release.yml

name: Build and Release

on:
  push:
    tags:
      - 'v*'

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 samtools + bcftools via MSYS2 (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

      - name: Stage tools and DLLs (Windows)
        if: runner.os == 'Windows'
        shell: msys2 {0}
        run: |
          mkdir -p /c/yleaf-tools
          for tool in samtools bcftools; do
            cp /mingw64/bin/${tool}.exe /c/yleaf-tools/
            ldd /mingw64/bin/${tool}.exe \
              | grep '/mingw64' | awk '{print $3}' \
              | while read f; do cp "$f" /c/yleaf-tools/ 2>/dev/null || true; done
          done
          echo "Staged $(ls /c/yleaf-tools | wc -l) files"

      - name: Download minimap2 Windows binary (Windows)
        if: runner.os == 'Windows'
        shell: pwsh
        run: |
          $releases = gh release list --repo lh3/minimap2 --json tagName --limit 10 | ConvertFrom-Json
          foreach ($rel in $releases) {
            $assets = gh release view $rel.tagName --repo lh3/minimap2 --json assets | ConvertFrom-Json
            $winAsset = $assets.assets | Where-Object { $_.name -match 'win' } | Select-Object -First 1
            if ($winAsset) {
              Write-Host "Found Windows binary in $($rel.tagName): $($winAsset.name)"
              Invoke-WebRequest $winAsset.browserDownloadUrl -OutFile mm2-win.zip
              Expand-Archive mm2-win.zip -DestinationPath C:/mm2-tmp
              $exe = Get-ChildItem -Recurse C:/mm2-tmp -Filter "minimap2*.exe" | Select-Object -First 1
              if ($exe) {
                Copy-Item $exe.FullName "C:/yleaf-tools/minimap2.exe"
                Write-Host "minimap2.exe staged"
              }
              break
            }
          }
          if (-not (Test-Path "C:/yleaf-tools/minimap2.exe")) {
            Write-Host "No Windows minimap2 binary found — FASTQ mode unavailable on Windows"
          }
        env:
          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

      - 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 samtools + bcftools via MSYS2 (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

      - name: Stage tools and DLLs (Windows)
        if: runner.os == 'Windows'
        shell: msys2 {0}
        run: |
          mkdir -p /c/yleaf-tools
          for tool in samtools bcftools; do
            cp /mingw64/bin/${tool}.exe /c/yleaf-tools/
            ldd /mingw64/bin/${tool}.exe \
              | grep '/mingw64' | awk '{print $3}' \
              | while read f; do cp "$f" /c/yleaf-tools/ 2>/dev/null || true; done
          done
          echo "Staged $(ls /c/yleaf-tools | wc -l) files"

      - name: Download minimap2 Windows binary (Windows)
        if: runner.os == 'Windows'
        shell: pwsh
        run: |
          $releases = gh release list --repo lh3/minimap2 --json tagName --limit 10 | ConvertFrom-Json
          foreach ($rel in $releases) {
            $assets = gh release view $rel.tagName --repo lh3/minimap2 --json assets | ConvertFrom-Json
            $winAsset = $assets.assets | Where-Object { $_.name -match 'win' } | Select-Object -First 1
            if ($winAsset) {
              Invoke-WebRequest $winAsset.browserDownloadUrl -OutFile mm2-win.zip
              Expand-Archive mm2-win.zip -DestinationPath C:/mm2-tmp
              $exe = Get-ChildItem -Recurse C:/mm2-tmp -Filter "minimap2*.exe" | Select-Object -First 1
              if ($exe) { Copy-Item $exe.FullName "C:/yleaf-tools/minimap2.exe" }
              break
            }
          }
        env:
          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

      - 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: |
          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
          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 (filenames may contain spaces from productName)
          for f in *.AppImage *.deb *.dmg *.exe *.msi; do
            [ -f "$f" ] && ASSETS+=("$f")
          done
          gh release create ${{ github.ref_name }} \
            --title "Yleaf ${{ github.ref_name }}" \
            --notes-file release_notes.txt \
            "${ASSETS[@]}"
        env:
          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}