commit ce8155ef5e1fb5f842080c628cb57e82d34d2e76dc6b06a905debfe513d4539d Author: Adrian Schröter Date: Fri May 3 22:55:55 2024 +0200 Sync from SUSE:SLFO:Main python-scipy revision f1d5ed61112f27fc01c44c6800750656 diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..9b03811 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,23 @@ +## Default LFS +*.7z filter=lfs diff=lfs merge=lfs -text +*.bsp filter=lfs diff=lfs merge=lfs -text +*.bz2 filter=lfs diff=lfs merge=lfs -text +*.gem filter=lfs diff=lfs merge=lfs -text +*.gz filter=lfs diff=lfs merge=lfs -text +*.jar filter=lfs diff=lfs merge=lfs -text +*.lz filter=lfs diff=lfs merge=lfs -text +*.lzma filter=lfs diff=lfs merge=lfs -text +*.obscpio filter=lfs diff=lfs merge=lfs -text +*.oxt filter=lfs diff=lfs merge=lfs -text +*.pdf filter=lfs diff=lfs merge=lfs -text +*.png filter=lfs diff=lfs merge=lfs -text +*.rpm filter=lfs diff=lfs merge=lfs -text +*.tbz filter=lfs diff=lfs merge=lfs -text +*.tbz2 filter=lfs diff=lfs merge=lfs -text +*.tgz filter=lfs diff=lfs merge=lfs -text +*.ttf filter=lfs diff=lfs merge=lfs -text +*.txz filter=lfs diff=lfs merge=lfs -text +*.whl filter=lfs diff=lfs merge=lfs -text +*.xz filter=lfs diff=lfs merge=lfs -text +*.zip filter=lfs diff=lfs merge=lfs -text +*.zst filter=lfs diff=lfs merge=lfs -text diff --git a/_multibuild b/_multibuild new file mode 100644 index 0000000..40a268f --- /dev/null +++ b/_multibuild @@ -0,0 +1,4 @@ + + gnu-hpc + test + diff --git a/python-scipy.changes b/python-scipy.changes new file mode 100644 index 0000000..5c59d0d --- /dev/null +++ b/python-scipy.changes @@ -0,0 +1,1867 @@ +------------------------------------------------------------------- +Mon Jan 22 12:20:49 UTC 2024 - Daniel Garcia + +- Disable broken tests in s390x, gh#scipy/scipy#18878, bsc#1218608 + +------------------------------------------------------------------- +Tue Nov 21 04:25:02 UTC 2023 - Steve Kowalik + +- Update to 1.11.4: + * MAINT: ensure cobyla objective returns scalar + * MAINT: fixup dep warning + * BUG: interpolate: fix spalde with len(c) < len(t) + * BUG: pass unused xrtol in fmin_bfgs to _minimize_bfgs + * BUG: Regression test for lsq trf boundary error + * BUG: lsq trf gives x=1e-10 if x0 is near a bound + * BUG: make Bessel-roots function not hang and not skip roots + * io/matlab: Fix loading of mat files containing fn handles when + simplify_cells=True + * BUG: make L-BFGS-B work with single precision gradient + * MAINT: stats: fix NumPy DeprecationWarnings + * BUG: sparse.linalg: Cast to intc before SuperLU + * MAINT: Use deb_system scheme to match meson's path inference & fix aarch64 + * BUG: Fix python3.12 distutils dev.py build + * BUG: stats: remove use of `BOOST_MATH_DECLARE_SPECIAL_FUNCTIONS` + * MAINT: fix libquadmath licence + * MAINT: newton, make sure x0 is an inexact type + * MAINT: stats.CovViaEigendecomposition: fix _colorize for singular + covariance + * TST: fix `TestODR.test_implicit` test failure with tolerance bump + * BUG: signal: freqz rfft grid fix + * BUG: Support sparse arrays in scipy.sparse.csgraph.laplacian + * MAINT: signal: Remove the cval parameter from the private function + _pad_test. + * BLD: Avoid absolute pathnames in .pyx files + * BUG: Add back make_strictly_feasible to lsq trf. + * MAINT: should not be using np.float64() on arrays + * BUG: trust-constr Bounds exclusive + * BUG: sparse.csgraph: Support int64 indices in traversal.pyx + * BUG: add infeasibility checks to min_weight_full_bipartite_matching + * DOC, MAINT: workaround for py311 docs + * BUG: Fix typecasting problem in scipy.sparse.lil_matrix truediv + * BUG: In least_squares make initial guess sufficiently feasible w.r.t. + to bounds for method 'trf' + * BUG: fix pow method for sparrays with power zero + * BUG: set idx_dtype in sparse dia_array.tocoo +- Drop patch intc.patch, included. + +------------------------------------------------------------------- +Mon Oct 9 06:52:54 UTC 2023 - ecsos + +- Let it build for Leap 15.6 also. + +------------------------------------------------------------------- +Thu Jul 27 13:31:24 UTC 2023 - Markéta Machová + +- Add upstream intc.patch to fix gh#scipy/scipy#18603 + +------------------------------------------------------------------- +Tue Jul 25 10:04:04 UTC 2023 - Markéta Machová + +- Update to 1.11.1 + * Several scipy.sparse array API improvements, including sparse.sparray, + a new public base class distinct from the older sparse.spmatrix class, + proper 64-bit index support, and numerous deprecations paving the way + to a modern sparse array experience. + * scipy.stats added tools for survival analysis, multiple hypothesis + testing, sensitivity analysis, and working with censored data. + * A new function was added for quasi-Monte Carlo integration, and linear + algebra functions det and lu now accept nD-arrays. + * An axes argument was added broadly to ndimage functions, facilitating + analysis of stacked image data. + +------------------------------------------------------------------- +Thu Jun 29 07:21:08 UTC 2023 - Andreas Schneider + +- Use sle15_python_module_pythons +- Require GCC >= 8 + +------------------------------------------------------------------- +Fri Mar 10 14:18:09 UTC 2023 - Martin Liška + +- Fix i686 tests for GCC 13 due to: + https://gcc.gnu.org/gcc-13/porting_to.html#excess-precision + +------------------------------------------------------------------- +Sun Feb 26 00:27:35 UTC 2023 - Ben Greiner + +- Update to 1.10.1 + * bug-fix release with no new features compared to 1.10.0 +- Drop scipy-pr17717-ro-interpn.patch + +------------------------------------------------------------------- +Mon Jan 16 22:06:27 UTC 2023 - Ben Greiner + +- Highlights of the 1.10.0 release + * A new dedicated datasets submodule (scipy.datasets) has been + added, and is now preferred over usage of scipy.misc for + dataset retrieval. + * A new scipy.interpolate.make_smoothing_spline function was + added. This function constructs a smoothing cubic spline from + noisy data, using the generalized cross-validation (GCV) + criterion to find the tradeoff between smoothness and proximity + to data points. + * scipy.stats has three new distributions, two new hypothesis + tests, three new sample statistics, a class for greater control + over calculations involving covariance matrices, and many other + enhancements. +- Add scipy-pr17717-ro-interpn.patch gh#scipy/scipy#17717 + * Fixes gh#spacetelescope/gwcs#433 +- Provide scipy-datasets.tar.gz for pooch cache and tests without + needing to download during test time. + +------------------------------------------------------------------- +Wed Jan 11 07:35:47 UTC 2023 - Guillaume GARDET + +- Update to version 1.10.0 +- Drop upstream pacthes: + * fix-tests.patch + * fix-tests-pytest72.patch + * scipy-pr17467-no-np.int0.patch + +------------------------------------------------------------------- +Fri Dec 23 16:37:30 UTC 2022 - Ben Greiner + +- Add scipy-pr17467-no-np.int0.patch gh#scipy/scipy#17467 +- Move the flavored packaganame definition so that quilt does not + fail + +------------------------------------------------------------------- +Thu Dec 8 17:07:18 UTC 2022 - Dominique Leuenberger + +- Ensure the test flavor has a different source name than the main + flavor: OBS uses the source names to create the dep-chain. With + the test package having the same name as the mani flavor, all + builds behind python-scipy are blocked until the test suite + passed. + +------------------------------------------------------------------- +Wed Dec 7 11:11:11 UTC 2022 - Daniel Garcia + +- Add fix-tests-pytest72.patch to fix the tests that fails with pytest 7 + gh#scipy/scipy#17296 + +------------------------------------------------------------------- +Fri Dec 2 11:56:35 UTC 2022 - Daniel Garcia + +- Add fix-tests.patch gh#scipy/scipy#16926#issuecomment-1287507634 + +------------------------------------------------------------------- +Thu Oct 20 15:05:16 UTC 2022 - Ben Greiner + +- Update to version 1.9.3 + * SciPy 1.9.3 is a bug-fix release with no new features compared + to 1.9.2. + * #3691: scipy.interpolate.UnivariateSpline segfault + * #5286: BUG: multivariate_normal returns a pdf for values + outside its… + * #6551: BUG: stats: inconsistency in docs and behavior of gmean + and hmean + * #9245: running + scipy.interpolate.tests.test_fitpack::test_bisplev_integer_overflow… + * #12471: test_bisplev_integer_overflow: Segmentation fault (core + dumped) + * #13321: Bug: setting iprint=0 hides all output from + fmin_l_bfgs_b, but… + * #13730: `scipy.stats.mood` does not correct for ties + * #14019: ks_2samp throws `RuntimeWarning: overflow encountered + in double_scalars` + * #14589: `shgo` error since scipy 1.8.0.dev0+1529.803e52d + * #14591: Input data validation for RectSphereBivariateSpline + * #15101: BUG: binom.pmf - RuntimeWarning: divide by zero + * #15342: BUG: scipy.optimize.minimize: Powell’s method function + evaluated… + * #15964: BUG: lombscargle fails if argument is a view + * #16211: BUG: Possible bug when using winsorize on pandas data + instead… + * #16459: BUG: stats.ttest_ind returns wrong p-values with + permutations + * #16500: odr.Model default meta value fails with __getattr__ + * #16519: BUG: Error in error message for incorrect sample + dimension in… + * #16527: BUG: dimension of isuppz in syevr is mistranslated + * #16600: BUG: `KDTree`’s optional argument `eps` seems to have + no… + * #16656: dtype not preserved with operations on sparse arrays + * #16751: BUG: `stats.fit` on `boltzmann` expects `bound` for + `lambda`,… + * #17012: BUG: Small oversight in sparse.linalg.lsmr? + * #17020: BUG: Build failure due to problems with shebang line in + cythoner.py + * #17088: BUG: stats.rayleigh.fit: returns `loc` that is + inconsistent… + * #17104: BUG? Incorrect branch in `LAMV` / `_specfunc.lamv` + * #17196: DOC: keepdims in stats.mode is incorrectly documented +- Move multibuild flavor ":standard" to unflavored build +- Test in parallel (pytest-xdist) + +------------------------------------------------------------------- +Tue Oct 11 08:36:20 UTC 2022 - Ben Greiner + +- Update to version 1.9.2 + * SciPy 1.9.2 is a bug-fix release with no new features compared + to 1.9.1. + +------------------------------------------------------------------- +Sat Sep 10 23:43:22 UTC 2022 - Ben Greiner + +- Update to version 1.9.1 + * SciPy 1.9.1 is a bug-fix release with no new features compared + to 1.9.0. Notably, some important meson build fixes are + included. +- Release 1.9.0 + * Full changelog at + https://docs.scipy.org/doc/scipy/release.1.9.0.html +- Highlights of the 1.9.0 release: + * We have modernized our build system to use meson, + substantially improving our build performance, and providing + better build-time configuration and cross-compilation support, + * Added scipy.optimize.milp, new function for mixed-integer + linear programming, + * Added scipy.stats.fit for fitting discrete and continuous + distributions to data, + * Tensor-product spline interpolation modes were added to + scipy.interpolate.RegularGridInterpolator, + * A new global optimizer (DIviding RECTangles algorithm) + scipy.optimize.direct. +- Switch to meson-python PEP517 build + +------------------------------------------------------------------- +Mon Jul 18 15:23:43 UTC 2022 - Ben Greiner + +- Keep lowercase egg-info despite setuptools 60+ + +------------------------------------------------------------------- +Sat May 21 08:12:51 UTC 2022 - andy great + +- Update to version 1.8.1. + * Bug-fix release with no new features. + +------------------------------------------------------------------- +Tue Apr 12 12:20:43 UTC 2022 - Martin Liška + +- With the previously added -ffloat-store, some tests that fail on i586. + Disable them. + +------------------------------------------------------------------- +Tue Apr 12 06:36:01 UTC 2022 - Martin Liška + +- Limit double floating point precision for x87, triggered by GCC 12. + Fixes test_kolmogorov.py Fatal Python error: Floating point exception + which is a double floating-point test. + +------------------------------------------------------------------- +Mon Mar 28 18:16:15 UTC 2022 - Ben Greiner + +- Update to version 1.8.0 + * https://scipy.github.io/devdocs/release.1.8.0.html + * SciPy 1.8.0 is the culmination of 6 months of hard work. It + contains many new features, numerous bug-fixes, improved test + coverage and better documentation. There have been a number of + deprecations and API changes in this release. 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). + * A sparse array API has been added for early testing and + feedback; this work is ongoing, and users should expect minor + API refinements over the next few releases. + * The sparse SVD library PROPACK is now vendored with SciPy, and + an interface is exposed via scipy.sparse.svds with + solver='PROPACK'. It is currently default-off due to potential + issues on Windows that we aim to resolve in the next release, + but can be optionally enabled at runtime for friendly testing + with an environment variable setting of USE_PROPACK=1. + * A new scipy.stats.sampling submodule that leverages the UNU.RAN + C library to sample from arbitrary univariate non-uniform + continuous and discrete distributions + * All namespaces that were private but happened to miss + underscores in their names have been deprecated. + * Backwards incompatible changes + - SciPy has raised the minimum compiler versions to GCC 6.3 on + linux and VS2019 on windows. In particular, this means that + SciPy may now use C99 and C++14 features. For more details + see here. + - The result for empty bins for scipy.stats.binned_statistic + with the builtin 'std' metric is now nan, for consistency + with np.std. + - The function scipy.spatial.distance.wminkowski has been + removed. To achieve the same results as before, please use + the minkowski distance function with the (optional) w= + keyword-argument for the given weight. + +------------------------------------------------------------------- +Sat Jan 29 20:44:30 UTC 2022 - Ben Greiner + +- Provide empty debuginfo extraction for :test flavor + +------------------------------------------------------------------- +Sun Jan 23 17:52:38 UTC 2022 - Ben Greiner + +- Update to version 1.7.3 + * 3rd bugfix release since 1.7.0 +- Highlights from the 1.7.0 release + * A new submodule for quasi-Monte Carlo, scipy.stats.qmc, was + added + * The documentation design was updated to use the same + PyData-Sphinx theme as NumPy and other ecosystem libraries. + * We now vendor and leverage the Boost C++ library to enable + numerous improvements for long-standing weaknesses in + scipy.stats + * scipy.stats has six new distributions, eight new (or + overhauled) hypothesis tests, a new function for bootstrapping, + a class that enables fast random variate sampling and + percentile point function evaluation, and many other + enhancements. + * cdist and pdist distance calculations are faster for several + metrics, especially weighted cases, thanks to a rewrite to a + new C++ backend framework + * A new class for radial basis function interpolation, + RBFInterpolator, was added to address issues with the Rbf + class. +- Enable fast part of the test suite + +------------------------------------------------------------------- +Mon Jul 26 14:37:33 UTC 2021 - Andreas Schwab + +- Enable openblas on riscv64 + +------------------------------------------------------------------- +Mon May 3 01:31:43 UTC 2021 - Arun Persaud + +- update to version 1.6.3: + * Issues closed + + #13772: Divide by zero in distance.yule + + #13796: CI: prerelease_deps failures + + #13890: TST: spatial rotation failure in (1.6.3) wheels repo + (ARM64) + * Pull requests + + #13755: CI: fix the matplotlib warning emitted during builing + docs + + #13773: BUG: Divide by zero in yule dissimilarity of constant + vectors + + #13799: CI/MAINT: deprecated np.typeDict + + #13819: substitute np.math.factorial with math.factorial + + #13895: TST: add random seeds in Rotation module + +------------------------------------------------------------------- +Sun Apr 4 16:40:00 UTC 2021 - Arun Persaud + +- update to version 1.6.2: + * Issues closed for 1.6.2 + + #13512: `stats.gaussian_kde.evaluate` broken on S390X + + #13584: rotation._compute_euler_from_matrix() creates an array + with negative... + + #13585: Behavior change in coo_matrix when dtype=None + + #13686: delta0 argument of scipy.odr.ODR() ignored + * Pull requests for 1.6.2 + + #12862: REL: put upper bounds on versions of dependencies + + #13575: BUG: fix `gaussian_kernel_estimate` on S390X + + #13586: BUG: sparse: Create a utility function `getdata` + + #13598: MAINT, BUG: enforce contiguous layout for output array + in Rotation.as_euler + + #13687: BUG: fix scipy.odr to consider given delta0 argument + +------------------------------------------------------------------- +Wed Mar 3 19:09:30 UTC 2021 - Arun Persaud + +- update to version 1.6.1: + * Issues closed + + #13072: BLD: Quadpack undefined references + + #13241: Not enough values to unpack when passing tuple to + `blocksize`... + + #13329: Large sparse matrices of big integers lose information + + #13342: fftn crashes if shape arguments are supplied as ndarrays + + #13356: LSQBivariateSpline segmentation fault when quitting the + Python... + + #13358: scipy.spatial.transform.Rotation object can not be + deepcopied... + + #13408: Type of `has_sorted_indices` property + + #13412: Sorting spherical Voronoi vertices leads to crash in + area calculation + + #13421: linear_sum_assignment - support for matrices with more + than 2^31... + + #13428: `stats.exponnorm.cdf` returns `nan` for small values of + `K`... + + #13465: KDTree.count_neighbors : 0xC0000005 error for tuple of + different... + + #13468: directed_hausdorff issue with shuffle + + #13472: Failures on FutureWarnings with numpy 1.20.0 for + lfilter, sosfilt... + + #13565: BUG: 32-bit wheels repo test failure in optimize + * Pull requests + + #13318: REL: prepare for SciPy 1.6.1 + + #13344: BUG: fftpack doesn't work with ndarray shape argument + + #13345: MAINT: Replace scipy.take with numpy.take in FFT + function docstrings. + + #13354: BUG: optimize: rename private functions to include + leading underscore + + #13387: BUG: Support big-endian platforms and big-endian WAVs + + #13394: BUG: Fix Python crash by allocating larger array in + LSQBivariateSpline + + #13400: BUG: sparse: Better validation for BSR ctor + + #13403: BUG: sparse: Propagate dtype through CSR/CSC + constructors + + #13414: BUG: maintain dtype of SphericalVoronoi regions + + #13422: FIX: optimize: use npy_intp to store array dims for lsap + + #13425: BUG: spatial: make Rotation picklable + + #13426: BUG: `has_sorted_indices` and `has_canonical_format` + should... + + #13430: BUG: stats: Fix exponnorm.cdf and exponnorm.sf for small + K + + #13470: MAINT: silence warning generated by + `spatial.directed_hausdorff` + + #13473: TST: fix failures due to new FutureWarnings in NumPy + 1.21.dev0 + + #13479: MAINT: update directed_hausdorff Cython code + + #13485: BUG: KDTree weighted count_neighbors doesn't work + between two... + + #13503: TST: fix `test_fortranfile_read_mixed_record` on + big-endian... + + #13518: DOC: document that pip >= 20.3.3 is needed for macOS 11 + + #13520: BLD: update reqs based on oldest-supported-numpy in + pyproject.toml + + #13567: TST, BUG: adjust tol on test_equivalence + +------------------------------------------------------------------- +Sat Jan 16 17:14:26 UTC 2021 - Benjamin Greiner + +- NEP 29: Last minorversion bump deprecated Python 3.6 + https://numpy.org/neps/nep-0029-deprecation_policy.html +- Fix hpc setup for coinstallable python3 flavors, needs + gh#openSUSE/hpc#3 + +------------------------------------------------------------------- +Tue Jan 5 07:57:30 UTC 2021 - Paolo Stivanin + +- Update to 1.6.0: + * scipy.ndimage improvements: Fixes and ehancements to boundary extension + modes for interpolation functions. Support for complex-valued inputs + in many filtering and interpolation functions. New grid_mode option + for scipy.ndimage.zoom to enable results consistent with scikit-image’s rescale. + * scipy.optimize.linprog has fast, new methods for large, sparse + problems from the HiGHS library. + * scipy.stats improvements including new distributions, a new test, + and enhancements to existing distributions and tests + * scipy.special now has improved support for 64-bit LAPACK backend + * scipy.odr now has support for 64-bit integer BLAS + * scipy.odr.ODR has gained an optional overwrite argument so that + existing files may be overwritten. + * scipy.cluster.hierarchy.DisjointSet has been added for incremental + connectivity queries. + * scipy.cluster.hierarchy.dendrogram return value now also includes + leaf color information in leaves_color_list. + * scipy.interpolate.interp1d has a new method nearest-up, similar to + the existing method nearest but rounds half-integers up instead of down. + * scipy.ndimage.convolve, scipy.ndimage.correlate and their 1d counterparts + now accept both complex-valued images and/or complex-valued filter kernels. + All convolution-based filters also now accept complex-valued inputs + * scipy.optimize.linprog has fast, new methods for large, sparse problems + from the HiGHS C++ library + * scipy.optimize.quadratic_assignment has been added for approximate solution of + the quadratic assignment problem. + * scipy.optimize.linear_sum_assignment now has a substantially reduced + overhead for small cost matrix sizes + * scipy.optimize.least_squares has improved performance when the user + provides the jacobian as a sparse jacobian already in csr_matrix format + * scipy.signal.gammatone has been added to design FIR or IIR filters that + model the human auditory system. + * scipy.signal.iircomb has been added to design IIR peaking/notching + comb filters that can boost/attenuate a frequency from a signal. + * scipy.signal.sosfilt performance has been improved to avoid some + previously- observed slowdowns + * scipy.signal.windows.taylor has been added–the Taylor window function + is commonly used in radar digital signal processing + * scipy.signal.gauss_spline now supports list type input for consistency + with other related SciPy functions + * scipy.signal.correlation_lags has been added to allow calculation of + the lag/ displacement indices array for 1D cross-correlation. + +------------------------------------------------------------------- +Fri Dec 18 20:29:48 UTC 2020 - andy great + +- Update to version 1.5.4. + * Bug fix release with no new feature. +- Updates for 1.5.3. + * Bug fix release with no new feature. + +------------------------------------------------------------------- +Thu Aug 13 07:23:03 UTC 2020 - Marketa Calabkova + +- Update to 1.5.2 + * wrappers for more than a dozen new LAPACK routines are now available in scipy.linalg.lapack + * Improved support for leveraging 64-bit integer size from linear algebra backends + * addition of the probability distribution for two-sided one-sample Kolmogorov-Smirnov tests + * see upstream changelog for more detailed info +- Drop breaking patch no_implicit_decl.patch + * the problem is with lapacke + +------------------------------------------------------------------- +Thu Mar 19 08:05:49 UTC 2020 - Martin Liška + +- Add -std=legacy in order to build with GCC10: + https://gcc.gnu.org/gcc-10/porting_to.html#argument-mismatch + +------------------------------------------------------------------- +Mon Mar 16 13:51:18 UTC 2020 - Egbert Eich + +- 'umpfack' is a runtime dependency of scipy. No build time + dependency to suitesparse is required (jsc#SLE-11732). +- Get rid of site.cfg entirely as it is used nowhwere in scipy. + +------------------------------------------------------------------- +Wed Jan 15 12:56:20 UTC 2020 - Tomáš Chvátal + +- Fix pybind11 devel dependency to match real name + +------------------------------------------------------------------- +Fri Dec 20 01:27:36 UTC 2019 - Todd R + +- Update to 1.4.1 + * SciPy 1.4.1 is a bug-fix release with no new features compared + to 1.4.0. Importantly, it aims to fix a problem where an older + version of pybind11 may cause a segmentation fault when + imported alongside incompatible libraries. + +------------------------------------------------------------------- +Tue Dec 17 20:48:57 UTC 2019 - Todd R + +- Update to 1.4.0 + + Highlights of this release + * a new submodule, `scipy.fft`, now supersedes `scipy.fftpack`; this + means support for ``long double`` transforms, faster multi-dimensional + transforms, improved algorithm time complexity, release of the global + intepreter lock, and control over threading behavior + * support for ``pydata/sparse`` arrays in `scipy.sparse.linalg` + * substantial improvement to the documentation and functionality of + several `scipy.special` functions, and some new additions + * the generalized inverse Gaussian distribution has been added to + `scipy.stats` + * an implementation of the Edmonds-Karp algorithm in + `scipy.sparse.csgraph.maximum_flow` + * `scipy.spatial.SphericalVoronoi` now supports n-dimensional input, + has linear memory complexity, improved performance, and + supports single-hemisphere generators + + New features + > Infrastructure + * Documentation can now be built with ``runtests.py --doc`` + * A ``Dockerfile`` is now available in the ``scipy/scipy-dev`` repository to + acilitate getting started with SciPy development. + > `scipy.constants` improvements + * `scipy.constants` has been updated with the CODATA 2018 constants. + > `scipy.fft` added + * `scipy.fft` is a new submodule that supersedes the `scipy.fftpack` submodule. + or the most part, this is a drop-in replacement for ``numpy.fft`` and + scipy.fftpack` alike. With some important differences, `scipy.fft`: + * uses NumPy's conventions for real transforms (``rfft``). This means the + eturn value is a complex array, half the size of the full ``fft`` output. + his is different from the output of ``fftpack`` which returned a real array + epresenting complex components packed together. + * the inverse real to real transforms (``idct`` and ``idst``) are normalized + or ``norm=None`` in thesame way as ``ifft``. This means the identity + `idct(dct(x)) == x`` is now ``True`` for all norm modes. + * does not include the convolutions or pseudo-differential operators + rom ``fftpack``. + * This submodule is based on the ``pypocketfft`` library, developed by the + uthor of ``pocketfft`` which was recently adopted by NumPy as well. + `pypocketfft`` offers a number of advantages over fortran ``FFTPACK``: + * support for long double (``np.longfloat``) precision transforms. + * faster multi-dimensional transforms using vectorisation + * Bluestein’s algorithm removes the worst-case ``O(n^2)`` complexity of + `FFTPACK`` + * the global interpreter lock (``GIL``) is released during transforms + * optional multithreading of multi-dimensional transforms via the ``workers`` + rgument + * Note that `scipy.fftpack` has not been deprecated and will continue to be + aintained but is now considered legacy. New code is recommended to use + scipy.fft` instead, where possible. + > `scipy.fftpack` improvements + * `scipy.fftpack` now uses pypocketfft to perform its FFTs, offering the same + peed and accuracy benefits listed for scipy.fft above but without the + mproved API. + > `scipy.integrate` improvements + * The function `scipy.integrate.solve_ivp` now has an ``args`` argument. + his allows the user-defined functions passed to the function to have + dditional parameters without having to create wrapper functions or + ambda expressions for them. + * `scipy.integrate.solve_ivp` can now return a ``y_events`` attribute + epresenting the solution of the ODE at event times + * New ``OdeSolver`` is implemented --- ``DOP853``. This is a high-order explicit + unge-Kutta method originally implemented in Fortran. Now we provide a pure + ython implementation usable through ``solve_ivp`` with all its features. + * `scipy.integrate.quad` provides better user feedback when break points are + pecified with a weighted integrand. + * `scipy.integrate.quad_vec` is now available for general purpose integration + f vector-valued functions + > `scipy.interpolate` improvements + * `scipy.interpolate.pade` now handles complex input data gracefully + * `scipy.interpolate.Rbf` can now interpolate multi-dimensional functions + > `scipy.io` improvements + * `scipy.io.wavfile.read` can now read data from a `WAV` file that has a + alformed header, similar to other modern `WAV` file parsers + * `scipy.io.FortranFile` now has an expanded set of available ``Exception`` + lasses for handling poorly-formatted files + > `scipy.linalg` improvements + * The function ``scipy.linalg.subspace_angles(A, B)`` now gives correct + esults for complex-valued matrices. Before this, the function only returned + orrect values for real-valued matrices. + * New boolean keyword argument ``check_finite`` for `scipy.linalg.norm`; whether + o check that the input matrix contains only finite numbers. Disabling may + ive a performance gain, but may result in problems (crashes, non-termination) + f the inputs do contain infinities or NaNs. + * `scipy.linalg.solve_triangular` has improved performance for a C-ordered + riangular matrix + * ``LAPACK`` wrappers have been added for ``?geequ``, ``?geequb``, ``?syequb``, + nd ``?heequb`` + * Some performance improvements may be observed due to an internal optimization + n operations involving LAPACK routines via ``_compute_lwork``. This is + articularly true for operations on small arrays. + * Block ``QR`` wrappers are now available in `scipy.linalg.lapack` + > `scipy.optimize` improvements + * It is now possible to use linear and non-linear constraints with + scipy.optimize.differential_evolution`. + * `scipy.optimize.linear_sum_assignment` has been re-written in C++ to improve + erformance, and now allows input costs to be infinite. + * A ``ScalarFunction.fun_and_grad`` method was added for convenient simultaneous + etrieval of a function and gradient evaluation + * `scipy.optimize.minimize` ``BFGS`` method has improved performance by avoiding + uplicate evaluations in some cases + * Better user feedback is provided when an objective function returns an array + nstead of a scalar. + > `scipy.signal` improvements + * Added a new function to calculate convolution using the overlap-add method, + amed `scipy.signal.oaconvolve`. Like `scipy.signal.fftconvolve`, this + unction supports specifying dimensions along which to do the convolution. + * `scipy.signal.cwt` now supports complex wavelets. + * The implementation of ``choose_conv_method`` has been updated to reflect the + ew FFT implementation. In addition, the performance has been significantly + mproved (with rather drastic improvements in edge cases). + * The function ``upfirdn`` now has a ``mode`` keyword argument that can be used + o select the signal extension mode used at the signal boundaries. These modes + re also available for use in ``resample_poly`` via a newly added ``padtype`` + rgument. + * `scipy.signal.sosfilt` now benefits from Cython code for improved performance + * `scipy.signal.resample` should be more efficient by leveraging ``rfft`` when + ossible + > `scipy.sparse` improvements + * It is now possible to use the LOBPCG method in `scipy.sparse.linalg.svds`. + * `scipy.sparse.linalg.LinearOperator` now supports the operation ``rmatmat`` + or adjoint matrix-matrix multiplication, in addition to ``rmatvec``. + * Multiple stability updates enable float32 support in the LOBPCG eigenvalue + olver for symmetric and Hermitian eigenvalues problems in + `scipy.sparse.linalg.lobpcg``. + * A solver for the maximum flow problem has been added as + scipy.sparse.csgraph.maximum_flow`. + * `scipy.sparse.csgraph.maximum_bipartite_matching` now allows non-square inputs, + o longer requires a perfect matching to exist, and has improved performance. + * `scipy.sparse.lil_matrix` conversions now perform better in some scenarios + * Basic support is available for ``pydata/sparse`` arrays in + scipy.sparse.linalg` + * `scipy.sparse.linalg.spsolve_triangular` now supports the ``unit_diagonal`` + rgument to improve call signature similarity with its dense counterpart, + scipy.linalg.solve_triangular` + * ``assertAlmostEqual`` may now be used with sparse matrices, which have added + upport for ``__round__`` + > `scipy.spatial` improvements + * The bundled Qhull library was upgraded to version 2019.1, fixing several + ssues. Scipy-specific patches are no longer applied to it. + * `scipy.spatial.SphericalVoronoi` now has linear memory complexity, improved + erformance, and supports single-hemisphere generators. Support has also been + dded for handling generators that lie on a great circle arc (geodesic input) + nd for generators in n-dimensions. + * `scipy.spatial.transform.Rotation` now includes functions for calculation of a + ean rotation, generation of the 3D rotation groups, and reduction of rotations + ith rotational symmetries. + * `scipy.spatial.transform.Slerp` is now callable with a scalar argument + * `scipy.spatial.voronoi_plot_2d` now supports furthest site Voronoi diagrams + * `scipy.spatial.Delaunay` and `scipy.spatial.Voronoi` now have attributes + or tracking whether they are furthest site diagrams + > `scipy.special` improvements + * The Voigt profile has been added as `scipy.special.voigt_profile`. + * A real dispatch has been added for the Wright Omega function + `scipy.special.wrightomega`). + * The analytic continuation of the Riemann zeta function has been added. (The + iemann zeta function is the one-argument variant of `scipy.special.zeta`.) + * The complete elliptic integral of the first kind (`scipy.special.ellipk`) is + ow available in `scipy.special.cython_special`. + * The accuracy of `scipy.special.hyp1f1` for real arguments has been improved. + * The documentation of many functions has been improved. + > `scipy.stats` improvements + * `scipy.stats.multiscale_graphcorr` added as an independence test that + perates on high dimensional and nonlinear data sets. It has higher statistical + ower than other `scipy.stats` tests while being the only one that operates on + ultivariate data. + * The generalized inverse Gaussian distribution (`scipy.stats.geninvgauss`) has + een added. + * It is now possible to efficiently reuse `scipy.stats.binned_statistic_dd` + ith new values by providing the result of a previous call to the function. + * `scipy.stats.hmean` now handles input with zeros more gracefully. + * The beta-binomial distribution is now available in `scipy.stats.betabinom`. + * `scipy.stats.zscore`, `scipy.stats.circmean`, `scipy.stats.circstd`, and + scipy.stats.circvar` now support the ``nan_policy`` argument for enhanced + andling of ``NaN`` values + * `scipy.stats.entropy` now accepts an ``axis`` argument + * `scipy.stats.gaussian_kde.resample` now accepts a ``seed`` argument to empower + eproducibility + * `scipy.stats.kendalltau` performance has improved, especially for large inputs, + ue to improved cache usage + * `scipy.stats.truncnorm` distribution has been rewritten to support much wider + ails + + Deprecated features + > `scipy` deprecations + * Support for NumPy functions exposed via the root SciPy namespace is deprecated + nd will be removed in 2.0.0. For example, if you use ``scipy.rand`` or + `scipy.diag``, you should change your code to directly use + `numpy.random.default_rng`` or ``numpy.diag``, respectively. + hey remain available in the currently continuing Scipy 1.x release series. + * The exception to this rule is using ``scipy.fft`` as a function -- + mod:`scipy.fft` is now meant to be used only as a module, so the ability to + all ``scipy.fft(...)`` will be removed in SciPy 1.5.0. + * In `scipy.spatial.Rotation` methods ``from_dcm``, ``as_dcm`` were renamed to + `from_matrix``, ``as_matrix`` respectively. The old names will be removed in + ciPy 1.6.0. + * Method ``Rotation.match_vectors`` was deprecated in favor of + `Rotation.align_vectors``, which provides a more logical and + eneral API to the same functionality. The old method + ill be removed in SciPy 1.6.0. + + Backwards incompatible changes + > `scipy.special` changes + * The deprecated functions ``hyp2f0``, ``hyp1f2``, and ``hyp3f0`` have been + emoved. + * The deprecated function ``bessel_diff_formula`` has been removed. + * The function ``i0`` is no longer registered with ``numpy.dual``, so that + `numpy.dual.i0`` will unconditionally refer to the NumPy version regardless + f whether `scipy.special` is imported. + * The function ``expn`` has been changed to return ``nan`` outside of its + omain of definition (``x, n < 0``) instead of ``inf``. + > `scipy.sparse` changes + * Sparse matrix reshape now raises an error if shape is not two-dimensional, + rather than guessing what was meant. The behavior is now the same as before + ciPy 1.1.0. + * ``CSR`` and ``CSC`` sparse matrix classes should now return empty matrices + f the same type when indexed out of bounds. Previously, for some versions + f SciPy, this would raise an ``IndexError``. The change is largely motivated + y greater consistency with ``ndarray`` and ``numpy.matrix`` semantics. + > `scipy.signal` changes + * `scipy.signal.resample` behavior for length-1 signal inputs has been + ixed to output a constant (DC) value rather than an impulse, consistent with + he assumption of signal periodicity in the FFT method. + * `scipy.signal.cwt` now performs complex conjugation and time-reversal of + avelet data, which is a backwards-incompatible bugfix for + ime-asymmetric wavelets. + > `scipy.stats` changes + * `scipy.stats.loguniform` added with better documentation as (an alias for + `scipy.stats.reciprocal``). ``loguniform`` generates random variables + hat are equally likely in the log space; e.g., ``1``, ``10`` and ``100`` + re all equally likely if ``loguniform(10 ** 0, 10 ** 2).rvs()`` is used. + + Other changes + * The ``LSODA`` method of `scipy.integrate.solve_ivp` now correctly detects stiff + roblems. + * `scipy.spatial.cKDTree` now accepts and correctly handles empty input data + * `scipy.stats.binned_statistic_dd` now calculates the standard deviation + tatistic in a numerically stable way. + * `scipy.stats.binned_statistic_dd` now throws an error if the input data + ontains either ``np.nan`` or ``np.inf``. Similarly, in `scipy.stats` now all + ontinuous distributions' ``.fit()`` methods throw an error if the input data + ontain any instance of either ``np.nan`` or ``np.inf``. +- Rebase no_implicit_decl.patch + +------------------------------------------------------------------- +Tue Dec 10 14:24:29 UTC 2019 - Todd R + +- Update to 1.3.3 + * Fix deadlock on osx for python 3.8 + * MAINT: TST: Skip tests with multiprocessing that use "spawn" start method + +------------------------------------------------------------------- +Tue Nov 19 20:08:41 UTC 2019 - Todd R + +- Update to 1.3.2 + * Bug in unique_roots in scipy.signal.signaltools.py for roots... + * Optimizers reporting success when the minimum is NaN + * ValueError raised if scipy.sparse.linalg.expm recieves array... + * linprog(method='revised simplex') doctest bug + * Graph shortest path with Floyd-Warshall removes explicit zeros. + * BUG: stats: Formula for the variance of the noncentral F distribution... + * BUG: Assignation issues in csr_matrix with fancy indexing + * root_scalar fails when passed a function wrapped with functools.lru_cache + * CI: travis osx build failure + * macOS build failure in SuperLU on maintenance/1.3.x + * Typo in sp.stats.wilcoxon docstring + +------------------------------------------------------------------- +Fri Aug 16 15:00:19 UTC 2019 - Todd R + +- Update to 1.3.1 + * BUG: Empty data handling of (c)KDTrees + * lsoda fails to detect stiff problem when called from solve_ivp + * sparse matrices indexing with scipy 1.3 + * Exception in loadarff with quoted nominal attributes in scipy... + * DOC/REL: Some sections of the release notes are not nested correctly. + * BUG: optimize: `linprog` failing TestLinprogSimplexBland::test_unbounded_below_no_presolve_corrected + * TST: Travis CI fails (with pytest 5.0 ?) + * CircleCI doc build failing on new warnings + * Scipy 1.3.0 build broken in AIX + * BUG: scipy.spatial.HalfspaceIntersection works incorrectly + * BUG: cKDTree GIL handling is incorrect + * TST: master branch CI failures + * BUG: ckdtree query_ball_point errors on discontiguous input + * BUG: No warning on PchipInterpolator changing from bernstein base to local power base + +------------------------------------------------------------------- +Sun May 19 02:47:42 UTC 2019 - Todd R + +- Update to 1.3.0 + + Highlights of this release + * Three new ``stats`` functions, a rewrite of ``pearsonr``, and an exact + computation of the Kolmogorov-Smirnov two-sample test + * A new Cython API for bounded scalar-function root-finders in `scipy.optimize` + * Substantial ``CSR`` and ``CSC`` sparse matrix indexing performance + improvements + * Added support for interpolation of rotations with continuous angular + rate and acceleration in ``RotationSpline`` + + New features + > `scipy.interpolate` improvements + * A new class ``CubicHermiteSpline`` is introduced. It is a piecewise-cubic + interpolator which matches observed values and first derivatives. Existing + cubic interpolators ``CubicSpline``, ``PchipInterpolator`` and + ``Akima1DInterpolator`` were made subclasses of ``CubicHermiteSpline``. + > `scipy.io` improvements + * For the Attribute-Relation File Format (ARFF) `scipy.io.arff.loadarff` + now supports relational attributes. + * `scipy.io.mmread` can now parse Matrix Market format files with empty lines. + > `scipy.linalg` improvements + * Added wrappers for ``?syconv`` routines, which convert a symmetric matrix + given by a triangular matrix factorization into two matrices and vice versa. + * `scipy.linalg.clarkson_woodruff_transform` now uses an algorithm that leverages + sparsity. This may provide a 60-90 percent speedup for dense input matrices. + Truly sparse input matrices should also benefit from the improved sketch + algorithm, which now correctly runs in ``O(nnz(A))`` time. + * Added new functions to calculate symmetric Fiedler matrices and + Fiedler companion matrices, named `scipy.linalg.fiedler` and + `scipy.linalg.fiedler_companion`, respectively. These may be used + for root finding. + > `scipy.ndimage` improvements + * Gaussian filter performances may improve by an order of magnitude in + some cases, thanks to removal of a dependence on ``np.polynomial``. This + may impact `scipy.ndimage.gaussian_filter` for example. + > `scipy.optimize` improvements + * The `scipy.optimize.brute` minimizer obtained a new keyword ``workers``, which + can be used to parallelize computation. + * A Cython API for bounded scalar-function root-finders in `scipy.optimize` + is available in a new module `scipy.optimize.cython_optimize` via ``cimport``. + This API may be used with ``nogil`` and ``prange`` to loop + over an array of function arguments to solve for an array of roots more + quickly than with pure Python. + * ``'interior-point'`` is now the default method for ``linprog``, and + ``'interior-point'`` now uses SuiteSparse for sparse problems when the + required scikits (scikit-umfpack and scikit-sparse) are available. + On benchmark problems (gh-10026), execution time reductions by factors of 2-3 + were typical. Also, a new ``method='revised simplex'`` has been added. + It is not as fast or robust as ``method='interior-point'``, but it is a faster, + more robust, and equally accurate substitute for the legacy + ``method='simplex'``. + * ``differential_evolution`` can now use a ``Bounds`` class to specify the + bounds for the optimizing argument of a function. + * `scipy.optimize.dual_annealing` performance improvements related to + vectorisation of some internal code. + > `scipy.signal` improvements + * Two additional methods of discretization are now supported by + `scipy.signal.cont2discrete`: ``impulse`` and ``foh``. + * `scipy.signal.firls` now uses faster solvers + * `scipy.signal.detrend` now has a lower physical memory footprint in some + cases, which may be leveraged using the new ``overwrite_data`` keyword argument + * `scipy.signal.firwin` ``pass_zero`` argument now accepts new string arguments + that allow specification of the desired filter type: ``'bandpass'``, + ``'lowpass'``, ``'highpass'``, and ``'bandstop'`` + * `scipy.signal.sosfilt` may have improved performance due to lower retention + of the global interpreter lock (GIL) in algorithm + > `scipy.sparse` improvements + * A new keyword was added to ``csgraph.dijsktra`` that + allows users to query the shortest path to ANY of the passed in indices, + as opposed to the shortest path to EVERY passed index. + * `scipy.sparse.linalg.lsmr` performance has been improved by roughly 10 percent + on large problems + * Improved performance and reduced physical memory footprint of the algorithm + used by `scipy.sparse.linalg.lobpcg` + * ``CSR`` and ``CSC`` sparse matrix fancy indexing performance has been + improved substantially + > `scipy.spatial` improvements + * `scipy.spatial.ConvexHull` now has a ``good`` attribute that can be used + alongsize the ``QGn`` Qhull options to determine which external facets of a + convex hull are visible from an external query point. + * `scipy.spatial.cKDTree.query_ball_point` has been modernized to use some newer + Cython features, including GIL handling and exception translation. An issue + with ``return_sorted=True`` and scalar queries was fixed, and a new mode named + ``return_length`` was added. ``return_length`` only computes the length of the + returned indices list instead of allocating the array every time. + * `scipy.spatial.transform.RotationSpline` has been added to enable interpolation + of rotations with continuous angular rates and acceleration + > `scipy.stats` improvements + * Added a new function to compute the Epps-Singleton test statistic, + `scipy.stats.epps_singleton_2samp`, which can be applied to continuous and + discrete distributions. + * New functions `scipy.stats.median_absolute_deviation` and `scipy.stats.gstd` + (geometric standard deviation) were added. The `scipy.stats.combine_pvalues` + method now supports ``pearson``, ``tippett`` and ``mudholkar_george`` pvalue + combination methods. + * The `scipy.stats.ortho_group` and `scipy.stats.special_ortho_group` + ``rvs(dim)`` functions' algorithms were updated from a ``O(dim^4)`` + implementation to a ``O(dim^3)`` which gives large speed improvements + for ``dim>100``. + * A rewrite of `scipy.stats.pearsonr` to use a more robust algorithm, + provide meaningful exceptions and warnings on potentially pathological input, + and fix at least five separate reported issues in the original implementation. + * Improved the precision of ``hypergeom.logcdf`` and ``hypergeom.logsf``. + * Added exact computation for Kolmogorov-Smirnov (KS) two-sample test, replacing + the previously approximate computation for the two-sided test `stats.ks_2samp`. + Also added a one-sided, two-sample KS test, and a keyword ``alternative`` to + `stats.ks_2samp`. + + Backwards incompatible changes + > `scipy.interpolate` changes + * Functions from ``scipy.interpolate`` (``spleval``, ``spline``, ``splmake``, + and ``spltopp``) and functions from ``scipy.misc`` (``bytescale``, + ``fromimage``, ``imfilter``, ``imread``, ``imresize``, ``imrotate``, + ``imsave``, ``imshow``, ``toimage``) have been removed. The former set has + been deprecated since v0.19.0 and the latter has been deprecated since v1.0.0. + Similarly, aliases from ``scipy.misc`` (``comb``, ``factorial``, + ``factorial2``, ``factorialk``, ``logsumexp``, ``pade``, ``info``, ``source``, + ``who``) which have been deprecated since v1.0.0 are removed. + `SciPy documentation for + v1.1.0 `__ + can be used to track the new import locations for the relocated functions. + > `scipy.linalg` changes + * For ``pinv``, ``pinv2``, and ``pinvh``, the default cutoff values are changed + for consistency (see the docs for the actual values). + > `scipy.optimize` changes + * The default method for ``linprog`` is now ``'interior-point'``. The method's + robustness and speed come at a cost: solutions may not be accurate to + machine precision or correspond with a vertex of the polytope defined + by the constraints. To revert to the original simplex method, + include the argument ``method='simplex'``. + > `scipy.stats` changes + * Previously, ``ks_2samp(data1, data2)`` would run a two-sided test and return + the approximated p-value. The new signature, ``ks_2samp(data1, data2, + alternative="two-sided", method="auto")``, still runs the two-sided test by + default but returns the exact p-value for small samples and the approximated + value for large samples. ``method="asymp"`` would be equivalent to the + old version but ``auto`` is the better choice. + + Other changes + * Our tutorial has been expanded with a new section on global optimizers + * There has been a rework of the ``stats.distributions`` tutorials. + * `scipy.optimize` now correctly sets the convergence flag of the result to + ``CONVERR``, a convergence error, for bounded scalar-function root-finders + if the maximum iterations has been exceeded, ``disp`` is false, and + ``full_output`` is true. + * `scipy.optimize.curve_fit` no longer fails if ``xdata`` and ``ydata`` dtypes + differ; they are both now automatically cast to ``float64``. + * `scipy.ndimage` functions including ``binary_erosion``, ``binary_closing``, and + ``binary_dilation`` now require an integer value for the number of iterations, + which alleviates a number of reported issues. + * Fixed normal approximation in case ``zero_method == "pratt"`` in + `scipy.stats.wilcoxon`. + * Fixes for incorrect probabilities, broadcasting issues and thread-safety + related to stats distributions setting member variables inside ``_argcheck()``. + * `scipy.optimize.newton` now correctly raises a ``RuntimeError``, when default + arguments are used, in the case that a derivative of value zero is obtained, + which is a special case of failing to converge. + * A draft toolchain roadmap is now available, laying out a compatibility plan + including Python versions, C standards, and NumPy versions. +- Python 2 is no longer supported + +------------------------------------------------------------------- +Tue Mar 19 17:08:19 UTC 2019 - Todd R + +- Update to 1.2.1 + * SyntaxError: Non-ASCII character 'xe2' in file scipy/stats/_continuous_distns.py on line 3346, but no encoding declared + * Version 1.2.0 introduces `too many indices for array` error in `optimize.newton()` + * scipy.stats.gaussian_kde normalizes the weights keyword argument externally. + * scipy.linalg.qr_update gives NaN result + * CI: Is scipy.scipy Windows Python36-32bit-full working? + +------------------------------------------------------------------- +Fri Mar 1 20:45:50 UTC 2019 - Matej Cepl + +- Use direct number in the Version tag + +------------------------------------------------------------------- +Tue Feb 12 08:55:55 UTC 2019 - Egbert Eich + +bsc#1130564: Apply update from the openSUSE package + +- Properly create and tear down default version links when the + HPC master packages are installed/uninstalled. +- Make use of %hpc_modules_init to make modules also known to + client. +- Module file: + * remove PATH element. Package has no binary, + * make cosmetic changes. +- Remove use of %%python_module in dependency. + +------------------------------------------------------------------- +Mon Jan 21 19:11:15 UTC 2019 - Jan Engelhardt + +- Trim filler wording from description. + +------------------------------------------------------------------- +Fri Jan 18 11:33:14 UTC 2019 - eich@suse.com + +- Some futher changes: + * Remove the use of fftw. The code doesn't link against it + anywhere. For HPC we would have to build things separately + for different MPI flavors as fftw3 exists only with HPC + support there. + * restructure the build process: since the environment for + the right python version of Numpy needs to be loaded, wrap + entire build (and install) in %%{python_expand: ..}. + +------------------------------------------------------------------- +Thu Jan 17 23:58:18 UTC 2019 - jjolly@suse.com + +- Add support for HPC builds: + * Add _multibuild file + * Add standard and gnu-hpc builds + * Create initialization for both flavors to set the correct + target directories in macros and replace install paths + with these. + * Restructure the build process. + * Create 'master' packages for non-HPC builds. + * Create environment module information, + +------------------------------------------------------------------- +Sat Dec 22 02:01:08 UTC 2018 - Todd R + +- Update to version 1.2.0 + * Many changes. Please see changelog at: + https://github.com/scipy/scipy/blob/v1.2.0/doc/release/1.2.0-notes.rst + +------------------------------------------------------------------- +Fri May 11 20:17:12 UTC 2018 - toddrme2178@gmail.com + +- Fix build on SLE + +------------------------------------------------------------------- +Mon May 7 06:48:57 UTC 2018 - toddrme2178@gmail.com + +- Update to version 1.1.0 + * Many changes. Please see changelog at: + https://github.com/scipy/scipy/blob/v1.1.0/doc/release/1.1.0-notes.rst + +------------------------------------------------------------------- +Sun Apr 1 22:41:09 UTC 2018 - arun@gmx.de + +- update to version 1.0.1: + * Issues closed for 1.0.1 + + #7493: ndimage.morphology functions are broken with numpy 1.13.0 + + #8118: minimize_cobyla broken if disp=True passed + + #8142: scipy-v1.0.0 pdist with metric=`minkowski` raises + `ValueError:... + + #8173: scipy.stats.ortho_group produces all negative + determinants... + + #8207: gaussian_filter seg faults on float16 numpy arrays + + #8234: scipy.optimize.linprog interior-point presolve bug with + trivial... + + #8243: Make csgraph importable again via from scipy.sparse + import* + + #8320: scipy.root segfaults with optimizer 'lm' + * Pull requests for 1.0.1 + + #8068: BUG: fix numpy deprecation test failures + + #8082: BUG: fix solve_lyapunov import + + #8144: MRG: Fix for cobyla + + #8150: MAINT: resolve UPDATEIFCOPY deprecation errors + + #8156: BUG: missing check on minkowski w kwarg + + #8187: BUG: Sign of elements in random orthogonal 2D matrices in + "ortho_group_gen"... + + #8197: CI: uninstall oclint + + #8215: Fixes Numpy datatype compatibility issues + + #8237: BUG: optimize: fix bug when variables fixed by bounds are + inconsistent... + + #8248: BUG: declare "gfk" variable before call of terminate() in + newton-cg + + #8280: REV: reintroduce csgraph import in scipy.sparse + + #8322: MAINT: prevent scipy.optimize.root segfault closes #8320 + + #8334: TST: stats: don't use exact equality check for hdmedian + test + + #8477: BUG: signal/signaltools: fix wrong refcounting in + PyArray_OrderFilterND + + #8530: BUG: linalg: Fixed typo in flapack.pyf.src. + + #8566: CI: Temporarily pin Cython version to 0.27.3 + + #8573: Backports for 1.0.1 + + #8581: Fix Cython 0.28 build break of qhull.pyx + +------------------------------------------------------------------- +Tue Feb 13 12:48:45 UTC 2018 - schwab@suse.de + +- Don't use openblas on m68k and riscv64 + +------------------------------------------------------------------- +Thu Oct 26 03:22:32 UTC 2017 - toddrme2178@gmail.com + +- Update to version 1.0.0 + * Many changes. Please see changelog at: + https://github.com/scipy/scipy/blob/v1.0.0/doc/release/1.0.0-notes.rst#why-1-0-now +- Rebase no_implicit_decl.patch + +------------------------------------------------------------------- +Tue Jul 11 19:55:40 UTC 2017 - toddrme2178@gmail.com + +- More rpmlint fixes. + +------------------------------------------------------------------- +Mon Jul 10 18:25:30 UTC 2017 - toddrme2178@gmail.com + +- Update to version 0.19.1 + * #7214: Memory use in integrate.quad in scipy-0.19.0 + * #7258: linalg.matrix_balance gives wrong transformation matrix + * #7262: Segfault in daily testing + * #7273: scipy.interpolate._bspl.evaluate_spline gets wrong type + * #7335: scipy.signal.dlti(A,B,C,D).freqresp() fails + * #7211: BUG: convolve may yield inconsistent dtypes with method changed + * #7216: BUG: integrate: fix refcounting bug in quad() + * #7229: MAINT: special: Rewrite a test of wrightomega + * #7261: FIX: Corrected the transformation matrix permutation + * #7265: BUG: Fix broken axis handling in spectral functions + * #7266: FIX 7262: ckdtree crashes in query_knn. + * #7279: Upcast half- and single-precision floats to doubles in BSpline... + * #7336: BUG: Fix signal.dfreqresp for StateSpace systems + * #7419: Fix several issues in sparse.load_npz, save_npz + * #7420: BUG: stats: allow integers as kappa4 shape parameters +- Add no_implicit_decl.patch + Fixes implicit-pointer-decl warnings and implicit-fortify-decl error. +- Fix wrong-script-interpreter rpmlint error. + +------------------------------------------------------------------- +Wed Apr 19 18:52:04 UTC 2017 - toddrme2178@gmail.com + +- Update to version 0.19.0 + + Highlights + * A unified foreign function interface layer, `scipy.LowLevelCallable`. + * Cython API for scalar, typed versions of the universal functions from + the `scipy.special` module, via `cimport scipy.special.cython_special`. +- Removed weave subpackage. It was removed upstream in this release. + +------------------------------------------------------------------- +Fri Oct 21 19:12:29 UTC 2016 - toddrme2178@gmail.com + +- Switch to single-spec version +- update to version 0.18.1: + * #6357: scipy 0.17.1 piecewise cubic hermite interpolation does not + return... + * #6420: circmean() changed behaviour from 0.17 to 0.18 + * #6421: scipy.linalg.solve_banded overwrites input 'b' when the + inversion... + * #6425: cKDTree INF bug + * #6435: scipy.stats.ks_2samp returns different values on different + computers + * #6458: Error in scipy.integrate.dblquad when using variable + integration... + * #6405: BUG: sparse: fix elementwise divide for CSR/CSC + * #6431: BUG: result for insufficient neighbours from cKDTree is + wrong. + * #6432: BUG Issue #6421: scipy.linalg.solve_banded overwrites input + 'b'... + * #6455: DOC: add links to release notes + * #6462: BUG: interpolate: fix .roots method of PchipInterpolator + * #6492: BUG: Fix regression in dblquad: #6458 + * #6543: fix the regression in circmean + * #6545: Revert gh-5938, restore ks_2samp + * #6557: Backports for 0.18.1 +- update to version 0.18.0: + (see http://scipy.github.io/devdocs/release.0.18.0.html for full changelog) + * Highlights of this release include: + + A new ODE solver for two-point boundary value problems, + scipy.optimize.solve_bvp. + + A new class, CubicSpline, for cubic spline interpolation of + data. + + N-dimensional tensor product polynomials, + scipy.interpolate.NdPPoly. + + Spherical Voronoi diagrams, scipy.spatial.SphericalVoronoi. + + Support for discrete-time linear systems, scipy.signal.dlti. +- update to version 0.17.1: + * #5817: BUG: skew, kurtosis return np.nan instead of "propagate" + * #5850: Test failed with sgelsy + * #5898: interpolate.interp1d crashes using float128 + * #5953: Massive performance regression in cKDTree.query with L_inf + distance... + * #6062: mannwhitneyu breaks backward compatibility in 0.17.0 + * #6134: T test does not handle nans + * #5902: BUG: interpolate: make interp1d handle np.float128 again + * #5957: BUG: slow down with p=np.inf in 0.17 cKDTree.query + * #5970: Actually propagate nans through stats functions with + nan_policy="propagate" + * #5971: BUG: linalg: fix lwork check in *gelsy + * #6074: BUG: special: fixed violation of strict aliasing rules. + * #6083: BUG: Fix dtype for sum of linear operators + * #6100: BUG: Fix mannwhitneyu to be backward compatible + * #6135: Don't pass null pointers to LAPACK, even during workspace + queries. + * #6148: stats: fix handling of nan values in T tests and kendalltau +- specfile: + * updated source url to files.pythonhosted.org + * require setuptools + * Add openBLAS support. + This can improve performance in many situations. + * Drop ATLAS support. + +------------------------------------------------------------------- +Thu Jan 28 09:21:47 UTC 2016 - toddrme2178@gmail.com + +- specfile: + * update copyright year + +- update to version 0.17.0: + (see http://scipy.github.io/devdocs/release.0.17.0.html for full changelog) + * Highlights + + New functions for linear and nonlinear least squares + optimization with constraints: scipy.optimize.lsq_linear and + scipy.optimize.least_squares + + Support for fitting with bounds in scipy.optimize.curve_fit. + + Significant improvements to scipy.stats, providing many + functions with better handing of inputs which have NaNs or are + empty, improved documentation, and consistent behavior between + scipy.stats and scipy.stats.mstats. + + Significant performance improvements and new functionality in + scipy.spatial.cKDTree. + +------------------------------------------------------------------- +Fri Oct 30 09:04:05 UTC 2015 - toddrme2178@gmail.com + +- Update to 0.16.1 + SciPy 0.16.1 is a bug-fix release with no new features compared + to 0.16.0. + +------------------------------------------------------------------- +Mon Jul 27 15:24:02 UTC 2015 - toddrme2178@gmail.com + +- Remove Cython subpackage. The sources are not as cleanly + separated as the changelog implied. + +------------------------------------------------------------------- +Mon Jul 27 09:26:20 UTC 2015 - toddrme2178@gmail.com + +- Update to 0.16.0 + * Highlights of this release include: + - A Cython API for BLAS/LAPACK in scipy.linalg + - A new benchmark suite. It's now straightforward to add new benchmarks, + and they're routinely included with performance enhancement PRs. + - Support for the second order sections (SOS) format in scipy.signal. + * New features + - Benchmark suite + + The benchmark suite has switched to using Airspeed Velocity + for benchmarking. + - scipy.linalg improvements + + A full set of Cython wrappers for BLAS and LAPACK has been added in + the modules scipy.linalg.cython_blas and scipy.linalg.cython_lapack. + In Cython, these wrappers can now be cimported from their + corresponding modules and used without linking directly against BLAS + or LAPACK. + + The functions scipy.linalg.qr_delete, scipy.linalg.qr_insert and + scipy.linalg.qr_update for updating QR decompositions were added. + + The function scipy.linalg.solve_circulant solves a linear system with + a circulant coefficient matrix. + + The function scipy.linalg.invpascal computes the inverse of a Pascal matrix. + + The function scipy.linalg.solve_toeplitz, a Levinson-Durbin Toeplitz solver, + was added. + + Added wrapper for potentially useful LAPACK function *lasd4. It computes + the square root of the i-th updated eigenvalue of a positive symmetric rank-one + modification to a positive diagonal matrix. See its LAPACK documentation and + unit tests for it to get more info. + + Added two extra wrappers for LAPACK least-square solvers. Namely, they are + *gelsd and *gelsy. + + Wrappers for the LAPACK *lange functions, which calculate various matrix + norms, were added. + + Wrappers for *gtsv and *ptsv, which solve A*X = B for tri-diagonal + matrix A, were added. + - scipy.signal improvements + + Support for second order sections (SOS) as a format for IIR filters + was added. The new functions are: + * scipy.signal.sosfilt + * scipy.signal.sosfilt_zi, + * scipy.signal.sos2tf + * scipy.signal.sos2zpk + * scipy.signal.tf2sos + * scipy.signal.zpk2sos. + + Additionally, the filter design functions iirdesign, iirfilter, butter, + cheby1, cheby2, ellip, and bessel can return the filter in the SOS + format. + + The function scipy.signal.place_poles, which provides two methods to place + poles for linear systems, was added. + + The option to use Gustafsson's method for choosing the initial conditions + of the forward and backward passes was added to scipy.signal.filtfilt. + + New classes TransferFunction, StateSpace and ZerosPolesGain were + added. These classes are now returned when instantiating scipy.signal.lti. + Conversion between those classes can be done explicitly now. + + An exponential (Poisson) window was added as scipy.signal.exponential, and a + Tukey window was added as scipy.signal.tukey. + + The function for computing digital filter group delay was added as + scipy.signal.group_delay. + + The functionality for spectral analysis and spectral density estimation has + been significantly improved: scipy.signal.welch became ~8x faster and the + functions scipy.signal.spectrogram, scipy.signal.coherence and + scipy.signal.csd (cross-spectral density) were added. + + scipy.signal.lsim was rewritten - all known issues are fixed, so this + function can now be used instead of lsim2; lsim is orders of magnitude + faster than lsim2 in most cases. + - scipy.sparse improvements + + The function scipy.sparse.norm, which computes sparse matrix norms, was + added. + + The function scipy.sparse.random, which allows to draw random variates from + an arbitrary distribution, was added. + - scipy.spatial improvements + + scipy.spatial.cKDTree has seen a major rewrite, which improved the + performance of the query method significantly, added support for parallel + queries, pickling, and options that affect the tree layout. See pull request + 4374 for more details. + + The function scipy.spatial.procrustes for Procrustes analysis (statistical + shape analysis) was added. + - scipy.stats improvements + + The Wishart distribution and its inverse have been added, as + scipy.stats.wishart and scipy.stats.invwishart. + + The Exponentially Modified Normal distribution has been + added as scipy.stats.exponnorm. + + The Generalized Normal distribution has been added as scipy.stats.gennorm. + + All distributions now contain a random_state property and allow specifying a + specific numpy.random.RandomState random number generator when generating + random variates. + + Many statistical tests and other scipy.stats functions that have multiple + return values now return namedtuples. See pull request 4709 for details. + - scipy.optimize improvements + + A new derivative-free method DF-SANE has been added to the nonlinear equation + system solving function scipy.optimize.root. + * Deprecated features + - scipy.stats.pdf_fromgamma is deprecated. This function was undocumented, + untested and rarely used. Statsmodels provides equivalent functionality + with statsmodels.distributions.ExpandedNormal. + - scipy.stats.fastsort is deprecated. This function is unnecessary, + numpy.argsort can be used instead. + - scipy.stats.signaltonoise and scipy.stats.mstats.signaltonoise are + deprecated. These functions did not belong in scipy.stats and are rarely + used. See issue #609 for details. + - scipy.stats.histogram2 is deprecated. This function is unnecessary, + numpy.histogram2d can be used instead. + * Backwards incompatible changes + - The deprecated global optimizer scipy.optimize.anneal was removed. + - The following deprecated modules have been removed. They had been deprecated + since Scipy 0.12.0, the functionality should be accessed as scipy.linalg.blas + and scipy.linalg.lapack. + + scipy.lib.blas + + scipy.lib.lapack + + scipy.linalg.cblas + + scipy.linalg.fblas + + scipy.linalg.clapack + + scipy.linalg.flapack. + - The deprecated function scipy.special.all_mat has been removed. + - These deprecated functions have been removed from scipy.stats: + + scipy.stats.fprob + + scipy.stats.ksprob + + scipy.stats.zprob + + scipy.stats.randwcdf + + scipy.stats.randwppf + * Other changes + - The version numbering for development builds has been updated to comply with PEP 440. + - Building with python setup.py develop is now supported. +- Move Cython imports to another package + +------------------------------------------------------------------- +Mon Mar 2 15:57:12 UTC 2015 - toddrme2178@gmail.com + +- update to version 0.15.1: + * #4413: BUG: Tests too strict, f2py doesn't have to overwrite this array + * #4417: BLD: avoid using NPY_API_VERSION to check not using deprecated... + * #4418: Restore and deprecate scipy.linalg.calc_work + +------------------------------------------------------------------- +Mon Jan 12 13:36:00 UTC 2015 - toddrme2178@gmail.com + +- Update to 0.15.0 + * New features + * scipy.optimize improvements + * scipy.optimize.linprog now provides a generic + linear programming similar to the way scipy.optimize.minimize + provides a generic interface to nonlinear programming optimizers. + Currently the only method supported is simplex which provides + a two-phase, dense-matrix-based simplex algorithm. Callbacks + functions are supported,allowing the user to monitor the progress + of the algorithm. + * The differential_evolution function is available from the scipy.optimize + module. Differential Evolution is an algorithm used for finding the global + minimum of multivariate functions. It is stochastic in nature (does not use + gradient methods), and can search large areas of candidate space, but often + requires larger numbers of function evaluations than conventional gradient + based techniques. + * scipy.signal improvements + * The function max_len_seq was added, which computes a Maximum + Length Sequence (MLS) signal. + * scipy.integrate improvements + * The interface between the scipy.integrate module and the QUADPACK library was + redesigned. It is now possible to use scipy.integrate to integrate + multivariate ctypes functions, thus avoiding callbacks to Python and providing + better performance, especially for complex integrand functions. + * scipy.sparse improvements + * scipy.sparse.linalg.svds now takes a LinearOperator as its main input. + * scipy.stats improvements + * Added a Dirichlet distribution as multivariate distribution. + * The new function `scipy.stats.median_test` computes Mood's median test. + * `scipy.stats.describe` returns a namedtuple rather than a tuple, allowing + users to access results by index or by name. + * Deprecated features + * The scipy.weave module is deprecated. It was the only module never ported + to Python 3.x, and is not recommended to be used for new code - use Cython + instead. In order to support existing code, scipy.weave has been packaged + separately: https://github.com/scipy/weave. It is a pure Python package, so + can easily be installed with pip install weave. + * scipy.special.bessel_diff_formula is deprecated. It is a private function, + and therefore will be removed from the public API in a following release. + * Backwards incompatible changes + * scipy.ndimage + * The functions scipy.ndimage.minimum_positions, + scipy.ndimage.maximum_positions and scipy.ndimage.extrema return + positions as ints instead of floats. + * Other changes + * scipy.integrate + * The OPTPACK and QUADPACK code has been changed to use the LAPACK matrix + solvers rather than the bundled LINPACK code. This means that there is no + longer any need for the bundled LINPACK routines, so they have been removed. +- Update copyright year + +------------------------------------------------------------------- +Mon Aug 11 08:53:11 UTC 2014 - toddrme2178@gmail.com + +- Switch to pypi download location +- Minor spec file cleanups + +------------------------------------------------------------------- +Fri May 30 15:06:23 UTC 2014 - toddrme2178@gmail.com + +- Mark python-scipy-weave as deprecated. + Please use python-weave package instead. + +------------------------------------------------------------------- +Thu May 8 10:16:00 UTC 2014 - toddrme2178@gmail.com + +- Update to version 0.14.0 + * New features + * scipy.interpolate improvements + * A new wrapper function `scipy.interpolate.interpn` for + interpolation onregular grids has been added. `interpn` + supports linear and nearest-neighbor interpolation in + arbitrary dimensions and spline interpolation in two + dimensions. + * Faster implementations of piecewise polynomials in power + and Bernstein polynomial bases have been added as + `scipy.interpolate.PPoly` and `scipy.interpolate.BPoly`. + New users should use these in favor of + `scipy.interpolate.PiecewisePolynomial`. + * `scipy.interpolate.interp1d` now accepts non-monotonic + inputs and sorts them. If performance is critical, sorting + can be turned off by using the new ``assume_sorted`` + keyword. + * Functionality for evaluation of bivariate spline + derivatives in ``scipy.interpolate`` has been added. + * The new class `scipy.interpolate.Akima1DInterpolator` + implements the piecewise cubic polynomial interpolation + scheme devised by H. Akima. + * Functionality for fast interpolation on regular, unevenly + spaced grids in arbitrary dimensions has been added as + `scipy.interpolate.RegularGridInterpolator` . + * ``scipy.linalg`` improvements + * The new function `scipy.linalg.dft` computes the matrix of + the discrete Fourier transform. + * A condition number estimation function for matrix + exponential, `scipy.linalg.expm_cond`, has been added. + * ``scipy.optimize`` improvements + * A set of benchmarks for optimize, which can be run with + ``optimize.bench()``, has been added. + * `scipy.optimize.curve_fit` now has more controllable error + estimation via the ``absolute_sigma`` keyword. + * Support for passing custom minimization methods to + ``optimize.minimize()`` and ``optimize.minimize_scalar()`` + has been added, currently useful especially for combining + ``optimize.basinhopping()`` with custom local optimizer + routines. + * ``scipy.stats`` improvements + * A new class `scipy.stats.multivariate_normal` with + functionality for multivariate normal random variables + has been added. + * A lot of work on the ``scipy.stats`` distribution framework + has been done. Moment calculations (skew and kurtosis + mainly) are fixed and verified, all examples are now + runnable, and many small accuracy and performance + improvements for individual distributions were merged. + * The new function `scipy.stats.anderson_ksamp` computes the + k-sample Anderson-Darling test for the null hypothesis that + k samples come from the same parent population. + * ``scipy.signal`` improvements + * ``scipy.signal.iirfilter`` and related functions to design + Butterworth, Chebyshev, elliptical and Bessel IIR filters + now all use pole-zero ("zpk") format internally instead of + using transformations to numerator/denominator format. + The accuracy of the produced filters, especially high-order + ones, is improved significantly as a result. + * The new function `scipy.signal.vectorstrength` computes the + vector strength, a measure of phase synchrony, of a set of + events. + * ``scipy.special`` improvements + * The functions `scipy.special.boxcox` and + `scipy.special.boxcox1p`, which compute the + Box-Cox transformation, have been added. + * ``scipy.sparse`` improvements + * Significant performance improvement in CSR, CSC, and DOK + indexing speed. + * When using Numpy >= 1.9 (to be released in MM 2014), sparse + matrices function correctly when given to arguments of + ``np.dot``, ``np.multiply`` and other ufuncs. + With earlier Numpy and Scipy versions, the results of such + operations are undefined and usually unexpected. + * Sparse matrices are no longer limited to ``2^31`` nonzero + elements. They automatically switch to using 64-bit index + data type for matrices containing more elements. User code + written assuming the sparse matrices use int32 as the index + data type will continue to work, except for such large + matrices. Code dealing with larger matrices needs to accept + either int32 or int64 indices. + * Deprecated features + * ``anneal`` + * The global minimization function `scipy.optimize.anneal` is + deprecated. All users should use the + `scipy.optimize.basinhopping` function instead. + * ``scipy.stats`` + * ``randwcdf`` and ``randwppf`` functions are deprecated. + All users should use distribution-specific ``rvs`` methods + instead. + * Probability calculation aliases ``zprob``, ``fprob`` and + ``ksprob`` are deprecated. Use instead the ``sf`` methods + of the corresponding distributions or the ``special`` + functions directly. + * ``scipy.interpolate`` + * ``PiecewisePolynomial`` class is deprecated. + * Backwards incompatible changes + * scipy.special.lpmn + * ``lpmn`` no longer accepts complex-valued arguments. A new + function ``clpmn`` with uniform complex analytic behavior + has been added, and it should be used instead. + * scipy.sparse.linalg + * Eigenvectors in the case of generalized eigenvalue problem + are normalized to unit vectors in 2-norm, rather than + following the LAPACK normalization convention. + * The deprecated UMFPACK wrapper in ``scipy.sparse.linalg`` + has been removed due to license and install issues. If + available, ``scikits.umfpack`` is still used transparently + in the ``spsolve`` and ``factorized`` functions. + Otherwise, SuperLU is used instead in these functions. + * scipy.stats + * The deprecated functions ``glm``, ``oneway`` and + ``cmedian`` have been removed from ``scipy.stats``. + * ``stats.scoreatpercentile`` now returns an array instead of + a list of percentiles. + * scipy.interpolate + * The API for computing derivatives of a monotone piecewise + interpolation has changed: if `p` is a + ``PchipInterpolator`` object, `p.derivative(der)` + returns a callable object representing the derivative of + `p`. For in-place derivatives use the second argument of + the `__call__` method: `p(0.1, der=2)` evaluates the + second derivative of `p` at `x=0.1`. + * The method `p.derivatives` has been removed. + +------------------------------------------------------------------- +Sun Mar 2 04:22:42 UTC 2014 - arun@gmx.de + +- updated to version 0.13.3 + Issues fixed: + * 3148: fix a memory leak in ``ndimage.label``. + * 3216: fix weave issue with too long file names for MSVC. + Other changes: + * Update Sphinx theme used for html docs so ``>>>`` in examples can be toggled. + +------------------------------------------------------------------- +Wed Dec 11 14:15:25 UTC 2013 - toddrme2178@gmail.com + +- Update to version 0.13.2 + + require Cython 0.19, earlier versions have memory leaks in + fused types + + ndimage.label fix swapped 64-bitness test + + optimize.fmin_slsqp constraint violation +- Require python-Cython >= 0.19 + +------------------------------------------------------------------- +Tue Nov 19 21:23:02 UTC 2013 - p.drouand@gmail.com + +- Update to version 0.13.1 + + ``ndimage.label`` returns incorrect results in scipy 0.13.0 + + ``ndimage.label`` return type changed from int32 to uint32 + + `ndimage.find_objects`` doesn't work with int32 input in some cases + +------------------------------------------------------------------- +Fri Oct 25 15:17:10 UTC 2013 - toddrme2178@gmail.com + +- Update to 0.13.0 + * Highlights + * support for fancy indexing and boolean comparisons with + sparse matrices + * interpolative decompositions and matrix functions in the + linalg module + * two new trust-region solvers for unconstrained minimization + * scipy.integrate improvements + * N-dimensional numerical integration + * dopri* improvements + * scipy.linalg improvements + * Interpolative decompositions + * Polar decomposition + * BLAS level 3 functions + * Matrix functions + * scipy.optimize improvements + * Trust-region unconstrained minimization algorithms + * scipy.sparse improvements + * Boolean comparisons and sparse matrices + * CSR and CSC fancy indexing + * scipy.io improvements + * Unformatted Fortran file reader + * scipy.io.wavfile enhancements + * scipy.interpolate improvements + * B-spline derivatives and antiderivatives + * Deprecated features + * expm2 and expm3 + * scipy.stats functions + * Backwards incompatible changes + * LIL matrix assignment + * Deprecated radon function removed + * Removed deprecated keywords xa and xb from + stats.distributions + * Changes to MATLAB file readers / writers +- Add a new flag to easily enable/disable atlas support for if it + ever gets fixed in the future +- Added numpy version number to requires and buildrequires +- Updated rpmlint fixes + +------------------------------------------------------------------- +Sun Apr 14 04:43:43 UTC 2013 - termim@gmail.com + +- Update to version 0.12.0 + Some of the highlights of this release are: + * Completed QHull wrappers in scipy.spatial. + * cKDTree now a drop-in replacement for KDTree. + * A new global optimizer, basinhopping. + * Support for Python 2 and Python 3 from the same code base (no more 2to3). + +------------------------------------------------------------------- +Mon Oct 1 12:45:12 UTC 2012 - toddrme2178@gmail.com + +- Update to version 0.11.0: + * Sparse Graph Submodule + * scipy.optimize improvements + * A unified interface to minimizers of univariate and + multivariate functions has been added. + * A unified interface to root finding algorithms for + multivariate functions has been added. + * The L-BFGS-B algorithm has been updated to version 3.0. + * scipy.linalg improvements + * New matrix equation solvers + * QZ and QR Decomposition + * Pascal matrices + * Sparse matrix construction and operations + * LSMR iterative solver + * Discrete Sine Transform + * scipy.interpolate improvements + * Interpolation in spherical coordinates + * scipy.stats improvements + * Binned statistics +- Remove upstreamed patches + +------------------------------------------------------------------- +Mon Aug 27 09:12:38 UTC 2012 - toddrme2178@gmail.com + +- Disable broken libatlas3 + +------------------------------------------------------------------- +Mon Jun 4 15:32:19 UTC 2012 - toddrme2178@gmail.com + +- Add suitesparse buildrequires +- Remove blas/lapack tests since these build successfully on all + targets now + +------------------------------------------------------------------- +Tue May 29 19:51:34 UTC 2012 - cfarrell@suse.com + +- license update: BSD-3-Clause + No LGPL licenses found in the package + +------------------------------------------------------------------- +Tue May 29 11:28:00 UTC 2012 - toddrme2178@gmail.com + +- Don't build against libatlas on factory since libatlas doesn't + work there + +------------------------------------------------------------------- +Fri May 18 08:54:19 UTC 2012 - toddrme2178@gmail.com + +- Fix rmplint warnings +- Clean up spec file formatting + +------------------------------------------------------------------- +Mon Apr 30 15:17:34 UTC 2012 - toddrme2178@gmail.com + +- Removed tests for unsupported openSUSE versions + +------------------------------------------------------------------- +Tue Apr 24 12:06:38 UTC 2012 - toddrme2178@gmail.com + +- Add python 3 package + +------------------------------------------------------------------- +Sat Apr 14 03:11:58 UTC 2012 - badshah400@gmail.com + +- Modify BuildRequires to match recent name changes of lapack and + blas in project. + +------------------------------------------------------------------- +Tue Mar 27 09:35:10 UTC 2012 - saschpe@suse.de + +- Update to version 0.10.1: + * AFAICS, upstream provides no changelog +- Spec file cleanup: + * New sub-package weave provides the devel package (only headers in + a 'devel' package won't work) + * Don't ship testsuite and package weave examples as documentation + * Set license to SDPX style + +------------------------------------------------------------------- +Sun Oct 2 22:16:43 CEST 2011 - behrisch@users.sf.net + +- update to 0.10.0b2 +- added patch for fortran functions returning random data +- prepared addition of ufsparse + +------------------------------------------------------------------- +Mon Sep 13 08:13:03 UTC 2010 - coolo@novell.com + +- update to 0.8.0: + * Python 3 compat + * Major documentation improvements + * Deprecated features + o Swapping inputs for correlation functions (scipy.signal) + o Obsolete code deprecated (scipy.misc) + * New features + o DCT support (scipy.fftpack) + o Single precision support for fft functions (scipy.fftpack) + o Correlation functions now implement the usual definition (scipy.signal) + o Additions and modification to LTI functions (scipy.signal) + ... many more, see 0.8.0-notes.rst + +------------------------------------------------------------------- +Tue Jul 14 17:44:43 CEST 2009 - lars@linux-schulserver.de + +- update to 0.7.1: + + Several fixes in Matlab file IO + + Work around a failure with Python 2.6 + + Memory leak in lfilter have been fixed + + Several bugs of varying severity were fixed in the special + functions +- adapted patches to latest version +- also package release notes + +------------------------------------------------------------------- +Sun Jun 21 12:12:10 CEST 2009 - lars@linux-schulserver.de + +- update to 0.7.0.3 (0.7.1rc3): + + bugfix release +- adapted patches: + + scipy-0.7.1rc3-implicit-fortify-decl.patch (xerbla.c) + + scipy-0.7.1rc3-undefined_operation.patch (zutil.c; cutil.c) +- new patches: + + scipy-0.7.1rc3-umfpack-include.patch (fix to find umfpack) + + scipy-0.7.1rc3-atlas-include.patch (fix to find atlas) + + scipy-0.7.1rc3-superlu.patch (correct use of fprintf) +- enable umfpack, atlas and amd support +- drop devel subpackage +- enable mandriva build + +------------------------------------------------------------------- +Mon Mar 9 15:55:36 CET 2009 - lars@linux-schulserver.de + +- update to 0.7.0: + SciPy 0.7.0 is the culmination of 16 months of hard work. It + contains many new features, numerous bug-fixes, improved test + coverage and better documentation. + + Python 2.6 support (NOT Python 3.0) + + Major documentation improvements + + Support for NumScons has been added + + Sandbox Removed + + Sparse matrices have seen extensive improvements + + Statistical functions for masked arrays have been added + + The IO code in both NumPy and SciPy is being extensively + reworked + + New Hierarchical Clustering module + + New Spatial package + + Reworked fftpack package + + New Constants package + + New Radial Basis Function module + + New complex ODE integrator + + New generalized symmetric and hermitian eigenvalue problem solver + + Bug fixes in the interpolation package + + Weave clean up +- adapted patches to new source + +------------------------------------------------------------------- +Fri Dec 19 23:48:19 CET 2008 - lars@linux-schulserver.de + +- fix compile errors on 11.1 and Factory (should go upstream): + + scipy-0.6.0-implicit-fortify-decl.patch + + scipy-0.6.0-undefined_operation.patch + + scipy-0.6.0-no-return-in-nonvoid-function.patch + +------------------------------------------------------------------- +Thu Oct 30 21:29:56 CET 2008 - lars@linux-schulserver.de + +- temporary fix _Py_c_abs compile error on new python + +------------------------------------------------------------------- +Thu Sep 25 16:21:33 CEST 2008 - lars@linux-schulserver.de + +- moved to Education base repository + +------------------------------------------------------------------- +Thu Jul 01 14:10:10 CEST 2008 - andrea@opensuse-org + +- fixed spec file +- libblas-devel is now libblas3 and blas to avoid version conflicts +- devel package splitted out to make rpmlint happy + +------------------------------------------------------------------- +Sun May 11 18:11:16 CEST 2008 - lars@linux-schulserver.de + +- build for openSUSE-Education +- Require python-numpy-devel for build +- blas-devel is now libblas-devel +- beautify specfile + +------------------------------------------------------------------- +Tue Nov 06 00:00:00 CEST 2007 Felix Richter + +- version bump to 0.6.0 + +------------------------------------------------------------------- +Fri Oct 19 00:00:00 CEST 2007 Werner Hoch + +- removed blas/lapack-devel packages for newer distributions + +------------------------------------------------------------------- +Sat Sep 08 00:00:00 CEST 2007 Werner Hoch + +- new version 0.5.2.1 + +------------------------------------------------------------------- +Fri Jan 19 00:00:00 CEST 2007 Werner Hoch + +- version upgraded to 0.5.2 + +------------------------------------------------------------------- +Thu Dec 05 00:00:00 CEST 2006 Werner Hoch + +- added blas-devel and lapack-devel to BuildRequires + +------------------------------------------------------------------- +Thu Sep 28 00:00:00 CEST 2006 Werner Hoch + +- Initial build. diff --git a/python-scipy.spec b/python-scipy.spec new file mode 100644 index 0000000..6bb5c87 --- /dev/null +++ b/python-scipy.spec @@ -0,0 +1,338 @@ +# +# spec file +# +# Copyright (c) 2024 SUSE LLC +# +# All modifications and additions to the file contributed by third parties +# remain the property of their copyright owners, unless otherwise agreed +# upon. The license for this file, and modifications and additions to the +# file, is the same license as for the pristine package itself (unless the +# license for the pristine package is not an Open Source License, in which +# case the license is the MIT License). An "Open Source License" is a +# license that conforms to the Open Source Definition (Version 1.9) +# published by the Open Source Initiative. + +# Please submit bugfixes or comments via https://bugs.opensuse.org/ +# + + +%{?sle15_python_module_pythons} +%global flavor @BUILD_FLAVOR@%{nil} +%define _ver 1_11_4 +%define shortname scipy +%define pname python-%{shortname} +%define hpc_upcase_trans_hyph() %(echo %{**} | tr [a-z] [A-Z] | tr '-' '_') + +%if "%{flavor}" == "" + %bcond_with hpc + %ifarch armv6l s390 s390x m68k + %bcond_with openblas + %else + %if 0%{?sle_version} == 120200 + %ifarch i586 + %bcond_with openblas + %else + %bcond_without openblas + %endif + %else + %bcond_without openblas + %endif + %endif +%endif + +%if "%{flavor}" == "test" +%bcond_with hpc +%bcond_without test +%define package_name %{pname}-test +%else +%define package_name %{pname} +%bcond_with test +%endif + +%if "%{flavor}" == "gnu-hpc" + %define compiler_family gnu + %bcond_without hpc + %undefine c_f_ver +%endif +%if "%{flavor}" == "gnu7-hpc" + %define compiler_family gnu + %define c_f_ver 7 + %bcond_without hpc +%endif + +%{?with_hpc:%{hpc_requires}} +%bcond_with ringdisabled +%if %{without hpc} +# for file section +%define p_python_sitearch %{python_sitearch} +# for inside python_expand +%define p_python_sitearch_expand %{$python_sitearch} +%define p_prefix %{_prefix} +%define p_bindir %{_bindir} +%else +%{!?compiler_family:%global compiler_family gnu} +%{hpc_init -c %{compiler_family} %{?c_f_ver:-v %{c_f_ver}} %{?ext:-e %{ext}}} +%define package_name %{hpc_package_name %{_ver}} +# for file section +%define p_python_sitearch %{hpc_python_sitearch} +# for inside python_expand +%define p_python_sitearch_expand $($python -c "import sysconfig as s; print(s.get_paths(vars={'platbase':'%{hpc_prefix}','base':'%{hpc_prefix}'}).get('platlib'))") +%define p_prefix %{hpc_prefix} +%define p_bindir %{hpc_bindir} +# Magic for OBS Staging. Only build the flavors required by +# other packages in the ring. +%if %{with ringdisabled} +ExclusiveArch: do_not_build +%endif + %ifarch armv6l s390 s390x m68k i586 +ExclusiveArch: do_not_build + %endif +%{hpc_modules_init openblas} +%endif + +# TODO explore debundling Boost for standard and hpc + +Name: %{package_name} +Version: 1.11.4 +Release: 0 +Summary: Scientific Tools for Python +License: BSD-3-Clause AND LGPL-2.0-or-later AND BSL-1.0 +URL: https://www.scipy.org +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 +BuildRequires: %{python_module Cython >= 0.29.32} +BuildRequires: %{python_module devel >= 3.8} +BuildRequires: %{python_module meson-python >= 0.9.0} +BuildRequires: %{python_module pip} +BuildRequires: %{python_module pybind11 >= 2.4.3} +BuildRequires: %{python_module pybind11-devel >= 2.4.3} +BuildRequires: %{python_module pythran >= 0.9.12} +BuildRequires: %{python_module wheel} +BuildRequires: fdupes +BuildRequires: meson >= 0.62.2 +BuildRequires: pkg-config +BuildRequires: python-rpm-macros >= 20220911 +%if %{with test} +BuildRequires: %{python_module pooch} +BuildRequires: %{python_module pytest-timeout} +BuildRequires: %{python_module pytest-xdist} +BuildRequires: %{python_module pytest} +BuildRequires: %{python_module scipy = %{version}} +BuildRequires: %{python_module threadpoolctl} +%endif +%if %{without hpc} +BuildRequires: %{python_module numpy-devel >= 1.18.5} +%if 0%{?sle_version} && 0%{?sle_version} <= 150600 +# The default gcc on SLE15 is gcc7 we need something newer +BuildRequires: gcc10-c++ +BuildRequires: gcc10-fortran +%else +BuildRequires: gcc-c++ >= 8 +BuildRequires: gcc-fortran >= 8 +%endif +Requires: python-numpy >= 1.18.5 +Requires: python-pybind11 >= 2.4.3 +Suggests: python-pooch + %if %{with openblas} +BuildRequires: openblas-devel + %else +BuildRequires: blas-devel +BuildRequires: lapack-devel + %endif +%else +BuildRequires: %{compiler_family}%{?c_f_ver}-compilers-hpc-macros-devel >= 1.3 +BuildRequires: %{python_module numpy%{?hpc_ext}-%{compiler_family}%{?c_f_ver}-hpc-devel} +BuildRequires: libopenblas%{?hpc_ext}-%{compiler_family}%{?c_f_ver}-hpc-devel +BuildRequires: lua-lmod +BuildRequires: suse-hpc >= 0.3 +Requires: libopenblas%{?hpc_ext}-%{compiler_family}%{?c_f_ver}-hpc +Requires: python-numpy%{?hpc_ext}-%{compiler_family}%{?c_f_ver}-hpc >= 1.18.5 +%endif +%python_subpackages + +%description +Scipy is open-source software for mathematics, science, and +engineering. The core library is NumPy which provides convenient and +fast N-dimensional array manipulation. The SciPy library is built to +work with NumPy arrays, and provides many numerical routines such as +for numerical integration and optimization. + +%{?with_hpc:%{hpc_python_master_package -L -a }} + +%prep +%autosetup -p1 -n scipy-%{version} -a1 +sed -i '1{/env python/d}' scipy/sparse/linalg/_isolve/tests/test_gcrotmk.py +chmod a-x scipy/stats/tests/test_distributions.py + +%ifarch i586 +# Limit double floating point precision for x87, triggered by GCC 12. +%global optflags %(echo "%{optflags} -ffloat-store") +%endif + +%if !%{with openblas} +# Edit the options file until we have a way to provide options to meson-python from command line or environment +# https://github.com/mesonbuild/meson-python/issues/230 https://github.com/mesonbuild/meson-python/issues/235 +sed -i "s/option('blas', type: 'string', value: 'openblas'/option('blas', type: 'string', value: 'blas'/" meson_options.txt +sed -i "s/option('lapack', type: 'string', value: 'openblas'/option('lapack', type: 'string', value: 'lapack'/" meson_options.txt +%endif + +%if !%{with test} +%build +%if 0%{?sle_version} && 0%{?sle_version} <= 150600 +# We need gcc >= 8 for SLE15 +export CC=gcc-10 +export CXX=g++-10 +export FC=gfortran-10 +%endif +# makes sure that the cython and pythran commands from the correct flavor are in PATH +%python_flavored_alternatives +%{python_expand # +%if %{with hpc} +py_ver=%{$python_version} +%hpc_setup +module load $python-numpy +%endif +export CFLAGS="%{optflags} -fno-strict-aliasing" +%{$python_pyproject_wheel} +} + +%install +%{python_expand # +%if %{with hpc} +%hpc_setup +module load $python-numpy +%endif +%{$python_pyproject_install --prefix %{p_prefix}} +# https://github.com/scipy/scipy/issues/16310, delete in order to avoid rpmlint errors +rm %{buildroot}%{p_python_sitearch_expand}/scipy/linalg/_blas_subroutines.h +rm %{buildroot}%{p_python_sitearch_expand}/scipy/linalg/_lapack_subroutines.h +rm %{buildroot}%{p_python_sitearch_expand}/scipy/special/_ufuncs_cxx_defs.h +rm %{buildroot}%{p_python_sitearch_expand}/scipy/special/_ufuncs_defs.h +%fdupes %{buildroot}%{p_python_sitearch_expand} +} + +%if %{with hpc} +%define hpc_module_pname ${python_flavor}-%{shortname} +%{python_expand # +rm -rf %{buildroot}%{p_python_sitearch_expand}/scipy/{,core,distutils,f2py,fft,lib,linalg,ma,matrixlib,oldnumeric,polynomial,random,testing}/tests +%hpc_write_modules_files +#%%Module1.0##################################################################### + +proc ModulesHelp { } { + +puts stderr " " +puts stderr "This module loads the %{pname} library built with the %{compiler_family} compiler " +puts stderr "toolchain." +puts stderr "\nVersion %{version}\n" + +} +module-whatis "Name: %{pname} built with %{compiler_family} toolchain." +module-whatis "Version: %{version}" +module-whatis "Category: python module" +module-whatis "Description: %{SUMMARY}" +module-whatis "URL %{url}" + +set version %{version} + +depends-on $python-numpy + +prepend-path PYTHONPATH ${sitesearch_path} + +setenv %{hpc_upcase_trans_hyph %{pname}}_DIR %{hpc_prefix} +setenv %{hpc_upcase_trans_hyph %{pname}}_BIN %{hpc_bindir} + +family %{shortname} +EOF +} +%endif +%endif + +%if %{with test} +%check +# pooch cache (extracted SOURCE1) +export XDG_CACHE_HOME=$PWD/scipy-datasets +# (occasional) precision errors +donttest="(TestLinprogIPSpecific and test_solver_select)" +donttest+=" or test_gh12922" +donttest+=" or (TestPeriodogram and test_nd_axis_m1)" +donttest+=" or (TestPeriodogram and test_nd_axis_0)" +donttest+=" or (TestPdist and test_pdist_jensenshannon_iris)" +donttest+=" or (test_rotation and test_align_vectors_single_vector)" +donttest+=" or (test_lobpcg and test_tolerance_float32)" +donttest+=" or (test_iterative and test_maxiter_worsening)" +donttest+=" or (test_resampling and test_bootstrap_alternative)" +%ifarch %ix86 +donttest+=" or (test_solvers and test_solve_generalized_discrete_are)" +# Skip the following tests that fail with GCC 13 due to the excess precision change: +# https://gcc.gnu.org/gcc-13/porting_to.html#excess-precision +donttest+=" or (test_fitpack or test_fitpack2 or test_splint or test_integrate or test_boost)" +%endif +# fails on big endian +donttest+=" or (TestNoData and test_nodata)" +# oom +donttest+=" or (TestBSR and test_scalar_idx_dtype)" +# error while getting entropy +donttest+=" or (test_cont_basic and 500-200-ncf-arg74)" +# https://github.com/scipy/scipy/issues/16927 +donttest+=" or (test_lobpcg and test_failure_to_run_iterations)" +%ifarch %ix86 %arm +# fails on 32bit +mark32bit="or xfail_on_32bit" +# precision errors +donttest+=" or (test_peak_finding and TestFindPeaksCwt and test_find_peaks_exact)" +donttest+=" or (test_peak_finding and TestFindPeaksCwt and test_find_peaks_withnoise)" +donttest+=" or (test_iterative and test_x0_equals_Mb and bicgstab)" +donttest+=" or (test_orthogonal and test_roots_gegenbauer)" +donttest+=" or (test_discrete_basic and test_rv_sample)" +donttest+=" or (test_distributions and TestLevyStable and nolan_samples and pct_range0-alpha_range0-beta_range0)" +donttest+=" or (test_distributions and TestLevyStable and test_location_scale and pdf)" +donttest+=" or (test_data and test_boost and (betainc or btdtr))" +donttest+=" or (test_mstats_basic and test_skewtest_2D_WithMask)" +%endif +%ifarch %ix86 +# illegal instruction (?) +donttest+=" or (test_fftlog and test_fht_identity)" +%endif +%ifarch %arm +donttest+=" or (test_cython_api and eval_sh_chebyt)" +donttest+=" or (test_stats_boost_ufunc)" +%endif + +%ifarch s390x +# gh#scipy/scipy#18878 +donttest+=" or (test_distance_transform_cdt05)" +donttest+=" or (test_svd_maxiter)" +%endif + +# not enough precison on 32 bits +if [ $(getconf LONG_BIT) -eq 32 ]; then + donttest+=" or (TestCheby1 and test_basic)" +fi +mv scipy scipy.dont-import-me +%pytest_arch --pyargs scipy -n auto -m "not (slow or xslow $mark32bit)" -k "not ($donttest)" +# prevent failing debuginfo extraction because we did not create anything for testing +touch debugsourcefiles.list +%endif + +%if !%{with test} +%if %{with hpc} +%post +%{hpc_module_delete_if_default} +%endif + +%files %{python_files} +%license LICENSE.txt +%{p_python_sitearch}/scipy/ +%{p_python_sitearch}/scipy-%{version}*-info + +%if %{with hpc} +%define hpc_module_pname %{python_flavor}-scipy +%{hpc_modules_files} +%{hpc_dirs} +%dir %{hpc_libdir}/python%{hpc_python_version} +%dir %{p_python_sitearch} +%endif +%endif + +%changelog diff --git a/scipy-1.11.4.tar.gz b/scipy-1.11.4.tar.gz new file mode 100644 index 0000000..31737e1 --- /dev/null +++ b/scipy-1.11.4.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:90a2b78e7f5733b9de748f589f09225013685f9b218275257f8a8168ededaeaa +size 56336202 diff --git a/scipy-datasets.tar.gz b/scipy-datasets.tar.gz new file mode 100644 index 0000000..cb5743d --- /dev/null +++ b/scipy-datasets.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6aa96107c15d6d74f8395f535aeaa083af04f0c360305d47755c4f798b2f3771 +size 1874187