feat(panel): validate hashing marker ids and keep collapsed bases

[Aratz]

Summary

• Hashing marker ids must have a numeric suffix, must not nest, and must not duplicate another marker id.
• Sample calling keeps a collapsed hashing base in the count matrix when that base is not itself on the panel.
• The isotype mask is taken from the panel, because that collapsed base has no control value in var.
• First panel pull request in the stack. The panel-sources pull request is based on this branch.

Test plan

• CI passes (ruff, ruff format, mypy, pytest)
• Duplicate marker ids and nested hashing suffixes are rejected
• Sample calling keeps a collapsed base that the panel does not define

Made with Cursor

[cursor]

Stale Bugbot comment from a previous run.

[cursor]

Collapsed bases break panel reload

Medium Severity

Sample calling now keeps a collapsed hashing base in var when that id is not a panel row, so control and sequences are missing. PNAAntibodyPanel.from_adata treats every var row as a panel marker, and validation then fails. Denoise reloads the panel from the pxl file and only catches KeyError, so a dehashed file with an extra collapsed base crashes that step.

Additional Locations (1)

• src/pixelator/pna/config/panel.py#L173-L206

 

^{Reviewed by Cursor Bugbot for commit e475f94. Configure here.}

[elhb]

lets ignore this bugbot comment, wont apply once we merge the stack

[cursor]

Cursor Bugbot has reviewed your changes using high effort and found 1 potential issue.

There are 2 total unresolved issues (including 1 from previous review).

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^{Reviewed by Cursor Bugbot for commit 3e00755. Configure here.}

[cursor]

Off-panel markers break panel reload

Medium Severity

pna_edgelist_to_anndata can now put collapsed hashing bases that are not on the panel into var. add_panel_information left-joins those rows, so control and sequences become missing. from_adata then treats every var row as a panel row and validation fails, so from_pxl_dataset cannot reload a dehashed file that kept an off-panel base.

Additional Locations (2)

• src/pixelator/pna/config/panel/antibody_panel.py#L162-L167
• src/pixelator/pna/sample_calling/__init__.py#L249-L258

 

^{Reviewed by Cursor Bugbot for commit 3e00755. Configure here.}