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github.com/scipy/scipy

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

Merge pull request #19788 from mdhaber/trim_mean

DOC: stats.trim_mean: correct documentation

ea4d1f1330950bee74396e427fe6330424907621 authored almost 1 year ago by Ralf Gommers <[email protected]>
DEP: deprecate complex dtypes in `PchipInterpolator` and `Akima1DInterpolator` (#19752)

* DEP: interpolate: deprecate complex dtypes where they give nonsense
In `PchipInterpolator` an...

7fb9df70aba3169adb4fa881b1bd620dfd7e072a authored almost 1 year ago by Lucas Colley <[email protected]>
Merge pull request #19787 from lucascolley/brew-openblas

DOC/BLD: macOS Homebrew OpenBlas detection advice

bb72c159743832d6f6835f85702c606f5890d0e7 authored almost 1 year ago by Ralf Gommers <[email protected]>
Merge pull request #19800 from h-vetinari/tols

TST: loosen tolerances for tests that fail otherwise on windows+MKL

fe41110dc6cd4b8cf08bdc76d8ccf7a3e2870a06 authored almost 1 year ago by Ralf Gommers <[email protected]>
MAINT: stats.mannwhitneyu: use new _rankdata

e8fdbfe477205a3371b15a987cdec59d48e100cb authored almost 1 year ago by Matt Haberland <[email protected]>
Merge remote-tracking branch 'upstream/main' into gh19642

fc91f1520abff924434b95d40d4530aa77b8d852 authored almost 1 year ago by Matt Haberland <[email protected]>
Merge pull request #19776 from mdhaber/rankdata

ENH: stats.rankdata: vectorize calculation

c77938cd5efc24c0a87867dbd5a37b85889e19cd authored about 1 year ago by Atsushi Sakai <[email protected]>
TST: loosen tolerances for tests that fail otherwise on windows+MKL

349be0b0c39be5673c8cbf9c455cd0d5d0836620 authored about 1 year ago by H. Vetinari <[email protected]>
DOC: Small documentation and docstring corrections for ShortTimeFFT. (#19555)

* Marked function stft(), istft() and spectrogram as legacy in docstring.
* In Python code exam...

16e58d0afe1bdeff99f73775a2ee4d0e62b1220a authored about 1 year ago by Dietrich Brunn <[email protected]>
DOC: update release notes with all deprecations for 1.12 release (#19735)

Co-authored-by: h-vetinari <[email protected]>

d13120499e987c10856f43fffe7f15af711ed560 authored about 1 year ago by Jake Bowhay <[email protected]>
Merge pull request #19792 from dschmitz89/MAINT_t_logpdf_poch

MAINT: simplify `t.logpdf`

08a5b6ff37b8ac39ce885df1fee737edda80d3fc authored about 1 year ago by Matt Haberland <[email protected]>
MAINT: simplify t.logpdf

7d5a5bea802e5371a20c82b35580a721c75bf3ea authored about 1 year ago by dschmitz89 <[email protected]>
Fixed docstrings

17159fe1b205b6559a2f9c141d6d38d9be20d31d authored about 1 year ago by sidsrinivasan <[email protected]>
BENCH: added benchmarks for the individual, non-batched distance

metrics in distance.py.

6524168429401b9fe9e4bc903f86bbf74d655e33 authored about 1 year ago by sidsrinivasan <[email protected]>
MAINT: stats.rankdata: adjust per code review

caed4e4735585d1b60428dc1cae6b058e2d912d5 authored about 1 year ago by Matt Haberland <[email protected]>
DOC: stats.trim_mean: correct documentation

[docs only]

150c93bdf96ef1aa7c5ac3437fbb6b6c2fbe5318 authored about 1 year ago by Matt Haberland <[email protected]>
DOC/BLD: macOS Homebrew OpenBlas detection advice

[docs only]

bc4dfb4c2f00ebfb957e0ae202835f85a52e5c15 authored about 1 year ago by Lucas Colley <[email protected]>
Merge pull request #19786 from rgommers/fix-install-tags

BLD: fix "Failed to guess install tag" in meson-log.txt, add explicit tags

3eb93f5c6d8ec66baed453c49cbeba5f781ba85d authored about 1 year ago by Tyler Reddy <[email protected]>
BLD: fix "Failed to guess install tag" in meson-log.txt, add explicit tags

Removed about ~40 lines from `meson-log.txt`. For `custom_target`,
`configure_file` and other su...

8a6d0512f458bacb452575f9a5d943ad5a76addd authored about 1 year ago by Ralf Gommers <[email protected]>
CI, MAINT: switch to stable python release (#19781)

* Update .github/workflows/linux_meson.yml

---------

Co-authored-by: Lucas Colley <lucas.c...

05e26d633b8e95cc53c0128d4a94f121c95813d6 authored about 1 year ago by Aman Atman <[email protected]>
DOC: stats.moment: correct 'moments' -> 'order'

[skip ci]

843d938a6f37ad8200bfa7ab0bcdda1c0a1a7132 authored about 1 year ago by Matt Haberland <[email protected]>
MAINT: stats.moment: change remaining occurences of keyword 'moment' to 'order'

47e5b4e82a46a2bb6b76432a748bbe61c54534c6 authored about 1 year ago by Matt Haberland <[email protected]>
BUG: stats.nbinom.logcdf: fix IndexError

* BUG: stats.nbinom.logcdf: fix IndexError

ae3ca70a72ef04547fbc28501009246cef5ee6c8 authored about 1 year ago by Daniel Schmitz <[email protected]>
DOC, MAINT: fix make dist in rel process (#19778)

* gh-19750 broke the `make dist` doc building
used in the release process, so fixing it here

fc715ba7ac0323ff3358d7eb5fbdf028e04c0865 authored about 1 year ago by Tyler Reddy <[email protected]>
DOC: Docstring and examples for Rotation.concatenate (#19775)

Co-authored-by: Jake Bowhay <[email protected]>

d4c0eaf0070014bf3ccf1acc91f8a1c8768615f1 authored about 1 year ago by Scott Shambaugh <[email protected]>
ENH: stats.rankdata: vectorize calculation

617081d9208a6a68ba7c95762b985186c29a9aca authored about 1 year ago by Matt Haberland <[email protected]>
MAINT: Avoid use of aligned_alloc in pocketfft on windows (#19761)

* MSVC is too non-conformant and broken...
* Also harden detection of cpp standard on MSVC plat...

35e98491fff54cd0fab61988e0fee16e1521aeaf authored about 1 year ago by Matt Borland <[email protected]>
Merge pull request #19743 from dschult/minmax-1d

ENH: sparse: Add min-max 1d support and tests

6452a48c9611d16140b160091de6cf5299fadd9f authored about 1 year ago by Tyler Reddy <[email protected]>
Merge pull request #19750 from lucascolley/requirements

DEV/BLD: generate `requirements/*` files to simplify build

30a0d13605a1675e863ab47b6b07cc4cb653f86f authored about 1 year ago by Ralf Gommers <[email protected]>
DOC: docstring for scipy.stats.crystalball needs an adjustment (#19773)

Co-authored-by: Francis Allanah <[email protected]>

6735ca637bc35b90fdc72770cf0388228d7f0572 authored about 1 year ago by Francis Allanah <[email protected]>
DOC/DEV: update building from source instructions

[docs only]

c217e3d6bae68635450f3c4d8bfd3d1b0f79a589 authored about 1 year ago by Lucas Colley <[email protected]>
DEV/BLD/CI: generate `requirements/*` files

[skip circle]

8567df4213957e87f104d7116f780711c3d999ca authored about 1 year ago by Lucas Colley <[email protected]>
MAINT: remove redundant `pyproject.toml` entry

a657e8f3b1e542ade173055174b81d229b17db3b authored about 1 year ago by Lucas Colley <[email protected]>
MAINT/CI: remove `*_requirements.txt` files

b8d019d0abb805938b9bf4b0cec421de498b9f41 authored about 1 year ago by Lucas Colley <[email protected]>
BLD: script to generate requirements files

Co-authored-by: Mike Taves <[email protected]>

bda50bf0e0070d89762971f8c422e1ac59905956 authored about 1 year ago by Lucas Colley <[email protected]>
TST: stats.moment: test equivalence of parameter order/moment

d8be39851819cca9e532733c1fb102216130c435 authored about 1 year ago by Matt Haberland <[email protected]>
Merge pull request #19768 from alugowski/superluwarn

MAINT: SuperLU upstream fix for compile warnings

bee9b9ae027eaac16dd8bf67c53c7ec084653b9e authored about 1 year ago by Ralf Gommers <[email protected]>
MAINT: SuperLU upstream fix for compile warnings

9268664d1552eb8aec2f40e8e0e05a9bd980480e authored about 1 year ago by Adam Lugowski <[email protected]>
update ValueError msgs and tests

1866fedb93acede914edc39255a1e889e12112f8 authored about 1 year ago by Dan Schult <[email protected]>
remove extraneous comments

120fa26315347d95526e6d4318df1c00b7969846 authored about 1 year ago by Dan Schult <[email protected]>
MAINT: interpolate: remove dead code (#19760)

ec98497595cd7eb39069ba5ab9117d306fe89579 authored about 1 year ago by Evgeni Burovski <[email protected]>
MAINT: correct inaccurate comment (#19758)

b391a93997b4d79b8ce932afd5ec9cec24d5ef0e authored about 1 year ago by Lucas Colley <[email protected]>
Merge pull request #19755 from lucascolley/walk-packages

MAINT/TST: ignore backend import errors when not in array API mode

bc41135d2dc01b5d99ac2b0a1ae28951fa42f9e5 authored about 1 year ago by Tyler Reddy <[email protected]>
MAINT: ignore backend import errors when not in array API mode

[skip circle]

d29975e72d2b161706b799e202ea66fe1c5989fc authored about 1 year ago by lucascolley <[email protected]>
CI: add labeler based on issue/PR titles (#19746)

42fdb0ec4a298d108819004298821fabb8021945 authored about 1 year ago by Lucas Colley <[email protected]>
Merge pull request #19751 from alugowski/fmmlocal

BUG: Make FMM classes `py::module_local` (fix for 1.12RC)

a313d7b81506cb4b41b49d864868967a9d758467 authored about 1 year ago by Ralf Gommers <[email protected]>
STY: stats.mannwhitneyu: light refactor

5e51fa5df43f10b727369fd60e36afe5e6f78280 authored about 1 year ago by Matt Haberland <[email protected]>
MAINT: stats.mannwhitneyu: minor adjustments

bcb7583d7cb20c9fd1110c00a0d9feefe022cb36 authored about 1 year ago by Matt Haberland <[email protected]>
BUG: Make FMM classes `py::module_local`

7ff50ff840d78097066a0bf65400a650df7364ed authored about 1 year ago by Adam Lugowski <[email protected]>
ENH: stats.mannwhitneyu: vectorize statistic calculations

ab04993f9b0b33d2d98b1e83293001e55b1d3220 authored about 1 year ago by Matt Haberland <[email protected]>
Merge pull request #19672 from j-bowhay/gh-17455-follow-up

DEP: signal: remove scipy.signal.{bspline,quadratic,cubic}

aa7bac2252b5e30e1b988a72b1bf64076e696ec2 authored about 1 year ago by Evgeni Burovski <[email protected]>
TST: skip RGI(..., method="pchip" for complex values) (#19748)

PchipInterpolator is nonlinear in data, hence does not guarantee that
pchip(x, y) == pchip(x, y...

3983e83028b3976514a2ca4ab66899333c3d8b93 authored about 1 year ago by Evgeni Burovski <[email protected]>
ENH: stats.mannwhitneyu: speed up statistic computation

c06dc2a6075e9d237bab55be44a3f1dccb91e223 authored about 1 year ago by Matt Haberland <[email protected]>
TST: fortranfiles fix (#19745)

* Fixes #19737

* the deprecation is obviously coming from https://github.com/numpy/numpy/pull...

d29977a8c5c9a1f6085d25fdd5fea50f54ceb59f authored about 1 year ago by Tyler Reddy <[email protected]>
CI: fix PR labeler config file (#19742)

f187aa25bbdd7023e9cdedb6c5da7f789742dcf8 authored about 1 year ago by Lucas Colley <[email protected]>
ENH: stats.mannwhitneyu: add support for PermutationMethod

9f9f7110aa37eba00ab59d746ffdd073b9156e75 authored about 1 year ago by Matt Haberland <[email protected]>
ENH: stats.mannwhitneyu: exploit symmetry of null distribution

6bae45d6f9a76ae42e07f3b0668bf6422ab4f4d3 authored about 1 year ago by Matt Haberland <[email protected]>
ENH: stats.mannwhitneyu: avoid redundant calculation and unnecessary cache growth

6dffb74b7c26c3434445646933e847bd17b8f3f4 authored about 1 year ago by Matt Haberland <[email protected]>
Add min-max 1d support with 1d tests

5d92dcf4aec5fab409898adce25a57cdfd82275d authored about 1 year ago by Dan Schult <[email protected]>
ENH: sparse: Generalize coo_array to support 1d shapes (#18530)

* Squashed changes

* fix misc test and mypy errors

* Minor tweaks on top of Dan's PR

* ...

ccee92ebe3c215319e77893bfdb33ec4593c09ff authored about 1 year ago by CJ Carey <[email protected]>
Merge pull request #19738 from lucascolley/pythran-min-version

BLD: require `pythran>=0.14.0`

9740431f42b846c5d5d0b3b6774a7cc9a0f60fcf authored about 1 year ago by Tyler Reddy <[email protected]>
Merge branch 'brunnermunzel_anp' into friedman_anp

664ba9ee7c8a12df70e45cdc54d2bb556e8e0f63 authored about 1 year ago by Matt Haberland <[email protected]>
Merge remote-tracking branch 'upstream/main' into friedman_anp

4b70f3c2f104e9a6ce88f28629d320386af4fd64 authored about 1 year ago by Matt Haberland <[email protected]>
CI: undo `pythran` pin in linux_meson 3.12-dev

457e0f5c6c06a84b7e62396c4e785f1a4f165511 authored about 1 year ago by lucascolley <[email protected]>
BLD: require `pythran>=0.14.0`

[skip circle]

a6d0d659ccabd7a61947261b824c725d63f26be4 authored about 1 year ago by lucascolley <[email protected]>
ENH: stats.mood: add nan_policy / keepdims support (#19731)

* ENH: stats.mood: add axis tuple / nan_policy / keepdims support

9975ae1069aa0572e9aadef4ae948fd20bd30347 authored about 1 year ago by Matt Haberland <[email protected]>
Merge pull request #19703 from h-vetinari/factorial_int_array

DEP: non-integers in `factorial(..., exact=True)`: deprecate for scalars and execute deprecation...

8cd805980852386324e18507a38380d18f3be4ef authored about 1 year ago by Jake Bowhay <[email protected]>
MAINT: enhance the configuration for the `pull-request-labeler` workflow (#19728)

* MAINT, ENH: move labeler permissions to the level of the job

See #19088. These permissions...

0f2a49fab3182c422f5472d9d15eff3d089ccd43 authored about 1 year ago by Agriya Khetarpal <[email protected]>
Merge pull request #19730 from tylerjereddy/treddy_bs4_dep_maint

MAINT: bs4 deprecation shim

3b332041522eb6128f040eba98caab5622abf397 authored about 1 year ago by Ralf Gommers <[email protected]>
TST: remove an obsolete DeprecationWarning filter

12fca6bd08a1dfd15a50c174c58df8b155327299 authored about 1 year ago by H. Vetinari <[email protected]>
MAINT: bs4 deprecation shim

* deals with the following deprecation warnings I've been seeing
during the release process for ...

bd91a7e0df8d27bd4741845cc29910b00ba84451 authored about 1 year ago by Tyler Reddy <[email protected]>
ENH: add the modified Akima method to `interpolate.Akima1DInterpolator` (#19696)

* ENH: add `modified` arg to `interpolate.Akima1DInterpolator`

* TST: add TestAkima1DInterpol...

1c38ce56f2af760459bfa27ce53ca53764d2ea5d authored about 1 year ago by Takumasa N <[email protected]>
MNT: use int instead of long in cython code (#19725)

https://github.com/cython/cython/pull/5830 /
d7e95912b6ed7d20e190fbf1aecb9f2a997d479 in cython ...

217748476403a1e5726a921cedb674e7ffbc952e authored about 1 year ago by Thomas A Caswell <[email protected]>
DEP: signal: remove scipy.signal.{lsim2,impulse2,step2} (#19675)

* DEP: signal: remove scipy.signal.{lsim2,impulse2,step2}

e72de0714f0ad6e9b93c9107be84ee68ef70a5db authored about 1 year ago by Jake Bowhay <[email protected]>
DOC: update release version procedure (#19722)

* we now need to adjust `version` in `pyproject.toml`
in the release process, so update the rel...

b3ba73a1526441824935e0c3d424415892bec84a authored about 1 year ago by Tyler Reddy <[email protected]>
DOC: add rationale for 88 char line length (#19721)

e86ebaf2d4b88dce2d9137c4632e4f5497e42af1 authored about 1 year ago by Lucas Colley <[email protected]>
DEP: also deprecated non-integer scalars for factorial(..., exact=True)

18bb04b95df98d5264bd3e522b8adde916f17e05 authored about 1 year ago by H. Vetinari <[email protected]>
DEP: execute deprecation of non-integer arrays in factorial(..., exact=True)

f5265e529c088f9affbeb7d9698dbcb48821c58f authored about 1 year ago by H. Vetinari <[email protected]>
Merge pull request #19714 from rgommers/cython3-upgrade

BLD: require Cython >=3.0.4, drop 0.29.X support

309bfd5c257737cbf44ff1d6a0ac284db0c6f709 authored about 1 year ago by Tyler Reddy <[email protected]>
BLD: require Cython >=3.0.4, drop 0.29.X support

This will make maintenance a bit easier, and it's time; NumPy
dropped Cython 0.29.X support mont...

09401057668f2fae6916373b9751ea131f86916d authored about 1 year ago by Ralf Gommers <[email protected]>
Merge pull request #19710 from rgommers/fix-editable-install-test-errors

TST: fix pytest discovery errors with editable installs

7f9d04bf0df6cdd6f4c9d5754d0e248f5440f3e8 authored about 1 year ago by Matt Haberland <[email protected]>
Merge pull request #19701 from lucascolley/array-api-compat-import

MAINT: make import of `array_api_compat` nicer

6f104d6a2d5ab51e6cd83179af18bf5fd2da8a8d authored about 1 year ago by Ralf Gommers <[email protected]>
MAINT: use nicer `array_api_compat` import

ace4ac47d1d4d46557e780f576a3b052a1ace632 authored about 1 year ago by lucascolley <[email protected]>
MAINT: make import of `array_api_compat` nicer

8bda22e036fa875009d0d309449e5427a0392d0b authored about 1 year ago by lucascolley <[email protected]>
DOC: clarify ttest_1samp argument (#19711)

The original has "Sample observation" as the description of the first
input argument, but this ...

704bf8a256d66f903d59b64fca9804ff37bc5dc7 authored about 1 year ago by Matthew Brett <[email protected]>
TST: fix discovery error of npz files under `special/tests/data`

With editable installs, these generated .npz files will live in a
build directory. The only way ...

2ddb28bad6c283f237861c1276eb9a564452e837 authored about 1 year ago by Ralf Gommers <[email protected]>
TST: add `norecursedirs` to pytest.ini, avoid picking up vendored tests

The ones in the highs git submodule were actually causing `pytest scipy`
to error on discovery. ...

307a3d24a4973a9fb43102c920547440e39dab13 authored about 1 year ago by Ralf Gommers <[email protected]>
TST: fix issue with `test_scipy_version.py` and editable installs

This file was installed in a different submodule than it was defined,
which led `pytest scipy` t...

7b1dc9fef76c4b08bf7e3a3920a7611c4efe2703 authored about 1 year ago by Ralf Gommers <[email protected]>
Merge pull request #19702 from h-vetinari/atol

4a6db1500dc62870865fe7827524abd332a88fd9 authored about 1 year ago by Pamphile Roy <[email protected]>
Merge pull request #19708 from lucascolley/optional

777a48b7bcaa04d983dd16f74c4b6e8c79c84bd2 authored about 1 year ago by Pamphile Roy <[email protected]>
BUG: fix negative overflow in stats.boxcox_normmax (#19691)

* MAINT: stats.boxcox_normmax: avoid negative overflow

Co-authored-by: Matt Haberland <mhaber...

a725b5ae891938492e34817cbb7f310e9346cd60 authored about 1 year ago by Xuefeng Xu <[email protected]>
homogenize escaping for tol/atol/rtol in docstrings

as well as the format of the SciPy version for which we announce the change

99367eb56e0147265ef969cb40c31e42656269a1 authored about 1 year ago by H. Vetinari <[email protected]>
remove obsolete warning filter

8b5f4681852bcb42cee431dc6a86a52373bd77ce authored about 1 year ago by H. Vetinari <[email protected]>
DOC: spatial.distance: missing optional param markers

[docs only]

0c583a4a2c109ed85dfc8aba242b6f099cb90f21 authored about 1 year ago by Lucas Colley <[email protected]>
fix C&P error

43f6836e33dde52644105f44ab577a6e809acfea authored about 1 year ago by H. Vetinari <[email protected]>
don't (re)calculate norm of b in _get_atol_rtol; ensure we raise warnings before returning

5715dd6000b945f26d72952cba90a824c958ab9f authored about 1 year ago by H. Vetinari <[email protected]>
adapt to tol->rtol renaming in test_iterative.py

very strange that this did not fail before already

5ae5901e6c177e4be274d829ae3c60417c94ccd6 authored about 1 year ago by H. Vetinari <[email protected]>
also apply tol->rtol deprecation for minres / tfqmr

6e612d3fef4d445a42be02d7e5dc7da7b28e0e4c authored about 1 year ago by H. Vetinari <[email protected]>
avoid spurious complex values in tfqmr

6937e3b36cb12ad1ee98e43f1ea15d1755975c26 authored about 1 year ago by H. Vetinari <[email protected]>
replace callers of assert_normclose with single-line code used elsewhere

e266e33eaf533fe301448725f345616605711714 authored about 1 year ago by H. Vetinari <[email protected]>