perpetual 2.0.0

on:
  pull_request:
  workflow_dispatch:

permissions:
  id-token: write
  contents: read

jobs:
  # 1. Job to create and upload the resources/data files
  prepare-resources:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
      - name: Setup Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.11" # Choose a single, compatible python version
          architecture: x64
      - name: Setup uv
        uses: astral-sh/setup-uv@v5
        with:
          enable-cache: true
      - name: Install dependencies for resource creation
        run: |
          uv pip install --system numpy pandas seaborn scikit-learn toml
          cp README.md package-python/README_PYTHON.md
          cp LICENSE package-python/LICENSE  
          cp LICENSE package-r/LICENSE
          mkdir -p resources
          cd package-python
          uv pip install --system -e .[dev]
          cd ..
      - name: Cache resources
        id: cache-resources
        uses: actions/cache@v4
        with:
          path: resources
          key: resources-${{ hashFiles('scripts/make_resources.py') }}
      - name: Build test data (create resources)
        if: steps.cache-resources.outputs.cache-hit != 'true'
        run: python scripts/make_resources.py

  # 2. Windows Build and Test Job (depends on resources)
  windows-build-test:
    if: github.event_name != 'push'
    needs: prepare-resources # This job waits for prepare-resources to complete
    strategy:
      matrix:
        pyversion: ["3.10", "3.11", "3.12", "3.13", "3.14"]
    runs-on: "windows-latest"
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
      - name: Setup uv
        uses: astral-sh/setup-uv@v5
        with:
          enable-cache: true
      - name: Restore resources cache
        id: restore-resources
        uses: actions/cache@v4
        with:
          path: resources
          key: resources-${{ hashFiles('scripts/make_resources.py') }}
      - name: Install latest stable Rust
        uses: dtolnay/rust-toolchain@stable
        with:
          toolchain: stable
      - uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.pyversion }}
          architecture: x64
      - name: Install deps
        run: uv pip install --system numpy pandas seaborn scikit-learn toml
      - run: |
          cp README.md package-python/README_PYTHON.md
          cp LICENSE package-python/LICENSE
          cp LICENSE package-r/LICENSE
      - name: Build test data (Install perpetual with its dev dependencies)
        run: |
          cd package-python
          uv pip install --system -e .[dev]
          cd ..
      - name: Fallback build resources
        if: steps.restore-resources.outputs.cache-hit != 'true'
        run: python scripts/make_resources.py
      - name: Build wheels with maturin
        uses: PyO3/maturin-action@v1
        with:
          target: x86_64
          command: build
          args: --release --strip --interpreter python --manifest-path package-python/Cargo.toml --out dist --sdist
      - name: Install wheel
        run: uv pip install --system perpetual --no-index --find-links dist --no-deps --force-reinstall
      - name: Run Package Tests
        run: |
          uv pip install --system pytest pytest-cov ruff setuptools typing-extensions --upgrade
          cd package-python
          ruff check .
          ruff format --check .
          pytest --cov=perpetual --cov-report=xml tests
          cd ..
      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v5
        with:
          use_oidc: true
          slug: ${{ github.repository }}
          directory: ./package-python
          flags: windows,python
          fail_ci_if_error: true
          verbose: true
      - name: Save Artifacts
        uses: actions/upload-artifact@v4
        with:
          name: dist-windows-${{ matrix.pyversion }}
          path: dist

  # 3. macOS Build and Test Job (depends on resources)
  macos-build-test:
    if: github.event_name != 'push'
    needs: prepare-resources
    strategy:
      matrix:
        pyversion: ["3.11", "3.12", "3.13", "3.14"]
        os: [macos-latest, macos-latest-large]
    runs-on: ${{ matrix.os }}
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
      - name: Setup uv
        uses: astral-sh/setup-uv@v5
        with:
          enable-cache: true
      - name: Install OpenMP
        run: brew install libomp
      - name: Restore resources cache
        id: restore-resources
        uses: actions/cache@v4
        with:
          path: resources
          key: resources-${{ hashFiles('scripts/make_resources.py') }}
      - name: Install latest stable Rust
        uses: dtolnay/rust-toolchain@stable
        with:
          toolchain: stable
      - uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.pyversion }}
      - name: Install deps
        run: uv pip install --system numpy pandas seaborn scikit-learn toml
      - run: |
          cp README.md package-python/README_PYTHON.md
          cp LICENSE package-python/LICENSE
          cp LICENSE package-r/LICENSE
      - name: Build test data (Install perpetual with its dev dependencies)
        run: |
          cd package-python
          uv pip install --system -e .[dev]
          cd ..
      - name: Fallback build resources
        if: steps.restore-resources.outputs.cache-hit != 'true'
        run: python scripts/make_resources.py
      - name: Build wheels with maturin
        uses: PyO3/maturin-action@v1
        with:
          command: build
          args: --release --strip --interpreter python --manifest-path package-python/Cargo.toml --out dist --sdist
      - name: Install wheel
        run: uv pip install --system perpetual --no-index --find-links dist --no-deps --force-reinstall
      - name: Run Package Tests
        run: |
          uv pip install --system pytest pytest-cov ruff setuptools typing-extensions --upgrade
          cd package-python
          ruff check .
          ruff format --check .
          pytest --cov=perpetual --cov-report=xml tests
          cd ..
      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v5
        with:
          use_oidc: true
          slug: ${{ github.repository }}
          directory: ./package-python
          flags: macos,python
          fail_ci_if_error: true
          verbose: true
      - name: Save Artifacts
        uses: actions/upload-artifact@v4
        with:
          name: dist-${{ matrix.os }}-${{ matrix.pyversion }}
          path: dist

  # 4. Linux x64 Build and Test Job (depends on resources)
  linux-build-test:
    if: github.event_name != 'push'
    needs: prepare-resources
    runs-on: ubuntu-latest
    strategy:
      matrix:
        pyversion: ["3.10", "3.11", "3.12", "3.13", "3.14"]
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
      - name: Setup uv
        uses: astral-sh/setup-uv@v5
        with:
          enable-cache: true
      - name: Restore resources cache
        id: restore-resources
        uses: actions/cache@v4
        with:
          path: resources
          key: resources-${{ hashFiles('scripts/make_resources.py') }}
      - name: Install latest stable Rust
        uses: dtolnay/rust-toolchain@stable
        with:
          toolchain: stable
      - uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.pyversion }}
          architecture: x64
      - name: Install deps
        run: uv pip install --system numpy pandas seaborn scikit-learn toml
      - run: |
          cp README.md package-python/README_PYTHON.md
          cp LICENSE package-python/LICENSE
          cp LICENSE package-r/LICENSE
      - name: Build test data (Install perpetual with its dev dependencies)
        run: |
          cd package-python
          uv pip install --system -e .[dev]
          cd ..
      - name: Fallback build resources
        if: steps.restore-resources.outputs.cache-hit != 'true'
        run: python scripts/make_resources.py
      - name: Build wheels with maturin
        uses: PyO3/maturin-action@v1
        with:
          target: x86_64
          manylinux: auto
          command: build
          args: --release --strip --interpreter python${{ matrix.pyversion }} --manifest-path package-python/Cargo.toml --out dist --sdist
      - name: Install wheel
        run: uv pip install --system perpetual --no-index --find-links dist --no-deps --force-reinstall
      - name: Run Package Tests
        run: |
          uv pip install --system pytest pytest-cov ruff setuptools typing-extensions --upgrade
          cd package-python
          ruff check .
          ruff format --check .
          pytest --cov=perpetual --cov-report=xml tests
          cd ..
      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v5
        with:
          use_oidc: true
          slug: ${{ github.repository }}
          directory: ./package-python
          flags: linux-x64,python
          fail_ci_if_error: true
          verbose: true
      - name: Save Artifacts
        uses: actions/upload-artifact@v4
        with:
          name: dist-linux-${{ matrix.pyversion }}
          path: dist

  # 5. Linux ARM Build and Test Job (depends on resources)
  linux-arm-build-test:
    if: github.event_name != 'push'
    needs: prepare-resources
    runs-on: ubuntu-24.04-arm
    strategy:
      matrix:
        pyversion: ["3.10", "3.11", "3.12", "3.13", "3.14"]
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
      - name: Setup uv
        uses: astral-sh/setup-uv@v5
        with:
          enable-cache: true
      - name: Restore resources cache
        id: restore-resources
        uses: actions/cache@v4
        with:
          path: resources
          key: resources-${{ hashFiles('scripts/make_resources.py') }}
      - name: Install latest stable Rust
        uses: dtolnay/rust-toolchain@stable
        with:
          toolchain: stable
      - uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.pyversion }}
          architecture: arm64
      - name: Install deps
        run: uv pip install --system numpy pandas seaborn scikit-learn toml
      - run: |
          cp README.md package-python/README_PYTHON.md
          cp LICENSE package-python/LICENSE
          cp LICENSE package-r/LICENSE
      - name: Build test data (Install perpetual with its dev dependencies)
        run: |
          cd package-python
          uv pip install --system -e .[dev]
          cd ..
      - name: Fallback build resources
        if: steps.restore-resources.outputs.cache-hit != 'true'
        run: python scripts/make_resources.py
      - name: Build wheels with maturin
        uses: PyO3/maturin-action@v1
        with:
          manylinux: auto
          command: build
          args: --release --strip --interpreter python${{ matrix.pyversion }} --manifest-path package-python/Cargo.toml --out dist --sdist
      - name: Install wheel
        run: uv pip install --system perpetual --no-index --find-links dist --no-deps --force-reinstall
      - name: Run Package Tests
        run: |
          uv pip install --system pytest pytest-cov ruff setuptools typing-extensions --upgrade
          cd package-python
          ruff check .
          ruff format --check .
          pytest --cov=perpetual --cov-report=xml tests
          cd ..
      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v5
        with:
          use_oidc: true
          slug: ${{ github.repository }}
          directory: ./package-python
          flags: linux-arm,python
          fail_ci_if_error: true
          verbose: true
      - name: Save Artifacts
        uses: actions/upload-artifact@v4
        with:
          name: dist-linux-arm-${{ matrix.pyversion }}
          path: dist

  # 6. Cargo Test Job (depends on resources)
  cargo-build-test:
    if: github.event_name != 'push'
    needs: prepare-resources
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
      - name: Setup uv
        uses: astral-sh/setup-uv@v5
        with:
          enable-cache: true
      - name: Restore resources cache
        id: restore-resources
        uses: actions/cache@v4
        with:
          path: resources
          key: resources-${{ hashFiles('scripts/make_resources.py') }}
      - name: Install latest stable Rust
        uses: dtolnay/rust-toolchain@stable
        with:
          toolchain: stable
      - uses: actions/setup-python@v5
        with:
          python-version: "3.11"
          architecture: x64
      - name: Install deps
        run: uv pip install --system numpy pandas seaborn scikit-learn toml
      - run: |
          cp README.md package-python/README_PYTHON.md
          cp LICENSE package-python/LICENSE
          cp LICENSE package-r/LICENSE
      - name: Build test data (Install perpetual with its dev dependencies)
        run: |
          cd package-python
          uv pip install --system -e .[dev]
          cd ..
      - name: Fallback build resources
        if: steps.restore-resources.outputs.cache-hit != 'true'
        run: python scripts/make_resources.py
      - name: Run tests
        # Cargo tests in the Rust package might still need the 'resources' folder
        # to exist and contain the data, which is now guaranteed by the download step.
        run: cargo test --verbose
      - name: Install cargo-tarpaulin
        uses: taiki-e/install-action@cargo-tarpaulin
      - name: Run coverage
        run: cargo tarpaulin --verbose --out Xml
      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v5
        with:
          use_oidc: true
          slug: ${{ github.repository }}
          files: ./cobertura.xml
          flags: rust
          fail_ci_if_error: true
          verbose: true

  # 7. R Package Check Job (depends on resources)
  R-CMD-check:
    needs: prepare-resources
    runs-on: ${{ matrix.config.os }}
    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: ubuntu-latest,   r: 'release'}
          - {os: windows-latest,  r: 'release'}

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes
      PERPETUAL_REQ_RESOURCES: true

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

      - name: Restore resources cache
        id: restore-resources
        uses: actions/cache@v4
        with:
          path: resources
          key: resources-${{ hashFiles('scripts/make_resources.py') }}

      - name: Restore fallback deps (Python) for resource generation
        if: steps.restore-resources.outputs.cache-hit != 'true'
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"

      - name: Install dependencies for resource creation (Fallback)
        if: steps.restore-resources.outputs.cache-hit != 'true'
        run: |
          pip install numpy pandas seaborn scikit-learn toml
          cd package-python
          pip install -e .
          cd ..
      
      - name: Fallback build resources
        if: steps.restore-resources.outputs.cache-hit != 'true'
        run: python scripts/make_resources.py

      - name: Copy Resources for Tests
        run: |
          mkdir -p package-r/tests/testthat/resources
          cp -r resources/* package-r/tests/testthat/resources/
        shell: bash

      - name: Setup Rust
        uses: dtolnay/rust-toolchain@master
        with:
          toolchain: nightly
          targets: ${{ runner.os == 'Windows' && 'x86_64-pc-windows-gnu' || '' }}

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          use-public-rspm: true

      - name: Vendor core Rust logic
        run: python scripts/vendor_r.py

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::rcmdcheck, any::devtools, any::testthat, any::roxygen2, any::jsonlite, any::covr
          needs: check
          working-directory: package-r

      - name: Generate Documentation
        run: |
          Rscript -e "roxygen2::roxygenise('package-r')"
        shell: bash

      - name: Debug - List files before build
        run: |
          ls -R package-r/src/rust/core | head -n 20
        shell: bash

      - name: Manual Build
        run: |
          R CMD build package-r --no-manual --no-build-vignettes
        shell: bash

      - name: Manual Install Test
        run: |
          tarball=$(ls perpetual_*.tar.gz | head -n 1)
          R CMD INSTALL "$tarball" --no-test-load
        shell: bash

      - name: Dump all check files on failure
        if: failure()
        shell: bash
        run: |
          echo "Listing all files in package-r/check:"
          ls -R package-r/check || true
          echo "Dumping 00install.out if it exists:"
          find . -name "00install.out" -print -exec cat {} \; || true
          echo "Dumping 00check.log if it exists:"
          find . -name "00check.log" -print -exec cat {} \; || true
          echo "Verifying vendored directory:"
          ls -R package-r/src/rust/core || true

      - name: Fix file permissions for R CMD check
        if: runner.os != 'Windows'
        run: |
          # R CMD check warns about executable files in source packages.
          # Strip execute permissions from all source files.
          find package-r/src -type f -exec chmod -x {} +
        shell: bash

      - name: Check
        uses: r-lib/actions/check-r-package@v2
        with:
          working-directory: package-r
          error-on: ${{ runner.os == 'Windows' && '"error"' || '"warning"' }}

      - name: Check Coverage
        if: success() && matrix.config.os == 'ubuntu-latest'
        run: |
           Rscript -e "cov <- covr::package_coverage('package-r'); covr::to_cobertura(cov, filename = 'package-r/cobertura.xml')"
        shell: bash
      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v5
        with:
          use_oidc: true
          slug: ${{ github.repository }}
          files: package-r/cobertura.xml
          flags: r
          fail_ci_if_error: true
          verbose: true