fix: update dependencies and add missing tools (closes #11)

.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: ['3.9', '3.10', '3.11']
+
+    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-action@stable
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install maturin pytest pytest-cov
+          pip install numpy pandas polars scipy pysam pybedtools typer rich
+
+      - name: Build Rust extension
+        run: |
+          maturin develop --release -m rust/Cargo.toml
+
+      - name: Run tests with coverage
+        run: |
+          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-action@stable
+
+      - name: Check Rust
+        run: |
+          cd rust
+          cargo check
+          cargo clippy -- -D warnings || true
+          cargo fmt --check || true

.github/workflows/docs.yml

@@ -0,0 +1,52 @@
+name: Build and Deploy Docs
+
+on:
+  push:
+    branches: [master, main, rust-optimization]
+  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 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

@@ -0,0 +1,130 @@
+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

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+        name: Remove trailing whitespace
+      - id: end-of-file-fixer
+        name: Fix end of files
+      - id: check-yaml
+        name: Check YAML syntax
+      - id: check-added-large-files
+        name: Check for large files
+        args: ['--maxkb=5000']
+      - id: check-merge-conflict
+        name: Check for merge conflicts
+      - id: check-case-conflict
+        name: Check for case conflicts
+      - id: mixed-line-ending
+        name: Fix mixed line endings
+
+  - repo: https://github.com/psf/black
+    rev: 23.12.1
+    hooks:
+      - id: black
+        name: Format Python code with Black
+        language_version: python3.11
+        args: ['--line-length=100']
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+        name: Lint Python code with Flake8
+        args: ['--max-line-length=100', '--ignore=E203,W503']
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
+    hooks:
+      - id: mypy
+        name: Type check with mypy
+        additional_dependencies:
+          - types-all
+          - numpy
+          - pandas
+        args:
+          - --ignore-missing-imports
+          - --no-strict-optional
+        files: ^src/
+
+  - repo: local
+    hooks:
+      - id: pytest-quick
+        name: Run quick regression tests
+        entry: python -m pytest tests/regression/ -v -m "not slow" --tb=short
+        language: system
+        pass_filenames: false
+        always_run: true
+        stages: [commit]
+
+ci:
+  autofix_commit_msg: |
+    [pre-commit.ci] auto fixes from pre-commit.com hooks
+
+    for more information, see https://pre-commit.ci
+  autofix_prs: true
+  autoupdate_branch: ''
+  autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+  autoupdate_schedule: weekly
+  skip: []
+  submodules: false