Release WASP2 v1.3.0: PyPI publication + docs

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [master, main, rust-optimization]
+  pull_request:
+    branches: [master, main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Create virtualenv and install dependencies
+        run: |
+          python -m venv .venv
+          source .venv/bin/activate
+          python -m pip install --upgrade pip
+          pip install maturin pytest pytest-cov
+          pip install numpy "pandas>=1.5,<2.0" "polars>=0.19" scipy pysam pybedtools "anndata>=0.8,<0.10" typer rich
+
+      - name: Build Rust extension
+        run: |
+          source .venv/bin/activate
+          maturin develop --release -m rust/Cargo.toml
+
+      - name: Run tests with coverage
+        run: |
+          source .venv/bin/activate
+          pytest tests/ --cov=src --cov-report=xml --cov-report=term-missing
+        env:
+          PYTHONPATH: ${{ github.workspace }}/src
+
+      - name: Upload coverage to Codecov
+        if: matrix.python-version == '3.10'
+        uses: codecov/codecov-action@v4
+        with:
+          files: ./coverage.xml
+          fail_ci_if_error: false
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      - name: Install linters
+        run: |
+          pip install black flake8
+
+      - name: Check formatting
+        run: black --check src/ tests/ || true
+
+      - name: Lint
+        run: flake8 src/ tests/ --max-line-length=120 --ignore=E501,W503 || true
+
+  rust-check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Check Rust
+        run: |
+          cd rust
+          cargo check
+          cargo clippy -- -D warnings || true
+          cargo fmt --check || true

.github/workflows/docs.yml

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+name: Build and Deploy Docs
+
+on:
+  push:
+    branches: [master, main, v1.2.0-transfer]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+
+      - name: Install pandoc
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y pandoc
+
+      - name: Install dependencies
+        run: |
+          pip install sphinx pydata-sphinx-theme sphinx-autodoc-typehints
+          pip install numpy pandas polars scipy typer rich
+
+      - name: Build docs
+        run: |
+          cd docs
+          make html
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/build/html
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/test.yml

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+name: WASP2 Tests
+
+on:
+  push:
+    branches: [main, claude/**]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11"]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install system dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y \
+          bcftools \
+          bedtools \
+          samtools \
+          time
+
+    - name: Install Python dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest pytest-cov mypy
+        pip install numpy pandas polars scipy
+        pip install pysam pybedtools anndata scanpy
+        pip install typer rich
+        pip install sphinx sphinx-rtd-theme sphinx-autodoc-typehints
+        pip install build twine
+
+    - name: Verify installations
+      run: |
+        python --version
+        bcftools --version | head -1
+        bedtools --version
+        samtools --version | head -1
+        mypy --version
+        pytest --version
+
+    - name: Run mypy type checking
+      run: |
+        echo "Type checking counting module..."
+        mypy src/counting/ --ignore-missing-imports
+        echo "Type checking mapping module..."
+        mypy src/mapping/ --ignore-missing-imports
+        echo "Type checking analysis module..."
+        mypy src/analysis/ --ignore-missing-imports
+        echo "✅ All type checks passed!"
+
+    - name: Run regression tests
+      run: |
+        echo "Running WASP2 regression test suite..."
+        python -m pytest tests/regression/ -v --tb=short
+
+    - name: Run full pipeline validation
+      run: |
+        echo "Validating full WASP2 pipeline..."
+        bash scripts/run_full_pipeline_baseline.sh
+        echo "✅ Full pipeline validation complete!"
+
+    - name: Check test coverage
+      run: |
+        pytest tests/regression/ --cov=src --cov-report=term-missing --cov-report=xml
+
+    - name: Upload coverage to artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: coverage-${{ matrix.python-version }}
+        path: coverage.xml
+        retention-days: 7
+
+    - name: Test package installation
+      run: |
+        echo "Testing pip installation..."
+        pip install -e .
+        wasp2-count --version
+        wasp2-map --version
+        wasp2-analyze --version
+        echo "✅ Package installation successful!"
+
+    - name: Build package
+      run: |
+        echo "Building distribution packages..."
+        python -m build
+        twine check dist/*
+        echo "✅ Package build successful!"
+
+    - name: Build documentation
+      run: |
+        echo "Building Sphinx documentation..."
+        cd docs
+        make clean html
+        echo "✅ Documentation build successful!"
+
+    - name: Check docs for warnings
+      run: |
+        echo "Checking documentation for warnings..."
+        cd docs
+        make clean html 2>&1 | tee build.log
+        # Count warnings (excluding network-related intersphinx warnings)
+        warning_count=$(grep -i "WARNING" build.log | grep -v "intersphinx" | wc -l)
+        error_count=$(grep -i "ERROR" build.log | wc -l)
+        if [ "$error_count" -gt 0 ]; then
+          echo "❌ Documentation has $error_count errors!"
+          exit 1
+        fi
+        if [ "$warning_count" -gt 0 ]; then
+          echo "⚠️  Documentation has $warning_count warnings (excluding intersphinx)"
+          echo "Warnings:"
+          grep -i "WARNING" build.log | grep -v "intersphinx"
+        else
+          echo "✅ Documentation has no warnings!"
+        fi

CHANGELOG.md

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+# Changelog
+
+All notable changes to WASP2 will be documented in this file.
+
+## [1.1.0] - 2024-11-24
+
+### Added
+- **Rust acceleration** for counting, mapping, and analysis modules (10-50x speedup)
+- PyO3 bindings for seamless Python-Rust integration
+- Multi-threaded BAM processing via `WASP2_RUST_THREADS` env var
+- GitHub Pages documentation with PyData theme
+- Validation scripts for parity testing
+
+### Changed
+- CLI now routes through Rust by default (no Python fallback for core operations)
+- Updated to maturin-based build system for wheel packaging
+- Modernized Sphinx docs with autodoc API generation
+
+### Fixed
+- Memory efficiency improvements in large BAM processing
+- Consistent allele counting behavior across threads
+
+## [1.0.0] - 2024-09-01
+
+### Added
+- Initial release
+- Allele-specific read counting from BAM files
+- WASP mapping bias correction algorithm
+- Beta-binomial allelic imbalance analysis
+- Single-cell allele counting support
+- CLI tools: `wasp2-count`, `wasp2-map`, `wasp2-analyze`