Make pyproject.toml the single definition for lint tool versions and settings by hjmjohnson · Pull Request #9067 · Project-MONAI/MONAI

hjmjohnson · 2026-08-22T21:13:29Z

Several people have converged on the same goal from different directions: @Borda opened #8683 asking that linting "rely solely on the repository's pre-commit configuration ... the exact same versions and rules are applied everywhere", @ericspod listed "Move black and isort formatting into pre-commit" in #9058 and raised the tool-version concern on #8683, and @aymuos15 prototyped a "remove everything and only do ruff" branch off that thread. This PR implements the shared requirement — one definition per tool — without changing a single source file.

Concretely: pyproject.toml becomes the only place a lint tool's version or settings are declared, and a CI job runs pre-commit on a lint-only environment.

For reviewers: this does not compete with #9061. #9061 adds black and isort hooks and notes that their versions "need to be set in the .pre-commit-config.yaml file separately from wherever else they're specified, so when versions are changed they need to be synced between files." This removes that requirement, so the two can be rebased onto each other in either order.

It also fills the gap left when the Pre-Commit-Lite approach was struck from the #9058 checklist. That approach existed to "ensure the versions of black and isort match what would be used locally"; with it withdrawn in favour of "regular pre-commit may just be fine", nothing currently makes those versions match. Declaring them once is the smaller way to get the same guarantee.

The drift is already real, not hypothetical

On dev today:

Setting	`pyproject.toml`	elsewhere
ruff version	`ruff>=0.14.11,<0.15`	`.pre-commit-config.yaml` → `rev: v0.15.20`
pycln version	absent	`.pre-commit-config.yaml` → `rev: v2.6.0`
ruff excludes	absent	`runtests.sh:602,604` and the ruff hook

The two ruff ranges are disjoint, so a contributor following CONTRIBUTING.md and pre-commit.ci could not run the same linter even in principle. Building an environment from pyproject.toml on this machine gives ruff 0.14.14; pre-commit.ci runs 0.15.20.

Because the excludes live in the callers, a plain ruff check --fix . — what an editor or a one-off invocation runs — does not get them, and rewrites versioneer.py and monai/_version.py. Before this PR that command reports 111 violations (84 UP031, 11 N806, 7 N801, 6 UP035, 2 N818, 1 B904), every one inside those two files.

runtests.sh also called ruff as a bare PATH executable while isort, black, pylint and pytype all go through "${PY_EXE}" -m. The guard above it, is_pip_installed ruff, tests importlib.util.find_spec using PY_EXE — so the check interrogated one environment and the invocation ran whatever ruff PATH happened to offer. In a clean virtualenv built per CONTRIBUTING.md, ./runtests.sh --codeformat fails outright with ruff: command not found.

What changed

pyproject.toml — a lint optional-dependency group holds the tools that .pre-commit-config.yaml and runtests.sh both invoke; testing pulls it in via monai[lint] so developers still have one install. The group excludes torch and the optional dependencies, so a lint-only environment can be built from it alone.

extend-exclude added to [tool.ruff] for the two vendored files
ruff pinned to 0.16.4, the newest release that leaves this codebase unchanged
pycln==2.6.0 added — it was pinned only in the hook and never installed by runtests.sh
[tool.black] switches from exclude to force-exclude, same regex

.pre-commit-config.yaml — ruff and pycln become repo: local hooks with language: system, and black and isort join them, so pre-commit runs the tools from that environment instead of building its own from a second set of pins. There is no rev: left to keep in sync. The hygiene hooks from pre-commit-hooks keep theirs — they have no pyproject.toml counterpart and are already single-definition.

runtests.sh — ruff goes through "${PY_EXE}" -m like every other tool; its duplicated --exclude flags are dropped.

monai/config/print_dependencies.py — parse_dependencies() expands self-referential requirements, normalizing both the project name and the extra names so case and -/_/. spellings resolve to one group; PEP 503 and PEP 685 specify the same rule. A requirement naming a different project, such as versioneer[toml] in build-system.requires, passes through untouched. install_deps feeds its output to pip install -r, where an unexpanded monai[lint] would resolve against the package index rather than the checkout. This is the only Python change; no source file is reformatted.

.github/workflows/cicd_tests.yml — a pre-commit job. pre-commit has never run in GitHub Actions; only the external pre-commit.ci service ran it, and the hooks above need an environment that service does not build, so they are listed under ci.skip and this job runs them. It reads the lint extra out of pyproject.toml at run time rather than restating versions in YAML. static-checks is left unchanged, so its copyright and pyrefly coverage is kept and CI fails if the two routes ever disagree.

Why each exclusion flag on the hook entries is load-bearing

language: system hooks receive explicit filenames, and most tools ignore their configured excludes in that mode. Run directly against the two vendored files:

tool	with the flag	without
black (`force-exclude`)	nothing to do	2 files would be reformatted
ruff (`--force-exclude`)	no files found	200 errors
isort (`--filter-files`)	skipped 2 files	2 sort errors

This is also why [tool.black] moves from exclude to force-exclude: black ignores exclude for filenames given on the command line, which is exactly how pre-commit calls it.

Verification

Ruff 0.16.4 was chosen by sweeping every release from 0.14.11 to 0.16.4 against dev. They are indistinguishable on this codebase — same violations before, same files touched by --fix — so the bump carries no lint-behaviour change.

check	result
`pre-commit run --all-files`, full environment	all hooks pass, tree unmodified
`pre-commit run --all-files`, torch-free lint env (as CI)	all hooks pass, tree unmodified
`./runtests.sh --codeformat`, venv not on PATH	copyright 1360 files, isort, black, ruff 0.16.4, pyrefly 0 errors
`./runtests.sh --autofix`	0 Python files changed
`./runtests.sh -u --net --coverage`	18196 tests, failure set identical to unmodified `dev`

Both routes now resolve the same ruff, 0.16.4, which is the point of the change.

The full suite was run twice from separate worktrees, once on this branch and once on unmodified dev, so the comparison is a controlled one. Both report 18196 tests and the same 39 failures, from pre-existing dependency incompatibilities unrelated to this PR (zarr 3.x, scipy 1.18 dropping sqrtm(disp=), matplotlib baseline images, and a None reaching a numeric comparison in fall_back_tuple). The dev run additionally failed test_optim_novograd test_step_6 and test_step_7, which pass in isolation on both trees across repeated runs and appear to be order-dependent flakes.

Note for anyone reproducing: use Python 3.10, matching PYTHON_VER1. The all extra has no upper bounds, so Python 3.12 resolves zarr 3.3.0, scipy 1.18.1 and matplotlib 3.11.1 — versions that Python 3.10 cannot reach and that CI therefore never sees. Rebuilding on 3.10 clears most of the failures above.

Nothing here changes which tools are used. Whether ruff should replace black and isort outright is a separate question with its own trade-offs, raised in #9066; this PR is a prerequisite for that either way, since otherwise such a swap has to be made in pyproject.toml, .pre-commit-config.yaml and runtests.sh simultaneously and kept in sync.

coderabbitai · 2026-08-22T21:13:40Z

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📝 Walkthrough

Walkthrough

The project adds a shared lint dependency group and updates tool exclusions. Pre-commit uses project-installed lint tools through local hooks. A new Ubuntu CI job installs the lint dependencies and runs all pre-commit hooks. runtests.sh invokes Ruff through the configured Python executable. Dependency parsing now expands self-referential extras and handles cyclic groups.

Estimated code review effort: 3 (Moderate) | ~20 minutes

Merge Risk: 🔵 Low · up to 466b1

The PR is otherwise mergeable, but dependency installation can select the published package instead of the local checkout when equivalent project-name spellings use different separators; this bounded correctness risk should receive explicit owner follow-up.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 3 functions across 3 files.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Title check	✅ Passed	The title clearly and concisely describes the main change: centralizing lint tool versions and settings in pyproject.toml.
Description check	✅ Passed	The description is detailed, relevant, and documents the changes and verification results. It does not reproduce the template's formal issue and types-of-changes sections, but it provides the required…

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The description is detailed, relevant, and documents the changes and verification results. It does not reproduce the template's formal issue and types-of-changes sections, but it provides the required context and is substantially complete.

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hjmjohnson · 2026-08-22T21:35:21Z

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In @.github/workflows/cicd_tests.yml:
- Around line 55-58: Update the pre-commit job to grant only contents read
permission at the job level, and configure its actions/checkout step with
persist-credentials disabled while preserving the existing checkout behavior.

In `@pyproject.toml`:
- Around line 169-170: Update the testing dependency group to expand the lint
requirements directly instead of referencing monai[lint], ensuring
parse_dependencies() includes all five lint packages before install_deps runs.
Alternatively, implement recursive group expansion in parse_dependencies() while
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coderabbitai · 2026-08-22T21:45:20Z

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hjmjohnson · 2026-08-22T22:36:17Z

Thanks — the token concern is fixed in c5eb18c; the dependency-resolution one I believe is a false positive, evidence below.

Token persistence — fixed. Fair catch. This job runs the hooks named by a PR's own .pre-commit-config.yaml, so leaving a usable credential in .git/config for that hook code to reach is the wrong default. The job now uses persist-credentials: false and permissions: contents: read.

Dependency resolution — tested, resolves from the checkout

The concern is that testing = ["monai[lint]", ...] could resolve monai from PyPI rather than the local tree. It does not: pip recognises the self-reference as the project already being installed.

Tested against the worst case — a throwaway project named monai (the name does exist on PyPI) at version 9.9.9, with the same extras shape, resolved by pip:

Collecting ruff==0.16.4 (from monai==9.9.9)
Would install coverage-7.15.4 monai-9.9.9 ruff-0.16.4

  monai      9.9.9      <- LOCAL CHECKOUT
  ruff       0.16.4     <- REMOTE (pypi)
  coverage   7.15.4     <- REMOTE (pypi)

monai came from the checkout, and ruff==0.16.4 came from the local lint extra — no published MONAI has a lint extra, so had this resolved from PyPI the pin could not have appeared. Confirmed independently with uv: installing .[all,testing] in an existing environment bumped ruff 0.14.14 → 0.16.4 and added pycln, both of which only exist in this branch's lint extra.

Separately, the CI job here never exercises that path at all — it reads the lint pins straight out of pyproject.toml and installs those, so no monai distribution is resolved either way.

Phase 3 recognised exactly one reviewer, greptile-apps[bot]. Any other review bot fell through is_bot() into "bot_other", a bucket the skill documents as "non-blocking, skip unless explicitly asked". On Project-MONAI/MONAI#9065 that put a genuine actionable CodeRabbit finding in the ignore pile; it was only acted on because the raw JSON was read by hand. The single GREPTILE_LOGIN constant becomes AI_REVIEW_PROVIDERS, keyed by bot login and carrying what differs per provider: how a review is requested, how one is forced for an already-reviewed head, and which in-repo file indicates the provider is configured. Findings are parsed per provider and normalised to P1/P2/P3, so CodeRabbit's Critical/Major/Minor maps onto the vocabulary the phase logic already speaks and one rule covers both. Two bugs surfaced while testing this against real PRs. The greptile parser never matched inline findings. Its pattern was alt="(P[123])"[^>]*>\s*\*\*([^*]+)\*\* but the badge is an <img> wrapped in an <a>, so a closing </a> sits between the badge and the bold title and \s* cannot span it. Most findings are inline, so Phase 3 has been running "address every P1/P2" against an empty list. InsightSoftwareConsortium/ITK#6777 reports 0 findings before this change and 2 P1s after. Provider detection read config files relative to the working directory, so triaging owner/repo#N from an unrelated checkout reported whatever that checkout happened to contain. It now queries the target repo. Unrecognised bots go to a new "bot_unknown" bucket rather than "bot_other". The two are documented differently on purpose: bot_other is ignorable, bot_unknown means nobody has classified this bot yet and it must be read before the phase can be called clean. That is the failure mode above, closed for the next review bot as well as this one. phase_3_ai_review also carries CodeRabbit's PR-level signals, merge_risk and failed_pre_merge_checks, which have no greptile equivalent and no inline comment to hang off. On Project-MONAI/MONAI#9067 merge_risk was "High" with zero inline findings — a credential-exposure issue in a workflow that would otherwise have been reported as Phase 3 clean. phase_3_greptile is retained as an alias so callers written against the old report keep working. ghtp_reply.py is untouched: replying and resolving are provider-agnostic. Verified against ITK#6714 and ITK#6777 (greptile) and MONAI#9065 and MONAI#9067 (coderabbit); test_ghtp_workstate.py still passes.

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In `@monai/config/print_dependencies.py`:
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In `@monai/config/print_dependencies.py`:
- Around line 63-67: Normalize extra names according to PEP 685 before the
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same normalization to requested and declared option keys so case and -, _, and .
variants resolve identically. Update or add tests covering these equivalences,
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monai/config/print_dependencies.py (1)
35-35: 📐 Maintainability & Code Quality | 🔵 Trivial | ⚡ Quick win

Document _normalize_extra inputs and result.

Add Google-style Args and Returns sections. The current docstring does not describe name or the returned value.

As per path instructions, definitions must include Google-style docstrings that describe each variable and return value.
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In `@monai/config/print_dependencies.py` at line 35, Update the _normalize_extra
docstring to use Google-style Args and Returns sections, documenting the name
input and the normalized string returned; preserve the existing normalization
behavior.
Source: Path instructions

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Inline comments:
In `@monai/config/print_dependencies.py`:
- Line 57: Update parse_dependencies to normalize both the project name and
captured requirement names using the packaging normalization rules before
filtering self-references, so underscore, hyphen, and dot variants match
equivalently. Preserve extras parsing and add regression coverage for each name
variant to ensure the self-reference is excluded.

---

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In `@monai/config/print_dependencies.py`:
- Line 35: Update the _normalize_extra docstring to use Google-style Args and
Returns sections, documenting the name input and the normalized string returned;
preserve the existing normalization behavior.

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Ruff is the only formatting/linting tool whose exclusion of the two vendored/generated files is not declared in pyproject.toml. Black has it in [tool.black] exclude and pyrefly has it in [tool.pyrefly] project-excludes; ruff's copy lives in the callers instead: runtests.sh:602,604 --exclude versioneer.py --exclude monai/_version.py .pre-commit-config.yaml exclude: (?x)(^versioneer.py|^monai/_version.py) Two consequences follow from that placement. First, the exclusion only applies when ruff is reached through one of those two callers. A one-off developer or IDE invocation -- plainly "ruff check --fix ." at the repository root -- does not get it, and rewrites versioneer.py and monai/_version.py. Before this change that call reports 111 violations (84 UP031, 11 N806, 7 N801, 6 UP035, 2 N818, 1 B904), every one of them inside those two files, and --fix modifies both. After it, "ruff check ." reports "All checks passed!" and --fix is a no-op. Verified on ruff 0.14.14 (the version pyproject currently resolves to) and on 0.16.4 (latest); the whole 0.14.11-0.16.4 range behaves identically here. Second, the setting has to be restated once per caller, so each new way of invoking a tool adds another copy that can drift. Project-MONAI#9061 shows the shape of this: it adds black and isort pre-commit hooks, and each one carries its own exclude block, with the accompanying note that "black will be given individual file names and so will ignore the excludes in pyproject.toml". Declaring the setting where the tool looks for it by default keeps one definition no matter how many routes reach the tool. This commit only adds the declaration; the now-redundant copies in runtests.sh and .pre-commit-config.yaml are left in place so this change is inert on its own and can be verified independently. They become removable once this has landed. No source files are changed. runtests.sh --codeformat passes on all four legs (copyright 1360 files, isort, black, ruff, pyrefly 0 errors) and pre-commit run --all-files passes. Signed-off-by: Hans Johnson <hans-johnson@uiowa.edu>

Tool versions were declared twice and could not agree. pyproject.toml asked for "ruff>=0.14.11,<0.15" while .pre-commit-config.yaml pinned rev v0.15.20 -- disjoint ranges, so a developer following CONTRIBUTING.md and pre-commit.ci were guaranteed to run different linters. pycln was pinned only in the hook and never installed by runtests.sh at all. pyproject.toml now owns both the versions and the settings: - a "lint" optional-dependency group holds the tools that .pre-commit-config.yaml and runtests.sh both invoke, and "testing" pulls it in via monai[lint] so developers still have one install. The group excludes torch and the optional dependencies, so a lint-only environment can be built from it alone. - ruff is pinned to 0.16.4, the newest release that leaves this codebase unchanged. Every release from 0.14.11 to 0.16.4 was run against dev and they are indistinguishable here: same violations before, same files touched by --fix, and "All checks passed!" on each. - pycln is added at 2.6.0, the version its hook used. - [tool.black] switches from exclude to force-exclude with the same regex, because black ignores exclude for filenames given on the command line, which is how pre-commit invokes it. The ruff and pycln hooks become local hooks with language: system, and black and isort join them, so pre-commit runs the tools from that environment rather than building its own from a second set of pins. There is no longer a rev: to keep in sync. The hygiene hooks from pre-commit-hooks keep their rev:, as they have no counterpart in pyproject.toml and so are already single-definition. The flags on those entries make the pyproject settings apply to the explicit filenames pre-commit passes. Each is load-bearing; run against the two vendored files directly: black with force-exclude nothing to do / without: 2 would be reformatted ruff with --force-exclude no files found / without: 200 errors isort with --filter-files skipped 2 files / without: 2 sort errors Because these hooks need an environment pre-commit.ci does not build, they are listed under ci.skip; the pre-commit job added to cicd_tests.yml runs them instead. parse_dependencies() gains expansion of self-referential requirements. runtests.sh's install_deps writes its output to a requirements file and runs "pip install -r" on it, and the parser appended each group verbatim, so "monai[lint]" reached pip as a plain requirement with no local path. pip would have resolved it against the package index -- installing the published release over the checkout under test, and none of the five lint tools. Self-references are now replaced by the group they name, with a seen-set so a group that refers to itself terminates. Covered by new cases in tests/config/test_print_dependencies.py, including the cyclic one. No source file is reformatted; the only Python change is that parser. pre-commit run --all-files and runtests.sh --autofix both leave the tree untouched. Signed-off-by: Hans Johnson <hans-johnson@uiowa.edu>

runtests.sh called ruff as a bare executable on PATH while isort, black, pylint and pytype all go through "${PY_EXE}" -m. The guard above it, is_pip_installed ruff, tests importlib.util.find_spec using PY_EXE, so the check interrogated one environment and the invocation ran whatever ruff PATH happened to offer. In a clean virtualenv built per CONTRIBUTING.md this makes ./runtests.sh --codeformat fail outright: ruff ./runtests.sh: line 598: ruff: command not found Check failed! and where a system ruff does exist it silently wins over the pinned one. The --exclude versioneer.py --exclude monai/_version.py flags are dropped because [tool.ruff] extend-exclude now carries them, so they apply however ruff is reached rather than only through this script. --unsafe-fixes is left on the fix path as-is; making it symmetric with the check path is a behaviour change and belongs on its own. Signed-off-by: Hans Johnson <hans-johnson@uiowa.edu>

pre-commit has never run in GitHub Actions; only the external pre-commit.ci service ran it. Now that the formatting hooks are skipped there, because they need an environment that service does not build, this job runs them. It installs the "lint" extra alone, read out of pyproject.toml at run time so the versions are not restated in the workflow. That needs neither torch nor the optional dependencies, unlike static-checks, which installs .[all,testing] before running formatters. static-checks is left unchanged. Running both routes keeps the copyright and pyrefly coverage it provides, and makes CI fail if pre-commit and runtests.sh ever disagree about the same files. Signed-off-by: Hans Johnson <hans-johnson@uiowa.edu>

ericspod · 2026-09-01T11:30:35Z

Hi @hjmjohnson thanks for looking into this and I do agree that we'd be better with a single place for defining the versions of tools. I had thought about exactly this sort of approach with an action that uses Pre-Commit Lite to push reformatted code back to the branch. The reason for sticking with doing this through the pre-commit file and the regular Pre-Commit app is that this runs much faster than a regular action and typically before the others run. Since reformatting code is important to do early so not to waste time testing code that'll be changed anyway. I don't believe there's a way of controlling action order or priority, and setting up the action to run the black/isort is much slower than using Pre-commit's provided small VMs. I would still say that we merge my approach for these reasons.

hjmjohnson force-pushed the ruff-odr-exclude branch from ea4bef1 to b6052ba Compare August 22, 2026 21:27

hjmjohnson marked this pull request as ready for review August 22, 2026 21:34

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hjmjohnson force-pushed the ruff-odr-exclude branch from c5eb18c to a721d5e Compare August 23, 2026 13:51

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hjmjohnson force-pushed the ruff-odr-exclude branch from 733c6ce to 466b1ee Compare August 31, 2026 15:27

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Comment thread monai/config/print_dependencies.py Outdated

hjmjohnson force-pushed the ruff-odr-exclude branch from 466b1ee to 840ad26 Compare August 31, 2026 15:36

hjmjohnson added 3 commits August 31, 2026 10:37

hjmjohnson force-pushed the ruff-odr-exclude branch from 840ad26 to a07ad28 Compare August 31, 2026 15:37

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Make pyproject.toml the single definition for lint tool versions and settings - #9067

Make pyproject.toml the single definition for lint tool versions and settings#9067
hjmjohnson wants to merge 4 commits into
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hjmjohnson commented Aug 22, 2026 •

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hjmjohnson commented Aug 22, 2026 •

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