openvax / gtfparse / 25808853095
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coverage: 93.78% (+7.3%) from 86.471%
25808853095

Pull #67

github

iskandr 
Address review: bug fixes + real GENCODE coverage

Fixes from PR review:

1. _apply_attribute_aliases: two aliases targeting the same canonical
   (e.g. both gene_type and a hypothetical gene_kind -> gene_biotype)
   silently produced a duplicate-column rename. Track renames in a
   running set so the second collision is flagged the same way as a
   pre-existing canonical (drop + warn). First in iteration order wins.

2. usecols + attribute_aliases: usecols was enforced at parse time
   (inside parse_gtf_and_expand_attributes) before aliases could run,
   so requesting `usecols=["gene_biotype"]` against a GENCODE GTF that
   only had gene_type returned an empty frame. Expand the parse-time
   filter to pull alias source columns through when their canonical is
   in usecols. End-of-function usecols filter still narrows down to
   the canonical name only.

New test coverage (18 new tests, 54 total):

  * explicit attribute_aliases=None matches implicit default
  * result_type="dict" with both kwargs
  * multiple aliases -> same canonical: first wins, second warned+dropped
  * alias-chain semantics pinned (no chasing — each rule judged against
    the pre-rename column set)
  * aliasing preserves all unrelated columns
  * usecols composes with attribute_aliases
  * gene_version=0 round-trips as Int64(0), not pd.NA
  * malformed version string ("v3") coerces to pd.NA (lenient by design)
  * version cast idempotent across repeated reads (global polars cache safety)

Real GENCODE fixture (tests/data/gencode.real.head.gtf) reflecting the
on-disk shape — versioned IDs embedded in gene_id/transcript_id rather
than separate *_version attrs, GENCODE-only fields (level, hgnc_id,
havana_gene/transcript, tag, transcript_support_level), and chr-prefixed
seqnames — plus 7 tests against it:

  * alias rename works on the real shape
  * no synthesized *_version columns when attrs absent
  * versioned ID strings preserved verbatim (ENSG/ENST/ENSP/ENSE)
  * GENCODE-only ... (continued)
Pull Request #67: Add attribute_aliases + cast_version_columns to read_gtf (closes #63, #64)

196 of 209 relevant lines covered (93.78%)

0.94 hits per line

Coverage Regressions

Lines Coverage ∆ File
8
93.55
 14.72% read_gtf.py
Jobs
ID Job ID Ran Files Coverage
1 25808853095.1 5
93.78
 GitHub Action Run
Source Files on build 25808853095