v1.16.0

What's Changed

• add ncbiblastapi services (alternative to ncbiblast from ebi)

Full Changelog: v1.15.0...v1.16.0

v1.15.0

What's Changed

• Add InterPro service wrapper by @Copilot in #318
• Add InterPro Jupyter notebook by @Copilot in #325
• Update UniProt notebook to current REST API (post-June 2022) by @Copilot in #324
• Add STRING-DB service; export MyGeneInfo and Panther from package root by @Copilot in #321
• Merge string and stringdb modules into a single unified STRING interface by @Copilot in #328
• Add notebook test suite and modernise all tutorial notebooks by @Copilot in #327
• Modernize Entrez_EUtils notebook and add InterPro notebook by @Copilot in #329
• Add Integrated Drug Discovery Pipeline notebook by @Copilot in #330
• Add bioservices protein CLI command group with 6 subcommands by @Copilot in #331
• Add gene CLI command group with 7 subcommands by @Copilot in #333

Full Changelog: v1.14.0...v1.15.0

v1.14.0

What's Changed

• Overhaul PubChem module to cover PUG REST API comprehensively by @Copilot in #299
• Fix savePathwayAs by switching to WikiPathways static assets URL by @Copilot in #302
• Simplify BioGRID: remove intermediary Search class by @Copilot in #303
• [WIP] Fix circular import issue with uniprot by @Copilot in #304
• Fix ReadTheDocs build: remove failing sphinxcontrib-googleanalytics, enable sphinx_copybutton by @Copilot in #306
• Fix CI: install pytest via [project.optional-dependencies] by @Copilot in #308
• Fix eutils tests failing on Python 3.11/3.12 due to numpy fork incompatibility by @Copilot in #309
• Fix PRIDE CI failures: handle new list-based API responses and stats 404 by @Copilot in #310
• Fix Python 3.11/3.12 CI regression: pin numpy <2.4 by @Copilot in #313
• Add EBI Proteins API service by @Copilot in #314
• Fix parse_kgml_pathway: missing graphics crash, silent relation drops, and sub-pathway docs by @Copilot in #316

Full Changelog: v0.13.0...v1.14.0

v0.13.0

What's Changed

• Update PDBe to v2 API by @dcroote in #283
• Use data parameter for MyGeneInfo by @JoshLoecker in #284
• Fix false "URL unreachable" warning when server returns HTTP error codes by @Copilot in #289
• Add Python 3.13 and 3.14 compatibility by @Copilot in #290
• Fix BioMart tests erroring with ValueError: unknown url type: 'undefined' by @Copilot in #293
• Migrate ChEBI from retired SOAP API to new REST API by @Copilot in #292
• Fix BioMart add_filter_to_xml to accept list values by @Copilot in #295

New Contributors

• @dcroote made their first contribution in #283

Full Changelog: v1.12.1...v0.13.0

v1.12.1

fix pyproject to use pandas>2.2

Full Changelog: v1.12.0...v1.12.1

v1.12.0

What's Changed

Update to fix pyproject, CI, tests

Full Changelog: v1.11.2...v1.12.0

v1.11.2

What's Changed

• Fix issue with compress in uniprot search. by @ArnaudBelcour in #249
• Updated logging instance by @JoshLoecker in #250
• Fix uniprot failedids by @cokelaer in #251
• COG module update to automatically fetch all pages

New Contributors

• @ArnaudBelcour made their first contribution in #249
• @JoshLoecker made their first contribution in #250

Full Changelog: v1.11.1...v1.11.2

v1.11.1

What's Changed

• Fix regression in uniprot module by @cokelaer in #246

Full Changelog: v1.11.0...v1.11.1

v1.11.0

• Fix uniprot issue with limitation of 25 items.
• remove deprecated classes
• removed rnaseq_ebi (deprecated service)
• major cleanup (no changes of functionalities)

v1.10.4

What's Changed

• Fix uniprot field (issue #226 by @GianArauz in #232)
• Added documentation by @PoorRican in #240
• Fix FutureWarning from Pandas by @GianArauz in #238
• This release replaced v1.10.3 that was faulty

New Contributors

• @GianArauz made their first contribution in #232
• @PoorRican made their first contribution in #240

Full Changelog: v1.10.1...v1.10.4