{"id":39084323,"url":"https://github.com/rise-unibas/clean-code","last_synced_at":"2026-01-17T18:35:11.025Z","repository":{"id":65923828,"uuid":"594037645","full_name":"RISE-UNIBAS/clean-code","owner":"RISE-UNIBAS","description":"Training materials and slides for courses on version control, clean code and documentation with practical examples and exercises in Python and R","archived":false,"fork":false,"pushed_at":"2025-08-25T09:05:08.000Z","size":17612,"stargazers_count":3,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-09-04T20:52:30.024Z","etag":null,"topics":["clean-code","documentation","fair4rs","git","python","r","training-materials","versioning"],"latest_commit_sha":null,"homepage":"","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc-by-4.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/RISE-UNIBAS.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2023-01-27T13:02:49.000Z","updated_at":"2025-08-25T09:05:11.000Z","dependencies_parsed_at":"2024-04-15T15:10:44.543Z","dependency_job_id":"ab039497-4c4a-4b62-ae6a-5a4e98a05c25","html_url":"https://github.com/RISE-UNIBAS/clean-code","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/RISE-UNIBAS/clean-code","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/RISE-UNIBAS%2Fclean-code","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/RISE-UNIBAS%2Fclean-code/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/RISE-UNIBAS%2Fclean-code/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/RISE-UNIBAS%2Fclean-code/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/RISE-UNIBAS","download_url":"https://codeload.github.com/RISE-UNIBAS/clean-code/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/RISE-UNIBAS%2Fclean-code/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28516083,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-17T18:28:00.501Z","status":"ssl_error","status_checked_at":"2026-01-17T18:28:00.150Z","response_time":85,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["clean-code","documentation","fair4rs","git","python","r","training-materials","versioning"],"created_at":"2026-01-17T18:35:10.943Z","updated_at":"2026-01-17T18:35:11.002Z","avatar_url":"https://github.com/RISE-UNIBAS.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Version control, clean code and documentation\n\nComprehensive training materials for teaching researchers how to write maintainable, well-documented code and collaborate effectively using version control. Includes crash courses and a full 4-day course with practical examples in Python and R, plus AI-assisted coding workflows.\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15099964.svg)](https://doi.org/10.5281/zenodo.15099964)\n\n## What's Included\n\n- **Full 4-day course** (15+ hours) covering Git, GitHub, clean code principles, documentation, AI-assisted coding, and research data publishing\n- **Quick crash courses** (3-6 hours) for focused topics\n- Hands-on exercises and real-world examples in Python and R\n- Ready-to-use slides and materials for instructors\n- New for 2026: AI-assisted coding session with Claude Code and PyCharm\n\n## Creator\n\nThese materials were created by the University of Basel's Research and Infrastructure Support RISE (rise@unibas.ch) between 2023 and 2026. \n\n## Documentation\n\n[Read this file on GitHub pages](https://rise-unibas.github.io/clean-code/).\n\n## Course Variants\n\nNote that there are [different versions of this course](https://github.com/RISE-UNIBAS/clean-code/releases), see the [changelog](CHANGELOG.md) for details.\n\n### Full 4-Day Course\n**[Course on version control, clean code and documentation](course/README.md)** in [`clean-code/course`](https://github.com/RISE-UNIBAS/clean-code/tree/main/course)\n\nComprehensive 4-day hands-on course (15+ hours) covering:\n- Git and GitHub fundamentals\n- Clean code principles and file organization\n- Documentation with Sphinx and docstrings\n- AI-assisted coding with Claude Code and PyCharm (new for 2026)\n- PyCharm integration and automated workflows\n- Research data publishing with GitHub-Zenodo\n\n**Target audience**: Researchers and graduate students wanting comprehensive software development skills\n\n### Crash Courses (Condensed Formats)\n\n**[Crash-course on version control, clean code and documentation](crash-course/README.md)** in [`clean-code/crash-course`](https://github.com/RISE-UNIBAS/clean-code/tree/main/crash-course)\n\nCondensed version covering core topics in 3-6 hours.\n\n**[Crash-course on version control and documentation with GitHub](crash-course-github/README.md)** in [`clean-code/crash-course-github`](https://github.com/RISE-UNIBAS/clean-code/tree/main/crash-course-github)\n\nFocused crash course on GitHub workflows and documentation.\n\n## License\n\n\u003ca rel=\"license\" href=\"http://creativecommons.org/licenses/by/4.0/\"\u003e\u003cimg alt=\"Creative Commons License\" style=\"border-width:0\" src=\"https://i.creativecommons.org/l/by/4.0/88x31.png\" /\u003e\u003c/a\u003e\u003cbr /\u003eThis work is licensed under a \u003ca rel=\"license\" href=\"http://creativecommons.org/licenses/by/4.0/\"\u003eCreative Commons Attribution 4.0 International License\u003c/a\u003e.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frise-unibas%2Fclean-code","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frise-unibas%2Fclean-code","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frise-unibas%2Fclean-code/lists"}