biolink/kgx: v2.7.0

Zenodo (CERN European Organization for Nuclear Research)

Abstract

What's Changed Bump requests from 2.32.3 to 2.32.4 by @dependabot[bot] in https://github.com/biolink/kgx/pull/515 Bump urllib3 from 2.4.0 to 2.5.0 by @dependabot[bot] in https://github.com/biolink/kgx/pull/516 Bump pillow from 11.2.1 to 11.3.0 by @dependabot[bot] in https://github.com/biolink/kgx/pull/519 Bump pypa/gh-action-pypi-publish from 1.2.2 to 1.13.0 in /.github/workflows by @dependabot[bot] in https://github.com/biolink/kgx/pull/521 Replace prefixcommons usages with curies by @cthoyt in https://github.com/biolink/kgx/pull/472 refactor documentation to include links to JSON schema by @sierra-moxon in https://github.com/biolink/kgx/pull/522 Kgx doc updates with KG class in Biolink by @sierra-moxon in https://github.com/biolink/kgx/pull/523 update bmt dependency by @sierra-moxon in https://github.com/biolink/kgx/pull/524 Add Jelly RDF format support by @lapkinvladimir in https://github.com/biolink/kgx/pull/531 add a skip to clean database by @sierra-moxon in https://github.com/biolink/kgx/pull/536 Ralatsdc/add arangodb support by @sierra-moxon in https://github.com/biolink/kgx/pull/537 Add ArangoDB support by @ralatsdc in https://github.com/biolink/kgx/pull/535 Bump urllib3 from 2.6.2 to 2.6.3 by @dependabot[bot] in https://github.com/biolink/kgx/pull/532 Bump virtualenv from 20.35.4 to 20.36.1 by @dependabot[bot] in https://github.com/biolink/kgx/pull/533 Bump protobuf from 6.33.2 to 6.33.5 by @dependabot[bot] in https://github.com/biolink/kgx/pull/534 Bump pygments from 2.19.2 to 2.20.0 by @dependabot[bot] in https://github.com/biolink/kgx/pull/538 Bump pyjwt from 2.11.0 to 2.12.0 by @dependabot[bot] in https://github.com/biolink/kgx/pull/539 Bump tornado from 6.5.4 to 6.5.5 by @dependabot[bot] in https://github.com/biolink/kgx/pull/540 Smoxon/remove python 3.9 support, migrate to uv by @sierra-moxon in https://github.com/biolink/kgx/pull/541 pin click to resolve kgx schema by @sierra-moxon in https://github.com/biolink/kgx/pull/542 Versioning up pyarrow from 18 to 22. This makes using it in uv enviornments much easier since the pyarrow binary is bundled alongside the python starting in this version. by @DnlRKorn in https://github.com/biolink/kgx/pull/543 Fix obograph_source prefix-map destruction and predicate mapping by @kevinschaper in https://github.com/biolink/kgx/pull/548 Optimize RDF export performance in RdfSink by @kevinschaper in https://github.com/biolink/kgx/pull/545 Bump urllib3 from 2.6.3 to 2.7.0 by @dependabot[bot] in https://github.com/biolink/kgx/pull/549 Bump idna from 3.11 to 3.15 by @dependabot[bot] in https://github.com/biolink/kgx/pull/550 New Contributors @cthoyt made their first contribution in https://github.com/biolink/kgx/pull/472 @lapkinvladimir made their first contribution in https://github.com/biolink/kgx/pull/531 @ralatsdc made their first contribution in https://github.com/biolink/kgx/pull/535 @DnlRKorn made their first contribution in https://github.com/biolink/kgx/pull/543 Full Changelog: https://github.com/biolink/kgx/compare/v2.6.0...v2.7.0

Authors 27

1. Deepak

   SIB Swiss Institute of Bioinformatics

   Affiliation as printed

   SIB Swiss Institute of Bioinformatics

2. Sierra Moxon

   Lawrence Berkeley National Laboratory

   Affiliation as printed

   Lawrence Berkeley National Lab

3. Lance M. Hannestad
   Affiliation as printed

   @STARInformatics

4. Chris J Mungall

   Lawrence Berkeley National Laboratory

   Affiliation as printed

   Lawrence Berkeley National Laboratory

5. Richard Bruskiewich
   Affiliation as printed

   Delphinai

6. Kevin Schaper
7. Harry Caufield

   Lawrence Berkeley National Laboratory

   Affiliation as printed

   Lawrence Berkeley National Laboratory

8. Kenneth Bruskiewicz
9. Raymond Leclair
10. Harshad
11. Volodymyr Lapkin
    Affiliation as printed

    PJATK

12. Carlo Kroll
13. Phil Owen
14. Charles Tapley Hoyt Aachen

    RWTH Aachen University

    Affiliation as printed

    RWTH Aachen University

15. Harold Solbrig
    Affiliation as printed

    Solbrig Informatics, LLC

16. Greg Rosenblatt
17. Andrew Su

    Scripps Research Institute

    Affiliation as printed

    Scripps Research

18. Damien Goutte-Gattat

    German BioImaging – Gesellschaft für Mikroskopie und Bildanalyse

    Affiliation as printed

    German BioImaging e.V

19. Daniel Himmelstein
    Affiliation as printed

    @radoverlay

20. DnlRKorn
21. Eric Douglass
22. Evan Morris

    Renaissance Computing Institute

    Affiliation as printed

    RENCI

23. HyeongSik Kim

    Robert Bosch (United States)

    Affiliation as printed

    Robert Bosch LLC

24. Kent Shefchek
    Affiliation as printed

    @myhelix

25. Nicolas Matentzoglu
    Affiliation as printed

    semanticly.ai

26. YaphetKG
27. cbizon