Add comprehensive test suite, CI/CD workflows, and multi-platform publishing

.codecov.yml

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+# Codecov configuration for fa2_modified
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 5%
+    patch:
+      default:
+        target: auto
+        threshold: 5%
+
+ignore:
+  - "tests/"
+  - "examples/"
+  - "setup.py"
+  - "fa2_modified/fa2util.c"  # Generated C file
+
+comment:
+  layout: "reach, diff, flags, files"
+  behavior: default
+  require_changes: false
+

.github/workflows/ci.yml

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+name: Continuous Integration
+
+on:
+  push:
+    branches: [ main, master ]
+  pull_request:
+    branches: [ main, master, dev ]
+  schedule:
+    # Run tests weekly on Monday at 00:00 UTC
+    - cron: '0 0 * * 1'
+  workflow_dispatch:
+
+jobs:
+  quick-test:
+    name: Quick test (Python 3.11, Ubuntu)
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+        cache: 'pip'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install Cython
+        pip install -e .
+        pip install pytest networkx
+
+    - name: Run quick tests
+      run: |
+        pytest tests/test_fa2util.py tests/test_forceatlas2.py -v
+
+  full-test:
+    name: Full test suite
+    needs: quick-test
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.8', '3.10', '3.11', '3.12', '3.13']
+        exclude:
+          - os: macos-latest
+            python-version: '3.8'
+          - os: windows-latest
+            python-version: '3.8'
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+
+    - name: Install system dependencies (Ubuntu)
+      if: runner.os == 'Linux'
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y build-essential
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install Cython
+        pip install -e .
+        pip install pytest pytest-cov networkx
+
+    - name: Install igraph (non-Windows)
+      if: runner.os != 'Windows'
+      continue-on-error: true
+      run: pip install python-igraph
+
+    - name: Run tests
+      run: |
+        pytest tests/ -v --cov=fa2_modified --cov-report=xml
+
+    - name: Upload coverage
+      if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
+      uses: codecov/codecov-action@v4
+      with:
+        file: ./coverage.xml
+        flags: unittests
+        fail_ci_if_error: false
+

.github/workflows/code-quality.yml

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+name: Code Quality
+
+on:
+  pull_request:
+    branches: [ main, master, dev ]
+  push:
+    branches: [ main, master ]
+
+jobs:
+  lint:
+    name: Linting (flake8)
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+
+    - name: Install flake8
+      run: pip install flake8
+
+    - name: Lint with flake8
+      run: |
+        # Stop the build if there are Python syntax errors or undefined names
+        flake8 fa2_modified --count --select=E9,F63,F7,F82 --show-source --statistics
+        # Exit-zero treats all errors as warnings
+        flake8 fa2_modified --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+  format-check:
+    name: Code Formatting (black)
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+
+    - name: Install black
+      run: pip install black
+
+    - name: Check formatting
+      run: black --check --diff fa2_modified/ tests/
+
+  import-sort:
+    name: Import Sorting (isort)
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+
+    - name: Install isort
+      run: pip install isort
+
+    - name: Check import sorting
+      run: isort --check-only --diff fa2_modified/ tests/
+
+  type-check:
+    name: Type Checking (mypy)
+    runs-on: ubuntu-latest
+    continue-on-error: true  # Don't fail the build on type errors for now
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+
+    - name: Install dependencies
+      run: |
+        pip install mypy numpy scipy tqdm
+
+    - name: Type check with mypy
+      run: mypy fa2_modified/ --ignore-missing-imports || echo "Type checking found issues (not blocking)"
+

.github/workflows/python-publish.yml

@@ -1,45 +1,101 @@
-# This workflow will upload a Python Package using Twine when a release is created
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
-
-# This workflow uses actions that are not certified by GitHub.
-# They are provided by a third-party and are governed by
-# separate terms of service, privacy policy, and support
-# documentation.
-
-name: Upload Python Package
+name: Build and Publish Wheels
 
 on:
   release:
     types: [published]
+  workflow_dispatch:
 
 permissions:
   contents: read
 
 jobs:
-  deploy:
+  build-wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Set up QEMU for Linux ARM builds
+        if: runner.os == 'Linux'
+        uses: docker/setup-qemu-action@v3
+        with:
+          platforms: arm64
+
+      - name: Install cibuildwheel
+        run: |
+          python -m pip install --upgrade pip
+          pip install cibuildwheel==2.16.5
 
+      - name: Build wheels
+        env:
+          CIBW_BUILD: "cp38-* cp39-* cp310-* cp311-* cp312-* cp313-*"
+          CIBW_SKIP: "pp* *-musllinux_*"
+          CIBW_BEFORE_BUILD: "pip install -U pip setuptools wheel Cython numpy"
+          CIBW_BEFORE_BUILD_LINUX: "pip install -U pip setuptools wheel Cython numpy && yum install -y gcc"
+          CIBW_TEST_COMMAND: "python -c \"import fa2_modified; print('Import successful')\""
+          CIBW_TEST_REQUIRES: "numpy scipy tqdm"
+          CIBW_ARCHS_MACOS: "x86_64 arm64"
+          CIBW_ARCHS_WINDOWS: "AMD64"
+          CIBW_ARCHS_LINUX: "x86_64 aarch64"
+          CIBW_BUILD_VERBOSITY: 1
+        run: |
+          python -m cibuildwheel --output-dir wheelhouse
+
+      - name: Build sdist (source)
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          python -m pip install build Cython
+          python -m build --sdist --outdir wheelhouse
+
+      - name: List built wheels
+        run: ls -lh wheelhouse/
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: wheelhouse/*
+          if-no-files-found: error
+
+  publish:
+    name: Publish to PyPI
+    needs: build-wheels
     runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/fa2-modified
+    permissions:
+      id-token: write
+      contents: read
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: docker://quay.io/pypa/manylinux2014_x86_64
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine auditwheel
-    - name: Build package
-      run: |
-        python3 -m pip install --upgrade build
-        python3 -m build
-    - name: Repair wheels
-      run: |
-        auditwheel repair --wheel-dir dist dist/*.whl
-        rm -rf dist/*linux_x86_64*.whl
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN_GITHUB }}
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          merge-multiple: true
+
+      - name: List all files to publish
+        run: ls -lh dist/
+
+      - name: Verify wheels
+        run: |
+          pip install twine
+          twine check dist/*
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN_GITHUB }}
+          packages-dir: dist
+          verbose: true
+          print-hash: true