Update dependency scipy to v1.14.1

[renovate]

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
scipy (source)	==1.12.0 -> ==1.14.1

---

Release Notes

scipy/scipy (scipy)

v1.14.1: SciPy 1.14.1

Compare Source

SciPy 1.14.1 Release Notes

SciPy 1.14.1 adds support for Python 3.13, including binary
wheels on PyPI. Apart from that, it is a bug-fix release with
no new features compared to 1.14.0.

Authors

• Name (commits)
• h-vetinari (1)
• Evgeni Burovski (1)
• CJ Carey (2)
• Lucas Colley (3)
• Ralf Gommers (3)
• Melissa Weber Mendonça (1)
• Andrew Nelson (3)
• Nick ODell (1)
• Tyler Reddy (36)
• Daniel Schmitz (1)
• Dan Schult (4)
• Albert Steppi (2)
• Ewout ter Hoeven (1)
• Tibor Völcker (2) +
• Adam Turner (1) +
• Warren Weckesser (2)
• ਗਗਨਦੀਪ ਸਿੰਘ (Gagandeep Singh) (1)

A total of 17 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.

v1.14.0: SciPy 1.14.0

Compare Source

SciPy 1.14.0 Release Notes

SciPy 1.14.0 is the culmination of 3 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
1.14.x branch, and on adding new features on the main branch.

This release requires Python 3.10+ and NumPy 1.23.5 or greater.

For running on PyPy, PyPy3 6.0+ is required.

Highlights of this release

• SciPy now supports the new Accelerate library introduced in macOS 13.3, and
  has wheels built against Accelerate for macOS >=14 resulting in significant
  performance improvements for many linear algebra operations.
• A new method, cobyqa, has been added to scipy.optimize.minimize - this
  is an interface for COBYQA (Constrained Optimization BY Quadratic
  Approximations), a derivative-free optimization solver, designed to
  supersede COBYLA, developed by the Department of Applied Mathematics, The
  Hong Kong Polytechnic University.
• scipy.sparse.linalg.spsolve_triangular is now more than an order of
  magnitude faster in many cases.

New features

scipy.fft improvements

• A new function, scipy.fft.prev_fast_len, has been added. This function
  finds the largest composite of FFT radices that is less than the target
  length. It is useful for discarding a minimal number of samples before FFT.

scipy.io improvements

• wavfile now supports reading and writing of wav files in the RF64
  format, allowing files greater than 4 GB in size to be handled.

scipy.constants improvements

• Experimental support for the array API standard has been added.

scipy.interpolate improvements

• scipy.interpolate.Akima1DInterpolator now supports extrapolation via the
  extrapolate argument.

scipy.optimize improvements

• scipy.optimize.HessianUpdateStrategy now also accepts square arrays for
  init_scale.
• A new method, cobyqa, has been added to scipy.optimize.minimize - this
  is an interface for COBYQA (Constrained Optimization BY Quadratic
  Approximations), a derivative-free optimization solver, designed to
  supersede COBYLA, developed by the Department of Applied Mathematics, The
  Hong Kong Polytechnic University.
• There are some performance improvements in
  scipy.optimize.differential_evolution.
• scipy.optimize.approx_fprime now has linear space complexity.

scipy.signal improvements

• scipy.signal.minimum_phase has a new argument half, allowing the
  provision of a filter of the same length as the linear-phase FIR filter
  coefficients and with the same magnitude spectrum.

scipy.sparse improvements

• Sparse arrays now support 1D shapes in COO, DOK and CSR formats.
  These are all the formats we currently intend to support 1D shapes.
  Other sparse array formats raise an exception for 1D input.
• Sparse array methods min/nanmin/argmin and max analogs now return 1D arrays.
  Results are still COO format sparse arrays for min/nanmin and
  dense np.ndarray for argmin.
• Sparse matrix and array objects improve their repr and str output.
• A special case has been added to handle multiplying a dia_array by a
  scalar, which avoids a potentially costly conversion to CSR format.
• scipy.sparse.csgraph.yen has been added, allowing usage of Yen's K-Shortest
  Paths algorithm on a directed on undirected graph.
• Addition between DIA-format sparse arrays and matrices is now faster.
• scipy.sparse.linalg.spsolve_triangular is now more than an order of
  magnitude faster in many cases.

scipy.spatial improvements

• Rotation supports an alternative "scalar-first" convention of quaternion
  component ordering. It is available via the keyword argument scalar_first
  of from_quat and as_quat methods.
• Some minor performance improvements for inverting of Rotation objects.

scipy.special improvements

• Added scipy.special.log_wright_bessel, for calculation of the logarithm of
  Wright's Bessel function.
• The relative error in scipy.special.hyp2f1 calculations has improved
  substantially.
• Improved behavior of boxcox, inv_boxcox, boxcox1p, and
  inv_boxcox1p by preventing premature overflow.

scipy.stats improvements

• A new function scipy.stats.power can be used for simulating the power
  of a hypothesis test with respect to a specified alternative.
• The Irwin-Hall (AKA Uniform Sum) distribution has been added as
  scipy.stats.irwinhall.
• Exact p-value calculations of scipy.stats.mannwhitneyu are much faster
  and use less memory.
• scipy.stats.pearsonr now accepts n-D arrays and computes the statistic
  along a specified axis.
• scipy.stats.kstat, scipy.stats.kstatvar, and scipy.stats.bartlett
  are faster at performing calculations along an axis of a large n-D array.

Array API Standard Support

Experimental support for array libraries other than NumPy has been added to
existing sub-packages in recent versions of SciPy. Please consider testing
these features by setting an environment variable SCIPY_ARRAY_API=1 and
providing PyTorch, JAX, or CuPy arrays as array arguments.

As of 1.14.0, there is support for

• scipy.cluster

• scipy.fft

• scipy.constants

• scipy.special: (select functions)

  • scipy.special.log_ndtr
  • scipy.special.ndtr
  • scipy.special.ndtri
  • scipy.special.erf
  • scipy.special.erfc
  • scipy.special.i0
  • scipy.special.i0e
  • scipy.special.i1
  • scipy.special.i1e
  • scipy.special.gammaln
  • scipy.special.gammainc
  • scipy.special.gammaincc
  • scipy.special.logit
  • scipy.special.expit
  • scipy.special.entr
  • scipy.special.rel_entr
  • scipy.special.xlogy
  • scipy.special.chdtrc

• scipy.stats: (select functions)

  • scipy.stats.describe
  • scipy.stats.moment
  • scipy.stats.skew
  • scipy.stats.kurtosis
  • scipy.stats.kstat
  • scipy.stats.kstatvar
  • scipy.stats.circmean
  • scipy.stats.circvar
  • scipy.stats.circstd
  • scipy.stats.entropy
  • scipy.stats.variation
  • scipy.stats.sem
  • scipy.stats.ttest_1samp
  • scipy.stats.pearsonr
  • scipy.stats.chisquare
  • scipy.stats.skewtest
  • scipy.stats.kurtosistest
  • scipy.stats.normaltest
  • scipy.stats.jarque_bera
  • scipy.stats.bartlett
  • scipy.stats.power_divergence
  • scipy.stats.monte_carlo_test

Deprecated features

• scipy.stats.gstd, scipy.stats.chisquare, and
  scipy.stats.power_divergence have deprecated support for masked array
  input.
• scipy.stats.linregress has deprecated support for specifying both samples
  in one argument; x and y are to be provided as separate arguments.
• The conjtransp method for scipy.sparse.dok_array and
  scipy.sparse.dok_matrix has been deprecated and will be removed in SciPy
  1.16.0.
• The option quadrature="trapz" in scipy.integrate.quad_vec has been
  deprecated in favour of quadrature="trapezoid" and will be removed in
  SciPy 1.16.0.
• scipy.special.{comb,perm} have deprecated support for use of exact=True in
  conjunction with non-integral N and/or k.

Backwards incompatible changes

• Many scipy.stats functions now produce a standardized warning message when
  an input sample is too small (e.g. zero size). Previously, these functions
  may have raised an error, emitted one or more less informative warnings, or
  emitted no warnings. In most cases, returned results are unchanged; in almost
  all cases the correct result is NaN.

Expired deprecations

There is an ongoing effort to follow through on long-standing deprecations.
The following previously deprecated features are affected:

• Several previously deprecated methods for sparse arrays were removed:
  asfptype, getrow, getcol, get_shape, getmaxprint,
  set_shape, getnnz, and getformat. Additionally, the .A and
  .H attributes were removed.

• scipy.integrate.{simps,trapz,cumtrapz} have been removed in favour of
  simpson, trapezoid, and cumulative_trapezoid.

• The tol argument of scipy.sparse.linalg.{bcg,bicstab,cg,cgs,gcrotmk, mres,lgmres,minres,qmr,tfqmr} has been removed in favour of rtol.
  Furthermore, the default value of atol for these functions has changed
  to 0.0.

• The restrt argument of scipy.sparse.linalg.gmres has been removed in
  favour of restart.

• The initial_lexsort argument of scipy.stats.kendalltau has been
  removed.

• The cond and rcond arguments of scipy.linalg.pinv have been
  removed.

• The even argument of scipy.integrate.simpson has been removed.

• The turbo and eigvals arguments from scipy.linalg.{eigh,eigvalsh}
  have been removed.

• The legacy argument of scipy.special.comb has been removed.

• The hz/nyq argument of signal.{firls, firwin, firwin2, remez} has
  been removed.

• Objects that weren't part of the public interface but were accessible through
  deprecated submodules have been removed.

• float128, float96, and object arrays now raise an error in
  scipy.signal.medfilt and scipy.signal.order_filter.

• scipy.interpolate.interp2d has been replaced by an empty stub (to be
  removed completely in the future).

• Coinciding with changes to function signatures (e.g. removal of a deprecated
  keyword), we had deprecated positional use of keyword arguments for the
  affected functions, which will now raise an error. Affected functions are:

  • sparse.linalg.{bicg, bicgstab, cg, cgs, gcrotmk, gmres, lgmres, minres, qmr, tfqmr}
  • stats.kendalltau
  • linalg.pinv
  • integrate.simpson
  • linalg.{eigh,eigvalsh}
  • special.comb
  • signal.{firls, firwin, firwin2, remez}

Other changes

• SciPy now uses C17 as the C standard to build with, instead of C99. The C++
  standard remains C++17.
• macOS Accelerate, which got a major upgrade in macOS 13.3, is now supported.
  This results in significant performance improvements for linear algebra
  operations, as well as smaller binary wheels.
• Cross-compilation should be smoother and QEMU or similar is no longer needed
  to run the cross interpreter.
• Experimental array API support for the JAX backend has been added to several
  parts of SciPy.

Authors

• Name (commits)
• h-vetinari (34)
• Steven Adams (1) +
• Max Aehle (1) +
• Ataf Fazledin Ahamed (2) +
• Luiz Eduardo Amaral (1) +
• Trinh Quoc Anh (1) +
• Miguel A. Batalla (7) +
• Tim Beyer (1) +
• Andrea Blengino (1) +
• boatwrong (1)
• Jake Bowhay (51)
• Dietrich Brunn (2)
• Evgeni Burovski (177)
• Tim Butters (7) +
• CJ Carey (5)
• Sean Cheah (46)
• Lucas Colley (73)
• Giuseppe "Peppe" Dilillo (1) +
• DWesl (2)
• Pieter Eendebak (5)
• Kenji S Emerson (1) +
• Jonas Eschle (1)
• fancidev (2)
• Anthony Frazier (1) +
• Ilan Gold (1) +
• Ralf Gommers (125)
• Rohit Goswami (28)
• Ben Greiner (1) +
• Lorenzo Gualniera (1) +
• Matt Haberland (260)
• Shawn Hsu (1) +
• Budjen Jovan (3) +
• Jozsef Kutas (1)
• Eric Larson (3)
• Gregory R. Lee (4)
• Philip Loche (1) +
• Christian Lorentzen (5)
• Sijo Valayakkad Manikandan (2) +
• marinelay (2) +
• Nikolay Mayorov (1)
• Nicholas McKibben (2)
• Melissa Weber Mendonça (7)
• João Mendes (1) +
• Samuel Le Meur-Diebolt (1) +
• Tomiță Militaru (2) +
• Andrew Nelson (35)
• Lysandros Nikolaou (1)
• Nick ODell (5) +
• Jacob Ogle (1) +
• Pearu Peterson (1)
• Matti Picus (5)
• Ilhan Polat (9)
• pwcnorthrop (3) +
• Bharat Raghunathan (1)
• Tom M. Ragonneau (2) +
• Tyler Reddy (101)
• Pamphile Roy (18)
• Atsushi Sakai (9)
• Daniel Schmitz (5)
• Julien Schueller (2) +
• Dan Schult (13)
• Tomer Sery (7)
• Scott Shambaugh (4)
• Tuhin Sharma (1) +
• Sheila-nk (4)
• Skylake (1) +
• Albert Steppi (215)
• Kai Striega (6)
• Zhibing Sun (2) +
• Nimish Telang (1) +
• toofooboo (1) +
• tpl2go (1) +
• Edgar Andrés Margffoy Tuay (44)
• Andrew Valentine (1)
• Valerix (1) +
• Christian Veenhuis (1)
• void (2) +
• Warren Weckesser (3)
• Xuefeng Xu (1)
• Rory Yorke (1)
• Xiao Yuan (1)
• Irwin Zaid (35)
• Elmar Zander (1) +
• Zaikun ZHANG (1)
• ਗਗਨਦੀਪ ਸਿੰਘ (Gagandeep Singh) (4) +

A total of 85 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.

v1.13.1: SciPy 1.13.1

Compare Source

SciPy 1.13.1 Release Notes

SciPy 1.13.1 is a bug-fix release with no new features
compared to 1.13.0. The version of OpenBLAS shipped with
the PyPI binaries has been increased to 0.3.27.

Authors

• Name (commits)
• h-vetinari (1)
• Jake Bowhay (2)
• Evgeni Burovski (6)
• Sean Cheah (2)
• Lucas Colley (2)
• DWesl (2)
• Ralf Gommers (7)
• Ben Greiner (1) +
• Matt Haberland (2)
• Gregory R. Lee (1)
• Philip Loche (1) +
• Sijo Valayakkad Manikandan (1) +
• Matti Picus (1)
• Tyler Reddy (62)
• Atsushi Sakai (1)
• Daniel Schmitz (2)
• Dan Schult (3)
• Scott Shambaugh (2)
• Edgar Andrés Margffoy Tuay (1)

A total of 19 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.

v1.13.0: SciPy 1.13.0

Compare Source

SciPy 1.13.0 Release Notes

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.dev.

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.
• New method BSpline.insert_knot inserts a knot into a BSpline instance.
  This routine is similar to the module-level scipy.interpolate.insert
  function, and works with the BSpline objects instead of tck tuples.
• 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 (65)
• Matthias Bussonnier (4)
• Tim Butters (1) +
• Cale (1) +
• CJ Carey (5)
• 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 (147)
• Matt Haberland (81)
• Tessa van der Heiden (2) +
• Shawn Hsu (1) +
• inky (3) +
• Jannes Münchmeyer (2) +
• Aditya Vidyadhar Kamath (2) +
• Agriya Khetarpal (1) +
• Andrew Landau (1) +
• Eric Larson (7)
• Zhen-Qi Liu (1) +
• Christian Lorentzen (2)
• 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 (27)
• Praveer Nidamaluri (1)
• Yagiz Olmez (5) +
• Dimitri Papadopoulos Orfanos (1)
• Drew Parsons (1) +
• Tirth Patel (7)
• Pearu Peterson (1)
• Matti Picus (3)
• Rambaud Pierrick (1) +
• Ilhan Polat (30)
• Quentin Barthélemy (1)
• Tyler Reddy (117)
• Pamphile Roy (10)
• Atsushi Sakai (8)
• Daniel Schmitz (10)
• Dan Schult (17)
• Eli Schwartz (4)
• Stefanie Senger (1) +
• Scott Shambaugh (2)
• Kevin Sheppard (2)
• sidsrinivasan (4) +
• Samuel St-Jean (1)
• Albert Steppi (31)
• 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 (8)
• Elmar Zander (1) +
• Mathias Zechmeister (1) +

A total of 96 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.

---

Configuration

📅 Schedule: Branch creation - At any time (no schedule defined), Automerge - At any time (no schedule defined).

🚦 Automerge: Disabled by config. Please merge this manually once you are satisfied.

♻ Rebasing: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox.

🔕 Ignore: Close this PR and you won't be reminded about these updates again.

---

• If you want to rebase/retry this PR, check this box

---

This PR was generated by Mend Renovate. View the repository job log.