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lagrulagru
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Merge branch 'main' into sk2-gray-morph-followup
2 parents 5d184ef + 862aaf6 commit 4ce6a08

21 files changed

Lines changed: 89 additions & 141 deletions

‎.coderabbit.yaml‎

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@@ -5,43 +5,7 @@ reviews:
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high_level_summary: false
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request_changes_workflow: false
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estimate_code_review_effort: true
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labeling_instructions:
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- label: ":scroll: type: API"
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instructions: >-
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For backward-incompatible changes to the API and deprecations.
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Only apply if no "type:" label is already assigned.
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- label: ":baby: type: New feature"
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instructions: >-
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For new features that previously did not exist.
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New features for tooling, infrastructure and such shouldn't use this label.
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Only apply if no "type:" label is already assigned.
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- label: ":wrench: type: Maintenance"
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instructions: >-
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For internal code changes and cleanups.
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Only apply if no "type:" label is already assigned.
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- label: ":adhesive_bandage: type: Bug fix"
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instructions: >-
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For bug fixes that apply to user facing API.
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Fixes for tooling, infrastructure and such shouldn't use this label.
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Only apply if no "type:" label is already assigned.
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- label: ":page_facing_up: type: Documentation"
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instructions: >-
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For changes dedicated to documentation (i.e., not as part of a new feature).
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Only apply if no "type:" label is already assigned.
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- label: ":robot: type: Infrastructure"
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instructions: >-
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Fixes to CI and other infrastructure.
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Only apply if no "type:" label is already assigned.
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- label: ":fast_forward: type: Enhancement"
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instructions: >-
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Improvements made to an existing feature.
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Improvements for tooling, infrastructure and such shouldn't use this label.
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Only apply if no "type:" label is already assigned.
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- label: ":chart_with_upwards_trend: type: Performance"
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instructions: >-
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For changes intended to improve performance.
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Only apply if no "type:" label is already assigned.
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auto_apply_labels: true
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auto_apply_labels: false
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in_progress_fortune: false
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poem: false
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enable_prompt_for_ai_agents: false

‎.github/workflows/label-check.yaml‎

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This file was deleted.

‎.github/workflows/test-pyodide.yaml‎

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# The appropriate version combinations can be found in the Pyodide repodata.json
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# "info" field, or in Makefile.envs:
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# https://github.com/pyodide/pyodide/blob/main/Makefile.envs#L2
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PYODIDE_VERSION: ["0.29.0"]
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PYODIDE_VERSION: ["0.29.3"]
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PYTHON_VERSION: ["3.13"]
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EMSCRIPTEN_VERSION: ["4.0.9"]
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NODE_VERSION: ["24"]
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PYODIDE_BUILD_VERSION: ["0.30.8"]
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PYODIDE_BUILD_VERSION: ["0.33.0"]
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steps:
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- name: Checkout scikit-image

‎environment.yml‎

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@@ -3,14 +3,14 @@ channels:
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- conda-forge
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dependencies:
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# base
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- numpy>=1.24
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- scipy>=1.11.4
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- numpy>=2.1
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- scipy>=1.15
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- networkx>=3.0
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- pillow>=10.1
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- imageio>=2.33,!=2.35.0
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- tifffile>=2022.8.12
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- packaging>=21
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- lazy-loader>=0.4
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- tifffile>=2025.1.10
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- packaging>=24
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- lazy-loader>=0.5
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# build
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- meson-python>=0.16
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- ninja>=1.11.1.1
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- numpydoc>=1.7
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- sphinx-copybutton
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- sphinx-togglebutton
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- matplotlib-base>=3.7
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- dask>=2023.2.0
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- matplotlib-base>=3.10
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- dask>=2025.1.0
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- pandas>=2.0
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- seaborn>=0.11
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- pooch>=1.6
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- tifffile>=2022.8.12
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- tifffile>=2025.1.10
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- myst-parser
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- intersphinx-registry>=0.2411.14
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- ipywidgets
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- ipykernel
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- plotly>=5.20
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- python-kaleido==0.2.1
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- scikit-learn>=1.2
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- scikit-learn>=1.6
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- sphinx-design>=0.5
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- pydata-sphinx-theme>=0.16
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- PyWavelets>=1.6
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- PyWavelets>=1.7
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- pytest-doctestplus>=1.6.0
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# optional
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- SimpleITK
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- scikit-learn>=1.2
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- scikit-learn>=1.6
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- pyamg>=5.2
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# optional_free_threaded
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- astropy-base>=6.0
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- dask>=2023.2.0
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- matplotlib-base>=3.7
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- astropy-base>=6.1
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- dask>=2025.1.0
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- matplotlib-base>=3.10
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- pooch>=1.6.0
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- PyWavelets>=1.6
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- PyWavelets>=1.7
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# test
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- numpydoc>=1.7
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- pooch>=1.6.0

‎meson.options‎

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‎pyproject.toml‎

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]
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dynamic = ['version']
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dependencies = [
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'numpy>=1.24',
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'scipy>=1.11.4',
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'numpy>=2.1',
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'scipy>=1.15; sys_platform != "emscripten"',
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'scipy>=1.14; sys_platform == "emscripten"',
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'networkx>=3.0',
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'pillow>=10.1',
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'imageio>=2.33,!=2.35.0',
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'tifffile>=2022.8.12',
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'packaging>=21',
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'lazy-loader>=0.4',
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'tifffile>=2025.1.10',
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'packaging>=24',
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'lazy-loader>=0.5',
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]
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[[project.maintainers]]
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'numpydoc>=1.7',
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'sphinx-copybutton',
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'sphinx-togglebutton',
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'matplotlib>=3.7',
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'dask[array]>=2023.2.0',
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'matplotlib>=3.10',
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'dask[array]>=2025.1.0',
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'pandas>=2.0',
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'seaborn>=0.11',
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'pooch>=1.6',
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'tifffile>=2022.8.12',
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'tifffile>=2025.1.10',
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'myst-parser',
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'intersphinx-registry>=0.2411.14',
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'ipywidgets',
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'ipykernel', # needed until https://github.com/jupyter-widgets/ipywidgets/issues/3731 is resolved
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'plotly>=5.20',
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'kaleido==0.2.1',
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'scikit-learn>=1.2',
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'scikit-learn>=1.6',
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'sphinx_design>=0.5',
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'pydata-sphinx-theme>=0.16',
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'PyWavelets>=1.6',
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'PyWavelets>=1.7',
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'pytest-doctestplus>=1.6.0',
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]
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optional = [
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'SimpleITK; sys_platform != "emscripten"',
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'scikit-learn>=1.2',
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'scikit-learn>=1.6',
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'pyamg>=5.2; sys_platform != "emscripten" and python_version < "3.14"', # not packaged for Pyodide yet
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'scikit-image[optional_free_threaded]'
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]
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optional_free_threaded = [
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'astropy>=6.0',
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'dask[array]>=2023.2.0',
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'matplotlib>=3.7',
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'astropy>=6.1',
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'dask[array]>=2025.1.0',
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'matplotlib>=3.10',
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'pooch>=1.6.0; sys_platform != "emscripten"', # requires stack switching with alternative pytest runner
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'PyWavelets>=1.6',
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'PyWavelets>=1.7',
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]
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test = [
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'meson-python>=0.16',
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'Cython>=3.0.10,!=3.2.0b1',
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'pythran>=0.16',
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'lazy_loader>=0.4',
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'lazy_loader>=0.5',
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'numpy>=2.0',
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]
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# https://github.com/joblib/threadpoolctl/pull/201 is released
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"ignore:.*JsProxy\\.as_object_map.*:RuntimeWarning",
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# Warning caused by matplotlib 3.7.0 because it uses deprecated API of pyparsing 3.3.1
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"ignore:.*(parseString|resetCache|enablePackrat).*:DeprecationWarning:matplotlib",
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"ignore:.*(parseString|resetCache|enablePackrat|oneOf).*:DeprecationWarning:matplotlib",
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# tifffile (v2025.12.20) uses deprecated NumPy API
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"ignore:Setting the shape on a NumPy array:DeprecationWarning:tifffile",
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]
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norecursedirs = ["io/_plugins"]
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enable="cpython-freethreading"
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[tool.cibuildwheel.config-settings]
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setup-args = "-Dinclude-v2=false"
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# Could be overwritten using CIBW_CONFIG_SETTINGS environment variable
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[[tool.cibuildwheel.overrides]]

‎requirements/default.txt‎

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# Generated via tools/generate_requirements.py and pre-commit hook.
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# Do not edit this file; modify pyproject.toml instead.
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numpy>=1.24
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scipy>=1.11.4
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numpy>=2.1
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scipy>=1.15; sys_platform != "emscripten"
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scipy>=1.14; sys_platform == "emscripten"
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networkx>=3.0
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pillow>=10.1
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imageio>=2.33,!=2.35.0
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tifffile>=2022.8.12
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packaging>=21
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lazy-loader>=0.4
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tifffile>=2025.1.10
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packaging>=24
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lazy-loader>=0.5

‎requirements/docs.txt‎

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numpydoc>=1.7
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sphinx-copybutton
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sphinx-togglebutton
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matplotlib>=3.7
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dask[array]>=2023.2.0
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matplotlib>=3.10
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dask[array]>=2025.1.0
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pandas>=2.0
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seaborn>=0.11
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pooch>=1.6
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tifffile>=2022.8.12
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tifffile>=2025.1.10
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myst-parser
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intersphinx-registry>=0.2411.14
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ipywidgets
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ipykernel
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plotly>=5.20
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kaleido==0.2.1
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scikit-learn>=1.2
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scikit-learn>=1.6
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sphinx_design>=0.5
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pydata-sphinx-theme>=0.16
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PyWavelets>=1.6
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PyWavelets>=1.7
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pytest-doctestplus>=1.6.0

‎requirements/optional.txt‎

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# Generated via tools/generate_requirements.py and pre-commit hook.
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# Do not edit this file; modify pyproject.toml instead.
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SimpleITK; sys_platform != "emscripten"
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scikit-learn>=1.2
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scikit-learn>=1.6
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pyamg>=5.2; sys_platform != "emscripten" and python_version < "3.14"
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astropy>=6.0
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dask[array]>=2023.2.0
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matplotlib>=3.7
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astropy>=6.1
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dask[array]>=2025.1.0
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matplotlib>=3.10
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pooch>=1.6.0; sys_platform != "emscripten"
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PyWavelets>=1.6
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PyWavelets>=1.7

‎requirements/optional_free_threaded.txt‎

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# Generated via tools/generate_requirements.py and pre-commit hook.
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# Do not edit this file; modify pyproject.toml instead.
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astropy>=6.0
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dask[array]>=2023.2.0
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matplotlib>=3.7
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astropy>=6.1
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dask[array]>=2025.1.0
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matplotlib>=3.10
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pooch>=1.6.0; sys_platform != "emscripten"
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PyWavelets>=1.6
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PyWavelets>=1.7

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