Handle mixed CDR3 lengths in logoplots

[AtharvaKatiyar]

Summary

Fixes #691.

pl.logoplot_cdr3_motif now handles mixed CDR3 sequence lengths by automatically creating one logo subplot per detected length.

Changes

• Group CDR3 sequences by length before calling alignment_to_matrix.
• Keep existing behavior for equal-length input (returns a single logomaker.Logo).
• For mixed lengths, auto-create stacked subplots and return list[logomaker.Logo].
• Raise clear ValueError when mixed lengths are provided with a single user-supplied ax.

Validation

• pytest -q src/scirpy/tests/test_plotting.py -k logoplot
• pytest -q (983 passed, 2 deselected)

[Copilot]

Pull request overview

This PR fixes scirpy issue #691 by enabling pl.logoplot_cdr3_motif to handle mixed CDR3 sequence lengths: it now splits sequences by length and renders one logo plot per detected length instead of failing.

Changes:

• Group CDR3 sequences by length and generate one logo plot per length when mixed lengths are present.
• Preserve existing single-length behavior (returning a single logomaker.Logo) and return list[logomaker.Logo] only for mixed lengths.
• Add tests for mixed-length behavior and for the error raised when a single user-supplied ax is provided with mixed lengths.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File	Description
src/scirpy/pl/_logoplots.py	Implements length-splitting logic, multi-subplot rendering, updated return type, and a clearer error for ax misuse.
src/scirpy/tests/test_plotting.py	Adds regression tests covering mixed-length return type and the single-ax error path.

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[Copilot]

sequence_list can be empty (e.g., when the selected chains/cdr3_col are all missing after subsetting). In that case n_lengths becomes 0 and the function falls through to plt.subplots(n_lengths, ...), which will raise a low-level Matplotlib error (nrows must be > 0). Add an explicit check for no sequences and raise a clear ValueError (e.g., "No CDR3 sequences found for the selected chains/column").

Suggested change

	n_lengths = len(sequences_by_length)
	n_lengths = len(sequences_by_length)
	if n_lengths == 0:
	raise ValueError("No CDR3 sequences found for the selected chains/column")

[Copilot]

The docstring says fig_kws is passed to matplotlib.pyplot.figure, but this function uses _init_ax(fig_kws) / plt.subplots(..., **fig_kws) (and _init_ax itself wraps plt.subplots). Please update the parameter description to match the actual call site (i.e. plt.subplots/figure creation kwargs) so users know which keys are supported.

Suggested change

	Parameters passed to the :func:`matplotlib.pyplot.figure` call
	if no `ax` is specified.
	Parameters passed to the axes/figure creation call via
	:func:`matplotlib.pyplot.subplots` if no `ax` is specified.

[codecov]

Codecov Report

❌ Patch coverage is 0% with 32 lines in your changes missing coverage. Please review.
✅ Project coverage is 19.18%. Comparing base (2ce57d1) to head (0b12a3a).

Files with missing lines	Patch %	Lines
src/scirpy/pl/_logoplots.py	0.00%	32 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #692      +/-   ##
==========================================
- Coverage   19.30%   19.18%   -0.13%     
==========================================
  Files          51       51              
  Lines        4636     4655      +19     
==========================================
- Hits          895      893       -2     
- Misses       3741     3762      +21     

Files with missing lines	Coverage Δ
src/scirpy/pl/_logoplots.py	21.15% <0.00%> (-12.18%)	⬇️

... and 1 file with indirect coverage changes

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