commit python-scikit-image for openSUSE:Factory

Hello community, here is the log from the commit of package python-scikit-image for openSUSE:Factory checked in at 2019-07-26 12:43:00 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/python-scikit-image (Old) and /work/SRC/openSUSE:Factory/.python-scikit-image.new.4126 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Package is "python-scikit-image" Fri Jul 26 12:43:00 2019 rev:6 rq:718626 version:0.15.0 Changes: -------- --- /work/SRC/openSUSE:Factory/python-scikit-image/python-scikit-image.changes 2019-01-21 11:03:26.547036121 +0100 +++ /work/SRC/openSUSE:Factory/.python-scikit-image.new.4126/python-scikit-image.changes 2019-07-26 12:43:07.097836454 +0200 @@ -1,0 +2,348 @@ +Tue Jul 23 17:22:19 UTC 2019 - Todd R + + + New Features + * N-dimensional flood fill, with tolerance + * Attribute operators + * Extension of register_translation to enable subpixel precision in 3D and + optionally disable error calculation + * unsharp mask filtering + * New options ``connectivity``, ``indices`` and ``allow_borders`` for + ``skimage.morphology.local_maxima`` and ``local_minima``. + * Image translation registration for masked data + (``skimage.feature.masked_register_translation``) + * Frangi (vesselness), Meijering (neuriteness), and Sato (tubeness) filters + * Allow float->float conversion of any range + * Let lower precision float arrays pass through ``img_as_float`` + * Lazy apply_parallel (allows optimization of dask array operations) + * Add range option for histogram. + * Add histogram matching + + Improvements + * Replace ``morphology.local_maxima`` with faster flood-fill based Cython + version + * ``skivi`` is now using ``qtpy`` for Qt4/Qt5/PySide/PySide2 compatibility (a + new optional dependency). + * Performance is now monitored by + `Airspeed Velocity https://asv.readthedocs.io/en/stable/`_. Benchmark + results will appear at https://pandas.pydata.org/speed/ + * Speed up inner loop of GLCM + * Allow tuple to define kernel in threshold_niblack and threshold_sauvola + * Add support for anisotropic blob detection in blob_log and blob_dog + + API Changes + * ``skimage.transform.seam_carve`` has been removed because the algorithm is + patented. + * Parameter ``dynamic_range`` in ``skimage.measure.compare_psnr`` has been + removed. Use parameter ``data_range`` instead. + * imageio is now the preferred plugin for reading and writing images. + * imageio is now a dependency of scikit-image. + * ``regular_grid`` now returns a tuple instead of a list for compatibility + with numpy 1.15 + * ``colorconv.separate_stains`` and ``colorconv.combine_stains`` now uses + base10 instead of the natural logarithm as discussed in issue #2995. + * Default value of ``clip_negative`` parameter in ``skimage.util.dtype_limits`` + has been set to ``False``. + * Default value of ``circle`` parameter in ``skimage.transform.radon`` + has been set to ``True``. + * Default value of ``circle`` parameter in ``skimage.transform.iradon`` + has been set to ``True``. + * Default value of ``mode`` parameter in ``skimage.transform.swirl`` + has been set to ``reflect``. + * Deprecated ``skimage.filters.threshold_adaptive`` has been removed. + Use ``skimage.filters.threshold_local`` instead. + * Default value of ``multichannel`` parameter in + ``skimage.restoration.denoise_bilateral`` has been set to ``False``. + * Default value of ``multichannel`` parameter in + ``skimage.restoration.denoise_nl_means`` has been set to ``False``. + * Default value of ``mode`` parameter in ``skimage.transform.resize`` + and ``skimage.transform.rescale`` has been set to ``reflect``. + * Default value of ``anti_aliasing`` parameter in ``skimage.transform.resize`` + and ``skimage.transform.rescale`` has been set to ``True``. + * Removed the ``skimage.test`` function. This functionality can be achieved + by calling ``pytest`` directly. + * ``morphology.local_maxima`` now returns a boolean array + + Bugfixes + * Correct bright ridge detection for Frangi filter + * ``skimage.morphology.local_maxima`` and ``skimage.morphology.local_minima`` + no longer raise an error if any dimension of the image is smaller 3 and + the keyword ``allow_borders`` was false. + * ``skimage.morphology.local_maxima`` and ``skimage.morphology.local_minima`` + will return a boolean array instead of an array of 0s and 1s if the + parameter ``indices`` was false. + * When ``compare_ssim`` is used with ``gaussian_weights`` set to True, the + boundary crop used when computing the mean structural similarity will now + exactly match the width of the Gaussian used. The Gaussian filter window is + also now truncated at 3.5 rather than 4.0 standard deviations to exactly match + the original publication on the SSIM. These changes should produce only a very + small change in the computed SSIM value. There is no change to the existing + behavior when ``gaussian_weights`` is False. + * erroneous use of cython wrap around + * Speed up block reduce by providing the appropriate parameters to numpy + * Add urllib.request again + * Repeat pixels in reflect mode when image has dimension 1 + * Improve Li thresholding + + Deprecations + * Python 2 support has been dropped. Users should have Python >= 3.5. + * ``skimage.util.montage2d`` has been removed. Use ``skimage.util.montage`` instead. + * ``skimage.novice`` is deprecated and will be removed in 0.16. + * ``skimage.transform.resize`` and ``skimage.transform.rescale`` option + ``anti_aliasing`` has been enabled by default. + * ``regionprops`` will use row-column coordinates in 0.16. You can start + using them now with ``regionprops(..., coordinates='rc')``. You can silence + warning messages, and retain the old behavior, with + ``regionprops(..., coordinates='xy')``. However, that option will go away + in 0.16 and result in an error. This change has a number of consequences. + Specifically, the "orientation" region property will measure the + anticlockwise angle from a *vertical* line, i.e. from the vector (1, 0) in + row-column coordinates. + * ``skimage.morphology.remove_small_holes`` ``min_size`` argument is deprecated + and will be removed in 0.16. Use ``area_threshold`` instead. + * ``skimage.filters.median`` will change behavior in the future to have an + identical behavior as ``scipy.ndimage.median_filter``. This behavior can be + set already using ``behavior='ndimage'``. In 0.16, it will be the default + behavior and removed in 0.17 as well as the parameter of the previous + behavior (i.e., ``mask``, ``shift_x``, ``shift_y``) will be removed. + + Documentation improvements + * Correct rotate method's center parameter doc + * Add Sphinx copybutton + * Add glossary to the documentation + * Add image of retina to our data + * Add microaneurysms() to gallery + * Better document remove_small_objects behaviour: int vs bool + * Linking preserve_range parameter calls to docs + * Update the documentation regarding datalocality + * Specify conda-forge channel for scikit-image conda install + * Turn DOIs into web links in docstrings + * Update documentation for regionprops + * DOC: Improve the RANSAC gallery example + * DOC: "feature.peak_local_max" : explanation of multiple same-intensity peaks returned by the function; added details on ``exclude_border`` parameter + + Improvements + * MNT: handle a deprecation warning for np.linspace and floats for the num parameter + * TST: numpy empty arrays are not inherently Falsy + * handle warning in scipy cdist for unused parameters + * MNT: don't use filter_warnings in test suite. + * Add doc notes on setting up the build environment + * Release the GIL in numerous cython functions + * Cython touchups to use float32 and float64 + * rank_filters: Change how the bitdepth and max_bin are computed to ensure exact warnings. + * Rank: Optimize OTSU filter + * Rank - Fix rank entropy and OTSU tests + * delay importing pyplot in manual segmentation + * Get rid of the requirements-parser dependency + * filter warning from ``correct_mesh_orientation`` in tests + * cloudpickle is really a doc dependency, not a core one + * optional dependencies on pip + * Fewer test warnings in 3.7 + * collections.abc nit + * Streamlined issue template + * Tighten the PR Template + * Use language level to 3 in cython for future compatibility + * Update ISSUE_TEMPLATE.md with info about numpy and skimage versions + * Use relative imports for many cython modules + * Pass tests that don't raise floating point exceptions on arm with soft-fp + + Other improvements + * BUG: Fix greycoprops correlation always returning 1 + * Add section on API discovery via ``skimage.lookfor`` + * Speedup 2D warping for affine transformations + * Credit Reviewers in Release Notes + * Added small galleries in the API + * Use skimage gaussian filter to avoid integer rounding artifacts + * Remove Python 2 compatibility + * Add ``rectangle_perimeter`` feature to ``skimage.draw`` + * Update installation instructions to reference existing requirements specification + * Updated release notes with pre 0.13.1 phase + * Release guidelines update + * Ensure we are installing with / running on Python 3 + * Hide warnings in test_unsharp_mask + * Process 0.15 deprecations + * Documentation: always use dev branch javascript + * Add initial airspeed velocity (asv) framework + * Supress warnings for flatten during io testing + * Recover from exceptions in filters.try_all_threshold() + * Fix skimage.test() to run the unittests + * skivi: Use qtpy to handle different Qt versions + * Refactor python version checking. + * Move data_dir to within ``data/__init__.py`` + * Move the definition of lookfor out of __init__.py + * Normalize the package number to PEP440 + * Remove skimage.test as it was never used. + * Added a message about qtpy to the INSTALL.rst + * Regression fix: Travis should fail if tests fail + * Set minimum cython version to ``0.23.4`` + * Add rgba2rgb to API docs + * Minor doc formatting fixes in video.rst + * Decrease the verbosity of the testing + * Speedup rgb2gray using matrix multiply + * Add instructions for meeseeksdev to PR template + * Remove installation instructions for video packages + * Big image labeling fix + * Handle dask deprecation in cycle_spin + * Fix Qt viewer painttool indexing + * build_versions.py is no longer hard coded. + * Remove dtype constructor call in exposure.rescale_intensity + * Various updates to the ASV benchmarks + * Add a link to stack overflow on github README + * MAINT: remove encoding information in file headers (python 3) + * Build tools: Dedicate a --pre build in appveyor and ensure other builds don't download --pre + * Fix the human readable error message on a bad build. + * Respect input array type in apply_parallel by default + * Travis cleanup pip commands + * Add benchmarks for morphology.watershed + * Correcte docstring formatting so that code block is displayed as code + * Defer skimage.io import of matplotlib.pyplot until needed + * Add benchmark for Sobel filters + * Remove cython md5 hashing since it breaks the build process + * Fix typo in documentation. + * Issue 3156: skimage/__init__.py Update docstring and fix import * + * Object detector module + * Do not import submodules while building + * Add benchmark suite for canny ++++ 151 more lines (skipped) ++++ between /work/SRC/openSUSE:Factory/python-scikit-image/python-scikit-image.changes ++++ and /work/SRC/openSUSE:Factory/.python-scikit-image.new.4126/python-scikit-image.changes Old: ---- scikit-image-0.14.2.tar.gz New: ---- fix_numpy_matrix_warning_test.patch scikit-image-0.15.0.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ python-scikit-image.spec ++++++ --- /var/tmp/diff_new_pack.QEdtUg/_old 2019-07-26 12:43:10.901834824 +0200 +++ /var/tmp/diff_new_pack.QEdtUg/_new 2019-07-26 12:43:10.901834824 +0200 @@ -17,17 +17,17 @@ %{?!python_module:%define python_module() python-%{**} python3-%{**}} -%define oldpython python -# Test discovery issues -%bcond_with tests +%define skip_python2 1 Name: python-scikit-image -Version: 0.14.2 +Version: 0.15.0 Release: 0 Summary: Collection of algorithms for image processing in Python License: BSD-3-Clause Group: Productivity/Scientific/Other URL: http://scikit-image.org/ Source0: https://files.pythonhosted.org/packages/source/s/scikit-image/scikit-image-%{version}.tar.gz +# PATCH-FEATURE-UPSTREAM fix_numpy_matrix_warning_test.patch -- gh#scikit-image/scikit-image#3869 +Patch0: fix_numpy_matrix_warning_test.patch BuildRequires: %{python_module Cython >= 0.23.4} BuildRequires: %{python_module devel} BuildRequires: %{python_module numpy-devel >= 1.11} @@ -53,19 +53,15 @@ Recommends: python-imread Recommends: python-pyamg Recommends: python-qt4 -%if %{with tests} -# Runtime dependencies +# SECTION test requirements BuildRequires: %{python_module Pillow >= 2.1.0} BuildRequires: %{python_module PyWavelets >= 0.4.0} BuildRequires: %{python_module matplotlib >= 1.3.1} BuildRequires: %{python_module networkx >= 1.8} BuildRequires: %{python_module nose} BuildRequires: %{python_module pytest} -%endif -%ifpython2 -Provides: %{oldpython}-scikits-image = %{version} -Obsoletes: %{oldpython}-scikits-image < %{version} -%endif +BuildRequires: %{python_module pytest-localserver} +# /SECTION %python_subpackages %description @@ -74,6 +70,7 @@ %prep %setup -q -n scikit-image-%{version} +%patch0 -p1 %build %python_build @@ -90,20 +87,16 @@ %preun %python_uninstall_alternative skivi -%if %{with tests} %check -mkdir tester -pushd tester +mv skimage skimage_temp %{python_expand export PYTHONPATH=%{buildroot}%{$python_sitearch} -py.test-%{$python_bin_suffix} -v skimage +py.test-%{$python_bin_suffix} -v %{buildroot}%{$python_sitearch}/skimage } -popd -rm -r tester -%endif +mv skimage_temp skimage %files %{python_files} %license LICENSE.txt -%doc CONTRIBUTING.txt CONTRIBUTORS.txt TODO.txt +%doc CONTRIBUTORS.txt TODO.txt %python_alternative %{_bindir}/skivi %{python_sitearch}/skimage/ %{python_sitearch}/scikit_image-%{version}-py*.egg-info ++++++ fix_numpy_matrix_warning_test.patch ++++++

From 0fc57bba3ce353d48801f435ff4eb422183c4703 Mon Sep 17 00:00:00 2001 From: Mark Harfouche Date: Tue, 30 Apr 2019 09:18:19 -0400 Subject: Fixup the test for the warnings for scipy 1.3 and the matrix subsclass

--- skimage/segmentation/tests/test_random_walker.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/skimage/segmentation/tests/test_random_walker.py b/skimage/segmentation/tests/test_random_walker.py index f2f731cdc7..43ddcec523 100644 --- a/skimage/segmentation/tests/test_random_walker.py +++ b/skimage/segmentation/tests/test_random_walker.py @@ -15,7 +15,7 @@ PYAMG_MISSING_WARNING = r'pyamg|\A\Z' PYAMG_OR_SCIPY_WARNING = SCIPY_RANK_WARNING + '|' + PYAMG_MISSING_WARNING -if (Version(np.__version__) >= '1.15.0'): +if Version(np.__version__) >= '1.15.0' and Version(scipy.__version__) < '1.3': NUMPY_MATRIX_WARNING = 'matrix subclass' else: NUMPY_MATRIX_WARNING = None @@ -352,7 +352,7 @@ def test_trivial_cases(): output_labels = random_walker(img, markers) assert np.all(output_labels[markers == 1] == 1) # Here 0-labeled pixels could not be determined (no connexion to seed) - assert np.all(output_labels[markers == 0] == -1) + assert np.all(output_labels[markers == 0] == -1) with expected_warnings(["Returning provided labels"]): test = random_walker(img, markers, return_full_prob=True) ++++++ scikit-image-0.14.2.tar.gz -> scikit-image-0.15.0.tar.gz ++++++ /work/SRC/openSUSE:Factory/python-scikit-image/scikit-image-0.14.2.tar.gz /work/SRC/openSUSE:Factory/.python-scikit-image.new.4126/scikit-image-0.15.0.tar.gz differ: char 5, line 1