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Package is "python-scipy" Wed Jul 3 20:29:17 2024 rev:74 rq:1184871 version:1.14.0 Changes: -------- --- /work/SRC/openSUSE:Factory/python-scipy/python-scipy.changes 2024-05-29 19:35:37.523996432 +0200 +++ /work/SRC/openSUSE:Factory/.python-scipy.new.18349/python-scipy.changes 2024-07-03 20:29:46.891925885 +0200 @@ -1,0 +2,208 @@ +Mon Jul 1 13:35:29 UTC 2024 - John Paul Adrian Glaubitz <[email protected]> + +- Update to 1.14.0 + ## 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. +- Cherry-pick upstream patch to fix build with GCC 14 + * https://github.com/scipy/scipy/pull/21063.patch +- Update BuildRequires from pyproject.toml + +------------------------------------------------------------------- Old: ---- scipy-1.13.1.tar.gz New: ---- 21063.patch scipy-1.14.0.tar.gz BETA DEBUG BEGIN: New:- Cherry-pick upstream patch to fix build with GCC 14 * https://github.com/scipy/scipy/pull/21063.patch - Update BuildRequires from pyproject.toml BETA DEBUG END: ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ python-scipy.spec ++++++ --- /var/tmp/diff_new_pack.QaJOJa/_old 2024-07-03 20:29:48.227974785 +0200 +++ /var/tmp/diff_new_pack.QaJOJa/_new 2024-07-03 20:29:48.231974931 +0200 @@ -93,7 +93,7 @@ # TODO explore debundling Boost for standard and hpc Name: %{package_name} -Version: 1.13.1 +Version: 1.14.0 Release: 0 Summary: Scientific Tools for Python License: BSD-3-Clause AND LGPL-2.0-or-later AND BSL-1.0 @@ -101,6 +101,8 @@ Source0: https://files.pythonhosted.org/packages/source/s/scipy/scipy-%{version}.tar.gz # Create with pooch: `python3 scipy-%%{version}/scipy/datasets/_download_all.py scipy-datasets/scipy-data; tar czf scipy-datasets.tar.gz scipy-datasets` Source1: scipy-datasets.tar.gz +# PATCH-FIX-UPSTREAM - MAINT: gcc-14 test_region5 tol bump +Patch: https://github.com/scipy/scipy/pull/21063.patch BuildRequires: %{python_module Cython >= 3.0.8 with %python-Cython < 3.1} BuildRequires: %{python_module devel >= 3.9} BuildRequires: %{python_module meson-python >= 0.15.0 with %python-meson-python < 0.18} @@ -123,7 +125,7 @@ BuildRequires: %{python_module threadpoolctl} %endif %if %{without hpc} -BuildRequires: %{python_module numpy-devel >= 1.18.5 with %python-numpy-devel < 2.3} +BuildRequires: %{python_module numpy-devel >= 1.23.5 with %python-numpy-devel < 2.3} %if 0%{?sle_version} && 0%{?sle_version} <= 150600 # The default gcc on SLE15 is gcc7 we need something newer BuildRequires: gcc10-c++ ++++++ 21063.patch ++++++ >From c485c78ae3918ed26d4c1208e77b029a7f918f0d Mon Sep 17 00:00:00 2001 From: Tyler Reddy <[email protected]> Date: Thu, 27 Jun 2024 09:56:23 -0600 Subject: [PATCH] MAINT: gcc-14 test_region5 tol bump * Fixes #21059 * A small tolerance bump in `TestHyp2f1.test_region5` needed for one its test cases to pass when compiling SciPy with gcc-14 series. [ci skip] [skip ci] --- scipy/special/tests/test_hyp2f1.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scipy/special/tests/test_hyp2f1.py b/scipy/special/tests/test_hyp2f1.py index 6c2f6ec103bf..adef4e2584c8 100644 --- a/scipy/special/tests/test_hyp2f1.py +++ b/scipy/special/tests/test_hyp2f1.py @@ -2093,7 +2093,7 @@ def test_region4(self, hyp2f1_test_case): c=-15.5, z=(0.3413793103448277-0.9482758620689655j), expected=(-1.0509834850116921-1.1145522325486075j), - rtol=1e-14, + rtol=1.1e-14, ), ), pytest.param( ++++++ scipy-1.13.1.tar.gz -> scipy-1.14.0.tar.gz ++++++ /work/SRC/openSUSE:Factory/python-scipy/scipy-1.13.1.tar.gz /work/SRC/openSUSE:Factory/.python-scipy.new.18349/scipy-1.14.0.tar.gz differ: char 5, line 1
