* [gentoo-commits] repo/gentoo:master commit in: dev-python/scikit-image/, dev-python/scikit-image/files/
@ 2024-08-14 7:36 Michał Górny
0 siblings, 0 replies; 2+ messages in thread
From: Michał Górny @ 2024-08-14 7:36 UTC (permalink / raw
To: gentoo-commits
commit: 2efdb7eea7ffc763b1280cc156025fb809e23a0d
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Wed Aug 14 07:24:11 2024 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Wed Aug 14 07:36:13 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2efdb7ee
dev-python/scikit-image: Enable py3.13
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>
.../files/scikit-image-0.24.0-py313.patch | 82 ++++++++++++++++++++++
dev-python/scikit-image/scikit-image-0.24.0.ebuild | 8 ++-
2 files changed, 89 insertions(+), 1 deletion(-)
diff --git a/dev-python/scikit-image/files/scikit-image-0.24.0-py313.patch b/dev-python/scikit-image/files/scikit-image-0.24.0-py313.patch
new file mode 100644
index 000000000000..664a2388c08e
--- /dev/null
+++ b/dev-python/scikit-image/files/scikit-image-0.24.0-py313.patch
@@ -0,0 +1,82 @@
+From ee41933e3ea15769cea32a514cdaeecbe84b70b9 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Edgar=20Andr=C3=A9s=20Margffoy=20Tuay?= <andfoy@gmail.com>
+Date: Wed, 31 Jul 2024 11:43:59 -0500
+Subject: [PATCH] Add CI to test scikit-image against free-threaded Python 3.13
+ (#7463)
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+enables testing scikit-image against free-threaded Python,
+this is part of the ongoing effort to test projects against the
+changes proposed in PEP703
+
+---------
+
+Co-authored-by: Stefan van der Walt <sjvdwalt@gmail.com>
+Co-authored-by: Lars Grüter <lagru+github@mailbox.org>
+---
+ .github/workflows/tests.yml | 26 ++++++++++++++++++++++++++
+ TODO.txt | 2 ++
+ meson.build | 2 +-
+ skimage/measure/_regionprops.py | 9 ++++++---
+ skimage/meson.build | 10 +++++++++-
+ skimage/transform/_geometric.py | 2 +-
+ skimage/util/_map_array.py | 2 +-
+ tools/github/before_install.sh | 6 ++++++
+ 8 files changed, 52 insertions(+), 7 deletions(-)
+
+diff --git a/skimage/measure/_regionprops.py b/skimage/measure/_regionprops.py
+index 9f34d6a1c..82a03b394 100644
+--- a/skimage/measure/_regionprops.py
++++ b/skimage/measure/_regionprops.py
+@@ -1,4 +1,5 @@
+ import inspect
++import sys
+ from functools import wraps
+ from math import atan2
+ from math import pi as PI
+@@ -1406,9 +1407,11 @@ def _parse_docs():
+ import textwrap
+
+ doc = regionprops.__doc__ or ''
+- matches = re.finditer(
+- r'\*\*(\w+)\*\* \:.*?\n(.*?)(?=\n [\*\S]+)', doc, flags=re.DOTALL
+- )
++ arg_regex = r'\*\*(\w+)\*\* \:.*?\n(.*?)(?=\n [\*\S]+)'
++ if sys.version_info >= (3, 13):
++ arg_regex = r'\*\*(\w+)\*\* \:.*?\n(.*?)(?=\n[\*\S]+)'
++
++ matches = re.finditer(arg_regex, doc, flags=re.DOTALL)
+ prop_doc = {m.group(1): textwrap.dedent(m.group(2)) for m in matches}
+
+ return prop_doc
+diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
+index 6f696e95b..56cedae63 100644
+--- a/skimage/transform/_geometric.py
++++ b/skimage/transform/_geometric.py
+@@ -687,7 +687,7 @@ class ProjectiveTransform(_GeometricTransform):
+
+ return dst[:, :ndim]
+
+- def __array__(self, dtype=None):
++ def __array__(self, dtype=None, copy=None):
+ if dtype is None:
+ return self.params
+ else:
+diff --git a/skimage/util/_map_array.py b/skimage/util/_map_array.py
+index 1f852fdb6..125dfb211 100644
+--- a/skimage/util/_map_array.py
++++ b/skimage/util/_map_array.py
+@@ -129,7 +129,7 @@ class ArrayMap:
+ """Return one more than the maximum label value being remapped."""
+ return np.max(self.in_values) + 1
+
+- def __array__(self, dtype=None):
++ def __array__(self, dtype=None, copy=None):
+ """Return an array that behaves like the arraymap when indexed.
+
+ This array can be very large: it is the size of the largest value
+--
+2.45.2
+
diff --git a/dev-python/scikit-image/scikit-image-0.24.0.ebuild b/dev-python/scikit-image/scikit-image-0.24.0.ebuild
index 2ec63290c17b..5bffa476e8a6 100644
--- a/dev-python/scikit-image/scikit-image-0.24.0.ebuild
+++ b/dev-python/scikit-image/scikit-image-0.24.0.ebuild
@@ -5,7 +5,7 @@ EAPI=8
DISTUTILS_USE_PEP517=meson-python
DISTUTILS_EXT=1
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{10..13} )
inherit distutils-r1 optfeature pypi
@@ -51,6 +51,12 @@ distutils_enable_tests pytest
# There is a programmable error in your configuration file:
#distutils_enable_sphinx doc/source dev-python/numpydoc dev-python/myst-parser
+PATCHES=(
+ # https://github.com/scikit-image/scikit-image/pull/7463
+ # stripped down to minimal 3.13 support
+ "${FILESDIR}/${P}-py313.patch"
+)
+
src_test() {
# for some reason, upstream refetches data that's already in the tarball
# sigh
^ permalink raw reply related [flat|nested] 2+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: dev-python/scikit-image/, dev-python/scikit-image/files/
@ 2024-04-21 2:35 Michał Górny
0 siblings, 0 replies; 2+ messages in thread
From: Michał Górny @ 2024-04-21 2:35 UTC (permalink / raw
To: gentoo-commits
commit: 0e29ce1cb465c9f7f0e91eac15b86f693048484d
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 21 01:41:43 2024 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sun Apr 21 02:35:02 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0e29ce1c
dev-python/scikit-image: Remove old
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>
dev-python/scikit-image/Manifest | 2 -
.../files/scikit-image-0.22.0-no-numpydoc.patch | 42 ----------
dev-python/scikit-image/scikit-image-0.22.0.ebuild | 64 --------------
.../scikit-image/scikit-image-0.23.0_rc2.ebuild | 97 ----------------------
4 files changed, 205 deletions(-)
diff --git a/dev-python/scikit-image/Manifest b/dev-python/scikit-image/Manifest
index 19374f7c05eb..0c576d024015 100644
--- a/dev-python/scikit-image/Manifest
+++ b/dev-python/scikit-image/Manifest
@@ -1,4 +1,2 @@
DIST scikit-image-data-15735b54e85c02427f07c71e6456723495034805.tar.bz2 143900901 BLAKE2B c1352e76337250fe1a9d6e07f08b6c9b1e0aed922ab8e0a3a4a1ea175f593b3375522e59550d30a22d392c34fef26d638c007c2af3d991887e02e7c68e56ebbb SHA512 d113dd258b35be710d841f9900cfbfe7103d1190b042489de88dd504b56277edac9a98fed5517e57725c5292fe26528267a06ff313bf6500b669d872c4481146
-DIST scikit_image-0.22.0.tar.gz 22685018 BLAKE2B 7d0a65f75f5a58211e21501d6cc6a638f1d36e9a2198a3ad9ff2f230890496c41d5e6cdaed02bbaa62f26aa57fd24fc993656cbdfc2c9c9750147d0f325e56f1 SHA512 4b8c097cd5465f57b1c0879363fe3bdc0941decf2d1f8a881f13f2b7f3207c425f3a0cdcb4be0eed7b33d3ac2f3f8b1835d1cfa69cd3fa2ff5e0be11385fef48
-DIST scikit_image-0.23.0rc2.tar.gz 22677632 BLAKE2B b663065650e25a33ffec80ddd05df622bc62b1c1d3d0a831488d4dd23291b4f125458ae335782762b1d4dc1efa8cbedd5fcd7e6bbe62003967209e4ca4179bca SHA512 aa5f27d571ea49276aba8443a691b30a576d52145a17f13b8ea080a2abf0ed01c57fe50324c05e72bb4662a9ddbb480be94be6784ac3220ed6853b12d94ae06b
DIST scikit_image-0.23.1.tar.gz 22676819 BLAKE2B 2d02bab4f8d6217c842f428a6758d467393a73a05ac741a49cd27fa6ee48335cf8fed4cc104296388d0e23c61ac3603f72d7bab44986c0d3d4073da383f89726 SHA512 7450387c3adcac15148c3ae4f43fd7da97ceabf3522302b7f3ab4cd02e5a9ec2cd9623f29e4aec3bb47668a231e0900724804619bb91aaaf97283d29c34392e6
diff --git a/dev-python/scikit-image/files/scikit-image-0.22.0-no-numpydoc.patch b/dev-python/scikit-image/files/scikit-image-0.22.0-no-numpydoc.patch
deleted file mode 100644
index 25137b5167c8..000000000000
--- a/dev-python/scikit-image/files/scikit-image-0.22.0-no-numpydoc.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-From 9b27f8e802c9513952c8a42450a4459fa357b89c Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= <mgorny@gentoo.org>
-Date: Fri, 26 Jan 2024 20:25:16 +0100
-Subject: [PATCH] Make it possible to run tests without numpydoc
-
-Skip the three tests requiring numpydoc when it is not installed.
-For `skimage/_shared/tests/test_utils.py`, use the existing
-`have_numpydoc` constant.
-For `skimage/measure/tests/test_regionprops.py`, use the standard
-`pytest.importorskip()` function.
-
-This makes it possible to successfully run the test suite when
-`numpydoc` is not installed. This would be convenient for Gentoo
-since numpydoc is facing neverending test regressions (in its own test
-suite).
----
- skimage/measure/tests/test_regionprops.py | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/skimage/measure/tests/test_regionprops.py b/skimage/measure/tests/test_regionprops.py
-index 01a59dfbf..0b74d30a4 100644
---- a/skimage/measure/tests/test_regionprops.py
-+++ b/skimage/measure/tests/test_regionprops.py
-@@ -4,7 +4,6 @@ import re
- import numpy as np
- import pytest
- import scipy.ndimage as ndi
--import numpydoc
- from numpy.testing import (assert_allclose, assert_almost_equal,
- assert_array_almost_equal, assert_array_equal,
- assert_equal)
-@@ -1261,6 +1260,7 @@ def test_column_dtypes_correct():
-
-
- def test_all_documented_items_in_col_dtypes():
-+ numpydoc = pytest.importorskip("numpydoc")
- docstring = numpydoc.docscrape.FunctionDoc(regionprops)
- notes_lines = docstring['Notes']
- property_lines = filter(lambda line: line.startswith('**'), notes_lines)
---
-2.43.0
-
diff --git a/dev-python/scikit-image/scikit-image-0.22.0.ebuild b/dev-python/scikit-image/scikit-image-0.22.0.ebuild
deleted file mode 100644
index 62ff8da8a3eb..000000000000
--- a/dev-python/scikit-image/scikit-image-0.22.0.ebuild
+++ /dev/null
@@ -1,64 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=meson-python
-DISTUTILS_EXT=1
-PYTHON_COMPAT=( python3_{10..12} )
-
-inherit distutils-r1 optfeature pypi
-
-DESCRIPTION="Image processing routines for SciPy"
-HOMEPAGE="
- https://scikit-image.org/
- https://github.com/scikit-image/scikit-image/
- https://pypi.org/project/scikit-image/
-"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~arm64 ~x86"
-PROPERTIES="test_network"
-RESTRICT="test"
-
-RDEPEND="
- >=dev-python/imageio-2.27[${PYTHON_USEDEP}]
- >=dev-python/lazy-loader-0.3[${PYTHON_USEDEP}]
- >=dev-python/networkx-2.8[${PYTHON_USEDEP}]
- >=dev-python/numpy-1.22[${PYTHON_USEDEP}]
- >=dev-python/pillow-9.0.1[${PYTHON_USEDEP}]
- >=dev-python/scipy-1.8[sparse(+),${PYTHON_USEDEP}]
- >=dev-python/tifffile-2022.8.12[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
-"
-
-DOCS=( CONTRIBUTORS.txt RELEASE.txt )
-
-distutils_enable_tests pytest
-# There is a programmable error in your configuration file:
-#distutils_enable_sphinx doc/source dev-python/numpydoc dev-python/myst-parser
-
-PATCHES=(
- # https://github.com/scikit-image/scikit-image/pull/7307
- "${FILESDIR}/${P}-no-numpydoc.patch"
-)
-
-python_test() {
- rm -rf skimage || die
- epytest --pyargs skimage
-}
-
-pkg_postinst() {
- optfeature "FITS io capability" dev-python/astropy
- optfeature "GTK" dev-python/pygtk
- optfeature "Parallel computation" dev-python/dask
- optfeature "io plugin providing most standard formats" dev-python/imread
- optfeature "plotting" dev-python/matplotlib
- optfeature "wavelet transformations" dev-python/pywavelets
- optfeature "io plugin providing a wide variety of formats, including specialized formats using in medical imaging." dev-python/simpleitk
-}
diff --git a/dev-python/scikit-image/scikit-image-0.23.0_rc2.ebuild b/dev-python/scikit-image/scikit-image-0.23.0_rc2.ebuild
deleted file mode 100644
index a4314f655ffc..000000000000
--- a/dev-python/scikit-image/scikit-image-0.23.0_rc2.ebuild
+++ /dev/null
@@ -1,97 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=meson-python
-DISTUTILS_EXT=1
-PYTHON_COMPAT=( python3_{10..12} )
-
-inherit distutils-r1 optfeature pypi
-
-TEST_DATA_COMMIT=15735b54e85c02427f07c71e6456723495034805
-DESCRIPTION="Image processing routines for SciPy"
-HOMEPAGE="
- https://scikit-image.org/
- https://github.com/scikit-image/scikit-image/
- https://pypi.org/project/scikit-image/
-"
-SRC_URI+="
- test? (
- https://gitlab.com/scikit-image/data/-/archive/${TEST_DATA_COMMIT}/scikit-image-data-${TEST_DATA_COMMIT}.tar.bz2
- )
-"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~arm64 ~x86"
-
-RDEPEND="
- >=dev-python/imageio-2.33[${PYTHON_USEDEP}]
- >=dev-python/lazy-loader-0.3[${PYTHON_USEDEP}]
- >=dev-python/networkx-2.8[${PYTHON_USEDEP}]
- >=dev-python/numpy-1.23[${PYTHON_USEDEP}]
- >=dev-python/pillow-9.1[${PYTHON_USEDEP}]
- >=dev-python/scipy-1.9[sparse(+),${PYTHON_USEDEP}]
- >=dev-python/tifffile-2022.8.12[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
- >=dev-python/cython-3.0.4[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- test? (
- dev-python/pytest-localserver[${PYTHON_USEDEP}]
- )
-"
-
-DOCS=( CONTRIBUTORS.txt RELEASE.txt )
-
-# xdist does not work with this test suite
-distutils_enable_tests pytest
-# There is a programmable error in your configuration file:
-#distutils_enable_sphinx doc/source dev-python/numpydoc dev-python/myst-parser
-
-src_test() {
- # for some reason, upstream refetches data that's already in the tarball
- # sigh
- mkdir -p "${HOME}/.cache/scikit-image" || die
- mv skimage "${HOME}/.cache/scikit-image/${PV/_/}" || die
-
- # This is a true horror, sigh
- local cache_dir=${HOME}/.cache/scikit-image/${PV/_/}/data
- pushd "${WORKDIR}/data-${TEST_DATA_COMMIT}" >/dev/null || die
- cp Tests_besides_Equalize_Otsu/add18_entropy/rank_filters_tests_3d.npz \
- Tests_besides_Equalize_Otsu/gray_morph_output.npz \
- brain.tiff cells3d.tif eagle.png \
- "${cache_dir}/" || die
- cp Normal_Epidermis_and_Dermis_with_Intradermal_Nevus_10x.JPG "${cache_dir}"/skin.jpg || die
- cp pivchallenge/B/B001_1.tif "${cache_dir}"/pivchallenge-B-B001_1.tif || die
- cp pivchallenge/B/B001_2.tif "${cache_dir}"/pivchallenge-B-B001_2.tif || die
- cp kidney-tissue-fluorescence.tif "${cache_dir}"/kidney.tif || die
- cp lily-of-the-valley-fluorescence.tif "${cache_dir}"/lily.tif || die
- cp astronaut_rl.npy "${cache_dir}/../restoration/tests/" || die
- popd > /dev/null || die
-
- distutils-r1_src_test
-}
-
-python_test() {
- local EPYTEST_DESELECT=(
- # tests for downloading all data files, including these not needed
- # by any actual tests
- data/tests/test_data.py::test_download_all_with_pooch
- )
-
- local -x PYTEST_DISABLE_PLUGIN_AUTOLOAD=1
- epytest --pyargs skimage -p localserver -o xfail_strict=False
-}
-
-pkg_postinst() {
- optfeature "FITS io capability" dev-python/astropy
- optfeature "GTK" dev-python/pygtk
- optfeature "Parallel computation" dev-python/dask
- optfeature "io plugin providing most standard formats" dev-python/imread
- optfeature "plotting" dev-python/matplotlib
- optfeature "wavelet transformations" dev-python/pywavelets
- optfeature "io plugin providing a wide variety of formats, including specialized formats using in medical imaging." dev-python/simpleitk
-}
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