[chore] Stricter ruff rules by fjosw · Pull Request #282 · fjosw/pyerrors

fjosw · 2026-04-20T17:49:33Z

This PR imposes stricter ruff rules and fixes the parts which raise errors now. Main changes:

Remove mutables as default argument (was part of [Fix] Remove mutables as default argument and fix smaller issues #249)
Removes printf style string formatting
Imposes strict zipping

jkuhl-uni

lgtm

jkuhl-uni · 2026-04-21T13:07:08Z

Thank you for all the work on the code style!
I think having these slightly stricter rules makes sense. I have to familiarize myself with some of the reasoning behind the ruff rules, but I think it is a good idea overall.

s-kuberski · 2026-04-23T16:47:16Z

Hi! Thanks for taking the time to implement this! I am still in the process of looking through the changes.

I was wondering about the change of the handling of random numbers. I understand that switching to np.random.default_rng() is considered to be the proper modern solution. However, I am asking myself if this change, hidden inside the large number of other changes, could lead to unexpected behavior.

As I understand it, changing the numpy random seed will not affect the state of the random number generator anymore, right? So there won't be any way to fix the seed in the random number generator in the future, when its initialization is hidden in the module. Could this lead to problems?

Restore use of the global np.random state in pseudo_Obs (misc.py) and the prior id generation (fits.py), keeping seed behavior unchanged. The switch to a module-local generator is out of scope for this lint-focused PR.

The RNG migration was reverted to keep np.random.seed() behavior, so add per-line noqa: NPY002 on the three legacy np.random calls instead of the Generator API.

fjosw · 2026-06-18T09:00:46Z

After quite some time I had another look at this PR. I agree with leaving the RNG changes out of this PR and potentially do them separately or not at all. I removed the rng changes from the diff. Could you review the changes that are left @s-kuberski @jkuhl-uni ?

jkuhl-uni · 2026-06-19T06:43:24Z

Hi,
thank you again for the work.
I think moving the changes to another PR is a good idea. I haven't had time to think more about the calls within NumPy. If the current call from pyerrors is considered legacy, I hope there is an alternative that would have the same properties in regard to the seed and instantiation of the RNG as the legacy call.

s-kuberski · 2026-07-03T10:07:06Z

Thanks for the adaption! This looks good to me and can be merged from my side.

There are only two very small things we might still want to fix before merging, that I noticed in lines that were touched in this pull request:

in pyerrors/linalg.py, in prune, the error message for Ntrunc >= basematrix.N seems to have the inequality reversed/misleading;
in pyerrors/covobs.py, the error message for a non-symmetric covariance matrix is missing a closing parenthesis.

Neither is blocking from my side, these are really minor.

Copilot

Pull request overview

This PR tightens the repository’s Ruff linting configuration and updates code/tests to satisfy the stricter rules, including safer iteration patterns (zip(..., strict=True)), removal of mutable default arguments, and modernization away from printf-style formatting.

Changes:

Added/expanded Ruff configuration in pyproject.toml and updated CI/docs to use Ruff instead of flake8.
Refactored multiple modules to address new lint violations (e.g., strict zip, f-strings/formatting, loop-variable hygiene, safer exception chaining, stacklevel on warnings).
Added regression tests covering strict-zip mismatches and unhashability expectations for Corr/CObs, plus an integration-derivative closure binding test.

Reviewed changes

Copilot reviewed 33 out of 33 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/obs_test.py	Adds tests for `Obs` mismatched lengths, fractional `N_sigma` formatting in `details()`, and `CObs` unhashability.
tests/integrate_test.py	Adds a regression test ensuring per-parameter derivatives don’t collapse due to a closure-binding bug.
tests/correlators_test.py	Adds tests ensuring `Corr` padding default isn’t shared and `Corr` is unhashable.
setup.py	Removes `flake8` from test extras (Ruff is now the lint tool).
pyproject.toml	Introduces Ruff target version and stricter lint rule selection/ignores.
pyerrors/special.py	Reformats imports/`__all__` for lint compliance and readability.
pyerrors/roots.py	Minor formatting cleanup (blank line).
pyerrors/obs.py	Enforces strict zips, modernizes formatting, adds warning stacklevels, binds closure variables safely, and updates various small lint-driven refactors.
pyerrors/mpm.py	Normalizes import ordering.
pyerrors/misc.py	Lint-driven refactors; affects `pseudo_Obs()` implementation.
pyerrors/linalg.py	Normalizes imports and addresses unused loop variables / strict zip.
pyerrors/integrate.py	Fixes closure binding for `i` inside a vectorized lambda and normalizes imports.
pyerrors/input/utils.py	Addresses unused `os.walk` variables and improves last-line tracking in param files.
pyerrors/input/sfcf.py	Removes mutable default args, strict-zips name/type pairs, improves exception chaining, adds warning stacklevels.
pyerrors/input/pandas.py	Import ordering tweaks and adds `stacklevel` to warnings.
pyerrors/input/openQCD.py	Import cleanup, warning `stacklevel`, safer defaults, and small formatting refactors.
pyerrors/input/misc.py	Import ordering tweaks and warning `stacklevel`.
pyerrors/input/json.py	Import ordering cleanup and conversion of printf-style formatting to f-strings.
pyerrors/input/hadrons.py	Removes mutable default args and strict-zips correlated iterables.
pyerrors/input/dobs.py	Removes mutable default args and converts many format strings to f-strings.
pyerrors/input/bdio.py	Refactors loops/formatting, strict-zips correlated iterables, and updates tuple construction.
pyerrors/fits.py	Import ordering, exception chaining, closure binding fixes, strict zips, and warning stacklevels.
pyerrors/dirac.py	Removes an extra blank line.
pyerrors/covobs.py	Improves exception formatting (fixes malformed message).
pyerrors/correlators.py	Removes mutable default args, adds warning `stacklevel`, makes `Corr` unhashable, and includes small lint refactors.
pyerrors/init.py	Reorders imports/exports to satisfy linting and style expectations.
CONTRIBUTING.md	Updates contributor guidance from flake8 to Ruff (including commands).
.github/workflows/ruff.yml	Updates Ruff workflow action versions.
.github/workflows/release.yml	Updates checkout action version.
.github/workflows/pytest.yml	Updates checkout action version.
.github/workflows/flake8.yml	Removes flake8 workflow.
.github/workflows/examples.yml	Updates checkout action version.
.github/workflows/docs.yml	Updates checkout action version.

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+            deltas = [np.random.normal(0.0, dvalue * np.sqrt(samples), samples)]  # noqa: NPY002
            deltas -= np.mean(deltas)
-            deltas *= dvalue / np.sqrt((np.var(deltas) / samples)) / np.sqrt(1 + 3 / samples)
+            deltas *= dvalue / np.sqrt(np.var(deltas) / samples) / np.sqrt(1 + 3 / samples)
            deltas += value
            res = Obs(deltas, [name])


+                last_line = ''
                for line in fp:
-                    pass
-                last_line = line
+                    last_line = line
                if last_line.split()[2] != param_hash:
                    rep_nums += file.split("_")[1] + ','


[chore] Stricter ruff rules

c896843

fjosw marked this pull request as ready for review April 20, 2026 17:49

fjosw requested review from jkuhl-uni and s-kuberski as code owners April 20, 2026 17:49

fjosw added 2 commits April 20, 2026 20:28

[chore] Furture lint rules and removal of flake8

d9ffa33

[ci] Bump github action versions

16e4c35

jkuhl-uni reviewed Apr 21, 2026

View reviewed changes

[chore] Add additional test coverage

157279a

fjosw added 3 commits June 18, 2026 10:46

Merge branch 'develop' into ruff_rules_strict

6961917

Revert RNG switch to np.random.default_rng()

9be9fb6

Restore use of the global np.random state in pseudo_Obs (misc.py) and the prior id generation (fits.py), keeping seed behavior unchanged. The switch to a module-local generator is out of scope for this lint-focused PR.

Silence NPY002 on intentional legacy np.random calls

3ca4b18

The RNG migration was reverted to keep np.random.seed() behavior, so add per-line noqa: NPY002 on the three legacy np.random calls instead of the Generator API.

jkuhl-uni approved these changes Jun 19, 2026

View reviewed changes

fjosw added 2 commits July 6, 2026 10:55

[Fix] Fix exception messages

0f22d9f

Merge branch 'develop' into ruff_rules_strict

236c52b

fjosw requested a review from Copilot July 6, 2026 08:58

Copilot started reviewing on behalf of fjosw July 6, 2026 08:59 View session

Copilot AI reviewed Jul 6, 2026

View reviewed changes

fjosw merged commit e72949b into develop Jul 6, 2026
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[chore] Stricter ruff rules - #282

[chore] Stricter ruff rules#282
fjosw merged 9 commits into
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ruff_rules_strict

fjosw commented Apr 20, 2026

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jkuhl-uni left a comment

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jkuhl-uni commented Apr 21, 2026

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s-kuberski commented Apr 23, 2026

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fjosw commented Jun 18, 2026

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jkuhl-uni commented Jun 19, 2026

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s-kuberski commented Jul 3, 2026

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fjosw commented Apr 20, 2026

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jkuhl-uni commented Apr 21, 2026

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s-kuberski commented Apr 23, 2026

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fjosw commented Jun 18, 2026

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jkuhl-uni commented Jun 19, 2026

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s-kuberski commented Jul 3, 2026

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