Mailman 3 - NumPy-Discussion

dtype=object arrays not treated like Python list?
by Steven G. Johnson 29 Mar '24

29 Mar '24

Should a dtype=object array be treated more like Python lists for type detection/coercion reasons? Currently, they are treated quite differently: >>> import numpy as np >>> np.isfinite([1,2,3]) array([ True, True, True]) >>> np.isfinite(np.asarray([1,2,3], dtype=object)) Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: ufunc 'isfinite' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe'' The reason I ask is that we ran into something similar when trying to pass wrappers around Julia arrays to Python. A Julia `Any[]` array is much like a Python list or a Numpy `object` array, and exposed in Python as a subtype of MutableSequence, but we found that it was treated by NumPy as more like a Numpy `object` array than a Python list (https://github.com/JuliaPy/PythonCall.jl/issues/486). Would it be desirable to treat a 1d Numpy `object` array more like a Python `list`? Or is there a way for externally defined types to opt-in to the `list` behavior? (I couldn't figure out in the numpy source code where `list` is being special-cased?)

4 3

Polyfit error in displacement
by Luca Bertolotti 26 Mar '24

26 Mar '24

Hello in a vb program they use 3rd degree approx and get this value including displacement:(SC) [image: image.png] Ii think that i'm doing the same with numpy but I get different value does anyone can help me please radious = [1821, 1284, 957, 603,450, 245] y = [6722, 6940, 7227, 7864,8472, 10458] p = np.polyfit(radious, y, 3,) t = np.polyval(p, radious) [ 6703.33694696 7061.23784145 7051.49974149 7838.84623289 8654.47847319 10373.60076402] You can see polyval is difference from the sc. of the table Any help is really appreciated

5 8

Automatic Clipping of array to upper / lower bounds of dtype
by Dom Grigonis 25 Mar '24

25 Mar '24

Hello, Can't find answer to this anywhere. What I would like is to automatically clip the values if they breach the bounds. I have done a simple clipping, and overwritten __iadd__, __isub__, __setitem__, … But I am wandering if there is a specified way to do this. Or maybe at least a centralised place exists to do such thing? E.g. Only 1 method to override? Regards and thanks, dgpb

5 7

ANN: DataLab v0.14
by Pierre Raybaut 22 Mar '24

22 Mar '24

Hello everyone, We're thrilled to announce the release of DataLab v0.14! https://datalab-platform.com DataLab is an open-source platform for scientific and technical data processing and visualization, based on NumPy, SciPy, ... and Qt. It's extendable with plugins, and works seamlessly as a complementary tool with your IDE (e.g. #Spyder, VSCode, ...) and Project Jupyter notebooks. Once again, this release is the result of the feedback and contributions of our early adopters. We're grateful for your support and look forward to your continued insights. 💥 New Features: - Brand new HDF5 browser: now shows all datasets, group properties and attributes. - New "Text file import assistant: various enhancements. - Other improvements (colormap inversion, signal/image histogram, ...) 🚀 New Binder environment to test DataLab online without installing anything: https://mybinder.org/v2/gh/DataLab-Platform/DataLab/binder-environments?url… 💡 You have a project or a use case in mind? (we can even write a tutorial for you...) You want to contribute? We'd love to hear from you! So please, don't hesitate to contact us or to open an issue ( https://github.com/Codra-Ingenierie-Informatique/DataLab/issues/new/choose) on our GitHub project for any request or question. Thank you for taking the time to read my announcement. Looking forward to your thoughts. Best, Pierre Raybaut

1 0

Accelerated NumPy with Weld compiler
by Hemant Singh 21 Mar '24

21 Mar '24

Stanford and MIT jointly developed the Weld language and compiler to run NumPy and Pandas significantly faster, 10x-250x. My company has changed the compiler to be production ready. Anyone interested in trialing this compiler, please contact me with your work email. Best, Hemant

2 1

Add to NumPy a function to compute cumulative sums from 0.
by john.dawson＠camlingroup.com 20 Mar '24

20 Mar '24

`cumsum` computes the sum of the first k summands for every k from 1. Judging by my experience, it is more often useful to compute the sum of the first k summands for every k from 0, as `cumsum`'s behaviour leads to fencepost-like problems. https://en.wikipedia.org/wiki/Off-by-one_error#Fencepost_error For example, `cumsum` is not the inverse of `diff`. I propose adding a function to NumPy to compute cumulative sums beginning with 0, that is, an inverse of `diff`. It might be called `cumsum0`. The following code is probably not the best way to implement it, but it illustrates the desired behaviour. ``` def cumsum0(a, axis=None, dtype=None, out=None): """ Return the cumulative sum of the elements along a given axis, beginning with 0. cumsum0 does the same as cumsum except that cumsum computes the sum of the first k summands for every k from 1 and cumsum, from 0. Parameters ---------- a : array_like Input array. axis : int, optional Axis along which the cumulative sum is computed. The default (None) is to compute the cumulative sum over the flattened array. dtype : dtype, optional Type of the returned array and of the accumulator in which the elements are summed. If `dtype` is not specified, it defaults to the dtype of `a`, unless `a` has an integer dtype with a precision less than that of the default platform integer. In that case, the default platform integer is used. out : ndarray, optional Alternative output array in which to place the result. It must have the same shape and buffer length as the expected output but the type will be cast if necessary. See :ref:`ufuncs-output-type` for more details. Returns ------- cumsum0_along_axis : ndarray. A new array holding the result is returned unless `out` is specified, in which case a reference to `out` is returned. If `axis` is not None the result has the same shape as `a` except along `axis`, where the dimension is smaller by 1. See Also -------- cumsum : Cumulatively sum array elements, beginning with the first. sum : Sum array elements. trapz : Integration of array values using the composite trapezoidal rule. diff : Calculate the n-th discrete difference along given axis. Notes ----- Arithmetic is modular when using integer types, and no error is raised on overflow. ``cumsum0(a)[-1]`` may not be equal to ``sum(a)`` for floating-point values since ``sum`` may use a pairwise summation routine, reducing the roundoff-error. See `sum` for more information. Examples -------- >>> a = np.array([[1, 2, 3], [4, 5, 6]]) >>> a array([[1, 2, 3], [4, 5, 6]]) >>> np.cumsum0(a) array([ 0, 1, 3, 6, 10, 15, 21]) >>> np.cumsum0(a, dtype=float) # specifies type of output value(s) array([ 0., 1., 3., 6., 10., 15., 21.]) >>> np.cumsum0(a, axis=0) # sum over rows for each of the 3 columns array([[0, 0, 0], [1, 2, 3], [5, 7, 9]]) >>> np.cumsum0(a, axis=1) # sum over columns for each of the 2 rows array([[ 0, 1, 3, 6], [ 0, 4, 9, 15]]) ``cumsum(b)[-1]`` may not be equal to ``sum(b)`` >>> b = np.array([1, 2e-9, 3e-9] * 1000000) >>> np.cumsum0(b)[-1] 1000000.0050045159 >>> b.sum() 1000000.0050000029 """ empty = a.take([], axis=axis) zero = empty.sum(axis, dtype=dtype, keepdims=True) later_cumsum = a.cumsum(axis, dtype=dtype) return concatenate([zero, later_cumsum], axis=axis, dtype=dtype, out=out) ```

14 25

ANN: SciPy 1.13.0rc1 -- please test
by Tyler Reddy 20 Mar '24

20 Mar '24

Hi all, On behalf of the SciPy development team I'm pleased to announce the release candidate SciPy 1.13.0rc1. Please help us test this pre-release. Sources and binary wheels can be found at: https://pypi.org/project/scipy/ and at: https://github.com/scipy/scipy/releases/tag/v1.13.0rc1 One of a few ways to install the release candidate with pip: pip install scipy==1.13.0rc1 ========================== SciPy 1.13.0 Release Notes ========================== Note: SciPy 1.13.0 is not released yet! SciPy 1.13.0 is the culmination of 3 months of hard work. This out-of-band release aims to support NumPy ``2.0.0``, and is backwards compatible to NumPy ``1.22.4``. The version of OpenBLAS used to build the PyPI wheels has been increased to ``0.3.26``. This release requires Python 3.9+ and NumPy 1.22.4 or greater. For running on PyPy, PyPy3 6.0+ is required. ************************** Highlights of this release ************************** - Support for NumPy ``2.0.0``. - Interactive examples have been added to the documentation, allowing users to run the examples locally on embedded Jupyterlite notebooks in their browser. - Preliminary 1D array support for the COO and DOK sparse formats. - Several `scipy.stats` functions have gained support for additional ``axis``, ``nan_policy``, and ``keepdims`` arguments. `scipy.stats` also has several performance and accuracy improvements. ************ New features ************ `scipy.integrate` improvements ============================== - The ``terminal`` attribute of `scipy.integrate.solve_ivp` ``events`` callables now additionally accepts integer values to specify a number of occurrences required for termination, rather than the previous restriction of only accepting a ``bool`` value to terminate on the first registered event. `scipy.io` improvements ======================= - `scipy.io.wavfile.write` has improved ``dtype`` input validation. `scipy.interpolate` improvements ================================ - The Modified Akima Interpolation has been added to ``interpolate.Akima1DInterpolator``, available via the new ``method`` argument. - ``RegularGridInterpolator`` gained the functionality to compute derivatives in place. For instance, ``RegularGridInterolator((x, y), values, method="cubic")(xi, nu=(1, 1))`` evaluates the mixed second derivative, :math:`\partial^2 / \partial x \partial y` at ``xi``. - Performance characteristics of tensor-product spline methods of ``RegularGridInterpolator`` have been changed: evaluations should be significantly faster, while construction might be slower. If you experience issues with construction times, you may need to experiment with optional keyword arguments ``solver`` and ``solver_args``. Previous behavior (fast construction, slow evaluations) can be obtained via `"*_legacy"` methods: ``method="cubic_legacy"`` is exactly equivalent to ``method="cubic"`` in previous releases. See ``gh-19633`` for details. `scipy.signal` improvements =========================== - Many filter design functions now have improved input validation for the sampling frequency (``fs``). `scipy.sparse` improvements =========================== - ``coo_array`` now supports 1D shapes, and has additional 1D support for ``min``, ``max``, ``argmin``, and ``argmax``. The DOK format now has preliminary 1D support as well, though only supports simple integer indices at the time of writing. - Experimental support has been added for ``pydata/sparse`` array inputs to `scipy.sparse.csgraph`. - ``dok_array`` and ``dok_matrix`` now have proper implementations of ``fromkeys``. - ``csr`` and ``csc`` formats now have improved ``setdiag`` performance. `scipy.spatial` improvements ============================ - ``voronoi_plot_2d`` now draws Voronoi edges to infinity more clearly when the aspect ratio is skewed. `scipy.special` improvements ============================ - All Fortran code, namely, ``AMOS``, ``specfun``, and ``cdflib`` libraries that the majority of special functions depend on, is ported to Cython/C. - The function ``factorialk`` now also supports faster, approximate calculation using ``exact=False``. `scipy.stats` improvements ========================== - `scipy.stats.rankdata` and `scipy.stats.wilcoxon` have been vectorized, improving their performance and the performance of hypothesis tests that depend on them. - ``stats.mannwhitneyu`` should now be faster due to a vectorized statistic calculation, improved caching, improved exploitation of symmetry, and a memory reduction. ``PermutationMethod`` support was also added. - `scipy.stats.mood` now has ``nan_policy`` and ``keepdims`` support. - `scipy.stats.brunnermunzel` now has ``axis`` and ``keepdims`` support. - `scipy.stats.friedmanchisquare`, `scipy.stats.shapiro`, `scipy.stats.normaltest`, `scipy.stats.skewtest`, `scipy.stats.kurtosistest`, `scipy.stats.f_oneway`, `scipy.stats.alexandergovern`, `scipy.stats.combine_pvalues`, and `scipy.stats.kstest` have gained ``axis``, ``nan_policy`` and ``keepdims`` support. - `scipy.stats.boxcox_normmax` has gained a ``ymax`` parameter to allow user specification of the maximum value of the transformed data. - `scipy.stats.vonmises` ``pdf`` method has been extended to support ``kappa=0``. The ``fit`` method is also more performant due to the use of non-trivial bounds to solve for ``kappa``. - High order ``moment`` calculations for `scipy.stats.powerlaw` are now more accurate. - The ``fit`` methods of `scipy.stats.gamma` (with ``method='mm'``) and `scipy.stats.loglaplace` are faster and more reliable. - `scipy.stats.goodness_of_fit` now supports the use of a custom ``statistic`` provided by the user. - `scipy.stats.wilcoxon` now supports ``PermutationMethod``, enabling calculation of accurate p-values in the presence of ties and zeros. - `scipy.stats.monte_carlo_test` now has improved robustness in the face of numerical noise. - `scipy.stats.wasserstein_distance_nd` was introduced to compute the Wasserstein-1 distance between two N-D discrete distributions. ******************* Deprecated features ******************* - Complex dtypes in ``PchipInterpolator`` and ``Akima1DInterpolator`` have been deprecated and will raise an error in SciPy 1.15.0. If you are trying to use the real components of the passed array, use ``np.real`` on ``y``. ****************************** Backwards incompatible changes ****************************** ************* Other changes ************* - The second argument of `scipy.stats.moment` has been renamed to ``order`` while maintaining backward compatibility. ******* Authors ******* * Name (commits) * h-vetinari (50) * acceptacross (1) + * Petteri Aimonen (1) + * Francis Allanah (2) + * Jonas Kock am Brink (1) + * anupriyakkumari (12) + * Aman Atman (2) + * Aaditya Bansal (1) + * Christoph Baumgarten (2) * Sebastian Berg (4) * Nicolas Bloyet (2) + * Matt Borland (1) * Jonas Bosse (1) + * Jake Bowhay (25) * Matthew Brett (1) * Dietrich Brunn (7) * Evgeni Burovski (48) * Matthias Bussonnier (4) * Cale (1) + * CJ Carey (4) * Thomas A Caswell (1) * Sean Cheah (44) + * Lucas Colley (97) * com3dian (1) * Gianluca Detommaso (1) + * Thomas Duvernay (1) * DWesl (2) * f380cedric (1) + * fancidev (13) + * Daniel Garcia (1) + * Lukas Geiger (3) * Ralf Gommers (139) * Matt Haberland (79) * Tessa van der Heiden (2) + * inky (3) + * Jannes Münchmeyer (2) + * Aditya Vidyadhar Kamath (2) + * Agriya Khetarpal (1) + * Andrew Landau (1) + * Eric Larson (7) * Zhen-Qi Liu (1) + * Adam Lugowski (4) * m-maggi (6) + * Chethin Manage (1) + * Ben Mares (1) * Chris Markiewicz (1) + * Mateusz Sokół (3) * Daniel McCloy (1) + * Melissa Weber Mendonça (6) * Josue Melka (1) * Michał Górny (4) * Juan Montesinos (1) + * Juan F. Montesinos (1) + * Takumasa Nakamura (1) * Andrew Nelson (26) * Praveer Nidamaluri (1) * Yagiz Olmez (5) + * Dimitri Papadopoulos Orfanos (1) * Drew Parsons (1) + * Tirth Patel (7) * Matti Picus (3) * Rambaud Pierrick (1) + * Ilhan Polat (30) * Quentin Barthélemy (1) * Tyler Reddy (81) * Pamphile Roy (10) * Atsushi Sakai (4) * Daniel Schmitz (10) * Dan Schult (16) * Eli Schwartz (4) * Stefanie Senger (1) + * Scott Shambaugh (2) * Kevin Sheppard (2) * sidsrinivasan (4) + * Samuel St-Jean (1) * Albert Steppi (30) * Adam J. Stewart (4) * Kai Striega (3) * Ruikang Sun (1) + * Mike Taves (1) * Nicolas Tessore (3) * Benedict T Thekkel (1) + * Will Tirone (4) * Jacob Vanderplas (2) * Christian Veenhuis (1) * Isaac Virshup (2) * Ben Wallace (1) + * Xuefeng Xu (3) * Xiao Yuan (5) * Irwin Zaid (6) * Mathias Zechmeister (1) + A total of 91 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 1.13.0 ************************ * `#1603 <https://github.com/scipy/scipy/issues/1603>`__: binomial ppf gives bogus results for small binomial probability... * `#2254 <https://github.com/scipy/scipy/issues/2254>`__: linalg.eig test failure (test_singular) (Trac #1735) * `#8398 <https://github.com/scipy/scipy/issues/8398>`__: Precision of CDFLIB too low * `#9950 <https://github.com/scipy/scipy/issues/9950>`__: "++" initialization in kmeans2 fails for univariate data * `#10317 <https://github.com/scipy/scipy/issues/10317>`__: scipy.stats.nbinom.interval returns wrong result for p=1 * `#10569 <https://github.com/scipy/scipy/issues/10569>`__: API: \`s\` argument different in scipy.fft and numpy.fft * `#11577 <https://github.com/scipy/scipy/issues/11577>`__: generalized eigenvalues are sometimes wrong (on some hardware) * `#14176 <https://github.com/scipy/scipy/issues/14176>`__: Add option for terminating solver after n events * `#14220 <https://github.com/scipy/scipy/issues/14220>`__: Documentation for dctn/idctn s-parameter is confusing * `#14450 <https://github.com/scipy/scipy/issues/14450>`__: Passing a numpy array as sampling frequency to signal.iirfilter... * `#14586 <https://github.com/scipy/scipy/issues/14586>`__: Problem with freeing-up memory of matrix * `#15039 <https://github.com/scipy/scipy/issues/15039>`__: BUG: sparse.dok_matrix.fromkeys method totally nonfunctional * `#15108 <https://github.com/scipy/scipy/issues/15108>`__: BUG: Seg. fault in scipy.sparse.linalg tests in PROPACK * `#16098 <https://github.com/scipy/scipy/issues/16098>`__: BLD:1.8.0: SciPy is not LTO ready * `#16792 <https://github.com/scipy/scipy/issues/16792>`__: BUG: Manually vectorizing scipy.linalg.expm fails in version... * `#17172 <https://github.com/scipy/scipy/issues/17172>`__: BUG: scipy.linalg.expm, coshm, sinhm and tanhm fail for read-only... * `#17436 <https://github.com/scipy/scipy/issues/17436>`__: BUG: linalg.cholesky: segmentation fault with large matrix * `#17530 <https://github.com/scipy/scipy/issues/17530>`__: Unnecessary approximation in \`scipy.stats.wilcoxon(x, y)\` * `#17681 <https://github.com/scipy/scipy/issues/17681>`__: BUG: special: \`pbvv_seq\` is broken. * `#18086 <https://github.com/scipy/scipy/issues/18086>`__: BUG: \`scipy.linalg.expm\` generates inconsistent results between... * `#18089 <https://github.com/scipy/scipy/issues/18089>`__: DOC: <Scaling due to window not clear for spectrum and density> * `#18166 <https://github.com/scipy/scipy/issues/18166>`__: ENH: stats.vonmises.pdf: return 1/(2pi) when kappa=0 * `#18408 <https://github.com/scipy/scipy/issues/18408>`__: MAINT: status of C++17 in the interregnum of meson without native... * `#18423 <https://github.com/scipy/scipy/issues/18423>`__: ENH: Adding the SDMN Fortran routine to the python Wrapped functions. * `#18678 <https://github.com/scipy/scipy/issues/18678>`__: BUG: scipy.special.stdtrit is not thread-safe for df.size > 500 * `#18722 <https://github.com/scipy/scipy/issues/18722>`__: DOC: in optimize.quadratic_assignment 2opt method, partial_match... * `#18902 <https://github.com/scipy/scipy/issues/18902>`__: DOC: make default bounds in scipy.optimize.linprog more obvious * `#19088 <https://github.com/scipy/scipy/issues/19088>`__: \`pull-request-labeler\` misbehaving and therefore disabled again * `#19181 <https://github.com/scipy/scipy/issues/19181>`__: TST: improve array API test skip decorators * `#19225 <https://github.com/scipy/scipy/issues/19225>`__: stats.t.fit() with own optimizer (e.g. to use Nelder-Mead) fails... * `#19486 <https://github.com/scipy/scipy/issues/19486>`__: Query: Where is cdflib used in SciPy code? * `#19573 <https://github.com/scipy/scipy/issues/19573>`__: scipy.fft.fht - documentation issue * `#19584 <https://github.com/scipy/scipy/issues/19584>`__: BUG: MATLAB expm vs scipy.linalg.expm: overflow/invalid value... * `#19596 <https://github.com/scipy/scipy/issues/19596>`__: BENCH: spatial.distance.\* "non-xdist" benchmarks * `#19605 <https://github.com/scipy/scipy/issues/19605>`__: BUG: wheel runs have a \*lot\* of test fails at the moment. * `#19642 <https://github.com/scipy/scipy/issues/19642>`__: Speeding up Mann-Whitney U-Test * `#19653 <https://github.com/scipy/scipy/issues/19653>`__: ENH: Voronoi diagram gives unexpected results from scipy.spatial * `#19659 <https://github.com/scipy/scipy/issues/19659>`__: BUG: savemat(..., format="4") throws ValueError errorneously... * `#19678 <https://github.com/scipy/scipy/issues/19678>`__: BUG: scipy.stats.theilslopes returns invalid data when input... * `#19683 <https://github.com/scipy/scipy/issues/19683>`__: BUG/TST: cluster: incorrect test for \`seed\` param of {\`kmeans\`,... * `#19729 <https://github.com/scipy/scipy/issues/19729>`__: DOC: Add interactive examples with jupyterlite-sphinx * `#19732 <https://github.com/scipy/scipy/issues/19732>`__: DOC: Likelihood function depending on censoring type * `#19733 <https://github.com/scipy/scipy/issues/19733>`__: BUG: \`pythran\` min version not enforced * `#19737 <https://github.com/scipy/scipy/issues/19737>`__: TST: io: \`test_fortranfiles_mixed_record\` fails with numpy... * `#19739 <https://github.com/scipy/scipy/issues/19739>`__: BUG: pchip interpolation of complex values is buggy due to sign... * `#19740 <https://github.com/scipy/scipy/issues/19740>`__: CI, MAINT: some easy cleanups for Python version * `#19754 <https://github.com/scipy/scipy/issues/19754>`__: MAINT, TST: test_public_api.py can fail with NumPy main, via... * `#19767 <https://github.com/scipy/scipy/issues/19767>`__: Build warnings from SuperLU fixed upstream * `#19772 <https://github.com/scipy/scipy/issues/19772>`__: DOC: stats: The docstring for \`scipy.stats.crystalball\` needs... * `#19774 <https://github.com/scipy/scipy/issues/19774>`__: DOC: Detail what "concatenate" means in the context of \`spatial.transform.Rotation.concatenate\` * `#19799 <https://github.com/scipy/scipy/issues/19799>`__: DOC: array types: update array validation guidance * `#19813 <https://github.com/scipy/scipy/issues/19813>`__: BUG: typo in specfun.f? * `#19831 <https://github.com/scipy/scipy/issues/19831>`__: Test failures with OpenBLAS 0.3.26 * `#19835 <https://github.com/scipy/scipy/issues/19835>`__: DOC: \`fft\` missing from list of subpackages * `#19836 <https://github.com/scipy/scipy/issues/19836>`__: DOC: remove incorrect sentence about subpackage imports * `#19846 <https://github.com/scipy/scipy/issues/19846>`__: CI: pre-release Linux job isn't using NumPy pre-release anymore * `#19848 <https://github.com/scipy/scipy/issues/19848>`__: \`_lib._util.MapWrapper\` uses multiprocessing with \`fork\`,... * `#19854 <https://github.com/scipy/scipy/issues/19854>`__: scipy.special.logsumexp for complex input with return_sign=True... * `#19862 <https://github.com/scipy/scipy/issues/19862>`__: DOC: documentation for transpose operator for sparse matrices... * `#19867 <https://github.com/scipy/scipy/issues/19867>`__: New ndimage and RBFInterpolator test failures in pre-release... * `#19896 <https://github.com/scipy/scipy/issues/19896>`__: BUG: \`special.nctdtr\` broken in main * `#19897 <https://github.com/scipy/scipy/issues/19897>`__: DOC: scipy.stats.unitary_group does not specify dim>1 * `#19928 <https://github.com/scipy/scipy/issues/19928>`__: TST: special: array types: test tol failure with \`torch\` backend * `#19943 <https://github.com/scipy/scipy/issues/19943>`__: BUG: sparse: CSC.setdiag is slower than converting to LIL and... * `#19948 <https://github.com/scipy/scipy/issues/19948>`__: BUG: scipy.sparse.linalg.gmres fails when provided x0 solves... * `#19951 <https://github.com/scipy/scipy/issues/19951>`__: BUG: boolean masking broken for sparse array classes * `#19963 <https://github.com/scipy/scipy/issues/19963>`__: DOC: scipy.optimize with large differences in parameter scales * `#19974 <https://github.com/scipy/scipy/issues/19974>`__: DOC/REL: retroactively add missing expired deprecations to 1.12.0... * `#19993 <https://github.com/scipy/scipy/issues/19993>`__: BUG: F_INT type conflict with f2py translation of INTEGER type... * `#19998 <https://github.com/scipy/scipy/issues/19998>`__: DOC: Boundary conditions in splrep * `#20001 <https://github.com/scipy/scipy/issues/20001>`__: BUG: scipy.stats.loglaplace may return negative moments * `#20009 <https://github.com/scipy/scipy/issues/20009>`__: BUG: ShortTimeFFT fails with complex input * `#20012 <https://github.com/scipy/scipy/issues/20012>`__: MAINT: Use NumPy sliding_window_view instead of as_strided in... * `#20014 <https://github.com/scipy/scipy/issues/20014>`__: TST: signal: TestCorrelateReal failing on Meson 3.12 job * `#20031 <https://github.com/scipy/scipy/issues/20031>`__: TST: prefer \`pytest.warns\` over \`np.testing.assert_warns\` * `#20034 <https://github.com/scipy/scipy/issues/20034>`__: TST: linalg: test_decomp_cossin.py::test_cossin_separate[float64]... * `#20036 <https://github.com/scipy/scipy/issues/20036>`__: MAINT: implement scipy.stats.powerlaw._munp * `#20041 <https://github.com/scipy/scipy/issues/20041>`__: BUG: Using LinearConstraint with optimize.differential_evolution * `#20042 <https://github.com/scipy/scipy/issues/20042>`__: BUG: scipy.stats.percentileofscore has a mistake * `#20043 <https://github.com/scipy/scipy/issues/20043>`__: equality used to compare floating point numbers (test_bootstrap_alternative) * `#20060 <https://github.com/scipy/scipy/issues/20060>`__: BUG: stacking two dok_array produces a NotImplementedError about... * `#20062 <https://github.com/scipy/scipy/issues/20062>`__: MAINT, TST: test failures against NumPy main * `#20071 <https://github.com/scipy/scipy/issues/20071>`__: MAINT: doc build warnings * `#20075 <https://github.com/scipy/scipy/issues/20075>`__: BUG: \`eigh_tridiagonal\` with \`select="i"\` fails for 1x1 matrices * `#20084 <https://github.com/scipy/scipy/issues/20084>`__: BUG: \`import scipy._lib._testutils\` raises exception in some... * `#20100 <https://github.com/scipy/scipy/issues/20100>`__: ENH: Expose NoConvergence error class in the scipy.optimize namespace * `#20107 <https://github.com/scipy/scipy/issues/20107>`__: MAINT: builds broken against NumPy main * `#20129 <https://github.com/scipy/scipy/issues/20129>`__: BUG: regression: eval_chebyt gives wrong results for complex... * `#20131 <https://github.com/scipy/scipy/issues/20131>`__: DOC: linalg: Unclear description for the output \`P\` of \`qr\`. * `#20142 <https://github.com/scipy/scipy/issues/20142>`__: Typo in the doc of the Kstwobign distribution * `#20157 <https://github.com/scipy/scipy/issues/20157>`__: MAINT, TST: test_svds_parameter_tol failures * `#20161 <https://github.com/scipy/scipy/issues/20161>`__: \`dev.py test\` fails to accept both \`--argument\` and \`--... * `#20170 <https://github.com/scipy/scipy/issues/20170>`__: Test failures due to \`asarray(..., copy=False)\` semantics change... * `#20180 <https://github.com/scipy/scipy/issues/20180>`__: deprecation warnings for Node.js 16 on GHA wheel build jobs * `#20182 <https://github.com/scipy/scipy/issues/20182>`__: BUG: \`csr_row_index\` and \`csr_column_index\` error for mixed... * `#20188 <https://github.com/scipy/scipy/issues/20188>`__: BUG: Raising scipy.spatial.transform.Rotation to power of 0 adds... * `#20220 <https://github.com/scipy/scipy/issues/20220>`__: new problem on Cirrus with Homebrew Python in macOS arm64 jobs * `#20225 <https://github.com/scipy/scipy/issues/20225>`__: CI/MAINT: \`choco\` error for invalid credentials * `#20230 <https://github.com/scipy/scipy/issues/20230>`__: CI, DOC, TST: failure related to scipy/stats/_distn_infrastructure.py... ************************ Pull requests for 1.13.0 ************************ * `#8404 <https://github.com/scipy/scipy/pull/8404>`__: ENH:special:Tighten cdflib precision to 1e-15 * `#14771 <https://github.com/scipy/scipy/pull/14771>`__: ENH: integrate.solve_ivp: allow event \`terminal\` attribute... * `#16660 <https://github.com/scipy/scipy/pull/16660>`__: DOC: update pydata-sphinx theme * `#17265 <https://github.com/scipy/scipy/pull/17265>`__: Doc: fix linalg.lstsq documentation on residues * `#17525 <https://github.com/scipy/scipy/pull/17525>`__: TST: linalg: temporarily silence failure in test_solve_generalized_discrete_are * `#18530 <https://github.com/scipy/scipy/pull/18530>`__: ENH: sparse: Generalize coo_array to support 1d shapes * `#18541 <https://github.com/scipy/scipy/pull/18541>`__: MAINT: sparse: Stop supporting multi-Ellipsis indexing * `#18828 <https://github.com/scipy/scipy/pull/18828>`__: ENH: improve dtype check in wavfile.write * `#19444 <https://github.com/scipy/scipy/pull/19444>`__: ENH: Add faster inverse-Wishart rvs and logpdf * `#19488 <https://github.com/scipy/scipy/pull/19488>`__: DOC: Improving "Spectral Analysis" section in User Guide * `#19541 <https://github.com/scipy/scipy/pull/19541>`__: BUG: fix cosine distance result type * `#19545 <https://github.com/scipy/scipy/pull/19545>`__: ENH: integrate._tanhsinh: support vector-valued functions * `#19555 <https://github.com/scipy/scipy/pull/19555>`__: DOC: Small documentation and docstring corrections for \`ShortTimeFFT\` * `#19560 <https://github.com/scipy/scipy/pull/19560>`__: ENH:MAINT:special:Cythonize cdflib * `#19587 <https://github.com/scipy/scipy/pull/19587>`__: ENH:MAINT:special:Rewrite amos F77 code * `#19631 <https://github.com/scipy/scipy/pull/19631>`__: ENH: add parameter ymax in stats.boxcox_normmax * `#19633 <https://github.com/scipy/scipy/pull/19633>`__: ENH: use NdBSpline in RegularGridInterpolator to speed up evaluations * `#19650 <https://github.com/scipy/scipy/pull/19650>`__: ENH: stats.kstests: add axis / nan_policy / keepdims support * `#19662 <https://github.com/scipy/scipy/pull/19662>`__: ENH: stats.normaltest/skewtest/kurtosistest: add axis / nan_policy... * `#19663 <https://github.com/scipy/scipy/pull/19663>`__: DOC: Add example to rv_continuous.fit * `#19664 <https://github.com/scipy/scipy/pull/19664>`__: DOC: Add example for mstats.brunnermunzel * `#19666 <https://github.com/scipy/scipy/pull/19666>`__: DOC: Add Example to lbfgsb docstring * `#19667 <https://github.com/scipy/scipy/pull/19667>`__: ENH: integrate._nsum: function for finite and infinite summation * `#19669 <https://github.com/scipy/scipy/pull/19669>`__: REL: set version to 1.13.0.dev0 * `#19672 <https://github.com/scipy/scipy/pull/19672>`__: DEP: signal: remove scipy.signal.{bspline,quadratic,cubic} * `#19674 <https://github.com/scipy/scipy/pull/19674>`__: DEP: linalg: remove tri{,u,l} * `#19675 <https://github.com/scipy/scipy/pull/19675>`__: DEP: signal: remove scipy.signal.{lsim2,impulse2,step2} * `#19676 <https://github.com/scipy/scipy/pull/19676>`__: DEP: signal: remove ability to import window functions from signal... * `#19679 <https://github.com/scipy/scipy/pull/19679>`__: MAINT: stats.theilslopes: consistent promotion of \`x\` and \`y\` * `#19680 <https://github.com/scipy/scipy/pull/19680>`__: ENH: stats.shapiro: add axis / nan_policy / keepdims support * `#19681 <https://github.com/scipy/scipy/pull/19681>`__: MAINT: Add binom to new C++ special lib along with its cephes... * `#19682 <https://github.com/scipy/scipy/pull/19682>`__: TST: consolidate array API test skip decorators * `#19687 <https://github.com/scipy/scipy/pull/19687>`__: MAINT:linalg: Remove redundant det and lu Fortran files * `#19689 <https://github.com/scipy/scipy/pull/19689>`__: MAINT: stats.moment: rename parameter \`moment\` to \`order\` * `#19694 <https://github.com/scipy/scipy/pull/19694>`__: MAINT: Remove \`PDistWeightedMetricWrapper\` and \`CDistWeightedMetricWrapper\` * `#19695 <https://github.com/scipy/scipy/pull/19695>`__: MAINT: Prefer \`np.fill_diagonal\` over \`diag_indices\` * `#19696 <https://github.com/scipy/scipy/pull/19696>`__: ENH: add \`method\` arg to \`interpolate.Akima1DInterpolator\` * `#19698 <https://github.com/scipy/scipy/pull/19698>`__: MAINT: bump project version * `#19701 <https://github.com/scipy/scipy/pull/19701>`__: MAINT: make import of \`array_api_compat\` nicer * `#19703 <https://github.com/scipy/scipy/pull/19703>`__: DEP: non-integers in \`factorial(..., exact=True)\`: deprecate... * `#19708 <https://github.com/scipy/scipy/pull/19708>`__: DOC: spatial.distance: add missing optional param markers * `#19710 <https://github.com/scipy/scipy/pull/19710>`__: TST: fix pytest discovery errors with editable installs * `#19711 <https://github.com/scipy/scipy/pull/19711>`__: DOC: clarify ttest_1samp argument * `#19714 <https://github.com/scipy/scipy/pull/19714>`__: BLD: require Cython >=3.0.4, drop 0.29.X support * `#19715 <https://github.com/scipy/scipy/pull/19715>`__: ENH: sparse: Add DOK support for 1d (without indexing) * `#19716 <https://github.com/scipy/scipy/pull/19716>`__: ENH: enable approximation for factorialk * `#19721 <https://github.com/scipy/scipy/pull/19721>`__: DOC: add rationale for 88 char line length * `#19722 <https://github.com/scipy/scipy/pull/19722>`__: DOC: update release version procedure * `#19723 <https://github.com/scipy/scipy/pull/19723>`__: ENH, MAINT: voronoi_plot_2d nicer inf lines * `#19724 <https://github.com/scipy/scipy/pull/19724>`__: MAINT: Windows NumPy 2.x int shims * `#19725 <https://github.com/scipy/scipy/pull/19725>`__: MNT: use int instead of long in cython code * `#19728 <https://github.com/scipy/scipy/pull/19728>`__: MAINT: enhance the configuration for the \`pull-request-labeler\`... * `#19730 <https://github.com/scipy/scipy/pull/19730>`__: MAINT: bs4 deprecation shim * `#19731 <https://github.com/scipy/scipy/pull/19731>`__: ENH: stats.mood: add nan_policy / keepdims support * `#19738 <https://github.com/scipy/scipy/pull/19738>`__: BLD: require \`pythran>=0.14.0\` * `#19741 <https://github.com/scipy/scipy/pull/19741>`__: ENH: stats.friedmanchisquare/brunnermunzel: add axis / nan_policy... * `#19742 <https://github.com/scipy/scipy/pull/19742>`__: CI: fix PR labeler config file * `#19743 <https://github.com/scipy/scipy/pull/19743>`__: ENH: sparse: Add min-max 1d support and tests * `#19744 <https://github.com/scipy/scipy/pull/19744>`__: ENH: stats.mannwhitneyu: speed improvement, memory reduction,... * `#19745 <https://github.com/scipy/scipy/pull/19745>`__: TST: fortranfiles fix * `#19746 <https://github.com/scipy/scipy/pull/19746>`__: CI: add labeler based on issue/PR titles * `#19749 <https://github.com/scipy/scipy/pull/19749>`__: ENH: stats.mannwhitneyu: vectorize statistic calculation * `#19750 <https://github.com/scipy/scipy/pull/19750>`__: DEV/BLD: generate \`requirements/\*\` files to simplify build * `#19752 <https://github.com/scipy/scipy/pull/19752>`__: DEP: deprecate complex dtypes in \`PchipInterpolator\` and \`Akima1DInterpolator\` * `#19755 <https://github.com/scipy/scipy/pull/19755>`__: MAINT/TST: ignore backend import errors when not in array API... * `#19757 <https://github.com/scipy/scipy/pull/19757>`__: ENH: Add vectorized scalar minimization bracket finder * `#19758 <https://github.com/scipy/scipy/pull/19758>`__: MAINT: correct inaccurate comment * `#19760 <https://github.com/scipy/scipy/pull/19760>`__: MAINT: interpolate: remove dead code * `#19762 <https://github.com/scipy/scipy/pull/19762>`__: ENH: stats.monte_carlo_test: account for inexact calculation... * `#19763 <https://github.com/scipy/scipy/pull/19763>`__: MAINT: integrate._nsum: adjust algorithm for determining number... * `#19768 <https://github.com/scipy/scipy/pull/19768>`__: MAINT: SuperLU upstream fix for compile warnings * `#19770 <https://github.com/scipy/scipy/pull/19770>`__: ENH: stats.wilcoxon: rewrite for speed and clarity; add PermutationMethod... * `#19773 <https://github.com/scipy/scipy/pull/19773>`__: DOC: stats: The docstring for scipy.stats.crystalball needs an... * `#19775 <https://github.com/scipy/scipy/pull/19775>`__: DOC: Docstring and examples for Rotation.concatenate * `#19776 <https://github.com/scipy/scipy/pull/19776>`__: ENH: stats.rankdata: vectorize calculation * `#19778 <https://github.com/scipy/scipy/pull/19778>`__: DOC, MAINT: fix make dist in rel process * `#19780 <https://github.com/scipy/scipy/pull/19780>`__: MAINT: scipy.stats: replace \`_normtest_finish\`/\`_ttest_finish\`/etc...... * `#19781 <https://github.com/scipy/scipy/pull/19781>`__: CI, MAINT: switch to stable python release * `#19786 <https://github.com/scipy/scipy/pull/19786>`__: BLD: fix "Failed to guess install tag" in meson-log.txt, add... * `#19787 <https://github.com/scipy/scipy/pull/19787>`__: DOC/BLD: macOS Homebrew OpenBlas detection advice * `#19788 <https://github.com/scipy/scipy/pull/19788>`__: DOC: stats.trim_mean: correct documentation * `#19790 <https://github.com/scipy/scipy/pull/19790>`__: BENCH: Added benchmarks for individual distance metrics * `#19792 <https://github.com/scipy/scipy/pull/19792>`__: MAINT: simplify \`t.logpdf\` * `#19796 <https://github.com/scipy/scipy/pull/19796>`__: API: Enable \`pydata/sparse\` input for csgraph module * `#19803 <https://github.com/scipy/scipy/pull/19803>`__: TST: stats: compare geometric zscore to naive version instead... * `#19807 <https://github.com/scipy/scipy/pull/19807>`__: DOC: fft: add note about FHT formulas * `#19808 <https://github.com/scipy/scipy/pull/19808>`__: MAINT: move elementwise algorithms and framework * `#19810 <https://github.com/scipy/scipy/pull/19810>`__: MAINT: set \`NPY_NO_DEPRECATED_API\` also for Cython code * `#19811 <https://github.com/scipy/scipy/pull/19811>`__: BLD: set default \`cpp_std\` to \`c++17\` * `#19818 <https://github.com/scipy/scipy/pull/19818>`__: MAINT: uarray CXX version hex cleanup * `#19820 <https://github.com/scipy/scipy/pull/19820>`__: TST: linalg: Test Cython LAPACK complex ladiv * `#19821 <https://github.com/scipy/scipy/pull/19821>`__: BLD: resolve missing prototype warnings in lsoda/vode * `#19822 <https://github.com/scipy/scipy/pull/19822>`__: BLD: propack: resolve missing return value warnings * `#19823 <https://github.com/scipy/scipy/pull/19823>`__: CI/DEV: add some new auto-labels * `#19824 <https://github.com/scipy/scipy/pull/19824>`__: ENH:Rewrite specfun F77 code in C * `#19825 <https://github.com/scipy/scipy/pull/19825>`__: MAINT: \`CODEOWNERS\` syntax fix and changes * `#19827 <https://github.com/scipy/scipy/pull/19827>`__: MAINT: spatial: fix build warnings in \`ckdtree\` code * `#19828 <https://github.com/scipy/scipy/pull/19828>`__: CI/DEV: fix and simplify \`label-globs\` syntax * `#19829 <https://github.com/scipy/scipy/pull/19829>`__: MAINT: interpolate: fix build warning from \`_ppoly.pyx\` * `#19837 <https://github.com/scipy/scipy/pull/19837>`__: MAINT: special: fix meson deprecation warning * `#19838 <https://github.com/scipy/scipy/pull/19838>`__: DOC: fft: improve \`s\` description for real transforms * `#19843 <https://github.com/scipy/scipy/pull/19843>`__: DOC: Add \`fft\` to list of submodules in tutorial * `#19844 <https://github.com/scipy/scipy/pull/19844>`__: TST: fix more cases of fd leaks from np.load() * `#19849 <https://github.com/scipy/scipy/pull/19849>`__: CI: fix prerelease job to use numpy 2.0, and add a second job... * `#19853 <https://github.com/scipy/scipy/pull/19853>`__: ENH: sparse: foundation for 1D arrays (add test suite, round... * `#19855 <https://github.com/scipy/scipy/pull/19855>`__: BLD: Revamp BLAS/LAPACK G77 ABI wrappers and fix PROPACK segfaults * `#19856 <https://github.com/scipy/scipy/pull/19856>`__: BLD: simplify pythran version requirement in meson * `#19857 <https://github.com/scipy/scipy/pull/19857>`__: BLD: make scipy build warning-free with LTO enabled * `#19860 <https://github.com/scipy/scipy/pull/19860>`__: MAINT: fix BLD label typo * `#19861 <https://github.com/scipy/scipy/pull/19861>`__: BUG:io:Skip arr_to_chars call for single code points * `#19864 <https://github.com/scipy/scipy/pull/19864>`__: Add documentation to explain behavior for transposing csr or... * `#19866 <https://github.com/scipy/scipy/pull/19866>`__: DOC: Change default for bounds in scipy.optimize.linprog * `#19868 <https://github.com/scipy/scipy/pull/19868>`__: MAINT: fix use of \`unique(..., return_inverse=True)\` * `#19869 <https://github.com/scipy/scipy/pull/19869>`__: MAINT: array types: rename \`as_xparray\` to \`_asarray\` * `#19870 <https://github.com/scipy/scipy/pull/19870>`__: MAINT: logsumexp: properly handle complex sign * `#19871 <https://github.com/scipy/scipy/pull/19871>`__: MAINT: make isinstance check in \`stats._distn_infrastructure\`... * `#19874 <https://github.com/scipy/scipy/pull/19874>`__: rankdata: ensure correct shape for empty inputs * `#19876 <https://github.com/scipy/scipy/pull/19876>`__: MAINT: stats: Add tests to ensure consistency between \`wasserstein_distance\` and different backends of \`wasserstein_distance_nd\` * `#19882 <https://github.com/scipy/scipy/pull/19882>`__: MAINT: vendor \`pocketfft\` as git submodule * `#19885 <https://github.com/scipy/scipy/pull/19885>`__: MAINT: fix some small array API support issues * `#19886 <https://github.com/scipy/scipy/pull/19886>`__: TST: stats: fix a few issues with non-reproducible seeding * `#19891 <https://github.com/scipy/scipy/pull/19891>`__: MAINT: stats: fix editable install issue in \`qmc\` and MPL-related... * `#19893 <https://github.com/scipy/scipy/pull/19893>`__: MAINT: remove unused itertools-import in scipy.interpolate._interpolate * `#19901 <https://github.com/scipy/scipy/pull/19901>`__: MAINT: special: remove use of \`numpy.math\` from \`_cdflib.pyx\` * `#19902 <https://github.com/scipy/scipy/pull/19902>`__: BUG:special:cdflib: Correct cdftnc Cython bugs * `#19908 <https://github.com/scipy/scipy/pull/19908>`__: Fix AIX build break. * `#19909 <https://github.com/scipy/scipy/pull/19909>`__: MAINT:linalg:Adjust lwork/liwork changes OpenBLAS 0.3.26 * `#19916 <https://github.com/scipy/scipy/pull/19916>`__: MAINT: update pocketfft git submodule location * `#19917 <https://github.com/scipy/scipy/pull/19917>`__: MAINT: replicate FITPACK's \`fpchec\` routine in python * `#19924 <https://github.com/scipy/scipy/pull/19924>`__: TST: cluster: fix test_kmeans_and_kmeans2_random_seed * `#19925 <https://github.com/scipy/scipy/pull/19925>`__: MAINT: forward port 1.12.0 relnotes * `#19927 <https://github.com/scipy/scipy/pull/19927>`__: BUG: cluster.kmeans\*: array types: accept \`int\`s for k * `#19929 <https://github.com/scipy/scipy/pull/19929>`__: DOC: updated incorrect sentence about subpackage imports. See... * `#19931 <https://github.com/scipy/scipy/pull/19931>`__: MAINT:special:cdflib:Refine the tolerances further * `#19932 <https://github.com/scipy/scipy/pull/19932>`__: ENH:stats:Use explicit formula for gamma.fit('mm') * `#19933 <https://github.com/scipy/scipy/pull/19933>`__: BUG: Correct handling of -inf in special stdr funcs * `#19934 <https://github.com/scipy/scipy/pull/19934>`__: BUG:special:amos: Fix some mistakes in the AMOS C translation * `#19937 <https://github.com/scipy/scipy/pull/19937>`__: TST: Add RNG seeds for TestInvgauss and TestLaplace * `#19938 <https://github.com/scipy/scipy/pull/19938>`__: MAINT: special: array types: fix warning when not in array API... * `#19939 <https://github.com/scipy/scipy/pull/19939>`__: BUG:special:amos: Fix exit path in \`amos_asyi\` * `#19942 <https://github.com/scipy/scipy/pull/19942>`__: MAINT: hypothesis: document minimum required version * `#19944 <https://github.com/scipy/scipy/pull/19944>`__: BUG: Correct handling of inf support in binomial * `#19945 <https://github.com/scipy/scipy/pull/19945>`__: BLD: fix issue with escape sequences in \`__config__.py\` * `#19947 <https://github.com/scipy/scipy/pull/19947>`__: BUG:special:amos: Fix typo in \`amos_mlri\` * `#19950 <https://github.com/scipy/scipy/pull/19950>`__: DOC: stats.logrank: fix typo that affect survival curves in manual * `#19952 <https://github.com/scipy/scipy/pull/19952>`__: BUG:sparse:Add early exit to gmres when x0 already solves problem * `#19957 <https://github.com/scipy/scipy/pull/19957>`__: defect: sparse: 1d bool mask with wrong shape should raise IndexError * `#19961 <https://github.com/scipy/scipy/pull/19961>`__: DOC: Add version warning banner to documentation * `#19962 <https://github.com/scipy/scipy/pull/19962>`__: ENH: sparse: speedup csr/csc setdiag by converting to coo * `#19965 <https://github.com/scipy/scipy/pull/19965>`__: DOC: scale of parameters in optimize.curve_fit * `#19969 <https://github.com/scipy/scipy/pull/19969>`__: DOC: Fix landing page images for dark theme * `#19971 <https://github.com/scipy/scipy/pull/19971>`__: ENH: Input validation for sampling frequency in signal.filter... * `#19975 <https://github.com/scipy/scipy/pull/19975>`__: ENH: support custom statistic in goodness_of_fit function (gh-19894) * `#19977 <https://github.com/scipy/scipy/pull/19977>`__: DOC: document a common alternative parameterization of invgauss. * `#19978 <https://github.com/scipy/scipy/pull/19978>`__: DOC: fix autosummary for scipy.signal.ShortTimeFFT.t/T under... * `#19980 <https://github.com/scipy/scipy/pull/19980>`__: ENH: stats: add axis/nan_policy support to \`f_oneway\` and \`alexandergovern\` * `#19981 <https://github.com/scipy/scipy/pull/19981>`__: TST: correct typo in TestGamma.test_fit_mm function. * `#19995 <https://github.com/scipy/scipy/pull/19995>`__: TST, MAINT: test_immediate_updating fix * `#19997 <https://github.com/scipy/scipy/pull/19997>`__: MAINT: Adjust the codebase to the new \`np.array\`'s \`copy\`... * `#20000 <https://github.com/scipy/scipy/pull/20000>`__: MAINT: interpolate: address review comments on NdBSpline/RGI * `#20003 <https://github.com/scipy/scipy/pull/20003>`__: MAINT: sparse: change coo_matrix.indices to coo_matrix.coords * `#20004 <https://github.com/scipy/scipy/pull/20004>`__: MAINT: sparse: change method names _mul_\* to _matmul_\* all... * `#20005 <https://github.com/scipy/scipy/pull/20005>`__: MAINT: Remove partial from \`__all__\` (removed from submodule) * `#20006 <https://github.com/scipy/scipy/pull/20006>`__: BENCH: optimize: add timings to global optimizers benchmarks * `#20010 <https://github.com/scipy/scipy/pull/20010>`__: BUG: Add proper error message for \`ShortTimeFFT\` for onesided... * `#20013 <https://github.com/scipy/scipy/pull/20013>`__: MAINT: signal: use \`sliding_window_view\` instead of \`as_strided\` * `#20016 <https://github.com/scipy/scipy/pull/20016>`__: DOC: update release docs to reflect new version banner * `#20017 <https://github.com/scipy/scipy/pull/20017>`__: BUG: loglaplace moment should be non-negative. * `#20018 <https://github.com/scipy/scipy/pull/20018>`__: ENH: refer to the Laplace distribution in log-Laplace documentation. * `#20019 <https://github.com/scipy/scipy/pull/20019>`__: DOC: Add support for interactive examples with jupyterlite-sphinx * `#20020 <https://github.com/scipy/scipy/pull/20020>`__: TST: TestCorrelateReal overflow shim * `#20021 <https://github.com/scipy/scipy/pull/20021>`__: ENH: fix numerical instability around zero in boxcox_llf * `#20023 <https://github.com/scipy/scipy/pull/20023>`__: ENH: use analytic formula for log-laplace MLE when loc is known. * `#20024 <https://github.com/scipy/scipy/pull/20024>`__: ENH:stats: Add multivariate Wasserstein distance as a separate... * `#20032 <https://github.com/scipy/scipy/pull/20032>`__: MAINT: Adjust some comments in special C++ library * `#20033 <https://github.com/scipy/scipy/pull/20033>`__: MAINT: sparse: Un-deprecate getnnz() * `#20037 <https://github.com/scipy/scipy/pull/20037>`__: MAINT: Add special handling for complex infinite input in digamma * `#20039 <https://github.com/scipy/scipy/pull/20039>`__: ENH: use analytical formula in scipy.stats.powerlaw._munp(). * `#20044 <https://github.com/scipy/scipy/pull/20044>`__: TST: _ConstraintWrapper returns a violation of the correct shape * `#20045 <https://github.com/scipy/scipy/pull/20045>`__: DOC: add missing np. in tutorial * `#20047 <https://github.com/scipy/scipy/pull/20047>`__: TST: use assert_allclose in test_bootstrap_alternative * `#20052 <https://github.com/scipy/scipy/pull/20052>`__: FIX: Allow any dtype-specifier for ndimage output * `#20053 <https://github.com/scipy/scipy/pull/20053>`__: Add sorting requirement for partial_match and partial_guess * `#20054 <https://github.com/scipy/scipy/pull/20054>`__: BUG: SciPy.interpolate.CubicSpline with periodic data * `#20063 <https://github.com/scipy/scipy/pull/20063>`__: ENH: optimize._differentiate: add option preserve_shape * `#20065 <https://github.com/scipy/scipy/pull/20065>`__: MAINT Fix broken link in \`scipy.stats._multivariate.py\` * `#20067 <https://github.com/scipy/scipy/pull/20067>`__: TST: shims for NumPy fft changes * `#20068 <https://github.com/scipy/scipy/pull/20068>`__: Changed assert_warns in stats testing to pytest.warns. * `#20069 <https://github.com/scipy/scipy/pull/20069>`__: MAINT/DOC: \`special.nrdtrimn/nrdtrisd\` docstring fixes * `#20070 <https://github.com/scipy/scipy/pull/20070>`__: MAINT: silence ruff deprecation warning * `#20076 <https://github.com/scipy/scipy/pull/20076>`__: BUG:linalg:Add early exit to eigh_tridiagonal for 1x1 input * `#20078 <https://github.com/scipy/scipy/pull/20078>`__: CI: update github actions and cibuildwheel * `#20080 <https://github.com/scipy/scipy/pull/20080>`__: BUG: sparse: Fix hstack, etc for dok_array * `#20086 <https://github.com/scipy/scipy/pull/20086>`__: MAINT: detect musl differently. * `#20087 <https://github.com/scipy/scipy/pull/20087>`__: MAINT: switch from \`numpy.array_api\` to \`array-api-strict\` * `#20092 <https://github.com/scipy/scipy/pull/20092>`__: DOC: Fix a could of places that are parsed as substitution references... * `#20093 <https://github.com/scipy/scipy/pull/20093>`__: DOC: Fix small typos in \`signal.rst\` and \`_short_time_fft.py\` * `#20095 <https://github.com/scipy/scipy/pull/20095>`__: DOC: tick tensor product splines off the roadmap * `#20096 <https://github.com/scipy/scipy/pull/20096>`__: TST:linalg:Reduce the size of the cossin test * `#20098 <https://github.com/scipy/scipy/pull/20098>`__: MAINT: minor array API skip improvements * `#20101 <https://github.com/scipy/scipy/pull/20101>`__: MAINT: editorial changes in the doc string of scipy.stats.vonmises. * `#20102 <https://github.com/scipy/scipy/pull/20102>`__: ENH: use non-trivial bounds to solve for kappa of vonmises MLE. * `#20103 <https://github.com/scipy/scipy/pull/20103>`__: MAINT: optimize: expose \`NoConvergence\` * `#20104 <https://github.com/scipy/scipy/pull/20104>`__: ENH: allow shape parameter kappa to be zero in vonmises distribution. * `#20106 <https://github.com/scipy/scipy/pull/20106>`__: DOC: update docstring of stats.percentileofscore * `#20108 <https://github.com/scipy/scipy/pull/20108>`__: MAINT: shim for descr->f access * `#20111 <https://github.com/scipy/scipy/pull/20111>`__: DOC: clarify accepted values for \`dim\` in \`unitary_group\`. * `#20112 <https://github.com/scipy/scipy/pull/20112>`__: BLD: signal: do not install Pythran source alongside the Cython... * `#20119 <https://github.com/scipy/scipy/pull/20119>`__: Fix small issues in docstrings * `#20121 <https://github.com/scipy/scipy/pull/20121>`__: BLD: simplifications in meson.build files * `#20122 <https://github.com/scipy/scipy/pull/20122>`__: MAINT: update Boost.Math to 1.83.0 * `#20123 <https://github.com/scipy/scipy/pull/20123>`__: MAINT: stats: fix test failure in \`kendalltau_seasonal\` * `#20130 <https://github.com/scipy/scipy/pull/20130>`__: BUG: Use Cython implementation of complex hyp2f1 in orthogonal_eval.pxd * `#20135 <https://github.com/scipy/scipy/pull/20135>`__: MAINT: interpolate: define \`F_INT\` as \`int\` rather than \`npy_int32\` * `#20138 <https://github.com/scipy/scipy/pull/20138>`__: TST: optimize: silence the output from calling cobyla with disp=True * `#20141 <https://github.com/scipy/scipy/pull/20141>`__: MAINT/CI: special/array types: test alternative backends in CI * `#20143 <https://github.com/scipy/scipy/pull/20143>`__: DOC: stats: Fix typo in the doc of the Kstwobign distribution * `#20144 <https://github.com/scipy/scipy/pull/20144>`__: MAINT, ENH: Hausdorff simplification * `#20145 <https://github.com/scipy/scipy/pull/20145>`__: TST: special: bump tolerances for new \`cdftnc\` regression tests * `#20146 <https://github.com/scipy/scipy/pull/20146>`__: MAINT: fix incorrect \`noexcept\` usage in Cython functions * `#20149 <https://github.com/scipy/scipy/pull/20149>`__: BLD: Ensure Python.h is included before system headers. * `#20153 <https://github.com/scipy/scipy/pull/20153>`__: BLD: interpolate: _interpnd_info does not need installing * `#20154 <https://github.com/scipy/scipy/pull/20154>`__: ENH: sparse: implement fromkeys for _dok_base * `#20163 <https://github.com/scipy/scipy/pull/20163>`__: MAINT: dev.py: allow --args after -- * `#20172 <https://github.com/scipy/scipy/pull/20172>`__: MAINT: (additional) array copy semantics shims * `#20173 <https://github.com/scipy/scipy/pull/20173>`__: TST:special:Add partial tests for nrdtrimn and nrdtrisd * `#20174 <https://github.com/scipy/scipy/pull/20174>`__: DOC: interpolate: \`splrep\` default boundary condition * `#20176 <https://github.com/scipy/scipy/pull/20176>`__: MAINT: vulture/ruff fixups * `#20181 <https://github.com/scipy/scipy/pull/20181>`__: MAINT: Avoid \`descr->elsize\` and use intp for it. * `#20183 <https://github.com/scipy/scipy/pull/20183>`__: BUG: Fix fancy indexing on compressed sparse arrays with mixed... * `#20184 <https://github.com/scipy/scipy/pull/20184>`__: DOC, DX: Remove version warning banner in latest version * `#20186 <https://github.com/scipy/scipy/pull/20186>`__: MAINT: update action. Closes #20180 * `#20191 <https://github.com/scipy/scipy/pull/20191>`__: BUG: Fix shape of single Rotation raised to the 0 or 1 power * `#20193 <https://github.com/scipy/scipy/pull/20193>`__: MAINT: Bump \`npy2_compat.h\` and add temporary pybind11 workaround * `#20195 <https://github.com/scipy/scipy/pull/20195>`__: ENH: linalg: allow readonly arrays in expm et al * `#20198 <https://github.com/scipy/scipy/pull/20198>`__: BLD: update minimum Cython version to 3.0.8 * `#20203 <https://github.com/scipy/scipy/pull/20203>`__: TST: linalg: undo xfail TestEig::test_singular * `#20204 <https://github.com/scipy/scipy/pull/20204>`__: TST: linalg: add a regression test for a gen eig problem * `#20205 <https://github.com/scipy/scipy/pull/20205>`__: BUG: Fixed \`fftshift()\` in \`ShortTimeFFT\`. * `#20206 <https://github.com/scipy/scipy/pull/20206>`__: DOC: clarify role of p in linalg.qr. * `#20209 <https://github.com/scipy/scipy/pull/20209>`__: CI: move regular macosx_arm64 from cirrus to GHA * `#20210 <https://github.com/scipy/scipy/pull/20210>`__: BLD: macosx_arm64 wheel build on GHA instead of cirrus * `#20212 <https://github.com/scipy/scipy/pull/20212>`__: BUG: linalg/sqrtm: more robust check for real->complex Schur... * `#20215 <https://github.com/scipy/scipy/pull/20215>`__: MAINT: bump OpenBLAS "the old way" * `#20217 <https://github.com/scipy/scipy/pull/20217>`__: DOC/MAINT: add examples for nctdtridf, nctdtrinc, nctdtrit * `#20218 <https://github.com/scipy/scipy/pull/20218>`__: TST: mark linalg.sqrtm test as xfail * `#20221 <https://github.com/scipy/scipy/pull/20221>`__: TST: Tweak tols and ignore warnings for more reliable SVD tests * `#20222 <https://github.com/scipy/scipy/pull/20222>`__: DOC add likelihood formula to stats.CensoredData * `#20224 <https://github.com/scipy/scipy/pull/20224>`__: BUG: fix \`cluster.vq.kmeans2\` with minit='++' for 1D data * `#20227 <https://github.com/scipy/scipy/pull/20227>`__: MAINT: remove repeated "the" typos * `#20229 <https://github.com/scipy/scipy/pull/20229>`__: BUG: linalg: fix int overflow in Cholesky (potrf) * `#20231 <https://github.com/scipy/scipy/pull/20231>`__: DOC/DX: array types: update \`_asarray\` description * `#20232 <https://github.com/scipy/scipy/pull/20232>`__: BLD: Refactor BLAS/LAPACK wrapper infrastructure * `#20233 <https://github.com/scipy/scipy/pull/20233>`__: DOC: stats.rv_continuous.fit: fix backslashes * `#20235 <https://github.com/scipy/scipy/pull/20235>`__: DOC: add reference for ARGUS distribution in scipy.stats * `#20236 <https://github.com/scipy/scipy/pull/20236>`__: DOC: fix small typo in array API docs * `#20237 <https://github.com/scipy/scipy/pull/20237>`__: MAINT: optimize: update \`_direct\` for typos * `#20238 <https://github.com/scipy/scipy/pull/20238>`__: MAINT: revert ARPACK changes from #20227 * `#20241 <https://github.com/scipy/scipy/pull/20241>`__: BLD: remove use of \`NPY_VISIBILITY_HIDDEN\` * `#20243 <https://github.com/scipy/scipy/pull/20243>`__: MAINT: Specfun translation into C++ * `#20245 <https://github.com/scipy/scipy/pull/20245>`__: MAINT: Updated _specfun.pyx * `#20248 <https://github.com/scipy/scipy/pull/20248>`__: MAINT: Removed specfun_lib and updated specfun_wrappers * `#20250 <https://github.com/scipy/scipy/pull/20250>`__: MAINT: interpolate: const qualify cython arrays * `#20251 <https://github.com/scipy/scipy/pull/20251>`__: MAINT:special:Adjust inf values for cdflib * `#20254 <https://github.com/scipy/scipy/pull/20254>`__: MAINT: linalg: readability refactor Riccati equation solver tests * `#20259 <https://github.com/scipy/scipy/pull/20259>`__: BUG: linalg: fix \`expm\` for large arrays * `#20261 <https://github.com/scipy/scipy/pull/20261>`__: BUG:linalg:Remove the 2x2 branch in expm * `#20263 <https://github.com/scipy/scipy/pull/20263>`__: DOC/REL: add missing expired deprecations to 1.12.0 notes Checksums ========= MD5 ~~~ a04fee9623677e6eec6c3a2ea7adb15d Changelog c1f15e49cd7f5b3d2327558a134611ba README.txt 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next NumPy triage meeting - now starting at 5 pm UTC
by Inessa Pawson 17 Mar '24

17 Mar '24

The next NumPy triage meeting will be held this Wednesday, January 11th at 5 pm UTC. (Please note the new time!) This is a meeting where we synchronously triage prioritized PRs and issues. Join us via Zoom: https://numfocus-org.zoom.us/j/82096749952?pwd=MW9oUmtKQ1c3a2gydGk1RTdYUUVX… Everyone is welcome to attend and contribute to a conversation. Please notify us of issues or PRs that you’d like to have reviewed by adding a GitHub link to them in the meeting agenda: https://hackmd.io/68i_JvOYQfy9ERiHgXMPvg. -- Cheers, Inessa Inessa Pawson Contributor Experience Lead | NumPy https://numpy.org/ GitHub: inessapawson

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Improved 2DFFT Approach
by camrymanjr＠me.com 15 Mar '24

15 Mar '24

Good day! My name is Alexander Levin. My colleague and I did a project on optimisation of two-dimensional Fourier transform algorithm six months ago. We took your implementation of numpy fft2d as a unit of quality. In the course of our research we found out that initially mathematically the method uses a far from optimal algorithm. As you may know, your operation goes first by rows then by columns applying a one-dimensional transformation. After spending some time researching mathematical papers on this topic, we found and implemented a new approach, the so-called Cooley-Tukey butterfly, optimised by Russian mathematicians in 2016. The output is a completely new approach, where we immediately apply a two-dimensional operation and save a serious proportion of time on it. As a result, we wrote a C++ package for Python, using Cython as a wrapper. The result was the package and an article on Medium describing the process. On tests for matrices ranging in size from 2048x512 to 8192x8192, our algorithm outperformed the NumPy transformation by an average of 50% in time. After discussing this matter with my colleague with whom we did the above development, we came to a common desire to share our results with you. Your company has been making a huge contribution to the IT community for almost 20 years on a pro bono basis. We share your philosophy and so we want to make the CS world a better place by providing you with our code to optimise the approach in an existing operation in your package. We would like to offer you our development version, though it'll need some minor improvements, we'd love to finish them collaboratively with you and hear your thoughts regarding what we have discovered and done so far. We'd be honored to help you and become NumPy contributors. I trust that our vision will resonate with you and that you will agree with us. I invite you to read our quick article about the process, which I have linked below, and our fully functioning package and share your views on our contribution to NumPy. We are willing to edit the code to fit your standards, as we believe that the best use of our work will be to contribute to the development of technology in the world. Thank you for your time. We look forward to your response and opinion. Medium Article about the process: https://medium.com/p/7963c3b2f3c9 GitHub Source code Repository: https://github.com/2D-FFT-Project/2d-fft

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Arrays of variable itemsize
by Dom Grigonis 13 Mar '24

13 Mar '24

Hi all, Say python’s builtin `int` type. It can be as large as memory allows. np.ndarray on the other hand is optimized for vectorization via strides, memory structure and many things that I probably don’t know. Well the point is that it is convenient and efficient to use for many things in comparison to python’s built-in list of integers. So, I am thinking whether something in between exists? (And obviously something more clever than np.array(dtype=object)) Probably something similar to `StringDType`, but for integers and floats. (It’s just my guess. I don’t know anything about `StringDType`, but just guessing it must be better than np.array(dtype=object) in combination with np.vectorize) Regards, dgpb

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