Mailman 3 December 2020 - scikit-image

Important updates to scipy.ndimage
by Stefan van der Walt 31 Dec '20

31 Dec '20

Please see below for the SciPy 1.6 release notes. Greg did a great job on fixing and reconciliating boundary handling in ndimage (this has been on the roadmap for many years, and closes a whole slew of issues!). Best regards, Stéfan ----- Original message ----- From: Tyler Reddy <tyler.je.reddy(a)gmail.com> To: SciPy Developers List <scipy-dev(a)python.org>, Discussion of Numerical Python <numpy-discussion(a)python.org>, python-announce-list(a)python.org Subject: [SciPy-Dev] ANN: SciPy 1.6.0 Date: Thursday, December 31, 2020 07:58 Hi all, On behalf of the SciPy development team I'm pleased to announce the release of SciPy 1.6.0. Sources and binary wheels can be found at: https://pypi.org/project/scipy/ and at: https://github.com/scipy/scipy/releases/tag/v1.6.0 One of a few ways to install this release with pip: pip install scipy==1.6.0 ===================== SciPy 1.6.0 Release Notes ===================== SciPy 1.6.0 is the culmination of 6 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with ``python -Wd`` and check for ``DeprecationWarning`` s). Our development attention will now shift to bug-fix releases on the 1.6.x branch, and on adding new features on the master branch. This release requires Python 3.7+ and NumPy 1.16.5 or greater. For running on PyPy, PyPy3 6.0+ is required. Highlights of this release --------------------------------- - `scipy.ndimage` improvements: Fixes and ehancements to boundary extension modes for interpolation functions. Support for complex-valued inputs in many filtering and interpolation functions. New ``grid_mode`` option for `scipy.ndimage.zoom` to enable results consistent with scikit-image's ``rescale``. - `scipy.optimize.linprog` has fast, new methods for large, sparse problems from the ``HiGHS`` library. - `scipy.stats` improvements including new distributions, a new test, and enhancements to existing distributions and tests New features ========== `scipy.special` improvements --------------------------------------- `scipy.special` now has improved support for 64-bit ``LAPACK`` backend `scipy.odr` improvements ---------------------------------- `scipy.odr` now has support for 64-bit integer ``BLAS`` `scipy.odr.ODR` has gained an optional ``overwrite`` argument so that existing files may be overwritten. `scipy.integrate` improvements ------------------------------------------ Some renames of functions with poor names were done, with the old names retained without being in the reference guide for backwards compatibility reasons: - ``integrate.simps`` was renamed to ``integrate.simpson`` - ``integrate.trapz`` was renamed to ``integrate.trapezoid`` - ``integrate.cumtrapz`` was renamed to ``integrate.cumulative_trapezoid`` `scipy.cluster` improvements --------------------------------------- `scipy.cluster.hierarchy.DisjointSet` has been added for incremental connectivity queries. `scipy.cluster.hierarchy.dendrogram` return value now also includes leaf color information in `leaves_color_list`. `scipy.interpolate` improvements -------------------------------------------- `scipy.interpolate.interp1d` has a new method ``nearest-up``, similar to the existing method ``nearest`` but rounds half-integers up instead of down. `scipy.io` improvements -------------------------------- Support has been added for reading arbitrary bit depth integer PCM WAV files from 1- to 32-bit, including the commonly-requested 24-bit depth. `scipy.linalg` improvements ------------------------------------- The new function `scipy.linalg.matmul_toeplitz` uses the FFT to compute the product of a Toeplitz matrix with another matrix. `scipy.linalg.sqrtm` and `scipy.linalg.logm` have performance improvements thanks to additional Cython code. Python ``LAPACK`` wrappers have been added for ``pptrf``, ``pptrs``, ``ppsv``, ``pptri``, and ``ppcon``. `scipy.linalg.norm` and the ``svd`` family of functions will now use 64-bit integer backends when available. `scipy.ndimage` improvements ------------------------------------------ `scipy.ndimage.convolve`, `scipy.ndimage.correlate` and their 1d counterparts now accept both complex-valued images and/or complex-valued filter kernels. All convolution-based filters also now accept complex-valued inputs (e.g. ``gaussian_filter``, ``uniform_filter``, etc.). Multiple fixes and enhancements to boundary handling were introduced to `scipy.ndimage` interpolation functions (i.e. ``affine_transform``, ``geometric_transform``, ``map_coordinates``, ``rotate``, ``shift``, ``zoom``). A new boundary mode, ``grid-wrap`` was added which wraps images periodically, using a period equal to the shape of the input image grid. This is in contrast to the existing ``wrap`` mode which uses a period that is one sample smaller than the original signal extent along each dimension. A long-standing bug in the ``reflect`` boundary condition has been fixed and the mode ``grid-mirror`` was introduced as a synonym for ``reflect``. A new boundary mode, ``grid-constant`` is now available. This is similar to the existing ndimage ``constant`` mode, but interpolation will still performed at coordinate values outside of the original image extent. This ``grid-constant`` mode is consistent with OpenCV's ``BORDER_CONSTANT`` mode and scikit-image's ``constant`` mode. Spline pre-filtering (used internally by ``ndimage`` interpolation functions when ``order >= 2``), now supports all boundary modes rather than always defaulting to mirror boundary conditions. The standalone functions ``spline_filter`` and ``spline_filter1d`` have analytical boundary conditions that match modes ``mirror``, ``grid-wrap`` and ``reflect``. `scipy.ndimage` interpolation functions now accept complex-valued inputs. In this case, the interpolation is applied independently to the real and imaginary components. The ``ndimage`` tutorials (https://docs.scipy.org/doc/scipy/reference/tutorial/ndimage.html) have been updated with new figures to better clarify the exact behavior of all of the interpolation boundary modes. `scipy.ndimage.zoom` now has a ``grid_mode`` option that changes the coordinate of the center of the first pixel along an axis from 0 to 0.5. This allows resizing in a manner that is consistent with the behavior of scikit-image's ``resize`` and ``rescale`` functions (and OpenCV's ``cv2.resize``). `scipy.optimize` improvements ----------------------------------------- `scipy.optimize.linprog` has fast, new methods for large, sparse problems from the ``HiGHS`` C++ library. ``method='highs-ds'`` uses a high performance dual revised simplex implementation (HSOL), ``method='highs-ipm'`` uses an interior-point method with crossover, and ``method='highs'`` chooses between the two automatically. These methods are typically much faster and often exceed the accuracy of other ``linprog`` methods, so we recommend explicitly specifying one of these three method values when using ``linprog``. `scipy.optimize.quadratic_assignment` has been added for approximate solution of the quadratic assignment problem. `scipy.optimize.linear_sum_assignment` now has a substantially reduced overhead for small cost matrix sizes `scipy.optimize.least_squares` has improved performance when the user provides the jacobian as a sparse jacobian already in ``csr_matrix`` format `scipy.optimize.linprog` now has an ``rr_method`` argument for specification of the method used for redundancy handling, and a new method for this purpose is available based on the interpolative decomposition approach. `scipy.signal` improvements -------------------------------------- `scipy.signal.gammatone` has been added to design FIR or IIR filters that model the human auditory system. `scipy.signal.iircomb` has been added to design IIR peaking/notching comb filters that can boost/attenuate a frequency from a signal. `scipy.signal.sosfilt` performance has been improved to avoid some previously- observed slowdowns `scipy.signal.windows.taylor` has been added--the Taylor window function is commonly used in radar digital signal processing `scipy.signal.gauss_spline` now supports ``list`` type input for consistency with other related SciPy functions `scipy.signal.correlation_lags` has been added to allow calculation of the lag/ displacement indices array for 1D cross-correlation. `scipy.sparse` improvements --------------------------------------- A solver for the minimum weight full matching problem for bipartite graphs, also known as the linear assignment problem, has been added in `scipy.sparse.csgraph.min_weight_full_bipartite_matching`. In particular, this provides functionality analogous to that of `scipy.optimize.linear_sum_assignment`, but with improved performance for sparse inputs, and the ability to handle inputs whose dense representations would not fit in memory. The time complexity of `scipy.sparse.block_diag` has been improved dramatically from quadratic to linear. `scipy.sparse.linalg` improvements ----------------------------------------------- The vendored version of ``SuperLU`` has been updated `scipy.fft` improvements -------------------------------- The vendored ``pocketfft`` library now supports compiling with ARM neon vector extensions and has improved thread pool behavior. `scipy.spatial` improvements --------------------------------------- The python implementation of ``KDTree`` has been dropped and ``KDTree`` is now implemented in terms of ``cKDTree``. You can now expect ``cKDTree``-like performance by default. This also means ``sys.setrecursionlimit`` no longer needs to be increased for querying large trees. ``transform.Rotation`` has been updated with support for Modified Rodrigues Parameters alongside the existing rotation representations (PR gh-12667). `scipy.spatial.transform.Rotation` has been partially cythonized, with some performance improvements observed `scipy.spatial.distance.cdist` has improved performance with the ``minkowski`` metric, especially for p-norm values of 1 or 2. `scipy.stats` improvements ------------------------------------ New distributions have been added to `scipy.stats`: - The asymmetric Laplace continuous distribution has been added as `scipy.stats.laplace_asymmetric`. - The negative hypergeometric distribution has been added as `scipy.stats.nhypergeom`. - The multivariate t distribution has been added as `scipy.stats.multivariate_t`. - The multivariate hypergeometric distribution has been added as `scipy.stats.multivariate_hypergeom`. The ``fit`` method has been overridden for several distributions (``laplace``, ``pareto``, ``rayleigh``, ``invgauss``, ``logistic``, ``gumbel_l``, ``gumbel_r``); they now use analytical, distribution-specific maximum likelihood estimation results for greater speed and accuracy than the generic (numerical optimization) implementation. The one-sample Cramér-von Mises test has been added as `scipy.stats.cramervonmises`. An option to compute one-sided p-values was added to `scipy.stats.ttest_1samp`, `scipy.stats.ttest_ind_from_stats`, `scipy.stats.ttest_ind` and `scipy.stats.ttest_rel`. The function `scipy.stats.kendalltau` now has an option to compute Kendall's tau-c (also known as Stuart's tau-c), and support has been added for exact p-value calculations for sample sizes ``> 171``. `stats.trapz` was renamed to `stats.trapezoid`, with the former name retained as an alias for backwards compatibility reasons. The function `scipy.stats.linregress` now includes the standard error of the intercept in its return value. The ``_logpdf``, ``_sf``, and ``_isf`` methods have been added to `scipy.stats.nakagami`; ``_sf`` and ``_isf`` methods also added to `scipy.stats.gumbel_r` The ``sf`` method has been added to `scipy.stats.levy` and `scipy.stats.levy_l` for improved precision. `scipy.stats.binned_statistic_dd` performance improvements for the following computed statistics: ``max``, ``min``, ``median``, and ``std``. We gratefully acknowledge the Chan-Zuckerberg Initiative Essential Open Source Software for Science program for supporting many of these improvements to `scipy.stats`. Deprecated features ================ `scipy.spatial` changes ------------------------------- Calling ``KDTree.query`` with ``k=None`` to find all neighbours is deprecated. Use ``KDTree.query_ball_point`` instead. ``distance.wminkowski`` was deprecated; use ``distance.minkowski`` and supply weights with the ``w`` keyword instead. Backwards incompatible changes ========================== `scipy` changes --------------------- Using `scipy.fft` as a function aliasing ``numpy.fft.fft`` was removed after being deprecated in SciPy ``1.4.0``. As a result, the `scipy.fft` submodule must be explicitly imported now, in line with other SciPy subpackages. `scipy.signal` changes ------------------------------- The output of ``decimate``, ``lfilter_zi``, ``lfiltic``, ``sos2tf``, and ``sosfilt_zi`` have been changed to match ``numpy.result_type`` of their inputs. The window function ``slepian`` was removed. It had been deprecated since SciPy ``1.1``. `scipy.spatial` changes ------------------------------- ``cKDTree.query`` now returns 64-bit rather than 32-bit integers on Windows, making behaviour consistent between platforms (PR gh-12673). `scipy.stats` changes ----------------------------- The ``frechet_l`` and ``frechet_r`` distributions were removed. They were deprecated since SciPy ``1.0``. Other changes ============= ``setup_requires`` was removed from ``setup.py``. This means that users invoking ``python setup.py install`` without having numpy already installed will now get an error, rather than having numpy installed for them via ``easy_install``. This install method was always fragile and problematic, users are encouraged to use ``pip`` when installing from source. - Fixed a bug in `scipy.optimize.dual_annealing` ``accept_reject`` calculation that caused uphill jumps to be accepted less frequently. - The time required for (un)pickling of `scipy.stats.rv_continuous`, `scipy.stats.rv_discrete`, and `scipy.stats.rv_frozen` has been significantly reduced (gh12550). Inheriting subclasses should note that ``__setstate__`` no longer calls ``__init__`` upon unpickling. Authors ======= * @endolith * @vkk800 * aditya + * George Bateman + * Christoph Baumgarten * Peter Bell * Tobias Biester + * Keaton J. Burns + * Evgeni Burovski * Rüdiger Busche + * Matthias Bussonnier * Dominic C + * Corallus Caninus + * CJ Carey * Thomas A Caswell * chapochn + * Lucía Cheung * Zach Colbert + * Coloquinte + * Yannick Copin + * Devin Crowley + * Terry Davis + * Michaël Defferrard + * devonwp + * Didier + * divenex + * Thomas Duvernay + * Eoghan O'Connell + * Gökçen Eraslan * Kristian Eschenburg + * Ralf Gommers * Thomas Grainger + * GreatV + * Gregory Gundersen + * h-vetinari + * Matt Haberland * Mark Harfouche + * He He + * Alex Henrie * Chun-Ming Huang + * Martin James McHugh III + * Alex Izvorski + * Joey + * ST John + * Jonas Jonker + * Julius Bier Kirkegaard * Marcin Konowalczyk + * Konrad0 * Sam Van Kooten + * Sergey Koposov + * Peter Mahler Larsen * Eric Larson * Antony Lee * Gregory R. Lee * Loïc Estève * Jean-Luc Margot + * MarkusKoebis + * Nikolay Mayorov * G. D. McBain * Andrew McCluskey + * Nicholas McKibben * Sturla Molden * Denali Molitor + * Eric Moore * Shashaank N + * Prashanth Nadukandi + * nbelakovski + * Andrew Nelson * Nick + * Nikola Forró + * odidev * ofirr + * Sambit Panda * Dima Pasechnik * Tirth Patel + * Matti Picus * Paweł Redzyński + * Vladimir Philipenko + * Philipp Thölke + * Ilhan Polat * Eugene Prilepin + * Vladyslav Rachek * Ram Rachum + * Tyler Reddy * Martin Reinecke + * Simon Segerblom Rex + * Lucas Roberts * Benjamin Rowell + * Eli Rykoff + * Atsushi Sakai * Moritz Schulte + * Daniel B. Smith * Steve Smith + * Jan Soedingrekso + * Victor Stinner + * Jose Storopoli + * Diana Sukhoverkhova + * Søren Fuglede Jørgensen * taoky + * Mike Taves + * Ian Thomas + * Will Tirone + * Frank Torres + * Seth Troisi * Ronald van Elburg + * Hugo van Kemenade * Paul van Mulbregt * Saul Ivan Rivas Vega + * Pauli Virtanen * Jan Vleeshouwers * Samuel Wallan * Warren Weckesser * Ben West + * Eric Wieser * WillTirone + * Levi John Wolf + * Zhiqing Xiao * Rory Yorke + * Yun Wang (Maigo) + * Egor Zemlyanoy + * ZhihuiChen0903 + * Jacob Zhong + A total of 122 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete. Issues closed for 1.6.0 ------------------------------- * `#1323 <https://github.com/scipy/scipy/issues/1323>`__: ndimage.shift destroys data from edges (Trac #796) * `#1892 <https://github.com/scipy/scipy/issues/1892>`__: using rptfile= with an existing file causes a Fortran runtime... * `#1903 <https://github.com/scipy/scipy/issues/1903>`__: ndimage.rotate misses some values (Trac #1378) * `#1930 <https://github.com/scipy/scipy/issues/1930>`__: scipy.io.wavfile should be able to read 24 bit signed wave (Trac... * `#3158 <https://github.com/scipy/scipy/issues/3158>`__: Odd casting behaviour of signal.filtfilt * `#3203 <https://github.com/scipy/scipy/issues/3203>`__: interpolation.zoom incorrect output for certain cases * `#3645 <https://github.com/scipy/scipy/issues/3645>`__: BUG: stats: mstats.pearsonr calculation is wrong if the masks... * `#3665 <https://github.com/scipy/scipy/issues/3665>`__: Return Bunch objects from stats functions * `#4922 <https://github.com/scipy/scipy/issues/4922>`__: unexpected zero output values from zoom * `#5202 <https://github.com/scipy/scipy/issues/5202>`__: BUG: stats: Spurious warnings from the pdf method of several... * `#5223 <https://github.com/scipy/scipy/issues/5223>`__: Zoom does not return the same values when resizing a sub-array... * `#5396 <https://github.com/scipy/scipy/issues/5396>`__: scipy.spatial.distance.pdist documention bug * `#5489 <https://github.com/scipy/scipy/issues/5489>`__: ValueError: failed to create intent(cache|hide)|optional array--... * `#6096 <https://github.com/scipy/scipy/issues/6096>`__: loadmat drops dtype of empty arrays when squeeze_me=True * `#6713 <https://github.com/scipy/scipy/issues/6713>`__: sicpy.ndimage.zoom returns artefacts and boundaries in some cases * `#7125 <https://github.com/scipy/scipy/issues/7125>`__: Impossible to know number of dimensions in c function used by... * `#7324 <https://github.com/scipy/scipy/issues/7324>`__: scipy.ndimage.zoom bad interpolation when downsampling (zoom... * `#8131 <https://github.com/scipy/scipy/issues/8131>`__: BUG: geometric_transform wrap mode possible bug * `#8163 <https://github.com/scipy/scipy/issues/8163>`__: LSMR fails on some random values when providing an x0 * `#8210 <https://github.com/scipy/scipy/issues/8210>`__: Why should I choose order > 1 for scipy.ndimage.zoom? * `#8465 <https://github.com/scipy/scipy/issues/8465>`__: Unexpected behavior with reflect mode of ndimage.rotate * `#8776 <https://github.com/scipy/scipy/issues/8776>`__: cdist behavior with Minkowsky and np.inf * `#9168 <https://github.com/scipy/scipy/issues/9168>`__: documentation of pearson3 in scipy.stats unclear * `#9223 <https://github.com/scipy/scipy/issues/9223>`__: Faster implementation of scipy.sparse.block_diag * `#9476 <https://github.com/scipy/scipy/issues/9476>`__: Invalid index in signal.medfilt2d's QUICK_SELECT * `#9857 <https://github.com/scipy/scipy/issues/9857>`__: scipy.odr.Output.sd_beta is not standard error * `#9865 <https://github.com/scipy/scipy/issues/9865>`__: Strange behavior of \`ndimage.shift\` and \`ndimage.affine_transform\` * `#10042 <https://github.com/scipy/scipy/issues/10042>`__: Consider support for multivariate student-t distribution? * `#10134 <https://github.com/scipy/scipy/issues/10134>`__: gausshyper distribution accepts invalid parameters * `#10179 <https://github.com/scipy/scipy/issues/10179>`__: str+bytes concatenation error in test_lapack.py * `#10216 <https://github.com/scipy/scipy/issues/10216>`__: cKDTree.query_ball_point speed regression * `#10463 <https://github.com/scipy/scipy/issues/10463>`__: ENH: vectorize scipy.fft for more CPU architectures * `#10593 <https://github.com/scipy/scipy/issues/10593>`__: Rename \`sum\` ndimage function * `#10595 <https://github.com/scipy/scipy/issues/10595>`__: scipy.stats.ttest_1samp should support alternative hypothesis * `#10610 <https://github.com/scipy/scipy/issues/10610>`__: ndimage.interpolation.spline_filter1d default value of mode * `#10620 <https://github.com/scipy/scipy/issues/10620>`__: ndimage.interpolation.zoom() option to work like skimage.transform.resize() * `#10711 <https://github.com/scipy/scipy/issues/10711>`__: Array Shapes Not Aligned Bug in scipy.optimize._lsq.lsq_linear.py * `#10782 <https://github.com/scipy/scipy/issues/10782>`__: BUG: optimize: methods unknown to \`scipy.optimize.show_options\` * `#10892 <https://github.com/scipy/scipy/issues/10892>`__: Possible typo in an equation of optimize/dual_annealing * `#11020 <https://github.com/scipy/scipy/issues/11020>`__: signal.fftconvolve return a tuple including lag information * `#11093 <https://github.com/scipy/scipy/issues/11093>`__: scipy.interpolate.interp1d can not handle datetime64 * `#11170 <https://github.com/scipy/scipy/issues/11170>`__: Use manylinux2014 to get aarch64/ppc64le support * `#11186 <https://github.com/scipy/scipy/issues/11186>`__: BUG: stats: pearson3 CDF and SF functions incorrect when skew... * `#11366 <https://github.com/scipy/scipy/issues/11366>`__: DeprecationWarning due to invalid escape sequences * `#11403 <https://github.com/scipy/scipy/issues/11403>`__: Optimize raises "ValueError: \`x0\` violates bound constraints"... * `#11558 <https://github.com/scipy/scipy/issues/11558>`__: ENH: IIR comb filter * `#11559 <https://github.com/scipy/scipy/issues/11559>`__: BUG: iirdesign doesn't fail for frequencies above Nyquist * `#11567 <https://github.com/scipy/scipy/issues/11567>`__: scipy.signal.iirdesign doesn't check consistency of wp and ws... * `#11654 <https://github.com/scipy/scipy/issues/11654>`__: ENH: Add Negative Hypergeometric Distribution * `#11720 <https://github.com/scipy/scipy/issues/11720>`__: BUG: stats: wrong shape from median_absolute_deviation for arrays... * `#11746 <https://github.com/scipy/scipy/issues/11746>`__: BUG: stats: pearson3 returns size 1 arrays where other distributions... * `#11756 <https://github.com/scipy/scipy/issues/11756>`__: Improve and fix \*Spline docstrings and code * `#11758 <https://github.com/scipy/scipy/issues/11758>`__: BUG: of scipy.interpolate.CubicSpline when \`bc_type' is set... * `#11925 <https://github.com/scipy/scipy/issues/11925>`__: MAINT: remove character encoding check in CI? * `#11963 <https://github.com/scipy/scipy/issues/11963>`__: Test failures - TestLinprogIPSparseCholmod * `#12102 <https://github.com/scipy/scipy/issues/12102>`__: incorrect first moment of non central t-distribution * `#12113 <https://github.com/scipy/scipy/issues/12113>`__: scipy.stats.poisson docs for rate = 0 * `#12152 <https://github.com/scipy/scipy/issues/12152>`__: ENH: signal.gauss_spline should accept a list * `#12157 <https://github.com/scipy/scipy/issues/12157>`__: BUG: Iteration index initialisation is wrong in scipy.optimize.linesearch.scalar_search_wolfe2 * `#12162 <https://github.com/scipy/scipy/issues/12162>`__: Storing Rotation object in NumPy array returns an array with... * `#12176 <https://github.com/scipy/scipy/issues/12176>`__: cannot modify the slice of an array returned by \`wavfile.read\` * `#12190 <https://github.com/scipy/scipy/issues/12190>`__: retrieve leave colors from dendrogram * `#12196 <https://github.com/scipy/scipy/issues/12196>`__: PERF: scipy.linalg.pinv is very slow compared to numpy.linalg.pinv * `#12222 <https://github.com/scipy/scipy/issues/12222>`__: Interpolating categorical data (interp1d) * `#12231 <https://github.com/scipy/scipy/issues/12231>`__: Is the p-value of the Kruskal-Wallis test two-sided? * `#12249 <https://github.com/scipy/scipy/issues/12249>`__: ENH: least_squares: should not re-instanciate csr_matrix if already... * `#12264 <https://github.com/scipy/scipy/issues/12264>`__: DOC: optimize: linprog method-specific function signature * `#12290 <https://github.com/scipy/scipy/issues/12290>`__: DOC: Convex Hull areas are actually perimeters for 2-dimensional... * `#12308 <https://github.com/scipy/scipy/issues/12308>`__: integrate.solve_ivp with DOP853 method fails when yDot = 0 * `#12326 <https://github.com/scipy/scipy/issues/12326>`__: BUG: stats.exponnorm.pdf returns 0 for small K * `#12337 <https://github.com/scipy/scipy/issues/12337>`__: scipy.sparse.linalg.eigsh documentation is misleading * `#12339 <https://github.com/scipy/scipy/issues/12339>`__: scipy.io.wavfile.write documentation has wrong example * `#12340 <https://github.com/scipy/scipy/issues/12340>`__: sparse.lil_matrix.tocsr() fails silently on matrices with nzn... * `#12350 <https://github.com/scipy/scipy/issues/12350>`__: Create a 2-parameter version of the gamma distribution * `#12369 <https://github.com/scipy/scipy/issues/12369>`__: scipy.signal.correlate has an error in the documentation, examples... * `#12373 <https://github.com/scipy/scipy/issues/12373>`__: interp1d returns incorrect values for step functions * `#12378 <https://github.com/scipy/scipy/issues/12378>`__: interpolate.NearestNDInterpolator.__call__ & LinearNDInterpolator.__call__... * `#12411 <https://github.com/scipy/scipy/issues/12411>`__: scipy.stats.spearmanr mishandles nan variables with "propogate" * `#12413 <https://github.com/scipy/scipy/issues/12413>`__: DOC: Remove the "Basic functions" section from the SciPy tutorial. * `#12415 <https://github.com/scipy/scipy/issues/12415>`__: scipy.stats.dirichlet documentation issue * `#12419 <https://github.com/scipy/scipy/issues/12419>`__: least_squares ValueError with 'lm' method - regression from 1.4.1... * `#12431 <https://github.com/scipy/scipy/issues/12431>`__: Request for Python wrapper for LAPACK's ?pptrf (Cholesky factorization... * `#12458 <https://github.com/scipy/scipy/issues/12458>`__: spearmanr with entire NaN columns produces errors * `#12477 <https://github.com/scipy/scipy/issues/12477>`__: WIP: Addition of MLE for stats.invgauss/wald * `#12483 <https://github.com/scipy/scipy/issues/12483>`__: reading .wav fails when the file is too big on python 3.6.0 * `#12490 <https://github.com/scipy/scipy/issues/12490>`__: BUG: stats: logistic and genlogistic logpdf overflow for large... * `#12499 <https://github.com/scipy/scipy/issues/12499>`__: LinearNDInterpolator raises ValueError when value array has writeable=False... * `#12523 <https://github.com/scipy/scipy/issues/12523>`__: Wrong key in __odrpack.c * `#12547 <https://github.com/scipy/scipy/issues/12547>`__: typo in scipy/cluster/_hierarchy.pyx * `#12549 <https://github.com/scipy/scipy/issues/12549>`__: DOC: least_squares return type is poorly formatted. * `#12578 <https://github.com/scipy/scipy/issues/12578>`__: TST: test_bounds_infeasible_2 failing on wheels repo cron jobs * `#12585 <https://github.com/scipy/scipy/issues/12585>`__: ENH: Add Multivariate Hypergeometric Distribution * `#12604 <https://github.com/scipy/scipy/issues/12604>`__: unintuitive conversion in \`scipy.constants.lambda2nu\` * `#12606 <https://github.com/scipy/scipy/issues/12606>`__: DOC: Invalid syntax in example. * `#12665 <https://github.com/scipy/scipy/issues/12665>`__: List of possible bugs found by automated code analysis * `#12696 <https://github.com/scipy/scipy/issues/12696>`__: scipy.optimize.fminbound, numpy depreciation warning Creating... * `#12699 <https://github.com/scipy/scipy/issues/12699>`__: TestProjections.test_iterative_refinements_dense failure * `#12701 <https://github.com/scipy/scipy/issues/12701>`__: TestDifferentialEvolutionSolver::test_L4 failing * `#12719 <https://github.com/scipy/scipy/issues/12719>`__: Misleading scipy.signal.get_window() docstring with 'exponential'... * `#12740 <https://github.com/scipy/scipy/issues/12740>`__: circstd doesn't handle R = hypot(S, C) > 1 * `#12749 <https://github.com/scipy/scipy/issues/12749>`__: ENH: interp1d Matlab compatibility * `#12773 <https://github.com/scipy/scipy/issues/12773>`__: Meta-issue: ndimage spline boundary handling (NumFOCUS proposal) * `#12813 <https://github.com/scipy/scipy/issues/12813>`__: optimize.root(method="krylov") fails if options["tol_norm"] expects... * `#12815 <https://github.com/scipy/scipy/issues/12815>`__: stats.zscore inconsistent behavior when all values are the same * `#12840 <https://github.com/scipy/scipy/issues/12840>`__: scipy.signal.windows.dpss docstring typo * `#12874 <https://github.com/scipy/scipy/issues/12874>`__: Rotation.random vs stats.special_ortho_group * `#12881 <https://github.com/scipy/scipy/issues/12881>`__: FFT - documentation - examples - linspace construction * `#12904 <https://github.com/scipy/scipy/issues/12904>`__: BUG: parsing in loadarff() * `#12917 <https://github.com/scipy/scipy/issues/12917>`__: GitHub Actions nightly build triggered on forks * `#12919 <https://github.com/scipy/scipy/issues/12919>`__: BUG: numerical precision, use gammaln in nct.mean * `#12924 <https://github.com/scipy/scipy/issues/12924>`__: Rename Sample Based Integration Methods to Comply with Code of... * `#12940 <https://github.com/scipy/scipy/issues/12940>`__: Should the minimum numpy for AIX be bumped to 1.16.5 * `#12951 <https://github.com/scipy/scipy/issues/12951>`__: A possible typo in scipy.stats.weightedtau * `#12952 <https://github.com/scipy/scipy/issues/12952>`__: [Documentation question] Would it be more precise to specify... * `#12970 <https://github.com/scipy/scipy/issues/12970>`__: Documentation presents second order sections as the correct choice... * `#12982 <https://github.com/scipy/scipy/issues/12982>`__: Calculate standard error of the intercept in linregress * `#12985 <https://github.com/scipy/scipy/issues/12985>`__: Possible wrong link in scipy.stats.wilcoxon doc * `#12991 <https://github.com/scipy/scipy/issues/12991>`__: least_squares broken with float32 * `#13001 <https://github.com/scipy/scipy/issues/13001>`__: \`OptimizeResult.message\` from \`L-BFGS-B\` is a bytes, not... * `#13030 <https://github.com/scipy/scipy/issues/13030>`__: BUG: lint_diff.py still fails for backport PRs * `#13077 <https://github.com/scipy/scipy/issues/13077>`__: CI: codecov proper patch diffs * `#13085 <https://github.com/scipy/scipy/issues/13085>`__: Build failing on main branch after HiGHS solver merge * `#13088 <https://github.com/scipy/scipy/issues/13088>`__: BLD, BUG: wheel builds failure with HiGHS/optimize * `#13099 <https://github.com/scipy/scipy/issues/13099>`__: Wrong output format for empty sparse results of kron * `#13108 <https://github.com/scipy/scipy/issues/13108>`__: TST, CI: GitHub Actions MacOS Failures * `#13111 <https://github.com/scipy/scipy/issues/13111>`__: BUG, DOC: refguide check is failing * `#13127 <https://github.com/scipy/scipy/issues/13127>`__: ODR output file writing broken in conda env with system compilers * `#13134 <https://github.com/scipy/scipy/issues/13134>`__: FromTravis migration tracker * `#13140 <https://github.com/scipy/scipy/issues/13140>`__: BUG: signal: \`ss2tf\` incorrectly truncates output to integers. * `#13179 <https://github.com/scipy/scipy/issues/13179>`__: CI: lint is failing because of output to stderr * `#13182 <https://github.com/scipy/scipy/issues/13182>`__: Key appears twice in \`test_optimize.test_show_options\` * `#13191 <https://github.com/scipy/scipy/issues/13191>`__: \`scipy.linalg.lapack.dgesjv\` overwrites original arrays if... * `#13207 <https://github.com/scipy/scipy/issues/13207>`__: TST: Erratic test failure in test_cossin_separate * `#13221 <https://github.com/scipy/scipy/issues/13221>`__: BUG: pavement.py glitch * `#13239 <https://github.com/scipy/scipy/issues/13239>`__: Segmentation fault with \`eigh(..., driver="evx")\` for 10x10... * `#13248 <https://github.com/scipy/scipy/issues/13248>`__: ndimage: improper cval handling for complex-valued inputs Pull requests for 1.6.0 ------------------------------ * `#8032 <https://github.com/scipy/scipy/pull/8032>`__: ENH: Add in taylor window common in Radar processing * `#8779 <https://github.com/scipy/scipy/pull/8779>`__: CI: Run benchmarks * `#9361 <https://github.com/scipy/scipy/pull/9361>`__: ENH: Add Kendall's tau-a and tau-c variants to scipy.stats.kendalltau() * `#11068 <https://github.com/scipy/scipy/pull/11068>`__: ENH: Adds correlation_lags function to scipy.signal * `#11119 <https://github.com/scipy/scipy/pull/11119>`__: ENH: add Cramer-von-Mises (one-sample) test to scipy.stats * `#11249 <https://github.com/scipy/scipy/pull/11249>`__: ENH: optimize: interpolative decomposition redundancy removal... * `#11346 <https://github.com/scipy/scipy/pull/11346>`__: ENH: add fast toeplitz matrix multiplication using FFT * `#11413 <https://github.com/scipy/scipy/pull/11413>`__: ENH: Multivariate t-distribution (stale) * `#11563 <https://github.com/scipy/scipy/pull/11563>`__: ENH: exact p-value in stats.kendalltau() for sample sizes > 171 * `#11691 <https://github.com/scipy/scipy/pull/11691>`__: ENH: add a stack of reversal functions to linprog * `#12043 <https://github.com/scipy/scipy/pull/12043>`__: ENH: optimize: add HiGHS methods to linprog - continued * `#12061 <https://github.com/scipy/scipy/pull/12061>`__: Check parameter consistensy in signal.iirdesign * `#12067 <https://github.com/scipy/scipy/pull/12067>`__: MAINT: Cleanup OLDAPI in ndimage/src/_ctest.c * `#12069 <https://github.com/scipy/scipy/pull/12069>`__: DOC: Add developer guidelines for implementing the nan_policy... * `#12077 <https://github.com/scipy/scipy/pull/12077>`__: MAINT: malloc return value checks for cython * `#12080 <https://github.com/scipy/scipy/pull/12080>`__: MAINT: Remove suppress_warnings * `#12085 <https://github.com/scipy/scipy/pull/12085>`__: ENH: special: support ILP64 Lapack * `#12086 <https://github.com/scipy/scipy/pull/12086>`__: MAINT: Cleanup PyMODINIT_FUNC used during 2to3 * `#12097 <https://github.com/scipy/scipy/pull/12097>`__: ENH: stats: override stats.rayleigh.fit with analytical MLE * `#12112 <https://github.com/scipy/scipy/pull/12112>`__: DOC: Improve integrate.nquad docstring * `#12125 <https://github.com/scipy/scipy/pull/12125>`__: TST: Add a test for stats.gmean with negative input * `#12139 <https://github.com/scipy/scipy/pull/12139>`__: TST: Reduce flakiness in lsmr test * `#12142 <https://github.com/scipy/scipy/pull/12142>`__: DOC: add a note in poisson distribution when mu=0 and k=0 in... * `#12144 <https://github.com/scipy/scipy/pull/12144>`__: DOC: Update ndimage.morphology.distance_transform\* * `#12154 <https://github.com/scipy/scipy/pull/12154>`__: ENH: scipy.signal: allow lists in gauss_spline * `#12170 <https://github.com/scipy/scipy/pull/12170>`__: ENH: scipy.stats: add negative hypergeometric distribution * `#12177 <https://github.com/scipy/scipy/pull/12177>`__: MAINT: Correctly add input line to ValueError * `#12183 <https://github.com/scipy/scipy/pull/12183>`__: ENH: Use fromfile where possible * `#12186 <https://github.com/scipy/scipy/pull/12186>`__: MAINT: generalize tests in SphericalVoronoi * `#12198 <https://github.com/scipy/scipy/pull/12198>`__: TST: Fix str + bytes error * `#12199 <https://github.com/scipy/scipy/pull/12199>`__: ENH: match np.result_type behaviour in some scipy.signal functions * `#12200 <https://github.com/scipy/scipy/pull/12200>`__: ENH: add FIR and IIR gammatone filters to scipy.signal * `#12204 <https://github.com/scipy/scipy/pull/12204>`__: ENH: Add overwrite argument for odr.ODR() and its test. * `#12206 <https://github.com/scipy/scipy/pull/12206>`__: MAINT:lstsq: Switch to tranposed problem if the array is tall * `#12208 <https://github.com/scipy/scipy/pull/12208>`__: wavfile bugfixes and maintenance * `#12214 <https://github.com/scipy/scipy/pull/12214>`__: DOC: fix docstring of "sd_beta" of odr.Output. * `#12234 <https://github.com/scipy/scipy/pull/12234>`__: MAINT: prevent divide by zero warnings in scipy.optimize BFGS... * `#12235 <https://github.com/scipy/scipy/pull/12235>`__: REL: set version to 1.6.0.dev0 * `#12237 <https://github.com/scipy/scipy/pull/12237>`__: BUG: Fix exit condition for QUICK_SELECT pivot * `#12242 <https://github.com/scipy/scipy/pull/12242>`__: ENH: Rename ndimage.sum to ndimage.sum_labels (keep sum as alias) * `#12243 <https://github.com/scipy/scipy/pull/12243>`__: EHN: Update SuperLU * `#12244 <https://github.com/scipy/scipy/pull/12244>`__: MAINT: stats: avoid spurious warnings in ncx2.pdf * `#12245 <https://github.com/scipy/scipy/pull/12245>`__: DOC: Fixed incorrect default for mode in scipy.ndimage.spline_filter1d * `#12248 <https://github.com/scipy/scipy/pull/12248>`__: MAINT: clean up pavement.py * `#12250 <https://github.com/scipy/scipy/pull/12250>`__: ENH: Replaced csr_matrix() by tocsr() and complemented docstring * `#12253 <https://github.com/scipy/scipy/pull/12253>`__: TST, CI: turn on codecov patch diffs * `#12259 <https://github.com/scipy/scipy/pull/12259>`__: MAINT: Remove duplicated test for import cycles * `#12263 <https://github.com/scipy/scipy/pull/12263>`__: ENH: Rename LocalSearchWrapper bounds * `#12265 <https://github.com/scipy/scipy/pull/12265>`__: BUG optimize: Accept np.matrix in lsq_linear * `#12266 <https://github.com/scipy/scipy/pull/12266>`__: BUG: Fix paren error in dual annealing accept_reject calculation * `#12269 <https://github.com/scipy/scipy/pull/12269>`__: MAINT: Included mismatched shapes in error messages. * `#12279 <https://github.com/scipy/scipy/pull/12279>`__: MAINT: \`__array__\` and array protocols cannot be used in sparse. * `#12281 <https://github.com/scipy/scipy/pull/12281>`__: DOC: update wheel DL docs * `#12283 <https://github.com/scipy/scipy/pull/12283>`__: ENH: odr: ILP64 Blas support in ODR * `#12284 <https://github.com/scipy/scipy/pull/12284>`__: ENH: linalg: support for ILP64 BLAS/LAPACK in f2py wrappers * `#12286 <https://github.com/scipy/scipy/pull/12286>`__: ENH: Cythonize scipy.spatial.transform.Rotation * `#12287 <https://github.com/scipy/scipy/pull/12287>`__: ENH: Read arbitrary bit depth (including 24-bit) WAVs * `#12292 <https://github.com/scipy/scipy/pull/12292>`__: BLD: fix musl compilation * `#12293 <https://github.com/scipy/scipy/pull/12293>`__: MAINT: Fix a DeprecationWarning in validate_runtests_log.py. * `#12296 <https://github.com/scipy/scipy/pull/12296>`__: DOC: Clarify area/volume in scipy.spatial.ConvexHull docstrings * `#12302 <https://github.com/scipy/scipy/pull/12302>`__: CI: Run travis builds on master to keep cache up to date * `#12305 <https://github.com/scipy/scipy/pull/12305>`__: TST: Cleanup print statements in tests * `#12323 <https://github.com/scipy/scipy/pull/12323>`__: ENH: Add a Bunch-like class to use as a backwards compatible... * `#12324 <https://github.com/scipy/scipy/pull/12324>`__: BUG: io: Fix an error that occurs when attempting to raise a... * `#12327 <https://github.com/scipy/scipy/pull/12327>`__: DOC: clarify docstrings of \`query_ball_tree\` and \`query_pairs\` * `#12334 <https://github.com/scipy/scipy/pull/12334>`__: PERF: Improve cKDTree.query_ball_point constant time cython overhead * `#12338 <https://github.com/scipy/scipy/pull/12338>`__: DOC: improve consistency and clarity of docs in linalg and sparse/linalg * `#12341 <https://github.com/scipy/scipy/pull/12341>`__: DOC: add Examples for KDTree query_ball_tree and query_pairs * `#12343 <https://github.com/scipy/scipy/pull/12343>`__: DOC: add examples for special.eval_legendre() * `#12349 <https://github.com/scipy/scipy/pull/12349>`__: BUG: avoid overflow in sum() for 32-bit systems * `#12351 <https://github.com/scipy/scipy/pull/12351>`__: DOC: Fix example wavfile to be 16bit * `#12352 <https://github.com/scipy/scipy/pull/12352>`__: [BUG] Consider 0/0 division in DOP853 error estimation * `#12353 <https://github.com/scipy/scipy/pull/12353>`__: Fix exception causes in vq.py * `#12354 <https://github.com/scipy/scipy/pull/12354>`__: MAINT: Cleanup unneeded void\* cast in setlist.pxd * `#12355 <https://github.com/scipy/scipy/pull/12355>`__: TST: Remove hack for old win-amd64 bug * `#12356 <https://github.com/scipy/scipy/pull/12356>`__: ENH: Faster implementation of scipy.sparse.block_diag (#9411... * `#12357 <https://github.com/scipy/scipy/pull/12357>`__: MAINT,TST: update and run scipy/special/utils/convert.py * `#12358 <https://github.com/scipy/scipy/pull/12358>`__: TST: Check mstat.skewtest pvalue * `#12359 <https://github.com/scipy/scipy/pull/12359>`__: TST: Sparse matrix test with int64 indptr and indices * `#12363 <https://github.com/scipy/scipy/pull/12363>`__: DOC: ref. in CloughTocher2DInterpolator * `#12364 <https://github.com/scipy/scipy/pull/12364>`__: DOC: \`sparse_distance_matrix\` and \`count_neighbors\` examples * `#12371 <https://github.com/scipy/scipy/pull/12371>`__: MAINT, CI: bump to latest stable OpenBLAS * `#12372 <https://github.com/scipy/scipy/pull/12372>`__: MAINT: Minor cleanup of (c)KDTree tests * `#12374 <https://github.com/scipy/scipy/pull/12374>`__: DEP: Deprecate \`distance.wminkowski\` * `#12375 <https://github.com/scipy/scipy/pull/12375>`__: ENH: Add fast path for minkowski distance with p=1,2 and support... * `#12376 <https://github.com/scipy/scipy/pull/12376>`__: Fix exception causes in most of the codebase * `#12377 <https://github.com/scipy/scipy/pull/12377>`__: DOC: Quick fix - adds newline to correlation_lags docstring Examples... * `#12381 <https://github.com/scipy/scipy/pull/12381>`__: BENCH: remove obsolete goal_time param * `#12382 <https://github.com/scipy/scipy/pull/12382>`__: ENH: Replace KDTree with a thin wrapper over cKDTree * `#12385 <https://github.com/scipy/scipy/pull/12385>`__: DOC: improve docstrings of interpolate.NearestNDInterpolator.__call__... * `#12387 <https://github.com/scipy/scipy/pull/12387>`__: DOC/STY: add example to scipy.signal.correlate * `#12393 <https://github.com/scipy/scipy/pull/12393>`__: CI: Replace the existing check for non-ASCII characters with... * `#12394 <https://github.com/scipy/scipy/pull/12394>`__: CI: arm64 numpy now available * `#12395 <https://github.com/scipy/scipy/pull/12395>`__: ENH: improve stats.binned_statistic_dd performance * `#12396 <https://github.com/scipy/scipy/pull/12396>`__: DOC, MAINT: forward port 1.5.0 relnotes * `#12398 <https://github.com/scipy/scipy/pull/12398>`__: API: Disable len() and indexing of Rotation instances with single... * `#12399 <https://github.com/scipy/scipy/pull/12399>`__: MAINT: Replace some Unicode dash-like chars with an ASCII hyphen. * `#12402 <https://github.com/scipy/scipy/pull/12402>`__: update .mailmap * `#12404 <https://github.com/scipy/scipy/pull/12404>`__: MAINT: io: Change the encoding comment of test_mio.py to utf-8. * `#12416 <https://github.com/scipy/scipy/pull/12416>`__: CI: cache mingw, azure pipelines * `#12427 <https://github.com/scipy/scipy/pull/12427>`__: BUG: logic error in loop unrolling (cKDTree) * `#12432 <https://github.com/scipy/scipy/pull/12432>`__: DOC: Remove the "Basic functions" section from the SciPy tutorial. * `#12434 <https://github.com/scipy/scipy/pull/12434>`__: ENH:linalg: Add LAPACK wrappers pptrf/pptrs/ppsv/pptri/ppcon * `#12435 <https://github.com/scipy/scipy/pull/12435>`__: DOC: fix simplex math for scipy.stats.dirichlet documentation * `#12439 <https://github.com/scipy/scipy/pull/12439>`__: DOC: add API methods summary for NdPPoly * `#12443 <https://github.com/scipy/scipy/pull/12443>`__: BUG: stats: Improve calculation of exponnorm.pdf * `#12448 <https://github.com/scipy/scipy/pull/12448>`__: DOC: stats: Add "Examples" to the ansari docstring. * `#12450 <https://github.com/scipy/scipy/pull/12450>`__: ENH: add \`leaves_color_list\` for cluster.dendrogram dictionary. * `#12451 <https://github.com/scipy/scipy/pull/12451>`__: MAINT: remove "blacklist" terminology from code base * `#12452 <https://github.com/scipy/scipy/pull/12452>`__: DOC: clarify the meaning of whitening for cluster.vq.whiten() * `#12455 <https://github.com/scipy/scipy/pull/12455>`__: MAINT: clearer error message in setup.py * `#12457 <https://github.com/scipy/scipy/pull/12457>`__: ENH: stats: override stats.pareto.fit with analytical MLE * `#12460 <https://github.com/scipy/scipy/pull/12460>`__: check if column in spearman rho is entirely NaN or Inf * `#12463 <https://github.com/scipy/scipy/pull/12463>`__: DOC: improve and clean up \*Spline docstrings in fitpack2.py * `#12474 <https://github.com/scipy/scipy/pull/12474>`__: ENH: linalg: speedup _sqrtm_triu by moving tight loop to Cython * `#12476 <https://github.com/scipy/scipy/pull/12476>`__: ENH: add IIR comb filter to scipy.signal * `#12484 <https://github.com/scipy/scipy/pull/12484>`__: Fix documentation for minimize * `#12486 <https://github.com/scipy/scipy/pull/12486>`__: DOC: add a note in poisson distribution when mu=0 and k=0 in... * `#12491 <https://github.com/scipy/scipy/pull/12491>`__: MAINT: forward port 1.5.1 release notes * `#12508 <https://github.com/scipy/scipy/pull/12508>`__: Fix exception causes all over the codebase * `#12514 <https://github.com/scipy/scipy/pull/12514>`__: ENH: stats: override stats.invgauss.fit with analytical MLE * `#12519 <https://github.com/scipy/scipy/pull/12519>`__: PERF: Avoid np.zeros when custom initialization is needed anyway * `#12520 <https://github.com/scipy/scipy/pull/12520>`__: DOC: Minor RST section renaming. * `#12521 <https://github.com/scipy/scipy/pull/12521>`__: MAINT: Remove unused imports * `#12522 <https://github.com/scipy/scipy/pull/12522>`__: PERF: Get rid of unnececssary allocation in VarReader5.cread_fieldnames * `#12524 <https://github.com/scipy/scipy/pull/12524>`__: DOC: special: Set Axes3D rect to avoid clipping labels in plot. * `#12525 <https://github.com/scipy/scipy/pull/12525>`__: Fix large sparse nnz * `#12526 <https://github.com/scipy/scipy/pull/12526>`__: DOC: Remove double section and too long header underline. * `#12527 <https://github.com/scipy/scipy/pull/12527>`__: Improve error message for wrong interpolation type * `#12530 <https://github.com/scipy/scipy/pull/12530>`__: Move redundant logic outside loop for conditional speedup in... * `#12532 <https://github.com/scipy/scipy/pull/12532>`__: ENH: Add norm={"forward", "backward"} to \`scipy.fft\` * `#12535 <https://github.com/scipy/scipy/pull/12535>`__: MAINT: Avoid sphinx deprecated aliases for SeeAlso and Only * `#12540 <https://github.com/scipy/scipy/pull/12540>`__: BUG: fix odr.output.work_ind key bug and add its test. * `#12541 <https://github.com/scipy/scipy/pull/12541>`__: ENH: add solver for minimum weight full bipartite matching * `#12550 <https://github.com/scipy/scipy/pull/12550>`__: PERF: pickling speed of rv\* * `#12551 <https://github.com/scipy/scipy/pull/12551>`__: DOC: fix typo in cluster/_hierarchy.pyx * `#12552 <https://github.com/scipy/scipy/pull/12552>`__: CI: Cleanup travis pip installs * `#12556 <https://github.com/scipy/scipy/pull/12556>`__: BUG: Fix problem with Scipy.integrate.solve_bvp for big problems * `#12557 <https://github.com/scipy/scipy/pull/12557>`__: MAINT: Use extern templates to improve sparsetools compile time * `#12558 <https://github.com/scipy/scipy/pull/12558>`__: MAINT: Remove hack to allow scipy.fft to act like a function * `#12563 <https://github.com/scipy/scipy/pull/12563>`__: MAINT: Remove unused mu0 in special/orthogonal.py * `#12564 <https://github.com/scipy/scipy/pull/12564>`__: DOC: fix return type docstring for least_squares * `#12565 <https://github.com/scipy/scipy/pull/12565>`__: DOC: stats: respond to query about Kruskal-Wallis test being... * `#12566 <https://github.com/scipy/scipy/pull/12566>`__: BUG: Interpolate: use stable sort * `#12568 <https://github.com/scipy/scipy/pull/12568>`__: Updated documentation for as_quat * `#12571 <https://github.com/scipy/scipy/pull/12571>`__: DEP: remove deprecated slepian window * `#12573 <https://github.com/scipy/scipy/pull/12573>`__: DEP: remove \`frechet_l\` and \`frechet_r\` * `#12575 <https://github.com/scipy/scipy/pull/12575>`__: BUG: stats: fix multinomial.pmf NaNs when params sum > 1 * `#12576 <https://github.com/scipy/scipy/pull/12576>`__: MAINT: remove warning from LSQSphereBivariateSpline * `#12582 <https://github.com/scipy/scipy/pull/12582>`__: ENH: Multivariate t-distribution * `#12587 <https://github.com/scipy/scipy/pull/12587>`__: ENH: speed up rvs of gengamma in scipy.stats * `#12588 <https://github.com/scipy/scipy/pull/12588>`__: DOC: add Examples add see also sections for LinearNDInterpolator,... * `#12597 <https://github.com/scipy/scipy/pull/12597>`__: ENH: Add single-sided p-values to t-tests * `#12599 <https://github.com/scipy/scipy/pull/12599>`__: Small update to scipy FFT tutorial * `#12600 <https://github.com/scipy/scipy/pull/12600>`__: ENH: disjoint set data structure * `#12602 <https://github.com/scipy/scipy/pull/12602>`__: BUG: add const for Read-only views in interpnd.pyx * `#12605 <https://github.com/scipy/scipy/pull/12605>`__: BUG: correct \`np.asanyarray\` use in \`scipy.constants.lambda2nu\` * `#12610 <https://github.com/scipy/scipy/pull/12610>`__: MAINT: forward port 1.5.2 release notes * `#12612 <https://github.com/scipy/scipy/pull/12612>`__: MAINT: stats: Use explicit keyword parameters instead of \`\*\*kwds\`. * `#12616 <https://github.com/scipy/scipy/pull/12616>`__: DOC: make explicit docstring that interpolate.interp1d only accepts... * `#12618 <https://github.com/scipy/scipy/pull/12618>`__: DOC: Minor doc formatting. * `#12640 <https://github.com/scipy/scipy/pull/12640>`__: MAINT: stats: fix issues with scipy.stats.pearson3 docs, moment,... * `#12647 <https://github.com/scipy/scipy/pull/12647>`__: TST: Add Boost ellipr[cdfgj]_data test data * `#12648 <https://github.com/scipy/scipy/pull/12648>`__: DOC: Update special/utils/README with instructions * `#12649 <https://github.com/scipy/scipy/pull/12649>`__: DOC: simplified pip quickstart guide * `#12650 <https://github.com/scipy/scipy/pull/12650>`__: DOC: stats: Fix boxcox docstring: lambda can be negative. * `#12655 <https://github.com/scipy/scipy/pull/12655>`__: DOC: update Steering Council members listed in governance docs * `#12659 <https://github.com/scipy/scipy/pull/12659>`__: rv_sample expect bug * `#12663 <https://github.com/scipy/scipy/pull/12663>`__: DOC: optimize: try to fix linprog method-specific documentation * `#12664 <https://github.com/scipy/scipy/pull/12664>`__: BUG: stats: Fix logpdf with large negative values for logistic... * `#12666 <https://github.com/scipy/scipy/pull/12666>`__: MAINT: Fixes from static analysis * `#12667 <https://github.com/scipy/scipy/pull/12667>`__: ENH: Adding Modified Rodrigues Parameters to the Rotation class * `#12670 <https://github.com/scipy/scipy/pull/12670>`__: DOC: Update documentation for Gamma distribution * `#12673 <https://github.com/scipy/scipy/pull/12673>`__: API: Unconditionally return np.intp from cKDTree.query * `#12677 <https://github.com/scipy/scipy/pull/12677>`__: MAINT: Add Autogenerated notice to ufuncs.pyi * `#12682 <https://github.com/scipy/scipy/pull/12682>`__: MAINT: Remove _util._valarray * `#12688 <https://github.com/scipy/scipy/pull/12688>`__: MAINT: add f2py-generated scipy.integrate files to .gitignore * `#12689 <https://github.com/scipy/scipy/pull/12689>`__: BENCH: simplify benchmark setup, remove benchmarks/run.py * `#12694 <https://github.com/scipy/scipy/pull/12694>`__: scipy/stats: Add laplace_asymmetric continuous distribution * `#12695 <https://github.com/scipy/scipy/pull/12695>`__: DOC: update Ubuntu quickstart; conda compilers now work! * `#12698 <https://github.com/scipy/scipy/pull/12698>`__: MAINT: Replace np.max with np.maximum * `#12700 <https://github.com/scipy/scipy/pull/12700>`__: TST: bump test precision for constrained trustregion test * `#12702 <https://github.com/scipy/scipy/pull/12702>`__: TST: bump test tolerance for \`DifferentialEvolutionSolver.test_L4\` * `#12703 <https://github.com/scipy/scipy/pull/12703>`__: BUG: Improve input validation for sepfir2d * `#12708 <https://github.com/scipy/scipy/pull/12708>`__: MAINT: fix a typo in scipy.sparse * `#12709 <https://github.com/scipy/scipy/pull/12709>`__: BUG: bvls can fail catastrophically to converge * `#12711 <https://github.com/scipy/scipy/pull/12711>`__: MAINT: Use platform.python_implementation to determine IS_PYPY * `#12713 <https://github.com/scipy/scipy/pull/12713>`__: TST: Fix flaky test_lgmres * `#12716 <https://github.com/scipy/scipy/pull/12716>`__: DOC: add examples and tutorial links for interpolate functions... * `#12717 <https://github.com/scipy/scipy/pull/12717>`__: DOC: Fix Issue #5396 * `#12725 <https://github.com/scipy/scipy/pull/12725>`__: ENH: Support complex-valued images and kernels for many ndimage... * `#12729 <https://github.com/scipy/scipy/pull/12729>`__: DEP: remove setup_requires * `#12732 <https://github.com/scipy/scipy/pull/12732>`__: BENCH: skip benchmarks instead of hiding them when SCIPY_XSLOW=0 * `#12734 <https://github.com/scipy/scipy/pull/12734>`__: CI: Don't ignore line-length in the lint_diff check. * `#12736 <https://github.com/scipy/scipy/pull/12736>`__: DOC: Fix signal.windows.get_window() 'exponential' docstring * `#12737 <https://github.com/scipy/scipy/pull/12737>`__: ENH: stats: override stats.gumbel_r.fit and stats.gumbel_l.fit... * `#12738 <https://github.com/scipy/scipy/pull/12738>`__: ENH: stats: override stats.logistic.fit with system of equations... * `#12743 <https://github.com/scipy/scipy/pull/12743>`__: BUG: Avoid negative variances in circular statistics * `#12744 <https://github.com/scipy/scipy/pull/12744>`__: Prevent build error on GNU/Hurd * `#12746 <https://github.com/scipy/scipy/pull/12746>`__: TST: parameterize the test cases in test_ndimage.py * `#12752 <https://github.com/scipy/scipy/pull/12752>`__: DOC: Add examples for some root finding functions. * `#12754 <https://github.com/scipy/scipy/pull/12754>`__: MAINT, CI: Azure windows deps multiline * `#12756 <https://github.com/scipy/scipy/pull/12756>`__: ENH: stats: Add an sf method to levy for improved precision in... * `#12757 <https://github.com/scipy/scipy/pull/12757>`__: ENH: stats: Add an sf method to levy_l for improved precision. * `#12765 <https://github.com/scipy/scipy/pull/12765>`__: TST, MAINT: infeasible_2 context * `#12767 <https://github.com/scipy/scipy/pull/12767>`__: Fix spline interpolation boundary handling for modes reflect... * `#12769 <https://github.com/scipy/scipy/pull/12769>`__: DOC: syntax error in scipy.interpolate.bspl * `#12770 <https://github.com/scipy/scipy/pull/12770>`__: ENH: add nearest-up rounding to scipy.interpolate.interp1d * `#12771 <https://github.com/scipy/scipy/pull/12771>`__: TST: fix invalid input unit test for scipy.signal.gammatone * `#12775 <https://github.com/scipy/scipy/pull/12775>`__: ENH: Adds quadratic_assignment with two methods * `#12776 <https://github.com/scipy/scipy/pull/12776>`__: ENH: add grid-constant boundary handling in ndimage interpolation... * `#12777 <https://github.com/scipy/scipy/pull/12777>`__: Add Taylor Window function - Common in Radar DSP * `#12779 <https://github.com/scipy/scipy/pull/12779>`__: ENH: Improvements to pocketfft thread pool and ARM neon vectorization * `#12788 <https://github.com/scipy/scipy/pull/12788>`__: API: Rename cKDTree n_jobs argument to workers * `#12792 <https://github.com/scipy/scipy/pull/12792>`__: DOC: remove THANKS.txt file in favor of scipy.org * `#12793 <https://github.com/scipy/scipy/pull/12793>`__: Add new flag to authors tool * `#12802 <https://github.com/scipy/scipy/pull/12802>`__: BENCH: add scipy.ndimage.interpolation benchmarks * `#12803 <https://github.com/scipy/scipy/pull/12803>`__: Do not pin the version of numpy in unsupported python versions * `#12810 <https://github.com/scipy/scipy/pull/12810>`__: CI: fix 32-bit Linux build failure on Azure CI runs * `#12812 <https://github.com/scipy/scipy/pull/12812>`__: ENH: support interpolation of complex-valued images * `#12814 <https://github.com/scipy/scipy/pull/12814>`__: BUG: nonlin_solve shouldn't pass non-vector dx to tol_norm * `#12818 <https://github.com/scipy/scipy/pull/12818>`__: Update ckdtree.pyx * `#12822 <https://github.com/scipy/scipy/pull/12822>`__: MAINT: simplify directed_hausdorff * `#12827 <https://github.com/scipy/scipy/pull/12827>`__: DOC: Fix wrong name w being used instead of worN in docs. * `#12831 <https://github.com/scipy/scipy/pull/12831>`__: DOC: fix typo in sparse/base.py * `#12835 <https://github.com/scipy/scipy/pull/12835>`__: MAINT: stats: Improve vonmises PDF calculation. * `#12839 <https://github.com/scipy/scipy/pull/12839>`__: ENH: scipy.stats: add multivariate hypergeometric distribution * `#12843 <https://github.com/scipy/scipy/pull/12843>`__: changed M to N in windows.dpss * `#12846 <https://github.com/scipy/scipy/pull/12846>`__: MAINT: update minimum NumPy version to 1.16.5 * `#12847 <https://github.com/scipy/scipy/pull/12847>`__: DOC: Unify the formula in docs of scipy.stats.pearsonr() * `#12849 <https://github.com/scipy/scipy/pull/12849>`__: DOC: polish QAP docs for consistency and readability * `#12852 <https://github.com/scipy/scipy/pull/12852>`__: ENH, MAINT: Bring KDTree interface to feature-parity with cKDTree * `#12858 <https://github.com/scipy/scipy/pull/12858>`__: DOC: use :doi: and :arxiv: directives for references * `#12872 <https://github.com/scipy/scipy/pull/12872>`__: lazily import multiprocessing.Pool in MapWrapper * `#12878 <https://github.com/scipy/scipy/pull/12878>`__: DOC: document ScalarFunction * `#12882 <https://github.com/scipy/scipy/pull/12882>`__: MAINT: stats: Change a test to use <= instead of strictly less... * `#12885 <https://github.com/scipy/scipy/pull/12885>`__: numpy.linspace calls edited to ensure correct spacing. * `#12886 <https://github.com/scipy/scipy/pull/12886>`__: DOC: stats: Add 'versionadded' to cramervonmises docstring. * `#12899 <https://github.com/scipy/scipy/pull/12899>`__: TST: make a couple of tests expected to fail on 32-bit architectures * `#12903 <https://github.com/scipy/scipy/pull/12903>`__: DOC: update Windows build guide and move into contributor guide * `#12907 <https://github.com/scipy/scipy/pull/12907>`__: DOC: clarify which array the precenter option applies to * `#12908 <https://github.com/scipy/scipy/pull/12908>`__: MAINT: spatial: Remove two occurrences of unused variables in... * `#12909 <https://github.com/scipy/scipy/pull/12909>`__: ENH: stats: Add methods gumbel_r._sf and gumbel_r._isf * `#12910 <https://github.com/scipy/scipy/pull/12910>`__: CI: travis: Remove some unnecessary code from .travis.yml. * `#12911 <https://github.com/scipy/scipy/pull/12911>`__: Minor fixes to dendrogram plotting * `#12921 <https://github.com/scipy/scipy/pull/12921>`__: CI: don't run GitHub Actions on fork or in cron job * `#12927 <https://github.com/scipy/scipy/pull/12927>`__: MAINT: rename integrate.simps to simpson * `#12934 <https://github.com/scipy/scipy/pull/12934>`__: MAINT: rename trapz and cumtrapz to (cumulative\_)trapezoid * `#12936 <https://github.com/scipy/scipy/pull/12936>`__: MAINT: fix numerical precision in nct.stats * `#12938 <https://github.com/scipy/scipy/pull/12938>`__: MAINT: fix linter on master * `#12941 <https://github.com/scipy/scipy/pull/12941>`__: Update minimum AIX pinnings to match non AIX builds * `#12955 <https://github.com/scipy/scipy/pull/12955>`__: BUG: Fixed wrong NaNs check in scipy.stats.weightedtau * `#12958 <https://github.com/scipy/scipy/pull/12958>`__: ENH: stats: Implement _logpdf, _sf and _isf for nakagami. * `#12962 <https://github.com/scipy/scipy/pull/12962>`__: Correcting that p should be in [0,1] for a variety of discrete... * `#12964 <https://github.com/scipy/scipy/pull/12964>`__: BUG: added line.strip() to split_data_line() * `#12968 <https://github.com/scipy/scipy/pull/12968>`__: ENH: stats: Use only an analytical formula or scalar root-finding... * `#12971 <https://github.com/scipy/scipy/pull/12971>`__: MAINT: Declare support for Python 3.9 * `#12972 <https://github.com/scipy/scipy/pull/12972>`__: MAINT: Remove redundant Python < 3.6 code * `#12980 <https://github.com/scipy/scipy/pull/12980>`__: DOC: Update documentation on optimize.rosen * `#12983 <https://github.com/scipy/scipy/pull/12983>`__: ENH: improvements to stats.linregress * `#12990 <https://github.com/scipy/scipy/pull/12990>`__: DOC: Clarify that using sos as output type for iirdesign can... * `#12992 <https://github.com/scipy/scipy/pull/12992>`__: DOC: capitalization and formatting in lsmr * `#12995 <https://github.com/scipy/scipy/pull/12995>`__: DOC: stats: Several documentation fixes. * `#12996 <https://github.com/scipy/scipy/pull/12996>`__: BUG: Improve error messages for \`range\` arg of binned_statistic_dd * `#12998 <https://github.com/scipy/scipy/pull/12998>`__: MAINT: approx_derivative with FP32 closes #12991 * `#13004 <https://github.com/scipy/scipy/pull/13004>`__: TST: isinstance(OptimizeResult.message, str) closes #13001 * `#13006 <https://github.com/scipy/scipy/pull/13006>`__: Keep correct dtype when loading empty mat arrays. * `#13009 <https://github.com/scipy/scipy/pull/13009>`__: MAINT: clip SLSQP step within bounds * `#13012 <https://github.com/scipy/scipy/pull/13012>`__: DOC: fix bilinear_zpk example labels * `#13013 <https://github.com/scipy/scipy/pull/13013>`__: ENH: Add \`subset\` and \`subsets\` methods to \`DisjointSet\`... * `#13029 <https://github.com/scipy/scipy/pull/13029>`__: MAINT: basinhopping callback for initial mininmisation * `#13032 <https://github.com/scipy/scipy/pull/13032>`__: DOC: fix docstring errors in in stats.wilcoxon * `#13036 <https://github.com/scipy/scipy/pull/13036>`__: BUG: forward port lint_diff shims * `#13041 <https://github.com/scipy/scipy/pull/13041>`__: MAINT: dogbox ensure x is within bounds closes #11403 * `#13042 <https://github.com/scipy/scipy/pull/13042>`__: MAINT: forward port 1.5.4 release notes * `#13046 <https://github.com/scipy/scipy/pull/13046>`__: DOC: Update optimize.least_squares doc for all tolerance must... * `#13052 <https://github.com/scipy/scipy/pull/13052>`__: Typo fix for cluster documentation * `#13054 <https://github.com/scipy/scipy/pull/13054>`__: BUG: fix \`scipy.optimize.show_options\` for unknown methods.... * `#13056 <https://github.com/scipy/scipy/pull/13056>`__: MAINT: fft: Fix a C++ compiler warning. * `#13057 <https://github.com/scipy/scipy/pull/13057>`__: Minor fixes on doc of function csr_tocsc * `#13058 <https://github.com/scipy/scipy/pull/13058>`__: DOC: stats: Replace np.float with np.float64 in a tutorial file. * `#13059 <https://github.com/scipy/scipy/pull/13059>`__: DOC: stats: Update the "Returns" section of the linregress docstring. * `#13060 <https://github.com/scipy/scipy/pull/13060>`__: MAINT: clip_x_for_func should be private * `#13061 <https://github.com/scipy/scipy/pull/13061>`__: DOC: signal.win -> signal.windows.win in Examples * `#13063 <https://github.com/scipy/scipy/pull/13063>`__: MAINT: Add suite-sparse and sksparse installation check * `#13070 <https://github.com/scipy/scipy/pull/13070>`__: MAINT: stats: Remove a couple obsolete comments. * `#13073 <https://github.com/scipy/scipy/pull/13073>`__: BUG: Fix scalar_search_wolfe2 to resolve #12157 * `#13078 <https://github.com/scipy/scipy/pull/13078>`__: CI, MAINT: migrate Lint to Azure * `#13081 <https://github.com/scipy/scipy/pull/13081>`__: BLD: drop Python 3.6 support (NEP 29) * `#13082 <https://github.com/scipy/scipy/pull/13082>`__: MAINT: update minimum NumPy version to 1.16.5 in a couple more... * `#13083 <https://github.com/scipy/scipy/pull/13083>`__: DOC: update toolchain.rst * `#13086 <https://github.com/scipy/scipy/pull/13086>`__: DOC: Update the Parameters section of the correlation docstring * `#13087 <https://github.com/scipy/scipy/pull/13087>`__: ENH:signal: Speed-up Cython implementation of _sosfilt * `#13089 <https://github.com/scipy/scipy/pull/13089>`__: BLD, BUG: add c99 compiler flag to HiGHS basiclu library * `#13091 <https://github.com/scipy/scipy/pull/13091>`__: BUG: Fix GIL handling in _sosfilt * `#13094 <https://github.com/scipy/scipy/pull/13094>`__: DOC: clarify "location" in docstring of cKDTree.query * `#13095 <https://github.com/scipy/scipy/pull/13095>`__: Zoom resize update * `#13097 <https://github.com/scipy/scipy/pull/13097>`__: BUG: fix CubicSpline(..., bc_type="periodic") #11758 * `#13100 <https://github.com/scipy/scipy/pull/13100>`__: BUG: sparse: Correct output format of kron * `#13107 <https://github.com/scipy/scipy/pull/13107>`__: ENH: faster linear_sum_assignment for small cost matrices * `#13110 <https://github.com/scipy/scipy/pull/13110>`__: CI, MAINT: refguide/asv checks to azure * `#13112 <https://github.com/scipy/scipy/pull/13112>`__: CI: fix MacOS CI * `#13113 <https://github.com/scipy/scipy/pull/13113>`__: CI: Install word list package for refguide-check * `#13115 <https://github.com/scipy/scipy/pull/13115>`__: BUG: add value range check for signal.iirdesign() * `#13116 <https://github.com/scipy/scipy/pull/13116>`__: CI: Don't report name errors after an exception in refguide-check * `#13117 <https://github.com/scipy/scipy/pull/13117>`__: CI: move sdist/pre-release test Azure * `#13119 <https://github.com/scipy/scipy/pull/13119>`__: Improve error message on friedmanchisquare function * `#13121 <https://github.com/scipy/scipy/pull/13121>`__: Fix factorial() for NaN on Python 3.10 * `#13123 <https://github.com/scipy/scipy/pull/13123>`__: BLD: Specify file extension for language standard version tests * `#13128 <https://github.com/scipy/scipy/pull/13128>`__: TST: skip Fortran I/O test for ODR * `#13130 <https://github.com/scipy/scipy/pull/13130>`__: TST: skip factorial() float tests on Python 3.10 * `#13136 <https://github.com/scipy/scipy/pull/13136>`__: CI:Add python dbg run to GH Actions * `#13138 <https://github.com/scipy/scipy/pull/13138>`__: CI: Port coverage, 64-bit BLAS, GCC 4.8 build to azure * `#13139 <https://github.com/scipy/scipy/pull/13139>`__: Fix edge case for mode='nearest' in ndimage.interpolation functions * `#13141 <https://github.com/scipy/scipy/pull/13141>`__: BUG: signal: Fix data type of the numerator returned by ss2tf. * `#13144 <https://github.com/scipy/scipy/pull/13144>`__: MAINT: stats: restrict gausshyper z > -1 * `#13146 <https://github.com/scipy/scipy/pull/13146>`__: typo in csr.py * `#13148 <https://github.com/scipy/scipy/pull/13148>`__: BUG: stats: fix typo in stable rvs per gh-12870 * `#13149 <https://github.com/scipy/scipy/pull/13149>`__: DOC: spatial/stats: cross-ref random rotation matrix functions * `#13151 <https://github.com/scipy/scipy/pull/13151>`__: MAINT: stats: Fix a test and a couple PEP-8 issues. * `#13152 <https://github.com/scipy/scipy/pull/13152>`__: MAINT: stats: Use np.take_along_axis in the private function... * `#13154 <https://github.com/scipy/scipy/pull/13154>`__: ENH: stats: Implement defined handling of constant inputs in... * `#13156 <https://github.com/scipy/scipy/pull/13156>`__: DOC: maintain equal display range for ndimage.zoom example * `#13159 <https://github.com/scipy/scipy/pull/13159>`__: CI: Azure: Don't run tests on merge commits, except for coverage * `#13160 <https://github.com/scipy/scipy/pull/13160>`__: DOC: stats: disambiguate location-shifted/noncentral * `#13161 <https://github.com/scipy/scipy/pull/13161>`__: BUG: DifferentialEvolutionSolver.__del__ can fail in garbage... * `#13163 <https://github.com/scipy/scipy/pull/13163>`__: BUG: stats: fix bug in spearmanr nan propagation * `#13167 <https://github.com/scipy/scipy/pull/13167>`__: MAINT: stats: Fix a test. * `#13169 <https://github.com/scipy/scipy/pull/13169>`__: BUG: stats: Fix handling of misaligned masks in mstats.pearsonr. * `#13178 <https://github.com/scipy/scipy/pull/13178>`__: CI: testing.yml --> macos.yml * `#13181 <https://github.com/scipy/scipy/pull/13181>`__: CI: fix lint * `#13190 <https://github.com/scipy/scipy/pull/13190>`__: BUG: optimize: fix a duplicate key bug for \`test_show_options\` * `#13192 <https://github.com/scipy/scipy/pull/13192>`__: BUG:linalg: Add overwrite option to gejsv wrapper * `#13194 <https://github.com/scipy/scipy/pull/13194>`__: BUG: slsqp should be able to use rel_step * `#13199 <https://github.com/scipy/scipy/pull/13199>`__: [skip travis] DOC: 1.6.0 release notes * `#13203 <https://github.com/scipy/scipy/pull/13203>`__: fix typos * `#13209 <https://github.com/scipy/scipy/pull/13209>`__: TST:linalg: set the seed for cossin test * `#13212 <https://github.com/scipy/scipy/pull/13212>`__: [DOC] Backtick and directive consistency. * `#13217 <https://github.com/scipy/scipy/pull/13217>`__: REL: add necessary setuptools and numpy version pins in pyproject.toml... * `#13226 <https://github.com/scipy/scipy/pull/13226>`__: BUG: pavement.py file handle fixes * `#13249 <https://github.com/scipy/scipy/pull/13249>`__: Handle cval correctly for ndimage functions with complex-valued... * `#13253 <https://github.com/scipy/scipy/pull/13253>`__: BUG,MAINT: Ensure all Pool objects are closed * `#13255 <https://github.com/scipy/scipy/pull/13255>`__: BUG:linalg: Fix heevx wrappers and add new tests * `#13260 <https://github.com/scipy/scipy/pull/13260>`__: CI: fix macOS testing * `#13269 <https://github.com/scipy/scipy/pull/13269>`__: CI: github actions: In the linux dbg tests, update apt before... * `#13279 <https://github.com/scipy/scipy/pull/13279>`__: MAINT: 1.6.0 rc2 backports Checksums ========= MD5 ~~~ 8fd605d90e571560d33eecb3c2263abe scipy-1.6.0-cp37-cp37m-macosx_10_9_x86_64.whl ab345b6f61228d8d797083fbe4ecb9df scipy-1.6.0-cp37-cp37m-manylinux1_i686.whl 6df40fd888aacc66c7fa2f905fdc3c8b 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1 0

Enquiry regarding edge detector technqiues
by Rajarshi Roychoudhury 25 Dec '20

25 Dec '20

Hi, I need some help regarding the following piece of code If arr_1 is an image, I have used the prewitt edge detection technique. edge_prewitt = prewitt(arr_1) Is any thresholding applied here?

1 0

scikit-image 0.18.1
by Juan Nunez-Iglesias 23 Dec '20

23 Dec '20

Dear all, I’ve just released scikit-image 0.18.1, a small bug fix release on top of 0.18.0. Specifically: - Fix indexing error for labelling in large (>2GB) arrays (#5143, #5151) This was caused by a cdef in Cython using long rather than size_t for an indexing integer, which failed for big images in 32-bit platforms. Thanks to Riadh for the fix! - Only use retry_if_failed with recent pooch (#5148) Even though we added pooch 1.3 as an optional dependency, if the user had an *existing* pooch installation and didn’t request pooch from us, we would happily use their old pooch, but ask it to do new tricks that it didn’t know yet. This caused an error on importing skimage, because data/__init__ is executed by default. (We should fix this, but that was a bigger undertaking — I think this bandaid already makes things much better.) Enjoy! 😊 Juan.

2 1

Job opportunities in bioimage analysis
by Juan Nunez-Iglesias 23 Dec '20

23 Dec '20

Dear skimagers, There's been quite a few job openings in bioimage analysis in the past couple of months, which I thought worthwhile to bring up in the mailing list. Please pass on to anyone or any channel you think might be interested. - My friend/collaborator/napari co-founder Loic Royer is hiring at the Chan Zuckerberg Biohub in San Francisco: https://forum.image.sc/t/bioimage-scientist-image-processing-for-light-shee… Loic is building next-generation microscopes and has all kinds of cool applications in mind — from large array data management to 3D tracking. - The Turing Institute (London) is looking for a postdoctoral fellow to apply AI methods to cryo-electron microscopy data: https://cezanneondemand.intervieweb.it/turing/jobs/research_associate__mole… - Marta Zlatic at the Laboratory for Molecular Biology in Cambridge, UK is looking for a software engineer to help with image processing and analysis pipelines: https://www.nature.com/naturecareers/job/senior-investigator-scientist-soft… - Albert Cardona, also at LMB, is hiring to software engineers, one data scientist, and a postdoc (!). I don't have a direct link but get in touch with Albert: https://twitter.com/albertcardona/status/1336310286362480641 - Recursion Pharma is looking for data scientists and software engineers. Most positions are in Salt Lake City, Utah, but some (including "Senior Machine Learning Scientist, Computer Vision") are remote: https://www.recursionpharma.com/careers - Jan Eglinger at FMI in Basel, Switzerland is looking for machine learning and image analysis specialist: https://www.fmi.ch/education-careers/positions/jobdetails.html?jobID=264 - Tom Caswell's group at Brookhaven National Lab is looking for a software engineer: https://jobs.bnl.gov/job/upton/scientific-software-engineer/3437/2861985264 - The Open Microscopy Environment team (Dundee, UK) is hiring a software engineer. Remote work might be possible. https://www.lifesci.dundee.ac.uk/vacancies/2020/dec/3/research-software-eng… and https://twitter.com/notjustmoore/status/1336320005294592001 - Stephan Salfeeld, at Janelia Research Campus in Ashburn, VA, is looking for postdocs in large scale bioimage analysis and deep learning: https://www.nature.com/naturecareers/job/postdoctoral-associate-saalfeld-la… All in all, it seems like a great time to be in image analysis! 🎉 I know most of these people personally, they're all working on very cool science or infrastructure, and I'd recommend working with any of them. Good luck! Juan.

1 0

Re: Otsu thresholding
by Juan Nunez-Iglesias 22 Dec '20

22 Dec '20

Some methods, like Li, have some special handling for nan values, but that is not uniform across all our methods, as you have seen. 😂 I would suggest: ```python t = threshold_otsu(image[np.isfinite(image)]) ``` That will only pass the non-nan, non-inf pixels to Otsu to do the calculation. Hope this helps! Juan. > On 18 Dec 2020, at 7:19 am, Laurynas Gedminas <laurynasgedminas(a)gmail.com> wrote: > > Hello, > I have NDVI image, its not a square, and has some None values, > I am trying to create otsu threshold, but getting error: > autodetected range of [nan, nan] is not finite > > how to go around that? > > <image.png> > > Thank you,

3 5

scikit-image 0.18.0rc2 is out
by Juan Nunez-Iglesias 14 Dec '20

14 Dec '20

Dear skimagers, I’ve just pushed scikit-image 0.18.0 release candidate 2 to PyPI. I think this is the real one! If I don’t hear objections by tomorrow morning (~24h from the timestamp on this email), I’ll tag and (finally!) release 0.18.0. 🎉 Please try this release candidate out by using `pip install -U --pre scikit-image`. Since we have started adding further dependencies to our documentation examples, in order to run some of the examples you will need to `pip install -U --pre scikit-image[docs]`. Or, if you only want access to our new example datasets, you can use `pip install -U --pre scikit-image[data]`. Finally, if you want to systematically test this release on your machine, you can use `pip install -U --pre scikit-image[test]`, then run `pytest --pyargs skimage`. You can find the release notes below. Happy image analysis! Juan. Announcement: scikit-image 0.18.0 ================================= We're happy to announce the release of scikit-image v0.18.0! scikit-image is an image processing toolbox for SciPy that includes algorithms for segmentation, geometric transformations, color space manipulation, analysis, filtering, morphology, feature detection, and more. This release of scikit-image drops support for Python 3.6 in accordance with the `NEP-29 Python and Numpy version support community standard <https://numpy.org/neps/nep-0029-deprecation_policy.html>`_: Python 3.7 or newer is required to run this version. For more information, examples, and documentation, please visit our website: https://scikit-image.org New Features ------------ - Add the iterative Lucas-Kanade (iLK) optical flow method (#4161) - Add Feret diameter in region properties (#4379, #4820) - Add functions to compute Euler number and Crofton perimeter estimation (#4380) - Add a function to compute the Hausdorff distance (#4382) - Added 3D support for many filters in ``skimage.filters.rank``. - An experimental implementation of trainable pixel segmentation, aiming for compatibility with the scikit-learn API, has been added to ``skimage.future``. Try it out! (#4739) - Add a new function ``segmentation.expand_labels`` to dilate labels while preventing overlap (#4795) - It is now possible to pass extra measurement functions to ``measure.regionprops`` and ``regionprops_table`` (#4810) - Add rolling ball algorithm for background subtraction (#4851) - New sample images have been added in the ``data`` subpackage: ``data.eagle`` (#4922), ``data.human_mitosis`` (#4939), ``data.cells3d`` (#4951), and ``data.vortex`` (#5041). Also note that the image for ``data.camera`` has been changed due to copyright issues (#4913). - ``skimage.feature.structure_tensor`` now supports 3D (and nD) images as input (#5002) - Many thresholding methods can now receive a precomputed histogram as input, resulting in significant speedups if multiple methods are tried on the same image, or if a fast histogram method is used. (#5006) - ``measure.regionprops`` now supports multichannel intensity images (#5037) Documentation ------------- - Add an example to the flood fill tutorial (#4619) - Docstring enhancements for marching cubes and find_contours (#4641) - A new tutorial presenting a cell biology example has been added to the gallery (#4648). Special thanks to Pierre Poulain and Fred Bernard (Université de Paris and Institut Jacques Monod) for scientific review of this example! - Improve register rotation example with notes and references (#4723) - Add versionadded for new scalar type support for "scale" param in ``transform.AffineTransform`` (#4733) - New tutorial on `visualizing 3D data <https://scikit-image.org/docs/dev/auto_examples/applications/plot_3d_image_…>`_ (#4850) - Add example for 3D adaptive histogram equalization (AHE) (#4658) - Automatic formatting of docstrings for improved consistency (#4849) - Improved docstring for ``rgb2lab`` (#4839) and ``marching_cubes`` (#4846) - Improved docstring for ``measure.marching_cubes``, mentioning how to decimate a mesh using mayavi (#4846) - Document how to contribute a gallery example. (#4857) - Fix and improve entropy example (#4904) - expand the benchmarking section of the developer docs (#4905) - Improved docstring for ``util.random_noise`` (#5001) - Improved docstrings for ``morphology.h_maxima`` and ``morphology.h_minima`` (#4929). - Improved docstring for ``util.img_as_int`` (#4888). - A new example demonstrates interactive exploration of regionprops results using the PyData stack (pandas, seaborn) at <https://scikit-image.org/docs/dev/auto_examples/segmentation/plot_regionpro…>`_ (#5010). - Documentation has been added to explain `how to download example datasets <https://scikit-image.org/docs/dev/install.html#downloading-all-demo-datasets>`_ which are not installed with scikit-image (#4984). Similarly, the contributor guide has been updated to mention how to host new datasets in a gitlab repository (#4892). - The `benchmarking section of the developer documentation <https://scikit-image.org/docs/dev/contribute.html#benchmarks>`_ has been expanded (#4905). - Added links to the image.sc forum in example pages (#5094, #5096) - Added missing datasets to gallery examples (#5116, #5118) - Add farid filters in __all__, to populate the documentation (#5128, #5129) - Proofread gallery example for rank filters. (#5126, #5136) Improvements ------------ - float32 support for SLIC (#4683), ORB (#4684, #4697), BRIEF (#4685), ``pyramid_gaussian`` (#4696), Richardson-Lucy deconvolution (#4880) - In ``skimage.restoration.richardson_lucy``, computations are now done in single-precision when the input image is single-precision. This can give a substantial performance improvement when working with single precision data. - Richardson-Lucy deconvolution now has a ``filter_epsilon`` keyword argument to avoid division by very small numbers (#4823) - Add default level parameter (max-min) / 2 in ``measure.find_contours`` (#4862) - The performance of the SLIC superpixels algorithm (``skimage.segmentation.slice``) was improved for the case where a mask is supplied by the user (#4903). The specific superpixels produced by masked SLIC will not be identical to those produced by prior releases. - ``exposure.adjust_gamma`` has been accelerated for ``uint8`` images by using a look-up table (LUT) (#4966). - ``measure.label`` has been accelerated for boolean input images, by using ``scipy.ndimage``'s implementation for this case (#4945). - ``util.apply_parallel`` now works with multichannel data (#4927). - ``skimage.feature.peak_local_max`` supports now any Minkowski distance. - We now use sparse cross-correlation to accelerate local thresholding functions (#4912) - ``morphology.convex_hull_image`` now uses much less memory by checking hull inequalities in sequence (#5020) - Polygon rasterization is more precise and will no longer potentially exclude input vertices. (#5029) - Add data optional requirements to allow pip install scikit-image[data] (#5105, #5111) - OpenMP support in MSVC (#4924, #5111) - Restandardize handling of Multi-Image files (#2815, #5132) - Consistent zoom boundary behavior across SciPy versions (#5131, #5133) API Changes ----------- - ``skimage.restoration.richardson_lucy`` returns a single-precision output when the input is single-precision. Prior to this release, double-precision was always used. - The default value of ``threshold_rel`` in ``skimage.feature.corner`` has changed from 0.1 to None, which corresponds to letting ``skimage.feature.peak_local_max`` decide on the default. This is currently equivalent to ``threshold_rel=0``. - ``data.cat`` has been introduced as an alias of ``data.chelsea`` for a more descriptive name. - The ``level`` parameter of ``measure.find_contours`` is now a keyword argument, with a default value set to (max(image) - min(image)) / 2. - ``p_norm`` argument was added to ``skimage.feature.peak_local_max`` to add support for Minkowski distances. - In ``measure.label``, the deprecated ``neighbors`` parameter has been removed. (#4942) Bug fixes --------- - A bug in ``label2rgb`` has been fixed when the input image had np.uint8 dtype (#4661) - Fixed incorrect implementation of ``skimage.color.separate_stains`` (#4725) - Many bug fixes have been made in ``peak_local_max`` (#2592, #4756, #4760, #5047) - Fix bug in ``random_walker`` when input labels have negative values (#4771) - PSF flipping is now correct for Richardson-Lucy deconvolution work in >2D (#4823) - Fix equalize_adapthist (CLAHE) for clip value 1.0 (#4828) - For the RANSAC algorithm, improved the case where all data points are outliers, which was previously raising an error (#4844) - An error-causing bug has been corrected for the ``bg_color`` parameter in ``label2rgb`` when its value is a string (#4840) - A normalization bug was fixed in ``metrics.variation_of_information`` (#4875) - Euler characteristic property of ``skimage.measure.regionprops`` was erroneous for 3D objects, since it did not take tunnels into account. A new implementation based on integral geometry fixes this bug (#4380). - In ``skimage.morphology.selem.rectangle`` the ``height`` argument controlled the width and the ``width`` argument controlled the height. They have been replaced with ``nrow`` and ``ncol``. (#4906) - ``skimage.segmentation.flood_fill`` and ``skimage.segmentation.flood`` now consistently handle negative values for ``seed_point``. - Segmentation faults in ``segmentation.flood`` have been fixed (#4948, #4972) - A segfault in ``draw.polygon`` for the case of 0-d input has been fixed (#4943). - In ``registration.phase_cross_correlation``, a ``ValueError`` is raised when NaNs are found in the computation (as a result of NaNs in input images). Before this fix, an incorrect value could be returned where the input images had NaNs (#4886). - Fix edge filters not respecting padding mode (#4907) - Use v{} for version tags with pooch (#5104, #5110) - Fix compilation error in XCode 12 (#5107, #5111) Deprecations ------------ - The ``indices`` argument in ``skimage.feature.peak_local_max`` has been deprecated. Indices will always be returned. (#4752) - In ``skimage.feature.structure_tensor``, an ``order`` argument has been introduced which will default to 'rc' starting in version 0.20. (#4841) - ``skimage.feature.structure_tensor_eigvals`` has been deprecated and will be removed in version 0.20. Use ``skimage.feature.structure_tensor_eigenvalues`` instead. - The ``skimage.viewer`` subpackage and the ``skivi`` script have been deprecated and will be removed in version 0.20. For interactive visualization we recommend using dedicated tools such as `napari <https://napari.org>`_ or `plotly <https://plotly.com>`_. In a similar vein, the ``qt`` and ``skivi`` plugins of ``skimage.io`` have been deprecated and will be removed in version 0.20. (#4941, #4954) - In ``skimage.morphology.selem.rectangle`` the arguments ``width`` and ``height`` have been deprecated. Use ``nrow`` and ``ncol`` instead. - The explicit setting ``threshold_rel=0` was removed from the Examples of the following docstrings: ``skimage.feature.BRIEF``, ``skimage.feature.corner_harris``, ``skimage.feature.corner_shi_tomasi``, ``skimage.feature.corner_foerstner``, ``skimage.feature.corner_fast``, ``skimage.feature.corner_subpix``, ``skimage.feature.corner_peaks``, ``skimage.feature.corner_orientations``, and ``skimage.feature._detect_octave``. - In ``skimage.restoration._denoise``, the warning regarding ``rescale_sigma=None`` was removed. - In ``skimage.restoration._cycle_spin``, the ``# doctest: +SKIP`` was removed. Development process ------------------- - Fix #3327: Add functionality for benchmark coverage (#3329) - Release process notes have been improved. (#4228) - ``pyproject.toml`` has been added to the sdist. - Build and deploy dev/master documentation using GitHub Actions (#4852) - Website now deploys itself (#4870) - build doc on circle ci and link artifact (#4881) - Benchmarks can now run on older scikit-image commits (#4891) - Website analytics are tracked using plausible.io and can be visualized on https://plausible.io/scikit-image.org (#4893) - Artifacts for the documentation build are now found in each pull request (#4881). - Documentation source files can now be written in Markdown in addition to ReST, thanks to ``myst`` (#4863). - update trove classifiers and tests for Python 3.9 + fix pytest config (#5052) - fix Azure Pipelines, pytest config, and trove classifiers for Python 3.8 (#5054) - Moved our testing from Travis to GitHub Actions (#5074) - We now build our wheels on GitHub Actions on the main repo using cibuildwheel. Many thanks to the matplotlib and scikit-learn developers for paving the way for us! (#5080) - Disable Travis-CI builds (#5099, #5111) - Improvements to CircleCI build: no parallelization and caching) (#5097, #5119) Other Pull Requests ------------------- - Manage iradon input and output data type (#4298) - random walker: Display a warning when the probability is outsite [0,1] for a given tol (#4631) - MAINT: remove unused cython file (#4633) - Forget legacy data dir (#4662) - Setup longdesc markdown and switch to 0.18dev (#4663) - Optional pooch dependency (#4666) - Adding new default values to functions on doc/examples/segmentation/plot_ncut (#4676) - Reintroduced convert with a strong deprecation warning (#4681) - In release notes, better describe skimage's relationship to ecosystem (#4689) - Perform some todo tasks for 0.18 (#4690) - Perform todo tasks for 0.17! (#4691) - suppressing warnings from gallery examples (#4692) - release notes for 0.17.2 (#4702) - Fix gallery example mentioning deprecated argument (#4706) - Specify the encoding of files opened in the setup phase (#4713) - Remove duplicate fused type definition (#4724) - Blacklist cython version 0.29.18 (#4730) - Fix CI failures related to conversion of np.floating to dtype (#4731) - Fix Ci failures related to array ragged input numpy deprecation (#4735) - Unwrap decorators before resolving link to source (sphinx.ext.linkcode) (#4740) - Fix plotting error in j-invariant denoising tutorial (#4744) - Highlight all source lines with HTML doc "source" links (sphinx.ext.linkcode) (#4746) - Turn checklist boxes into bullet points inside the pull request template (#4747) - Deprecate (min_distance < 1) and (footprint.size < 2) in peak_local_max (#4753) - forbid dask 2.17.0 to fix CI (#4758) - try to fix ci which is broken because of pyqt5 last version (#4788) - Remove unused variable in j invariant docs (#4792) - include all md files in manifest.in (#4793) - Remove additional "::" to make plot directive work. (#4798) - Use optipng to compress images/thumbnails in our gallery (#4800) - Fix runtime warning in blob.py (#4803) - Add TODO task for sphinx-gallery>=0.9.0 to remove enforced thumbnail_size (#4804) - Change SSIM code example to use real MSE (#4807) - Let biomed example load image data with Pooch. (#4809) - Tweak threshold_otsu error checking - closes #4811 (#4812) - Ensure assert messages from Cython rank filters are informative (#4815) - Simplify equivalent_diameter function (#4819) - DOC: update subpackage descriptions (#4825) - style: be explicit when stacking arrays (#4826) - MAINT: import Iterable from collections.abc (Python 3.9 compatibility) (#4834) - Silence several warnings in the test suite (#4837) - Silence a few RuntimeWarnings in the test suite (#4838) - handle color string mapping correctly (#4840) - DOC: Autoformat docstrings in ``io.*.py`` (#4845) - Update min req for pillow due to CVE-2020-10379 and co. (#4861) - DOC: First pass at format conversion, rst -> myst (#4863) - Fixed typo in comment (#4867) - Alternative wording for install guide PR #4750 (#4871) - DOC: Clarify condition on unique vertices returned by marching cubes (#4872) - Remove unmaintained wiki page link in contributor guidelines (#4873) - new matomo config (#4879) - Fix Incorrect documentation for skimage.util.img_as_int Issue (#4888) - Minor edit for proper doc rendering (#4897) - Changelog back-log (#4898) - minor refactoring in phase_cross_correlation (#4901) - Fix draw.circle/disk deprecation message, fixes #4884 (#4908) - Add versionchanged tag for new opt param in measure.find_contours() (#4909) - Declare build dependencies (#4920) - Replace words with racial connotations (#4921) - Fixes to apply_parallel for functions working with multichannel data (#4927) - Improve description of h_maxima and h_minima functions (#4928) (#4929) - CI: Skip doc build for PYTHONOPTIMIZE=2 (#4930) - MAINT: Remove custom fused type in skimage/morphology/_max_tree.pyx (#4931) - MAINT: remove numpydoc option, issue fixed in numpydoc 1.0 (#4932) - modify development version string to allow use with NumpyVersion (#4947) - CI: Add verbose option to avoid travis timeout for OSX install script (#4956) - Fix CI: ban sphinx-gallery 0.8.0 (#4960) - Alias for data.chelsea: data.cat() (#4962) - Fix typo. (#4963) - CI: Use Travis wait improved to avoid timeout for OSX builds (#4965) - Small enhancement in "Contour finding" example: Removed unused variable n (#4967) - MAINT: remove unused imports (#4968) - MAINT: Remove conditional import on networkx (#4970) - forbid latest version of pyqt (#4973) - Remove warnings/explicit settings on feature, restoration (#4974) - Docstring improvements for label and regionprops_label (#4983) - try to fix timeout problem with circleci (#4986) - improve Euler number example (#4989) - [website] Standardize Documentation index page. (#4990) - Proofread INSTALL file. (#4991) - Catch leftover typos in INSTALL file. (#4992) - Let tifffile.imread handle additional keyword arguments (#4997) - Update docstring for random_noise function (#5001) - Update sphinx mapping for sklearn and numpy (#5003) - Update docstring slic superpixels (#5014) - Bump numpy versions to match scipy (kinda) (#5016) - Fix usage of numpy.pad for old versions of numpy (#5017) - [MRG] Update documentation to new data.camera() (#5018) - bumped plotly requirement for docs (#5021) - Fix IndexError when calling hough_line_peaks with too few angles (#5024) - Code simplification after latest numpy bump (#5027) - Fixes broken link to CODE_OF_CONDUCT.md (#5030) - Specify whether core dev should merge right after second approving review. (#5040) - Update pytest configuration to include ``test_`` functions (#5044) - MAINT Build fix for pyodide (#5059) - reduce OSX build time so that Travis is happy (#5067) - DOC: document the normalized kernel in prewitt_h, prewitt_v (#5076) - Some minor tweaks to CI (#5079) - removed usage of numpy's private functions from util.arraycrop (#5081) - peak_local_max: remove deprecated `indices` argument from examples (#5082) - Replace np.bool, np.float, and np.int with bool, float, and int (#5103, #5108) - change plausible script to track outbound links (#5115, #5123) - Remove Python 3.6 support (#5117, #5125) - Optimize ensure_spacing (#5062, #5135) 52 authors added to this release [alphabetical by first name or login] ---------------------------------------------------------------------- A warm thank you to all contributors who added to this release. A fraction of contributors were first-time contributors to open source and a much larger fraction first-time contributors to scikit-image. It's a great feeling for maintainers to welcome new contributors, and the diversity of scikit-image contributors is surely a big strength of the package. - Abhishek Arya - Abhishek Patil - Alexandre de Siqueira - Ben Nathanson - Cameron Blocker - Chris Roat - Christoph Gohlke - Clement Ng - Corey Harris - David McMahon - David Mellert - Devi Sandeep - Egor Panfilov - Emmanuelle Gouillart - François Boulogne - Genevieve Buckley - Gregory R. Lee - Harry Kwon - iofall (cedarfall) - Jan Funke - Juan Nunez-Iglesias - Julian Gilbey - Julien Jerphanion - kalpana - kolibril13 (kolibril13) - Kushaan Gupta - Lars Grüter - Marianne Corvellec - Mark Harfouche - Marvin Albert - Matthias Bussonnier - Max Frei - Nathan - neeraj3029 (neeraj3029) - Nick - notmatthancock (matt) - OGordon100 (OGordon100) - Owen Solberg - Riadh Fezzani - Robert Haase - Roman Yurchak - Ronak Sharma - Ross Barnowski - Ruby Werman - ryanlu41 (ryanlu41) - Sebastian Wallkötter - Shyam Saladi - Stefan van der Walt - Terence Honles - Volker Hilsenstein - Wendy Mak - Yogendra Sharma 41 reviewers added to this release [alphabetical by first name or login] ------------------------------------------------------------------------ - Abhishek Arya - Abhishek Patil - Alexandre de Siqueira - Ben Nathanson - Chris Roat - Clement Ng - Corey Harris - Cris Luengo - David Mellert - Egor Panfilov - Emmanuelle Gouillart - François Boulogne - Gregory R. Lee - Harry Kwon - Jan Funke - Juan Nunez-Iglesias - Julien Jerphanion - kalpana - Kushaan Gupta - Lars Grüter - Marianne Corvellec - Mark Harfouche - Marvin Albert - neeraj3029 - Nick - OGordon100 - Riadh Fezzani - Robert Haase - Ross Barnowski - Ruby Werman - ryanlu41 - Scott Trinkle - Sebastian Wallkötter - Stanley_Wang - Stefan van der Walt - Steven Brown - Stuart Mumford - Terence Honles - Volker Hilsenstein - Wendy Mak

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Re: scikit-image Digest, Vol 50, Issue 1
by Genevieve Buckley 13 Dec '20

13 Dec '20

Hi Chien-Cheng, The scikit-image release 0.18.0 is being prepared now (so hopefully it will be out soon). I think installing the release candidate will be the simplest way forward for you, until the official release 0.18.0 becomes available. You can install the latest release candidate into your anaconda environment with: pip install scikit-image==0.18.0rc2 Last, in case you are also interested to know what went wrong with trying to install the development version, I suspect the problem you had earlier is because of one of two possibilities: 1. You have not cloned the scikit-image repository from github, or 2. You have not changed directory in your terminal before running that conda install command. You'll need to move to the location of the scikit-image git repository with something like "cd Documents/Github/scikit-image" or "cd Documents\Github\scikit-image" before you can install it. There are a few other pre-requisites for a development installation (like a working C compiler, and a C++ compiler). These are listed as bullet points under the heading "Installing scikit-image for contributors" on the page you linked to: https://scikit-image.org/docs/dev/install.html#id4 I hope that helps, Genevieve On Fri, 11 Dec 2020 at 21:13, <scikit-image-request(a)python.org> wrote: > Send scikit-image mailing list submissions to > scikit-image(a)python.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.python.org/mailman3/lists/scikit-image.python.org/ > or, via email, send a message with subject or body 'help' to > scikit-image-request(a)python.org > > You can reach the person managing the list at > scikit-image-owner(a)python.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of scikit-image digest..." > > Today's Topics: > > 1. Installation question about skimage developer version > (Hung, C. (Chien-Cheng)) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 11 Dec 2020 10:01:12 +0000 > From: "Hung, C. (Chien-Cheng)" <c.hung(a)uu.nl> > Subject: [scikit-image] Installation question about skimage developer > version > To: "scikit-image(a)python.org" <scikit-image(a)python.org> > Message-ID: <AM6PR05MB4999E409E9F2D0A6FA8455808FCA0(a)AM6PR05MB4999.eur > prd05.prod.outlook.com> > Content-Type: multipart/related; boundary="_004_AM6PR05MB4999E4 > 09E9F2D0A6FA8455808FCA0AM6PR05MB4999eurp_"; > type="multipart/alternative" > > Dear scikit team, > > My name is Chien-Cheng and I am trying to use scikit-image to do some > image segmentation. > The method I choose is called "Training segmentation" ( > https://scikit-image.org/docs/dev/auto_examples/segmentation/plot_trainable… > ). > Currently, I am trying to run the example of the training method and I got > a few questions. > The latest skimage version I have in the Anaconda is 0.17.2. > But I found the training method seems only applicable for the developer > version 0.19.0.dev0 since some of the attribute in the script is missing in > the version of 0.17.2 (for example, there is an error called > AttributeError: module 'skimage.feature' has no attribute > 'multiscale_basic_features' after running the example script with 0.17.2). > Also, I cannot find the example of the training method in the version of > 0.17.2 so I figure the training methods require the developer version. > > I have tried installing the contributor/developer version in the conda > environment by following the instruction ( > https://scikit-image.org/docs/dev/install.html#id6) but when I was > running the third comment "conda install `for i in > requirements/{default,build,test}.txt; do echo -n " --file $i "; done`. The > console shows me the error below: > > [cid:image002.jpg@01D6CFE7.99D9EF80] > > I really don't know what the problem might be so I would like to turn to > your help. > There are two questions I have so far: > > 1. Do I need to install the developer version to use the training > methods? > 2. If so, did I install the developer version with the correct > procedure? If yes, how to solve the issue I have above? > > Looking forward to your reply, thanks! > > Best regards, > Chien-Cheng > > > > > > > > > > > > > > > > > > >

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Installation question about skimage developer version
by Hung, C. (Chien-Cheng) 12 Dec '20

12 Dec '20

Dear scikit team, My name is Chien-Cheng and I am trying to use scikit-image to do some image segmentation. The method I choose is called "Training segmentation" (https://scikit-image.org/docs/dev/auto_examples/segmentation/plot_trainable…). Currently, I am trying to run the example of the training method and I got a few questions. The latest skimage version I have in the Anaconda is 0.17.2. But I found the training method seems only applicable for the developer version 0.19.0.dev0 since some of the attribute in the script is missing in the version of 0.17.2 (for example, there is an error called AttributeError: module 'skimage.feature' has no attribute 'multiscale_basic_features' after running the example script with 0.17.2). Also, I cannot find the example of the training method in the version of 0.17.2 so I figure the training methods require the developer version. I have tried installing the contributor/developer version in the conda environment by following the instruction (https://scikit-image.org/docs/dev/install.html#id6) but when I was running the third comment "conda install `for i in requirements/{default,build,test}.txt; do echo -n " --file $i "; done`. The console shows me the error below: [cid:image002.jpg@01D6CFE7.99D9EF80] I really don't know what the problem might be so I would like to turn to your help. There are two questions I have so far: 1. Do I need to install the developer version to use the training methods? 2. If so, did I install the developer version with the correct procedure? If yes, how to solve the issue I have above? Looking forward to your reply, thanks! Best regards, Chien-Cheng

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Smil release 0.10.0
by Jose-Marcio Martins da Cruz 10 Dec '20

10 Dec '20

Hello, Although Smil is not part os Scikit-image, it may be of interest to some of you. I'm glad to announce the release 0.11.0 of Smil, our Mathematical Morphology library. Smil is a library completely written in C++ with a Python interface (thanks to Swig). This is maintenance release with some few changes. Smil is the successor of other Mathematical Morphology software we created since the 70s : Xlim, Xlim3D, Micromorph, Morph-M and now Smil. Mathematical Morphology is a discipline created at our research department in the 60s by Georges Matheron and Jean Serra. The web site of the library is : http://smil.cmm.mines-paristech.fr You can have have a quick global view of what functions are available inside Smil here : http://smil.cmm.mines-paristech.fr/publis/SmilQuickReference.pdf Release notes here : http://smil.cmm.mines-paristech.fr/doc/_release_notes.html Feel free to make comments or give some feedback. Best regards -- --------------------------------------------------------------- Jose Marcio MARTINS DA CRUZ, Ph.D. Ecole des Mines de Paris Centre de Morphologie Mathématique --------------------------------------------------------------- Spam : http://amzn.to/LEscRu ou http://bit.ly/SpamJM ---------------------------------------------------------------

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Smil release 0.10.0
by Jose Marcio Martins da Cruz 10 Dec '20

10 Dec '20

Hello, Although Smil is not part os Scikit-image, it may be of interest to some of you. I'm glad to announce the release 0.11.0 of Smil, our Mathematical Morphology library. Smil is a library completely written in C++ with a Python interface (thanks to Swig). This is maintenance release with some few changes. Smil is the successor of other Mathematical Morphology software we created since the 70s : Xlim, Xlim3D, Micromorph, Morph-M and now Smil. Mathematical Morphology is a discipline created at our research department in the 60s by Georges Matheron and Jean Serra. The web site of the library is : http://smil.cmm.mines-paristech.fr You can have have a quick global view of what functions are available inside Smil here : http://smil.cmm.mines-paristech.fr/publis/SmilQuickReference.pdf Release notes here : http://smil.cmm.mines-paristech.fr/doc/_release_notes.html Feel free to make comments or give some feedback. Best regards -- --------------------------------------------------------------- Jose Marcio MARTINS DA CRUZ, Ph.D. Ecole des Mines de Paris Centre de Morphologie Mathématique --------------------------------------------------------------- Spam : http://amzn.to/LEscRu ou http://bit.ly/SpamJM ---------------------------------------------------------------

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scikit-image December 2020