Clean up stale docstrings, history comments, and leftover CI/test cache files
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- Dominant language
- Python
- Stars
- 129
- Forks
- 34
- PR merge metrics
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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_gtfsays 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_attributesdocuments achunksizeparameter it doesn't take.gtfparse/read_gtf.py:419-426: an unrecognizedresult_typesilently returnsNone. It should raiseValueError.gtfparse/write_gtf.py:61-63: the docstring refers to "the naiveif value:check in earlier drafts".gtfparse/attribute_parsing.py:55-56: the comment explainsintern(str(...))(:81) as a Python 2 unicode workaround. On Python 3 thestr()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:1-4describes 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:3-4points to~/code/trufflepig/test.shfor 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 usescoverallsapp/github-action@v2.2.3..hypothesis/unicode_data/13.0.0/charmap.json.gzandtests/.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
- 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 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