pyg-hyper-bench 0.1.0__tar.gz

pyg_hyper_bench-0.1.0/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug Report
+description: Report a bug or issue with pyg-hyper-bench
+title: "[Bug]: "
+labels: ["bug", "needs-triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thank you for reporting a bug! Please provide the following information to help us resolve the issue quickly.
+
+  - type: dropdown
+    id: bug-area
+    attributes:
+      label: Bug Area
+      description: Where did the issue occur?
+      options:
+        - Evaluation Protocols (NodeClassificationProtocol, etc.)
+        - Single-Run Evaluator (SingleRunEvaluator)
+        - Multi-Run Evaluator (MultiRunEvaluator)
+        - Statistical Aggregation (mean, std, CI)
+        - Data Splitting (transductive/inductive)
+        - Reproducibility/Seeds
+        - Type Annotations/Type Checking
+        - Documentation
+        - Installation/Dependencies
+        - Tests
+        - Other
+    validations:
+      required: true
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description
+      description: What happened? What did you expect to happen?
+      placeholder: |
+        Example:
+        - MultiRunEvaluator produces inconsistent results
+        - NodeClassificationProtocol split ratios are incorrect
+        - Type checking fails with ty
+    validations:
+      required: true
+
+  - type: textarea
+    id: reproduction
+    attributes:
+      label: Steps to Reproduce
+      description: Provide minimal code to reproduce the issue
+      placeholder: |
+        ```python
+        from pyg_hyper_bench import MultiRunEvaluator, NodeClassificationProtocol
+        from pyg_hyper_data.datasets import CoraCocitation
+
+        dataset = CoraCocitation()
+        protocol = NodeClassificationProtocol()
+        evaluator = MultiRunEvaluator(dataset, protocol, n_runs=5)
+        # Error occurs here
+        ```
+      value: |
+        ```python
+        # Your code here
+        ```
+    validations:
+      required: true
+
+  - type: textarea
+    id: environment
+    attributes:
+      label: Environment
+      description: Please provide your environment information
+      value: |
+        - OS: [e.g. Ubuntu 22.04, macOS 14.0, Windows 11]
+        - Python version: [e.g. 3.12.0]
+        - PyTorch version: [e.g. 2.9.0]
+        - PyTorch Geometric version: [e.g. 2.6.0]
+        - pyg-hyper-bench version: [e.g. 0.1.0]
+        - pyg-hyper-data version: [e.g. 0.1.0]
+        - Installation method: [uv / pip]
+    validations:
+      required: true
+
+  - type: textarea
+    id: error-output
+    attributes:
+      label: Error Output
+      description: Paste the full error message or traceback
+      render: shell
+      placeholder: |
+        Traceback (most recent call last):
+          ...
+
+  - type: textarea
+    id: additional-context
+    attributes:
+      label: Additional Context
+      description: Any additional information, screenshots, or related issues
+
+  - type: checkboxes
+    id: checklist
+    attributes:
+      label: Checklist
+      options:
+        - label: I have searched existing issues and this is not a duplicate
+          required: true
+        - label: I am using the latest version of pyg-hyper-bench
+          required: true
+        - label: I have verified this is a bug in pyg-hyper-bench (not PyTorch/PyG/pyg-hyper-data)
+          required: false

pyg_hyper_bench-0.1.0/.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+  - name: Question or Discussion
+    url: https://github.com/nishide-dev/pyg-hyper-bench/discussions
+    about: Ask questions or discuss ideas with the community
+  - name: pyg-hyper-data Issues
+    url: https://github.com/nishide-dev/pyg-hyper-data/issues
+    about: Report issues with datasets or data utilities

pyg_hyper_bench-0.1.0/.github/ISSUE_TEMPLATE/documentation.yml

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+name: Documentation Issue
+description: Report an issue with documentation or suggest improvements
+title: "[Docs]: "
+labels: ["documentation", "needs-triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thank you for helping improve our documentation!
+
+  - type: dropdown
+    id: doc-area
+    attributes:
+      label: Documentation Area
+      description: Which part of the documentation needs improvement?
+      options:
+        - README.md
+        - API Documentation (docstrings)
+        - Usage Examples
+        - DESIGN.md
+        - Installation Instructions
+        - Quick Start Guide
+        - Integration Tests/Examples
+        - Type Annotations
+        - Other
+    validations:
+      required: true
+
+  - type: dropdown
+    id: issue-type
+    attributes:
+      label: Issue Type
+      description: What type of documentation issue is this?
+      options:
+        - Incorrect Information
+        - Missing Information
+        - Unclear/Confusing
+        - Outdated
+        - Typo/Grammar
+        - Code Example Doesn't Work
+        - Needs More Examples
+        - Other
+    validations:
+      required: true
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description
+      description: Describe the documentation issue
+      placeholder: |
+        Example:
+        - The example in README.md for MultiRunEvaluator is outdated
+        - Missing documentation for custom metrics
+        - Unclear explanation of statistical measures
+    validations:
+      required: true
+
+  - type: textarea
+    id: current
+    attributes:
+      label: Current Documentation
+      description: Quote the current documentation (if applicable)
+      placeholder: |
+        > Current text from docs...
+
+  - type: textarea
+    id: suggested
+    attributes:
+      label: Suggested Improvement
+      description: How should the documentation be improved?
+      placeholder: |
+        Suggested changes or additions...
+
+  - type: textarea
+    id: location
+    attributes:
+      label: Location
+      description: Where in the documentation is this issue?
+      placeholder: |
+        - File: README.md, line 123
+        - Section: "Quick Start > Multi-Run Evaluation"
+        - Function: MultiRunEvaluator.run_evaluation()
+
+  - type: textarea
+    id: additional-context
+    attributes:
+      label: Additional Context
+      description: Any additional information or screenshots
+
+  - type: checkboxes
+    id: checklist
+    attributes:
+      label: Checklist
+      options:
+        - label: I have checked the latest documentation
+          required: true
+        - label: I am willing to submit a PR to fix this
+          required: false

pyg_hyper_bench-0.1.0/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature Request
+description: Suggest a new feature or enhancement for pyg-hyper-bench
+title: "[Feature]: "
+labels: ["enhancement", "needs-triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thank you for suggesting a feature! Please provide details to help us understand your request.
+
+  - type: dropdown
+    id: feature-area
+    attributes:
+      label: Feature Area
+      description: Which area would this feature affect?
+      options:
+        - New Evaluation Protocol (link prediction, clustering, etc.)
+        - Evaluator Enhancement (SingleRunEvaluator, MultiRunEvaluator)
+        - Statistical Methods (new metrics, aggregation methods)
+        - Data Splitting (new split strategies)
+        - PyTorch Lightning Integration
+        - Visualization/Reporting
+        - Performance Optimization
+        - API/Usability
+        - Documentation
+        - Tests
+        - Other
+    validations:
+      required: true
+
+  - type: textarea
+    id: problem
+    attributes:
+      label: Problem Statement
+      description: What problem would this feature solve?
+      placeholder: |
+        Example:
+        - There is no protocol for hyperedge prediction tasks
+        - Multi-run results are difficult to visualize
+        - Need support for custom metrics
+    validations:
+      required: true
+
+  - type: textarea
+    id: solution
+    attributes:
+      label: Proposed Solution
+      description: How would you like to see this feature implemented?
+      placeholder: |
+        Example:
+        - Add LinkPredictionProtocol with AUC/MRR metrics
+        - Add plot() method to MultiRunResult for visualization
+        - Allow custom metric functions in protocols
+
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives Considered
+      description: Have you considered any alternative solutions or workarounds?
+
+  - type: textarea
+    id: example
+    attributes:
+      label: Example Usage
+      description: Show how you would use this feature (if applicable)
+      render: python
+      placeholder: |
+        # Example of how the feature would be used
+        from pyg_hyper_bench import LinkPredictionProtocol
+
+        protocol = LinkPredictionProtocol(
+            split_type="hyperedge_split",
+            metrics=["auc", "mrr", "hits@10"]
+        )
+
+  - type: textarea
+    id: additional-context
+    attributes:
+      label: Additional Context
+      description: Any additional information, references, or related work
+
+  - type: checkboxes
+    id: checklist
+    attributes:
+      label: Checklist
+      options:
+        - label: I have searched existing issues and this is not a duplicate
+          required: true
+        - label: This feature aligns with pyg-hyper-bench's purpose (benchmarking)
+          required: true
+        - label: I am willing to contribute a PR for this feature
+          required: false

pyg_hyper_bench-0.1.0/.github/pull_request_template.md

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+## Summary
+
+<!-- Briefly describe what this PR does -->
+
+## Type of Change
+
+<!-- Check all that apply -->
+
+- [ ] 🐛 Bug fix (fixes an issue with existing functionality)
+- [ ] ✨ New feature (adds new functionality)
+- [ ] 📝 Documentation (documentation only changes)
+- [ ] 🎨 Style (formatting, whitespace, no functional changes)
+- [ ] ♻️ Refactoring (code restructuring without changing behavior)
+- [ ] ⚡ Performance improvement
+- [ ] 🔒 Type safety (type annotations, type checking fixes)
+- [ ] 🧪 Tests (adding or updating tests)
+- [ ] 🔧 Configuration (pyproject.toml, CI/CD, etc.)
+- [ ] 📊 New Protocol (new evaluation protocol)
+
+## Related Issue
+
+<!-- Link to related issues -->
+
+Closes #<!-- Issue number -->
+
+## Changes Made
+
+<!-- Describe your changes in detail -->
+
+### Modified Files
+
+- `file/path.py`: Description of changes
+
+### Impact on Existing Code
+
+<!-- How does this change affect existing functionality? -->
+
+- [ ] New protocol added
+- [ ] API changes (breaking changes)
+- [ ] Evaluation logic changes
+- [ ] Performance improvements
+- [ ] Bug fixes
+- [ ] Documentation only
+- [ ] No impact on existing functionality
+
+### Breaking Changes
+
+<!-- Check if this introduces breaking changes -->
+
+- [ ] Yes (describe below)
+- [ ] No
+
+<!-- Details of breaking changes and migration guide -->
+```
+
+```
+
+## Testing
+
+<!-- Describe how you tested your changes -->
+
+### Test Commands
+
+```bash
+# Run all tests
+uv run pytest tests/ -v
+
+# Run specific test file
+uv run pytest tests/test_integration.py -v
+
+# Check code quality
+uv run ruff check
+uv run ruff format .
+uv run ty check
+
+# Run pre-commit hooks
+uv run pre-commit run --all-files
+```
+
+### Test Results
+
+```bash
+# Paste test output here
+```
+
+### Test Environment
+
+- OS: <!-- e.g. Ubuntu 22.04, macOS 14.0 -->
+- Python version: <!-- e.g. 3.12.0 -->
+- PyTorch version: <!-- e.g. 2.9.0 -->
+- PyTorch Geometric version: <!-- e.g. 2.6.0 -->
+- CUDA version (if applicable): <!-- e.g. 12.6 -->
+- GPU (if applicable): <!-- e.g. RTX 4090 -->
+
+## Screenshots (if applicable)
+
+<!-- Add screenshots for visual changes or output examples -->
+
+## Checklist
+
+<!-- Please check all items before requesting review -->
+
+### Code Quality
+
+- [ ] Code follows the project's style guidelines
+- [ ] Code is well-commented and self-documenting
+- [ ] All tests pass (`uv run pytest tests/`)
+- [ ] Code linting passes (`uv run ruff check`)
+- [ ] Code formatting is correct (`uv run ruff format .`)
+- [ ] Type checking passes (`uv run ty check`)
+- [ ] Pre-commit hooks pass (`uv run pre-commit run --all-files`)
+
+### Testing
+
+- [ ] Added tests for new functionality
+- [ ] Updated existing tests (if needed)
+- [ ] All edge cases are covered
+- [ ] Tests are reproducible with fixed seeds
+- [ ] Integration tests pass (if applicable)
+
+### Documentation
+
+- [ ] Updated README.md (if needed)
+- [ ] Added/updated docstrings for new/modified functions
+- [ ] Added usage examples (if new feature)
+- [ ] Updated type annotations
+- [ ] Added comments for complex logic
+
+### Protocols (if applicable)
+
+- [ ] Protocol implements BenchmarkProtocol interface
+- [ ] Data splitting works correctly
+- [ ] Evaluation metrics are accurate
+- [ ] Reproducible with seeds
+- [ ] Example usage is provided
+
+### Evaluators (if applicable)
+
+- [ ] Evaluator works with all protocols
+- [ ] Statistical aggregation is correct (if multi-run)
+- [ ] Confidence intervals are calculated properly
+- [ ] Seed management works correctly
+- [ ] Example usage is provided
+
+### Performance (if applicable)
+
+- [ ] Tested with large datasets
+- [ ] Memory usage is reasonable
+- [ ] No significant performance regression
+- [ ] Benchmarked against baseline (if optimization)
+
+### Backward Compatibility
+
+- [ ] Changes are backward compatible
+- [ ] If breaking changes exist, migration guide is provided
+- [ ] Deprecation warnings added (if removing features)
+
+## Reviewer Notes
+
+<!-- Any specific areas you'd like reviewers to focus on, or questions you have -->
+
+---
+
+**Thank you for your contribution!** 🙏
+
+<!--
+Review Guidelines:
+- Check code quality and style
+- Verify tests pass and cover edge cases
+- Review documentation completeness
+- Test the changes locally if possible
+- Provide constructive feedback
+-->

pyg_hyper_bench-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
+    branches: [main, dev]
+
+jobs:
+  code-quality:
+    name: Code Quality Checks
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      - name: Check code formatting with Ruff
+        run: uv run ruff format --check .
+
+      - name: Lint code with Ruff
+        run: uv run ruff check .
+
+      - name: Type check with ty
+        run: uv run ty check
+
+  tests:
+    name: Tests (Python ${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12", "3.13"]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      - name: Run unit tests
+        run: uv run pytest tests/test_multi_run_evaluator.py -v --cov=pyg_hyper_bench --cov-report=xml --cov-report=term
+
+      - name: Run integration tests
+        run: uv run pytest tests/test_integration.py -v
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        if: matrix.python-version == '3.12'
+        with:
+          file: ./coverage.xml
+          fail_ci_if_error: false
+
+  pre-commit:
+    name: Pre-commit Hooks
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      - name: Run pre-commit hooks
+        run: uv run pre-commit run --all-files
+
+  build:
+    name: Build Package
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Install dependencies for build test
+        run: uv sync --all-extras
+
+      - name: Build package
+        run: uv build --no-sources
+
+      - name: Check package installation
+        run: |
+          # Test that the built wheel is valid by checking its contents
+          python -m zipfile -l dist/*.whl | grep "pyg_hyper_bench/__init__.py"
+
+          # Test import in the existing environment (already has all deps)
+          uv run python -c "from pyg_hyper_bench import SingleRunEvaluator, MultiRunEvaluator, NodeClassificationProtocol; print('✅ Package imports successfully!')"
+
+      - name: Upload build artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish-testpypi:
+    name: Publish to TestPyPI
+    runs-on: ubuntu-latest
+    needs: [code-quality, tests, pre-commit, build]
+    if: github.event_name == 'push' && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/dev')
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      - name: Get current version
+        id: version
+        run: |
+          VERSION=$(grep '^version = ' pyproject.toml | sed 's/version = "\(.*\)"/\1/')
+          BRANCH_NAME=${GITHUB_REF#refs/heads/}
+          COMMIT_SHORT=${GITHUB_SHA:0:7}
+          DEV_VERSION="${VERSION}.dev$(date +%Y%m%d%H%M%S)"
+
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+          echo "dev_version=$DEV_VERSION" >> $GITHUB_OUTPUT
+          echo "branch=$BRANCH_NAME" >> $GITHUB_OUTPUT
+          echo "commit=$COMMIT_SHORT" >> $GITHUB_OUTPUT
+          echo "📦 Base version: $VERSION"
+          echo "🚀 TestPyPI version: $DEV_VERSION"
+          echo "🌿 Branch: $BRANCH_NAME"
+          echo "📝 Commit: $COMMIT_SHORT"
+
+      - name: Update version for TestPyPI
+        run: |
+          echo "Updating version to ${{ steps.version.outputs.dev_version }}"
+          sed -i 's/^version = ".*"/version = "${{ steps.version.outputs.dev_version }}"/' pyproject.toml
+          cat pyproject.toml | grep "^version"
+
+      - name: Build package
+        run: uv build --no-sources
+
+      - name: Publish to TestPyPI
+        env:
+          UV_PUBLISH_TOKEN: ${{ secrets.TESTPYPI_API_TOKEN }}
+        run: |
+          echo "🚀 Publishing pyg-hyper-bench ${{ steps.version.outputs.dev_version }} to TestPyPI..."
+          uv publish --index testpypi
+
+      - name: Create comment with TestPyPI link
+        if: github.event_name == 'push'
+        run: |
+          echo "✅ Published to TestPyPI: https://test.pypi.org/project/pyg-hyper-bench/${{ steps.version.outputs.dev_version }}/"
+          echo "🌿 Branch: ${{ steps.version.outputs.branch }}"
+          echo "📝 Commit: ${{ steps.version.outputs.commit }}"
+          echo ""
+          echo "Install with:"
+          echo "pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ pyg-hyper-bench==${{ steps.version.outputs.dev_version }}"