BibSpire

A Python tool to update .bib file entries with INSPIRE-HEP citations while preserving reference keys.

Overview

BibSpire reads a .bib file, searches each entry on inspire-hep.net, and replaces the entries with the official INSPIRE citations while keeping the same reference keys. This ensures your bibliography has the most accurate and complete citation information from INSPIRE-HEP.

Features

• Automatic INSPIRE Search: Searches INSPIRE-HEP for each bibliography entry
• Key Preservation: Keeps original reference keys while updating content
• Multiple Search Strategies: Uses title, author, eprint, and DOI for matching
• Robust Parsing: Handles complex BibTeX formats with nested braces
• Error Handling: Gracefully handles missing entries and API errors
• Rate Limiting: Configurable delays between API requests
• Code Quality: Enforced with Ruff linting and formatting
• Comprehensive Testing: Full test suite with unit and integration tests

Installation

From PyPI (Recommended)

pip install bibspire

From Source (Development)

# Clone the repository
git clone https://github.com/lorenzennio/bibspire.git
cd bibspire

# Install in development mode with dev dependencies
pip install -e ".[dev]"

From Built Package

# Build and install
python -m build
pip install dist/bibspire-1.0.0-py3-none-any.whl

Usage

Command Line Interface

# Basic usage - update file in place
bibspire input.bib

# Save to different file
bibspire input.bib -o output.bib

# Verbose output
bibspire input.bib -v

# Custom delay between API requests
bibspire input.bib -d 2.0

# Show help
bibspire --help

Run as Python Module

python -m bibspire input.bib -o output.bib -v

Programmatic Usage

from bibspire import BibSpire, BibParser

# Create BibSpire instance
bibspire = BibSpire(delay=1.0, verbose=True)

# Update a bibliography file
bibspire.update_bib_file("input.bib", "output.bib")

# Or work with entries directly
entries = BibParser.parse_bib_file("input.bib")
updated_entries = bibspire.update_entries(entries)

Testing

The project includes a comprehensive test suite:

# Run fast unit and integration tests
pytest tests/ -v -m "not slow"

# Run all tests including slow real API tests
pytest tests/ -v

# Run only slow tests (real API calls)
pytest tests/ -v -m "slow"

# Run tests with coverage
pytest tests/ --cov=bibspire --cov-report=html

Test Categories

• Unit Tests (test_core.py, test_cli.py): Fast tests with mocked dependencies
• Integration Tests (test_integration.py): Tests with mocked HTTP responses
• Slow Tests (test_slow.py): Real API calls to INSPIRE-HEP (marked as slow)

Development

Building and Testing

# Use Makefile targets
make help                   # Show all available targets
make all                    # Install deps, install pre-commit, run checks, and build
make check                  # Run linting, formatting, and fast tests
make ci                     # Run full CI checks with coverage
make pre-commit-install     # Install pre-commit hooks
make pre-commit-run         # Run pre-commit on all files
make test                   # Run fast tests only
make test-cov               # Run fast tests with coverage
make lint                   # Run linting
make format                 # Format code

# Manual commands
pip install -e ".[dev]"    # Install with dev dependencies
pytest tests/ -v           # Run tests
pytest tests/ -v --cov=bibspire  # Run tests with coverage
ruff check src/ tests/     # Run linting
ruff format src/ tests/    # Format code
python -m build            # Build package

Pre-commit Hooks

This project uses pre-commit hooks to ensure code quality. The hooks automatically run:

• Code linting and formatting with Ruff
• Trailing whitespace removal
• End-of-file fixes
• YAML and TOML validation
• Tests

To set up pre-commit hooks:

# Install and activate pre-commit hooks
make pre-commit-install

# Run pre-commit on all files manually
make pre-commit-run

Once installed, the hooks will run automatically on every commit. If any hook fails, the commit will be rejected until the issues are fixed.

Publishing

Manual Publishing

# Install twine for uploading
pip install twine

# Check package integrity
twine check dist/*

# Upload to PyPI (requires account and authentication)
python -m twine upload dist/*

Automatic Publishing

The package is automatically published to PyPI when a new version tag is pushed:

git tag v1.0.1
git push origin v1.0.1

This triggers the release workflow which:

• Builds the package
• Checks package integrity
• Publishes to PyPI
• Creates a GitHub release

Project Structure

bibspire/
├── .github/workflows/         # CI/CD workflows
├── src/bibspire/              # Main package
│   ├── __init__.py           # Package exports
│   ├── __main__.py           # Module entry point
│   ├── cli.py                # Command-line interface
│   └── core.py               # Core functionality
├── tests/                     # Test suite
│   ├── conftest.py           # Test fixtures
│   ├── test_core.py          # Core functionality tests
│   ├── test_cli.py           # CLI tests
│   ├── test_integration.py   # Integration tests
│   └── test_slow.py          # Slow API tests
├── pyproject.toml            # Package configuration
├── Makefile                  # Development commands
└── README.md                 # This file

Example

Given an input .bib file:

@article{mykey2023,
  title = {Observation of a new particle in the search for the Standard Model Higgs boson},
  author = {Aad, G. and others},
  year = {2012}
}

BibSpire will search INSPIRE, find the official record, and replace it with:

@article{mykey2023,
  author = {Aad, Georges and others},
  collaboration = {ATLAS},
  title = {{Observation of a new particle in the search for the Standard Model Higgs boson with the ATLAS detector at the LHC}},
  eprint = {1207.7214},
  archivePrefix = {arXiv},
  primaryClass = {hep-ex},
  doi = {10.1016/j.physletb.2012.08.020},
  journal = {Phys. Lett. B},
  volume = {716},
  pages = {1--29},
  year = {2012}
}

Note how the reference key mykey2023 is preserved while all other fields are updated with official INSPIRE data.

Dependencies

• Python ≥ 3.8
• requests ≥ 2.25.0

Development Dependencies

• pytest ≥ 6.0.0
• pytest-mock ≥ 3.6.0
• responses ≥ 0.21.0
• ruff ≥ 0.1.0 (linting and formatting)
• build ≥ 0.8.0 (package building)

Contributing

1. Fork the repository
2. Create a feature branch
3. Add tests for your changes
4. Run the test suite: pytest tests/ -v
5. Run linting: make lint or ruff check src/ tests/
6. Format code: make format or ruff format src/ tests/
7. Submit a pull request

Code Quality

This project uses Ruff for linting and code formatting. The configuration includes:

• Linting: Enforces Python best practices, code style, and catches common errors
• Formatting: Consistent code style with 88-character line length
• Import sorting: Automatic import organization and cleanup
• Type checking: Basic type hint validation

Run make check to run all quality checks before submitting changes.

Continuous Integration

This project uses GitHub Actions for automated testing and quality assurance:

CI Workflow

• Linting: Ruff checks for code quality and style
• Multi-Python Testing: Tests run on Python 3.8-3.12
• Coverage: Code coverage reporting with Codecov integration
• Integration Tests: Slow tests run on main branch and when labeled
• Package Building: Validates package can be built locally

Workflows

• ci.yml: Main CI pipeline for PRs and pushes
• release.yml: Automated publishing on version tags

Quality Gates

All PRs must pass:

• Ruff linting (no violations)
• Code formatting check
• Test suite (35+ tests)
• Package build validation

To trigger slow integration tests, add the run-slow-tests label to your PR.

License

MIT License - see LICENSE file for details.

Troubleshooting

Command Not Found

If bibspire command is not found:

# Use full path or activate virtual environment
/path/to/venv/bin/bibspire input.bib

# Or run as module
python -m bibspire input.bib

API Rate Limiting

If you encounter rate limiting:

# Increase delay between requests
bibspire input.bib -d 2.0

Test Failures

If tests fail:

# Check dependencies
pip install -e ".[test]"

# Run specific test
pytest tests/test_core.py::TestBibEntry::test_init -v