CVS commit: pkgsrc/math/py-scikit-image

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/math/py-scikit-image
From: "Adam Ciarcinski" <adam%netbsd.org@localhost>
Date: Tue, 11 Feb 2025 12:09:56 +0000

Module Name:    pkgsrc
Committed By:   adam
Date:           Tue Feb 11 12:09:56 UTC 2025

Modified Files:
        pkgsrc/math/py-scikit-image: Makefile PLIST distinfo

Log Message:
py-scikit-image: updated to 0.25.1

scikit-image 0.25.1

Bug Fixes

- Include ``centroid`` in ``__all__`` of the PYI file in ``skimage.measure``
- Improve numerical stability of ``blur_effect``
- Because under-determined fits are unreliable, ``skimage.measure.EllipseModel`` will now warn and return ``False`` (no fit) when fewer than 5 data points are provided
- Explicitly upcast ``data`` with dtype ``float16`` to ``float32`` in  ``skimage.segmentation.random_walker``; this fixes passing ``float16`` on NumPy 1.26

Documentation

- Don't use removed ``QuadContourSet.collections`` in gallery example
- Change old import convention in the gallery examples

scikit-image 0.25.0 (2024-12-13)

New Features

- Add the new Gray-Level Co-occurrence Matrix (GLCM) properties  "mean", "variance", "standard deviation" and "entropy" to  ``skimage.feature.texture.graycoprops``
- Add the new ``skimage.morphology.footprint_rectangle`` supporting generation of rectangular or hyper-rectangular footprints in one function

API Changes

- Complete the deprecation of and remove ``skimage.feature.plot_matches``. Use ``skimage.feature.plot_matched_features`` going forward
- Deprecate ``skimage.io.imshow``, ``skimage.io.imshow_collection`` and ``skimage.io.show``. Please use ``matplotlib``, ``napari``, etc. to visualize images
- Remove deprecated ``skimage.morphology.skeletonize_3d``;  use ``skimage.morphology.skeletonize`` instead
- Deprecate ``skimage.io`` plugin infrastructure
- Switched to using the ``scipy.sparse`` array interface. For more details, see the note about the new ``scipy.sparse`` array interface [here](https://docs.scipy.org/doc/scipy/reference/sparse.html)
- Deprecate ``skimage.morphology.rectangle`` in favor of the new function ``skimage.morphology.footprint_rectangle``
- Deprecate ``skimage.morphology.cube`` in favor of the new function ``skimage.morphology.footprint_rectangle``
- Deprecate ``skimage.morphology.square`` in favor of the new function ``skimage.morphology.footprint_rectangle``

Enhancements

- Improve numerical stability of ``skimage.morphology.local_minima`` for extremely small floats
- Allow passing a sequence of colors to the parameter ``matches_color`` in ``skimage.feature.plot_matched_features``
- Make sure that ``skimage.feature.plot_matched_features`` uses the same random colors, if ``matches_color`` isn't provided  explicitly

Performance

- ``skimage.feature.peak_local_max`` will now skip unnecessary distance computations in the case of ``min_distance=1``. This results in performance improvements to functions like 
``skimage.feature.blob_dog``, ``skimage.feature.blob_log``,  ``skimage.feature.blob_doh`` and ``skimage.feature.corner_peaks`` that call  ``peak_local_max`` internally
- In ``skimage.featurepeak_local_max``, skip unnecessary check for cases where  ``min_distance > 1`` is passed

Bug Fixes

- Ensure that ``skimage.morphology.remove_objects_by_distance`` doesn't fail  if the given integer dtype cannot be safely cast to the architecture specific size of ``intp``, e.g. on i386 architectures
- Fix degeneracy in ``skimage.draw.ellipsoid_stats`` when all semi-axes have the same length
- Prevent ``skimage.morphology.thin`` from accidentally  modifying the input image in case it is of dtype uint8
- Fix numerical precision error in ``skimage.measure.ransac``. In some cases, ``ransac`` was stopping at the first iteration
- Fix numerical precision error in ``skimage.measure.ransac``;  very small probabilities lead to -0 number of max trials
- Ensure that ``RegionProperties`` objects returned by ``skimage.measure.regionprops`` can be deserialized with pickle
- Fix edge case where setting ``watershed_lines=True`` in ``skimage.segmentation.watershed`` resulted in an incorrect solution
- Fix the behavior of ``skimage.segmentation.watershed`` when the markers don't align with local minima by making sure every marker is evaluated before successive pixels
- Fix dtype promotion in ``skimage.segmentation.join_segmentations`` if ``numpy.uint`` is used with NumPy<2

Documentation

- In ``skimage.morphology.skeletonize``, clarify the expected image dtypes and how objects of different intensities are handled
- Fix example section in docstring of ``skimage.feature.graycomatrix``
- Use conda-forge consistently in instructions for setting up the development environment
- Use new ``CITATION.cff`` instead of ``CITATION.bib``
- Use correct ``spin test --coverage`` in contribution guide
- Tweak advice to new developers; remove AI warning
- Rework installation instructions
- Improve the description of the ``image`` parameter in ``skimage.restoration.richardson_lucy``
- Account for empty arrays when counting segments per contour level in gallery example "Segment human cells (in mitosis)"
- Fix typo in morphology doc
- Change type description of parameter ``radius`` in  ``skimage.morphology.ball`` from ``int`` to ``float``


To generate a diff of this commit:
cvs rdiff -u -r1.24 -r1.25 pkgsrc/math/py-scikit-image/Makefile
cvs rdiff -u -r1.7 -r1.8 pkgsrc/math/py-scikit-image/PLIST
cvs rdiff -u -r1.10 -r1.11 pkgsrc/math/py-scikit-image/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/py-scikit-image/Makefile
diff -u pkgsrc/math/py-scikit-image/Makefile:1.24 pkgsrc/math/py-scikit-image/Makefile:1.25
--- pkgsrc/math/py-scikit-image/Makefile:1.24   Mon Oct 14 06:45:51 2024
+++ pkgsrc/math/py-scikit-image/Makefile        Tue Feb 11 12:09:55 2025
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.24 2024/10/14 06:45:51 wiz Exp $
+# $NetBSD: Makefile,v 1.25 2025/02/11 12:09:55 adam Exp $
 
-DISTNAME=      scikit_image-0.24.0
+DISTNAME=      scikit_image-0.25.1
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME:S/_/-/}
 CATEGORIES=    math graphics python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=s/scikit-image/}
@@ -10,21 +10,22 @@ HOMEPAGE=   https://scikit-image.org/
 COMMENT=       Image processing routines for SciPy
 LICENSE=       modified-bsd
 
-TOOL_DEPENDS+= ${PYPKGPREFIX}-cython>=0.29.32:../../devel/py-cython
-TOOL_DEPENDS+= ${PYPKGPREFIX}-meson_python>=0.13:../../devel/py-meson_python
-DEPENDS+=      ${PYPKGPREFIX}-Pillow>=9.1:../../graphics/py-Pillow
+TOOL_DEPENDS+= ${PYPKGPREFIX}-meson_python>=0.16:../../devel/py-meson_python
+TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools>=68:../../devel/py-setuptools
+DEPENDS+=      ${PYPKGPREFIX}-Pillow>=10.1:../../graphics/py-Pillow
 DEPENDS+=      ${PYPKGPREFIX}-imageio>=2.33:../../graphics/py-imageio
 DEPENDS+=      ${PYPKGPREFIX}-lazy_loader>=0.4:../../misc/py-lazy_loader
-DEPENDS+=      ${PYPKGPREFIX}-networkx>=2.8:../../math/py-networkx
-DEPENDS+=      ${PYPKGPREFIX}-numpy>=1.23:../../math/py-numpy
+DEPENDS+=      ${PYPKGPREFIX}-networkx>=3.0:../../math/py-networkx
+DEPENDS+=      ${PYPKGPREFIX}-numpy>=1.24:../../math/py-numpy
 DEPENDS+=      ${PYPKGPREFIX}-packaging>=21:../../devel/py-packaging
-DEPENDS+=      ${PYPKGPREFIX}-scipy>=1.9:../../math/py-scipy
+DEPENDS+=      ${PYPKGPREFIX}-scipy>=1.11.2:../../math/py-scipy
 DEPENDS+=      ${PYPKGPREFIX}-tifffile>=2022.8.12:../../graphics/py-tifffile
 # optional
-DEPENDS+=      ${PYPKGPREFIX}-matplotlib>=3.6:../../graphics/py-matplotlib
-DEPENDS+=      ${PYPKGPREFIX}-pywavelets>=1.1.1:../../math/py-pywavelets
+DEPENDS+=      ${PYPKGPREFIX}-matplotlib>=3.7:../../graphics/py-matplotlib
+DEPENDS+=      ${PYPKGPREFIX}-pywavelets>=1.6:../../math/py-pywavelets
 
 USE_LANGUAGES= c c++
+USE_TOOLS+=    pkg-config
 GCC_REQD+=     9
 
 PYTHON_VERSIONS_INCOMPATIBLE=  39

Index: pkgsrc/math/py-scikit-image/PLIST
diff -u pkgsrc/math/py-scikit-image/PLIST:1.7 pkgsrc/math/py-scikit-image/PLIST:1.8
--- pkgsrc/math/py-scikit-image/PLIST:1.7       Tue Aug  6 11:44:50 2024
+++ pkgsrc/math/py-scikit-image/PLIST   Tue Feb 11 12:09:55 2025
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.7 2024/08/06 11:44:50 adam Exp $
+@comment $NetBSD: PLIST,v 1.8 2025/02/11 12:09:55 adam Exp $
 ${PYSITELIB}/${WHEEL_INFODIR}/LICENSE.txt
 ${PYSITELIB}/${WHEEL_INFODIR}/METADATA
 ${PYSITELIB}/${WHEEL_INFODIR}/RECORD
@@ -549,8 +549,6 @@ ${PYSITELIB}/skimage/io/_io.pyo
 ${PYSITELIB}/skimage/io/_plugins/__init__.py
 ${PYSITELIB}/skimage/io/_plugins/__init__.pyc
 ${PYSITELIB}/skimage/io/_plugins/__init__.pyo
-${PYSITELIB}/skimage/io/_plugins/_colormixer.so
-${PYSITELIB}/skimage/io/_plugins/_histograms.so
 ${PYSITELIB}/skimage/io/_plugins/fits_plugin.ini
 ${PYSITELIB}/skimage/io/_plugins/fits_plugin.py
 ${PYSITELIB}/skimage/io/_plugins/fits_plugin.pyc
@@ -601,9 +599,6 @@ ${PYSITELIB}/skimage/io/tests/test_colle
 ${PYSITELIB}/skimage/io/tests/test_fits.py
 ${PYSITELIB}/skimage/io/tests/test_fits.pyc
 ${PYSITELIB}/skimage/io/tests/test_fits.pyo
-${PYSITELIB}/skimage/io/tests/test_histograms.py
-${PYSITELIB}/skimage/io/tests/test_histograms.pyc
-${PYSITELIB}/skimage/io/tests/test_histograms.pyo
 ${PYSITELIB}/skimage/io/tests/test_imageio.py
 ${PYSITELIB}/skimage/io/tests/test_imageio.pyc
 ${PYSITELIB}/skimage/io/tests/test_imageio.pyo
@@ -791,8 +786,8 @@ ${PYSITELIB}/skimage/morphology/_misc_cy
 ${PYSITELIB}/skimage/morphology/_skeletonize.py
 ${PYSITELIB}/skimage/morphology/_skeletonize.pyc
 ${PYSITELIB}/skimage/morphology/_skeletonize.pyo
-${PYSITELIB}/skimage/morphology/_skeletonize_3d_cy.so
-${PYSITELIB}/skimage/morphology/_skeletonize_cy.so
+${PYSITELIB}/skimage/morphology/_skeletonize_lee_cy.so
+${PYSITELIB}/skimage/morphology/_skeletonize_various_cy.so
 ${PYSITELIB}/skimage/morphology/_util.py
 ${PYSITELIB}/skimage/morphology/_util.pyc
 ${PYSITELIB}/skimage/morphology/_util.pyo
@@ -861,9 +856,6 @@ ${PYSITELIB}/skimage/morphology/tests/te
 ${PYSITELIB}/skimage/morphology/tests/test_skeletonize.py
 ${PYSITELIB}/skimage/morphology/tests/test_skeletonize.pyc
 ${PYSITELIB}/skimage/morphology/tests/test_skeletonize.pyo
-${PYSITELIB}/skimage/morphology/tests/test_skeletonize_3d.py
-${PYSITELIB}/skimage/morphology/tests/test_skeletonize_3d.pyc
-${PYSITELIB}/skimage/morphology/tests/test_skeletonize_3d.pyo
 ${PYSITELIB}/skimage/morphology/tests/test_util.py
 ${PYSITELIB}/skimage/morphology/tests/test_util.pyc
 ${PYSITELIB}/skimage/morphology/tests/test_util.pyo

Index: pkgsrc/math/py-scikit-image/distinfo
diff -u pkgsrc/math/py-scikit-image/distinfo:1.10 pkgsrc/math/py-scikit-image/distinfo:1.11
--- pkgsrc/math/py-scikit-image/distinfo:1.10   Tue Aug  6 11:44:50 2024
+++ pkgsrc/math/py-scikit-image/distinfo        Tue Feb 11 12:09:55 2025
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.10 2024/08/06 11:44:50 adam Exp $
+$NetBSD: distinfo,v 1.11 2025/02/11 12:09:55 adam Exp $
 
-BLAKE2s (scikit_image-0.24.0.tar.gz) = ccd2fdc6bf021c493e5f530a628b2cc2a91198e09a1189eeac0e9419f28b8b1e
-SHA512 (scikit_image-0.24.0.tar.gz) = becb062725b4c1f64e12a1f775175e48dbce1b989c1e8f40ec04ff79cb926740be514b9a0a68e3f9e17fb0d3c7b860c7451b91eb178bbae93521e02e3e8e92db
-Size (scikit_image-0.24.0.tar.gz) = 22693928 bytes
+BLAKE2s (scikit_image-0.25.1.tar.gz) = 5802312b8342ea7ce5b9b78accccc29242f063efd9eb8c0716925a0f4282adf8
+SHA512 (scikit_image-0.25.1.tar.gz) = ede7fa3fdfda2440e5590a14b46b161418da3908674158b8592299d0b611913cdf4821761fcab6673470a33d178ec336d4d60d03fb9a072ed23e4f178a3eb0d8
+Size (scikit_image-0.25.1.tar.gz) = 22697578 bytes

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