openvax / openvax/gtfparse

Triage: 11 open issues appear resolved on master

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#75 0 comments 0 reactions 0 assignees View on GitHub

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Dominant language
Python
Stars
129
Forks
34
PR merge metrics
No merged PRs in 30d

Description

Of the 21 open issues, 11 look fixed on master (2.8.0). I checked each one against the code and, where the report had input, ran it with polars 1.43 / pyarrow 25.

Fixed; can be closed

  • #36, #38 scan_csv() got an unexpected keyword argument 'sep': fixed by #42 (see the maintainer's comment on #36). read_gtf.py:118 now passes separator.
  • #40 logging.basicConfig at import: removed in 9e9222d (#71). There is no basicConfig anywhere in gtfparse/.
  • #50 dtypes deprecation: read_gtf.py:121 passes schema_overrides (5a740c9).
  • #49 'LazyFrame' object has no attribute 'lazy' (reported on 2.0.1 / Python 3.6): read_gtf.py:124 now uses eager read_csv(...).lazy(), and requires-python >= 3.9.
  • #19 Scallop GTF, "Integer column has NA values": the snippet from the issue parses into 30 rows × 13 columns. That error message no longer exists in the code.
  • #32 pyarrow undeclared, #52 pandas undeclared: both are in requirements.txt:2-3.
  • #47 pyarrow <14.1 pin: upper bounds removed in 1c50944 (#51).
  • #45 table_to_blockmanager (pyarrow 10) and #55 numpy 2 _ARRAY_API (old pyarrow): both come from old pyarrow builds, and pyarrow>=18.0.0 is now required. The commenter on #45 says upgrading pyarrow fixed it.

Not in this repo

  • #43: Bioconda recipe for 2.1.0.

Still reproduce

  • #44: description "part1; part2" parses as part1.
  • #23: attribute_parsing.py:71 still does split(" ", 2)[:2].

Not checked: #16, #53, #65, #66, #69. #13 is addressed by #74.

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reviewing the referenced issues, commits, and code locations in read_gtf.py and attribute_parsing.py. Confirm the listed fixes, close issues marked fixed, leave #43 for Bioconda, and keep #44 and #23 open because they still reproduce. Check the remaining unreviewed issues before finalizing the triage.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Documentation
Difficulty
3/5
Estimated time
1-2 days
Activity status
Active
Clarity
Mostly clear
Newbie friendliness
58/100

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