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, 6 Aug 2024 11:44:50 +0000

Module Name:    pkgsrc
Committed By:   adam
Date:           Tue Aug  6 11:44:50 UTC 2024

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

Log Message:
py-scikit-image: updated to 0.24.0

scikit-image 0.24.0 (2024-06-18)

Highlights

Add new class skimage.transform.ThinPlateSplineTransform, which can estimate and model non-linear transforms with thin-plate splines and allows image warping with skimage.transform.warp

New Features

Add new class skimage.transform.ThinPlateSplineTransform, which can estimate and model non-linear transforms with thin-plate splines and allows image warping with skimage.transform.warp
Add skimage.morphology.remove_objects_by_distance, which removes labeled objects, ordered by size (default), until the remaining objects are a given distance apart

Performance

In skimage.feature.corner_fast, test four directions earlier, which should more than half the computation time for most cases

Documentation

Remove obsolete instruction about documenting changes
Clarify description of data_range parameter in skimage.metrics.structural_similarity
Update release process notes
Fix typo in docstring of skimage.measure.regionprops
Fix typos in skimage.measure.find_contours
Add algorithmic complexity description + suggested alternatives to skimage.restoration.rolling_ball docstring
Remove ineffective PR contribution clause
Clarify objection period for lazy consensus in SKIP 1
Add a new gallery example “Use thin-plate splines for image warping”
Add a new gallery example on “Removing objects” based on their size or distance

Infrastructure

Escape user-controlled variables in GA workflow
Add generation of GitHub artifact attestations to built sdist and wheels before upload to PyPI
For publishing actions use the full length commit SHA
Be mindful of resources by canceling in-progress workflows
Add out-of-tree Pyodide builds in CI for scikit-image

Maintenance

Replace deprecated nose style setup/teardown with autouse fixtures
Temporarily pin macos-12 runner in CI
Fix NumPy2 dtype promotion issues in pywt dependent code
In skimage.util.compare_images, deprecate the parameter image2. Instead use image0, image1 to pass the compared images. Furthermore, all other parameters will be turned into keyword-only parameters 
once the deprecation is complete
Add support back for Python 3.9 to enhance compatibility with Numpy 2
Disable ruff/pyupgrade rule UP038
Stop verifying wheel attestations temporarily


To generate a diff of this commit:
cvs rdiff -u -r1.22 -r1.23 pkgsrc/math/py-scikit-image/Makefile
cvs rdiff -u -r1.6 -r1.7 pkgsrc/math/py-scikit-image/PLIST
cvs rdiff -u -r1.9 -r1.10 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:1.22 pkgsrc/math/py-scikit-image/Makefile:1.23
--- pkgsrc/math/py-scikit-image/Makefile:1.22   Sun Feb 18 11:15:04 2024
+++ pkgsrc/math/py-scikit-image/Makefile        Tue Aug  6 11:44:50 2024
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.22 2024/02/18 11:15:04 wiz Exp $
+# $NetBSD: Makefile,v 1.23 2024/08/06 11:44:50 adam Exp $
 
-DISTNAME=      scikit_image-0.22.0
+DISTNAME=      scikit_image-0.24.0
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME:S/_/-/}
 CATEGORIES=    math graphics python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=s/scikit-image/}
@@ -12,31 +12,27 @@ 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}-numpy>=1.21.1:../../math/py-numpy
-DEPENDS+=      ${PYPKGPREFIX}-scipy>=1.8:../../math/py-scipy
+DEPENDS+=      ${PYPKGPREFIX}-Pillow>=9.1:../../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}-Pillow>=9.0.1:../../graphics/py-Pillow
-DEPENDS+=      ${PYPKGPREFIX}-imageio>=2.27:../../graphics/py-imageio
-DEPENDS+=      ${PYPKGPREFIX}-tifffile>=2022.8.12:../../graphics/py-tifffile
-DEPENDS+=      ${PYPKGPREFIX}-pywavelets>=1.1.1:../../math/py-pywavelets
+DEPENDS+=      ${PYPKGPREFIX}-numpy>=1.23:../../math/py-numpy
 DEPENDS+=      ${PYPKGPREFIX}-packaging>=21:../../devel/py-packaging
-DEPENDS+=      ${PYPKGPREFIX}-lazy_loader>=0.2:../../misc/py-lazy_loader
+DEPENDS+=      ${PYPKGPREFIX}-scipy>=1.9:../../math/py-scipy
+DEPENDS+=      ${PYPKGPREFIX}-tifffile>=2022.8.12:../../graphics/py-tifffile
 # optional
-DEPENDS+=      ${PYPKGPREFIX}-matplotlib>=3.0.3:../../graphics/py-matplotlib
-TEST_DEPENDS+= ${PYPKGPREFIX}-test>=0:../../devel/py-test
+DEPENDS+=      ${PYPKGPREFIX}-matplotlib>=3.6:../../graphics/py-matplotlib
+DEPENDS+=      ${PYPKGPREFIX}-pywavelets>=1.1.1:../../math/py-pywavelets
 
 USE_LANGUAGES= c c++
-GCC_REQD+=     8
+GCC_REQD+=     9
 
-PYTHON_VERSIONS_INCOMPATIBLE=  27 38
+PYTHON_VERSIONS_INCOMPATIBLE=  27 38 39
 
 pre-configure:
        ${LN} -f -s ${PREFIX}/bin/cython-${PYVERSSUFFIX} ${BUILDLINK_DIR}/bin/cython
        ${LN} -f -s ${PREFIX}/bin/pythran-${PYVERSSUFFIX} ${BUILDLINK_DIR}/bin/pythran
 
-do-test:
-       cd ${WRKSRC} && ${SETENV} ${TEST_ENV} pytest-${PYVERSSUFFIX}
-
 .include "../../devel/py-cython/buildlink3.mk"
 .include "../../math/py-pythran/buildlink3.mk"
 .include "../../lang/python/wheel.mk"

Index: pkgsrc/math/py-scikit-image/PLIST
diff -u pkgsrc/math/py-scikit-image/PLIST:1.6 pkgsrc/math/py-scikit-image/PLIST:1.7
--- pkgsrc/math/py-scikit-image/PLIST:1.6       Thu Feb 15 22:14:14 2024
+++ pkgsrc/math/py-scikit-image/PLIST   Tue Aug  6 11:44:50 2024
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.6 2024/02/15 22:14:14 wiz Exp $
+@comment $NetBSD: PLIST,v 1.7 2024/08/06 11:44:50 adam Exp $
 ${PYSITELIB}/${WHEEL_INFODIR}/LICENSE.txt
 ${PYSITELIB}/${WHEEL_INFODIR}/METADATA
 ${PYSITELIB}/${WHEEL_INFODIR}/RECORD
@@ -22,9 +22,15 @@ ${PYSITELIB}/skimage/_shared/_tempfile.p
 ${PYSITELIB}/skimage/_shared/_warnings.py
 ${PYSITELIB}/skimage/_shared/_warnings.pyc
 ${PYSITELIB}/skimage/_shared/_warnings.pyo
+${PYSITELIB}/skimage/_shared/compat.py
+${PYSITELIB}/skimage/_shared/compat.pyc
+${PYSITELIB}/skimage/_shared/compat.pyo
 ${PYSITELIB}/skimage/_shared/coord.py
 ${PYSITELIB}/skimage/_shared/coord.pyc
 ${PYSITELIB}/skimage/_shared/coord.pyo
+${PYSITELIB}/skimage/_shared/dtype.py
+${PYSITELIB}/skimage/_shared/dtype.pyc
+${PYSITELIB}/skimage/_shared/dtype.pyo
 ${PYSITELIB}/skimage/_shared/fast_exp.h
 ${PYSITELIB}/skimage/_shared/fast_exp.so
 ${PYSITELIB}/skimage/_shared/filters.py
@@ -44,6 +50,9 @@ ${PYSITELIB}/skimage/_shared/tests/__ini
 ${PYSITELIB}/skimage/_shared/tests/test_coord.py
 ${PYSITELIB}/skimage/_shared/tests/test_coord.pyc
 ${PYSITELIB}/skimage/_shared/tests/test_coord.pyo
+${PYSITELIB}/skimage/_shared/tests/test_dtype.py
+${PYSITELIB}/skimage/_shared/tests/test_dtype.pyc
+${PYSITELIB}/skimage/_shared/tests/test_dtype.pyo
 ${PYSITELIB}/skimage/_shared/tests/test_fast_exp.py
 ${PYSITELIB}/skimage/_shared/tests/test_fast_exp.pyc
 ${PYSITELIB}/skimage/_shared/tests/test_fast_exp.pyo
@@ -75,6 +84,12 @@ ${PYSITELIB}/skimage/_shared/utils.pyo
 ${PYSITELIB}/skimage/_shared/version_requirements.py
 ${PYSITELIB}/skimage/_shared/version_requirements.pyc
 ${PYSITELIB}/skimage/_shared/version_requirements.pyo
+${PYSITELIB}/skimage/_vendored/__init__.py
+${PYSITELIB}/skimage/_vendored/__init__.pyc
+${PYSITELIB}/skimage/_vendored/__init__.pyo
+${PYSITELIB}/skimage/_vendored/numpy_lookfor.py
+${PYSITELIB}/skimage/_vendored/numpy_lookfor.pyc
+${PYSITELIB}/skimage/_vendored/numpy_lookfor.pyo
 ${PYSITELIB}/skimage/color/__init__.py
 ${PYSITELIB}/skimage/color/__init__.pyc
 ${PYSITELIB}/skimage/color/__init__.pyi
@@ -726,6 +741,7 @@ ${PYSITELIB}/skimage/measure/tests/test_
 ${PYSITELIB}/skimage/measure/tests/test_regionprops.pyo
 ${PYSITELIB}/skimage/metrics/__init__.py
 ${PYSITELIB}/skimage/metrics/__init__.pyc
+${PYSITELIB}/skimage/metrics/__init__.pyi
 ${PYSITELIB}/skimage/metrics/__init__.pyo
 ${PYSITELIB}/skimage/metrics/_adapted_rand_error.py
 ${PYSITELIB}/skimage/metrics/_adapted_rand_error.pyc
@@ -771,6 +787,7 @@ ${PYSITELIB}/skimage/morphology/_flood_f
 ${PYSITELIB}/skimage/morphology/_flood_fill_cy.so
 ${PYSITELIB}/skimage/morphology/_grayreconstruct.so
 ${PYSITELIB}/skimage/morphology/_max_tree.so
+${PYSITELIB}/skimage/morphology/_misc_cy.so
 ${PYSITELIB}/skimage/morphology/_skeletonize.py
 ${PYSITELIB}/skimage/morphology/_skeletonize.pyc
 ${PYSITELIB}/skimage/morphology/_skeletonize.pyo
@@ -1032,6 +1049,9 @@ ${PYSITELIB}/skimage/transform/_geometri
 ${PYSITELIB}/skimage/transform/_geometric.pyo
 ${PYSITELIB}/skimage/transform/_hough_transform.so
 ${PYSITELIB}/skimage/transform/_radon_transform.so
+${PYSITELIB}/skimage/transform/_thin_plate_splines.py
+${PYSITELIB}/skimage/transform/_thin_plate_splines.pyc
+${PYSITELIB}/skimage/transform/_thin_plate_splines.pyo
 ${PYSITELIB}/skimage/transform/_warps.py
 ${PYSITELIB}/skimage/transform/_warps.pyc
 ${PYSITELIB}/skimage/transform/_warps.pyo
@@ -1072,6 +1092,9 @@ ${PYSITELIB}/skimage/transform/tests/tes
 ${PYSITELIB}/skimage/transform/tests/test_radon_transform.py
 ${PYSITELIB}/skimage/transform/tests/test_radon_transform.pyc
 ${PYSITELIB}/skimage/transform/tests/test_radon_transform.pyo
+${PYSITELIB}/skimage/transform/tests/test_thin_plate_splines.py
+${PYSITELIB}/skimage/transform/tests/test_thin_plate_splines.pyc
+${PYSITELIB}/skimage/transform/tests/test_thin_plate_splines.pyo
 ${PYSITELIB}/skimage/transform/tests/test_warps.py
 ${PYSITELIB}/skimage/transform/tests/test_warps.pyc
 ${PYSITELIB}/skimage/transform/tests/test_warps.pyo
@@ -1139,6 +1162,9 @@ ${PYSITELIB}/skimage/util/tests/test_inv
 ${PYSITELIB}/skimage/util/tests/test_labels.py
 ${PYSITELIB}/skimage/util/tests/test_labels.pyc
 ${PYSITELIB}/skimage/util/tests/test_labels.pyo
+${PYSITELIB}/skimage/util/tests/test_lookfor.py
+${PYSITELIB}/skimage/util/tests/test_lookfor.pyc
+${PYSITELIB}/skimage/util/tests/test_lookfor.pyo
 ${PYSITELIB}/skimage/util/tests/test_map_array.py
 ${PYSITELIB}/skimage/util/tests/test_map_array.pyc
 ${PYSITELIB}/skimage/util/tests/test_map_array.pyo

Index: pkgsrc/math/py-scikit-image/distinfo
diff -u pkgsrc/math/py-scikit-image/distinfo:1.9 pkgsrc/math/py-scikit-image/distinfo:1.10
--- pkgsrc/math/py-scikit-image/distinfo:1.9    Thu Feb 15 22:14:14 2024
+++ pkgsrc/math/py-scikit-image/distinfo        Tue Aug  6 11:44:50 2024
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.9 2024/02/15 22:14:14 wiz Exp $
+$NetBSD: distinfo,v 1.10 2024/08/06 11:44:50 adam Exp $
 
-BLAKE2s (scikit_image-0.22.0.tar.gz) = 4792d53b9d1752e281e4f64e2bf60fede6c800cd4a437cac109d0ff1cecd1496
-SHA512 (scikit_image-0.22.0.tar.gz) = 4b8c097cd5465f57b1c0879363fe3bdc0941decf2d1f8a881f13f2b7f3207c425f3a0cdcb4be0eed7b33d3ac2f3f8b1835d1cfa69cd3fa2ff5e0be11385fef48
-Size (scikit_image-0.22.0.tar.gz) = 22685018 bytes
+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

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