Adding metadata

4 files changed, 4 insertions, 187 deletions

diff --git a/dev-python/scikit-image/Manifest b/dev-python/scikit-image/Manifest
index b94876414f28..1ca72e8a16df 100644
--- a/dev-python/scikit-image/Manifest
+++ b/dev-python/scikit-image/Manifest
@@ -1,4 +1,3 @@
 DIST scikit-image-data-15735b54e85c02427f07c71e6456723495034805.tar.bz2 143900901 BLAKE2B c1352e76337250fe1a9d6e07f08b6c9b1e0aed922ab8e0a3a4a1ea175f593b3375522e59550d30a22d392c34fef26d638c007c2af3d991887e02e7c68e56ebbb SHA512 d113dd258b35be710d841f9900cfbfe7103d1190b042489de88dd504b56277edac9a98fed5517e57725c5292fe26528267a06ff313bf6500b669d872c4481146
-DIST scikit_image-0.24.0.tar.gz 22693928 BLAKE2B f165f702908fe446b459de3db0ec056a4b79d7266f85bc81c991569c1e492c22d238e8553d8f035abd83d4d3c4b449304e74b55d8bf558cac977c3ea5f0c864a SHA512 becb062725b4c1f64e12a1f775175e48dbce1b989c1e8f40ec04ff79cb926740be514b9a0a68e3f9e17fb0d3c7b860c7451b91eb178bbae93521e02e3e8e92db
 DIST scikit_image-0.25.0.tar.gz 22696477 BLAKE2B 6a19d10c8475e4975f9648befad410362b9cdfffcb2dd39c510d79f0498f33c305374996f4492b6f8b3d267da913f8f763d8834faae1a5949363f314f0a43fbd SHA512 b8954dd74177838f93e15f3f818868cac0f463fef420c1fabc297e691ff7c6bf2b243715b562054d38ef7fa3483eebe5f95a9e045974bcee136b32a283e1902f
-DIST scikit_image-0.25.0rc2.tar.gz 22697011 BLAKE2B 55fa48357343ff7663c5a956042e8914b62fe78b82085035276fb11cf10864f1d06a3f31247b766c294b91419825c3199c22b533c4e6207b5bdb152090aefbcc SHA512 4c418f6eebba394dab7d297deafc518be815be205f7701458b1adf3a9d3102c7be76ebd93d72fac78d990bfa0e06e749925c995e23315f2c23da560f93cf6867
+DIST scikit_image-0.25.1.tar.gz 22697578 BLAKE2B ff4533d3d705f4dbb919578af3a976e1e09c1dadbcb26b15fe421aefe9cd1ce0d891a268844a21c47696db69470ffd6951db918496149accee47100c7d42521c SHA512 ede7fa3fdfda2440e5590a14b46b161418da3908674158b8592299d0b611913cdf4821761fcab6673470a33d178ec336d4d60d03fb9a072ed23e4f178a3eb0d8
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
deleted file mode 100644
index 664a2388c08e..000000000000
--- a/dev-python/scikit-image/files/scikit-image-0.24.0-py313.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-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
deleted file mode 100644
index ccf6d28d49d1..000000000000
--- a/dev-python/scikit-image/scikit-image-0.24.0.ebuild
+++ /dev/null
@@ -1,102 +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_{9,10,11,12,13} )
-
-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[${PYTHON_USEDEP}]
-	>=dev-python/lazy-loader-0.4[${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[${PYTHON_USEDEP}]
-	)
-"
-
-DOCS=( CONTRIBUTORS.txt RELEASE.txt )
-
-# xdist does not work with this test suite
-distutils_enable_tests pytest
-# There is a programmable error in your configuration file:
-#distutils_enable_sphinx doc/source dev-python/numpydoc dev-python/myst-parser
-
-PATCHES=(
-	# https://github.com/scikit-image/scikit-image/pull/7463
-	# stripped down to minimal 3.13 support
-	"${FILESDIR}/${P}-py313.patch"
-)
-
-src_test() {
-	# for some reason, upstream refetches data that's already in the tarball
-	# sigh
-	mkdir -p "${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 "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-0.25.0_rc2.ebuild b/dev-python/scikit-image/scikit-image-0.25.1.ebuild
index 1090121e651e..f48109fa6f66 100644
--- a/dev-python/scikit-image/scikit-image-0.25.0_rc2.ebuild
+++ b/dev-python/scikit-image/scikit-image-0.25.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -78,6 +78,8 @@ python_test() {
 		# tests for downloading all data files, including these not needed
 		# by any actual tests
 		data/tests/test_data.py::test_download_all_with_pooch
+		# hangs? TODO
+		graph/tests/test_rag.py::test_reproducibility
 	)
 
 	local -x PYTEST_DISABLE_PLUGIN_AUTOLOAD=1