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dev-python/scikit-image: Remove old
Signed-off-by: Michał Górny <mgorny@gentoo.org>
This commit is contained in:
Michał Górny
@@ -1,4 +1,2 @@
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DIST scikit-image-data-15735b54e85c02427f07c71e6456723495034805.tar.bz2 143900901 BLAKE2B c1352e76337250fe1a9d6e07f08b6c9b1e0aed922ab8e0a3a4a1ea175f593b3375522e59550d30a22d392c34fef26d638c007c2af3d991887e02e7c68e56ebbb SHA512 d113dd258b35be710d841f9900cfbfe7103d1190b042489de88dd504b56277edac9a98fed5517e57725c5292fe26528267a06ff313bf6500b669d872c4481146
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DIST scikit_image-0.22.0.tar.gz 22685018 BLAKE2B 7d0a65f75f5a58211e21501d6cc6a638f1d36e9a2198a3ad9ff2f230890496c41d5e6cdaed02bbaa62f26aa57fd24fc993656cbdfc2c9c9750147d0f325e56f1 SHA512 4b8c097cd5465f57b1c0879363fe3bdc0941decf2d1f8a881f13f2b7f3207c425f3a0cdcb4be0eed7b33d3ac2f3f8b1835d1cfa69cd3fa2ff5e0be11385fef48
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DIST scikit_image-0.23.0rc2.tar.gz 22677632 BLAKE2B b663065650e25a33ffec80ddd05df622bc62b1c1d3d0a831488d4dd23291b4f125458ae335782762b1d4dc1efa8cbedd5fcd7e6bbe62003967209e4ca4179bca SHA512 aa5f27d571ea49276aba8443a691b30a576d52145a17f13b8ea080a2abf0ed01c57fe50324c05e72bb4662a9ddbb480be94be6784ac3220ed6853b12d94ae06b
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DIST scikit_image-0.23.1.tar.gz 22676819 BLAKE2B 2d02bab4f8d6217c842f428a6758d467393a73a05ac741a49cd27fa6ee48335cf8fed4cc104296388d0e23c61ac3603f72d7bab44986c0d3d4073da383f89726 SHA512 7450387c3adcac15148c3ae4f43fd7da97ceabf3522302b7f3ab4cd02e5a9ec2cd9623f29e4aec3bb47668a231e0900724804619bb91aaaf97283d29c34392e6
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@@ -1,42 +0,0 @@
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From 9b27f8e802c9513952c8a42450a4459fa357b89c Mon Sep 17 00:00:00 2001
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From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= <mgorny@gentoo.org>
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Date: Fri, 26 Jan 2024 20:25:16 +0100
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Subject: [PATCH] Make it possible to run tests without numpydoc
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Skip the three tests requiring numpydoc when it is not installed.
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For `skimage/_shared/tests/test_utils.py`, use the existing
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`have_numpydoc` constant.
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For `skimage/measure/tests/test_regionprops.py`, use the standard
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`pytest.importorskip()` function.
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This makes it possible to successfully run the test suite when
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`numpydoc` is not installed. This would be convenient for Gentoo
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since numpydoc is facing neverending test regressions (in its own test
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suite).
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---
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skimage/measure/tests/test_regionprops.py | 2 +-
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1 file changed, 1 insertion(+), 1 deletion(-)
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diff --git a/skimage/measure/tests/test_regionprops.py b/skimage/measure/tests/test_regionprops.py
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index 01a59dfbf..0b74d30a4 100644
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--- a/skimage/measure/tests/test_regionprops.py
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+++ b/skimage/measure/tests/test_regionprops.py
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@@ -4,7 +4,6 @@ import re
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import numpy as np
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import pytest
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import scipy.ndimage as ndi
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-import numpydoc
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from numpy.testing import (assert_allclose, assert_almost_equal,
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assert_array_almost_equal, assert_array_equal,
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assert_equal)
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@@ -1261,6 +1260,7 @@ def test_column_dtypes_correct():
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def test_all_documented_items_in_col_dtypes():
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+ numpydoc = pytest.importorskip("numpydoc")
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docstring = numpydoc.docscrape.FunctionDoc(regionprops)
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notes_lines = docstring['Notes']
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property_lines = filter(lambda line: line.startswith('**'), notes_lines)
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--
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2.43.0
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@@ -1,64 +0,0 @@
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# Copyright 1999-2024 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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DISTUTILS_USE_PEP517=meson-python
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DISTUTILS_EXT=1
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PYTHON_COMPAT=( python3_{10..12} )
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inherit distutils-r1 optfeature pypi
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DESCRIPTION="Image processing routines for SciPy"
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HOMEPAGE="
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https://scikit-image.org/
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https://github.com/scikit-image/scikit-image/
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https://pypi.org/project/scikit-image/
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"
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LICENSE="BSD"
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SLOT="0"
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KEYWORDS="~amd64 ~arm64 ~x86"
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PROPERTIES="test_network"
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RESTRICT="test"
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RDEPEND="
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>=dev-python/imageio-2.27[${PYTHON_USEDEP}]
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>=dev-python/lazy-loader-0.3[${PYTHON_USEDEP}]
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>=dev-python/networkx-2.8[${PYTHON_USEDEP}]
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>=dev-python/numpy-1.22[${PYTHON_USEDEP}]
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>=dev-python/pillow-9.0.1[${PYTHON_USEDEP}]
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>=dev-python/scipy-1.8[sparse(+),${PYTHON_USEDEP}]
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>=dev-python/tifffile-2022.8.12[${PYTHON_USEDEP}]
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"
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DEPEND="${RDEPEND}"
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BDEPEND="
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dev-python/cython[${PYTHON_USEDEP}]
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dev-python/packaging[${PYTHON_USEDEP}]
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"
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DOCS=( CONTRIBUTORS.txt RELEASE.txt )
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distutils_enable_tests pytest
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# There is a programmable error in your configuration file:
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#distutils_enable_sphinx doc/source dev-python/numpydoc dev-python/myst-parser
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PATCHES=(
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# https://github.com/scikit-image/scikit-image/pull/7307
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"${FILESDIR}/${P}-no-numpydoc.patch"
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)
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python_test() {
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rm -rf skimage || die
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epytest --pyargs skimage
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}
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pkg_postinst() {
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optfeature "FITS io capability" dev-python/astropy
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optfeature "GTK" dev-python/pygtk
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optfeature "Parallel computation" dev-python/dask
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optfeature "io plugin providing most standard formats" dev-python/imread
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optfeature "plotting" dev-python/matplotlib
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optfeature "wavelet transformations" dev-python/pywavelets
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optfeature "io plugin providing a wide variety of formats, including specialized formats using in medical imaging." dev-python/simpleitk
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}
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@@ -1,97 +0,0 @@
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# Copyright 1999-2024 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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DISTUTILS_USE_PEP517=meson-python
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DISTUTILS_EXT=1
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PYTHON_COMPAT=( python3_{10..12} )
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inherit distutils-r1 optfeature pypi
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TEST_DATA_COMMIT=15735b54e85c02427f07c71e6456723495034805
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DESCRIPTION="Image processing routines for SciPy"
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HOMEPAGE="
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https://scikit-image.org/
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https://github.com/scikit-image/scikit-image/
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https://pypi.org/project/scikit-image/
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"
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SRC_URI+="
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test? (
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https://gitlab.com/scikit-image/data/-/archive/${TEST_DATA_COMMIT}/scikit-image-data-${TEST_DATA_COMMIT}.tar.bz2
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)
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"
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LICENSE="BSD"
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SLOT="0"
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KEYWORDS="~amd64 ~arm64 ~x86"
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RDEPEND="
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>=dev-python/imageio-2.33[${PYTHON_USEDEP}]
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>=dev-python/lazy-loader-0.3[${PYTHON_USEDEP}]
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>=dev-python/networkx-2.8[${PYTHON_USEDEP}]
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>=dev-python/numpy-1.23[${PYTHON_USEDEP}]
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>=dev-python/pillow-9.1[${PYTHON_USEDEP}]
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>=dev-python/scipy-1.9[sparse(+),${PYTHON_USEDEP}]
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>=dev-python/tifffile-2022.8.12[${PYTHON_USEDEP}]
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"
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DEPEND="${RDEPEND}"
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BDEPEND="
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>=dev-python/cython-3.0.4[${PYTHON_USEDEP}]
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dev-python/packaging[${PYTHON_USEDEP}]
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test? (
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dev-python/pytest-localserver[${PYTHON_USEDEP}]
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)
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"
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DOCS=( CONTRIBUTORS.txt RELEASE.txt )
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# xdist does not work with this test suite
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distutils_enable_tests pytest
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# There is a programmable error in your configuration file:
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#distutils_enable_sphinx doc/source dev-python/numpydoc dev-python/myst-parser
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src_test() {
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# for some reason, upstream refetches data that's already in the tarball
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# sigh
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mkdir -p "${HOME}/.cache/scikit-image" || die
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mv skimage "${HOME}/.cache/scikit-image/${PV/_/}" || die
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# This is a true horror, sigh
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local cache_dir=${HOME}/.cache/scikit-image/${PV/_/}/data
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pushd "${WORKDIR}/data-${TEST_DATA_COMMIT}" >/dev/null || die
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cp Tests_besides_Equalize_Otsu/add18_entropy/rank_filters_tests_3d.npz \
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Tests_besides_Equalize_Otsu/gray_morph_output.npz \
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brain.tiff cells3d.tif eagle.png \
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"${cache_dir}/" || die
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cp Normal_Epidermis_and_Dermis_with_Intradermal_Nevus_10x.JPG "${cache_dir}"/skin.jpg || die
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cp pivchallenge/B/B001_1.tif "${cache_dir}"/pivchallenge-B-B001_1.tif || die
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cp pivchallenge/B/B001_2.tif "${cache_dir}"/pivchallenge-B-B001_2.tif || die
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cp kidney-tissue-fluorescence.tif "${cache_dir}"/kidney.tif || die
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cp lily-of-the-valley-fluorescence.tif "${cache_dir}"/lily.tif || die
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cp astronaut_rl.npy "${cache_dir}/../restoration/tests/" || die
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popd > /dev/null || die
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distutils-r1_src_test
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}
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python_test() {
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local EPYTEST_DESELECT=(
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# tests for downloading all data files, including these not needed
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# by any actual tests
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data/tests/test_data.py::test_download_all_with_pooch
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)
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local -x PYTEST_DISABLE_PLUGIN_AUTOLOAD=1
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epytest --pyargs skimage -p localserver -o xfail_strict=False
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}
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pkg_postinst() {
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optfeature "FITS io capability" dev-python/astropy
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optfeature "GTK" dev-python/pygtk
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optfeature "Parallel computation" dev-python/dask
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optfeature "io plugin providing most standard formats" dev-python/imread
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optfeature "plotting" dev-python/matplotlib
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optfeature "wavelet transformations" dev-python/pywavelets
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optfeature "io plugin providing a wide variety of formats, including specialized formats using in medical imaging." dev-python/simpleitk
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}
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