MAINT: backports for 1.11.0rc2 #18671

tylerjereddy · 2023-06-13T23:11:52Z

Still TODO:

need to deal with BUG: dev.py notes needs a small shim #18595 (that's easy enough)
sparse release notes likely need a bit of tweaking, or at least for the reversion that happened cc @perimosocordiae @stefanv
good to check with conda release manager @h-vetinari if there are any concerns I'm not addressing?

Backports Included here:

[skip ci]

[skip actions] [skip circle]

… add tests

The ppc64le one is a small test bump. The PyPy-on-Windows one is a real bug in PyPy, but it's not planned to be fixed any time soon, so the test is xfail-ed here. Closes scipygh-18632 [skip circle] [skip cirrus]

…cipy#18659) Co-authored-by: Pamphile Roy <roy.pamphile@gmail.com>

* update the SciPy 1.11.0 release notes following a set of RC2 backports

h-vetinari · 2023-06-13T23:43:43Z

good to check with conda release manager @h-vetinari if there are any concerns I'm not addressing?

Would be good to have #18630. @rgommers marked it as a backport-candidate already (but also milestoned it for 1.12? 🤔 In any case, if it's not backported, I'll have to carry it on the feedstock, at least for ppc; this would also be manageable).

Otherwise there are no additional PRs that I'm aware of that we need for the conda-forge side, thanks for checking!

rgommers · 2023-06-14T06:21:30Z

Would be good to have #18630. @rgommers marked it as a backport-candidate already (but also milestoned it for 1.12? 🤔

Agreed. Merged now, would be good to add to the backports here. That PR is going into 1.12; this backport PR pulls it into 1.11 - the milestones on the respective PRs indicate that; the issue itself is also marked for 1.11.0.

rgommers · 2023-06-14T07:33:52Z

The pre-release job is failing with meson.build:57:2: ERROR: Problem encountered: SciPy requires Cython < 3.0. Let's remove that check again from meson.build - for details, see https://github.com/scipy/scipy/pull/18591/files#r1229148530.

rgommers · 2023-06-14T07:40:39Z

The musllinux job is crashing due to pulling in numpy 2.0.0.dev - the --pre flag had to be added for the 1.25.0 pre-release wheel, but we shouldn't be tested 2.0 nightlies in the 1.11.x branch.

I pushed a commit that should fix both of the failing jobs.

h-vetinari · 2023-06-14T07:45:21Z

The musllinux job is crashing due to pulling in numpy 2.0.0.dev

Speaking of numpy, does the condition numpy <1.28.0 still make sense now that the main branch targets 2.0? Doesn't have to be changed in this PR (and of course we can backport numpy 2.0 compatibility patches if we want to), but more out of curiosity.

rgommers · 2023-06-14T07:55:04Z

Speaking of numpy, does the condition numpy <1.28.0 still make sense now that the main branch targets 2.0?

Yes it does - the N+3 condition still holds. A numpy 1.26.0 is planned; it's unlikely that there'll be any more minor releases beyond that, but you never know.

rgommers · 2023-06-14T08:33:30Z

Hmm, musllinux got further but is still crashing in linalg/tests/test_decomp.py on TestSVD_GESDD.test_random_complex. It passes on main, with what looks like the same version of OpenBLAS (0.3.23). That seems to be related to #17630 (comment) and commit 5055c7e.

EDIT: that test has a random number seeding issue, which may explain why it behaves differently on different branches. I'll try to fix that on main first.

EDIT 2: it passed on a second run, without making a relevant change. So it's a flake or related to seeding - let's ignore it on the 1.11.x branch.

These tests crash in a quite flaky way, as seen in scipygh-18671 and previously also in scipygh-17630. So to make sure it's not due to test ordering, avoid use of the global RandomState instance.

tupui

Thanks Tyler! LGTM from my perspective.

About the release notes, can we do some tweaking here? I had some talk with Matt and we might want to highlight other things in stats and in general.

tylerjereddy · 2023-06-14T15:59:58Z

About the release notes, can we do some tweaking here? I had some talk with Matt and we might want to highlight other things in stats and in general.

Yes, please do make release notes suggestions here, or you can even open a PR against my branch or whatever suits. Apart from Matt, I think the feedback on the release notes was pretty light initially, probably the usual reason of folks being busy.

…18630) [skip ci] --------- Co-authored-by: Ralf Gommers <ralf.gommers@gmail.com>

* Fixes scipy#18595 * use `git apply` to directly apply the patch from scipygh-18595 that worked during the RC1 phase of current release cycle; I'll skip the CI--it isn't tested there which is why the patch is needed in the first place [skip ci]

tylerjereddy · 2023-06-14T16:47:28Z

the two additional backports have been added in, and the summary comment at the top of this PR has been updated accordingly
at the time of writing, the only outstanding item is making the release notes "better" + sparse relnotes updates probably

tupui · 2023-06-14T17:47:49Z

at the time of writing, the only outstanding item is making the release notes "better" + sparse relnotes updates probably

I will raise this to the sparse team on discord.

tupui · 2023-06-14T18:02:07Z

@jjerphan is going to help for the sparse part tomorrow 😃 Thanks!!

jjerphan · 2023-06-14T18:08:05Z

Or later tonight. 🦉

…linux (#18677) * CI: remove setuptools install from musllinux job No longer used/needed, since we removed the need for it from Pythran. * TST: improve seeding of problematic linalg tests + add `IS_MUSL` These tests crash in a quite flaky way, as seen in gh-18671 and previously also in gh-17630. So to make sure it's not due to test ordering, avoid use of the global RandomState instance.

mdhaber

Please consider tylerjereddy#73.

jjerphan · 2023-06-14T21:52:49Z

I just opened tylerjereddy#74.

tylerjereddy · 2023-06-15T18:44:53Z

I merged the release notes PRs from Matt and Julien, making minor tweaks to the latter
I noticed we still hadn't removed the reference to diags_array in the release notes despite Revert "ENH: sparse: Add _array version of diags creation functions… #18599, so I removed that mention
noticed another last-minute PR to backport, BUG: signal: fix detrend with array-like bp #18676, and pulled that in
Updated the author/PR lists again, checked doc build + test suite locally at least
Updated summary comment above, which appears to have no oustanding items left as far as I can tell

rgommers

LGTM and CI is green modulo 3 unrelated failures, so good to go I'd say. I'd recommend either squash-merging this though or (preferably) squashing the ~10 separate commits that tweak the release notes entry for sparse array stuff.

* update the SciPy 1.11.0rc2 release notes following additional backports DOC: suggestions for `scipy.sparse` release notes Signed-off-by: Julien Jerphanion <git@jjerphan.xyz> Reword some sentences Remove mentions of n-dimensional sparse arrays Apply suggestions from code review DOC: update release notes for scipy.stats DOC: PR 18671 revisions * remove `diags_array` from release notes per scipygh-18599 DOC: PR 18671 revisions * update release notes after more activity

* release notes updates after another backport to 1.11.0rc2 PR

tylerjereddy · 2023-06-16T02:30:01Z

squashing the ~10 separate commits that tweak the release notes entry for sparse array stuff.

I took note of the status of the PR before the interactive rebasing adventure: 27 commits, +169 −158
then after doing the squasing/merge conflict resolution the PR now shows: 17 commits, +169 −158

That looks about right I think, a bit unfortunate that a backport got interwoven or I could have condensed even more, but that's a reduction by 10.

rgommers · 2023-06-16T08:23:38Z

LGTM now, thanks @tylerjereddy. In it goes. The hang on CirrusCI is unrelated; there's one doc warning which seems to be due to a new version of Matplotlib. That's not blocking for the release, let's deal with that in main.

dschult and others added 11 commits June 13, 2023 16:31

MAINT: io: replace isspmatrix with issparse in mmio module (scipy#18556)

c66dade

[skip ci]

DOC: Fix sidebar for API reference pages (scipy#18596)

0fbdecf

CI: fix wheel upload to anaconda [wheel build] (scipy#18598)

5325ccb

[skip actions] [skip circle]

DEP: fix typo of module name in deprecation warning (scipy#18608)

5acc007

Mark void functions as noexcept in _rotation.pyx

905dc2e

MAINT: stats.truncnorm/stats.betaprime: fix _munp for higher moments,…

60b438a

… add tests

ENH: stats.betaprime._munp: override for arbitrary order

246d716

MAINT: fix 'no such option' error in build_scipy CI (scipy#18657)

5291233

TST: fix two test failures that showed up on conda-forge

e971d05

The ppc64le one is a small test bump. The PyPy-on-Windows one is a real bug in PyPy, but it's not planned to be fixed any time soon, so the test is xfail-ed here. Closes scipygh-18632 [skip circle] [skip cirrus]

DOC:sobol_indices: correct statement about sums of Sobol' indices (s…

191a110

…cipy#18659) Co-authored-by: Pamphile Roy <roy.pamphile@gmail.com>

DOC: update relnotes

5792643

* update the SciPy 1.11.0 release notes following a set of RC2 backports

tylerjereddy added the maintenance Items related to regular maintenance tasks label Jun 13, 2023

tylerjereddy added this to the 1.11.0 milestone Jun 13, 2023

tylerjereddy requested review from tupui, larsoner, andyfaff and ilayn as code owners June 13, 2023 23:11

github-actions bot added scipy.io scipy.optimize scipy.signal scipy.spatial scipy.special scipy.stats labels Jun 13, 2023

rgommers self-requested a review as a code owner June 14, 2023 07:40

rgommers force-pushed the treddy_1_11_rc2_prep branch from ae47882 to e8614d1 Compare June 14, 2023 08:23

rgommers mentioned this pull request Jun 14, 2023

MAINT: shims/notes for NumPy 1.24.0 #17630

Closed

rgommers mentioned this pull request Jun 14, 2023

TST: linalg: improve seeding of some tests that are a problem on musllinux #18677

Merged

tupui approved these changes Jun 14, 2023

View reviewed changes

mckib2 and others added 2 commits June 14, 2023 10:27

MAINT: stats: remove long double support for all boost ufuncs (scipy#…

536510e

…18630) [skip ci] --------- Co-authored-by: Ralf Gommers <ralf.gommers@gmail.com>

BUG: small shim for release process

dfdc43f

* Fixes scipy#18595 * use `git apply` to directly apply the patch from scipygh-18595 that worked during the RC1 phase of current release cycle; I'll skip the CI--it isn't tested there which is why the patch is needed in the first place [skip ci]

mdhaber mentioned this pull request Jun 14, 2023

DOC: update release notes for scipy.stats tylerjereddy/scipy#73

Merged

ilayn approved these changes Jun 14, 2023

View reviewed changes

mdhaber requested changes Jun 14, 2023

View reviewed changes

jjerphan mentioned this pull request Jun 14, 2023

DOC: suggestions for scipy.sparse release notes tylerjereddy/scipy#74

Merged

rgommers approved these changes Jun 15, 2023

View reviewed changes

tylerjereddy and others added 3 commits June 15, 2023 20:25

BUG: signal: fix detrend with array-like bp (scipy#18676)

9c1d262

DOC: update 1.11.0 relnotes

08dc19a

* release notes updates after another backport to 1.11.0rc2 PR

tylerjereddy force-pushed the treddy_1_11_rc2_prep branch from 64b5cfe to 08dc19a Compare June 16, 2023 02:26

rgommers merged commit a41ac77 into scipy:maintenance/1.11.x Jun 16, 2023
17 of 18 checks passed

tylerjereddy deleted the treddy_1_11_rc2_prep branch June 16, 2023 15:36

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MAINT: backports for 1.11.0rc2 #18671

MAINT: backports for 1.11.0rc2 #18671

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MAINT: backports for 1.11.0rc2 #18671

MAINT: backports for 1.11.0rc2 #18671

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