Triage: 11 open issues appear resolved on master
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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:118now passesseparator. - #40
logging.basicConfigat import: removed in 9e9222d (#71). There is nobasicConfiganywhere ingtfparse/. - #50
dtypesdeprecation:read_gtf.py:121passesschema_overrides(5a740c9). - #49
'LazyFrame' object has no attribute 'lazy'(reported on 2.0.1 / Python 3.6):read_gtf.py:124now uses eagerread_csv(...).lazy(), andrequires-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
<14.1pin: 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, andpyarrow>=18.0.0is 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 aspart1. - #23:
attribute_parsing.py:71still doessplit(" ", 2)[:2].
Not checked: #16, #53, #65, #66, #69. #13 is addressed by #74.
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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