Avoid deprecated assign to ndarray.shape by lagru · Pull Request #8020 · scikit-image/scikit-image

lagru · 2026-01-13T19:51:46Z

Description

Closes #8019, closes #8025. Still testing locally because there's no way to trigger the failing nightly job directly – it will run once merged into main though.

Checklist

A descriptive but concise pull request title
Docstrings for all functions
Unit tests
A gallery example in ./doc/examples for new features
Contribution guide is followed

Release note

For maintainers and optionally contributors, please refer to the instructions on how to document this PR for the release notes.

...

src/skimage/io/_plugins/pil_plugin.py

lagru · 2026-01-14T19:26:55Z

@stefanv, as I said on Zulip, feel very welcome to take over this PR. :) I'm focusing on the typing stuff this week.

coderabbitai · 2026-01-21T01:20:26Z

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📝 Walkthrough

Walkthrough

Updated dependency constraints across multiple manifests, removed the Meson include-v2 option and unconditionally include skimage2 in the build, and replaced deprecated in-place NumPy shape assignments with explicit np.reshape(..., copy=False) calls and related comment/docstring updates.

Changes

Cohort / File(s)	Summary
Dependency Version Updates `environment.yml`, `pyproject.toml`, `requirements/default.txt`, `requirements/docs.txt`, `requirements/optional.txt`, `requirements/optional_free_threaded.txt`	Bumped minimum versions for core and optional packages (notably `numpy` → >=2.1, `scipy` → >=1.14, `tifffile` → >=2025.1.10, `matplotlib` → >=3.10, `dask` → >=2025.1.0, `scikit-learn` → >=1.6, `PyWavelets` → >=1.7, `astropy` → >=6.1). Adjusted docs/test warning filters and removed a `cibuildwheel` setup-args entry.
Build Configuration `meson.options`, `src/meson.build`	Removed the Meson boolean option `include-v2` and its runtime conditional; `skimage2` subdirectory is now added unconditionally to the build.
Array reshape migrations (NumPy 2.5 compatibility) `src/skimage/io/_plugins/pil_plugin.py`, `src/skimage/measure/_marching_cubes_lewiner.py`, `src/skimage/morphology/grayreconstruct.py`, `src/skimage/util/_map_array.py`	Replaced assignments to `array.shape = ...` with `np.reshape(..., copy=False)` to avoid deprecated in-place shape mutation while preserving view/no-copy semantics.
Comments / Docstrings `src/skimage/feature/sift.py`, `src/skimage/graph/_mcp.pyx`, `src/skimage/restoration/_rolling_ball_cy.pyx`	Updated inline comments and docstrings to describe reshape/view semantics (reflecting the change from direct shape assignment to `np.reshape(..., copy=False)`).
CI / Workflow `.github/workflows/test-pyodide.yaml`	Updated Pyodide versions in the workflow matrix (PYODIDE_VERSION and PYODIDE_BUILD_VERSION).

Sequence Diagram(s)

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Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Out of Scope Changes check	❓ Inconclusive	While most changes directly address the linked issues (shape assignment replacements) and related compatibility, the pull request includes substantial out-of-scope changes: broad dependency version upgrades (numpy, scipy, dask, matplotlib, etc.), removal of the include-v2 option, and workflow updates that are not directly related to the ndarray.shape deprecation issue.	Clarify whether dependency upgrades and include-v2 removal should be part of this PR or should be separated into distinct pull requests focused on their respective objectives.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title 'Avoid deprecated assign to ndarray.shape' is concise (40 characters), clearly describes the main objective of the PR, and does not end with a period.
Description check	✅ Passed	The description clearly relates to the changeset by explaining the PR closes issues `#8019` and `#8025` related to deprecated ndarray.shape assignments, and references NumPy 2.5 deprecation warnings addressed in the code changes.
Linked Issues check	✅ Passed	The code changes comprehensively address both linked issues: replacements of deprecated ndarray.shape assignments with np.reshape(copy=False) throughout multiple files (pil_plugin.py, marching_cubes_lewiner.py, grayreconstruct.py, rolling_ball_cy.pyx, _map_array.py), plus dependency upgrades to NumPy 2.1+ and build configuration adjustments.
Docstring Coverage	✅ Passed	Docstring coverage is 83.33% which is sufficient. The required threshold is 80.00%.

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src/skimage/io/_plugins/pil_plugin.py

src/skimage/measure/_marching_cubes_lewiner.py

src/skimage/morphology/grayreconstruct.py

src/skimage/util/_map_array.py

Use `.reshape(..., copy=False)` instead as recommended by NumPy. I'm a bit scared because our test suite seems to have only triggered one instance of these warnings (in grayreconstruct.py", line 216, in `reconstruction`)?

lagru · 2026-03-03T20:45:15Z

Will review shortly.

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Actionable comments posted: 3

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Reviewing files that changed from the base of the PR and between 5d0aded and 87d5597.

📒 Files selected for processing (15)

environment.yml
meson.options
pyproject.toml
requirements/default.txt
requirements/docs.txt
requirements/optional.txt
requirements/optional_free_threaded.txt
src/meson.build
src/skimage/feature/sift.py
src/skimage/graph/_mcp.pyx
src/skimage/io/_plugins/pil_plugin.py
src/skimage/measure/_marching_cubes_lewiner.py
src/skimage/morphology/grayreconstruct.py
src/skimage/restoration/_rolling_ball_cy.pyx
src/skimage/util/_map_array.py

💤 Files with no reviewable changes (1)

meson.options

pyproject.toml

src/meson.build

src/skimage/util/_map_array.py

lagru · 2026-03-04T14:38:57Z

requirements/default.txt

 # Do not edit this file; modify pyproject.toml instead.
-numpy>=1.24
-scipy>=1.11.4
+numpy>=2.1


What about SPEC0 saying that we still need to support v2.0? Are you anticipating that our next release is after that can be dropped?

Yes, I think so (Q3 2026).

lagru · 2026-03-04T14:41:57Z

pyproject.toml

@stefanv I know you mentioned that you needed to update a few dependencies here, but I don't remember why. Could you maybe briefly summarize why?

I think I had to update NumPy, and then another dependency to match that etc. etc. It was the standard cascade. But I was pretty careful not to pull in very new packages.

coderabbitai

🧹 Nitpick comments (1)

environment.yml (1)

11-12: Consider removing duplicate tifffile entry.

tifffile>=2025.1.10 appears both in the base section (line 11) and the docs section (line 40). Since docs dependencies implicitly include base dependencies, the entry on line 40 is redundant.

Also applies to: 40-40

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environment.yml
pyproject.toml

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🧹 Nitpick comments (1)

pyproject.toml (1)
228-230: Improve warning filter comments to decouple from upstream versions.

The comments at lines 227–230 tie suppressions to specific upstream versions, creating maintenance burden. Reword them to track upstream status generically and establish clear removal conditions:
♻️ Suggested wording update
-    # Warning caused by matplotlib 3.7.0 because it uses deprecated API of pyparsing 3.3.1
+    # Upstream matplotlib emits pyparsing deprecation warnings; remove when matplotlib>=3.10.7 or fixes the deprecated calls.
     "ignore:.*(parseString|resetCache|enablePackrat|oneOf).*:DeprecationWarning:matplotlib",
-    # tifffile (v2025.12.20) uses deprecated NumPy API
+    # Upstream tifffile emits ndarray.shape deprecation warnings; remove when upstream fix is released.
     "ignore:Setting the shape on a NumPy array:DeprecationWarning:tifffile",
The matplotlib case is solvable (fix available in v3.10.7+). The tifffile case awaits upstream action on the ndarray.shape setter issue. Either way, the comments should orient maintainers toward removal conditions rather than version snapshots.

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requirements/default.txt

* origin/main: (27 commits) Move `_shared` to `_skimage2` (#8102) Port `pad_footprint` & `mirror_footprint` to `skimage2` (#8094) Add rescaling API to skimage2 (#8075) Move `skimage2` implementation into `_skimage2` (#8093) Undo (double) mirroring in `ski2.morphology.dilation` (#8060) Grammar (#8091) Move `ensure_spacing` into `skimage2` (#8067) Ensure that `skimage2` does not eagerly import `skimage` (#8087) Use lazy-loader 0.5 (#8080) MAINT: make ellipse fitting forward compatible (#8054) Avoid deprecated assign to ndarray.shape (#8020) Avoid circular import in `feature/corner.py` (#8077) Turn off coderabbit auto-labeling & label checks (#8070) Fix GIL being re-enabled by C++ extensions (#8059) Fix conventions following docstub and misc. (#8055) Port grayscale morphology operators to skimage2 (#8046) Add revised `peak_local_max` to `skimage2` (#8039) Allow read-only arrays as input to remap (#7535) Add `prescale` parameter to "blob functions" (#7858) Try to make coderabbit respect exisiting type labels (#8042) ...

lagru added the 🔧 type: Maintenance Refactoring and maintenance of internals label Jan 13, 2026

lagru changed the title ~~Upd deprecated shape assign~~ Avoid deprecated assign to ndarray.shape Jan 13, 2026

lagru assigned stefanv Jan 13, 2026

stefanv reviewed Jan 14, 2026

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src/skimage/io/_plugins/pil_plugin.py Outdated Show resolved Hide resolved

lagru mentioned this pull request Jan 16, 2026

DeprecationWarning: Setting the shape on a NumPy array has been deprecated in NumPy 2.5. #8025

Closed

stefanv force-pushed the upd-deprecated-shape-assign branch from 4c0b25d to 9976947 Compare January 21, 2026 01:20

stefanv reviewed Feb 6, 2026

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lagru and others added 4 commits February 5, 2026 17:15

Avoid deprecated assign to ndarray.shape

fd28e53

Use `.reshape(..., copy=False)` instead as recommended by NumPy. I'm a bit scared because our test suite seems to have only triggered one instance of these warnings (in grayreconstruct.py", line 216, in `reconstruction`)?

Ignore deprecation warning in tifffile

27dc953

Use np.reshape(x, ..., copy=False) instead of x = x.reshape.

3227e05

Satisfy linter

ba5595f

stefanv force-pushed the upd-deprecated-shape-assign branch from c571516 to ba5595f Compare February 6, 2026 01:15

stefanv added 12 commits February 5, 2026 22:13

Re-enable v2 namespace

433f013

Add back reshape assignments

b88d3a8

Update minimum version of NumPy

e39acc2

Move to NumPy 2.1, which has copy keyword in reshape

66bdde9

Update SciPy to 1.13

1a96869

Further package updates

ad2d4aa

Update tifffile

bde9a67

Update package: packaging

a0036fe

Add back matplotlib warning filter

3af179f

Catch additional pyparsing warning

1bd3610

Update scikit-learn

795f055

Update dask

87d5597

lagru marked this pull request as ready for review March 3, 2026 20:43

stefanv approved these changes Mar 3, 2026

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stefanv self-requested a review March 3, 2026 20:44

lagru marked this pull request as draft March 3, 2026 20:44

coderabbitai bot reviewed Mar 3, 2026

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lagru commented Mar 4, 2026

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lagru and others added 3 commits March 4, 2026 15:44

Fix typo

f544e36

Merge branch 'main' into upd-deprecated-shape-assign

3b73519

v2 is now always included

7dc6f18

stefanv marked this pull request as ready for review March 5, 2026 08:50

coderabbitai bot reviewed Mar 5, 2026

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stefanv added 2 commits March 5, 2026 01:11

Try with SciPy 1.15

6eb8aa9

Try latest pyodide/pyodide-build

01a5f66

coderabbitai bot reviewed Mar 5, 2026

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stefanv force-pushed the upd-deprecated-shape-assign branch from c3459ed to 01a5f66 Compare March 5, 2026 19:59

Use SciPy 1.14 for pyodide; avoid duplicates in environment.yml

a018bf3

stefanv merged commit 7737c04 into scikit-image:main Mar 5, 2026
25 checks passed

stefanv added this to the 0.27 milestone Mar 5, 2026

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