docs

name	docs
description	missense-kinase-toolkit Sphinx docs; extends my central `docs` skill. Use when adding/removing public API, fixing docstrings, or regenerating the docs/generated stubs (then rebuild with make clean && make html).

missense-kinase-toolkit documentation

Baseline — fetch first

Apply my canonical docs conventions (MolSSI cookiecutter-cms Sphinx layout, autosummary + autodoc + napoleon for NumPy docstrings, recursive custom templates, make clean && make html, the never-hand-edit-generated/ rule, Read the Docs) before the repo-specific notes below. WebFetch and follow:

https://raw.githubusercontent.com/jessicaw9910/skills/main/.claude/skills/docs/SKILL.md

If the fetch fails (no network / non-200), tell me the central docs skill could not be retrieved and confirm how to proceed — do not silently skip the baseline.

Repo-specific additions

• Docs live in docs/ at the repo root. docs/api.rst drives autosummary and lists the two top-level packages: mkt.schema and mkt.databases (recursion covers the submodules/classes). Add any new top-level package there.
• Build it with the two scripts in docs/ (not the conda docs env):
  • docs/create_docs_venv.sh [py_version] — creates an isolated venv at docs/.venv (gitignored), installs sphinx + sphinx-rtd-theme, then editable-installs mkt-schema then mkt-databases (databases depends on schema). Uses uv if present, else python -m venv + pip. Default Python 3.12 (mkt requires >=3.9,<3.13).
  • docs/build_docs.sh — activates docs/.venv, removes docs/_build and the untracked docs/generated stubs, sets SPHINX_BUILD=1, then runs python -m sphinx -b html . _build/html and opens the result.
• Why a venv and not the conda docs env: the conda docs env is py3.13, outside mkt's supported range, so mkt.databases can't be installed there. Both mkt.schema and mkt.databases are imported in docs/conf.py, so autodoc needs them importable.
• OneDrive gotcha: this repo lives under OneDrive, which silently rewrites a venv's interpreter symlinks into plain text files — the old root-level docs_env/ died this way (bin/python became a 10-byte text file, so it ran but produced no output). If docs/.venv ever goes quiet/empty, just rerun docs/create_docs_venv.sh to recreate it.
• docs/generated/*.rst are untracked autosummary output; build_docs.sh deletes and regenerates them, so removed/renamed API drops out automatically. Never hand-edit them.
• Custom templates: docs/_templates/custom-{module,class}-template.rst.
• Read the Docs config is readthedocs.yml at the repo root (not .readthedocs.yaml); RTD installs doc deps from docs/requirements.yaml.