[padix-key]

Since #949 plot_sequence_logo() only accepts a color scheme name or a ColorScheme, but rbs_identification.py still passes a plain list of colors, which makes the full documentation build fail with TypeError: Expected a color scheme name or 'ColorScheme', but got 'list'.

The other gallery fixes found in the same documentation build are in #964, which targets main.

[codspeed]

Merging this PR will regress 2 benchmarks

⚡ 13 improved benchmarks
❌ 2 regressed benchmarks
✅ 94 untouched benchmarks
⏩ 14 skipped benchmarks¹

Warning

Please fix the performance issues or acknowledge them on CodSpeed.

Performance Changes

	Benchmark	BASE	HEAD	Efficiency
❌	benchmark_structural_alphabet_methods[to_protein_blocks]	6.7 ms	10 ms	-32.79%
❌	benchmark_match_kmer_selection[KmerTable-11*11*1*1***111]	244.4 µs	276.5 µs	-11.61%
⚡	benchmark_set_structure[cif-False]	93 ms	31.7 ms	×2.9
⚡	benchmark_set_structure[cif-True]	103.4 ms	41.8 ms	×2.5
⚡	benchmark_connect[connect_via_distances]	3.2 ms	1.7 ms	+86.27%
⚡	benchmark_superimpose_multi_model[superimpose]	9 ms	5.6 ms	+60.76%
⚡	benchmark_superimpose[superimpose]	2 ms	1.3 ms	+56.55%
⚡	benchmark_serialize_pdbx[cif]	178.2 ms	121.4 ms	+46.77%
⚡	benchmark_infer_bond_types	1,202.5 µs	829.2 µs	+45.01%
⚡	benchmark_clustering[neighbor_joining]	556.6 µs	394.9 µs	+40.96%
⚡	benchmark_set_structure	9.4 ms	6.9 ms	+36%
⚡	benchmark_set_structure_with_bonds	9.7 ms	7.2 ms	+35.45%
⚡	benchmark_match_kmer_selection[KmerTable-None]	278 µs	244.8 µs	+13.55%
⚡	benchmark_superimpose_multi_model[superimpose_homologs]	36.1 ms	32.1 ms	+12.49%
⚡	benchmark_match[KmerTable-None]	326.8 µs	294.2 µs	+11.06%

Tip

Investigate this regression by commenting @codspeedbot fix this regression on this PR, or directly use the CodSpeed MCP with your agent.

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_{Comparing padix-key:color-scheme-example (83b9dc5) with main (78a2c93)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 v2 (eeb3637) during the generation of this report, so main (78a2c93) was used instead as the comparison base. There might be some changes unrelated to this pull request in this report. ↩