Use NumPy 2.0 API

[padix-key]

Resolves #919

[codspeed]

Merging this PR will improve performance by 62.64%

⚠️ Different runtime environments detected

Some benchmarks with significant performance changes were compared across different runtime environments,
which may affect the accuracy of the results.

Open the report in CodSpeed to investigate

⚡ 7 improved benchmarks
❌ 1 (👁 1) regressed benchmark
✅ 101 untouched benchmarks
⏩ 14 skipped benchmarks¹

Performance Changes

	Benchmark	BASE	HEAD	Efficiency
⚡	benchmark_set_structure[cif-False]	92.9 ms	31.7 ms	×2.9
⚡	benchmark_set_structure[cif-True]	103.5 ms	41.8 ms	×2.5
⚡	benchmark_connect[connect_via_distances]	3.2 ms	1.7 ms	+87.43%
⚡	benchmark_serialize_pdbx[cif]	177.7 ms	120.5 ms	+47.45%
⚡	benchmark_infer_bond_types	1,203 µs	822.1 µs	+46.33%
⚡	benchmark_set_structure	9.4 ms	6.8 ms	+38.04%
⚡	benchmark_set_structure_with_bonds	9.6 ms	7.1 ms	+36.38%
👁	benchmark_match_kmer_selection[KmerTable-None]	246.2 µs	277.3 µs	-11.23%

Tip

Curious why performance improved? Comment @codspeedbot explain why performance improved on this PR, or directly use the CodSpeed MCP with your agent.

---

_{Comparing padix-key:issue-919 (9059962) with main (1aaf784)}

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. ↩