Migrate documentation from Sphinx to MkDocs#17
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5h4ng
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Mar 12, 2026
5h4ng
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- Replace Sphinx setup (docs/source/, Makefile, make.bat) with MkDocs
- Add mkdocs.yml with Material theme and mkdocstrings (numpy style)
- Add new docs pages: index, installation, usage, api, examples
- Update .readthedocs.yaml to build with MkDocs on Python 3.11
- Update docs/requirements.txt for MkDocs dependencies
- Remove committed Sphinx HTML build artifacts from docs/source/_build/
- Replace Sphinx setup (docs/source/, Makefile, make.bat) with MkDocs - Add mkdocs.yml with Material theme and mkdocstrings (numpy style) - Add new docs pages: index, installation, usage, api, examples - Update .readthedocs.yaml to build with MkDocs on Python 3.11 - Update docs/requirements.txt for MkDocs dependencies - Remove committed Sphinx HTML build artifacts from docs/source/_build/ Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Reorganize flat MkDocs pages into a proper multi-section hierarchy: - getting-started/: detailed installation guide (including NetMHCpan/II PATH setup) and a quickstart walkthrough from config to output - tutorial/: pipeline workflow explanation (5 stages), examples, and per-feature deep-dive pages covering formulas and configuration - api/: split API reference into Core, I/O, Features, Rescore, Visualization, and CLI pages - development/: contributor setup guide (uv, pytest, ruff, pre-commit) Also: - Expand docs/index.md with a pipeline diagram and numbered steps - Add navigation.indexes to mkdocs.yml for section index pages - Add local docs/javascripts/mathjax.js for MathJax configuration - Fix site_name capitalization (optiMHC → OptiMHC) - Update README.md description for clarity Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- antigen-presentation: simplify output tables to show only best-allele mode columns and remove mode parameter from config examples - index: move selenocysteine handling note to a collapsible admonition - original: credit mokapot for the log-transformation approach - overlapping: reframe intro around OLC-inspired algorithm and ladder presentation hotspots - pwm: add SysteMHC Atlas v1/v2 citations for PWM matrix provenance - rt-deviation: remove stale DeepRescore attribution for Rt formula - spectral-similarity: update Koina URL, add Koina paper citation and spectral entropy (Li et al. 2021) citation; simplify requirements note Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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