Releases | Open Source Science

https://github.com/biolink/kgx - v2.5.1

What's Changed

re-enable dynamic versioning by @kevinschaper in https://github.com/biolink/kgx/pull/512

Full Changelog: https://github.com/biolink/kgx/compare/2.5.0...v2.5.1

- Python
Published by kevinschaper about 1 year ago

https://github.com/biolink/kgx - 2.5.0

What's Changed

Bump jinja2 from 3.1.3 to 3.1.5 by @dependabot in https://github.com/biolink/kgx/pull/503
Checks if synonym val exists before access by @matentzn in https://github.com/biolink/kgx/pull/502
Bump requests from 2.31.0 to 2.32.0 by @dependabot in https://github.com/biolink/kgx/pull/493
Bump virtualenv from 20.25.1 to 20.26.6 by @dependabot in https://github.com/biolink/kgx/pull/504
fix docs, refresh sphinx, regenerate index by @sierra-moxon in https://github.com/biolink/kgx/pull/507
trapi source/sink stubs and transform docs by @sierra-moxon in https://github.com/biolink/kgx/pull/506
refactor docs to all be in the same place by @sierra-moxon in https://github.com/biolink/kgx/pull/508
fix link in documentation by @andrewsu in https://github.com/biolink/kgx/pull/510
Preserve 'exactSynonym' when transforming OBOJSON to KGX TSV by @iQuxLE in https://github.com/biolink/kgx/pull/511

New Contributors

@matentzn made their first contribution in https://github.com/biolink/kgx/pull/502
@andrewsu made their first contribution in https://github.com/biolink/kgx/pull/510
@iQuxLE made their first contribution in https://github.com/biolink/kgx/pull/511

Full Changelog: https://github.com/biolink/kgx/compare/v2.4.2...2.5.0

- Python
Published by kevinschaper about 1 year ago

https://github.com/biolink/kgx - v2.5.0-rc1

What's Changed

Bump jinja2 from 3.1.3 to 3.1.5 by @dependabot in https://github.com/biolink/kgx/pull/503
Checks if synonym val exists before access by @matentzn in https://github.com/biolink/kgx/pull/502
Bump requests from 2.31.0 to 2.32.0 by @dependabot in https://github.com/biolink/kgx/pull/493
Bump virtualenv from 20.25.1 to 20.26.6 by @dependabot in https://github.com/biolink/kgx/pull/504
fix docs, refresh sphinx, regenerate index by @sierra-moxon in https://github.com/biolink/kgx/pull/507
trapi source/sink stubs and transform docs by @sierra-moxon in https://github.com/biolink/kgx/pull/506

New Contributors

@matentzn made their first contribution in https://github.com/biolink/kgx/pull/502

Full Changelog: https://github.com/biolink/kgx/compare/v2.4.2...v2.5.0-rc1

- Python
Published by sierra-moxon about 1 year ago

https://github.com/biolink/kgx - v2.4.2

What's Changed

Updated versions of packages by @hrshdhgd in https://github.com/biolink/kgx/pull/499

Full Changelog: https://github.com/biolink/kgx/compare/v2.4.1...v2.4.2

- Python
Published by hrshdhgd almost 2 years ago

https://github.com/biolink/kgx - v2.4.1

What's Changed

add "parquet source" mapped to "GraphSource" to support parquet sink support by @sierra-moxon in https://github.com/biolink/kgx/pull/490
Bump urllib3 from 2.1.0 to 2.2.2 by @dependabot in https://github.com/biolink/kgx/pull/494
Bump certifi from 2023.11.17 to 2024.7.4 by @dependabot in https://github.com/biolink/kgx/pull/495
Bump zipp from 3.17.0 to 3.19.1 by @dependabot in https://github.com/biolink/kgx/pull/496
Bump setuptools from 69.0.2 to 70.0.0 by @dependabot in https://github.com/biolink/kgx/pull/497
Update neo4j dependency version by @hrshdhgd in https://github.com/biolink/kgx/pull/498

Full Changelog: https://github.com/biolink/kgx/compare/v2.4.0...v2.4.1

- Python
Published by hrshdhgd almost 2 years ago

https://github.com/biolink/kgx - v2.4.0

What's Changed

update bmt to 1.4.0 by @sierra-moxon in https://github.com/biolink/kgx/pull/489

Full Changelog: https://github.com/biolink/kgx/compare/v2.3.3...v2.4.0

- Python
Published by sierra-moxon about 2 years ago

https://github.com/biolink/kgx - v2.3.3

What's Changed

upgrade bmt to 1.3.0 by @sierra-moxon in https://github.com/biolink/kgx/pull/486
Add Parquet sink support by @caufieldjh in https://github.com/biolink/kgx/pull/483
Bump idna from 3.6 to 3.7 by @dependabot in https://github.com/biolink/kgx/pull/487
Fixing KGX to support testing knowledgelevel and agenttype by @sierra-moxon in https://github.com/biolink/kgx/pull/488

Full Changelog: https://github.com/biolink/kgx/compare/v2.3.2...v2.3.3

- Python
Published by sierra-moxon about 2 years ago

https://github.com/biolink/kgx - v2.3.2

What's Changed

update linkml, linkml-runtime, bmt, tests to take advantage of newer biolink model by @sierra-moxon in https://github.com/biolink/kgx/pull/485

Full Changelog: https://github.com/biolink/kgx/compare/v2.3.1...v2.3.2

- Python
Published by sierra-moxon about 2 years ago

https://github.com/biolink/kgx - v2.3.1

What's Changed

Updating jsonlines dependecy version. by @hrshdhgd in https://github.com/biolink/kgx/pull/480

Full Changelog: https://github.com/biolink/kgx/compare/v2.3.0...v2.3.1

- Python
Published by caufieldjh about 2 years ago

https://github.com/biolink/kgx - v2.3.0

What's Changed

Update tox for biolink-model compatibility by @glass-ships in https://github.com/biolink/kgx/pull/476
Bump jinja2 from 3.1.2 to 3.1.3 by @dependabot in https://github.com/biolink/kgx/pull/477
Update links to biolink model docs in kgx-format.md by @deepakunni3 in https://github.com/biolink/kgx/pull/478
Updating tox version by @hrshdhgd in https://github.com/biolink/kgx/pull/479

New Contributors

@glass-ships made their first contribution in https://github.com/biolink/kgx/pull/476

Full Changelog: https://github.com/biolink/kgx/compare/v2.2.5...v2.3.0

- Python
Published by sierra-moxon over 2 years ago

https://github.com/biolink/kgx - Partially resolves issue #470

Resolves issue https://github.com/biolink/kgx/issues/470 - propagation failure for 'deprecate' tag.

- Python
Published by RichardBruskiewich over 2 years ago

https://github.com/biolink/kgx - v2.2.4

What's Changed

fix auto-assignment of category by @sierra-moxon in https://github.com/biolink/kgx/pull/473

Full Changelog: https://github.com/biolink/kgx/compare/v2.2.3...v2.2.4

- Python
Published by sierra-moxon over 2 years ago

https://github.com/biolink/kgx - v2.2.3

What's Changed

Bump urllib3 from 2.0.3 to 2.0.7 by @dependabot in https://github.com/biolink/kgx/pull/467
Bump certifi from 2023.5.7 to 2023.7.22 by @dependabot in https://github.com/biolink/kgx/pull/469
update sparqlwrapper by @sierra-moxon in https://github.com/biolink/kgx/pull/468

Full Changelog: https://github.com/biolink/kgx/compare/v2.2.2...v2.2.3

- Python
Published by sierra-moxon over 2 years ago

https://github.com/biolink/kgx - v2.2.2

What's Changed

Changed networkx and rdflib dependency to version = * by @hrshdhgd in https://github.com/biolink/kgx/pull/464
kgx-format.md: TOC links and JSON Lines consistency by @dhimmel in https://github.com/biolink/kgx/pull/466

New Contributors

@dhimmel made their first contribution in https://github.com/biolink/kgx/pull/466

Full Changelog: https://github.com/biolink/kgx/compare/v2.2.1...v2.2.2

- Python
Published by sierra-moxon over 2 years ago

https://github.com/biolink/kgx - v2.2.1

What's Changed

Ran poetry update for pandas by @hrshdhgd in https://github.com/biolink/kgx/pull/462

Full Changelog: https://github.com/biolink/kgx/compare/v2.2.0...v2.2.1

- Python
Published by hrshdhgd almost 3 years ago

https://github.com/biolink/kgx - v2.2.0

What's Changed

Remove unused closurizer dependency by @kevinschaper in https://github.com/biolink/kgx/pull/457
Update kgx-format.md - typo fix by @caufieldjh in https://github.com/biolink/kgx/pull/459
Bump requests from 2.28.2 to 2.31.0 by @dependabot in https://github.com/biolink/kgx/pull/455
update to bmt 1.1.0 by @sierra-moxon in https://github.com/biolink/kgx/pull/460

New Contributors

@caufieldjh made their first contribution in https://github.com/biolink/kgx/pull/459

Full Changelog: https://github.com/biolink/kgx/compare/v2.1.0...v2.2.0

- Python
Published by sierra-moxon almost 3 years ago

https://github.com/biolink/kgx - v2.1.0

What's Changed

add examples to readme of running key functionality from command line by @sierra-moxon in https://github.com/biolink/kgx/pull/453
update bmt dependency by @sierra-moxon in https://github.com/biolink/kgx/pull/456

Full Changelog: https://github.com/biolink/kgx/compare/v2.0.8...v2.1.0

- Python
Published by sierra-moxon about 3 years ago

https://github.com/biolink/kgx - v2.0.8

What's Changed

Update kgx-format.md to remove relation by @sierra-moxon in https://github.com/biolink/kgx/pull/450
add test for CPATH by @sierra-moxon in https://github.com/biolink/kgx/pull/451
update bmt by @sierra-moxon in https://github.com/biolink/kgx/pull/452

Full Changelog: https://github.com/biolink/kgx/compare/v2.0.7...v2.0.8

- Python
Published by sierra-moxon about 3 years ago

https://github.com/biolink/kgx - v2.0.7

What's Changed

Make sure the multivalued slot list is cached by @kevinschaper in https://github.com/biolink/kgx/pull/448
update bmt to latest release to grab update infores dictionary by @sierra-moxon in https://github.com/biolink/kgx/pull/449

Full Changelog: https://github.com/biolink/kgx/compare/v2.0.6...v2.0.7

- Python
Published by sierra-moxon about 3 years ago

https://github.com/biolink/kgx - v2.0.6

What's Changed

Speed up rdf sink (and more?) with lru_cache on text utils by @kevinschaper in https://github.com/biolink/kgx/pull/447

Full Changelog: https://github.com/biolink/kgx/compare/v2.0.5...v2.0.6

- Python
Published by kevinschaper about 3 years ago

https://github.com/biolink/kgx - v2.0.5

What's Changed

if property is 'type' assume uriorcurie datatype, fixes #445 by @sierra-moxon in https://github.com/biolink/kgx/pull/446

Full Changelog: https://github.com/biolink/kgx/compare/v2.0.4...v2.0.5

- Python
Published by sierra-moxon about 3 years ago

https://github.com/biolink/kgx - v2.0.4

What's Changed

Sql sink, fixes #443 by @sierra-moxon in https://github.com/biolink/kgx/pull/442
Change default reification behavior to true to avoid tossing important qualifiers by default (like negation!) by @kevinschaper in https://github.com/biolink/kgx/pull/444

Full Changelog: https://github.com/biolink/kgx/compare/v2.0.3...v2.0.4

- Python
Published by sierra-moxon about 3 years ago

https://github.com/biolink/kgx - v2.0.3

What's Changed

scalars and lists - make list unique by @sierra-moxon in https://github.com/biolink/kgx/pull/439
validation: speed up log_error method by @sierra-moxon in https://github.com/biolink/kgx/pull/441

Full Changelog: https://github.com/biolink/kgx/compare/v2.0.2...v2.0.3

- Python
Published by sierra-moxon about 3 years ago

https://github.com/biolink/kgx - v2.0.2

What's Changed

fixing cli after poetry migration by @sierra-moxon in https://github.com/biolink/kgx/pull/437

Full Changelog: https://github.com/biolink/kgx/compare/v2.0.1...v2.0.2

- Python
Published by sierra-moxon about 3 years ago

https://github.com/biolink/kgx - v2.0.1

What's Changed

fix up Dockerfile to work with poetry by @sierra-moxon in https://github.com/biolink/kgx/pull/426
fixing token name by @sierra-moxon in https://github.com/biolink/kgx/pull/427
Bump markdown-it-py from 2.1.0 to 2.2.0 by @dependabot in https://github.com/biolink/kgx/pull/429
Add poetry dynamic versioning config to pyproject.toml by @kevinschaper in https://github.com/biolink/kgx/pull/433

New Contributors

@dependabot made their first contribution in https://github.com/biolink/kgx/pull/429

Full Changelog: https://github.com/biolink/kgx/compare/v2.0.0...v2.0.1

- Python
Published by sierra-moxon about 3 years ago

https://github.com/biolink/kgx - v2.0.0

What's Changed

adding poetry, fixes #423, #403 by @sierra-moxon in https://github.com/biolink/kgx/pull/418

Full Changelog: https://github.com/biolink/kgx/compare/v1.7.0...v2.0.0

- Python
Published by sierra-moxon over 3 years ago

https://github.com/biolink/kgx - v1.7.0

What's Changed

handling edge provenance when it comes from both the edge file and the transform configuration fixes #407 by @sierra-moxon in https://github.com/biolink/kgx/pull/408
Clarify TSV list value formatting by @RichardBruskiewich in https://github.com/biolink/kgx/pull/410
more tests of knowledge source provenance by @sierra-moxon in https://github.com/biolink/kgx/pull/409
Bump version to 1.7.0 in preparation of a release by @sierra-moxon in https://github.com/biolink/kgx/pull/411

Full Changelog: https://github.com/biolink/kgx/compare/1.6.2...v1.7.0

- Python
Published by sierra-moxon almost 4 years ago

https://github.com/biolink/kgx - 1.6.1

What's Changed

remove extra docker commands, add test to expose provided_by exclusion fixes #400 by @sierra-moxon in https://github.com/biolink/kgx/pull/406

Full Changelog: https://github.com/biolink/kgx/compare/1.6.0...1.6.1

- Python
Published by sierra-moxon almost 4 years ago

https://github.com/biolink/kgx - 1.6.0

What's Changed

Biolink 3 upgrade fixes #399 by @sierra-moxon in https://github.com/biolink/kgx/pull/405

Full Changelog: https://github.com/biolink/kgx/compare/1.5.9...1.6.0

- Python
Published by sierra-moxon almost 4 years ago

https://github.com/biolink/kgx - 1.5.9

What's Changed

removed version anchor for sphinx and related pkgs by @hrshdhgd in https://github.com/biolink/kgx/pull/397
Issue 384 remove stream from graph summary and validate commands by @RichardBruskiewich @sierra-moxon in https://github.com/biolink/kgx/pull/388

New Contributors

@hrshdhgd made their first contribution in https://github.com/biolink/kgx/pull/397

Full Changelog: https://github.com/biolink/kgx/compare/1.5.8...1.5.9

- Python
Published by sierra-moxon almost 4 years ago

https://github.com/biolink/kgx - 1.5.8

What's Changed

Removes some noisy print statements from neo4j_sink by @kevinschaper in https://github.com/biolink/kgx/pull/390

Full Changelog: https://github.com/biolink/kgx/compare/1.5.7...1.5.8

- Python
Published by kevinschaper almost 4 years ago

https://github.com/biolink/kgx - 1.5.7

What's Changed

Validator prefix fix by @kevinschaper in https://github.com/biolink/kgx/pull/382
add streaming to merge Transformer by @sierra-moxon in https://github.com/biolink/kgx/pull/386

Full Changelog: https://github.com/biolink/kgx/compare/1.5.6...1.5.7

- Python
Published by sierra-moxon about 4 years ago

https://github.com/biolink/kgx - 1.5.6

What's Changed

update Click, update tox support to fix kgx black/click conflicts. by @sierra-moxon in https://github.com/biolink/kgx/pull/375
ID Generation Patch by @YaphetKG in https://github.com/biolink/kgx/pull/374
Correct tests by @sierra-moxon in https://github.com/biolink/kgx/pull/376
fix requirements to allow build in venv fixes #339 by @sierra-moxon in https://github.com/biolink/kgx/pull/377

New Contributors

@YaphetKG made their first contribution in https://github.com/biolink/kgx/pull/374

Full Changelog: https://github.com/biolink/kgx/compare/1.5.5...1.5.6

- Python
Published by sierra-moxon about 4 years ago

https://github.com/biolink/kgx - 1.5.5

What's Changed

Add jsonlines to the spec. by @cbizon in https://github.com/biolink/kgx/pull/340
Patch for issues 348 by @RichardBruskiewich in https://github.com/biolink/kgx/pull/349
Patch to resolve issue 360 remove !!set and other odd markup in yaml output of graph-summary output by @RichardBruskiewich in https://github.com/biolink/kgx/pull/361
Issue 359 error exit codes by @RichardBruskiewich @sierra-moxon in https://github.com/biolink/kgx/pull/362
update bmt to get new biolink-model, fix linkml changes, add test coverage to click in order to pass sonarcloud coverage requirements by @sierra-moxon in https://github.com/biolink/kgx/pull/367
list delimiters (issue 345) by @EvanDietzMorris in https://github.com/biolink/kgx/pull/370
Switch from neo4jrestclient to neo4j for Neo4j 4.3 compatibility by @kevinschaper @RichardBruskiewich @sierra-moxon in https://github.com/biolink/kgx/pull/343
Issue 338 enhanced kgx transform logging by @RichardBruskiewich @sierra-moxon in https://github.com/biolink/kgx/pull/365

New Contributors

@cbizon made their first contribution in https://github.com/biolink/kgx/pull/340
@EvanDietzMorris made their first contribution in https://github.com/biolink/kgx/pull/370

Full Changelog: https://github.com/biolink/kgx/compare/1.5.4...1.5.5

- Python
Published by sierra-moxon over 4 years ago

https://github.com/biolink/kgx - 1.5.4

update to use new version of bmt, thus new version (2.2.5) of biolink-model.

- Python
Published by sierra-moxon over 4 years ago

https://github.com/biolink/kgx - 1.5.3

remove pystache requirement

- Python
Published by sierra-moxon over 4 years ago

https://github.com/biolink/kgx - 1.5.1

Keep track of edge properties in owl source

- Python
Published by sierra-moxon almost 5 years ago

https://github.com/biolink/kgx - 1.5.0

Support mixins in ancestors hierarchy
Invalidate mixins as categories
Maintenance and bug fixes

- Python
Published by sierra-moxon almost 5 years ago

https://github.com/biolink/kgx - Biolink 2.* update

This version replaces the previously hard-coded config.yaml Biolink Model release number with use of the current Biolink Model Toolkit default model release value.
Users of the KGX 'validate' functionality can also reset the Biolink Model (SemVer) release number at the CLI, and programmatically, with the Validator.set_biolink_model() class method.
KGX made Biolink Model 2.0++ aware with respect to new provenance slots - knowledge_source and its descendant slot definitions. These slot properties need to be explicitly specified in the Transformer.transform input_args dictionary.
Some support for heuristic auto-generation of candidate format-compliant CURIES Biolink Model 2.0++ Information Resource ("InfoRes") CURIES. The new code also provides a regular expression and meta-data based rewrite of knowledge source names into such CURIES.
Some additional clarification in the 'readTheDocs' documentation including for 1.3.0 streaming release features.

- Python
Published by RichardBruskiewich almost 5 years ago

https://github.com/biolink/kgx - 1.3.0

Add streaming option to validation

- Python
Published by sierra-moxon almost 5 years ago

https://github.com/biolink/kgx - 1.2.0

Update BMT to 0.7.2
Update LinkML to 1.0.0
Pin some major release versions in requirements.txt

- Python
Published by sierra-moxon almost 5 years ago

https://github.com/biolink/kgx - 1.1.0

Migrate to LinkML from BiolinkML

- Python
Published by sierra-moxon about 5 years ago

https://github.com/biolink/kgx -

Fix bug with caching records in RdfSource
Add shortcuts for arguments in all CLI operations
Fix usage in CLI

- Python
Published by deepakunni3 about 5 years ago

https://github.com/biolink/kgx -

Fixed caching bug in RdfSource
Fixed bug when setting 'provided_by' for a source

- Python
Published by deepakunni3 about 5 years ago

https://github.com/biolink/kgx -

Added Source implementation for reading from various data stores
Added Sink implementation for writing to various data stores
Added a simplified Transformer that is agnostic
Refactor KGX to make use of Sources and Sinks
Added ability to stream graphs (Thanks to @gregr for the inspiration)

- Python
Published by deepakunni3 about 5 years ago