[gentoo-commits] repo/gentoo:master commit in: dev-python/scikit-image/

["Michał Górny" <mgorny@gentoo.org>]

commit:     d17ed39019a981e55c6ab0408f8858164c52e53c
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 27 06:24:24 2025 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Mon Jan 27 07:28:48 2025 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d17ed390

dev-python/scikit-image: Bump to 0.25.1

Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>

 dev-python/scikit-image/Manifest                   |  1 +
 dev-python/scikit-image/scikit-image-0.25.1.ebuild | 96 ++++++++++++++++++++++
 2 files changed, 97 insertions(+)

diff --git a/dev-python/scikit-image/Manifest b/dev-python/scikit-image/Manifest
index 8a8c3741abed..1ca72e8a16df 100644
--- a/dev-python/scikit-image/Manifest
+++ b/dev-python/scikit-image/Manifest
@@ -1,2 +1,3 @@
 DIST scikit-image-data-15735b54e85c02427f07c71e6456723495034805.tar.bz2 143900901 BLAKE2B c1352e76337250fe1a9d6e07f08b6c9b1e0aed922ab8e0a3a4a1ea175f593b3375522e59550d30a22d392c34fef26d638c007c2af3d991887e02e7c68e56ebbb SHA512 d113dd258b35be710d841f9900cfbfe7103d1190b042489de88dd504b56277edac9a98fed5517e57725c5292fe26528267a06ff313bf6500b669d872c4481146
 DIST scikit_image-0.25.0.tar.gz 22696477 BLAKE2B 6a19d10c8475e4975f9648befad410362b9cdfffcb2dd39c510d79f0498f33c305374996f4492b6f8b3d267da913f8f763d8834faae1a5949363f314f0a43fbd SHA512 b8954dd74177838f93e15f3f818868cac0f463fef420c1fabc297e691ff7c6bf2b243715b562054d38ef7fa3483eebe5f95a9e045974bcee136b32a283e1902f
+DIST scikit_image-0.25.1.tar.gz 22697578 BLAKE2B ff4533d3d705f4dbb919578af3a976e1e09c1dadbcb26b15fe421aefe9cd1ce0d891a268844a21c47696db69470ffd6951db918496149accee47100c7d42521c SHA512 ede7fa3fdfda2440e5590a14b46b161418da3908674158b8592299d0b611913cdf4821761fcab6673470a33d178ec336d4d60d03fb9a072ed23e4f178a3eb0d8

diff --git a/dev-python/scikit-image/scikit-image-0.25.1.ebuild b/dev-python/scikit-image/scikit-image-0.25.1.ebuild
new file mode 100644
index 000000000000..385fcfede7ab
--- /dev/null
+++ b/dev-python/scikit-image/scikit-image-0.25.1.ebuild
@@ -0,0 +1,96 @@
+# Copyright 1999-2025 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..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-2.36[${PYTHON_USEDEP}]
+	>=dev-python/lazy-loader-0.4[${PYTHON_USEDEP}]
+	>=dev-python/networkx-3.0[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.24[${PYTHON_USEDEP}]
+	>=dev-python/pillow-10.1[${PYTHON_USEDEP}]
+	>=dev-python/scipy-1.11.2[sparse(+),${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[${PYTHON_USEDEP}]
+	)
+"
+
+# xdist does not work with this test suite
+distutils_enable_tests pytest
+# There is a programmable error in your configuration file:
+#distutils_enable_sphinx doc/source dev-python/numpydoc dev-python/myst-parser
+
+src_test() {
+	# for some reason, upstream refetches data that's already in the tarball
+	# sigh
+	mkdir -p "${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
+		# hangs? TODO
+		graph/tests/test_rag.py::test_reproducibility
+	)
+
+	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
+}