Initial commit

.claude-plugin/plugin.json

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+{
+  "name": "github-repo-skill",
+  "description": "Best practice for repository creation, maintenance, and hygeiebe",
+  "version": "0.0.0-2025.11.28",
+  "author": {
+    "name": "Chris Mungall",
+    "email": "cjmungall@lbl.gov"
+  },
+  "skills": [
+    "./skills/github-repo-skill"
+  ]
+}

README.md

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+# github-repo-skill
+
+Best practice for repository creation, maintenance, and hygeiebe

plugin.lock.json

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skills/github-repo-skill/SKILL.md

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+---
+name: github-repo-skill
+description: Guide for creating new GitHub repos and best practice for existing GitHub repos, applicable to both code and non-code projects
+license: CC-0
+---
+
+# github-repo-skill
+
+## overview
+
+To create and maintain high-quality repos that conform to Mungall group / BBOP best practice, use this skill. Use this skill regardless of whether the repo is for code or non-code (ontology, linkml schemas, curated content, analyses, websites). Use this skill for both new repos, for migrating legacy repos, or for ongoing maintenance.
+
+---
+
+# Principles
+
+## Follow existing copier templates
+
+The Mungall group favors the use of [copier](https://copier.readthedocs.io/) and blesses the following templates:
+
+* For LinkML schemas: https://github.com/linkml/linkml-project-copier
+* For code: https://github.com/monarch-initiative/monarch-project-copier
+* For ontologies: https://github.com/INCATools/ontology-development-kit (uses bespoke framework, not copier)
+
+These should always be used for new repos. Pre-existing repos should try and follow these or migrate towards them.
+
+Additionally the group uses additional drop-in templates for AI integrations:
+
+* https://github.com/ai4curation/github-ai-integrations
+
+## Favored tools
+
+These are included in the templates above but some general over-arching preferences: 
+
+* modern python dev stack: `uv`, `ruff`
+* for builds, both `just` and `make` are favored, with `just` favored for non-pipeline cases
+
+## Engineering best practice
+
+* pydantic or pydantic generated from LinkML for data models and data access objects (dataclasses are fine for engine objects)
+* always use typing
+* testing:
+   * follow TDD, use pytest-style tests, `@pytest.mark.parametrize` is good for combinatorial testing
+   * always use doctests: make them informative for humans but also serving as additional tests
+   * ensure unit tests and tests that depend on external APIs, infrastructure etc are separated (e.g. `pytest.mark.integration`)
+   * do not create mock tests unless explicitly requested
+   * for data-oriented projects, yaml, tsvs, etc can go in `tests/input` or smilar
+   * for schemas, following the linkml templates, and ensure schemas and example test data is validated
+   * for ontologies, follow ODK best practice and ensure ontologies are comprehensively axiomatized to allow for reasoner-based checking
+* jupyter notebooks are good for documentation, dashboards, and analysis, but ensure that core logic is separated out and has unit tests
+* CLIs, APIs, and MCPs should be shims on top of core logic, and should have their own tests
+* Every library should have a fully featured CLI. typer is favored, but click is also good.
+
+## Dependency management
+
+* `uv add` to add new dependencies (or `uv add --dev` or similar for dev dependencies)
+* libraries should allow somewhat relaxed dependencies to avoid diamond dependency problems. applications and infra can pin more tightly.
+
+## Git and GitHub Practices
+
+* always work on branches, commit early and often, make PRs early
+* in general, ne PR = one issue (avoid mixing orthogonal concerns). Always reference issues in commits/PR messages
+* use `gh` on command line for operations like finding issues, creating PRs
+* all the group copier templates include extensive github actions for ensuring PRs are high quality
+* github repo should have adequate metadata, links to docs, tags
+
+## Documentation
+
+* Follow [Diátaxis framework](https://diataxis.fr/): tutorial, how-to, reference, explanation
+* Use examples extensively - examples can double as tests
+* frameworks: mkdocs is generally favored due to simplicity but sphinx is ok for older projects
+* Every project must have a comprehensive up to date README.md (or the README.md can point to site generated from mkdocs)
+