What's Changed
Package structure and dependencies
- Python and pandas compatibility adjustments by @bgyori in #1404
- Migrate testing from nosetests to pytest by @bgyori in #1405
- Update dependencies by @bgyori in #1417
- Move markupsafe version constraint by @bgyori in #1440
- Remove pandas version restriction by @bgyori in #1441
- Extend to Python 3.12 compatibility by @bgyori in #1443
- Networkx 3 compatibility by @kkaris in #1447
- Add Python 3.10 testing by @bgyori in #1410
- Update Flask, Flask Restx, unpin Gilda by @kkaris in #1452
Documentation
- Update documentation by @cthoyt in #1408
- Use RTD config for docs build by @bgyori in #1425
- Documentation fixes by @bgyori in #1451
Core assembly modules
- Add optional residue/position feature to CountScorer by @johnbachman in #1396
- Remove mesh cycle from bio-ontology by @kkaris in #1433
- Add version to file docstring and log message in bio ontology CLI by @kkaris in #1432
Knowledge sources
- Handle more UP/HGNC corner cases in BioPAX by @bgyori in #1390
- Improve BioPAX conversion processing and extend API by @bgyori in #1392
- Fix quotes in Reach processor run command by @kwalcock in #1397
- Propagate section information from new Reach implementation by @bgyori in #1399
- Allow extracting all Agents from Reach entities by @bgyori in #1400
- Db sources updates by @kkaris in #1423
- Processor improvements by @bgyori in #1450
- Update SIGNOR processor and FamPlex by @bgyori in #1409
- Add coordinate info to Agent extraction endpoints from readers by @bgyori in #1412
- Handle underscores in agent IDs for DB query by @bgyori in #1414
- Add fix for issue with latest SIGNOR release by @bgyori in #1453
- Fixes to input processors due to changes in sources by @haohangyan in #1454
Output assemblers
Resources and database clients
- Implement client for MGI resources by @bgyori in #1391
- Update MeSH resources and ontology by @bgyori in #1395
- Standardize MeSH 2022 by @cthoyt in #1411
- Update MeSH to 2024 by @bgyori in #1431
- Update HGNC resource by @bgyori in #1415
- Reimplement cBioPortal client for new API by @bgyori in #1435
- Update resource files by @bgyori in #1436
- Add client for RGD database by @bgyori in #1449
- Add Ensembl info for MGI genes by @bgyori in #1429
Literature clients
- Improve PubMed metadata extraction handling by @bgyori in #1430
- Implement retrieving more than 10k PMIDs and all metadata by @bgyori in #1424
- Journal info by @kkaris in #1416
- Allow enhanced author parsing by @pagreene in #1406
- Get article references, either just PMIDs or details by @pagreene in #1407
- PubMed XML save option by @bgyori in #1413
- Add more robust retry to the pubmed client's send_request by @kkaris in #1426
Other
- Various fixes and improvements by @bgyori in #1402
- Fix syntax warnings and styling by @bgyori in #1455
- Remove lib2to3 logging patch by @bgyori in #1437
Full Changelog: 1.22.0...1.23.0
Contributors
johnbachman, kkaris, and 5 other contributors