[docs+build]: P-value docs, autodoc, metadata + dependency/arch modernization (improve-docs + upgrade-dependencies) - #37
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…encies) OpenSpec change: upgrade-dependencies. Aligns declared pins/config with the tested modern stack (numpy 2.x / numba / pandas 3 / pybind11 3 / py3.12 / CUDA 12.x) and broadens GPU support. - build-system: drop setuptools/wheel; add scikit-build-core>=0.10; pin pybind11>=2.13,<4 (verified building on 3.0.3). - CUDA architectures 75 -> 75;80;86;89;90 (native SASS for Turing..Hopper; verified via cuobjdump). Reconciled a single CMake floor (3.26...4.0) across pyproject and CMakeLists.txt. - Extras [project.optional-dependencies]: plots, research, test — so the core install stays lean and research modules install on demand. - plots.py: replaced the private seaborn._freedman_diaconis_bins import with a public reimplementation (numerically identical). - environment: environment-gpu.yml is now the real single lock source (py3.12/ numpy2/numba/CUDA12.x); folded benchmark/toolchain env files into extras; new environment/README.md documents the conda-lock regen command. - cibuildwheel: toolkit 12.5->12.8 (fixed the stale "12.9" comment), arch list, Python range 3.10-3.14. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
OpenSpec change: improve-docs. - P-VALUE DOCS (the reported gap): rewrote the pvalue_n_perms docstring in impl.py and impl_gpu.py — one-sided permutation test, estimator (count+1)/(n_perms+1), interpretation, min resolvable p ~ 1/(n_perms+1), returned tuple shapes, and a cost warning for 2d inputs (a p-value per pair x n_perms extra evaluations). Fixed typos (cm_vlaues, pvalue_n_permutations, returns_parts, coordiates, maximimized). Added a "Computing p-values" section to usage.rst and expanded the README. - Fixed ccc() return-type annotations to the real polymorphic return. - Version single-sourcing: ccc.__version__ via importlib.metadata; conf.py reads package metadata; CITATION.cff -> 0.2.4. One version everywhere (0.2.4). - LICENSE: aligned CITATION.cff (was MIT), README, and pyproject classifier to the authoritative LICENSE file (BSD-2-Clause-Patent). SEE PR NOTE — confirm. - Sphinx: added an autodoc API page (api.rst) rendering ccc(); switched theme to sphinx_rtd_theme; filled the bindings.rst stub; de-duplicated PUBLISHING.md; added Marc Subirana-Granes to authors; corrected the stale citation in introduction.rst (Bioinformatics 2026, btag068). - Added a benchmarking.rst page for the ccc-gpu-bench CLI + README pointer. - Reconciled README/docs claims (real PyPI install, CUDA/CC floor, Python range). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…codex) Addresses the two codex findings on PR E: - [P1] conda-lock.yml still resolved Python 3.10 / NumPy 1.26 and referenced the removed environment-gpu-new.yml, so the documented `conda-lock install` built the OLD stack. Slimmed environment-gpu.yml to the reproducible build/test/docs env (Python 3.12, NumPy 2.x, numba, CUDA 12.5 toolkit, pybind11 3.x, sphinx), removing the research/analysis-only deps (minepy/seaborn/etc. — minepy has no modern-Python build and blocked the solve), and regenerated conda-lock.yml from scratch. The lock now matches the declared source. - [P2] Removed the `plots` and `research` optional-dependency extras: the modules they target (ccc.plots/methods/giant) are intentionally excluded from the wheel (cleanup change), so `pip install cccgpu[plots]` could never provide them. Their deps are documented for source-checkout/analysis use instead. Kept `test`. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Codex review returned two findings, both fixed in cf2f3b7:
(Reminder: the LICENSE alignment to BSD-2-Clause-Patent is flagged in the PR description for your confirmation.) |
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Implements upgrade-dependencies (proposal 7) + improve-docs (proposal 6). Two commits.
The
LICENSEfile is BSD-2-Clause Plus Patent, butCITATION.cffsaid MIT. Treating the LICENSE file as authoritative, this PR aligns CITATION.cff, the README badge/text, and the pyproject license to BSD-2-Clause-Patent. If MIT was intended, say so and I'll flip it the other way instead.upgrade-dependencies
scikit-build-core>=0.10, pinpybind11>=2.13,<4, single CMake floor3.26...4.0.cuobjdump); resolves the README-vs-wheel CC contradiction..sois 7.8 MB.[project.optional-dependencies](plots/research/test); replaced the privateseaborn._freedman_diaconis_binsimport inplots.pywith a public reimplementation.environment-gpu.ymlis now the real single conda-lock source (py3.12/numpy2/CUDA12.x); folded stray env files into extras;environment/README.mddocuments the regen command. cibuildwheel toolkit 12.5→12.8, arch, Python range (correct-by-inspection; not run here). conda-lock not regenerated (best-effort; documented).improve-docs
pvalue_n_permsinimpl.py+impl_gpu.py— one-sided permutation test, estimator(count+1)/(n_perms+1), interpretation, min resolvable p, return shapes, and a 2D cost warning; fixed the typos (cm_vlaues,pvalue_n_permutations, …). Added a "Computing p-values" docs section + expanded README.ccc()return annotations; version single-sourced to 0.2.4 (ccc.__version__via importlib.metadata; conf.py + CITATION aligned).api.rst) rendersccc(); theme →sphinx_rtd_theme; filledbindings.rst; de-duped PUBLISHING; corrected the stale citation (Bioinformatics 2026, btag068); added abenchmarking.rstpage forccc-gpu-bench.Note: version bump
A 0.3.0 bump is warranted before the next release because the wheel-slimming across this initiative is a BREAKING packaging change. Not released/tagged here — left to you.
Testing (ccc-gpu-dev, RTX 4090)
Multi-arch rebuild OK;
ccc.__version__ == 0.2.4; CPU subset 139 passed, 4 skipped; GPU subset 79 passed;ccc-gpu-benchstdout pure JSONL; ruff/format clean;sphinx-build -W(mocked) rc=0, API page renders. cibuildwheel/RTD not executed locally.