Refactor: replace np.ndarray with npt.NDArray in type hints by maverickcodex18 · Pull Request #5346 · yt-project/yt

maverickcodex18 · 2025-12-06T21:31:39Z

Walkthrough: Updating NumPy Type Hints

I have updated the type hints in yt to use numpy.typing.NDArray (aliased as npt.NDArray) instead of np.ndarray. This change improves type checking precision and adheres to modern NumPy typing standards. The alias of numpy.typing is updated from npt to nptesting in testing.py.

Changes Overview

The following files were modified to use import numpy.typing as nptype and nptype.NDArray:

yt Core and Utilities

yt/utilities/io_handler.py
yt/loaders.py

`yt/visualization`

yt/visualization/plot_window.py
yt/visualization/fixed_resolution.py
yt/visualization/plot_modifications.py

`yt/frontends`

yt/frontends/rockstar/data_structures.py
yt/frontends/artio/data_structures.py
yt/frontends/ramses/io.py
yt/frontends/ramses/hilbert.py
yt/frontends/ramses/particle_handlers.py
yt/frontends/stream/misc.py

Verification

I verified the changes by:

Confirming that import numpy.typing as npt is replaced by import numpy.typing as nptype.
Confirming that usages of npt.NDArray are replaced by nptype.NDArray.
Ensuring no conflicts with numpy.testing as npt.

Files Checked But Not Modified

I inspected the following files and found they were either already compliant or only used np.ndarray in docstrings:

yt/visualization/fixed_resolution_filters.py (Already compliant)
yt/visualization/_handlers.py (Already compliant)
yt/geometry/geometry_handler.py (Already compliant)
yt/frontends/amrvac/io.py (Docstrings only)
yt/utilities/lib/cykdtree/plot.py (Docstrings only)

Excluded File where `np.ndarray` is present

yt/testing.py (Updated helper functions like fake_random_sph_ds, integrate_kernel, cubicspline_python, etc.)

Fixes: #5144

welcome · 2025-12-06T21:31:41Z

Hi! Welcome, and thanks for opening this pull request. We have some guidelines for new pull requests, and soon you'll hear back about the results of our tests and continuous integration checks. Thank you for your contribution!

maverickcodex18 · 2025-12-07T19:58:11Z

Fix Mypy Type Errors

Objective: Resolve type errors reported by mypy, specifically "Bad number of arguments for type alias" and "Incompatible type" errors.

Changes

A. Fix `npt.NDArray` Type Arguments

The error Bad number of arguments for type alias, expected 1, given 2 was occurring because npt.NDArray was being used with two arguments (e.g., npt.NDArray[Any, np.dtype[Type]]). numpy.typing.NDArray expects a single type argument representing the scalar type.
Files Corrected:

yt/geometry/coordinates/coordinate_handler.py: Corrected pixelize return type.
yt/frontends/ramses/hilbert.py: Corrected signatures for hilbert3d, get_intersecting_cpus, and get_cpu_list_cuboid.
yt/frontends/rockstar/data_structures.py: Corrected _Npart and _read_member.
Fix Pattern:

# Before
ijk: "nptype.NDArray[Any, np.dtype[np.int64]]"
# After
ijk: "nptype.NDArray[np.int64]"

chrishavlin

here's a quick note. also, i will not have time to review in detail for a few days.

chrishavlin · 2025-12-08T15:17:04Z

yt/loaders.py

 from urllib.parse import urlsplit

 import numpy as np
+import numpy.typing as nptype


let's use import numpy.typing as npt everywhere. You've got a mix of imports across files, please just stick to import numpy.typing as npt.

npt was already in use as an alias at some files , so I thought nptype would be better choice to avoid any issues .

Also can you help me add label to the pr , I don't know how to add it.

can you point out a spot where it's being used as an alias? I don't see it in this file or the other couple I just checked. npt is preferred. i'll add the label when I get to doing a full review.

The alias nptype was chosen to avoid conflicts with numpy.testing, which is often imported as npt.

it's true that we use npt for both namespaces, however I don't think they are ever imported in the same module (we don't have type hints in tests, and we shouldn't be using numpy.typing anywhere else), so, even if the meaning of npt is context-dependent, I don't think it's actually ambiguous.

Thanks @neutrinoceros
In testing.py , We are importing both numpy.typing and numpy.testing , otherwise everything looks good on using npt as alias.
Should I stick to npt alias for numpy.typing and revert type hints changes in 'testing.py' ?

ah, you mean this section?

yt/yt/testing.py

Lines 1880 to 1897 in 2973f4d

def _deprecated_numpy_testing_reexport(func):

import numpy.testing as npt

npt_func = getattr(npt, func.__name__)

@wraps(npt_func)

def retf(*args, **kwargs):

__tracebackhide__ = True # Hide traceback for pytest

issue_deprecation_warning(

f"yt.testing.{func.__name__} is a pure re-export of "

f"numpy.testing.{func.__name__}, it will stop working in the future. "

"Please import this function directly from numpy instead.",

since="4.2",

stacklevel=3,

)

return npt_func(*args, **kwargs)

return retf

ya, that's an unfortunate re-definition of npt in that function... I'd say (1) keep the import numpy.typing as npt at the top of the file and revert your changes and (2) adjust that testing import for clarity:

import numpy.testing as nptesting npt_func = getattr(nptesting, func.__name__)

Looks like there are a couple other minor spots where we do import numpy.testing as npt, but not in any of the files you're touching, so I'll submit a separate PR to fix those locations so we reserve npt for numpy.typing

Thanks! and FYI I'm hoping to take a detailed look this afternoon or tomorrow.

still need to update this import

Suggested change

import numpy.typing as nptype

import numpy.typing as npt

chrishavlin

looks pretty good! most of my comments are just a request to change all your imports to import numpy.typing as npt -- I didn't go through all the usages, so you'll need to update everywhere you've used nptype.

Also, there are a couple spots where I want to double check the dtype specification -- I will do that though since it will require a bit more familiarity with yt than I'd expect from a new contributor. Thanks for the work so far!

yt/frontends/ramses/hilbert.py

yt/_typing.py

yt/frontends/ramses/hilbert.py

yt/frontends/ramses/io.py

yt/frontends/ramses/particle_handlers.py

yt/utilities/io_handler.py

yt/visualization/plot_modifications.py

yt/visualization/plot_window.py

maverickcodex18 · 2025-12-12T20:01:37Z

Hi @chrishavlin , I have already made changes in new PR.
changing nptype to npt
reverting changes in testing.py
changing alias of numpy.testing to nptesting and npt_func = getattr(nptesting, func.__name__)

Please take a look in the new PR

chrishavlin

great! just one change that you missed

yt/frontends/ramses/hilbert.py

Co-authored-by: Chris Havlin <chris.havlin@gmail.com>

chrishavlin

Looks good to me! I'll try to drum up a second review. Thanks for the work!

chrishavlin · 2025-12-19T15:26:14Z

yt/frontends/ramses/hilbert.py

-    ijk: "np.ndarray[Any, np.dtype[np.int64]]", bit_length: int
-) -> "np.ndarray[Any, np.dtype[np.float64]]":
+    ijk: "npt.NDArray[np.int64]", bit_length: int
+) -> "npt.NDArray[np.int64]":


@cphyc mind double checking my fix here? the hilbert index arrays will always be int arrays from what I can see.

(also if you're up for reviewing the rest of the PR it'd be welcome!)

chrishavlin · 2025-12-19T15:36:08Z

yt/frontends/ramses/hilbert.py

    ds,
    region: YTRegion,
-    LE: Optional["np.ndarray[Any, np.dtype[np.float64]]"] = None,
+    LE: Optional["npt.NDArray[np.float64]"] = None,


oh! nothing to change here, but I just remembered: the Any in the original np.ndarray[Any, np.dtype[np.float64]] is a reference to the array shape. So the update here is equivalent as npt.NDArray[dtype] is a type alias to np.ndarray[tuple[Any,...], dtype]

(reference: https://numpy.org/devdocs/reference/typing.html#numpy.typing.NDArray )

chrishavlin · 2025-12-19T15:48:34Z

@maverickcodex18 just FYI I just pushed changes to your branch to fix the failing pre-commit checks (with your updates there were some lingering unused imports of Any). Nothing for you to do, but if the second reviewer suggests changes you'll want to make sure you pull in my changes locally to avoid merge conflicts.

Thanks for you work! Hopefully we'll get a second review soon (I'll send some messages around).

maverickcodex18 · 2025-12-20T10:16:34Z

@maverickcodex18 just FYI I just pushed changes to your branch to fix the failing pre-commit checks (with your updates there were some lingering unused imports of Any). Nothing for you to do, but if the second reviewer suggests changes you'll want to make sure you pull in my changes locally to avoid merge conflicts.

Thanks for you work! Hopefully we'll get a second review soon (I'll send some messages around).

Thankyou @chrishavlin

neutrinoceros

this is definitely going in the right direction. As I understand a naked np.ndarray was actually never meant to be used as a type hint, but this begs the question: is it correct to use a naked npt.NDArray (i.e., no dtype specified) ?
There are a couple question I need to investigate before I can sign off, but I'll try to get back to this tomorrow. Thank you for your work and patience !

neutrinoceros · 2026-01-28T21:49:45Z

yt/_typing.py


-MaskT = Optional["np.ndarray[Any, np.dtype[np.bool_]]"]
-AlphaT = Optional["np.ndarray[Any, np.dtype[np.float64]]"]
+MaskT = Optional["npt.NDArray[np.bool_]"]


We don't need Optional at all now that we dropped Python 3.9 (over a year ago). I don't understand why this wasn't auto-refactored already by ruff, but I want to find out.

gotcha: ruff is pulling back because of the stringed annotation within. Remove the quotes and we actually get Python 3.10 code. I think the original reason we used quotes there was backward compatibility with older versions of numpy, but we require 1.21+ now so numpy.typing.NDArray can always be assumed to be available

Refactor: replace np.ndarray with nptype.NDArray in type hints

511aab1

maverickcodex18 changed the title ~~Refactor: replace np.ndarray with nptype.NDArray in type hints~~ Refactor: replace np.ndarray with nptype.NDArray in type hints Fixes #5144 Dec 6, 2025

maverickcodex18 closed this Dec 6, 2025

maverickcodex18 deleted the fixIssue5144 branch December 6, 2025 21:39

maverickcodex18 restored the fixIssue5144 branch December 6, 2025 21:40

maverickcodex18 reopened this Dec 6, 2025

maverickcodex18 changed the title ~~Refactor: replace np.ndarray with nptype.NDArray in type hints Fixes #5144~~ Refactor: replace np.ndarray with nptype.NDArray in type hints Dec 6, 2025

MyPy Type Errors Fixed

44687be

chrishavlin self-requested a review December 8, 2025 15:15

chrishavlin requested changes Dec 8, 2025

View reviewed changes

chrishavlin added enhancement Making something better refactor improve readability, maintainability, modularity labels Dec 11, 2025

chrishavlin mentioned this pull request Dec 11, 2025

Reserve npt for numpy.typing #5349

Open

2 tasks

type hints fix

6a41449

chrishavlin requested changes Dec 12, 2025

View reviewed changes

chrishavlin added this to the 4.5.0 milestone Dec 12, 2025

type hints fix

02a690c

maverickcodex18 force-pushed the fixIssue5144 branch from ef380c1 to 02a690c Compare December 12, 2025 20:11

chrishavlin requested changes Dec 12, 2025

View reviewed changes

yt/frontends/ramses/hilbert.py Outdated Show resolved Hide resolved

maverickcodex18 and others added 4 commits December 13, 2025 10:58

Update yt/_typing.py

c8af3ab

Co-authored-by: Chris Havlin <chris.havlin@gmail.com>

Update yt/frontends/ramses/hilbert.py

1709f67

Co-authored-by: Chris Havlin <chris.havlin@gmail.com>

Merge branch 'yt-project:main' into fixIssue5144

2f935f8

Merge branch 'yt-project:main' into fixIssue5144

c8aad3d

maverickcodex18 changed the title ~~Refactor: replace np.ndarray with nptype.NDArray in type hints~~ Refactor: replace np.ndarray with npt.NDArray in type hints Dec 16, 2025

chrishavlin previously approved these changes Dec 19, 2025

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rm unused Any imports

fb0c7a7

chrishavlin dismissed their stale review via fb0c7a7 December 19, 2025 15:46

chrishavlin approved these changes Dec 19, 2025

View reviewed changes

Merge branch 'yt-project:main' into fixIssue5144

3a69c29

neutrinoceros reviewed Jan 28, 2026

View reviewed changes

	def _deprecated_numpy_testing_reexport(func):
	import numpy.testing as npt

	npt_func = getattr(npt, func.__name__)

	@wraps(npt_func)
	def retf(args, *kwargs):
	__tracebackhide__ = True # Hide traceback for pytest
	issue_deprecation_warning(
	f"yt.testing.{func.__name__} is a pure re-export of "
	f"numpy.testing.{func.__name__}, it will stop working in the future. "
	"Please import this function directly from numpy instead.",
	since="4.2",
	stacklevel=3,
	)
	return npt_func(args, *kwargs)

	return retf

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maverickcodex18 commented Dec 6, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Walkthrough: Updating NumPy Type Hints

Changes Overview

yt Core and Utilities

yt/visualization

yt/frontends

Verification

Files Checked But Not Modified

Excluded File where np.ndarray is present

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welcome bot commented Dec 6, 2025

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maverickcodex18 commented Dec 7, 2025

Fix Mypy Type Errors

Changes

A. Fix npt.NDArray Type Arguments

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maverickcodex18 commented Dec 6, 2025 •

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`yt/visualization`

`yt/frontends`

Excluded File where `np.ndarray` is present

A. Fix `npt.NDArray` Type Arguments

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maverickcodex18 commented Dec 12, 2025 •

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