Make uei_count optional

[johandahlberg]

Description

Make uei_count optional.

Fixes: pna-3264

Type of change

• New feature (non-breaking change which adds functionality)

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce it when relevant.

PR checklist:

• This comment contains a description of changes (with reason).
• I have performed a self-review of my own code
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• If a new tool or package is included, I have updated dependencies in pyproject.toml and cited it properly
• I have checked my code and documentation and corrected any misspellings
• I have documented any significant changes to the code in CHANGELOG.md

---

Note

Medium Risk
Touches graph statistics and sample-calling SQL paths; absent uei_count will report zero molecules, which could mislead downstream metrics if callers expect real molecule counts.

Overview
uei_count is now optional on PNA edgelists in sample calling and the graph component recovery path, so pipelines can run when that column is missing.

Shared helpers has_uei_count and n_molecules_sql detect the column via DuckDB DESCRIBE and either sum molecules or treat counts as 0. Graph recovery uses this for molecule totals and for create_working_edgelist (synthetic uei_count = 0 when absent). Sample calling omits uei_count from exported edgelists when it was not on the input.

CHANGELOG documents the behavior. Tests cover stats, working edgelist shaping, and end-to-end sample calling without uei_count.

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[ptajvar]

Thank you for the fix Johan!

[cursor]

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

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[cursor]

Non-aggregate molecule SQL fallback

Medium Severity

The n_molecules_sql helper returns a non-aggregate 0 when uei_count is missing. In component_recovery, using this directly in SELECT can cause an index error for empty edgelists or yield a column of zeros instead of a single total. get_count_statistics correctly embeds it within an aggregate query.

Additional Locations (1)

• src/pixelator/pna/graph/component_recovery.py#L119-L125

 

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[johandahlberg]

I will close this and open a new one, since for some reason I can't get GH to rebase this properly.