scverse
Sort output
This PR orders the results. By default, it's ordered by chrom, start, and id. Custom ordering can be provided using order_by.
If subsets of columns are selected, then the columns are sorted with available columns and finally by id.
I think we could do something like:
order_cols = []
if "gene" in tables:
order_cols += ["seq_name", "gene_seq_start"]
if "tx" in tables:
order_cols += ["tx_seq_start"]
if "exon" in tables:
order_cols += ["exon_seq_start"]
to have a consistent total order. But idk for sure.
Can this get some tests for expected behavior?
I updated it like that. It now sorts in a consistent order. I also added assertions to the tests to validate this functionality.
Codecov Report
Attention: Patch coverage is 95.23810% with 1 lines in your changes are missing coverage. Please review.
Project coverage is 93.01%. Comparing base (
ef33d87) to head (a5cdb15). Report is 1 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@
## main #64 +/- ##
==========================================
- Coverage 93.09% 93.01% -0.08%
==========================================
Files 6 6
Lines 333 358 +25
==========================================
+ Hits 310 333 +23
- Misses 23 25 +2
| Files | Coverage Δ | |
|---|---|---|
| src/genomic_features/ensembl/ensembldb.py | 93.02% <95.23%> (-0.14%) |
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Sorry for the delay on review/ approval but I wanted to dig into the duckdb behaviour we saw a bit more. An ibis maintainer believes this might be a duckdb bug.
- https://github.com/ibis-project/ibis/discussions/8896