From ed0a1596c807e379a19960170c94735aff22fa84 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sat, 27 Jan 2024 00:57:29 +0000 Subject: gentoo auto-resync : 27:01:2024 - 00:57:29 --- dev-python/scikit-image/Manifest | 6 ++ .../files/scikit-image-0.22.0-no-numpydoc.patch | 42 ++++++++++++++ dev-python/scikit-image/metadata.xml | 18 ++++++ .../scikit-image/scikit-image-0.19.3-r1.ebuild | 59 ++++++++++++++++++++ dev-python/scikit-image/scikit-image-0.22.0.ebuild | 64 ++++++++++++++++++++++ 5 files changed, 189 insertions(+) create mode 100644 dev-python/scikit-image/Manifest create mode 100644 dev-python/scikit-image/files/scikit-image-0.22.0-no-numpydoc.patch create mode 100644 dev-python/scikit-image/metadata.xml create mode 100644 dev-python/scikit-image/scikit-image-0.19.3-r1.ebuild create mode 100644 dev-python/scikit-image/scikit-image-0.22.0.ebuild (limited to 'dev-python/scikit-image') diff --git a/dev-python/scikit-image/Manifest b/dev-python/scikit-image/Manifest new file mode 100644 index 000000000000..a6f79a025926 --- /dev/null +++ b/dev-python/scikit-image/Manifest @@ -0,0 +1,6 @@ +AUX scikit-image-0.22.0-no-numpydoc.patch 1664 BLAKE2B 65a4b565069bf21a44deae1de9cd4e66a9788e7cf3928bdf52b65325be89952a287ae713f019530f97effd92e462ea2aa94b4ad334c41d0f03d8c8d66b759f92 SHA512 38c38f4755dcb106b0683ea091b75d0923aa63e123c0e8c09eead13beec573dc65a696df955e6d58e873fadc9ec2bc95f3823ba2cb875477b627c09caa32c029 +DIST scikit-image-0.19.3.tar.gz 22232287 BLAKE2B 855584be0e69ac6e0dc7a17a68a1bca6843b471073e63d098b4933bc301eab5246d4cd2b444960de7fcd37012b66f7ba8cd6030ac485a7ab3aa1d36501aef0c7 SHA512 cda1699200e19155da13e313eb129771b7bb895913e552b959a3374267fe4f73c33d5e6e2fa2d49326903c901925797e46b9f05342a78c5332df1c266d37471a +DIST scikit_image-0.22.0.tar.gz 22685018 BLAKE2B 7d0a65f75f5a58211e21501d6cc6a638f1d36e9a2198a3ad9ff2f230890496c41d5e6cdaed02bbaa62f26aa57fd24fc993656cbdfc2c9c9750147d0f325e56f1 SHA512 4b8c097cd5465f57b1c0879363fe3bdc0941decf2d1f8a881f13f2b7f3207c425f3a0cdcb4be0eed7b33d3ac2f3f8b1835d1cfa69cd3fa2ff5e0be11385fef48 +EBUILD scikit-image-0.19.3-r1.ebuild 1709 BLAKE2B edb21f44833c94e895727ddc0e64ac5caed225753b6b52cbb13f64517ce68450a72100adc27997bb781fce5978582028e14bf219e381a54da43b58267e68e257 SHA512 f6a0a17725e4cde03a3e271af53dfde5ee330ca7a08af88a25dab8b434e5dc940b2a1c5d1ac0ae400ef746a93bd66dc62ddf9266cb6d9e9f5c76a95100fe1e83 +EBUILD scikit-image-0.22.0.ebuild 1822 BLAKE2B 4e59a3b890c0fcaa173f05cf6b10db34a2e915fd97466b6b2dec59fbbc8caefce18171b4df97b0b8b585079e9bd3d803ba83a12c33aff620494dfb971cdaa349 SHA512 ff87e164b115cce39c730fb28f15d4d9091f831886a2b38611cde1c79827205fc40eab36ab60b2487bdf947333170d1452fcb1aee3a8922ef5b899a9792a1933 +MISC metadata.xml 695 BLAKE2B 11487b964bde2ce1a39a8680bc3cc62045c4a7e2e17844de830d5f0e043660c431cd002a2a0fc19acb4c0262289ee280195475dd1f8b35f6a51ce0df369871f8 SHA512 fca83587d443373fc7219911900105676bdba5a7ced07ac00a9ab5cbe361d8ca1175b02b04fa53cdbde6f198a986b21f989baf32139cd76b7d1b2b78034d3142 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 new file mode 100644 index 000000000000..25137b5167c8 --- /dev/null +++ b/dev-python/scikit-image/files/scikit-image-0.22.0-no-numpydoc.patch @@ -0,0 +1,42 @@ +From 9b27f8e802c9513952c8a42450a4459fa357b89c Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= +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/metadata.xml b/dev-python/scikit-image/metadata.xml new file mode 100644 index 000000000000..132691d57cb8 --- /dev/null +++ b/dev-python/scikit-image/metadata.xml @@ -0,0 +1,18 @@ + + + + + sci@gentoo.org + Gentoo Science Project + + + This SciKit (toolkit for SciPy) includes useful image processing + algorithms for use with Python and NumPy. While SciPy’s ndimage + provides low-level manipulation, scikits.image centres around + algorithms and applications. + + + scikit-image + scikit-image/scikit-image + + diff --git a/dev-python/scikit-image/scikit-image-0.19.3-r1.ebuild b/dev-python/scikit-image/scikit-image-0.19.3-r1.ebuild new file mode 100644 index 000000000000..3b0060a33375 --- /dev/null +++ b/dev-python/scikit-image/scikit-image-0.19.3-r1.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 +PYTHON_COMPAT=( python3_{10..11} ) + +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" +RESTRICT="test" + +RDEPEND=" + dev-python/imageio[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] + dev-python/pywavelets[${PYTHON_USEDEP}] + dev-python/scipy[sparse(+),${PYTHON_USEDEP}] + dev-python/tifffile[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] +" + +DOCS=( CONTRIBUTORS.txt RELEASE.txt ) + +distutils_enable_tests pytest +# There is a programmable error in your configuration file: +#distutils_enable_sphinx doc/source dev-python/numpydoc dev-python/myst-parser + +python_test() { + # This needs to be run in the install dir + cd "${WORKDIR}/${P}-${EPYTHON//./_}/install/usr/lib/${EPYTHON}/site-packages/skimage" || die + distutils-r1_python_test +} + +pkg_postinst() { + optfeature "FITS io capability" dev-python/astropy + optfeature "GTK" dev-python/pygtk + optfeature "Parallel computation" dev-python/dask + optfeature "io plugin providing most standard formats" dev-python/imread + # not in portage yet + #optfeature "io plugin providing a wide variety of formats, including specialized formats using in medical imaging." dev-python/simpleitk +} diff --git a/dev-python/scikit-image/scikit-image-0.22.0.ebuild b/dev-python/scikit-image/scikit-image-0.22.0.ebuild new file mode 100644 index 000000000000..c9fa7b6e7d77 --- /dev/null +++ b/dev-python/scikit-image/scikit-image-0.22.0.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=meson-python +DISTUTILS_EXT=1 +PYTHON_COMPAT=( python3_{10..12} ) + +inherit distutils-r1 optfeature pypi + +DESCRIPTION="Image processing routines for SciPy" +HOMEPAGE=" + https://scikit-image.org/ + https://github.com/scikit-image/scikit-image/ + https://pypi.org/project/scikit-image/ +" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~arm64 ~x86" +PROPERTIES="test_network" +RESTRICT="test" + +RDEPEND=" + >=dev-python/imageio-2.27[${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 +} -- cgit v1.2.3