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 <[email protected]>
+
+ + 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 <[email protected]>
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
