openvax / gtfparse / 28970605686

Builds Branch Commit Type Ran Committer Via Coverage
28970605686 master Merge pull request #72 from openvax/feature/21-write-gtf Add write_gtf: serialize a DataFrame back to GTF (fixes #21) push web-flow github
95.62
28970588144 feature/21-write-gtf Bump version to 2.8.0 Minor release: adds write_gtf, the inverse of read_gtf, for serializing a DataFrame of genomic features back to GTF (#21). Claude-Session: https://claude.ai/code/session_014fNxSBm5zvdsDNwN3nhmpS push iskandr github
95.62
28970590726 feature/21-write-gtf Merge 06fb59af1 into 6b2e0c73e Pull #72 web-flow github
95.62
28970419586 feature/21-write-gtf write_gtf: case-insensitive .gz, edge-case tests, doc caveat Follow-ups from review of #72: - Detect the gzip suffix case-insensitively (.GZ as well as .gz). - Note in the docstring that a literal tab or newline in an attribute value is unrepr... Pull #72 iskandr github
95.67
28969477314 feature/21-write-gtf write_gtf: robust, vectorized, gzip-aware; test both round-trip directions Addresses the review findings on the first draft: - Faithful missing-value handling. read_gtf represents an absent attribute as null (numeric *_version columns) or the ... Pull #72 iskandr github
95.28
28968358897 master Merge pull request #71 from openvax/fix/70-remove-basicconfig-at-import Fix #70: stop calling logging.basicConfig() at import time push web-flow github
95.15
28968279719 fix/70-remove-basicconfig-at-import Bump version to 2.7.2 Patch release: gtfparse no longer calls logging.basicConfig() at import time, so importing the library no longer reconfigures the host application's root logger (#70). Claude-Session: https://claude.ai/code/session_014fNxSB... Pull #71 iskandr github
95.15
28967537707 fix/70-remove-basicconfig-at-import Use lazy logging args instead of eager % interpolation Pass log message arguments to logger.info(...) rather than pre-formatting with the % operator, so the interpolation is skipped entirely when the log level is disabled (the standard logging id... Pull #71 iskandr github
95.15
28967540561 fix/70-remove-basicconfig-at-import Merge 2f24147c4 into 03668a374 Pull #71 web-flow github
95.15
28965821496 fix-70-no-import-time-basicconfig Fix #70: don't reconfigure root logging when importing gtfparse attribute_parsing, create_missing_features and read_gtf each called logging.basicConfig(level=logging.INFO) at import, which adds a handler to the ROOT logger and sets the root level... Pull #73 iskandr github
95.19
28965619839 feature/21-write-gtf Add write_gtf: serialize a DataFrame back to GTF (fixes #21) Adds the inverse of read_gtf. A DataFrame produced by read_gtf -- whether the attribute column was expanded into per-key columns or left as a raw 'attribute' string -- can be written ba... Pull #72 iskandr github
95.7
28953968093 fix/70-remove-basicconfig-at-import Fix #70: stop calling logging.basicConfig() at import time gtfparse called logging.basicConfig(level=logging.INFO) at module import in three modules (read_gtf, attribute_parsing, create_missing_features). As a library this is an anti-pattern: it ... Pull #71 iskandr github
95.15
25821451381 master test.sh: memory-aware pytest-xdist worker count Mirror the worker-cap logic from trufflepig/hitlist/tsarina/vaxrank so concurrent test runs across sibling repos can't fork-bomb the laptop. Picks min(cpu_reserve, available_RAM / PER_WORKER_GB), re... push iskandr github
95.22
25819759602 master Merge pull request #68 from openvax/fix/56-expand-attribute-column-false-nameerror Fix #56: NameError when expand_attribute_column=False push web-flow github
95.22
25819115218 fix/56-expand-attribute-column-false-nameerror Fix #56: NameError on expand_attribute_column=False The else branch in read_gtf passed `result_df` to parse_gtf before `result_df` had been assigned — a guaranteed NameError that survived because the branch was never tested. Replaced with the cor... Pull #68 iskandr github
95.22