API: Cleaning `numpy/init.py` and main namespace - Part 4 [NEP 52] #24445

mtsokol · 2023-08-18T10:49:44Z

~~Follow-up PR after #24376 is merged.~~ Can be merged independently.
Relevant issue: #24306.

Scope of the PR:

Deprecate row_stack (an alias for vstack) to be removed completely in 2.0
Deprecate trapz in favor of scipy.interpolate.trapezoid (scipy uses trapz implementation, therefore it must be moved there)
Deprecate in1d (instead use isin) and make in1d private in 2.0

Part of matplotlib#26422, xref numpy/numpy#24445

ngoldbaum

Overall looks great, just a couple comments.

numpy/lib/tests/test_arraysetops.py

ngoldbaum

LGTM. I see scipy/scipy#19100 got merged, are there other downstream PRs we should wait to get merged before this does?

mtsokol · 2023-08-22T18:23:44Z

LGTM. I see scipy/scipy#19100 got merged, are there other downstream PRs we should wait to get merged before this does?

There are still usages of them in SciPy and Pandas, I will create PRs shortly.

[EDIT] Done for Pandas, SciPy and scikit-learn. For matplotlib a draft PR was already created.

* replace deprecated `in1d` with `isin` calls per numpy/numpy#24445, as part of effort to remain NumPy `2.0` compliant * the testsuite seems happy locally--if there are any cases where `in1d` was potentially receiving arrays with `ndim > 1`, we may want to add `ravel()` to the outputs in these replacements just to be safe, but I've assumed the testsuite has us covered * for now, I've intentionally not adjusted the docstring of our Cython `_in2d`, which refers to `in1d`; seems less critical for now

tylerjereddy

The diff seems sensible to be me as well (there was some desire for a non-Quansight reviewer as well in last meeting).

I did wonder a little bit about whether it makes sense to delete the tests for i.e., trapz before the function is completely removed vs. suppressing the deprecation warnings on those tests until trapz disappears for good.

Downstream reception to the patches seems "ok" enough. I also opened a cross-listed PR to NumFOCUS project MDAnalysis and they seemed alright with it as well.

* MAINT: in1d -> isin * replace deprecated `in1d` with `isin` calls per numpy/numpy#24445, as part of effort to remain NumPy `2.0` compliant * the testsuite seems happy locally--if there are any cases where `in1d` was potentially receiving arrays with `ndim > 1`, we may want to add `ravel()` to the outputs in these replacements just to be safe, but I've assumed the testsuite has us covered * for now, I've intentionally not adjusted the docstring of our Cython `_in2d`, which refers to `in1d`; seems less critical for now * DOC: PR 4255 revisions * add an appropriate `CHANGELOG` entry per reviewer request * Update package/CHANGELOG --------- Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>

mtsokol · 2023-08-28T10:10:42Z

I did wonder a little bit about whether it makes sense to delete the tests for i.e., trapz before the function is completely removed vs. suppressing the deprecation warnings on those tests until trapz disappears for good.

@tylerjereddy I can reintroduce TestTrapz if needed - should I add them? The implementation with tests was already moved to SciPy.

ngoldbaum · 2023-08-28T16:00:36Z

I think keeping the tests for deprecated code around is worthwhile, the marginal cost of running a unit test is low and it's possible superficially unrelated code changes could break deprecated functionality and it would be nice to be aware of that.

mtsokol · 2023-08-28T16:23:14Z

I think keeping the tests for deprecated code around is worthwhile, the marginal cost of running a unit test is low and it's possible superficially unrelated code changes could break deprecated functionality and it would be nice to be aware of that.

Makes sense to me - I reintroduced trapz tests with a deprecation warnings filter.

rgommers · 2023-09-05T18:37:54Z

@mtsokol would you mind fixing the merge conflict?

mtsokol · 2023-09-05T19:15:34Z

@mtsokol would you mind fixing the merge conflict?

@rgommers Sure! Rebased.

rgommers

LGTM, this has been in the queue for 2 weeks, and it looks solid. In it goes, thanks @mtsokol!

pllim · 2023-09-07T16:01:01Z

numpy/lib/_function_base_impl.py

@@ -4880,6 +4883,14 @@ def trapz(y, x=None, dx=1.0, axis=-1):
    >>> np.trapz(a, axis=1)
    array([2.,  8.])
    """
+
+    # Deprecated in NumPy 2.0, 2023-08-18
+    warnings.warn(


This will affect a lot of analysis code... not just developers, but users.

FWIW, we did that same rename in scipy.integrate a few years ago, and got no complaints. This name is considered a slur, and that's an extra reason to get rid of it. We touched on this in the 2.0 dev call IIRC, and folks were in favor of names that are both more descriptive and more inclusive (cumsum & co too).

It's deprecated rather than outright removed here exactly because it's used quite a bit. So no code will actually break in the 2.0 release.

Huh, didn't know it's a slur. Thanks for the clarification!

Neither did I until scipy/scipy#12924.

charris · 2023-09-07T18:16:32Z

Never heard/read it myself. Lots of things can become slurs when it is convenient.

xref numpy#24445

ntessore · 2024-01-09T11:03:46Z

I don't know which issue, or even venue, is appropriate for this, but can I please register the strongest possible objection to removing the trapezoidal rule entirely from numpy, and relying on scipy? It is such a fundamental and common operation, that it would be an immense downside having to depend on scipy just for this.

rgommers · 2024-01-09T11:33:59Z

@ntessore could you please open a new issue instead? That way it's easier to discover and discuss. Expanding a little on the impact would be useful too (e.g., number of places it's used which don't already depend on SciPy).

This PR adds back the links that were removed from `trapz` in PR numpy#24445, finishing the migration to `trapezoid` in PR numpy#25738. Currently, no web docs appear for `trapezoid`.

This PR adds back the links that were removed from `trapz` in PR numpy#24445, finishing the migration to `trapezoid` in PR numpy#25738. Currently, no web docs appear for `trapezoid`. [skip actions] [skip azp] [skip cirrus]

mtsokol force-pushed the overhaul-of-main-namespace-part-4 branch from b812dfd to 35e072c Compare August 18, 2023 10:50

mtsokol changed the title ~~Overhaul of main namespace part 4~~ API: Cleaning numpy/__init__.py and main namespace - Part 4 [NEP 52] Aug 18, 2023

mtsokol force-pushed the overhaul-of-main-namespace-part-4 branch 2 times, most recently from fea696e to f9fd36d Compare August 21, 2023 10:35

ksunden mentioned this pull request Aug 21, 2023

MAINT: Numpy 2.0 deprecations for row_stack and in1d matplotlib/matplotlib#26566

Merged

1 task

ksunden added a commit to ksunden/matplotlib that referenced this pull request Aug 21, 2023

MAINT: Numpy 2.0 deprecations for row_stack and in1d

ef5689f

Part of matplotlib#26422, xref numpy/numpy#24445

ngoldbaum reviewed Aug 21, 2023

View reviewed changes

numpy/lib/tests/test_arraysetops.py Outdated Show resolved Hide resolved

numpy/lib/tests/test_arraysetops.py Show resolved Hide resolved

mtsokol requested a review from ngoldbaum August 22, 2023 15:49

ngoldbaum approved these changes Aug 22, 2023

View reviewed changes

This was referenced Aug 22, 2023

MAINT: Remove usages of np.row_stack and np.in1d scipy/scipy#19110

Merged

MAINT: Remove np.in1d function calls pandas-dev/pandas#54694

Merged

tylerjereddy mentioned this pull request Aug 22, 2023

MAINT: in1d -> isin MDAnalysis/mdanalysis#4255

Merged

This was referenced Aug 23, 2023

MAINT: Remove np.in1d and np.trapz usages scikit-learn/scikit-learn#27140

Merged

ENH: Reflect changes from numpy namespace refactor Part 4 jax-ml/jax#17244

Closed

mtsokol force-pushed the overhaul-of-main-namespace-part-4 branch from bebb3a2 to 732e6d5 Compare August 24, 2023 21:34

tylerjereddy added 30 - API 62 - Python API Changes or additions to the Python API. Mailing list should usually be notified. Numpy 2.0 API Changes labels Aug 25, 2023

tylerjereddy reviewed Aug 25, 2023

View reviewed changes

mtsokol force-pushed the overhaul-of-main-namespace-part-4 branch from 48ca8f8 to 448dd0d Compare August 28, 2023 10:01

mtsokol force-pushed the overhaul-of-main-namespace-part-4 branch from 0dfc32f to 41639e4 Compare August 28, 2023 10:33

mtsokol requested a review from tylerjereddy August 29, 2023 11:43

mtsokol self-assigned this Aug 29, 2023

mtsokol force-pushed the overhaul-of-main-namespace-part-4 branch from 41f19fa to c60bdc6 Compare August 30, 2023 09:39

mtsokol force-pushed the overhaul-of-main-namespace-part-4 branch 2 times, most recently from 2bb6fcd to 4f5b772 Compare September 1, 2023 10:37

rgommers added this to the 2.0.0 release milestone Sep 1, 2023

mtsokol added 9 commits September 5, 2023 21:03

ENH: Deprecate in1d, trapz, row_stack [skip ci]

f36df8f

MAINT: Move in1d implementation to a private function

5819ecf

Remove irrelevant comment

be17070

Add changelog file

475a492

Extend expired attributes

099a139

Tweak release note file

31cfe27

Reintroduce trapz tests

b438a7e

Fix after rebase

da1c585

Remove redundant variable

bf91c88

mtsokol force-pushed the overhaul-of-main-namespace-part-4 branch from 4f5b772 to bf91c88 Compare September 5, 2023 19:03

rgommers approved these changes Sep 5, 2023

View reviewed changes

rgommers merged commit 2f0bd6e into numpy:main Sep 5, 2023

mtsokol deleted the overhaul-of-main-namespace-part-4 branch September 5, 2023 19:58

neutrinoceros mentioned this pull request Sep 6, 2023

BUG: fix an incompatibility with numpy 2.0 (np.trapz and np.in2d are deprecated) yt-project/unyt#445

Merged

pllim mentioned this pull request Sep 6, 2023

TST: devdeps failing with numpy-dev failures from mpl astropy/astropy#15283

Closed

pllim reviewed Sep 7, 2023

View reviewed changes

pllim mentioned this pull request Sep 7, 2023

MNT: NumPy 2.0 compatibility spacetelescope/synphot_refactor#362

Closed

BvB93 added a commit to BvB93/numpy that referenced this pull request Dec 21, 2023

TYP: Remove trapz, in1d and row_stack leftovers

476d3d8

xref numpy#24445

BvB93 added a commit to BvB93/numpy that referenced this pull request Dec 21, 2023

TYP: Remove trapz, in1d and row_stack leftovers

97623ce

xref numpy#24445

bmwoodruff mentioned this pull request Jun 8, 2024

DOC: Enable web docs for numpy.trapezoid and add back links #26645

Merged

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

API: Cleaning `numpy/init.py` and main namespace - Part 4 [NEP 52] #24445

API: Cleaning `numpy/init.py` and main namespace - Part 4 [NEP 52] #24445

mtsokol commented Aug 18, 2023 •

edited

Loading

ngoldbaum left a comment

ngoldbaum left a comment

mtsokol commented Aug 22, 2023 •

edited

Loading

tylerjereddy left a comment

mtsokol commented Aug 28, 2023

ngoldbaum commented Aug 28, 2023

mtsokol commented Aug 28, 2023

rgommers commented Sep 5, 2023

mtsokol commented Sep 5, 2023 •

edited

Loading

rgommers left a comment

pllim Sep 7, 2023

rgommers Sep 7, 2023

pllim Sep 7, 2023

rgommers Sep 7, 2023 •

edited

Loading

charris commented Sep 7, 2023

ntessore commented Jan 9, 2024

rgommers commented Jan 9, 2024

API: Cleaning numpy/__init__.py and main namespace - Part 4 [NEP 52] #24445

API: Cleaning numpy/__init__.py and main namespace - Part 4 [NEP 52] #24445

Conversation

mtsokol commented Aug 18, 2023 • edited Loading

ngoldbaum left a comment

Choose a reason for hiding this comment

ngoldbaum left a comment

Choose a reason for hiding this comment

mtsokol commented Aug 22, 2023 • edited Loading

tylerjereddy left a comment

Choose a reason for hiding this comment

mtsokol commented Aug 28, 2023

ngoldbaum commented Aug 28, 2023

mtsokol commented Aug 28, 2023

rgommers commented Sep 5, 2023

mtsokol commented Sep 5, 2023 • edited Loading

rgommers left a comment

Choose a reason for hiding this comment

pllim Sep 7, 2023

Choose a reason for hiding this comment

rgommers Sep 7, 2023

Choose a reason for hiding this comment

pllim Sep 7, 2023

Choose a reason for hiding this comment

rgommers Sep 7, 2023 • edited Loading

Choose a reason for hiding this comment

charris commented Sep 7, 2023

ntessore commented Jan 9, 2024

rgommers commented Jan 9, 2024

API: Cleaning `numpy/init.py` and main namespace - Part 4 [NEP 52] #24445

API: Cleaning `numpy/init.py` and main namespace - Part 4 [NEP 52] #24445

mtsokol commented Aug 18, 2023 •

edited

Loading

mtsokol commented Aug 22, 2023 •

edited

Loading

mtsokol commented Sep 5, 2023 •

edited

Loading

rgommers Sep 7, 2023 •

edited

Loading