missense-kinase-toolkit

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-specific git conventions; extends my central `git` skill. Use when creating commits, branches, or pull requests.

missense-kinase-toolkit-specific testing conventions; extends my central `tests` skill. Use when adding or running tests, or debugging test failures.

How the Streamlit app and the reusable mkt.databases.app package fit together (SequenceAlignment, StructureConfig/Visualizer, PropertyTables) and the schema → databases → app dependency chain. Use when editing the Streamlit app or the mkt.databases.app modules, or wiring visualization logic between them.

How to add or modify a database/API client in mkt.databases (the APIClient hierarchy in api_schema.py, query datetime + cache provenance stamping, requests caching, token handling). Use when integrating a new data source (REST/Swagger/GraphQL) or editing an existing client like cbioportal, oncokb, uniprot, chembl, open_targets, hgnc, pfam, ncbi, protvar, cancer_hotspots.

missense-kinase-toolkit-specific CI/CD layout; extends my central `ci` skill. Use when editing .github/workflows, adding a sub-package, changing the test env, or debugging CI failures.

missense-kinase-toolkit-specific Python style; extends my central `formatting` skill. Use whenever writing or editing any Python code in this repo.

missense-kinase-toolkit-specific plotting conventions; extends my central `plotting` skill. Use whenever writing or editing figure code (e.g. `mkt.databases.plot`) or generating project figures.

How kinase structure visualization works in this repo: the StructureConfig/StructureVisualizer/PyMOLGenerator pipeline, the generate_pymol_files CLI, and when to use generated scripts (licensed PyMOL) vs in-process pymol2/SASA. Use when generating or editing PyMOL files, structure highlighting configs, or SASA computation.