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CI: enable codspeed for Python #3262

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Follow-up on #3231 with Python perf tracking.

This uses pytest-benchmark instead of asv, but I'm still not sure that's a good idea, because pytest-benchmark doesn't track memory usage as asv does.

update benchmarks

port ASV time benchmarks to pytest-benchmark, keep memory usage ones for now

simplify benchmarks

run codspeed for python

[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

add tox installation
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codecov bot commented Jul 25, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.74%. Comparing base (f621726) to head (19a0ccd).

Additional details and impacted files
@@           Coverage Diff           @@
##           latest    #3262   +/-   ##
=======================================
  Coverage   86.73%   86.74%           
=======================================
  Files         136      136           
  Lines       15871    15871           
  Branches     2728     2728           
=======================================
+ Hits        13766    13767    +1     
+ Misses       1796     1795    -1     
  Partials      309      309           
Flag Coverage Δ
hypothesis-py 25.40% <ø> (ø)
python 92.37% <ø> (ø)
rust 62.18% <ø> (+0.03%) ⬆️

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codspeed-hq bot commented Jul 25, 2024

CodSpeed Performance Report

Merging #3262 will create unknown performance changes

Comparing lirber/codspeed_python (19a0ccd) with latest (f621726)

Summary

⁉️ 21 dropped benchmarks

⚠️ Please fix the performance issues or acknowledge them on CodSpeed.

Benchmarks breakdown

Benchmark latest lirber/codspeed_python Change
⁉️ force with valid kmers 13.9 ms N/A N/A
⁉️ invalid kmers 10.3 ms N/A N/A
⁉️ lowercase 13.9 ms N/A N/A
⁉️ valid 13.9 ms N/A N/A
⁉️ force with valid kmers 396.4 ms N/A N/A
⁉️ invalid kmers 396.8 ms N/A N/A
⁉️ lowercase 396.3 ms N/A N/A
⁉️ valid 396.4 ms N/A N/A
⁉️ abund0_ani_ci0 560.5 µs N/A N/A
⁉️ abund0_ani_ci1 581.5 µs N/A N/A
⁉️ abund1_ani_ci0 770.9 µs N/A N/A
⁉️ abund1_ani_ci1 793.5 µs N/A N/A
⁉️ intersection 18.2 µs N/A N/A
⁉️ intersection_size 15.4 µs N/A N/A
⁉️ large intersection 9.1 ms N/A N/A
⁉️ large intersection btree 18 ms N/A N/A
⁉️ large intersection_size 7.5 ms N/A N/A
⁉️ large intersection_size btree 17.8 ms N/A N/A
⁉️ load nodegraph 187 µs N/A N/A
⁉️ save compressed nodegraph 1.4 ms N/A N/A
... ... ... ... ...

ℹ️ Only the first 20 benchmarks are displayed. Go to the app to view all benchmarks.

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