Triage: 11 open issues appear resolved on master #75

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1. iskandr commented on Sep 29, 2026

   

   iskandr

   on Sep 29, 2026

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   Verified against the published gtfparse 2.9.1 package on 2026-09-29. Ten of the eleven suspected-resolved reports are now closed, each with its own verification note. #19 remains open because the original input has not been reproduced faithfully.

   Reports	Disposition	Evidence
   #36, #38	Closed	The reader uses read_csv(separator=...); Ensembl parsing succeeds without the old sep error.
   #49	Closed	The StringTie fixture parses, and the lazy helper returns a collectable LazyFrame without calling .lazy() on one. Current metadata requires Python >=3.9.
   #50	Closed	schema_overrides replaces dtypes; parsing and pandas conversion pass with deprecations as errors.
   #40	Closed	A fresh-process import/read check makes zero calls to logging.basicConfig and preserves both unconfigured and application-configured root logging.
   #32, #52	Closed	A fresh normal PyPI install automatically installs PyArrow and pandas. Published metadata declares pyarrow>=18.0.0 and pandas>=2.1.0; imports and conversion pass.
   #47	Closed	The old PyArrow upper bound is absent; the requirement is pyarrow>=18.0.0. Parsing/conversion succeeds with 25.0.1 as well as 18.0.0.
   #45, #55	Closed	Import/parsing/pandas conversion works with PyArrow 18.0.0 and 25.0.1, pandas 3.0.6, and NumPy 2.5.3. The old table_to_blockmanager / _ARRAY_API failures do not reproduce on these supported combinations.
   #19	Kept open	The literal pasted snippet contains spaces rather than tabs and raises Wrong number of columns. Normalizing only field separators produces 30 rows × 13 columns, but the original hybrid.gtf file is unavailable. That normalized check does not establish that the original report is resolved.

   Checks ran in an isolated Python 3.12 environment installed from PyPI, with pip check passing and DeprecationWarning treated as an error. The tested dependency combinations were:

   • Polars 1.44.2 / PyArrow 25.0.1 / pandas 3.0.6 / NumPy 2.5.3.
   • Polars 1.44.2 / PyArrow 18.0.0 / pandas 3.0.6 / NumPy 2.5.3.
   • Polars 0.20.31 / PyArrow 18.0.0 / pandas 3.0.6 / NumPy 2.5.3.

   Fixture checks cover Ensembl (995 rows), StringTie (1,000 rows), RefSeq (24 rows), and the separator-normalized Scallop example (30 rows). Each was read into Polars and/or pandas as appropriate; the logging and lazy-reader checks exercise the installed release as well.

   New current bug found: #85. The declared polars>=0.20.2 floor is too low for the unconditional schema_overrides call. Polars 0.20.2 installs with pip check passing but fails on a valid one-line GTF. Polars 0.20.31 passes the targeted audit checks; its full API support still needs verification before changing the lower bound. The old Polars report closures link this separate current issue.

   Other dispositions from the original tracker: #23 and #44 shipped in 2.9.0 via #82; #53 shipped in 2.9.1 via #84. #43 remains a separate Bioconda packaging report. #13/#74, #16, #37, and feature/design work #65/#66/#69 remain separate open work and were not closed by this audit.

   Closing this triage tracker with the individual dispositions recorded. Follow-up is #85, plus the original input needed for #19.
2. iskandr

   closed this as completedon Sep 29, 2026