Resources

A curated collection of additional resources that complement the modules in this school. Suggestions and additions are welcome — please open an issue or pull request on GitHub.

Research software engineering

• The Turing Way: a handbook for reproducible, ethical, and collaborative data science.
• Software Carpentry: foundational lessons on the Unix shell, version control, and programming.
• The Missing Semester of Your CS Education: practical tooling skills often skipped in formal courses.
• US Research Software Engineer Association (US-RSE): community for people who write research software.

Environments and dependency management

• Python venv module: the built-in way to create virtual environments.
• uv: fast Rust-based tool covering environments, dependency resolution, locking, building, and publishing.
• miniforge and Pixi: conda-family package managers, useful when you need non-Python dependencies.
• conda-lock and pip-tools: lock files for exactly reproducible environments.

Python packaging and project structure

• Scientific Python Development Guide: modern best practices for building scientific Python packages.
• Python Packaging User Guide: the PyPA’s official packaging documentation and tutorials.
• pyOpenSci Python Package Guide: community standards and guidance for scientific Python packages.
• Hatch and PDM: modern packaging and environment tools.
• scientific-python/cookie: a project template covering 11+ build backends, CI, linting, and docs.
• PyPI Trusted Publishing: publish from GitHub Actions without API tokens.

Testing, style, and continuous integration

• pytest documentation: the de facto standard Python testing framework.
• Ruff: fast Python linter and formatter.
• pre-commit: manage and run Git pre-commit hooks.
• PEP 8: the Python style guide.

Version control and collaboration

• Pro Git book: comprehensive, free Git reference.
• GitHub Skills: interactive courses on Git and GitHub workflows.
• GitHub CLI (gh): forks, pull requests, and reviews from the terminal.
• GitHub rulesets: protect main with required reviews and status checks.

Jupyter notebooks under version control

• nbstripout: strip outputs and metadata from notebooks before committing.
• Jupytext: pair notebooks with plain-text .py or .md files for reviewable diffs.
• nbdime: notebook-aware diff and merge.

Documentation

• Sphinx and MyST parser: documentation generation for Python projects.
• Write the Docs: community and guides on documentation practice.

Open science, licensing, and citation

• Choose a License: help selecting an open-source license.
• Open Source Initiative — Licenses: the canonical list of approved open-source licenses.
• Journal of Open Source Software (JOSS): a venue for publishing and peer-reviewing research software.
• Zenodo: archive releases and mint DOIs for software.
• Software Citation Principles: the foundational paper on how and why to cite software.
• Citation File Format (CFF): a standard CITATION.cff format for making software citable.