Modernize pre-commit hooks & linting (PR 1/9) by Marius1311 · Pull Request #1282 · scverse/cellrank

Marius1311 · 2026-02-13T22:35:13Z

Summary

Replace the legacy linting/formatting stack (black, isort, flake8, doc8, pyupgrade) with ruff + biome + pyproject-fmt, require Python ≥3.12, and apply bulk reformatting.

This is the first in a series of modernization PRs to align CellRank with the scverse cookiecutter template.

Changes

Pre-commit hooks

Replace black + isort with ruff-format (single formatter)
Remove redundant hooks: flake8, doc8, pyupgrade, rst-backticks, yesqa (all subsumed by ruff)
Add biome (JSON formatting), pyproject-fmt, and useful pre-commit-hooks (check-ast, check-merge-conflict, check-added-large-files, etc.)
Bump all hook versions to latest

Python version & ruff config

Require python_requires = ">=3.12" — drop 3.10/3.11 classifiers
Consolidate ruff config: remove target-version (inferred from requires-python), add isort rules ("I"), enable docstring-code-format, add B905 to ignore (67 pre-existing zip() without strict= — to be addressed separately)

Code quality

Move 16 local imports to top level where they were only local for historical reasons; annotate all remaining ~21 local imports with # circular import comments
Fix bare # noqa comments — replaced with explicit rule codes (e.g., # noqa: BLE001) or removed where unnecessary (5 removed, 19 annotated)
Fix np.array → np.ndarray in 6 type annotations across 3 files — np.array is a function, not a type, so np.array | None raises TypeError at runtime (pre-existing bug exposed by ruff UP007/UP045 auto-fixes)

Bulk reformat

Ran pre-commit run --all-files to convergence — reformats ~67 files
Added .git-blame-ignore-revs so git blame (and GitHub blame UI) skips the reformat commit

Housekeeping

Updated .gitignore (add uv.lock, .github/prompts/)

Commits

#	Commit	Description
1	`91a3bdfd`	Replace black + isort with ruff-format
2	`edd7a132`	Remove redundant pre-commit hooks
3	`7ac027e7`	Add modern hooks: biome, pyproject-fmt; bump versions
4	`5e687f0f`	Require Python ≥3.12, update ruff config
5	`1dd1e667`	Move local imports to top level
6	`313b30a4`	Fix bare `# noqa` comments with explicit rule codes
7	`0a8f50a9`	Bulk reformat: `pre-commit run --all-files`
8	`e9bbac22`	Add `.git-blame-ignore-revs` for bulk reformat commit
9	`b3b8bd63`	Fix `np.array` type annotations → `np.ndarray`
10	`63cddb85`	Update `.gitignore`

Notes

All 14 pre-commit hooks pass cleanly
The bulk reformat commit (0a8f50a9) is listed in .git-blame-ignore-revs — GitHub will automatically ignore it in blame views
B905 (zip() without strict=) is intentionally deferred — 67 call sites need individual review for correctness

- Remove black and isort pre-commit hooks - Remove pretty-format-yaml hook (replaced by biome in 1c) - Rename ruff hook to ruff-check, add ruff-format hook - Add types_or: [python, pyi, jupyter] to both ruff hooks - Remove [tool.black] and [tool.isort] sections from pyproject.toml - Add I (isort) to [tool.ruff.lint] select

- Remove pyupgrade hook (ruff UP rules cover this) - Remove blacken-docs hook (ruff-format handles code blocks) - Remove rstcheck hook (CI lint-docs is more thorough) - Remove doc8 hook and [tool.doc8] from pyproject.toml

- Add biomejs/pre-commit v2.2.4 (biome-format) + biome.jsonc config - Add tox-dev/pyproject-fmt v2.6.0 - Bump pre-commit-hooks v4.6.0 → v6.0.0 - Bump ruff-pre-commit v0.6.5 → v0.13.2

- requires-python: '>=3.10' → '>=3.12' - Remove Python 3.10/3.11 classifiers - Remove target-version (inferred from requires-python) - Add src = ['src'] for first-party import detection - Add format.docstring-code-format = true

Move 16 safe-to-move local imports to module top level: - scanpy.plotting.palettes in _colors.py - numpy.linalg.norm, scipy.spatial.distance.jensenshannon, sklearn.feature_selection.mutual_info_regression in _lineage.py - networkx, cellrank._utils._parallelize.parallelize in _utils.py - cellrank._utils._key.Key in _base_kernel.py - scvelo.plotting.utils in _random_walk.py - cellrank.kernels._utils._ensure_numeric_ordered in _log_odds.py - mpl_toolkits.axes_grid1.Divider/Size in _heatmap.py - sklearn.svm.SVR in pl/_utils.py - cellrank._utils._linear_solver._is_petsc_slepc_available in _schur.py - cellrank._utils.Lineage, sklearn.utils.sparsefuncs in _cytotrace_kernel.py Add '# circular import' comments to all remaining local imports that must stay local to avoid circular import chains.

- Remove 5 unnecessary noqa comments (no rules triggered) - Add specific codes to 19 remaining noqa comments: D400/D401 for docrep %(copy)s templates D400 for multi-line docstring endings F821 for forward-reference type annotations F401 for unused petsc4py/slepc4py imports C408 for dict() call NPY001 for deprecated np.int alias B006 for mutable default argument

Run all pre-commit hooks on every file to apply consistent formatting: - ruff format: reformat all Python files - ruff check --fix: auto-fix UP007/UP045 (Union→X|Y), C420 (dict.fromkeys), UP042/UP047 (type params), remove unused Union/Optional imports - pyproject-fmt: normalize pyproject.toml - biome: format JSON files - Ignore B905 (zip without strict=) for now (67 pre-existing violations)

np.array is a function, not a type — using it in X | Y union syntax causes TypeError at runtime. These were pre-existing annotation bugs exposed by the ruff UP007/UP045 auto-fixes.

RTD was using Python 3.10, which now fails because requires-python >= 3.12.

Aligns with requires-python >= 3.12 set in commit 5e687f0.

- lint.yml: 3.10 → 3.12 - deployment.yml: 3.10 → 3.12 - docs/installation.rst: >= 3.8 → >= 3.12

Ruff UP017 auto-converted datetime.timezone.utc → datetime.UTC (the modern Python 3.11+ alias). The test's IncTime monkeypatch only exposed a 'timezone' property, not 'UTC'. Add the missing property to the mock.

codecov · 2026-02-13T23:13:54Z

Codecov Report

❌ Patch coverage is 93.96985% with 24 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.37%. Comparing base (be09075) to head (9c77017).
⚠️ Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
src/cellrank/_utils/_lineage.py	82.60%	4 Missing ⚠️
.../cellrank/estimators/mixins/_fate_probabilities.py	75.00%	0 Missing and 4 partials ⚠️
src/cellrank/_utils/_utils.py	93.54%	2 Missing ⚠️
src/cellrank/estimators/mixins/_lineage_drivers.py	83.33%	0 Missing and 2 partials ⚠️
src/cellrank/logging/_logging.py	77.77%	2 Missing ⚠️
src/cellrank/_utils/_docs.py	0.00%	0 Missing and 1 partial ⚠️
src/cellrank/_utils/_enum.py	75.00%	1 Missing ⚠️
src/cellrank/_utils/_linear_solver.py	87.50%	1 Missing ⚠️
...cellrank/estimators/mixins/decomposition/_eigen.py	83.33%	0 Missing and 1 partial ⚠️
...cellrank/estimators/mixins/decomposition/_schur.py	95.00%	0 Missing and 1 partial ⚠️
... and 5 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1282      +/-   ##
==========================================
- Coverage   79.38%   79.37%   -0.01%     
==========================================
  Files          51       51              
  Lines        8624     8627       +3     
  Branches     1492     1492              
==========================================
+ Hits         6846     6848       +2     
  Misses       1198     1198              
- Partials      580      581       +1

Files with missing lines	Coverage Δ
src/cellrank/_utils/_colors.py	`81.34% <100.00%> (ø)`
src/cellrank/_utils/_key.py	`94.80% <100.00%> (+0.06%)`	⬆️
src/cellrank/_utils/_parallelize.py	`73.33% <100.00%> (ø)`
src/cellrank/datasets.py	`44.44% <100.00%> (ø)`
src/cellrank/estimators/_base_estimator.py	`80.00% <100.00%> (ø)`
src/cellrank/estimators/mixins/_kernel.py	`100.00% <100.00%> (ø)`
src/cellrank/estimators/mixins/_utils.py	`89.18% <100.00%> (ø)`
src/cellrank/estimators/terminal_states/_cflare.py	`67.77% <100.00%> (ø)`
src/cellrank/estimators/terminal_states/_gpcca.py	`78.04% <100.00%> (ø)`
...timators/terminal_states/_term_states_estimator.py	`77.39% <100.00%> (ø)`
... and 38 more

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

Zethson

I love these kind of PRs. Sorry, just saw this while passing by

Tested locally: docs build succeeds on 3.13.7.

Marius1311 · 2026-02-18T17:07:14Z

Hi @Zethson, thanks a lot for your review, that's great! I'll go over it step by step, but for context, I planned a series of PRs to update CellRank, this is just the first one. I wanted to do the more "radical" changes, like switching to hatch, on a separate PR, that's why it's not included here.

Marius1311 · 2026-02-20T18:46:30Z

comments

Can use from numpy.typing import NDarray for type hints.

Marius1311 · 2026-02-20T20:04:13Z

comments

Can use from numpy.typing import NDarray for type hints.

Actually I wouldn't do it - that's only really useful if you want to be really strict about typing, i.e. use mypy. We're more leaninant on types, so I think it's fine.

Marius1311 added 11 commits February 13, 2026 16:26

Remove redundant pre-commit hooks

edd7a13

- Remove pyupgrade hook (ruff UP rules cover this) - Remove blacken-docs hook (ruff-format handles code blocks) - Remove rstcheck hook (CI lint-docs is more thorough) - Remove doc8 hook and [tool.doc8] from pyproject.toml

Add modern hooks: biome, pyproject-fmt; bump versions

7ac027e

- Add biomejs/pre-commit v2.2.4 (biome-format) + biome.jsonc config - Add tox-dev/pyproject-fmt v2.6.0 - Bump pre-commit-hooks v4.6.0 → v6.0.0 - Bump ruff-pre-commit v0.6.5 → v0.13.2

Require Python >=3.12, update ruff config

5e687f0

- requires-python: '>=3.10' → '>=3.12' - Remove Python 3.10/3.11 classifiers - Remove target-version (inferred from requires-python) - Add src = ['src'] for first-party import detection - Add format.docstring-code-format = true

Add .git-blame-ignore-revs for bulk reformat commit

e9bbac2

Fix np.array type annotations → np.ndarray

b3b8bd6

np.array is a function, not a type — using it in X | Y union syntax causes TypeError at runtime. These were pre-existing annotation bugs exposed by the ruff UP007/UP045 auto-fixes.

Update .gitignore: add uv.lock and .github/prompts/

63cddb8

Fix ReadTheDocs: use Python 3.12

48d867f

RTD was using Python 3.10, which now fails because requires-python >= 3.12.

Marius1311 requested a review from WeilerP February 13, 2026 22:50

Marius1311 added 3 commits February 13, 2026 17:51

Drop Python 3.10/3.11 from CI matrix and tox envlist

fb656ab

Aligns with requires-python >= 3.12 set in commit 5e687f0.

Update remaining Python version references to 3.12

a1efa96

- lint.yml: 3.10 → 3.12 - deployment.yml: 3.10 → 3.12 - docs/installation.rst: >= 3.8 → >= 3.12

Fix test_timing mock for datetime.UTC

0502869

Ruff UP017 auto-converted datetime.timezone.utc → datetime.UTC (the modern Python 3.11+ alias). The test's IncTime monkeypatch only exposed a 'timezone' property, not 'UTC'. Add the missing property to the mock.

Zethson reviewed Feb 18, 2026

View reviewed changes

Marius1311 added 2 commits February 18, 2026 11:21

Merge branch 'main' into modernize/pre-commit-linting

1e47bd0

Bump ReadTheDocs Python 3.12 → 3.13

8187bd2

Tested locally: docs build succeeds on 3.13.7.

Merge branch 'main' into modernize/pre-commit-linting

9c77017

Marius1311 merged commit c8f1975 into main Feb 20, 2026
6 of 7 checks passed

Marius1311 deleted the modernize/pre-commit-linting branch February 20, 2026 20:04

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Modernize pre-commit hooks & linting (PR 1/9)#1282

Modernize pre-commit hooks & linting (PR 1/9)#1282
Marius1311 merged 17 commits intomainfrom
modernize/pre-commit-linting

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Marius1311 commented Feb 13, 2026

Summary

Changes

Pre-commit hooks

Python version & ruff config

Code quality

Bulk reformat

Housekeeping

Commits

Notes

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