[padix-key]

import biotite.structure currently fails on main with NameError: name 'Any' is not defined.
#1012 removed the typing.Any import from structure/filter.py, while #1017 added a new annotation using Any.
Both PRs passed CI on their own, but their merge result does not.

Checked locally on main + this fix: ruff, ruff format, pyright, numpydoc and the test suite (11224 passed; the only failures are the local mmseqs binary version and the local version.py).

Authored by Claude

[codspeed]

Merging this PR will improve performance by 91.09%

1 warning

⚠️ 16 benchmarks with a significant change ran on different hardware

Their base and head results were measured on machines with a different CPU, core count or memory, so the changes might not come from the code. Run base and head on the same runner type.

Learn more about Macro Runners

See affected benchmarks

⚡ 16 improved benchmarks
✅ 93 untouched benchmarks
🆕 2 new benchmarks
⏩ 14 skipped benchmarks¹

Performance Changes

	Benchmark	BASE	HEAD	Efficiency
⚡	benchmark_find_rotatable_bonds	177.1 ms	26.8 ms	×6.6
⚡	benchmark_superimpose[superimpose]	3,198.9 µs	651.8 µs	×4.9
⚡	benchmark_hbond	29.7 ms	10.1 ms	×2.9
⚡	benchmark_similar_kmers	483 µs	200.5 µs	×2.4
⚡	benchmark_superimpose_multi_model[superimpose]	14.4 ms	6.4 ms	×2.3
⚡	benchmark_get_assembly	1,594.7 ms	835.6 ms	+90.84%
⚡	benchmark_superimpose[superimpose_homologs]	60.6 ms	33.5 ms	+80.65%
⚡	benchmark_score_threshold_rule[11*11*1*1***111]	3.3 s	1.9 s	+70.74%
⚡	benchmark_score_threshold_rule[None]	3.3 s	1.9 s	+70.64%
⚡	benchmark_superimpose_multi_model[superimpose_homologs]	74.2 ms	44.7 ms	+65.87%
⚡	benchmark_superimpose[superimpose_without_outliers]	31.9 ms	20.8 ms	+52.95%
⚡	benchmark_match_kmer_selection[KmerTable-None]	642.6 µs	525.3 µs	+22.32%
⚡	benchmark_superimpose[superimpose_structural_homologs]	53.4 ms	44.8 ms	+19.1%
⚡	benchmark_set_structure[bcif-True]	39 ms	32.8 ms	+19%
⚡	benchmark_match[KmerTable-None]	739.6 µs	626.7 µs	+18.02%
⚡	benchmark_set_structure[bcif-False]	17.7 ms	15.1 ms	+16.81%
🆕	benchmark_stack[10]	N/A	6.7 ms	N/A
🆕	benchmark_stack[2]	N/A	2 ms	N/A

Tip

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_{Comparing padix-key:fix/filter-any-import (57ea941) with main (81df912)²}

Footnotes

1. 14 benchmarks were skipped, so the baseline results were used instead. If they were deleted from the codebase, click here and archive them to remove them from the performance reports. ↩

2. No successful run was found on main (d690a09) during the generation of this report, so 81df912 was used instead as the comparison base. There might be some changes unrelated to this pull request in this report. ↩