openvax / openvax/gtfparse

Clean up stale docstrings, history comments, and leftover CI/test cache files

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Dominant language
Python
Stars
129
Forks
34
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Description

These are small, and each item is a deletion or a one-line docstring fix. I left them out of #74 so that PR stays docs-only.

Docstrings and comments that are wrong or narrate history

  • gtfparse/read_gtf.py:279: read_gtf says it returns "a dictionary mapping column names to sequences of values". It returns a Polars DataFrame by default.
  • gtfparse/read_gtf.py:183: parse_gtf_and_expand_attributes documents a chunksize parameter it doesn't take.
  • gtfparse/read_gtf.py:419-426: an unrecognized result_type silently returns None. It should raise ValueError.
  • gtfparse/write_gtf.py:61-63: the docstring refers to "the naive if value: check in earlier drafts".
  • gtfparse/attribute_parsing.py:55-56: the comment explains intern(str(...)) (:81) as a Python 2 unicode workaround. On Python 3 the str() call does nothing.
  • tests/test_gencode_gtf.py:17,102,160: section dividers labeled with issue numbers (#63, #64). tests/test_expand_attribute_column_false.py:1-4 describes the old NameError instead of the behavior under test.
  • pyproject.toml:74-80: ruff ignore comments like "out of scope for config PR".

Stale infrastructure

  • test.sh:3-4 points to ~/code/trufflepig/test.sh for its rationale. That path exists only on a local machine.
  • .github/workflows/tests.yml:4-8: the TODO block (cache ~/.cache/pyensembl, conda binaries, add a tests badge, update coveralls) doesn't apply. The badge is already in the README and Coveralls already uses coverallsapp/github-action@v2.2.3.
  • .hypothesis/unicode_data/13.0.0/charmap.json.gz and tests/.hypothesis/... are committed Hypothesis caches. Nothing imports Hypothesis. Delete them and add .hypothesis/ to .gitignore.

format.sh (apply formatting), lint.sh (ruff check plus format check), and lint-and-test.sh (lint, then test) don't overlap, so I'd keep all three.

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 with the listed locations in gtfparse/read_gtf.py, gtfparse/write_gtf.py, gtfparse/attribute_parsing.py, the named test files, pyproject.toml, test.sh, and .github/workflows/tests.yml; run lint-and-test.sh before changes. Done means the stale docstrings, comments, TODOs, local path, and committed Hypothesis caches are removed, the invalid result_type raises ValueError, .hypothesis/ is ignored, and the three helper scripts remain.

Written by the indexing model from the issue text.

Assessment

Tech stack
github-actions, python
Domain
ci-cd, testing-qa, tooling
Issue type
Refactor
Difficulty
3/5
Estimated time
1-2 days
Activity status
Active
Clarity
Mostly clear
Newbie friendliness
72/100

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