/src-tauri/binaries
          cp /tmp/sidecar-dist/yleaf dashboard/src-tauri/binaries/yleaf-${{ matrix.tauri_target }}
          chmod +x dashboard/src-tauri/binaries/yleaf-${{ matrix.tauri_target }}

      - name: Build sidecar (Windows)
        if: runner.os == 'Windows'
        shell: pwsh
        run: |
          python -m PyInstaller `
            --distpath C:\sidecar-dist `
            --workpath C:\sidecar-build `
            --noconfirm `
            dashboard\pyinstaller_yleaf.spec
          New-Item -ItemType Directory -Force -Path dashboard\src-tauri\binaries
          Copy-Item C:\sidecar-dist\yleaf.exe `
            dashboard\src-tauri\binaries\yleaf-${{ matrix.tauri_target }}.exe

      # ── Install Node.js + Rust, build Tauri app ───────────────────────────
      - name: Set up Node.js
        uses: actions/setup-node@v4
        with:
          node-version: '22'

      - name: Install Rust stable
        uses: dtolnay/rust-toolchain@stable

      - name: Install npm dependencies
        working-directory: dashboard
        run: npm ci

      - name: Build Tauri app (Linux/macOS)
        if: runner.os != 'Windows'
        working-directory: dashboard
        shell: bash -el {0}
        run: npm run tauri build

      - name: Build Tauri app (Windows)
        if: runner.os == 'Windows'
        working-directory: dashboard
        run: npm run tauri build

      # ── Collect and upload installer artifacts ────────────────────────────
      - name: Upload Linux installers
        if: runner.os == 'Linux'
        uses: actions/upload-artifact@v4
        with:
          name: dashboard-linux
          path: |
            dashboard/src-tauri/target/release/bundle/appimage/*.AppImage
            dashboard/src-tauri/target/release/bundle/deb/*.deb

      - name: Upload macOS installer
        if: runner.os == 'macOS'
        uses: actions/upload-artifact@v4
        with:
          name: dashboard-macos
          path: dashboard/src-tauri/target/release/bundle/dmg/*.dmg

      - name: Upload Windows installers
        if: runner.os == 'Windows'
        uses: actions/upload-artifact@v4
        with:
          name: dashboard-windows
          path: |
            dashboard/src-tauri/target/release/bundle/nsis/*.exe
            dashboard/src-tauri/target/release/bundle/msi/*.msi

  # ── Create GitHub Release with all artifacts ───────────────────────────────
  release:
    name: Create GitHub Release
    needs: [build, tauri-build]
    if: always()
    runs-on: ubuntu-latest
    permissions:
      contents: write

    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0

      - name: Download all artifacts
        uses: actions/download-artifact@v4
        with:
          merge-multiple: true

      - name: Generate changelog
        run: |
          NOTES_FILE="release_notes_${{ github.ref_name }}.md"
          if [ -f "$NOTES_FILE" ]; then
            cp "$NOTES_FILE" release_notes.txt
          else
            PREV=$(git tag --sort=-v:refname | sed -n '2p')
            RANGE="${PREV:+${PREV}..}HEAD"
            git log $RANGE --pretty=format:"- %s" \
              | grep -v "Co-Authored-By" > release_notes.txt
          fi
          cat release_notes.txt

      - name: Publish release
        run: |
          ASSETS=()
          # CLI executables
          [ -f yleaf-linux.tar.gz ]  && ASSETS+=("yleaf-linux.tar.gz")
          [ -f yleaf-macos.tar.gz ]  && ASSETS+=("yleaf-macos.tar.gz")
          [ -f yleaf-windows.zip ]   && ASSETS+=("yleaf-windows.zip")
          # Dashboard installers — search recursively because upload-artifact@v4
          # preserves subdirectory structure when multiple paths are specified
          while IFS= read -r -d '' f; do
            ASSETS+=("$f")
          done < <(find . \( -name "*.AppImage" -o -name "*.deb" -o -name "*.dmg" -o -name "*.exe" -o -name "*.msi" \) -print0)
          if gh release view ${{ github.ref_name }} &>/dev/null; then
            gh release upload ${{ github.ref_name }} "${ASSETS[@]}" --clobber
          else
            gh release create ${{ github.ref_name }} \
              --title "Yleaf ${{ github.ref_name }}" \
              --notes-file release_notes.txt \
              "${ASSETS[@]}"
          fi
        env:
          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}