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MarcoGorelli · 2026-07-20T17:29:29Z

Reference Issues/PRs

I've kept .mypy_cache excluded in .gitignore and some other places because contributors probably still have that folder (unchecked) locally, so this will avoid unexpected issue for them

What does this implement/fix? Explain your changes.

First time contributor introduction

AI usage disclosure

I used AI assistance for:

Code generation - I got claude to do a first-pass, and then did the rest manually

Any other comments?

MarcoGorelli · 2026-07-21T09:15:47Z

+[tool.pyrefly.errors]
+bad-override = false


there's hundreds of errors from bad-override due to incompatible constructors

mypy (with the current configuration) doesn't flag these

so, for now, i'd suggest not checking this with pyrefly either

MarcoGorelli · 2026-07-21T09:44:28Z

+                # as xfail.
+                status = "xfail"
+            else:
+                status = "failed"


i'm moving this up from L948 so that check_result can be instantiated with all fields present

MarcoGorelli · 2026-07-21T09:46:05Z

+[tool.pyrefly]
+project-includes = ["sklearn"]
+project-excludes = ["**/sklearn/externals*"]
+preset = "legacy"


this is similar to mypy's current level of strictness. if you want to opt in to a higher level of strictness, I'd suggest leaving that to a separate PR

DeaMariaLeon · 2026-07-21T15:48:43Z

I think there is a mypy mention in the documentation, maybe you want to change that as well?
It's in doc/developers/maintainer.rst ("To avoid type checker (e.g. mypy) errors...")

…cally

MarcoGorelli · 2026-07-22T09:45:07Z

 # FutureWarnings
 with warnings.catch_warnings():
    warnings.simplefilter("ignore", FutureWarning)
-    # mypy error: Module has no attribute "__path__"


__path__ doesn't appear here anyway, not sure what this comment was doing here 😄

MarcoGorelli · 2026-07-22T13:02:30Z

thanks for your review! have addressed

tagging @AnneBeyer and @adrinjalali as they were involved with #32737

adrinjalali

This is actually a nice improvement to what we have, I like it.

@AnneBeyer wanna have a look?

adrinjalali · 2026-07-23T13:58:11Z



 if TYPE_CHECKING:
-    # typing_extensions is available when mypy is installed


still need some sort of a comment here

sure thanks - i've rephrased a bit as it's not a dependency of pyrefly (like it is of mypy), but pyrefly can understand its symbols

lesteve · 2026-08-07T17:05:59Z

This is actually a nice improvement to what we have, I like it.

@adrinjalali so that we are on a similar page and remember what we were hoping for if we ever merge this PR: what do you like and what is the improvement exactly?

Here are a few guesses, there could be others:

pre-commit mypy check can be slowish, maybe a few seconds in the general use case. I noticed it but honestly I am not sure this is a high priority thing to fix.
you have high confidence that pyrefly is better-behaved (please add a few details) than mypy and that we are less likely to fight the typechecker. I can see that a few type annotations were removed in this PR, but I have no idea whether it's because pyrefly is "smarter" or whether the config was done in a way to be less pedantic.

My personal feeling is that broadly speaking there is not a strong interest about typing in scikit-learn and my guess is that it is unlikely that we invest time into adding more typing in the medium-term. Switching to a different typechecker (that feels like maybe a bit less standard) feels more like a risk, and the benefits are not 100% clear to me.

Having said this, I wish we were sometimes more adventurous in scikit-learn where possible and switching a developer tool doesn't affect users's experience too much, so I am open to change my mind if there are good arguments 🤷.

glevv · 2026-08-10T05:40:40Z

@lesteve in my experience, the default behaviour of pyrefly is configured to be very compatible with mypy while also is more "forgivable" in some ways.

There is an option to change preset to a stricter one, which will make contributors fight the typecheker for sure.

In general, default preset shouldn't make life harder for anybody and will speed up the check.

betatim · 2026-08-10T07:49:37Z

I'd be interested in a switch to a type checker that is faster than mypy. I don't really care for static typing in scikit-learn, so reducing the amount of time spent staring at the pre-commit messages waiting for mypy to "do its thing, what ever that might be" is something I'd be happy to support.

At the same time, because I don't find static typing to be all that useful I am interested in keeping type checking related churn down. This means that if we switch we should switch to a type checker that has some history in terms of being well maintained, widely used and still here in a few years time. From my little investigation about type checkers I think pyrefly ticks those boxes, maybe except for the last one??

lorentzenchr · 2026-08-10T11:34:42Z

I fully agree with what @betatim said and would like to merge this PR.
@lesteve Fine for you?

AnneBeyer

Thank you for taking this on @MarcoGorelli!
From what I understand, it doesn't change the behavior (still ignores the things we want to ignore) while cleaning up the code a bit and taking less time, so I would be happy to see this change as well.

Since we have the linting lock files and a running version in this PR, we can always pin it if future updates would create a maintenance overhead on our end.

One thing I noticed when checking out this PR and testing it by committing something (without changing anything in the installation of pre-commit): I didn't have to install pyrefly myself. The first commit took a bit longer, and from what I understand, it was installed automatically in ~/.cache/pre-commit/..., so we might not even have to add it to the installation instructions? In any case, it looks like it will not even disrupt the contributor experience (except for an unexpected delay on the first commit after merging main).

MarcoGorelli · 2026-08-10T12:07:32Z

thanks!

for pre-commit, in general, it doesn't require you to install anything, it handles it all for you

so:

if you run pre-commit run pyrefly --all-files, no setup (other than having pre-commit installed) is required
if you run pyrefly check yourself, you'll need to have pyrefly installed

same for all the other tools, this isn't unique to pyrefly

AnneBeyer · 2026-08-10T12:19:59Z

Ah, that makes sense. Thank you for the clarification! If I understand correctly, this means that, since we instruct contributors to use pre-commit, we could actually remove ruff and pyrefly from the installation instructions, right? This would be something for a follow-up PR, though.

lesteve · 2026-08-10T13:49:47Z

@lorentzenchr feel free to merge it and I guess you will be the main person to deal with the consequences if any 😜 🤞.

It seems like the consensus is:

as a project we don't care about typing too much
the pre-commit checks is fast instead of a few seconds with mypy and it looks like people care about this
we make the bet that pyrefly will be stable enough so we don't have to fight with the typechecker too much.

betatim · 2026-08-10T14:25:07Z

Something that we need to look out for is that existing PRs that do not merge main will not use pyrefly when the contributor adds new commits (I think). I'm not sure if the CI for those PRs will use pyrefly or not, I think they will. So there might be some errors due to this. I think the fix is to merge main into the contributors branch and make a commit.

lesteve · 2026-08-10T14:51:50Z

Good point, I am not 100% sure what will happen ... as maintainer, it's probably safer to click on "Update branch" and then set automerge rather than merging an not super recent PR directly?

I guess that was implicitly included in "deal with the consequences if any" 😉.

lesteve · 2026-08-11T04:52:52Z

For completeness and better awareness, if you push a commit into a branch where mypy is still used (i.e. the vast majority of PRs right now) you will get an error in the linting CI, merging main fixes it.

The error is something like this:

importlib.metadata.PackageNotFoundError: No package metadata was found for pyrefly

I saw this in #34676 (comment).

lesteve · 2026-08-11T05:03:13Z

Annoyingly (or at least semi-annoyingly) there is no bot linting comment when linting fails early, I opened #34719 about it.

MarcoGorelli changed the title ~~WIP Use pyrefly instead of mypy for type-checking~~ WIP MNT Use pyrefly instead of mypy for type-checking Jul 20, 2026

github-actions Bot added module:datasets module:utils labels Jul 20, 2026

MarcoGorelli force-pushed the pyrefly branch 3 times, most recently from cb2cb90 to f9bd7ff Compare July 21, 2026 09:04

MarcoGorelli commented Jul 21, 2026

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MarcoGorelli force-pushed the pyrefly branch from f9bd7ff to 196fba6 Compare July 21, 2026 09:34

MarcoGorelli added 2 commits July 21, 2026 10:34

MNT: Run pyrefly instead of mypy

c1ba020

🔥 remove mypy

1df7476

MarcoGorelli force-pushed the pyrefly branch from 196fba6 to 1df7476 Compare July 21, 2026 09:34

MarcoGorelli commented Jul 21, 2026

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MarcoGorelli marked this pull request as ready for review July 21, 2026 09:50

MarcoGorelli changed the title ~~WIP MNT Use pyrefly instead of mypy for type-checking~~ MNT Use pyrefly instead of mypy for type-checking Jul 21, 2026

DeaMariaLeon reviewed Jul 21, 2026

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Comment thread pyproject.toml

remove now-unnecessary type: ignores, standardise on pyrefly: ignore

360cb5f

revert all changes to externals

e056fd7

MarcoGorelli marked this pull request as draft July 21, 2026 15:51

AnneBeyer added the Build / CI label Jul 22, 2026

MarcoGorelli added 3 commits July 22, 2026 10:29

simplify ignore-missing-imports

9f38afe

update comment

1516d81

restore .mypy_cache ignores, in case people still have that folder lo…

13f6dd6

…cally

MarcoGorelli commented Jul 22, 2026

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MarcoGorelli marked this pull request as ready for review July 22, 2026 09:48

adrinjalali added the No Changelog Needed label Jul 23, 2026

adrinjalali approved these changes Jul 23, 2026

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restore and rephrase comment about typing_extensions

bc7828c

Merge remote-tracking branch 'upstream/main' into pyrefly

784b6c5

lesteve mentioned this pull request Aug 7, 2026

MNT Add tickboxes for AI disclosure in PR template #34677

Closed

MarcoGorelli added 2 commits August 10, 2026 09:45

Merge remote-tracking branch 'upstream/main' into pyrefly

906217f

bump to 1.2.0

107e8f9

AnneBeyer approved these changes Aug 10, 2026

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lorentzenchr approved these changes Aug 10, 2026

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lorentzenchr merged commit 94a85a8 into scikit-learn:main Aug 10, 2026
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prady0t pushed a commit to prady0t/scikit-learn that referenced this pull request Sep 2, 2026

MNT Use pyrefly instead of mypy for type-checking (scikit-learn#34527)

ca2b46a

jeremiedbb mentioned this pull request Sep 8, 2026

Release 1.9.1 #34905

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jeremiedbb pushed a commit to jeremiedbb/scikit-learn that referenced this pull request Sep 8, 2026

MNT Use pyrefly instead of mypy for type-checking (scikit-learn#34527)

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jeremiedbb pushed a commit to jeremiedbb/scikit-learn that referenced this pull request Sep 9, 2026

MNT Use pyrefly instead of mypy for type-checking (scikit-learn#34527)

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jeremiedbb pushed a commit to jeremiedbb/scikit-learn that referenced this pull request Sep 9, 2026

MNT Use pyrefly instead of mypy for type-checking (scikit-learn#34527)

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		if TYPE_CHECKING:
		# typing_extensions is available when mypy is installed

		[tool.pyrefly.errors]
		bad-override = false

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Reference Issues/PRs

What does this implement/fix? Explain your changes.

First time contributor introduction

AI usage disclosure

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