chore: linting, src layout, and sphinx docs#1
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- auto fix using vscode markdown lint operation.
- vscode settings.json (gitignored):
"MD033": {
"allowed_elements": ["details", "summary", "code"]
},
"MD060": false,
"MD032": false,
- missing \ in the table (broken table):
<<
per-gene `|score|` ranking (for a prediction) |
>>
per-gene `\|score\|` ranking (for a prediction) |
mypy / pyright were firing on small stuff, where the logic present was already preventing any issue. Add small type annotation & type ignore.
additionally applied RUF005: replace with iterable unpacking << key = (seed,) + tuple(zlib.crc32(str(t).encode()) for t in tags) >> key = (seed, *(zlib.crc32(str(t).encode()) for t in tags))
- README.md: use t-test_overestim_var in help text, restore ```txt fence - pyproject.toml: keep local ruff/mypy/pyright config; add test dependency-group (pytest) replacing project.optional-dependencies
- README trimmed to install + quick start + sample datasets pointer; full content moved to sphinx docs - user-guide/ folder with usage, scoring, protocols, building-blocks - installation.md with dev setup (moved from contributing) - tutorials.md placeholder - index.md: citation block, grid cards, toctree reorganization - references.bib: add Miller 2025 and Vollenweider 2026 entries - conf.py: show_navbar_depth for stable sidebar
Rename scoring.md → calibration.md and move it first in the user guide toctree, so readers encounter the conceptual framing (what a protocol is, what DRF and BDS measure) before the CLI usage page. Expand the page with proper math formalism: introduces s_bench notation, the two empirical controls, and the DRF/BDS formulas with inline interpretation. Add a single orienting sentence to user-guide/index.md. Update the cross-link in docs/index.md. Also include a pre-existing conf.py fix (bibtex_reference_style). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Add Attributes sections to all five dataclasses (RunConfig, Protocol,
Calibrator, DEResult, Param) so Sphinx tables are populated
- Add full Parameters/Returns to run_protocol, moments, bh, ttest_from_moments,
top_space, pca_space, degs_space, register_de_space
- Add {cite} Vollenweider_2026 to bh
- Add attribute docstrings with usage examples to DE_METHODS and SPACES
- Add docstring example to Registry class; one-liners for __getitem__/meta/names
- Document Context class (Parameters + Attributes) as light public API
- Fix weighted_mse ctx description: uses ctx.wmse_weights, was marked unused
- Add de_ttest, de_ttest_overestim, de_mwu to api.md autosummary
- Add Context section to api.md
- Add protocol_table.py Sphinx extension
- Simplify class.rst template: drop attribute/method summary tables and the
redundant Attributes block; keep only inline Methods section
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
src/layoutpyproject.toml;applied auto-fix and auto-format passes
requires-pythonto>=3.11(illico requires 3.11+)docs/conf.py, API reference, contributing guide, changelogtestdependency-group with pytest inpyproject.tomlStatus / still in progress
protocols, scoring) will move into the Sphinx docs instead
and extending the tool (new protocols, spaces, sources); loosely inspired by
the figure notebooks in scPertEval-figures but scoped to onboarding
(ruff, mypy/pyright, pyproject-fmt)
Test plan
pip install -e .works from the newsrc/layoutruff checkandmypypass cleansphinx-autobuild docs docs/_build)