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github.com/scipy/scipy

SciPy library main repository
https://github.com/scipy/scipy

MAINT:linalg:Adjust lwork/liwork changes OpenBLAS 0.3.26

See https://github.com/Reference-LAPACK/lapack/pull/942

8c96a1f742335bca283aae418763aaba62c03378 authored 12 months ago by Ilhan Polat <[email protected]>
Fix AIX build break.

This patch is a fix to AIX build break that happened due to a variable defined as hz in _amos.c....

e76a07ca7e26233f1f78a95f355227cb44f44e7e authored 12 months ago by Aditya Vidyadhar Kamath <[email protected]>
DEP: reflect extended deprecations also in release notes (#19903)

52732578a67e1f243b466e0668d99f6ec85d0d08 authored 12 months ago by h-vetinari <[email protected]>
Merge pull request #19901 from rgommers/cdflib-remove-npmath

MAINT: special: remove use of `numpy.math` from `_cdflib.pyx`

730010e77319606718b3d50a8fc402ba9cc629bc authored 12 months ago by Ilhan Polat <[email protected]>
MAINT: special: remove use of `numpy.math` from `_cdflib.pyx`

This Cython module should not be used, since it's likely to be
deprecated and we cleaned up all ...

aa85972894668f6dc92a3a22820cb1068c42f1a3 authored 12 months ago by Ralf Gommers <[email protected]>
Merge pull request #19891 from rgommers/fix-mpl-stats-failure

MAINT: stats: fix editable install issue in `qmc` and MPL-related issue in test

7ca49f47fa24887494c933185b29f9d2959aecc6 authored 12 months ago by Tyler Reddy <[email protected]>
Merge pull request #19869 from lucascolley/as_xparray

MAINT: array types: rename `as_xparray` to `_asarray`

2a4d6e978baa015935e009cd00537d2ddeee2531 authored 12 months ago by Ralf Gommers <[email protected]>
TST: array-api: improve tracebacks for testing functions

`__tracebackhide__ = True` should be used for all testing functions,
just like it is in `numpy.t...

7d9080691e210681c0c47ff47d8930ae009953dc authored 12 months ago by Ralf Gommers <[email protected]>
MAINT: fix some small array API support issues

These surfaced with the more strict reference implementation in
https://github.com/numpy/numpy/p...

f4900381e460122aea465a54cd59df4c219a7e63 authored 12 months ago by Ralf Gommers <[email protected]>
DEP: extend some announced deprecations due to out-of-band 1.13 release (#19892)

816d59dad58cd9820900062ba2279e807865a97f authored 12 months ago by h-vetinari <[email protected]>
Merge pull request #19811 from lucascolley/cpp17

BLD: set default `cpp_std` to `c++17`

736216d5ea2645cb76f4468d02addc2d18acd5c0 authored 12 months ago by Ralf Gommers <[email protected]>
Merge pull request #19893 from h-vetinari/itertools

MAINT: remove unused itertools-import in scipy.interpolate._interpolate

2353b154451fa77ee5f009b696ae82070ed8eab6 authored 12 months ago by Evgeni Burovski <[email protected]>
MAINT: remove unused itertools-import in scipy.interpolate._interpolate

this already got ignored due to the presence of `__all__` in that module

63a9298b1c7d9568eeb8891aada742dfc45fc0c4 authored 12 months ago by H. Vetinari <[email protected]>
BUG: stats.qmc: remove use of `__file__` to fix npz file loading

This code is broken when using an editable install, generating a lot
of hard to understand failu...

184c4e833cf08ded78290c607761da8fadd5f680 authored 12 months ago by Ralf Gommers <[email protected]>
BLD: set default `cpp_std` to `c++17`

[wheel build] [skip circle]

10c2a45586d8a169a0407efc90753ebfc0dbd626 authored 12 months ago by Lucas Colley <[email protected]>
MAINT: logsumexp: properly handle complex sign (#19870)

a403bde8346314fc39decfd5e60347c3d7a8df14 authored 12 months ago by Jake Vanderplas <[email protected]>
TST: avoid trying to use Matplotlib when it's not importable

Specific to numpy 2.0.0-dev. This test fails a lot when trying
to use the test suite in envs whi...

2f1bf7303f9efb0a964fd920040496bee9cb4c79 authored 12 months ago by Ralf Gommers <[email protected]>
Merge pull request #19882 from lucascolley/pocketfft

MAINT: vendor `pocketfft` as git submodule

6a71dd5820f5984208584f7e57e71946bd0d39f0 authored 12 months ago by Tyler Reddy <[email protected]>
Merge pull request #19886 from rgommers/fix-test-seeding

TST: stats: fix a few issues with non-reproducible seeding

909df2e270db9f6da2495f62326c337885b2a197 authored 12 months ago by Matt Haberland <[email protected]>
TST: stats: fix a few issues with non-reproducible seeding

The use of `hash('a_descriptive_string')` is cute, but unfortunately
hashes are not reproducible...

bff424e5e1467cdc052fe86d39b165846232dc62 authored 12 months ago by Ralf Gommers <[email protected]>
MAINT: pocketfft: use header from git submodule

f739fd4a9a58f5dfdcb6787d910257086680bea9 authored 12 months ago by lucascolley <[email protected]>
MAINT: pocketfft: define `CACHE_SIZE` in build

[skip circle]

e79dfb2ca5a866b90d37d171d2f4cc2889c116e4 authored 12 months ago by lucascolley <[email protected]>
MAINT: vendor `pocketfft` as git submodule

d527d30849f55799fbcdb647aef7f3ad603fcac8 authored 12 months ago by lucascolley <[email protected]>
ENH:MAINT:special:Rewrite amos F77 code (#19587)

* MAINT:special:amos:Remove AMOS Fortran library

[skip ci]

* ENH:special:amos:Rewrite publ...

8e9d43838b7db8d40fc4567f3aafeed68466b464 authored 12 months ago by Ilhan Polat <[email protected]>
DOC: 1.12 release notes tweaks (#19877)

* SciPy `1.12.0` release notes formatting improvements

e5f21298b62fb03732f000645d2caaa67aad8800 authored 12 months ago by Daniel Schmitz <[email protected]>
MAINT: stats.rankdata: ensure correct shape for empty inputs (#19874)

* MAINT: stats.rankdata: ensure correct shape for empty inputs

6ace6377c481e46ef154b45337ce5c2eb6452a6e authored 12 months ago by Jake Vanderplas <[email protected]>
DOC:optimize: Make default for bounds in scipy.optimize.linprog clearer

87f8428b227dd8962d8658482bd8a150a31292a4 authored 12 months ago by Chethin Manage <[email protected]>
add note on behavior for csr/csc arrays (#19864)

43a96e2d766b8751254b88887bca95e87fa50521 authored 12 months ago by Andrew Landau <[email protected]>
Merge pull request #19871 from rgommers/atleast1d-isinstance

MAINT: make isinstance check in `stats._distn_infrastructure` more ro…

a75b1f0e0fa59c175bb22baa6a8397f4b2cb9740 authored 12 months ago by Evgeni Burovski <[email protected]>
MAINT: make isinstance check in `stats._distn_infrastructure` more robust

This check for a list return type from `atleast_1d` may fail if
in NumPy 2.0 the return type wil...

80cc0193c8d6c15b98c939b40415aa708a5391d0 authored 12 months ago by Ralf Gommers <[email protected]>
MAINT: array types: rename `as_xparray` to `_asarray`

6bdb149afcfa6b5b0b78e366b19ea718919e4359 authored 12 months ago by lucascolley <[email protected]>
Merge pull request #19868 from rgommers/fix-unique-inverse

MAINT: fix use of `unique(..., return_inverse=True)`

c5197c435440be51152c7930e421525b876a1793 authored 12 months ago by Tyler Reddy <[email protected]>
MAINT: fix use of `unique(..., return_inverse=True)`

Code was written to expect a 1-D array with the inverse
indices, and that got changed in NumPy i...

c836e0292066dfed26786c4e4610f6b48da76d6c authored 12 months ago by Ralf Gommers <[email protected]>
ENH: stats.boxcox_normmax: add parameter ymax (#19631)

* ENH: stats.boxcox_normmax: add parameter ymax

19dad8405e3405c00845a8ef20b7461f5d0c490e authored 12 months ago by Xuefeng Xu <[email protected]>
Merge pull request #19859 from rgommers/fix-ci-rmtree-failure

BLD: improve scipy-openblas dependency check

4e69f71d587b3b4ebaf922b9b3a9d48f03d7b007 authored 12 months ago by Ralf Gommers <[email protected]>
Merge pull request #19857 from eli-schwartz/lto

BLD: make scipy build warning-free with LTO enabled

bd00d29cae54fd28ea58229c5ce5aa729ff52666 authored 12 months ago by Ralf Gommers <[email protected]>
Merge pull request #19860 from lucascolley/BLD-glob

MAINT: fix BLD label typo

29fe6bda96e2819a437f1fe6ae67acfa25dea295 authored 12 months ago by Ralf Gommers <[email protected]>
MAINT: fix BLD label typo

[skip ci]

1137d9d6dd6e2bfd59e5ecf02be2bd2fc746dab8 authored 12 months ago by lucascolley <[email protected]>
Merge pull request #19856 from eli-schwartz/pythran-version

BLD: simplify pythran version requirement in meson

2665b0c003c0b2b8d4ddb0db533721956ae11597 authored 12 months ago by Ralf Gommers <[email protected]>
BLD: improve scipy-openblas dependency check

This avoids looking for scipy-openblas with CMake (which we never want),
and avoids looking for ...

34e31cb9aa8d060b5e384088ba2289886f7bd77c authored 12 months ago by Ralf Gommers <[email protected]>
BLD: make scipy build warning-free with LTO enabled

Much fortran code is not LTO-safe, and would require modernizing that
fortran code, probably. We...

c604fdfaebea593434e2b722a55ad1cb2145e673 authored 12 months ago by Eli Schwartz <[email protected]>
BLD: simplify pythran version requirement in meson

For a find_program() invocation, the version check can be inlined into
the lookup. This is diffe...

3110372a3d0c86f332c471c08dc339a5aba75332 authored 12 months ago by Eli Schwartz <[email protected]>
DOC: stats.rv_continuous.fit: add example of custom optimizer (#19663)

* DOC: stats.rv_continuous.fit: add example of custom optimizer

89049ddf566cb34cc4a87383a467ca82a6724d1d authored 12 months ago by m-maggi <[email protected]>
Merge pull request #19849 from rgommers/fix-prerelease-job

CI: fix prerelease job to use numpy 2.0, and add a second job to test ABI compat

906e6cd9bb022e78a07b34636bee64813ce56afa authored 12 months ago by Tyler Reddy <[email protected]>
TST: signal: fix warning filter regex to avoid `buttord` test failure

The warning message in NumPy changed between 1.22 and 2.0, it used
to say "in true_divide" and n...

d919646752035177435cf5d531c1329e7b666554 authored 12 months ago by Ralf Gommers <[email protected]>
CI: add extra pre-release job that tests numpy 2.0/1.x ABI compat

Note that this job uses Python 3.11 rather than 3.12 to avoid the
problem with MapWrapper report...

f4707ecf926f32beccc7caec44bdb504394b359d authored 12 months ago by Ralf Gommers <[email protected]>
DOC: Add example for mstats.brunnermunzel (#19664)

* DOC: Add example for mstats.brunnermunzel

48e3215d5cd39da5d26c9c3b81a5881f5ea13783 authored 12 months ago by Stefanie Senger <[email protected]>
TST: stats: compare geometric zscore to naive version instead of hardcoded values (#19803)

* TST: stats: improve test for geometric zscore

12c37da2f57f895fe76248c51f6d621ad6baabf5 authored 12 months ago by Quentin Barthélemy <[email protected]>
CI: ensure we use numpy 2.0.0-dev in pre-release CI job

Closes gh-19846

d04c0e424a5d4f32949cb438b89748af3115057d authored 12 months ago by Ralf Gommers <[email protected]>
Merge pull request #19838 from lucascolley/real-transform-docs

DOC: fft: improve `s` description for real transforms

d23363809572e9a44074a3f06f66137083446b48 authored 12 months ago by Ralf Gommers <[email protected]>
Merge pull request #19842 from mgorny/pocketfft-test-fixture

TST: move reference data for test_real_transforms to a fixture

c927b4fc38f91e707749498439df0f0d9b5fb227 authored 12 months ago by Ralf Gommers <[email protected]>
Merge pull request #19844 from mgorny/np-load

TST: fix more cases of fd leaks from np.load()

6c01f51aa951a17202d55ed50a1115460520b7c9 authored 12 months ago by Evgeni Burovski <[email protected]>
TST: fix more cases of fd leaks from np.load()

Fix a few more cases of `np.load()` results not being closed.
To confirm them, I've used the fol...

9e07b524240e9c0598bab7776ffa79c0f9735971 authored 12 months ago by Michał Górny <[email protected]>
MAINT: special: fix meson deprecation warning (#19837)

[skip circle]

e60a60394d61fe0081fc5f05f68ee585e07e4406 authored 12 months ago by Lucas Colley <[email protected]>
Merge pull request #19843 from theplatypus/fft-submodule-docs

DOC: Add `fft` to list of submodules in tutorial

1691f1353125e110499b1184dfe175907e3fa8c4 authored 12 months ago by Ralf Gommers <[email protected]>
TST: move reference data for test_real_transforms to a fixture

Move the code for getting the reference data in test_real_transforms
to a fixture. This easily ...

8f470e09327933fc0f8e1bc4f29e8bda74c0d606 authored 12 months ago by Michał Górny <[email protected]>
DOC: Add `fft` to list of submodules in tutorial

c3dd6b15ca105a387fc871ad39e72ad1bf4a3aa3 authored 12 months ago by theplatypus <[email protected]>
Merge pull request #19810 from rgommers/cython-nodepr-api

MAINT: set `NPY_NO_DEPRECATED_API` also for Cython code

02aaf8dcf2e6afbd20c74b9274343e0871e4722a authored 12 months ago by Ilhan Polat <[email protected]>
DOC: fft: correct `s` description for real transforms

[docs only]

c5e08aa0d7a19d7351fa28294801ce844124a747 authored 12 months ago by Lucas Colley <[email protected]>
Merge pull request #19825 from lucascolley/codeowners

MAINT: `CODEOWNERS` syntax fix and changes

e7c6a0d1ce504c528ab00d19ddac6bdb1ae1cb36 authored 12 months ago by Tyler Reddy <[email protected]>
DOC: Improving "Spectral Analysis" section in User Guide (#19488)

* DOC: Improving "Spectral Analysis" section in User Guide

* DOC: Remove header comments of p...

446a9dbcab46c6351adb50369af7c4050f443a09 authored 12 months ago by Dietrich Brunn <[email protected]>
DOC: update Cython section of detailed roadmap.

d0d72e55760bbf4158f6672bc8e92c0c9a9a13b6 authored 12 months ago by Ralf Gommers <[email protected]>
BLD: clean up meson.build files for `numpy_nodepr_api` and warning flags

The one minor issue is a few "redefinition of macro" warnings because
Pythran defines `NPY_NO_DE...

ab7ca955c4e80debc6da740337d649c257164c43 authored 12 months ago by Ralf Gommers <[email protected]>
MAINT: set `NPY_NO_DEPRECATED_API` also for Cython code

This is a follow-up to gh-10840.

d447b2bf9741062d3f146914aba1affc9deb4628 authored 12 months ago by Ralf Gommers <[email protected]>
Merge pull request #19829 from rgommers/fix-ppoly-warning

MAINT: interpolate: fix build warning from `_ppoly.pyx`

88c60ff2b54e4a7fef2f578d010939343f9fd6ca authored 12 months ago by Evgeni Burovski <[email protected]>
Merge pull request #19666 from anupriyakkumari/main

DOC: Add Example to lbfgsb docstring

6ebea8296ee27630ef9ac52f443c5a8326ceeb68 authored 12 months ago by Kai <[email protected]>
CI/DEV: fix and simplify `label-globs` syntax (#19828)

94c115534d8624757dcea7f92f270bcc36380909 authored 12 months ago by Lucas Colley <[email protected]>
REL: bump copyright to 2024 (#19830)

c6c91f6269ae8b329f6b85c776ba5e6f8f1e1f0c authored 12 months ago by Lucas Colley <[email protected]>
MAINT: interpolate: fix build warning from `_ppoly.pyx`

This warning is new with GCC 12 (and a false positive, see cython#5937):

```
[6/7] Compiling C ...

4b22adcfaa7962d5ecfde81c313484f3c219e371 authored 12 months ago by Ralf Gommers <[email protected]>
MAINT: uarray CXX version hex cleanup (#19818)

68e65d3286e19a9209120b55732ae1cd099961d1 authored 12 months ago by Tyler Reddy <[email protected]>
Merge pull request #19827 from rgommers/fix-ckdtree-warnings

MAINT: spatial: fix build warnings in `ckdtree` code

67aac4648b4b02473c9f8ab6b43033a87dac6f20 authored 12 months ago by Tyler Reddy <[email protected]>
Merge pull request #19822 from thalassemia/propack_warn

BLD: propack: resolve missing return value warnings

d07d2d7ea5fc2628cd7353539081e0b3cbf9619b authored 12 months ago by Ralf Gommers <[email protected]>
Merge pull request #19820 from thalassemia/test_ladiv

TST: linalg: Test Cython LAPACK complex ladiv

5d67dff09578a9e5dca9eb30a2ea6a32c39504e2 authored 12 months ago by Ralf Gommers <[email protected]>
MAINT: spatial: fix build warnings in ckdtree code

First warning:

```
[5/8] Compiling C++ object scipy/spatial/_ckdtree.cpython-310-x86_64-linux-g...

fdd17ba451128ad654b03a475290f4029aec7083 authored 12 months ago by Ralf Gommers <[email protected]>
MAINT: Windows NumPy 2.x int shims (#19724)

* related to gh-19605

* fixes 213 test failures on Windows alongside NumPy `main`
by restori...

2d6be1c71322c33a7151f1620d633711715b6a7b authored 12 months ago by Tyler Reddy <[email protected]>
MAINT: `CODEOWNERS` syntax fix and changes

[skip ci]

527ba3755ceeca2e54fb2480dc936818345c67c7 authored 12 months ago by lucascolley <[email protected]>
Merge pull request #19821 from thalassemia/missing_proto

BLD: resolve missing prototype warnings in lsoda/vode

12763351358202d414064292489bdcdb952b0358 authored 12 months ago by Ralf Gommers <[email protected]>
CI/DEV: add some new auto-labels (#19823)

0348d2f7f47e11170bc7581b4f4b178c0db39f16 authored 12 months ago by Lucas Colley <[email protected]>
TST: linalg: Test Cython LAPACK complex ladiv

8b4eef3ccee86d9e6a40a9011a5dced4733473ec authored 12 months ago by thalassemia <[email protected]>
Apply suggestions from code review

Co-authored-by: Daniel Schmitz <[email protected]>

89d0012bb667f5ad0792275216a578293fac4c07 authored 12 months ago by anupriyakkumari <[email protected]>
BLD: resolve missing prototype warnings

a495138278ac9b95023b5ddbdb30d76eecf2ddab authored 12 months ago by thalassemia <[email protected]>
BLD: propack: resolve missing return value warnings

93a07f4a5ee0639944287b8370773997be1c0284 authored 12 months ago by thalassemia <[email protected]>
DOC: stats.mannwhitneyu: hopefully fix links

[docs only]

c7893feeb21ca933a1f2521cf920323986a079f6 authored 12 months ago by Matt Haberland <[email protected]>
DOC: stats.mannwhitneyu: fixups per review

[skip ci]

c9e6d27c2b61867d78b6789e39327f806987cda6 authored 12 months ago by Matt Haberland <[email protected]>
Apply suggestions from code review

Co-authored-by: Lucas Colley <[email protected]>
Co-authored-by: Daniel Schmitz <40656107+...

0e31f93ac37dc195a7716814d8326420d96b294c authored 12 months ago by anupriyakkumari <[email protected]>
Merge remote-tracking branch 'upstream/main'

e5fd9faa554e44e682191f83e0c0d3d2e084ff2d authored 12 months ago by anupriyakkumari <[email protected]>
Apply suggestions from code review

committing more suggestions

Co-authored-by: Lucas Colley <[email protected]>

7eca0697c3b75fb89111a57fceaed4866e91cbc7 authored 12 months ago by anupriyakkumari <[email protected]>
Apply suggestions from code review

Committing suggestions

Co-authored-by: Daniel Schmitz <[email protected]...

a892844f725dda442d139d4b14ef100496172252 authored 12 months ago by anupriyakkumari <[email protected]>
DOC: fft: add note about FHT formulas (#19807)

* add description

* shorten description

* shorten description

* inverse doc

* Update...

7ff74ee275de307d6a17bebff4ea10cf58d35dff authored 12 months ago by Aman Atman <[email protected]>
MAINT: Add binom to new C++ special lib along with its cephes dependencies (#19681)

093e6455732d27beedb9e1a91524139810299cdd authored 12 months ago by Albert Steppi <[email protected]>
Merge pull request #19749 from mdhaber/gh19642

ENH: stats.mannwhitneyu: vectorize statistic calculation #19749

e35407702d2ad72755bccf548ef93fff82014f42 authored 12 months ago by Atsushi Sakai <[email protected]>
Merge pull request #19790 from sidsrinivasan/distance-bench

BENCH: Added benchmarks for individual distance metrics

dbcd3dbf71ead579dbb5816dcf61ffe8adb5e5cb authored 12 months ago by Tyler Reddy <[email protected]>
ENH:MAINT:special:Cythonize cdflib (#19560)

* ENH:MAINT:special:Cythonize cdflib

[skip ci]

ENH:MAINT:special:Some fixes on cdfchn

E...

667b8d4d058024468c75b74fb35ab64abc3ccbd1 authored 12 months ago by Ilhan Polat <[email protected]>
BUG: support sparse Hessian in `Newton-CG` and `trust-constr` (#19785)

648ba8c633e35f02fa062ead1f882e804d8582af authored 12 months ago by Daniel Schmitz <[email protected]>
Merge pull request #19806 from h-vetinari/multi_warn

TST: fix compatibility with pytest 8

b91545ad6d42a0005c8a368dc61e967074bd44d8 authored 12 months ago by Ralf Gommers <[email protected]>
MAINT: integrate.cumulative_simpson: various improvements (#19709)

* MAINT: integrate.cumulative_simpson: various improvements

cff2279fdfabacf7f5110ff7ed697fe9910bf9be authored 12 months ago by Praveer Nidamaluri <[email protected]>
TST: separate two unrelated tests in test_signaltools.py

The second half of the test had nothing to do with test_none
ever since its introduction in ce7e...

79e6e852f2fce021a9cb10a990cbc72670d60512 authored almost 1 year ago by H. Vetinari <[email protected]>
TST: account for parasitic warnings for compatibility with pytest 8

By and large, these should all be filtered out in the implementation,
not in the tests, see #19805.

36dcd6057e8b2d70ce5084d6cebb487ead9eefda authored almost 1 year ago by H. Vetinari <[email protected]>
TST: account for multiple warnings where they are unavoidable

For example, in the deprecation of positional use of `tol=` in sparse solvers.

f20cdcee07cf21b49cb07b896001320db3c75fa3 authored almost 1 year ago by H. Vetinari <[email protected]>
MAINT: stats.mannwhitneyu: adjustments per comments

269673d30af06a14354f5dabf88c21673e607c04 authored almost 1 year ago by Matt Haberland <[email protected]>