Remove Numba as a dependency #2841

namurphy · 2024-08-28T17:12:27Z

Description

The purpose of this pull request is to test out dropping Numba as a dependency by dropping the numba.njit decorator from two formulary lite-functions. The lite-functions still exist as minimal functions that operate on NumPy arrays without any validations.

Motivation

It often takes Numba ∼3–5 months before it becomes compatible with a new release of Python each October. Depending on Numba has the following adverse consequences:

PlasmaPy is not able to run on the newest version of Python for a period of ∼3–5 months after the release of a new version of Python.
Packages that depend on PlasmaPy (like fiasco) likewise cannot be run on the newest version of Python for ∼3–5 months after a release.
The test suite for PlasmaPy cannot be run on release candidates for a new version of Python.

I did some timings (reported in this comment) and found that the performance gains from using Numba are ∼1–3% for the charged particle radiography tests, and that our full test suite runs ∼1% quicker without a Numba dependency.

My view is that we get enough performance gains from dropping units and validations for the lite-functions, and that the drawbacks from depending on Numba are much more significant than the slight performance gains.

Alternatives

I've been hoping we could Cythonize the lite functions so that we could drop the Numba dependency. However, we haven't had the capacity to complete this.

Related issues and pull requests

Closes #1342.

Related to #1098, #1145, #2104, #2256, #2372, #2634, #2786.

codecov · 2024-08-28T17:30:35Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.33%. Comparing base (1385eb4) to head (1b41756).
Report is 52 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2841      +/-   ##
==========================================
- Coverage   95.12%   94.33%   -0.79%     
==========================================
  Files         107      107              
  Lines        9617     9621       +4     
  Branches     2226     2228       +2     
==========================================
- Hits         9148     9076      -72     
- Misses        280      350      +70     
- Partials      189      195       +6

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namurphy · 2024-08-28T17:39:22Z

I ran the full test suite locally on my workstation with nox -s 'tests-all(3.12)' for both the main and denumbafy branches (with and without Numba, respectively). The overall test suite was a little bit quicker without Numba, while synthetic charged particle radiography tests were generally slightly slower.

test	`main` (with Numba)	`denumbafy` (without Numba)
Full suite	77.83	76.80 (-1%)
test_add_wire_mesh	18.97	19.14 (+1%)
test_multiple_grids	14.01	14.44 (+3%)
test_multiple_grids2	13.44	13.77 (+2%)
test_1D_deflections	3.40	3.35 (-1.5%)
test_run_options	2.40	2.38 (-1%)

namurphy · 2024-08-28T22:06:57Z

I did some timings to check the performance of jitted and non-jitted versions of plasma_frequency_lite. The relative differences in performance are high, but the absolute differences remain quite low.

inputs	jitted	not-jitted	absolute difference
floats	295 ns	772 ns	$4.77 × 10^{-7}$ s
1000-element arrays	3.22 μs	5.72 μs	$2.5 × 10^{-6}$ s
100000-element arrays	226 μs	366 μs	$1.4 × 10^{-4}$ s
10000000-element arrays	29.2 ms	77 ms	$0.04$ s

StanczakDominik

Alas, so it is. Perhaps Numba's still better for end users instead of libraries 🫡

namurphy · 2024-09-09T16:55:48Z

Alas, so it is. Perhaps Numba's still better for end users instead of libraries 🫡

It really is! Numba is a fantastic package, but the ∼3–5 month delays after a new release of Python outweigh the slight improvements in PlasmaPy's overall performance. The delays are also causing problems for fiasco which depends on PlasmaPy. Plus, depending on Numba also means that we can't test against Python beta releases and release candidates before the official release of Python. Sigh!

Also it is great as always to hear from you! I hope you have been doing really well!

pheuer

I also approve - give the scope of PlasmaPy, I think these minor enhancements from njit are not worth the operational issues. Thanks for running the comprehensive timing comparisons!

namurphy · 2024-09-09T18:16:38Z

Awesome, thank you! I'll go ahead and merge it. I suspect this will make @wtbarnes happy. 🙃

namurphy added 3 commits August 28, 2024 13:01

Remove Numba as a dependency

b9fcd3d

Continue removing Numba

7fe2a10

Remove global substitution for |Numba|

5572dd7

namurphy added the prototype 🏗️ Trying out an implementation on a trial basis label Aug 28, 2024

namurphy added 2 commits August 28, 2024 13:21

Continue removing Numba

3e72fa5

Remove check against py_func

e3ce4e4

namurphy added the run weekly tests in CI Add this label to PRs to additionally run weekly tests. label Aug 28, 2024

namurphy removed the run weekly tests in CI Add this label to PRs to additionally run weekly tests. label Aug 28, 2024

Edit changelog: 2841.internal.rst

6a7635f

github-actions bot added the maintenance General updates to package infrastructure label Aug 28, 2024

StanczakDominik approved these changes Aug 29, 2024

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namurphy mentioned this pull request Sep 5, 2024

Add Python 3.13 to test suite #2850

Closed

namurphy marked this pull request as ready for review September 9, 2024 16:55

namurphy requested review from rocco8773 and a team as code owners September 9, 2024 16:55

namurphy requested a review from pheuer September 9, 2024 16:55

pheuer approved these changes Sep 9, 2024

View reviewed changes

namurphy added 2 commits September 9, 2024 13:30

Merge branch 'main' into denumbafy

9a1def7

nox -s requirements

1b41756

namurphy merged commit 02ac744 into PlasmaPy:main Sep 9, 2024
19 checks passed

namurphy deleted the denumbafy branch September 9, 2024 18:16

github-actions bot removed the prototype 🏗️ Trying out an implementation on a trial basis label Sep 9, 2024

namurphy mentioned this pull request Oct 3, 2024

Include Python 3.13 in continuous integration test suite 🧪 wtbarnes/fiasco#334

Open

namurphy mentioned this pull request Oct 25, 2024

Add Python 3.13 to tests #2869

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Remove Numba as a dependency #2841

Remove Numba as a dependency #2841

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Remove Numba as a dependency #2841

Remove Numba as a dependency #2841

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namurphy commented Aug 28, 2024 • edited Loading

Description

Motivation

Alternatives

Related issues and pull requests

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