What's Changed
Enhancements and Cleanup:
ISA MODEL
- fix to Comments on several ISA objects
- fix to Datafile.py
- fix to Material.py
ISA TAB
- fix to isatab writer / reader and serialisation of Characteristics, Parameter and FactorValue values
- roundtrip testing
ISA JSON
- upgrade the all ISA json_schemas overcoming the silent schema validation failure
- fix to json serialiser affecting declaration/referencing of units
ISA Documentation:
- addition of several new jupyter notebooks documenting ISA object usages
- creation of jupyter notebooks documenting known limitations or anti patterns (i.e., "don't" when using ISA tab representations)
Versions update:
- Dropped python 3.8 and 3.9
- Added compatibility for python 3.12 (production ready)
- Added compatibility for python 3.13 (test only)
- Bump numpy, pandas, sqlAlchemy
New Contributors
special thanks for reporting and addressing issues in isatab writer
- @oyurekten made their first contribution in #590
special thanks for contributing the migration to uv
- @sorenwacker made their first contribution in #589
special thanks for contributing the sqlAlchemy upgrade
special thanks for code review, overall contribution and help.
Former Contributors
special thanks to @terazus for huge contribution to isa refactoring, isajson-ld among many other things.
More details
- Issue #399 addressed by #601 and #603
- Issue #409
- Issue #414 by @knirirr in https://github.com/ISA-tools/isa-api/pull/580/files
- Issue #416 in in #590
- Issue #427 by @knirirr and @proccaserra in #592
- Issue #483
- Merge from master by @terazus in #493
- merge from master by @terazus in #495
- Update requirements.txt by @terazus in #499
- Issue 497 fix by @proccaserra in #507
- Fix to determining JSON directory location. by @terazus in #546
- Testing changes to run on Windows. by @ptth222 in #549
- Update defaults.py by @ptth222 in #539
- More changes by @ptth222 in #550
- Rename i_df and investigation_df. by @ptth222 in #529
- Fix rule and check. by @terazus in #548
- Fairly significant changes to check_protocol_fields by @ptth222 in #531
- Changed messaging on study assays errors by @ptth222 in #530
- Extended 511 by @proccaserra in #551
- Added better messaging by @ptth222 in #527
- Refactor isatab loader by @terazus in #555
- Protocol types refactor by @ptth222 in #556
- Issue #511 by @proccaserra in #514
- Issue #520 by @knirirr in #592
- Issue #523 [Characteristic values are recast as string in ISA tab in https://github.com//pull/590
- Issue #540 relaxing requirement on Person Mid Initials in XML config.
- Issue #562 python312 by @proccaserra in #564
- Mock pubmed 557 by @knirirr in #567
- adjusting bh23 workbook, and model class by @proccaserra in #565
- issue #566
- Issue #570 by @oyurekten in #590
- Issue #571 by @oyurekten in #590
- Deprecation future warnings by @knirirr in #574
- Update README.md by @proccaserra in #576
- adding toml file, updates to setup.py, fixing broken shield and ... by @proccaserra in #577
- merging into master from develop to make a new release by @proccaserra in #573
- Issue #575 addressing SQLAlchemy breaking change when upgrading from 1.4 to 2.+ by @oyurekten in #590
- creating a lock file, updating toml file by @proccaserra in #578
- upping numpy and pandas version for isacookbok by @proccaserra in #579
- Issue #584 addressed in #590
- UV Package Manager Integration by @oyurekten in #590
- PR on dev by @proccaserra in #588
- Deprecation warnings prs by @proccaserra in #593
- check_isa_schemas updated to new json validator. #591 by @knirirr in #592
- Develop by @proccaserra in #580
- Removed references to deprecated materials in favour of other_material. by @knirirr in #594
- Hid some PerformanceWarnings... by @knirirr in #596
- fix to get_ols_ontology by @proccaserra in #599
- Re-enable some skipped tests. by @knirirr in #600
- Develop by @proccaserra in #595
- jupyter notebook testing and revisions/corrections by @proccaserra in #603
Full Changelog: v0.14.2...v0.14.3
Contributors
proccaserra, sorenwacker, and 4 other contributors