https://github.com/biolink/biolink-model-toolkit - v1.4.4

What's Changed

• Bump certifi from 2024.6.2 to 2024.7.4 by @dependabot in https://github.com/biolink/biolink-model-toolkit/pull/175
• bump biolink model version by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/176

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.4.3...v1.4.4

- Python
Published by sierra-moxon about 2 years ago

https://github.com/biolink/biolink-model-toolkit - get_association() patch

Code checks in get_associations() for subject/object categories or predicates unknown to the target Biolink Model, and returns empty matches (with log warnings)

- Python
Published by RichardBruskiewich about 2 years ago

https://github.com/biolink/biolink-model-toolkit - v1.4.2

What's Changed

• Added a couple of utility methods useful at my end but which seemed to belong in BMT by @RichardBruskiewich in https://github.com/biolink/biolink-model-toolkit/pull/169
• Bump requests from 2.31.0 to 2.32.0 by @dependabot in https://github.com/biolink/biolink-model-toolkit/pull/170
• add biolink curie formatting to get_associations method, fixes #171 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/172

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.4.1...v1.4.2

- Python
Published by sierra-moxon about 2 years ago

https://github.com/biolink/biolink-model-toolkit - v1.4.1

What's Changed

• Bump jinja2 from 3.1.3 to 3.1.4 by @dependabot in https://github.com/biolink/biolink-model-toolkit/pull/167
• bump biolink model version by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/168

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.4.0...v1.4.1

- Python
Published by sierra-moxon about 2 years ago

https://github.com/biolink/biolink-model-toolkit - v1.4.0

What's Changed

• Bump idna from 3.6 to 3.7 by @dependabot in https://github.com/biolink/biolink-model-toolkit/pull/165
• update biolink to 4.2.0 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/166

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.3.0...v1.4.0

- Python
Published by sierra-moxon over 2 years ago

https://github.com/biolink/biolink-model-toolkit - v1.3.0

What's Changed

• Handle aliases in queries for get_descendants by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/164
• upgrade linkml, linkml-runtime dependencies
• update GH action to check KGX dependency downstream.

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.2.1...v1.3.0

- Python
Published by sierra-moxon over 2 years ago

https://github.com/biolink/biolink-model-toolkit - v1.2.1

What's Changed

• update biolink version to 4.1.5 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/162

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.2.0...v1.2.1

- Python
Published by sierra-moxon over 2 years ago

https://github.com/biolink/biolink-model-toolkit - v1.2.0

What's Changed

• Bump jinja2 from 3.1.2 to 3.1.3 by @dependabot in https://github.com/biolink/biolink-model-toolkit/pull/160
• updating biolink 4.1.4 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/161

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.1.4...v1.2.0

- Python
Published by sierra-moxon over 2 years ago

https://github.com/biolink/biolink-model-toolkit - v1.1.4

What's Changed

• fuss with workflows to include an add of kgx with the current bmt by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/158
• Biolink model 4.0 and permissible value descendants and children methods by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/159

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.1.3...v1.1.4

- Python
Published by sierra-moxon over 2 years ago

https://github.com/biolink/biolink-model-toolkit - v1.1.3

What's Changed

• Bump urllib3 from 2.0.2 to 2.0.7 by @dependabot in https://github.com/biolink/biolink-model-toolkit/pull/153
• Biolink model 3.6.0 update, and extra dependency resolution action by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/157

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.1.2...v1.1.3

- Python
Published by sierra-moxon over 2 years ago

https://github.com/biolink/biolink-model-toolkit - v1.1.2

What's Changed

• Parameterized LATESTBIOLINKRELEASE and updated to 3.5.4 by @RichardBruskiewich in https://github.com/biolink/biolink-model-toolkit/pull/149
• get_associations repaired with added inverse matching by @RichardBruskiewich in https://github.com/biolink/biolink-model-toolkit/pull/148
• tweak-pr-148-per-suggestions by @RichardBruskiewich in https://github.com/biolink/biolink-model-toolkit/pull/150

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.1.1...v1.1.2

- Python
Published by sierra-moxon almost 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.1.1

What's Changed

• issue-139-enhance-qualifier-value-validation by @RichardBruskiewich in https://github.com/biolink/biolink-model-toolkit/pull/143
• Bump certifi from 2023.5.7 to 2023.7.22 by @dependabot in https://github.com/biolink/biolink-model-toolkit/pull/142
• small comment fix by @RichardBruskiewich in https://github.com/biolink/biolink-model-toolkit/pull/137
• issue-140-get-associations by @RichardBruskiewich in https://github.com/biolink/biolink-model-toolkit/pull/141
• update to biolink-model version 3.5.3 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/144

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.1.0...v1.1.1

- Python
Published by sierra-moxon almost 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.1.0

What's Changed

• Update toolkit.py by @RichardBruskiewich in https://github.com/biolink/biolink-model-toolkit/pull/136
• update to biolink 3.5.0 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/138

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.0.15...v1.1.0

- Python
Published by sierra-moxon about 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.0.15

What's Changed

• update oaklib by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/130
• Bump requests from 2.30.0 to 2.31.0 by @dependabot in https://github.com/biolink/biolink-model-toolkit/pull/133
• Remove oak dependency by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/134
• fix test; infores parameters no longer in biolink as slots by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/135

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.0.14...v1.0.15

- Python
Published by sierra-moxon about 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.0.14

What's Changed

• Bump pymdown-extensions from 9.11 to 10.0 by @dependabot in https://github.com/biolink/biolink-model-toolkit/pull/131
• Rustsim pinning by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/132

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.0.13...v1.0.14

- Python
Published by sierra-moxon about 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.0.13

What's Changed

• tweak validate_edge method to account for mixins without parentage ba… by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/126
• Update infores file format parser by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/128
• update to biolink-model v3.3.1 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/127

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.0.12...v1.0.13

- Python
Published by sierra-moxon about 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.0.12

What's Changed

• check bte meta knowledge graph for domain/range constraint violations by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/124
• Validate edge method for use in semmeddb domain/range constraint analysis by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/125

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.0.11...v1.0.12

- Python
Published by sierra-moxon over 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.0.11

What's Changed

• remove-duplicate-isreachablefrom_enum-call by @RichardBruskiewich in https://github.com/biolink/biolink-model-toolkit/pull/123

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.0.10...v1.0.11

- Python
Published by sierra-moxon over 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.0.10

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.0.9...v1.0.10

- Python
Published by sierra-moxon over 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.0.9

What's Changed

• Retrieve denormalized properties, fixes #121 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/122

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.0.8...v1.0.9

- Python
Published by sierra-moxon over 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.0.8

update version requirements per release of biolink 3.2.5

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.0.7...v1.0.8

- Python
Published by sierra-moxon over 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.0.7

What's Changed

• update to biolink-model 3.2.4 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/120

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.0.5...v1.0.7

- Python
Published by sierra-moxon over 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.0.6

What's Changed

• update to biolink-model 3.2.3 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/120

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.0.5...v1.0.6

- Python
Published by sierra-moxon over 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.0.5

What's Changed

• Update biolink 3.2.2 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/119

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.0.4...v1.0.5

- Python
Published by sierra-moxon over 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.0.4

What's Changed

• exact, narrow, broad, close, related mappings collection fixes #111 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/115
• Added tests for getallelementbymapping() by @gaurav in https://github.com/biolink/biolink-model-toolkit/pull/112
• add class and slot uris in get_element method, fixes #116 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/117

New Contributors

• @gaurav made their first contribution in https://github.com/biolink/biolink-model-toolkit/pull/112

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.0.3...v1.0.4

- Python
Published by sierra-moxon over 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.0.3

What's Changed

• update poetry.lock file to update bioregistry via oaklib, fixes #113 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/114

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.0.2...v1.0.3

- Python
Published by sierra-moxon over 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.0.2

What's Changed

• Patch small bugs v1.0.0 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/108

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.0.1...v1.0.2

- Python
Published by sierra-moxon over 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.0.1

What's Changed

• patch-small-bugs-v1.0.0 by @RichardBruskiewich in https://github.com/biolink/biolink-model-toolkit/pull/107
• Test type by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/106
• Bump aiohttp from 2.3.10 to 3.7.4 by @dependabot in https://github.com/biolink/biolink-model-toolkit/pull/105

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v1.0.0...v1.0.1

- Python
Published by sierra-moxon over 3 years ago

https://github.com/biolink/biolink-model-toolkit - v1.0.0

What's Changed

• added oaklib and ubergraph as dependencies (hence the major version update)
• Qualifier enum support by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/104

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v0.10.0...v1.0.0

- Python
Published by sierra-moxon over 3 years ago

https://github.com/biolink/biolink-model-toolkit - v0.10.0

What's Changed

• Replaced BMT's internal generator with LinkML SchemaView
• Bump certifi from 2022.9.24 to 2022.12.7 by @dependabot in https://github.com/biolink/biolink-model-toolkit/pull/98
• enum hierarchy support, remove linkml dependency by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/99
• Support predicate maps by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/100
• add test for and fixes #93, fixes #86 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/102

New Contributors

• @dependabot made their first contribution in https://github.com/biolink/biolink-model-toolkit/pull/98

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v0.9.0...v0.10.0

- Python
Published by sierra-moxon over 3 years ago

https://github.com/biolink/biolink-model-toolkit - v0.9.0

What's Changed

• Poetry by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/94
• Poetry by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/95
• push html files in gh-pages by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/96

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/0.8.12...v0.9.0

- Python
Published by sierra-moxon over 3 years ago

https://github.com/biolink/biolink-model-toolkit - v0.8.12

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/0.8.11...0.8.12

- Python
Published by sierra-moxon almost 4 years ago

https://github.com/biolink/biolink-model-toolkit - 0.8.10

What's Changed

• implement isnodeproperty() and isassociationslot() by @RichardBruskiewich in https://github.com/biolink/biolink-model-toolkit/pull/83

New Contributors

• @RichardBruskiewich made their first contribution in https://github.com/biolink/biolink-model-toolkit/pull/83

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/v0.8.9...0.8.10

- Python
Published by sierra-moxon almost 4 years ago

https://github.com/biolink/biolink-model-toolkit - v0.8.8_augustQotM

v0.8.8_augustQotM - special release for august QotM

- Python
Published by sierra-moxon about 4 years ago

https://github.com/biolink/biolink-model-toolkit - v0.8.9

What's Changed

• update biolink model to 3.0.0, fix tests for canonical predicate fixes #78 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/80
• fix up workflows to autodeploy to pypi by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/81

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/0.8.7...v0.8.9

- Python
Published by sierra-moxon about 4 years ago

https://github.com/biolink/biolink-model-toolkit - 0.8.8

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/0.8.6...0.8.8

- Python
Published by sierra-moxon about 4 years ago

https://github.com/biolink/biolink-model-toolkit - 0.8.7

What's Changed

• fix tests with updated model by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/79

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/0.8.6...0.8.7

- Python
Published by sierra-moxon about 4 years ago

https://github.com/biolink/biolink-model-toolkit - 0.8.6

Update version of Biolink Model used in the toolkit. Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/0.8.5...0.8.6

- Python
Published by sierra-moxon about 4 years ago

https://github.com/biolink/biolink-model-toolkit - 0.8.4

What's Changed

• fix tests to work with 2.2.16 bm release by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/77

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/0.8.3...0.8.4

- Python
Published by sierra-moxon over 4 years ago

https://github.com/biolink/biolink-model-toolkit - 0.8.2

What's Changed

• versions by @cbizon in https://github.com/biolink/biolink-model-toolkit/pull/72
• update linkml to 1.1.18 by @sierra-moxon in https://github.com/biolink/biolink-model-toolkit/pull/73

New Contributors

• @cbizon made their first contribution in https://github.com/biolink/biolink-model-toolkit/pull/72

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/0.8.1...0.8.2

- Python
Published by sierra-moxon over 4 years ago

https://github.com/biolink/biolink-model-toolkit - 0.8.1

update linkml and biolink model

Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/0.7.8...0.8.1

- Python
Published by sierra-moxon over 4 years ago

https://github.com/biolink/biolink-model-toolkit - 0.7.8

bumped the version of the biolink-model to 2.2.12 Full Changelog: https://github.com/biolink/biolink-model-toolkit/compare/0.7.7...0.7.8

- Python
Published by sierra-moxon over 4 years ago

https://github.com/biolink/biolink-model-toolkit - 0.7.7

bump version of biolink-model

- Python
Published by sierra-moxon over 4 years ago

https://github.com/biolink/biolink-model-toolkit - 0.7.4

• updated to biolink-model 2.2.3
• added tox, flake8, black formatting suggestions.

- Python
Published by sierra-moxon almost 5 years ago

https://github.com/biolink/biolink-model-toolkit - 0.7.3

adding support for finding mixins in ancestors/descendants methods pinning to biolink-model v2.2.0 add and fix tests

- Python
Published by sierra-moxon about 5 years ago

https://github.com/biolink/biolink-model-toolkit -

• Pin to Biolink Model 1.4.0
• Update methods to accommodate latest changes in the model
• Update tests
• Replace exceptions in get_element with warnings

- Python
Published by deepakunni3 over 5 years ago

https://github.com/biolink/biolink-model-toolkit -

• Fixed bug where get_element was not parsing input names properly
• Fixed bug where getancestors and getdescendants were returning derived slots
• Make lookup by name be case-insensitive as a fallback

- Python
Published by deepakunni3 over 5 years ago

https://github.com/biolink/biolink-model-toolkit -

• Added reflexive option to getancestors and getdescendants
• Added formatted option to return elements formatted as CURIEs
• Added support for parsing biolink names in sentence case, CamelCase, and snake_case
• Deprecated names method and add getallelements instead
• Added new methods to Toolkit class
• Added support for fetching elements based on their aliases

- Python
Published by deepakunni3 over 5 years ago

https://github.com/biolink/biolink-model-toolkit -

• Add missing methods that are to be deprecated
• Remove access to deprecated methods within BMT
• Tidy up logging

- Python
Published by deepakunni3 over 5 years ago

https://github.com/biolink/biolink-model-toolkit -

• Added more convenience methods
• Deprecated methods and add their replacement
• Updated tests
• Updated README.md
• Pin to Biolink Model v1.3.9

- Python
Published by deepakunni3 over 5 years ago