Added transformation return to orient_principal_components

[nablacart]

Modified transform.orient_principal_components to return an AffineTransformation of centering translation and cumulative rotation to align with specified axes, in addition to transformed coordinates. Updated tests to reflect changes.

Returning the transformation allows for downstream alignment to a specific component of the input structure.

Validated with:

• pixi run -e test test tests/structure/test_transform.py -q: 1135 passed

[padix-key]

I think this is a good idea 👍. However it changes the function signature, so it would put this into the biotite v2 release (which is already planned after the next release).

Otherwise, I left a minor review comment

[padix-key]

As we have a AffineTransformation at hand now, I see no reason to carry centered around. Instead we can simply

return transform.apply(atoms), transform

[padix-key]

I'll change the target branch to v2. Could you rebase your branch on it?

[padix-key]

If I see correctly you merged previous PRs from v2 into this one instead of rebasing, right? Could you instead run git rebase -i v2 and only keep the commits relevant to this PR?

[codspeed-hq]

Merging this PR will degrade performance by 12.43%

⚡ 1 improved benchmark
❌ 5 regressed benchmarks
✅ 97 untouched benchmarks
⏩ 17 skipped benchmarks¹

Warning

Please fix the performance issues or acknowledge them on CodSpeed.

Performance Changes

	Benchmark	BASE	HEAD	Efficiency
❌	benchmark_superimpose[superimpose_without_outliers]	13.5 ms	16.8 ms	-19.3%
❌	benchmark_superimpose[superimpose]	2 ms	2.4 ms	-17.66%
❌	benchmark_cell_list_compute_contacts[PAIRS]	15.8 ms	19.1 ms	-17.08%
❌	benchmark_cell_list_compute_contacts[MAPPING]	15.9 ms	19.2 ms	-17%
❌	benchmark_cell_list_compute_contacts[MASK]	18.5 ms	21.2 ms	-12.63%
⚡	benchmark_match_kmer_selection[KmerTable-11*11*1*1***111]	276.4 µs	245 µs	+12.83%

Tip

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

---

_{Comparing nablacart:orient_pc_return_transform (a2b02f4) with main (d9e7f49)²}

Footnotes

1. 17 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 (1b203c7) during the generation of this report, so main (d9e7f49) was used instead as the comparison base. There might be some changes unrelated to this pull request in this report. ↩

[nablacart]

If I see correctly you merged previous PRs from v2 into this one instead of rebasing, right? Could you instead run git rebase -i v2 and only keep the commits relevant to this PR?

My apologies, I am inexperienced with contributing from a fork instead of a branch. I did rebase on v2 but may have done so incorrectly, so I'll revert and try again.

[padix-key]

No worries, if you prefer I can also rerun the rebase (although I am not sure if GitHub allows me force-pushing to your branch afterwards)