linkml - v1.9.4-rc2

What's Changed

• update linkml-runtime dependency by @sierra-moxon in https://github.com/linkml/linkml/pull/2870

Full Changelog: https://github.com/linkml/linkml/compare/v1.9.4-rc1...v1.9.4-rc2

- Python
Published by sierra-moxon 10 months ago

linkml - v1.9.4-rc1

What's Changed

• Allow excluding abstract classes from ERD Diagram by @vladistan in https://github.com/linkml/linkml/pull/2840
• Sort output of ErdDiagram for repeatable output by @vladistan in https://github.com/linkml/linkml/pull/2846
• exclude entities from standard naming linter rule by @turbomam in https://github.com/linkml/linkml/pull/2793
• migrate to uv by @iQuxLE in https://github.com/linkml/linkml/pull/2779
• Update person schema by @vladistan in https://github.com/linkml/linkml/pull/2848
• Bump actions/checkout to v5 in github workflows (closes #2864) by @EOltmanns in https://github.com/linkml/linkml/pull/2865
• Update contributing.md by @cmungall in https://github.com/linkml/linkml/pull/2859
• Enabling some disabled schemaloader tests for improved test coverage by @ialarmedalien in https://github.com/linkml/linkml/pull/2834
• refactor: move cli utils by @Silvanoc in https://github.com/linkml/linkml/pull/2715
• Add tests to ensure that class_uri becomes exactMatch in JSON-LD and RDF by @Silvanoc in https://github.com/linkml/linkml/pull/2692

New Contributors

• @EOltmanns made their first contribution in https://github.com/linkml/linkml/pull/2865

Full Changelog: https://github.com/linkml/linkml/compare/v1.9.3...v1.9.4-rc1

- Python
Published by sierra-moxon 10 months ago

linkml - v1.9.3

What's Changed

• Use enum value rather than enum for click meta click option in pydanticgen by @kevinschaper in https://github.com/linkml/linkml/pull/2686
• Adding stub test for https://github.com/orgs/linkml/discussions/2154 by @cmungall in https://github.com/linkml/linkml/pull/2156
• Adding notebooks to dev path and adding notebooks for stackoverflow Qs by @cmungall in https://github.com/linkml/linkml/pull/1755
• test rewrite rules to pytest closes #1722 by @tfliss in https://github.com/linkml/linkml/pull/2704
• Add action to run tests with selected linkml-runtime branches by @dalito in https://github.com/linkml/linkml/pull/2575
• Remove special case for Windows in test_docgen by @dalito in https://github.com/linkml/linkml/pull/2698
• Bump docker/setup-qemu-action from 2 to 3 by @dependabot[bot] in https://github.com/linkml/linkml/pull/2739
• Bug fix: remove duplicate -d option in click options by @ialarmedalien in https://github.com/linkml/linkml/pull/2717
• Bump ts-graphviz/setup-graphviz from 1 to 2 by @dependabot[bot] in https://github.com/linkml/linkml/pull/2736
• Bump codecov/codecov-action from 5.4.2 to 5.4.3 by @dependabot[bot] in https://github.com/linkml/linkml/pull/2737
• Bump docker/metadata-action from 4 to 5 by @dependabot[bot] in https://github.com/linkml/linkml/pull/2738
• Issue2708 gen doc template fixes by @dalito in https://github.com/linkml/linkml/pull/2709
• Format misc repo files pre-commit compliant by @vladistan in https://github.com/linkml/linkml/pull/2758
• tests: validate context using rdf by @Silvanoc in https://github.com/linkml/linkml/pull/2678
• Show information about asserted rules on class documentation pages by @sujaypatil96 in https://github.com/linkml/linkml/pull/2640
• Reformat docs to be pre-commit compliant by @vladistan in https://github.com/linkml/linkml/pull/2761
• Make generator templates pre-commit compliant by @vladistan in https://github.com/linkml/linkml/pull/2762
• Add understand to the git ignore by @vladistan in https://github.com/linkml/linkml/pull/2764
• Make PersonInfo schema pre-commit compliant by @vladistan in https://github.com/linkml/linkml/pull/2765
• Remove py38 from action for testing unreleased linkml-runtime by @dalito in https://github.com/linkml/linkml/pull/2766
• Adding linter rule to find undeclared slots by @ialarmedalien in https://github.com/linkml/linkml/pull/2749
• Make person schema generated files pre-commit compliant by @vladistan in https://github.com/linkml/linkml/pull/2767
• Add .editorconfig by @dalito in https://github.com/linkml/linkml/pull/2763
• Update tox config and move it to pyproject.toml by @dalito in https://github.com/linkml/linkml/pull/2759
• Switch to using ruff for code formatting by @ialarmedalien in https://github.com/linkml/linkml/pull/2774
• Call sqla templates directly by @ialarmedalien in https://github.com/linkml/linkml/pull/2773
• Fix enum URL generation for Mermaid diagrams by @dalito in https://github.com/linkml/linkml/pull/2751
• Fix typo: name of sqlite3 in tutorial by @kimrutherford in https://github.com/linkml/linkml/pull/2784
• Make test code pre-commit compliant by @vladistan in https://github.com/linkml/linkml/pull/2771
• Documentation: Add enum RDF rendering to modeling.md by @matentzn in https://github.com/linkml/linkml/pull/2746
• Update Biolink model to 4.2.5 by @vladistan in https://github.com/linkml/linkml/pull/2783
• test(convert): fix and improve test by @Silvanoc in https://github.com/linkml/linkml/pull/2724
• Ignore vendored test data by @vladistan in https://github.com/linkml/linkml/pull/2780
• Adding linter rule to check that ranges are valid by @ialarmedalien in https://github.com/linkml/linkml/pull/2781
• Replace NMDC schema with a tiny file by @vladistan in https://github.com/linkml/linkml/pull/2801
• Adding linter rule to perform checks on schema types by @ialarmedalien in https://github.com/linkml/linkml/pull/2789
• Make pre-commit happy with test input data by @vladistan in https://github.com/linkml/linkml/pull/2770
• Minor Spelling fixes by @vladistan in https://github.com/linkml/linkml/pull/2804
• Small formatting fixes by @vladistan in https://github.com/linkml/linkml/pull/2806
• Make misc repo files pre-commit compliant by @vladistan in https://github.com/linkml/linkml/pull/2810
• Use Pathlib consistently when calling generators by @vladistan in https://github.com/linkml/linkml/pull/2811
• Fix json schema generator by @vladistan in https://github.com/linkml/linkml/pull/2815
• Fix markdown generator by @vladistan in https://github.com/linkml/linkml/pull/2817
• Fix generic generator by @vladistan in https://github.com/linkml/linkml/pull/2814
• Fix SQL Schema generator to create linter compliant files by @vladistan in https://github.com/linkml/linkml/pull/2816
• Delete unnecessary files from the repo by @vladistan in https://github.com/linkml/linkml/pull/2823
• Temporary allow spell check to ignore 2 typos coming from the runtime by @vladistan in https://github.com/linkml/linkml/pull/2824
• Convert invalid short form JSON to standard YAML by @vladistan in https://github.com/linkml/linkml/pull/2825
• Add pre-commit to code quality check by @vladistan in https://github.com/linkml/linkml/pull/2744
• Index creation by @VictoriaSavageNNL in https://github.com/linkml/linkml/pull/2775
• Clean-up emit_metadata as alias for metadata by @Silvanoc in https://github.com/linkml/linkml/pull/2796
• fix(generators): revert flag removal by @Silvanoc in https://github.com/linkml/linkml/pull/2835
• Pass permissible_value title to constructor in generated code by @pkalita-lbl in https://github.com/linkml/linkml/pull/2838
• update to linkml-runtime 1.9.4 by @sierra-moxon in https://github.com/linkml/linkml/pull/2839
• Fix doc generation to add PURL URIs for enums by @dalito in https://github.com/linkml/linkml/pull/2711

New Contributors

• @kimrutherford made their first contribution in https://github.com/linkml/linkml/pull/2784

Full Changelog: https://github.com/linkml/linkml/compare/v1.9.2...v1.9.3

- Python
Published by sierra-moxon 11 months ago

linkml - v1.9.3-rc3

What's Changed

• update to linkml-runtime 1.9.4 by @sierra-moxon in https://github.com/linkml/linkml/pull/2839
• Fix doc generation to add PURL URIs for enums by @dalito in https://github.com/linkml/linkml/pull/2711

Full Changelog: https://github.com/linkml/linkml/compare/v1.9.3-rc2...v1.9.3-rc3

- Python
Published by sierra-moxon 11 months ago

linkml - v1.9.3-rc2

What's Changed

• Issue2708 gen doc template fixes by @dalito in https://github.com/linkml/linkml/pull/2709
• Format misc repo files pre-commit compliant by @vladistan in https://github.com/linkml/linkml/pull/2758
• tests: validate context using rdf by @Silvanoc in https://github.com/linkml/linkml/pull/2678
• Show information about asserted rules on class documentation pages by @sujaypatil96 in https://github.com/linkml/linkml/pull/2640
• Reformat docs to be pre-commit compliant by @vladistan in https://github.com/linkml/linkml/pull/2761
• Make generator templates pre-commit compliant by @vladistan in https://github.com/linkml/linkml/pull/2762
• Add understand to the git ignore by @vladistan in https://github.com/linkml/linkml/pull/2764
• Make PersonInfo schema pre-commit compliant by @vladistan in https://github.com/linkml/linkml/pull/2765
• Remove py38 from action for testing unreleased linkml-runtime by @dalito in https://github.com/linkml/linkml/pull/2766
• Adding linter rule to find undeclared slots by @ialarmedalien in https://github.com/linkml/linkml/pull/2749
• Make person schema generated files pre-commit compliant by @vladistan in https://github.com/linkml/linkml/pull/2767
• Add .editorconfig by @dalito in https://github.com/linkml/linkml/pull/2763
• Update tox config and move it to pyproject.toml by @dalito in https://github.com/linkml/linkml/pull/2759
• Switch to using ruff for code formatting by @ialarmedalien in https://github.com/linkml/linkml/pull/2774
• Call sqla templates directly by @ialarmedalien in https://github.com/linkml/linkml/pull/2773
• Fix enum URL generation for Mermaid diagrams by @dalito in https://github.com/linkml/linkml/pull/2751
• Fix typo: name of sqlite3 in tutorial by @kimrutherford in https://github.com/linkml/linkml/pull/2784
• Make test code pre-commit compliant by @vladistan in https://github.com/linkml/linkml/pull/2771
• Documentation: Add enum RDF rendering to modeling.md by @matentzn in https://github.com/linkml/linkml/pull/2746
• Update Biolink model to 4.2.5 by @vladistan in https://github.com/linkml/linkml/pull/2783
• test(convert): fix and improve test by @Silvanoc in https://github.com/linkml/linkml/pull/2724
• Ignore vendored test data by @vladistan in https://github.com/linkml/linkml/pull/2780
• Adding linter rule to check that ranges are valid by @ialarmedalien in https://github.com/linkml/linkml/pull/2781
• Replace NMDC schema with a tiny file by @vladistan in https://github.com/linkml/linkml/pull/2801
• Adding linter rule to perform checks on schema types by @ialarmedalien in https://github.com/linkml/linkml/pull/2789
• Make pre-commit happy with test input data by @vladistan in https://github.com/linkml/linkml/pull/2770
• Minor Spelling fixes by @vladistan in https://github.com/linkml/linkml/pull/2804
• Small formatting fixes by @vladistan in https://github.com/linkml/linkml/pull/2806
• Make misc repo files pre-commit compliant by @vladistan in https://github.com/linkml/linkml/pull/2810
• Use Pathlib consistently when calling generators by @vladistan in https://github.com/linkml/linkml/pull/2811
• Fix json schema generator by @vladistan in https://github.com/linkml/linkml/pull/2815
• Fix markdown generator by @vladistan in https://github.com/linkml/linkml/pull/2817
• Fix generic generator by @vladistan in https://github.com/linkml/linkml/pull/2814
• Fix SQL Schema generator to create linter compliant files by @vladistan in https://github.com/linkml/linkml/pull/2816
• Delete unnecessary files from the repo by @vladistan in https://github.com/linkml/linkml/pull/2823
• Temporary allow spell check to ignore 2 typos coming from the runtime by @vladistan in https://github.com/linkml/linkml/pull/2824
• Convert invalid short form JSON to standard YAML by @vladistan in https://github.com/linkml/linkml/pull/2825
• Add pre-commit to code quality check by @vladistan in https://github.com/linkml/linkml/pull/2744
• Index creation by @VictoriaSavageNNL in https://github.com/linkml/linkml/pull/2775
• Clean-up emit_metadata as alias for metadata by @Silvanoc in https://github.com/linkml/linkml/pull/2796
• fix(generators): revert flag removal by @Silvanoc in https://github.com/linkml/linkml/pull/2835
• Pass permissible_value title to constructor in generated code by @pkalita-lbl in https://github.com/linkml/linkml/pull/2838

New Contributors

• @kimrutherford made their first contribution in https://github.com/linkml/linkml/pull/2784

Full Changelog: https://github.com/linkml/linkml/compare/v1.9.3-rc1...v1.9.3-rc2

- Python
Published by sierra-moxon 11 months ago

linkml - v1.9.3-rc1

What's Changed

• Use enum value rather than enum for click meta click option in pydanticgen by @kevinschaper in https://github.com/linkml/linkml/pull/2686
• Adding stub test for https://github.com/orgs/linkml/discussions/2154 by @cmungall in https://github.com/linkml/linkml/pull/2156
• Adding notebooks to dev path and adding notebooks for stackoverflow Qs by @cmungall in https://github.com/linkml/linkml/pull/1755
• test rewrite rules to pytest closes #1722 by @tfliss in https://github.com/linkml/linkml/pull/2704
• Add action to run tests with selected linkml-runtime branches by @dalito in https://github.com/linkml/linkml/pull/2575
• Remove special case for Windows in test_docgen by @dalito in https://github.com/linkml/linkml/pull/2698
• Bump docker/setup-qemu-action from 2 to 3 by @dependabot in https://github.com/linkml/linkml/pull/2739
• Bug fix: remove duplicate -d option in click options by @ialarmedalien in https://github.com/linkml/linkml/pull/2717
• Bump ts-graphviz/setup-graphviz from 1 to 2 by @dependabot in https://github.com/linkml/linkml/pull/2736
• Bump codecov/codecov-action from 5.4.2 to 5.4.3 by @dependabot in https://github.com/linkml/linkml/pull/2737
• Bump docker/metadata-action from 4 to 5 by @dependabot in https://github.com/linkml/linkml/pull/2738

Full Changelog: https://github.com/linkml/linkml/compare/v1.9.2...v1.9.3-rc1

- Python
Published by sierra-moxon about 1 year ago

linkml - v1.9.2

What's Changed

• Multiple tag/value pairs in annotations schema block should appear on different lines by @sujaypatil96 in https://github.com/linkml/linkml/pull/2611
• Appropriately handle linking of classes with slots that have a range: None asserted on them by @sujaypatil96 in https://github.com/linkml/linkml/pull/2601
• fix(recommendedslotsplugin): Fix warning output to correctly set slot location in RecommendedSlotsPlugin by @clevinson in https://github.com/linkml/linkml/pull/2629
• fix(jsonldgen): use correct ContextGenerator field by @Silvanoc in https://github.com/linkml/linkml/pull/2621
• Use URIs with element type for gen-doc option --subfolder-type-separation by @dalito in https://github.com/linkml/linkml/pull/2562
• Update csv.rst by @timalamenciak in https://github.com/linkml/linkml/pull/2588
• Addressing Issue #1915, CLI update and DDL generation update by @VictoriaSavageNNL in https://github.com/linkml/linkml/pull/2612
• Deprecate gen-markdown generator by @sujaypatil96 in https://github.com/linkml/linkml/pull/2637
• Incorrect syntax in docs page for markdown/documentation generator by @sujaypatil96 in https://github.com/linkml/linkml/pull/2643
• Restructuring content between Markdown/Documentation generator pages by @sujaypatil96 in https://github.com/linkml/linkml/pull/2646
• add several versions of logo / icon by @nlharris in https://github.com/linkml/linkml/pull/2656
• Update pyproject.toml & actions to poetry 2.x / PEP 621 by @dalito in https://github.com/linkml/linkml/pull/2633
• Don't try to upload coverage data for dependabot PRs by @dalito in https://github.com/linkml/linkml/pull/2664
• Fix execute tutorial script and update tutorials 1, 3, 4 by @rly in https://github.com/linkml/linkml/pull/2641
• Bump JamesIves/github-pages-deploy-action from 4.4.1 to 4.7.3 by @dependabot in https://github.com/linkml/linkml/pull/2657
• Addressing Issue #2414 and #2554 - Abstract Class DDL by @VictoriaSavageNNL in https://github.com/linkml/linkml/pull/2614
• Generator template fixes: ensure multiline descriptions are dealt with correctly by @ialarmedalien in https://github.com/linkml/linkml/pull/2607
• Bug fix: ensure that pydantic pattern field validators work correctly on multivalued entries by @ialarmedalien in https://github.com/linkml/linkml/pull/2668
• Misc SQL transform code and test edits by @ialarmedalien in https://github.com/linkml/linkml/pull/2649
• Bump docker/setup-buildx-action from 2 to 3 by @dependabot in https://github.com/linkml/linkml/pull/2658
• Bump docker/login-action from 2 to 3 by @dependabot in https://github.com/linkml/linkml/pull/2660
• rollup transformer implementation #2568 by @iQuxLE in https://github.com/linkml/linkml/pull/2618
• Bump docker/build-push-action from 3 to 6 by @dependabot in https://github.com/linkml/linkml/pull/2661
• Bump actions/create-github-app-token from 2.0.2 to 2.0.5 by @dependabot in https://github.com/linkml/linkml/pull/2662
• Dalito fork issue2578 fix uri in snapshot by @sierra-moxon in https://github.com/linkml/linkml/pull/2670
• Basic Pandera Generator for Initial Merge by @tfliss in https://github.com/linkml/linkml/pull/2587
• Removing cruft and adding a very basic test to the rollup transformer by @ialarmedalien in https://github.com/linkml/linkml/pull/2672
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2642
• Add truncate_descriptions option to docgen by @ialarmedalien in https://github.com/linkml/linkml/pull/2639
• Deprecate gen-yuml generator by @madanucd in https://github.com/linkml/linkml/pull/2665
• first pass at howto for ontologies as values by @cmungall in https://github.com/linkml/linkml/pull/1585
• remove context setting in mermaid diagram generator by @sierra-moxon, @dalito, @ialarmedalien in https://github.com/linkml/linkml/pull/2675

New Contributors

• @clevinson made their first contribution in https://github.com/linkml/linkml/pull/2629
• @VictoriaSavageNNL made their first contribution in https://github.com/linkml/linkml/pull/2612
• @dependabot made their first contribution in https://github.com/linkml/linkml/pull/2657
• @iQuxLE made their first contribution in https://github.com/linkml/linkml/pull/2618

Full Changelog: https://github.com/linkml/linkml/compare/v1.9.1...v1.9.2

- Python
Published by sierra-moxon about 1 year ago

linkml - v1.9.2-rc1

What's Changed

• Multiple tag/value pairs in annotations schema block should appear on different lines by @sujaypatil96 in https://github.com/linkml/linkml/pull/2611
• Appropriately handle linking of classes with slots that have a range: None asserted on them by @sujaypatil96 in https://github.com/linkml/linkml/pull/2601
• fix(recommendedslotsplugin): Fix warning output to correctly set slot location in RecommendedSlotsPlugin by @clevinson in https://github.com/linkml/linkml/pull/2629
• fix(jsonldgen): use correct ContextGenerator field by @Silvanoc in https://github.com/linkml/linkml/pull/2621
• Use URIs with element type for gen-doc option --subfolder-type-separation by @dalito in https://github.com/linkml/linkml/pull/2562
• Update csv.rst by @timalamenciak in https://github.com/linkml/linkml/pull/2588
• Addressing Issue #1915, CLI update and DDL generation update by @VictoriaSavageNNL in https://github.com/linkml/linkml/pull/2612
• Deprecate gen-markdown generator by @sujaypatil96 in https://github.com/linkml/linkml/pull/2637
• Incorrect syntax in docs page for markdown/documentation generator by @sujaypatil96 in https://github.com/linkml/linkml/pull/2643
• Restructuring content between Markdown/Documentation generator pages by @sujaypatil96 in https://github.com/linkml/linkml/pull/2646
• add several versions of logo / icon by @nlharris in https://github.com/linkml/linkml/pull/2656
• Update pyproject.toml & actions to poetry 2.x / PEP 621 by @dalito in https://github.com/linkml/linkml/pull/2633
• Don't try to upload coverage data for dependabot PRs by @dalito in https://github.com/linkml/linkml/pull/2664
• Fix execute tutorial script and update tutorials 1, 3, 4 by @rly in https://github.com/linkml/linkml/pull/2641
• Bump JamesIves/github-pages-deploy-action from 4.4.1 to 4.7.3 by @dependabot in https://github.com/linkml/linkml/pull/2657
• Addressing Issue #2414 and #2554 - Abstract Class DDL by @VictoriaSavageNNL in https://github.com/linkml/linkml/pull/2614
• Generator template fixes: ensure multiline descriptions are dealt with correctly by @ialarmedalien in https://github.com/linkml/linkml/pull/2607
• Bug fix: ensure that pydantic pattern field validators work correctly on multivalued entries by @ialarmedalien in https://github.com/linkml/linkml/pull/2668
• Misc SQL transform code and test edits by @ialarmedalien in https://github.com/linkml/linkml/pull/2649
• Bump docker/setup-buildx-action from 2 to 3 by @dependabot in https://github.com/linkml/linkml/pull/2658
• Bump docker/login-action from 2 to 3 by @dependabot in https://github.com/linkml/linkml/pull/2660
• rollup transformer implementation #2568 by @iQuxLE in https://github.com/linkml/linkml/pull/2618
• Bump docker/build-push-action from 3 to 6 by @dependabot in https://github.com/linkml/linkml/pull/2661
• Bump actions/create-github-app-token from 2.0.2 to 2.0.5 by @dependabot in https://github.com/linkml/linkml/pull/2662
• Dalito fork issue2578 fix uri in snapshot by @sierra-moxon in https://github.com/linkml/linkml/pull/2670
• Basic Pandera Generator for Initial Merge by @tfliss in https://github.com/linkml/linkml/pull/2587
• Removing cruft and adding a very basic test to the rollup transformer by @ialarmedalien in https://github.com/linkml/linkml/pull/2672
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2642
• Add truncate_descriptions option to docgen by @ialarmedalien in https://github.com/linkml/linkml/pull/2639
• Deprecate gen-yuml generator by @madanucd in https://github.com/linkml/linkml/pull/2665
• first pass at howto for ontologies as values by @cmungall in https://github.com/linkml/linkml/pull/1585
• remove context setting in mermaid diagram generator by @sierra-moxon in https://github.com/linkml/linkml/pull/2675

New Contributors

• @clevinson made their first contribution in https://github.com/linkml/linkml/pull/2629
• @VictoriaSavageNNL made their first contribution in https://github.com/linkml/linkml/pull/2612
• @dependabot made their first contribution in https://github.com/linkml/linkml/pull/2657
• @iQuxLE made their first contribution in https://github.com/linkml/linkml/pull/2618

Full Changelog: https://github.com/linkml/linkml/compare/v1.9.1...v1.9.2-rc1

- Python
Published by sierra-moxon about 1 year ago

linkml - v1.9.1

What's Changed

• Create model-property-graphs.md by @mbrush in https://github.com/linkml/linkml/pull/2549
• Add a new argument to the SHACL generator to exclude imported elements by @vincentkelleher in https://github.com/linkml/linkml/pull/2508
• Punning-related FAQ in Modeling Section by @madanucd in https://github.com/linkml/linkml/pull/2574
• Add deprecation banner/message to element documentation page titles – round 2 by @sujaypatil96 in https://github.com/linkml/linkml/pull/2583
• Behavior of alias in case it is asserted on slot in schema file by @sujaypatil96 in https://github.com/linkml/linkml/pull/2584
• Explicit --materialize-attributes and --materialize-patterns take precedence over --materialize by @sujaypatil96 in https://github.com/linkml/linkml/pull/2569
• fix test to be less rigid in formating issues to help push through li… by @sierra-moxon in https://github.com/linkml/linkml/pull/2597
• Fix nested relative imports by @will-0 in https://github.com/linkml/linkml/pull/2576
• Bump removed_from annotation in deprecation protocol, remove linkml dataops as it is causing errors in runtime "test with upstream" dependencies by @sierra-moxon in https://github.com/linkml/linkml/pull/2598
• linter config schema and python with exclude_type by @turbomam in https://github.com/linkml/linkml/pull/2524
• Pr 2358 - branch version of https://github.com/linkml/linkml/pull/2358 for ease of coordination by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2605
• Update pypi action, add test action for pypi dist deployment by @sierra-moxon in https://github.com/linkml/linkml/pull/2617
• update docker action to only push on release by @sierra-moxon in https://github.com/linkml/linkml/pull/2631

New Contributors

• @mbrush made their first contribution in https://github.com/linkml/linkml/pull/2549
• @will-0 made their first contribution in https://github.com/linkml/linkml/pull/2576

Full Changelog: https://github.com/linkml/linkml/compare/v1.8.7...v1.9.1

- Python
Published by sierra-moxon about 1 year ago

linkml - v1.9.1-rc3

What's Changed

• update docker action to only push on release by @sierra-moxon in https://github.com/linkml/linkml/pull/2631

Full Changelog: https://github.com/linkml/linkml/compare/v1.9.1-rc2...v1.9.1-rc3

- Python
Published by sierra-moxon about 1 year ago

linkml - v1.9.1-rc2

What's Changed

• Update pypi action, add test action for pypi dist deployment by @sierra-moxon in https://github.com/linkml/linkml/pull/2617

Full Changelog: https://github.com/linkml/linkml/compare/v1.9.1-rc1...v1.9.1-rc2

- Python
Published by sierra-moxon about 1 year ago

linkml - v1.9.1-rc1

What's Changed

• Fix nested relative imports by @will-0 in https://github.com/linkml/linkml/pull/2576
• Bump removed_from annotation in deprecation protocol, remove linkml dataops as it is causing errors in runtime "test with upstream" dependencies by @sierra-moxon in https://github.com/linkml/linkml/pull/2598
• linter config schema and python with exclude_type by @turbomam in https://github.com/linkml/linkml/pull/2524
• Pr 2358 - branch version of https://github.com/linkml/linkml/pull/2358 for ease of coordination by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2605

New Contributors

• @will-0 made their first contribution in https://github.com/linkml/linkml/pull/2576

Full Changelog: https://github.com/linkml/linkml/compare/v1.9.0-rc1...v1.9.1-rc1

- Python
Published by sierra-moxon about 1 year ago

linkml - v1.9.0-rc1

What's Changed

• Create model-property-graphs.md by @mbrush in https://github.com/linkml/linkml/pull/2549
• Add a new argument to the SHACL generator to exclude imported elements by @vincentkelleher in https://github.com/linkml/linkml/pull/2508
• Punning-related FAQ in Modeling Section by @madanucd in https://github.com/linkml/linkml/pull/2574
• Add deprecation banner/message to element documentation page titles – round 2 by @sujaypatil96 in https://github.com/linkml/linkml/pull/2583
• Behavior of alias in case it is asserted on slot in schema file by @sujaypatil96 in https://github.com/linkml/linkml/pull/2584
• Explicit --materialize-attributes and --materialize-patterns take precedence over --materialize by @sujaypatil96 in https://github.com/linkml/linkml/pull/2569
• fix test to be less rigid in formating issues to help push through li… by @sierra-moxon in https://github.com/linkml/linkml/pull/2597

New Contributors

• @mbrush made their first contribution in https://github.com/linkml/linkml/pull/2549

Full Changelog: https://github.com/linkml/linkml/compare/v1.8.7...v1.9.0-rc1

- Python
Published by sierra-moxon about 1 year ago

linkml - v1.8.7

What's Changed

• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2460
• 1720 convert tests in teststest notebooks to pytest by @tfliss in https://github.com/linkml/linkml/pull/2488
• Convert test_validation/ to pytest and logging by @tfliss in https://github.com/linkml/linkml/pull/2505
• Adds SHACL ifabsent handling for type uriorcurie by @jsheunis in https://github.com/linkml/linkml/pull/2503
• handle schemaview's prefixes as JsonObj instead of dict in gen-linkml by @sierra-moxon in https://github.com/linkml/linkml/pull/2470
• Fix handling of equalsstringin to use OWL enumerated datatypes by @Angatar in https://github.com/linkml/linkml/pull/2519
• [tests][ci] Run slow tests separately by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2389
• Enhancing OWL tests for equalsstringin by @cmungall in https://github.com/linkml/linkml/pull/2541
• Add standalone mermaid class diagram generator by @sujaypatil96 in https://github.com/linkml/linkml/pull/2529
• Add materialize patterns flag to JSON Schema generator by @madanucd in https://github.com/linkml/linkml/pull/2547
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2544

New Contributors

• @Angatar made their first contribution in https://github.com/linkml/linkml/pull/2519
• @madanucd made their first contribution in https://github.com/linkml/linkml/pull/2547

Full Changelog: https://github.com/linkml/linkml/compare/v1.8.6...v1.8.7

- Python
Published by sujaypatil96 over 1 year ago

linkml - v1.8.6

What's Changed

• gen-typescript print to stdout if output not specified by @kevinschaper in https://github.com/linkml/linkml/pull/2379
• Add deprecation warnings to validators by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2386
• [jsonschemagen] Add lifecycle methods to jsonschemagen by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2369
• Fix up wording on monotonicity -- it is existing ones to not be overridden by @yarikoptic in https://github.com/linkml/linkml/pull/2392
• Tests plantumlgen rest call by @Silvanoc in https://github.com/linkml/linkml/pull/2374
• feat: allow enum IRI separator override in owlgen.py by @egavard in https://github.com/linkml/linkml/pull/2376
• Bundle originating error/object to linkml.validator.report.ValidationResult by @candleindark in https://github.com/linkml/linkml/pull/2363
• Make materialization (attributes and patterns) default behaviour in gen-linkml by @sujaypatil96 in https://github.com/linkml/linkml/pull/2341
• Fix typo by @nlharris in https://github.com/linkml/linkml/pull/2396
• add 'linke' and 'moxon' to list of words to ignore by @nlharris in https://github.com/linkml/linkml/pull/2398
• add "All GitHub Contributors" by @nlharris in https://github.com/linkml/linkml/pull/2397
• Pass default values to pydantic via keyword argument by @ptgolden in https://github.com/linkml/linkml/pull/2390
• Add documentation on using URI as class for slot range by @amc-corey-cox in https://github.com/linkml/linkml/pull/2408
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2375
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2427
• fix(run-examples): handle inlined dictionaries by @Silvanoc in https://github.com/linkml/linkml/pull/2426
• SHACL generator: Support min/max/exact cardinality by @elichad in https://github.com/linkml/linkml/pull/2440
• rm http_cache.sqlite by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2410
• Issue 2419 tutorial2 validation fails by @joga4er in https://github.com/linkml/linkml/pull/2443
• Shacl generator: Include slot annotations when if any_of is used by @elichad in https://github.com/linkml/linkml/pull/2441
• Issue 2447 - add cli option for mermaid with or without markdown compatibility using existing 'format' parameter by @sierra-moxon in https://github.com/linkml/linkml/pull/2453
• add prefix map file by @GertjanBisschop in https://github.com/linkml/linkml/pull/2467
• Inlined types management by the JSON-LD context generator by @vincentkelleher in https://github.com/linkml/linkml/pull/2461
• add linter check that one and only one tree_root is found if TreeRootClassRule config rule is configured by @sierra-moxon in https://github.com/linkml/linkml/pull/2468
• Added rules FAQ to address issue #2452 by @timalamenciak in https://github.com/linkml/linkml/pull/2454
• Fix AnyShapeArrays re: recursive type aliases in recent versions of pydantic by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2481
• initial dbml generator by @sierra-moxon in https://github.com/linkml/linkml/pull/2480
• Issue 1719 convert test linter to pytests by @tfliss in https://github.com/linkml/linkml/pull/2484
• Issue 1720 convert test prefixes to pytests by @tfliss in https://github.com/linkml/linkml/pull/2486

New Contributors

• @egavard made their first contribution in https://github.com/linkml/linkml/pull/2376
• @ptgolden made their first contribution in https://github.com/linkml/linkml/pull/2390
• @elichad made their first contribution in https://github.com/linkml/linkml/pull/2440
• @joga4er made their first contribution in https://github.com/linkml/linkml/pull/2443
• @GertjanBisschop made their first contribution in https://github.com/linkml/linkml/pull/2467
• @timalamenciak made their first contribution in https://github.com/linkml/linkml/pull/2454
• @tfliss made their first contribution in https://github.com/linkml/linkml/pull/2484

Full Changelog: https://github.com/linkml/linkml/compare/v1.8.5...v1.8.6

- Python
Published by kevinschaper over 1 year ago

linkml - v1.8.5

What's Changed

• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2355
• [docgen] improve methods configurability for derived schemas by @Silvanoc in https://github.com/linkml/linkml/pull/2365
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2368
• [plantuml] mark and skip plantuml docker tests when docker not present by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2373
• fix 2279 - use base types in IfAbsentProcessor by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2281
• fix: generated python with ifabsent by @Silvanoc in https://github.com/linkml/linkml/pull/2329
• test: add pytest-xdist plugin for parallelization by @Silvanoc in https://github.com/linkml/linkml/pull/2347
• feat(graphql): add support for enumerations by @Silvanoc in https://github.com/linkml/linkml/pull/2303

Full Changelog: https://github.com/linkml/linkml/compare/v1.8.4...v1.8.5

- Python
Published by sierra-moxon over 1 year ago

linkml - v1.8.4

What's Changed

• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2278
• [pydanticgen] Sort Imports by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2287
• Added support for alias metaslot in pydantic by @cmungall in https://github.com/linkml/linkml/pull/2291
• Additional test for logicalmodeltransformer by @cmungall in https://github.com/linkml/linkml/pull/2290
• fix autogen'd pydantic regex pattern validator by @daniel-ji in https://github.com/linkml/linkml/pull/2273
• Addition to #2291, the import compliance test now marked pydantic-complete by @cmungall in https://github.com/linkml/linkml/pull/2293
• updating owlgen to use implements metaslot when available for permissible values by @cmungall in https://github.com/linkml/linkml/pull/2294
• [QoL] fix deprecation warnings by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2288
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2298
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2317
• add RDFGenerator to linkml/generators/init.py by @turbomam in https://github.com/linkml/linkml/pull/2311
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2327
• Array Representation 2: numpydantic by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2178
• [perf] minor pydanticgen perf boosts - remove unnecessary object creation by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2218
• SHACL generator ignore subclass properties by @vincentkelleher in https://github.com/linkml/linkml/pull/2318
• Add output option to TS generator by @vladistan in https://github.com/linkml/linkml/pull/2135
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2332
• Improve logging by replacing the use of the root logger by module-level loggers by @candleindark in https://github.com/linkml/linkml/pull/2323
• Introduce a docgen subfolder type separation argument by @vincentkelleher in https://github.com/linkml/linkml/pull/2306
• Adding uniqueness constraint tests. by @cmungall in https://github.com/linkml/linkml/pull/2338

New Contributors

• @candleindark made their first contribution in https://github.com/linkml/linkml/pull/2323

Full Changelog: https://github.com/linkml/linkml/compare/v1.8.3...v1.8.4

- Python
Published by madanucd over 1 year ago

linkml - v1.8.3

What's Changed

• simplify feature request template by @nlharris in https://github.com/linkml/linkml/pull/2266
• Windows testing fixes by @dalito in https://github.com/linkml/linkml/pull/2271
• Unify ifabsent processing for Shacl, Pydantic and Python by @vincentkelleher in https://github.com/linkml/linkml/pull/2175
• Remove @vocab from enums in JSON LD contexts by @vincentkelleher in https://github.com/linkml/linkml/pull/2152
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2269
• Add version option to high-level CLI groups by @pkalita-lbl in https://github.com/linkml/linkml/pull/2276
• Update java.rst - vs _ in output-directory option by @jjkoehorst in https://github.com/linkml/linkml/pull/2274

New Contributors

• @jjkoehorst made their first contribution in https://github.com/linkml/linkml/pull/2274

Full Changelog: https://github.com/linkml/linkml/compare/v1.8.2...v1.8.3

- Python
Published by amc-corey-cox almost 2 years ago

linkml - v1.8.2

What's Changed

• Remove support for pydantic v1 stage 1 by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2195
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2198
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2207
• [pydanticgen] Simplify pydantic generator render method by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2019
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2214
• [pydanticgen] Split generation :) by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2208
• gen-pydantic not properly handling multivalued, required fields. by @daniel-ji in https://github.com/linkml/linkml/pull/2201
• fix outdated cli command in docs and make it tested by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2226
• [pydanticgen][minor] Implement equals_string, equals_string_in by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2228
• [pydanticgen] make default for Optional[<T>] always be None by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2229
• Add note admonition for abstract slots by @sujaypatil96 in https://github.com/linkml/linkml/pull/2220
• [pydanticgen] lifecycle methods :) by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2209
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2237
• [pydanticgen] Don't include meta if empty by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2236
• Add cardinality constraints to Pydantic generation for list values by @daniel-ji in https://github.com/linkml/linkml/pull/2225
• Fix xsd:anyURI range in JSON-LD generator by @vincentkelleher in https://github.com/linkml/linkml/pull/2242
• add link to LinkML repo by @nlharris in https://github.com/linkml/linkml/pull/2244
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2253
• Adding tests and documentation for LogicalModelTransformer. by @cmungall in https://github.com/linkml/linkml/pull/2235
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2261
• Unified linkml CLI by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2227
• Support rdfs:subClassOf with the SHACL generator by @vincentkelleher in https://github.com/linkml/linkml/pull/2256
• Document contributing SOP for slow snapshot tests by @cmungall in https://github.com/linkml/linkml/pull/2183
• Allow "null" for optional slots in json schema gen by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2252
• Modify test in tests/test_generators/test_docgen.py that checks domain_of duplicity by @sujaypatil96 in https://github.com/linkml/linkml/pull/2262
• Add link to video by @nlharris in https://github.com/linkml/linkml/pull/2264
• allow a list of slots in schemabuilder by @cmungall in https://github.com/linkml/linkml/pull/2268
• fix mastodon link by @cmungall in https://github.com/linkml/linkml/pull/2267
• simplify bug report template by @nlharris in https://github.com/linkml/linkml/pull/2265
• [QoL] Pretty print - main package version by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2032

New Contributors

• @daniel-ji made their first contribution in https://github.com/linkml/linkml/pull/2201

Full Changelog: https://github.com/linkml/linkml/compare/v1.8.1...v1.8.2

- Python
Published by cmungall almost 2 years ago

linkml - v1.8.1

What's Changed

• Ensure jsonschemagen does not incorrectly invalidate arrays by @cmungall in https://github.com/linkml/linkml/pull/2189
• [pydanticgen] Add CLI options for linkml_meta mode, tests and bugfixes for linkml_meta by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2186
• Fix plantUML syntax bugs to do spacing and add suppor for SVG tooltips by @jsnyder-csdisco in https://github.com/linkml/linkml/pull/2161
• Adding test cases for complex values in annotations, expanded and unexpanded. by @cmungall in https://github.com/linkml/linkml/pull/2192

New Contributors

• @jsnyder-csdisco made their first contribution in https://github.com/linkml/linkml/pull/2161

Full Changelog: https://github.com/linkml/linkml/compare/v1.8.0...v1.8.1

- Python
Published by cmungall almost 2 years ago

linkml - v1.8.0

Major Changes

Metamodel

The 1.8.x series of LinkML is synced with 1.8.0 of the LinkML metamodel. See the metamodel release notes for a description of changes:

https://github.com/linkml/linkml-model/releases/tag/v1.8.0

See also the corresponding linkml-runtime release: https://github.com/linkml/linkml-runtime/releases/tag/v1.8.0

Pydanticgen

• Dropped support for pydantic v1
• Multiple enhancements to Pydantic generation from @sneakers-the-rat and others

What's Changed

• restore auto-versioning by @cmungall in https://github.com/linkml/linkml/pull/1886
• Add blurb about dev environment setup to contributing guide by @pkalita-lbl in https://github.com/linkml/linkml/pull/1892
• pydanticgen enum titles (issue 1810) by @kevinschaper in https://github.com/linkml/linkml/pull/1891
• Updating the docs on NDArrays to reflect 1.7 changes by @cmungall in https://github.com/linkml/linkml/pull/1893
• Correct import for sqlalchemy.pool.StaticPool by @bendichter in https://github.com/linkml/linkml/pull/1895
• Adding support for serializing inlined tuples as simple dicts in pydantic. by @cmungall in https://github.com/linkml/linkml/pull/1869
• Additional owlgen compliance tests. by @cmungall in https://github.com/linkml/linkml/pull/1894
• add database files to .gitignore by @bendichter in https://github.com/linkml/linkml/pull/1906
• Fix tutorial09.md typos by @bendichter in https://github.com/linkml/linkml/pull/1903
• Poetry extras removal by @dalito in https://github.com/linkml/linkml/pull/1900
• rmv unnecessary default_factories by @bendichter in https://github.com/linkml/linkml/pull/1905
• Update doc build instructions and add makefile command to build docs by @dalito in https://github.com/linkml/linkml/pull/1899
• Foreign keys should be of same type as the primary key they reference by @noahhl in https://github.com/linkml/linkml/pull/1907
• Pydantic generated models require importing Decimal by @noahhl in https://github.com/linkml/linkml/pull/1911
• fix some grammatical errors by @bendichter in https://github.com/linkml/linkml/pull/1913
• Pydanticgen: Inject imports, slots, and classes by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1916
• remove mutables as default arguments by @bendichter in https://github.com/linkml/linkml/pull/1912
• Adding tests for empty preconditions in rules. by @cmungall in https://github.com/linkml/linkml/pull/1926
• Add timeout to requests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1918
• [wip] fixing context generator for any_of with range by @djarecka in https://github.com/linkml/linkml/pull/1898
• Fix docstrings by @bendichter in https://github.com/linkml/linkml/pull/1929
• Update sqlalchemygen.py style by @bendichter in https://github.com/linkml/linkml/pull/1904
• Perf: Mark shex generator as slow, skip except for gh actions runner by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1921
• change methods to static where appropriate by @bendichter in https://github.com/linkml/linkml/pull/1908
• Add suggestions of permissive licenses by @nlharris in https://github.com/linkml/linkml/pull/1928
• Update gen-json-schema command in tutorial to use --top-class option by @pkalita-lbl in https://github.com/linkml/linkml/pull/1931
• [QoL] Make generating output optional in compliance tests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1941
• [QoL] Quiet warnings by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1939
• Deprecate SQLDDLGenerator and change references to SQLTableGenerator by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1940
• additional tests for patterns, mixins, and abstract classes. by @cmungall in https://github.com/linkml/linkml/pull/1947
• Cache network requests during tests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1949
• Pydanticgen - Modularize template by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1927
• Account for any_of ranges in documentation pages by @sujaypatil96 in https://github.com/linkml/linkml/pull/1856
• Unbreak the docs & test them by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1954
• [pydanticgen] Replace classmethod-property chain with init subclass by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1959
• Add any_of implementation to shaclgen.py by @anjastrunk in https://github.com/linkml/linkml/pull/1601
• Support ifabsent in the Shacl generator by @vincentkelleher in https://github.com/linkml/linkml/pull/1964
• remove tab in biolink model by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1971
• Replace metamodel with kitchen sink in script tests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1969
• [docker] Fix error from COPY .git directory by using ADD by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1980
• Add debug logs to doc-gen by @timothy-trinidad-ps in https://github.com/linkml/linkml/pull/1974
• Allow multiple files to be passed to linkml-sqldb dump by @cmungall in https://github.com/linkml/linkml/pull/1985
• Cast rdflib Namespace instances to strings when used as base for contextgen by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1982
• Adding imports tests to compliance test suite. by @cmungall in https://github.com/linkml/linkml/pull/1987
• use typing version of Tuple, not class for 3.8 compat by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1989
• Linter: add patterns in config for classes and slots by @linupi in https://github.com/linkml/linkml/pull/1979
• Fixing test for #25 by explicitly invoking jsonld1.1. by @cmungall in https://github.com/linkml/linkml/pull/1995
• Make pyshacl an extra by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1992
• Include python version in CI cache key by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1990
• Fix Node Kind for Custom Class Ranges by @vincentkelleher in https://github.com/linkml/linkml/pull/2003
• Adding documentation for linkml expression language by @turbomam in https://github.com/linkml/linkml/pull/2011
• owlgen - skip nested annotations by @cmungall in https://github.com/linkml/linkml/pull/2013
• Adding compliance tests for importing and subsetting metamodel, fixes #2015 by @cmungall in https://github.com/linkml/linkml/pull/2016
• Update lockfile by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2002
• Use fetch-depth: 0 in docker-build workflow by @pkalita-lbl in https://github.com/linkml/linkml/pull/2022
• JSON-LD Context Generator Fixes by @vincentkelleher in https://github.com/linkml/linkml/pull/1981
• Automatically PR to update poetry lockfile by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2023
• Add support for Python 3.12 by @Silvanoc in https://github.com/linkml/linkml/pull/1704
• [pydanticgen] Add list of lists array implementation by @rly in https://github.com/linkml/linkml/pull/1887
• Adding ifabsent tests. by @cmungall in https://github.com/linkml/linkml/pull/2014
• Automatically PR to update poetry lockfile v2 by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2028
• optimize rendering of Applicable classes section on slot documentation pages by @sujaypatil96 in https://github.com/linkml/linkml/pull/2009
• Ensure unique key constraints on foreign keys are mapped in SQL transform. by @cmungall in https://github.com/linkml/linkml/pull/2035
• fix link to "inlining" documentation by @nlharris in https://github.com/linkml/linkml/pull/2039
• Fix testing infrasucture for Pydantic 2 default by @pkalita-lbl in https://github.com/linkml/linkml/pull/2041
• [perf] Finish putting file I/O behind --with-output flag in compliance tests (and other free perf) by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2045
• Issue 2037: extend shaclgen.py to add the suffix "Shape" to the generated SHACL shape by @robertschubert in https://github.com/linkml/linkml/pull/2038
• Make docs dependencies optional and in a separate group by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1991
• Optimize logic in subset.md.jinja2 by @sujaypatil96 in https://github.com/linkml/linkml/pull/2046
• [tests] Remove test outputs and GeneratorTestCase by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1976
• WIP: Tests remove testcase by @pkalita-lbl in https://github.com/linkml/linkml/pull/2048
• Automatically PR to update poetry lockfile v3 by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2044
• convert test_data to pytest by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2050
• Run code quality checks only once in testing workflow by @pkalita-lbl in https://github.com/linkml/linkml/pull/2055
• convert enhancements to pytest by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2052
• Add --without-cache option to tests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2051
• Add deprecations module and add deprecation warnings for pydantic v1 by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1957
• feat: add '--version' to linkml-run-examples by @Silvanoc in https://github.com/linkml/linkml/pull/2058
• Pass strings rather than printing to stdout in generators by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2061
• [poetry] Update Lockfile by @github-actions in https://github.com/linkml/linkml/pull/2056
• Use app installation token in poetry update workflow by @pkalita-lbl in https://github.com/linkml/linkml/pull/2062
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2066
• Make class blocks in mermaid class diagrams clickable/hyperlinked by @sujaypatil96 in https://github.com/linkml/linkml/pull/2065
• Display single/multi-valuedness (cardinality) on slot edges by @sujaypatil96 in https://github.com/linkml/linkml/pull/2071
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2075
• Documentation: Recommend the official docker image in docs and improve structure of installation intro by @mkbrechtel in https://github.com/linkml/linkml/pull/2073
• Improve Dockerfile: Update Baseimages, make build work with Buildah/Podman and install python packages globally in runner by @mkbrechtel in https://github.com/linkml/linkml/pull/2074
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2083
• Ensure consistency of cardinality displayed on edges of Mermaid class diagram by @sujaypatil96 in https://github.com/linkml/linkml/pull/2080
• Minor fixes and improvements to text by @nlharris in https://github.com/linkml/linkml/pull/2082
• Add generator flag to include an import outside the normal import mechanism by @sierra-moxon in https://github.com/linkml/linkml/pull/2079
• plantuml: hide circle and empty members, remove quotes by @VladimirAlexiev in https://github.com/linkml/linkml/pull/2060
• Clarify use of slack channel in contribution docs by @matentzn in https://github.com/linkml/linkml/pull/2093
• Allow control over which OWL types are used for enums. Fixes #2090 by @cmungall in https://github.com/linkml/linkml/pull/2095
• validator: support including validator context when reporting errors by @paulmillar in https://github.com/linkml/linkml/pull/2089
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2098
• Adding link to expr lang docs by @cmungall in https://github.com/linkml/linkml/pull/2086
• Fix typo in docs (add missing closing parenthesis) by @eecavanna in https://github.com/linkml/linkml/pull/2097
• Update slot cardinality meaning on main linkml docs site by @sujaypatil96 in https://github.com/linkml/linkml/pull/2100
• genshacl: fix the propagation of types to SHACL sh:datatype and sh:nodeKind by @jsheunis in https://github.com/linkml/linkml/pull/2102
• Autodetect pydantic version in gen-pydantic issue #2077 by @manulera in https://github.com/linkml/linkml/pull/2078
• [pydanticgen] Embed extra metadata in modules, classes, and fields by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2036
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2106
• Adding documentation on monotonicity. by @cmungall in https://github.com/linkml/linkml/pull/2108
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2120
• Re-enable tests/testnotebooks/testexamples.py testdistributedmodels by @pkalita-lbl in https://github.com/linkml/linkml/pull/2119
• Make quality checks happy by @vladistan in https://github.com/linkml/linkml/pull/2136
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2137
• hotwo on deprecation by @sierra-moxon in https://github.com/linkml/linkml/pull/2127
• shaclgen: Add --include-annotations option to let annotations be part of shacl shapes by @jsheunis in https://github.com/linkml/linkml/pull/2111
• Erdiagram include upstream by @vladistan in https://github.com/linkml/linkml/pull/2139
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2143
• Adding tests for min/max as floats. by @cmungall in https://github.com/linkml/linkml/pull/2145
• Implement equalsstring and equalsstring_in; take 2 by @pkalita-lbl in https://github.com/linkml/linkml/pull/2150
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2151
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2173
• Mappings section should show on individual element pages and not just classes by @sujaypatil96 in https://github.com/linkml/linkml/pull/2172
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2184
• linkml-model-1.8.0rc by @cmungall in https://github.com/linkml/linkml/pull/2180

New Contributors

• @noahhl made their first contribution in https://github.com/linkml/linkml/pull/1907
• @djarecka made their first contribution in https://github.com/linkml/linkml/pull/1898
• @vincentkelleher made their first contribution in https://github.com/linkml/linkml/pull/1964
• @timothy-trinidad-ps made their first contribution in https://github.com/linkml/linkml/pull/1974
• @linupi made their first contribution in https://github.com/linkml/linkml/pull/1979
• @robertschubert made their first contribution in https://github.com/linkml/linkml/pull/2038
• @github-actions made their first contribution in https://github.com/linkml/linkml/pull/2056
• @linkml-pr-bot made their first contribution in https://github.com/linkml/linkml/pull/2066
• @mkbrechtel made their first contribution in https://github.com/linkml/linkml/pull/2073
• @VladimirAlexiev made their first contribution in https://github.com/linkml/linkml/pull/2060
• @matentzn made their first contribution in https://github.com/linkml/linkml/pull/2093
• @jsheunis made their first contribution in https://github.com/linkml/linkml/pull/2102
• @manulera made their first contribution in https://github.com/linkml/linkml/pull/2078
• @vladistan made their first contribution in https://github.com/linkml/linkml/pull/2136

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.0...v1.8.0

- Python
Published by cmungall almost 2 years ago

linkml - v1.8.0rc2

Major Changes

Metamodel

The 1.8.x series of LinkML is synced with 1.8.0 of the LinkML metamodel. See the metamodel release notes for a description of changes:

https://github.com/linkml/linkml-model/releases/tag/v1.8.0rc1

These are both at the release candidate stage

See also the corresponding linkml-runtime release: https://github.com/linkml/linkml-runtime/releases/tag/v1.8.0rc2

Pydanticgen

Multiple enhancements to Pydantic generation from @sneakers-the-rat and others

What's Changed

• restore auto-versioning by @cmungall in https://github.com/linkml/linkml/pull/1886
• Add blurb about dev environment setup to contributing guide by @pkalita-lbl in https://github.com/linkml/linkml/pull/1892
• pydanticgen enum titles (issue 1810) by @kevinschaper in https://github.com/linkml/linkml/pull/1891
• Updating the docs on NDArrays to reflect 1.7 changes by @cmungall in https://github.com/linkml/linkml/pull/1893
• Correct import for sqlalchemy.pool.StaticPool by @bendichter in https://github.com/linkml/linkml/pull/1895
• Adding support for serializing inlined tuples as simple dicts in pydantic. by @cmungall in https://github.com/linkml/linkml/pull/1869
• Additional owlgen compliance tests. by @cmungall in https://github.com/linkml/linkml/pull/1894
• add database files to .gitignore by @bendichter in https://github.com/linkml/linkml/pull/1906
• Fix tutorial09.md typos by @bendichter in https://github.com/linkml/linkml/pull/1903
• Poetry extras removal by @dalito in https://github.com/linkml/linkml/pull/1900
• rmv unnecessary default_factories by @bendichter in https://github.com/linkml/linkml/pull/1905
• Update doc build instructions and add makefile command to build docs by @dalito in https://github.com/linkml/linkml/pull/1899
• Foreign keys should be of same type as the primary key they reference by @noahhl in https://github.com/linkml/linkml/pull/1907
• Pydantic generated models require importing Decimal by @noahhl in https://github.com/linkml/linkml/pull/1911
• fix some grammatical errors by @bendichter in https://github.com/linkml/linkml/pull/1913
• Pydanticgen: Inject imports, slots, and classes by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1916
• remove mutables as default arguments by @bendichter in https://github.com/linkml/linkml/pull/1912
• Adding tests for empty preconditions in rules. by @cmungall in https://github.com/linkml/linkml/pull/1926
• Add timeout to requests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1918
• [wip] fixing context generator for any_of with range by @djarecka in https://github.com/linkml/linkml/pull/1898
• Fix docstrings by @bendichter in https://github.com/linkml/linkml/pull/1929
• Update sqlalchemygen.py style by @bendichter in https://github.com/linkml/linkml/pull/1904
• Perf: Mark shex generator as slow, skip except for gh actions runner by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1921
• change methods to static where appropriate by @bendichter in https://github.com/linkml/linkml/pull/1908
• Add suggestions of permissive licenses by @nlharris in https://github.com/linkml/linkml/pull/1928
• Update gen-json-schema command in tutorial to use --top-class option by @pkalita-lbl in https://github.com/linkml/linkml/pull/1931
• [QoL] Make generating output optional in compliance tests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1941
• [QoL] Quiet warnings by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1939
• Deprecate SQLDDLGenerator and change references to SQLTableGenerator by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1940
• additional tests for patterns, mixins, and abstract classes. by @cmungall in https://github.com/linkml/linkml/pull/1947
• Cache network requests during tests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1949
• Pydanticgen - Modularize template by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1927
• Account for any_of ranges in documentation pages by @sujaypatil96 in https://github.com/linkml/linkml/pull/1856
• Unbreak the docs & test them by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1954
• [pydanticgen] Replace classmethod-property chain with init subclass by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1959
• Add any_of implementation to shaclgen.py by @anjastrunk in https://github.com/linkml/linkml/pull/1601
• Support ifabsent in the Shacl generator by @vincentkelleher in https://github.com/linkml/linkml/pull/1964
• remove tab in biolink model by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1971
• Replace metamodel with kitchen sink in script tests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1969
• [docker] Fix error from COPY .git directory by using ADD by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1980
• Add debug logs to doc-gen by @timothy-trinidad-ps in https://github.com/linkml/linkml/pull/1974
• Allow multiple files to be passed to linkml-sqldb dump by @cmungall in https://github.com/linkml/linkml/pull/1985
• Cast rdflib Namespace instances to strings when used as base for contextgen by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1982
• Adding imports tests to compliance test suite. by @cmungall in https://github.com/linkml/linkml/pull/1987
• use typing version of Tuple, not class for 3.8 compat by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1989
• Linter: add patterns in config for classes and slots by @linupi in https://github.com/linkml/linkml/pull/1979
• Fixing test for #25 by explicitly invoking jsonld1.1. by @cmungall in https://github.com/linkml/linkml/pull/1995
• Make pyshacl an extra by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1992
• Include python version in CI cache key by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1990
• Fix Node Kind for Custom Class Ranges by @vincentkelleher in https://github.com/linkml/linkml/pull/2003
• Adding documentation for linkml expression language by @turbomam in https://github.com/linkml/linkml/pull/2011
• owlgen - skip nested annotations by @cmungall in https://github.com/linkml/linkml/pull/2013
• Adding compliance tests for importing and subsetting metamodel, fixes #2015 by @cmungall in https://github.com/linkml/linkml/pull/2016
• Update lockfile by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2002
• Use fetch-depth: 0 in docker-build workflow by @pkalita-lbl in https://github.com/linkml/linkml/pull/2022
• JSON-LD Context Generator Fixes by @vincentkelleher in https://github.com/linkml/linkml/pull/1981
• Automatically PR to update poetry lockfile by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2023
• Add support for Python 3.12 by @Silvanoc in https://github.com/linkml/linkml/pull/1704
• [pydanticgen] Add list of lists array implementation by @rly in https://github.com/linkml/linkml/pull/1887
• Adding ifabsent tests. by @cmungall in https://github.com/linkml/linkml/pull/2014
• Automatically PR to update poetry lockfile v2 by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2028
• optimize rendering of Applicable classes section on slot documentation pages by @sujaypatil96 in https://github.com/linkml/linkml/pull/2009
• Ensure unique key constraints on foreign keys are mapped in SQL transform. by @cmungall in https://github.com/linkml/linkml/pull/2035
• fix link to "inlining" documentation by @nlharris in https://github.com/linkml/linkml/pull/2039
• Fix testing infrasucture for Pydantic 2 default by @pkalita-lbl in https://github.com/linkml/linkml/pull/2041
• [perf] Finish putting file I/O behind --with-output flag in compliance tests (and other free perf) by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2045
• Issue 2037: extend shaclgen.py to add the suffix "Shape" to the generated SHACL shape by @robertschubert in https://github.com/linkml/linkml/pull/2038
• Make docs dependencies optional and in a separate group by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1991
• Optimize logic in subset.md.jinja2 by @sujaypatil96 in https://github.com/linkml/linkml/pull/2046
• [tests] Remove test outputs and GeneratorTestCase by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1976
• WIP: Tests remove testcase by @pkalita-lbl in https://github.com/linkml/linkml/pull/2048
• Automatically PR to update poetry lockfile v3 by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2044
• convert test_data to pytest by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2050
• Run code quality checks only once in testing workflow by @pkalita-lbl in https://github.com/linkml/linkml/pull/2055
• convert enhancements to pytest by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2052
• Add --without-cache option to tests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2051
• Add deprecations module and add deprecation warnings for pydantic v1 by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1957
• feat: add '--version' to linkml-run-examples by @Silvanoc in https://github.com/linkml/linkml/pull/2058
• Pass strings rather than printing to stdout in generators by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2061
• [poetry] Update Lockfile by @github-actions in https://github.com/linkml/linkml/pull/2056
• Use app installation token in poetry update workflow by @pkalita-lbl in https://github.com/linkml/linkml/pull/2062
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2066
• Make class blocks in mermaid class diagrams clickable/hyperlinked by @sujaypatil96 in https://github.com/linkml/linkml/pull/2065
• Display single/multi-valuedness (cardinality) on slot edges by @sujaypatil96 in https://github.com/linkml/linkml/pull/2071
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2075
• Documentation: Recommend the official docker image in docs and improve structure of installation intro by @mkbrechtel in https://github.com/linkml/linkml/pull/2073
• Improve Dockerfile: Update Baseimages, make build work with Buildah/Podman and install python packages globally in runner by @mkbrechtel in https://github.com/linkml/linkml/pull/2074
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2083
• Ensure consistency of cardinality displayed on edges of Mermaid class diagram by @sujaypatil96 in https://github.com/linkml/linkml/pull/2080
• Minor fixes and improvements to text by @nlharris in https://github.com/linkml/linkml/pull/2082
• Add generator flag to include an import outside the normal import mechanism by @sierra-moxon in https://github.com/linkml/linkml/pull/2079
• plantuml: hide circle and empty members, remove quotes by @VladimirAlexiev in https://github.com/linkml/linkml/pull/2060
• Clarify use of slack channel in contribution docs by @matentzn in https://github.com/linkml/linkml/pull/2093
• Allow control over which OWL types are used for enums. Fixes #2090 by @cmungall in https://github.com/linkml/linkml/pull/2095
• validator: support including validator context when reporting errors by @paulmillar in https://github.com/linkml/linkml/pull/2089
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2098
• Adding link to expr lang docs by @cmungall in https://github.com/linkml/linkml/pull/2086
• Fix typo in docs (add missing closing parenthesis) by @eecavanna in https://github.com/linkml/linkml/pull/2097
• Update slot cardinality meaning on main linkml docs site by @sujaypatil96 in https://github.com/linkml/linkml/pull/2100
• genshacl: fix the propagation of types to SHACL sh:datatype and sh:nodeKind by @jsheunis in https://github.com/linkml/linkml/pull/2102
• Autodetect pydantic version in gen-pydantic issue #2077 by @manulera in https://github.com/linkml/linkml/pull/2078
• [pydanticgen] Embed extra metadata in modules, classes, and fields by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2036
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2106
• Adding documentation on monotonicity. by @cmungall in https://github.com/linkml/linkml/pull/2108
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2120
• Re-enable tests/testnotebooks/testexamples.py testdistributedmodels by @pkalita-lbl in https://github.com/linkml/linkml/pull/2119
• Make quality checks happy by @vladistan in https://github.com/linkml/linkml/pull/2136
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2137
• hotwo on deprecation by @sierra-moxon in https://github.com/linkml/linkml/pull/2127
• shaclgen: Add --include-annotations option to let annotations be part of shacl shapes by @jsheunis in https://github.com/linkml/linkml/pull/2111
• Erdiagram include upstream by @vladistan in https://github.com/linkml/linkml/pull/2139
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2143
• Adding tests for min/max as floats. by @cmungall in https://github.com/linkml/linkml/pull/2145
• Implement equalsstring and equalsstring_in; take 2 by @pkalita-lbl in https://github.com/linkml/linkml/pull/2150
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2151
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2173
• Mappings section should show on individual element pages and not just classes by @sujaypatil96 in https://github.com/linkml/linkml/pull/2172

New Contributors

• @noahhl made their first contribution in https://github.com/linkml/linkml/pull/1907
• @djarecka made their first contribution in https://github.com/linkml/linkml/pull/1898
• @vincentkelleher made their first contribution in https://github.com/linkml/linkml/pull/1964
• @timothy-trinidad-ps made their first contribution in https://github.com/linkml/linkml/pull/1974
• @linupi made their first contribution in https://github.com/linkml/linkml/pull/1979
• @robertschubert made their first contribution in https://github.com/linkml/linkml/pull/2038
• @github-actions made their first contribution in https://github.com/linkml/linkml/pull/2056
• @linkml-pr-bot made their first contribution in https://github.com/linkml/linkml/pull/2066
• @mkbrechtel made their first contribution in https://github.com/linkml/linkml/pull/2073
• @VladimirAlexiev made their first contribution in https://github.com/linkml/linkml/pull/2060
• @matentzn made their first contribution in https://github.com/linkml/linkml/pull/2093
• @jsheunis made their first contribution in https://github.com/linkml/linkml/pull/2102
• @manulera made their first contribution in https://github.com/linkml/linkml/pull/2078
• @vladistan made their first contribution in https://github.com/linkml/linkml/pull/2136

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.0...v1.8.0rc2

- Python
Published by cmungall almost 2 years ago

linkml - v1.7.11rc1 Embed extra metadata in modules

What's Changed

• [pydanticgen] Embed extra metadata in modules, classes, and fields by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2036

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.10...v1.7.11rc1

- Python
Published by cmungall about 2 years ago

linkml - v1.7.10

What's Changed

• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2098
• Adding link to expr lang docs by @cmungall in https://github.com/linkml/linkml/pull/2086
• Fix typo in docs (add missing closing parenthesis) by @eecavanna in https://github.com/linkml/linkml/pull/2097
• Update slot cardinality meaning on main linkml docs site by @sujaypatil96 in https://github.com/linkml/linkml/pull/2100
• genshacl: fix the propagation of types to SHACL sh:datatype and sh:nodeKind by @jsheunis in https://github.com/linkml/linkml/pull/2102
• Autodetect pydantic version in gen-pydantic issue #2077 by @manulera in https://github.com/linkml/linkml/pull/2078

New Contributors

• @jsheunis made their first contribution in https://github.com/linkml/linkml/pull/2102
• @manulera made their first contribution in https://github.com/linkml/linkml/pull/2078

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.9...v1.7.10

- Python
Published by cmungall about 2 years ago

linkml - v1.7.9

What's Changed

• Add --without-cache option to tests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2051
• Add deprecations module and add deprecation warnings for pydantic v1 by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1957
• feat: add '--version' to linkml-run-examples by @Silvanoc in https://github.com/linkml/linkml/pull/2058
• Pass strings rather than printing to stdout in generators by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2061
• [poetry] Update Lockfile by @github-actions in https://github.com/linkml/linkml/pull/2056
• Use app installation token in poetry update workflow by @pkalita-lbl in https://github.com/linkml/linkml/pull/2062
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2066
• Make class blocks in mermaid class diagrams clickable/hyperlinked by @sujaypatil96 in https://github.com/linkml/linkml/pull/2065
• Display single/multi-valuedness (cardinality) on slot edges by @sujaypatil96 in https://github.com/linkml/linkml/pull/2071
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2075
• Documentation: Recommend the official docker image in docs and improve structure of installation intro by @mkbrechtel in https://github.com/linkml/linkml/pull/2073
• Improve Dockerfile: Update Baseimages, make build work with Buildah/Podman and install python packages globally in runner by @mkbrechtel in https://github.com/linkml/linkml/pull/2074
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2083
• Ensure consistency of cardinality displayed on edges of Mermaid class diagram by @sujaypatil96 in https://github.com/linkml/linkml/pull/2080
• Minor fixes and improvements to text by @nlharris in https://github.com/linkml/linkml/pull/2082
• Add generator flag to include an import outside the normal import mechanism by @sierra-moxon in https://github.com/linkml/linkml/pull/2079
• plantuml: hide circle and empty members, remove quotes by @VladimirAlexiev in https://github.com/linkml/linkml/pull/2060
• Clarify use of slack channel in contribution docs by @matentzn in https://github.com/linkml/linkml/pull/2093
• Allow control over which OWL types are used for enums. Fixes #2090 by @cmungall in https://github.com/linkml/linkml/pull/2095
• validator: support including validator context when reporting errors by @paulmillar in https://github.com/linkml/linkml/pull/2089

New Contributors

• @github-actions made their first contribution in https://github.com/linkml/linkml/pull/2056
• @linkml-pr-bot made their first contribution in https://github.com/linkml/linkml/pull/2066
• @mkbrechtel made their first contribution in https://github.com/linkml/linkml/pull/2073
• @VladimirAlexiev made their first contribution in https://github.com/linkml/linkml/pull/2060
• @matentzn made their first contribution in https://github.com/linkml/linkml/pull/2093

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.8...v1.7.9

- Python
Published by cmungall about 2 years ago

linkml - v1.7.8

What's Changed

• Ensure unique key constraints on foreign keys are mapped in SQL transform. by @cmungall in https://github.com/linkml/linkml/pull/2035
• fix link to "inlining" documentation by @nlharris in https://github.com/linkml/linkml/pull/2039
• Fix testing infrasucture for Pydantic 2 default by @pkalita-lbl in https://github.com/linkml/linkml/pull/2041
• [perf] Finish putting file I/O behind --with-output flag in compliance tests (and other free perf) by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2045
• Issue 2037: extend shaclgen.py to add the suffix "Shape" to the generated SHACL shape by @robertschubert in https://github.com/linkml/linkml/pull/2038
• Make docs dependencies optional and in a separate group by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1991
• Optimize logic in subset.md.jinja2 by @sujaypatil96 in https://github.com/linkml/linkml/pull/2046
• [tests] Remove test outputs and GeneratorTestCase by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1976
• WIP: Tests remove testcase by @pkalita-lbl in https://github.com/linkml/linkml/pull/2048
• Automatically PR to update poetry lockfile v3 by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2044
• convert test_data to pytest by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2050
• Run code quality checks only once in testing workflow by @pkalita-lbl in https://github.com/linkml/linkml/pull/2055
• convert enhancements to pytest by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2052

New Contributors

• @robertschubert made their first contribution in https://github.com/linkml/linkml/pull/2038

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.7...v1.7.8

- Python
Published by cmungall about 2 years ago

linkml - v1.7.7 (array support)

Highlights

• [pydanticgen] Add list of lists array implementation by @rly @sneakers-the-rat in https://github.com/linkml/linkml/pull/1887

This release sees the first implementation of the array spec in pydanticgen.

An overview of arrays is present in the schema guide: https://linkml.io/linkml/schemas/arrays

With the introduction of the 1.7.0 it has been possible to represent N-dimensional arrays, e.g.

yaml MyClass: attributes: data: range: integer array: minimum_number_dimensions: 3 maximum_number_dimensions: 5

This release equips pydanticgen with the ability to translate these to nested lists, and lays the framework for representation using numpytyping.

This implementation is the result of heroic efforts by the @linkml/ndarray-wg, and in particular, @sneakers-the-rat and @rly

🙏 🙏 🙏

What's Changed

• Fix Node Kind for Custom Class Ranges by @vincentkelleher in https://github.com/linkml/linkml/pull/2003
• Adding documentation for linkml expression language by @turbomam in https://github.com/linkml/linkml/pull/2011
• owlgen - skip nested annotations by @cmungall in https://github.com/linkml/linkml/pull/2013
• Adding compliance tests for importing and subsetting metamodel, fixes #2015 by @cmungall in https://github.com/linkml/linkml/pull/2016
• Update lockfile by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2002
• Use fetch-depth: 0 in docker-build workflow by @pkalita-lbl in https://github.com/linkml/linkml/pull/2022
• JSON-LD Context Generator Fixes by @vincentkelleher in https://github.com/linkml/linkml/pull/1981
• Automatically PR to update poetry lockfile by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2023
• Add support for Python 3.12 by @Silvanoc in https://github.com/linkml/linkml/pull/1704
• [pydanticgen] Add list of lists array implementation by @rly @sneakers-the-rat in https://github.com/linkml/linkml/pull/1887
• Adding ifabsent tests. by @cmungall in https://github.com/linkml/linkml/pull/2014
• Automatically PR to update poetry lockfile v2 by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2028
• optimize rendering of Applicable classes section on slot documentation pages by @sujaypatil96 in https://github.com/linkml/linkml/pull/2009

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.6...v1.7.7

- Python
Published by cmungall about 2 years ago

linkml - v1.7.6

What's Changed

• Cache network requests during tests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1949
• Pydanticgen - Modularize template by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1927
• Account for any_of ranges in documentation pages by @sujaypatil96 in https://github.com/linkml/linkml/pull/1856
• Unbreak the docs & test them by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1954
• [pydanticgen] Replace classmethod-property chain with init subclass by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1959
• Add any_of implementation to shaclgen.py by @anjastrunk in https://github.com/linkml/linkml/pull/1601
• Support ifabsent in the Shacl generator by @vincentkelleher in https://github.com/linkml/linkml/pull/1964
• remove tab in biolink model by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1971
• Replace metamodel with kitchen sink in script tests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1969
• [docker] Fix error from COPY .git directory by using ADD by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1980
• Add debug logs to doc-gen by @timothy-trinidad-ps in https://github.com/linkml/linkml/pull/1974
• Allow multiple files to be passed to linkml-sqldb dump by @cmungall in https://github.com/linkml/linkml/pull/1985
• Cast rdflib Namespace instances to strings when used as base for contextgen by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1982
• Adding imports tests to compliance test suite. by @cmungall in https://github.com/linkml/linkml/pull/1987
• use typing version of Tuple, not class for 3.8 compat by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1989
• Linter: add patterns in config for classes and slots by @linupi in https://github.com/linkml/linkml/pull/1979
• Fixing test for #25 by explicitly invoking jsonld1.1. by @cmungall in https://github.com/linkml/linkml/pull/1995
• Make pyshacl an extra by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1992
• Include python version in CI cache key by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1990

New Contributors

• @vincentkelleher made their first contribution in https://github.com/linkml/linkml/pull/1964
• @timothy-trinidad-ps made their first contribution in https://github.com/linkml/linkml/pull/1974
• @linupi made their first contribution in https://github.com/linkml/linkml/pull/1979

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.5...v1.7.6

- Python
Published by cmungall about 2 years ago

linkml - v1.7.5

What's Changed

• Fix docstrings by @bendichter in https://github.com/linkml/linkml/pull/1929
• Update sqlalchemygen.py style by @bendichter in https://github.com/linkml/linkml/pull/1904
• Perf: Mark shex generator as slow, skip except for gh actions runner by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1921
• change methods to static where appropriate by @bendichter in https://github.com/linkml/linkml/pull/1908
• Add suggestions of permissive licenses by @nlharris in https://github.com/linkml/linkml/pull/1928
• Update gen-json-schema command in tutorial to use --top-class option by @pkalita-lbl in https://github.com/linkml/linkml/pull/1931
• [QoL] Make generating output optional in compliance tests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1941
• [QoL] Quiet warnings by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1939
• Deprecate SQLDDLGenerator and change references to SQLTableGenerator by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1940
• additional tests for patterns, mixins, and abstract classes. by @cmungall in https://github.com/linkml/linkml/pull/1947

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.4...v1.7.5

- Python
Published by cmungall over 2 years ago

linkml - v1.7.4

What's Changed

• fix some grammatical errors by @bendichter in https://github.com/linkml/linkml/pull/1913
• Pydanticgen: Inject imports, slots, and classes by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1916
• remove mutables as default arguments by @bendichter in https://github.com/linkml/linkml/pull/1912
• Adding tests for empty preconditions in rules. by @cmungall in https://github.com/linkml/linkml/pull/1926
• Add timeout to requests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1918
• fixing context generator for any_of with range by @djarecka in https://github.com/linkml/linkml/pull/1898

New Contributors

• @djarecka made their first contribution in https://github.com/linkml/linkml/pull/1898

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.3...v1.7.4

- Python
Published by cmungall over 2 years ago

linkml - v1.7.3

What's Changed

• Add blurb about dev environment setup to contributing guide by @pkalita-lbl in https://github.com/linkml/linkml/pull/1892
• pydanticgen enum titles (issue 1810) by @kevinschaper in https://github.com/linkml/linkml/pull/1891
• Updating the docs on NDArrays to reflect 1.7 changes by @cmungall in https://github.com/linkml/linkml/pull/1893
• Correct import for sqlalchemy.pool.StaticPool by @bendichter in https://github.com/linkml/linkml/pull/1895
• Adding support for serializing inlined tuples as simple dicts in pydantic. by @cmungall in https://github.com/linkml/linkml/pull/1869
• Additional owlgen compliance tests. by @cmungall in https://github.com/linkml/linkml/pull/1894
• add database files to .gitignore by @bendichter in https://github.com/linkml/linkml/pull/1906
• Fix tutorial09.md typos by @bendichter in https://github.com/linkml/linkml/pull/1903
• Poetry extras removal by @dalito in https://github.com/linkml/linkml/pull/1900
• rmv unnecessary default_factories by @bendichter in https://github.com/linkml/linkml/pull/1905
• Update doc build instructions and add makefile command to build docs by @dalito in https://github.com/linkml/linkml/pull/1899
• Foreign keys should be of same type as the primary key they reference by @noahhl in https://github.com/linkml/linkml/pull/1907
• Pydantic generated models require importing Decimal by @noahhl in https://github.com/linkml/linkml/pull/1911

New Contributors

• @noahhl made their first contribution in https://github.com/linkml/linkml/pull/1907

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.2...v1.7.3

- Python
Published by cmungall over 2 years ago

linkml - v1.7.2

What's Changed

• restore auto-versioning by @cmungall in https://github.com/linkml/linkml/pull/1886

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.0...v1.7.2

- Python
Published by cmungall over 2 years ago

linkml - v1.7.1

This release is identical to 1.7.0. It was not released to pypi due to a sync error.

The first PyPI release in the 1.7.x series is https://github.com/linkml/linkml/releases/tag/v1.7.2

- Python
Published by cmungall over 2 years ago

linkml - v1.7.0

Array Support

The 1.7.x series of LinkML sees the introduction of first-class array support through the introduction of the linkml:array metamodel slot.

Basic example of usage, to define a 3D array: TemperatureDataset: attributes: temperature_matrix: range: float unit: ucum_code: K array: exact_number_dimensions: 3

Note that most frameworks will not yet support this new construct. Support and additional documentation will be rolled out in the 1.7.x linkml series.

Thanks to the work of the @linkml/ndarray-wg

• @bendichter
• @ialarmedalien
• @jmchandonia
• @melonora
• @nicholsn
• @oruebel
• @rly
• @sneakers-the-rat

This work was conducted as part of the LinkML Neurodata Hackashop sponsored by NeurodataWithoutBorders and DANDI and organized by @satra and @oruebel at Berkeley in Feb 2024.

Note: the first PyPI version in the 1.7.x series is 1.7.2 (https://github.com/linkml/linkml/releases/tag/v1.7.2).

What's Changed

• Fixes #1653 by @cmungall in https://github.com/linkml/linkml/pull/1654
• NMDC-inspired test for polymorphic collections, plus some spelling corrections by @turbomam in https://github.com/linkml/linkml/pull/1609
• Add option to JsonschemaValidationPlugin to provide pre-generated JSON Schema by @pkalita-lbl in https://github.com/linkml/linkml/pull/1663
• Pydantic 2 testing by @pkalita-lbl in https://github.com/linkml/linkml/pull/1660
• Fix typescript generator link in tutorial05.md by @rwblair in https://github.com/linkml/linkml/pull/1667
• Test Stub for Issue 163 by @nicholsn in https://github.com/linkml/linkml/pull/1642
• stub for test for #1422 by @cmungall in https://github.com/linkml/linkml/pull/1622
• 3 new FAQ questions from NWD, fixes #1568 by @sierra-moxon in https://github.com/linkml/linkml/pull/1580
• make line length consistent between black and ruff by @sierra-moxon in https://github.com/linkml/linkml/pull/1561
• Connect new validator module to linkml-validate CLI entry point by @pkalita-lbl in https://github.com/linkml/linkml/pull/1675
• owl enhancements by @cmungall in https://github.com/linkml/linkml/pull/1668
• Added ways to stay involved by @nlharris in https://github.com/linkml/linkml/pull/1683
• minor fix linkmllink->linkmllint, etc. by @sierra-moxon in https://github.com/linkml/linkml/pull/1687
• Fix broken enum and subset URI links by @sujaypatil96 in https://github.com/linkml/linkml/pull/1686
• Add missing simple data types by @anjastrunk in https://github.com/linkml/linkml/pull/1688
• Updated validation documentation by @pkalita-lbl in https://github.com/linkml/linkml/pull/1679
• Fix typo in name of example JSON property by @eecavanna in https://github.com/linkml/linkml/pull/1693
• Adds support for using typeof to generate the typescript type if type.base is not set by @kevinschaper in https://github.com/linkml/linkml/pull/1700
• Ensure source_file is populated on SchemaDefinition when it is loaded by Validator by @pkalita-lbl in https://github.com/linkml/linkml/pull/1697
• [gen-doc] Allow to rename the index document. by @gouttegd in https://github.com/linkml/linkml/pull/1709
• Added a compliance test for jsonpointer. by @cmungall in https://github.com/linkml/linkml/pull/1707
• Show headers for class, slot documentation pages similar to MIxS by @sujaypatil96 in https://github.com/linkml/linkml/pull/1705
• Remove calls to decode on output of Graph.serialize by @pkalita-lbl in https://github.com/linkml/linkml/pull/1714
• Additional compliance tests for boolean combinations, owlgen edge case fixes by @cmungall in https://github.com/linkml/linkml/pull/1736
• First pass at collaboration best practice doc 1744 by @cmungall in https://github.com/linkml/linkml/pull/1745
• Fix the rendering of date and time fields in Java code by @gouttegd in https://github.com/linkml/linkml/pull/1710
• update return types on shaclgen methods by @glass-ships in https://github.com/linkml/linkml/pull/1741
• Edits to collaboration guide by @cmungall in https://github.com/linkml/linkml/pull/1747
• Improve tutorial 02 (add docu for tree_root) by @dalito in https://github.com/linkml/linkml/pull/1753
• swap to a Apache2 license to match biolink by @sierra-moxon in https://github.com/linkml/linkml/pull/1754
• Adding test for 1446 by @cmungall in https://github.com/linkml/linkml/pull/1756
• Fix JSON Schema generation for inlined slots with class range descendants by @pkalita-lbl in https://github.com/linkml/linkml/pull/1758
• Add optional argument --use-class-uris to gen-doc by @sujaypatil96 in https://github.com/linkml/linkml/pull/1759
• PydanticGen CLI Updates by @glass-ships in https://github.com/linkml/linkml/pull/1729
• fix double close-parens by @nlharris in https://github.com/linkml/linkml/pull/1762
• Adding new how-to doc on recognizing and using different data shapes (structural forms) by @cmungall in https://github.com/linkml/linkml/pull/1761
• Add option to gen-excel to support splitting up workbook on a per class basis by @sujaypatil96 in https://github.com/linkml/linkml/pull/1732
• Adding a how-to on managing releases by @cmungall in https://github.com/linkml/linkml/pull/1765
• Issue 1696 pydantic regex support by @nicholsn in https://github.com/linkml/linkml/pull/1772
• Convert tests in tests/test_utils to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1768
• Convert tests in tests/test_validator to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1769
• Convert tests in tests/test_workspaces to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1770
• slots defined in an ancestor mixin, should be distributed to classes defined as having descendent mixins (pythongen) fixes #1671 by @sierra-moxon in https://github.com/linkml/linkml/pull/1752
• Pydantic gen pattern lists by @plbremer in https://github.com/linkml/linkml/pull/1779
• Convert tests in tests/test_scripts to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1783
• Added --preserve-name option to schema-fixer. by @cmungall in https://github.com/linkml/linkml/pull/1787
• Fix instructions for gen-yuml in tutorial02 by @dalito in https://github.com/linkml/linkml/pull/1773
• Ensure that logging level is set correctly in Generator CLIs by @pkalita-lbl in https://github.com/linkml/linkml/pull/1790
• Replace JsonSchemaDataValidator with Validator in ExampleRunner by @pkalita-lbl in https://github.com/linkml/linkml/pull/1778
• additional compliance tests redux2 by @cmungall in https://github.com/linkml/linkml/pull/1791
• Emit a warning from JsonSchemaGenerator when the top_class option doesn't correspond to an actual class name by @pkalita-lbl in https://github.com/linkml/linkml/pull/1795
• Account for required slot_conditions when handling rules in jsonschemagen by @pkalita-lbl in https://github.com/linkml/linkml/pull/1796
• Update SPECIFICATION.md by @cmungall in https://github.com/linkml/linkml/pull/1794
• Delete sparql directory by @cmungall in https://github.com/linkml/linkml/pull/1793
• Total length of data validation formula <= 255 characters for uncorrutped Excel file generation by @sujaypatil96 in https://github.com/linkml/linkml/pull/1798
• Add util functions for typescript in generator by @amc-corey-cox in https://github.com/linkml/linkml/pull/1799
• Add in optional argument to include/exclude Excel files for mixin classes by @sujaypatil96 in https://github.com/linkml/linkml/pull/1800
• Fix 1666 - Dont use callables for generated pydantic field defaults by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1797
• Generate basic Pydantic model for data arrays by @rly in https://github.com/linkml/linkml/pull/1397
• Fix typo in return for is{{interface}} by @amc-corey-cox in https://github.com/linkml/linkml/pull/1801
• Traverse class ancestors looking for rules to apply in JSON Schema output by @pkalita-lbl in https://github.com/linkml/linkml/pull/1805
• Allow non-object types in JSON Schema generated from unconstrained classes by @pkalita-lbl in https://github.com/linkml/linkml/pull/1809
• add test to confirm that example in ticket returns two annotations, e… by @sierra-moxon in https://github.com/linkml/linkml/pull/1814
• Move numpy dependency to tests group by @pkalita-lbl in https://github.com/linkml/linkml/pull/1822
• Choose between Mermaid/PlantUML in gen-doc UML class diagrams by @sujaypatil96 in https://github.com/linkml/linkml/pull/1819
• Parse enums properly when generating ShEx by @deepakunni3 in https://github.com/linkml/linkml/pull/1824
• Use --> for for class-to-class relationships based on slots by @sujaypatil96 in https://github.com/linkml/linkml/pull/1823
• replace calls to deprecated methods in schemaview by @cmungall in https://github.com/linkml/linkml/pull/1815
• linkml-lint: ignore dot files by default by @paulmillar in https://github.com/linkml/linkml/pull/1831
• gen-json-schema: support taking JSON Schema title from title slot by @paulmillar in https://github.com/linkml/linkml/pull/1838
• Adding --use-native-uris option to owlgen. by @cmungall in https://github.com/linkml/linkml/pull/1843
• Adding shaclgen to compliance tests by @cmungall in https://github.com/linkml/linkml/pull/1844
• Format with Black v24 by @pkalita-lbl in https://github.com/linkml/linkml/pull/1848
• Adding a compliance test for linkml:Any by @cmungall in https://github.com/linkml/linkml/pull/1849
• Add explicit record for Chris to unify him with cmungall in mailmap by @yarikoptic in https://github.com/linkml/linkml/pull/1863
• Update CITATION.cff by @nlharris in https://github.com/linkml/linkml/pull/1858
• expand simple dict processing by @cmungall in https://github.com/linkml/linkml/pull/1860
• Update tutorial09.md by @bendichter in https://github.com/linkml/linkml/pull/1874
• remove rdflibshim from _init__.py by @tgbugs in https://github.com/linkml/linkml/pull/1870
• attempt at fixing forward references when using imported schemas in p… by @kervel in https://github.com/linkml/linkml/pull/1859
• Fix some URLs, enable checking of w3id.org/linkml/ links by @yarikoptic in https://github.com/linkml/linkml/pull/1873
• Update pyproject.toml by @dalito in https://github.com/linkml/linkml/pull/1875
• Add instruction about installing poetry dev dependencies before makin… by @nlharris in https://github.com/linkml/linkml/pull/1879
• Update tutorial10.md by @cmungall in https://github.com/linkml/linkml/pull/1878
• 1.7.0 release candidate by @cmungall in https://github.com/linkml/linkml/pull/1847

New Contributors

• @rwblair made their first contribution in https://github.com/linkml/linkml/pull/1667
• @gouttegd made their first contribution in https://github.com/linkml/linkml/pull/1709
• @plbremer made their first contribution in https://github.com/linkml/linkml/pull/1779
• @sneakers-the-rat made their first contribution in https://github.com/linkml/linkml/pull/1797
• @paulmillar made their first contribution in https://github.com/linkml/linkml/pull/1831
• @bendichter made their first contribution in https://github.com/linkml/linkml/pull/1874
• @tgbugs made their first contribution in https://github.com/linkml/linkml/pull/1870

Full Changelog: https://github.com/linkml/linkml/compare/v1.6.0...v1.7.0

- Python
Published by cmungall over 2 years ago

linkml - v1.6.11

What's Changed

• Format with Black v24 by @pkalita-lbl in https://github.com/linkml/linkml/pull/1848
• Adding a compliance test for linkml:Any by @cmungall in https://github.com/linkml/linkml/pull/1849
• Add explicit record for Chris to unify him with cmungall in mailmap by @yarikoptic in https://github.com/linkml/linkml/pull/1863
• Update CITATION.cff by @nlharris in https://github.com/linkml/linkml/pull/1858
• expand simple dict processing by @cmungall in https://github.com/linkml/linkml/pull/1860

Full Changelog: https://github.com/linkml/linkml/compare/v1.6.10...v1.6.11

- Python
Published by cmungall over 2 years ago

linkml - v1.7.0rc2

Release Candidate for LinkML 1.7.0

Synced with:

• linkml-runtime 1.70.rc1
• linkml-model 1.7.0rc1

This release introduces two changes to the metamodel:

• Include LABEL in Permissible Value Formula Options by @nicholsn in https://github.com/linkml/linkml-model/pull/171
• Make maximumvalue and minimumvalue accept linkml:Any by @sneakers-the-rat in https://github.com/linkml/linkml-model/pull/176
• Update array metamodel and examples by @rly in https://github.com/linkml/linkml-model/pull/175

Note: this is a pre-release so it will not be installed by default.

If you want to test via poetry you will need to explicitly add in your schema, e.g.

bash poetry add --group dev linkml-1.7.0rc2

What's Changed (This package)

• Fixes #1653 by @cmungall in https://github.com/linkml/linkml/pull/1654
• NMDC-inspired test for polymorphic collections, plus some spelling corrections by @turbomam in https://github.com/linkml/linkml/pull/1609
• Add option to JsonschemaValidationPlugin to provide pre-generated JSON Schema by @pkalita-lbl in https://github.com/linkml/linkml/pull/1663
• Pydantic 2 testing by @pkalita-lbl in https://github.com/linkml/linkml/pull/1660
• Fix typescript generator link in tutorial05.md by @rwblair in https://github.com/linkml/linkml/pull/1667
• Test Stub for Issue 163 by @nicholsn in https://github.com/linkml/linkml/pull/1642
• stub for test for #1422 by @cmungall in https://github.com/linkml/linkml/pull/1622
• 3 new FAQ questions from NWD, fixes #1568 by @sierra-moxon in https://github.com/linkml/linkml/pull/1580
• make line length consistent between black and ruff by @sierra-moxon in https://github.com/linkml/linkml/pull/1561
• Connect new validator module to linkml-validate CLI entry point by @pkalita-lbl in https://github.com/linkml/linkml/pull/1675
• owl enhancements by @cmungall in https://github.com/linkml/linkml/pull/1668
• Added ways to stay involved by @nlharris in https://github.com/linkml/linkml/pull/1683
• minor fix linkmllink->linkmllint, etc. by @sierra-moxon in https://github.com/linkml/linkml/pull/1687
• Fix broken enum and subset URI links by @sujaypatil96 in https://github.com/linkml/linkml/pull/1686
• Add missing simple data types by @anjastrunk in https://github.com/linkml/linkml/pull/1688
• Updated validation documentation by @pkalita-lbl in https://github.com/linkml/linkml/pull/1679
• Fix typo in name of example JSON property by @eecavanna in https://github.com/linkml/linkml/pull/1693
• Adds support for using typeof to generate the typescript type if type.base is not set by @kevinschaper in https://github.com/linkml/linkml/pull/1700
• Ensure source_file is populated on SchemaDefinition when it is loaded by Validator by @pkalita-lbl in https://github.com/linkml/linkml/pull/1697
• [gen-doc] Allow to rename the index document. by @gouttegd in https://github.com/linkml/linkml/pull/1709
• Added a compliance test for jsonpointer. by @cmungall in https://github.com/linkml/linkml/pull/1707
• Show headers for class, slot documentation pages similar to MIxS by @sujaypatil96 in https://github.com/linkml/linkml/pull/1705
• Remove calls to decode on output of Graph.serialize by @pkalita-lbl in https://github.com/linkml/linkml/pull/1714
• Additional compliance tests for boolean combinations, owlgen edge case fixes by @cmungall in https://github.com/linkml/linkml/pull/1736
• First pass at collaboration best practice doc 1744 by @cmungall in https://github.com/linkml/linkml/pull/1745
• Fix the rendering of date and time fields in Java code by @gouttegd in https://github.com/linkml/linkml/pull/1710
• update return types on shaclgen methods by @glass-ships in https://github.com/linkml/linkml/pull/1741
• Edits to collaboration guide by @cmungall in https://github.com/linkml/linkml/pull/1747
• Improve tutorial 02 (add docu for tree_root) by @dalito in https://github.com/linkml/linkml/pull/1753
• swap to a Apache2 license to match biolink by @sierra-moxon in https://github.com/linkml/linkml/pull/1754
• Adding test for 1446 by @cmungall in https://github.com/linkml/linkml/pull/1756
• Fix JSON Schema generation for inlined slots with class range descendants by @pkalita-lbl in https://github.com/linkml/linkml/pull/1758
• Add optional argument --use-class-uris to gen-doc by @sujaypatil96 in https://github.com/linkml/linkml/pull/1759
• PydanticGen CLI Updates by @glass-ships in https://github.com/linkml/linkml/pull/1729
• fix double close-parens by @nlharris in https://github.com/linkml/linkml/pull/1762
• Adding new how-to doc on recognizing and using different data shapes (structural forms) by @cmungall in https://github.com/linkml/linkml/pull/1761
• Add option to gen-excel to support splitting up workbook on a per class basis by @sujaypatil96 in https://github.com/linkml/linkml/pull/1732
• Adding a how-to on managing releases by @cmungall in https://github.com/linkml/linkml/pull/1765
• Issue 1696 pydantic regex support by @nicholsn in https://github.com/linkml/linkml/pull/1772
• Convert tests in tests/test_utils to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1768
• Convert tests in tests/test_validator to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1769
• Convert tests in tests/test_workspaces to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1770
• slots defined in an ancestor mixin, should be distributed to classes defined as having descendent mixins (pythongen) fixes #1671 by @sierra-moxon in https://github.com/linkml/linkml/pull/1752
• Pydantic gen pattern lists by @plbremer in https://github.com/linkml/linkml/pull/1779
• Convert tests in tests/test_scripts to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1783
• Added --preserve-name option to schema-fixer. by @cmungall in https://github.com/linkml/linkml/pull/1787
• Fix instructions for gen-yuml in tutorial02 by @dalito in https://github.com/linkml/linkml/pull/1773
• Ensure that logging level is set correctly in Generator CLIs by @pkalita-lbl in https://github.com/linkml/linkml/pull/1790
• Replace JsonSchemaDataValidator with Validator in ExampleRunner by @pkalita-lbl in https://github.com/linkml/linkml/pull/1778
• additional compliance tests redux2 by @cmungall in https://github.com/linkml/linkml/pull/1791
• Emit a warning from JsonSchemaGenerator when the top_class option doesn't correspond to an actual class name by @pkalita-lbl in https://github.com/linkml/linkml/pull/1795
• Account for required slot_conditions when handling rules in jsonschemagen by @pkalita-lbl in https://github.com/linkml/linkml/pull/1796
• Update SPECIFICATION.md by @cmungall in https://github.com/linkml/linkml/pull/1794
• Delete sparql directory by @cmungall in https://github.com/linkml/linkml/pull/1793
• Total length of data validation formula <= 255 characters for uncorrutped Excel file generation by @sujaypatil96 in https://github.com/linkml/linkml/pull/1798
• Add util functions for typescript in generator by @amc-corey-cox in https://github.com/linkml/linkml/pull/1799
• Add in optional argument to include/exclude Excel files for mixin classes by @sujaypatil96 in https://github.com/linkml/linkml/pull/1800
• Fix 1666 - Dont use callables for generated pydantic field defaults by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1797
• Generate basic Pydantic model for data arrays by @rly in https://github.com/linkml/linkml/pull/1397
• Fix typo in return for is{{interface}} by @amc-corey-cox in https://github.com/linkml/linkml/pull/1801
• Traverse class ancestors looking for rules to apply in JSON Schema output by @pkalita-lbl in https://github.com/linkml/linkml/pull/1805
• Allow non-object types in JSON Schema generated from unconstrained classes by @pkalita-lbl in https://github.com/linkml/linkml/pull/1809
• add test to confirm that example in ticket returns two annotations, e… by @sierra-moxon in https://github.com/linkml/linkml/pull/1814
• Move numpy dependency to tests group by @pkalita-lbl in https://github.com/linkml/linkml/pull/1822
• Choose between Mermaid/PlantUML in gen-doc UML class diagrams by @sujaypatil96 in https://github.com/linkml/linkml/pull/1819
• Parse enums properly when generating ShEx by @deepakunni3 in https://github.com/linkml/linkml/pull/1824
• Use --> for for class-to-class relationships based on slots by @sujaypatil96 in https://github.com/linkml/linkml/pull/1823
• replace calls to deprecated methods in schemaview by @cmungall in https://github.com/linkml/linkml/pull/1815
• linkml-lint: ignore dot files by default by @paulmillar in https://github.com/linkml/linkml/pull/1831
• gen-json-schema: support taking JSON Schema title from title slot by @paulmillar in https://github.com/linkml/linkml/pull/1838
• Adding --use-native-uris option to owlgen. by @cmungall in https://github.com/linkml/linkml/pull/1843
• Adding shaclgen to compliance tests by @cmungall in https://github.com/linkml/linkml/pull/1844
• Format with Black v24 by @pkalita-lbl in https://github.com/linkml/linkml/pull/1848

New Contributors

• @rwblair made their first contribution in https://github.com/linkml/linkml/pull/1667
• @gouttegd made their first contribution in https://github.com/linkml/linkml/pull/1709
• @plbremer made their first contribution in https://github.com/linkml/linkml/pull/1779
• @sneakers-the-rat made their first contribution in https://github.com/linkml/linkml/pull/1797
• @paulmillar made their first contribution in https://github.com/linkml/linkml/pull/1831

Full Changelog: https://github.com/linkml/linkml/compare/v1.6.0...v1.7.0rc2

- Python
Published by cmungall over 2 years ago

linkml - v1.7.0rc1

What's Changed

• Fixes #1653 by @cmungall in https://github.com/linkml/linkml/pull/1654
• NMDC-inspired test for polymorphic collections, plus some spelling corrections by @turbomam in https://github.com/linkml/linkml/pull/1609
• Add option to JsonschemaValidationPlugin to provide pre-generated JSON Schema by @pkalita-lbl in https://github.com/linkml/linkml/pull/1663
• Pydantic 2 testing by @pkalita-lbl in https://github.com/linkml/linkml/pull/1660
• Fix typescript generator link in tutorial05.md by @rwblair in https://github.com/linkml/linkml/pull/1667
• Test Stub for Issue 163 by @nicholsn in https://github.com/linkml/linkml/pull/1642
• stub for test for #1422 by @cmungall in https://github.com/linkml/linkml/pull/1622
• 3 new FAQ questions from NWD, fixes #1568 by @sierra-moxon in https://github.com/linkml/linkml/pull/1580
• make line length consistent between black and ruff by @sierra-moxon in https://github.com/linkml/linkml/pull/1561
• Connect new validator module to linkml-validate CLI entry point by @pkalita-lbl in https://github.com/linkml/linkml/pull/1675
• owl enhancements by @cmungall in https://github.com/linkml/linkml/pull/1668
• Added ways to stay involved by @nlharris in https://github.com/linkml/linkml/pull/1683
• minor fix linkmllink->linkmllint, etc. by @sierra-moxon in https://github.com/linkml/linkml/pull/1687
• Fix broken enum and subset URI links by @sujaypatil96 in https://github.com/linkml/linkml/pull/1686
• Add missing simple data types by @anjastrunk in https://github.com/linkml/linkml/pull/1688
• Updated validation documentation by @pkalita-lbl in https://github.com/linkml/linkml/pull/1679
• Fix typo in name of example JSON property by @eecavanna in https://github.com/linkml/linkml/pull/1693
• Adds support for using typeof to generate the typescript type if type.base is not set by @kevinschaper in https://github.com/linkml/linkml/pull/1700
• Ensure source_file is populated on SchemaDefinition when it is loaded by Validator by @pkalita-lbl in https://github.com/linkml/linkml/pull/1697
• [gen-doc] Allow to rename the index document. by @gouttegd in https://github.com/linkml/linkml/pull/1709
• Added a compliance test for jsonpointer. by @cmungall in https://github.com/linkml/linkml/pull/1707
• Show headers for class, slot documentation pages similar to MIxS by @sujaypatil96 in https://github.com/linkml/linkml/pull/1705
• Remove calls to decode on output of Graph.serialize by @pkalita-lbl in https://github.com/linkml/linkml/pull/1714
• Additional compliance tests for boolean combinations, owlgen edge case fixes by @cmungall in https://github.com/linkml/linkml/pull/1736
• First pass at collaboration best practice doc 1744 by @cmungall in https://github.com/linkml/linkml/pull/1745
• Fix the rendering of date and time fields in Java code by @gouttegd in https://github.com/linkml/linkml/pull/1710
• update return types on shaclgen methods by @glass-ships in https://github.com/linkml/linkml/pull/1741
• Edits to collaboration guide by @cmungall in https://github.com/linkml/linkml/pull/1747
• Improve tutorial 02 (add docu for tree_root) by @dalito in https://github.com/linkml/linkml/pull/1753
• swap to a Apache2 license to match biolink by @sierra-moxon in https://github.com/linkml/linkml/pull/1754
• Adding test for 1446 by @cmungall in https://github.com/linkml/linkml/pull/1756
• Fix JSON Schema generation for inlined slots with class range descendants by @pkalita-lbl in https://github.com/linkml/linkml/pull/1758
• Add optional argument --use-class-uris to gen-doc by @sujaypatil96 in https://github.com/linkml/linkml/pull/1759
• PydanticGen CLI Updates by @glass-ships in https://github.com/linkml/linkml/pull/1729
• fix double close-parens by @nlharris in https://github.com/linkml/linkml/pull/1762
• Adding new how-to doc on recognizing and using different data shapes (structural forms) by @cmungall in https://github.com/linkml/linkml/pull/1761
• Add option to gen-excel to support splitting up workbook on a per class basis by @sujaypatil96 in https://github.com/linkml/linkml/pull/1732
• Adding a how-to on managing releases by @cmungall in https://github.com/linkml/linkml/pull/1765
• Issue 1696 pydantic regex support by @nicholsn in https://github.com/linkml/linkml/pull/1772
• Convert tests in tests/test_utils to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1768
• Convert tests in tests/test_validator to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1769
• Convert tests in tests/test_workspaces to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1770
• slots defined in an ancestor mixin, should be distributed to classes defined as having descendent mixins (pythongen) fixes #1671 by @sierra-moxon in https://github.com/linkml/linkml/pull/1752
• Pydantic gen pattern lists by @plbremer in https://github.com/linkml/linkml/pull/1779
• Convert tests in tests/test_scripts to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1783
• Added --preserve-name option to schema-fixer. by @cmungall in https://github.com/linkml/linkml/pull/1787
• Fix instructions for gen-yuml in tutorial02 by @dalito in https://github.com/linkml/linkml/pull/1773
• Ensure that logging level is set correctly in Generator CLIs by @pkalita-lbl in https://github.com/linkml/linkml/pull/1790
• Replace JsonSchemaDataValidator with Validator in ExampleRunner by @pkalita-lbl in https://github.com/linkml/linkml/pull/1778
• additional compliance tests redux2 by @cmungall in https://github.com/linkml/linkml/pull/1791
• Emit a warning from JsonSchemaGenerator when the top_class option doesn't correspond to an actual class name by @pkalita-lbl in https://github.com/linkml/linkml/pull/1795
• Account for required slot_conditions when handling rules in jsonschemagen by @pkalita-lbl in https://github.com/linkml/linkml/pull/1796
• Update SPECIFICATION.md by @cmungall in https://github.com/linkml/linkml/pull/1794
• Delete sparql directory by @cmungall in https://github.com/linkml/linkml/pull/1793
• Total length of data validation formula <= 255 characters for uncorrutped Excel file generation by @sujaypatil96 in https://github.com/linkml/linkml/pull/1798
• Add util functions for typescript in generator by @amc-corey-cox in https://github.com/linkml/linkml/pull/1799
• Add in optional argument to include/exclude Excel files for mixin classes by @sujaypatil96 in https://github.com/linkml/linkml/pull/1800
• Fix 1666 - Dont use callables for generated pydantic field defaults by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1797
• Generate basic Pydantic model for data arrays by @rly in https://github.com/linkml/linkml/pull/1397
• Fix typo in return for is{{interface}} by @amc-corey-cox in https://github.com/linkml/linkml/pull/1801
• Traverse class ancestors looking for rules to apply in JSON Schema output by @pkalita-lbl in https://github.com/linkml/linkml/pull/1805
• Allow non-object types in JSON Schema generated from unconstrained classes by @pkalita-lbl in https://github.com/linkml/linkml/pull/1809
• add test to confirm that example in ticket returns two annotations, e… by @sierra-moxon in https://github.com/linkml/linkml/pull/1814
• Move numpy dependency to tests group by @pkalita-lbl in https://github.com/linkml/linkml/pull/1822
• Choose between Mermaid/PlantUML in gen-doc UML class diagrams by @sujaypatil96 in https://github.com/linkml/linkml/pull/1819
• Parse enums properly when generating ShEx by @deepakunni3 in https://github.com/linkml/linkml/pull/1824
• Use --> for for class-to-class relationships based on slots by @sujaypatil96 in https://github.com/linkml/linkml/pull/1823
• replace calls to deprecated methods in schemaview by @cmungall in https://github.com/linkml/linkml/pull/1815
• linkml-lint: ignore dot files by default by @paulmillar in https://github.com/linkml/linkml/pull/1831
• gen-json-schema: support taking JSON Schema title from title slot by @paulmillar in https://github.com/linkml/linkml/pull/1838
• Adding --use-native-uris option to owlgen. by @cmungall in https://github.com/linkml/linkml/pull/1843
• Adding shaclgen to compliance tests by @cmungall in https://github.com/linkml/linkml/pull/1844
• Format with Black v24 by @pkalita-lbl in https://github.com/linkml/linkml/pull/1848

New Contributors

• @rwblair made their first contribution in https://github.com/linkml/linkml/pull/1667
• @gouttegd made their first contribution in https://github.com/linkml/linkml/pull/1709
• @plbremer made their first contribution in https://github.com/linkml/linkml/pull/1779
• @sneakers-the-rat made their first contribution in https://github.com/linkml/linkml/pull/1797
• @paulmillar made their first contribution in https://github.com/linkml/linkml/pull/1831

Full Changelog: https://github.com/linkml/linkml/compare/v1.6.0...v1.7.0rc1

- Python
Published by cmungall over 2 years ago

linkml - v1.6.10

What's Changed

• gen-json-schema: support taking JSON Schema title from title slot by @paulmillar in https://github.com/linkml/linkml/pull/1838
• Adding --use-native-uris option to owlgen. by @cmungall in https://github.com/linkml/linkml/pull/1843

Full Changelog: https://github.com/linkml/linkml/compare/v1.6.9...v1.6.10

- Python
Published by turbomam over 2 years ago

linkml - v1.6.9

What's Changed

• Choose between Mermaid/PlantUML in gen-doc UML class diagrams by @sujaypatil96 in https://github.com/linkml/linkml/pull/1819
• Parse enums properly when generating ShEx by @deepakunni3 in https://github.com/linkml/linkml/pull/1824
• Use --> for for class-to-class relationships based on slots by @sujaypatil96 in https://github.com/linkml/linkml/pull/1823
• replace calls to deprecated methods in schemaview by @cmungall in https://github.com/linkml/linkml/pull/1815
• linkml-lint: ignore dot files by default by @paulmillar in https://github.com/linkml/linkml/pull/1831

New Contributors

• @paulmillar made their first contribution in https://github.com/linkml/linkml/pull/1831

Full Changelog: https://github.com/linkml/linkml/compare/v1.6.8...v1.6.9

- Python
Published by cmungall over 2 years ago

linkml - v1.6.8

What's Changed

• Generate basic Pydantic model for data arrays by @rly in https://github.com/linkml/linkml/pull/1397
• Fix typo in return for is{{interface}} by @amc-corey-cox in https://github.com/linkml/linkml/pull/1801
• Traverse class ancestors looking for rules to apply in JSON Schema output by @pkalita-lbl in https://github.com/linkml/linkml/pull/1805
• Allow non-object types in JSON Schema generated from unconstrained classes by @pkalita-lbl in https://github.com/linkml/linkml/pull/1809
• add test to confirm that example in ticket returns two annotations, e… by @sierra-moxon in https://github.com/linkml/linkml/pull/1814
• Move numpy dependency to tests group by @pkalita-lbl in https://github.com/linkml/linkml/pull/1822

Full Changelog: https://github.com/linkml/linkml/compare/v1.6.7...v1.6.8

- Python
Published by pkalita-lbl over 2 years ago

linkml - v1.6.7

What's Changed

• Emit a warning from JsonSchemaGenerator when the top_class option doesn't correspond to an actual class name by @pkalita-lbl in https://github.com/linkml/linkml/pull/1795
• Account for required slot_conditions when handling rules in jsonschemagen by @pkalita-lbl in https://github.com/linkml/linkml/pull/1796
• Update SPECIFICATION.md by @cmungall in https://github.com/linkml/linkml/pull/1794
• Delete sparql directory by @cmungall in https://github.com/linkml/linkml/pull/1793
• Total length of data validation formula <= 255 characters for uncorrutped Excel file generation by @sujaypatil96 in https://github.com/linkml/linkml/pull/1798
• Add util functions for typescript in generator by @amc-corey-cox in https://github.com/linkml/linkml/pull/1799
• Add in optional argument to include/exclude Excel files for mixin classes by @sujaypatil96 in https://github.com/linkml/linkml/pull/1800
• Fix 1666 - Dont use callables for generated pydantic field defaults by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1797

New Contributors

• @sneakers-the-rat made their first contribution in https://github.com/linkml/linkml/pull/1797

Full Changelog: https://github.com/linkml/linkml/compare/v1.6.6...v1.6.7

- Python
Published by sujaypatil96 over 2 years ago

linkml - v1.6.6

What's Changed

• Pydantic gen pattern lists by @plbremer in https://github.com/linkml/linkml/pull/1779
• Convert tests in tests/test_scripts to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1783
• Added --preserve-name option to schema-fixer. by @cmungall in https://github.com/linkml/linkml/pull/1787
• Fix instructions for gen-yuml in tutorial02 by @dalito in https://github.com/linkml/linkml/pull/1773
• Ensure that logging level is set correctly in Generator CLIs by @pkalita-lbl in https://github.com/linkml/linkml/pull/1790
• Replace JsonSchemaDataValidator with Validator in ExampleRunner by @pkalita-lbl in https://github.com/linkml/linkml/pull/1778
• additional compliance tests by @cmungall in https://github.com/linkml/linkml/pull/1791

New Contributors

• @plbremer made their first contribution in https://github.com/linkml/linkml/pull/1779

Full Changelog: https://github.com/linkml/linkml/compare/v1.6.5...v1.6.6

- Python
Published by cmungall over 2 years ago

linkml - v1.6.5

What's Changed

• Add option to gen-excel to support splitting up workbook on a per class basis by @sujaypatil96 in https://github.com/linkml/linkml/pull/1732
• Adding a how-to on managing releases by @cmungall in https://github.com/linkml/linkml/pull/1765
• Issue 1696 pydantic regex support by @nicholsn in https://github.com/linkml/linkml/pull/1772
• Convert tests in tests/test_utils to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1768
• Convert tests in tests/test_validator to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1769
• Convert tests in tests/test_workspaces to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1770
• slots defined in an ancestor mixin, should be distributed to classes defined as having descendent mixins (pythongen) fixes #1671 by @sierra-moxon in https://github.com/linkml/linkml/pull/1752

Full Changelog: https://github.com/linkml/linkml/compare/v1.6.4...v1.6.5

- Python
Published by sujaypatil96 over 2 years ago

linkml - v1.6.4

What's Changed

• First pass at collaboration best practice doc 1744 by @cmungall in https://github.com/linkml/linkml/pull/1745
• Fix the rendering of date and time fields in Java code by @gouttegd in https://github.com/linkml/linkml/pull/1710
• update return types on shaclgen methods by @glass-ships in https://github.com/linkml/linkml/pull/1741
• Edits to collaboration guide by @cmungall in https://github.com/linkml/linkml/pull/1747
• Improve tutorial 02 (add docu for tree_root) by @dalito in https://github.com/linkml/linkml/pull/1753
• swap to a Apache2 license to match biolink by @sierra-moxon in https://github.com/linkml/linkml/pull/1754
• Adding test for 1446 by @cmungall in https://github.com/linkml/linkml/pull/1756
• Fix JSON Schema generation for inlined slots with class range descendants by @pkalita-lbl in https://github.com/linkml/linkml/pull/1758
• Add optional argument --use-class-uris to gen-doc by @sujaypatil96 in https://github.com/linkml/linkml/pull/1759
• PydanticGen CLI Updates by @glass-ships in https://github.com/linkml/linkml/pull/1729
• fix double close-parens by @nlharris in https://github.com/linkml/linkml/pull/1762
• Adding new how-to doc on recognizing and using different data shapes (structural forms) by @cmungall in https://github.com/linkml/linkml/pull/1761

Full Changelog: https://github.com/linkml/linkml/compare/v1.6.3...v1.6.4

- Python
Published by cmungall over 2 years ago

linkml - v1.6.3

What's Changed

• Fix typo in name of example JSON property by @eecavanna in https://github.com/linkml/linkml/pull/1693
• Adds support for using typeof to generate the typescript type if type.base is not set by @kevinschaper in https://github.com/linkml/linkml/pull/1700
• Ensure source_file is populated on SchemaDefinition when it is loaded by Validator by @pkalita-lbl in https://github.com/linkml/linkml/pull/1697
• [gen-doc] Allow to rename the index document. by @gouttegd in https://github.com/linkml/linkml/pull/1709
• Added a compliance test for jsonpointer. by @cmungall in https://github.com/linkml/linkml/pull/1707
• Show headers for class, slot documentation pages similar to MIxS by @sujaypatil96 in https://github.com/linkml/linkml/pull/1705
• Remove calls to decode on output of Graph.serialize by @pkalita-lbl in https://github.com/linkml/linkml/pull/1714
• Additional compliance tests for boolean combinations, owlgen edge case fixes by @cmungall in https://github.com/linkml/linkml/pull/1736

New Contributors

• @gouttegd made their first contribution in https://github.com/linkml/linkml/pull/1709

Full Changelog: https://github.com/linkml/linkml/compare/v1.6.2...v1.6.3

- Python
Published by turbomam over 2 years ago

linkml - v1.6.2

Highlights

JSON Schema Generation and Validation Framework

See the improved docs: https://linkml.io/linkml/data/validating-data.html

• Add option to JsonschemaValidationPlugin to provide pre-generated JSON Schema by @pkalita-lbl in https://github.com/linkml/linkml/pull/1663
• Connect new validator module to linkml-validate CLI entry point by @pkalita-lbl in https://github.com/linkml/linkml/pull/1675
• Updated validation documentation by @pkalita-lbl in https://github.com/linkml/linkml/pull/1679

OWL Generation

• owl enhancements by @cmungall in https://github.com/linkml/linkml/pull/1668

This adds two options to owlgen --add-root-classes, and --mixins-as-expressions. See the "tips" section on the owlgen docs: https://linkml.io/linkml/generators/owl.html#tips

Other changes

• NMDC-inspired test for polymorphic collections, plus some spelling corrections by @turbomam in https://github.com/linkml/linkml/pull/1609
• Pydantic 2 testing by @pkalita-lbl in https://github.com/linkml/linkml/pull/1660
• Fix typescript generator link in tutorial05.md by @rwblair in https://github.com/linkml/linkml/pull/1667
• Test Stub for Issue 163 by @nicholsn in https://github.com/linkml/linkml/pull/1642
• stub for test for #1422 by @cmungall in https://github.com/linkml/linkml/pull/1622
• 3 new FAQ questions from NWD, fixes #1568 by @sierra-moxon in https://github.com/linkml/linkml/pull/1580
• make line length consistent between black and ruff by @sierra-moxon in https://github.com/linkml/linkml/pull/1561
• Added ways to stay involved by @nlharris in https://github.com/linkml/linkml/pull/1683
• minor fix linkmllink->linkmllint, etc. by @sierra-moxon in https://github.com/linkml/linkml/pull/1687
• Fix broken enum and subset URI links by @sujaypatil96 in https://github.com/linkml/linkml/pull/1686
• Add missing simple data types by @anjastrunk in https://github.com/linkml/linkml/pull/1688

New Contributors

• @rwblair made their first contribution in https://github.com/linkml/linkml/pull/1667

Full Changelog: https://github.com/linkml/linkml/compare/v1.6.1...v1.6.2

- Python
Published by cmungall over 2 years ago

linkml - v1.6.1

What's Changed

More consistent use of SchemaView() in linkml/generators/owlgen.py and additional class-range elif

• Fixes #1653 by @cmungall in https://github.com/linkml/linkml/pull/1654

Full Changelog: https://github.com/linkml/linkml/compare/v1.6.0...v1.6.1

- Python
Published by turbomam over 2 years ago

linkml - v1.6.0

This release is synced with linkml-model-1.6.0

https://github.com/linkml/linkml-model/releases/tag/v1.6.0

Metamodel changes

• Adding instantiates metaslot by @cmungall in https://github.com/linkml/linkml-model/pull/163
• Adding AnyValue to the metamodel by @cmungall in https://github.com/linkml/linkml-model/pull/164
• changing the range of extensions (annotation values) from string to AnyValue by @cmungall in https://github.com/linkml/linkml-model/pull/162
• Added jsonpointer path types by @cmungall in https://github.com/linkml/linkml-model/pull/159
• Added missing "not" to partial_match slot description by @pkalita-lbl in https://github.com/linkml/linkml-model/pull/166

What's Changed

• fix(docgen): emphasizing multiline descriptions by @Silvanoc in https://github.com/linkml/linkml/pull/1351
• jsonschemavalidator should cache previous results of jsonschema generation by @cmungall in https://github.com/linkml/linkml/pull/1363
• Fix issue #1365 Type definitions not properly sorted in gen-python by @kervel in https://github.com/linkml/linkml/pull/1366
• logging in Excel generator by @sujaypatil96 in https://github.com/linkml/linkml/pull/1344
• Show min, max and pattern on slot pages by @sujaypatil96 in https://github.com/linkml/linkml/pull/1374
• notebook for Type Designators by @cmungall in https://github.com/linkml/linkml/pull/1378
• Add documentation about slot cardinality syntax by @sujaypatil96 in https://github.com/linkml/linkml/pull/1388
• howto docs for NDArray by @cmungall in https://github.com/linkml/linkml/pull/1376
• Misc. improvements to docgen by @sujaypatil96 in https://github.com/linkml/linkml/pull/1398
• slots modifying classes table by @amc-corey-cox in https://github.com/linkml/linkml/pull/1211
• Fix pydanticgen/pythongen to prevent code injection attacks by @ialarmedalien in https://github.com/linkml/linkml/pull/1402
• Configure useenumvalues to True on pydanticgen BaseModel by @kevinschaper in https://github.com/linkml/linkml/pull/1288
• Un-break the build (pydanticgen template fix) by @kevinschaper in https://github.com/linkml/linkml/pull/1414
• Ensure rules are translated at class level and optionally at top level by @pkalita-lbl in https://github.com/linkml/linkml/pull/1415
• Support has_member and all_members in JSON Schema generator by @pkalita-lbl in https://github.com/linkml/linkml/pull/1411
• Add schema validation to linkml-lint command by @pkalita-lbl in https://github.com/linkml/linkml/pull/1410
• pydanticgen: Include keys when checking for inlining by @cmungall in https://github.com/linkml/linkml/pull/1416
• jsonschemavalidator caching keyed on schema and entry point by @sujaypatil96 in https://github.com/linkml/linkml/pull/1420
• A first stab at a Golang generator by @jeff-cohere in https://github.com/linkml/linkml/pull/1418
• linkml-run-examples: validate from dict then try to instantiate by @cmungall in https://github.com/linkml/linkml/pull/1428
• Address linkml-convert issue in tutorial by @nicholsn in https://github.com/linkml/linkml/pull/1425
• Make Pydantic-generated required field have Field() not Field(None) by @rly in https://github.com/linkml/linkml/pull/1431
• regenerating test artefacts by @cmungall in https://github.com/linkml/linkml/pull/1437
• fixing spurious warnings by @cmungall in https://github.com/linkml/linkml/pull/1436
• Fix multivalued strings in typescriptgen by @kevinschaper in https://github.com/linkml/linkml/pull/1427
• Issue #1438 - required slots by @glass-ships in https://github.com/linkml/linkml/pull/1439
• Clean up print statements by @kevinschaper in https://github.com/linkml/linkml/pull/1442
• Fix erdiagramgen issue where mermaid output contains enum variable name by @nicholsn in https://github.com/linkml/linkml/pull/1433
• Adding compile_module to pydantic by @cmungall in https://github.com/linkml/linkml/pull/1377
• Update examples.ipynb by @andrawaag in https://github.com/linkml/linkml/pull/1443
• python 3.7 compatibility for pydanticgen by @kevinschaper in https://github.com/linkml/linkml/pull/1445
• Some workflow steps/jobs cannot run in forks by @Silvanoc in https://github.com/linkml/linkml/pull/1450
• add enum support to gen-typescript, fix it in gen-pydantic by @glass-ships in https://github.com/linkml/linkml/pull/1455
• Improve handling of range unions in jsonschemagen by @pkalita-lbl in https://github.com/linkml/linkml/pull/1461
• pydanticgen any_of conflict with default range by @kevinschaper in https://github.com/linkml/linkml/pull/1460
• Make hierarchical indented rendering of class table default by @sujaypatil96 in https://github.com/linkml/linkml/pull/1458
• Correct gen-doc command by @AlasdairGray in https://github.com/linkml/linkml/pull/1464
• Fix owlgen bug where JsonObjs were being ommitted, 1463. by @cmungall in https://github.com/linkml/linkml/pull/1466
• moving some dependencies to dev dependencies. Fixes 1467 by @cmungall in https://github.com/linkml/linkml/pull/1468
• fix #1472 by @nlharris in https://github.com/linkml/linkml/pull/1476
• Fix LinkML types appearing in generated JSON Schema by @pkalita-lbl in https://github.com/linkml/linkml/pull/1475
• Fix conversion to JSON-LD by @Silvanoc in https://github.com/linkml/linkml/pull/1482
• Delete [ character that was truncating hyperlink text (fixes #1473) by @eecavanna in https://github.com/linkml/linkml/pull/1477
• Add option to assert equivalentClass between a class and its class_uri by @deepakunni3 in https://github.com/linkml/linkml/pull/1484
• Various minor tune ups while going through the docs by @yarikoptic in https://github.com/linkml/linkml/pull/1491
• Codespell: config, workflog + some typos fixed by @yarikoptic in https://github.com/linkml/linkml/pull/1490
• Adding a how-to for combining LinkML and OpenAI 1499 by @cmungall in https://github.com/linkml/linkml/pull/1500
• Iterate over all errors found in JsonSchemaDataValidator by @pkalita-lbl in https://github.com/linkml/linkml/pull/1502
• More of codespell inspired fixes for some manually selected words by @yarikoptic in https://github.com/linkml/linkml/pull/1498
• Fix JsonSchemaDataValidator interaction with example runner by @pkalita-lbl in https://github.com/linkml/linkml/pull/1504
• Validation CLI improvements by @pkalita-lbl in https://github.com/linkml/linkml/pull/1510
• Add slot definitions for Tutorial 7 by @nicholsn in https://github.com/linkml/linkml/pull/1518
• Fix missing simple data types by @anjastrunk in https://github.com/linkml/linkml/pull/1523
• Include code quality checks in main workflow by @pkalita-lbl in https://github.com/linkml/linkml/pull/1520
• Fix shaclgen formatting by @pkalita-lbl in https://github.com/linkml/linkml/pull/1529
• update markdown generator documentation by @sujaypatil96 in https://github.com/linkml/linkml/pull/1528
• Documentation updates by @cmungall in https://github.com/linkml/linkml/pull/1527
• markdown documentation generation docs rst fixes by @sujaypatil96 in https://github.com/linkml/linkml/pull/1530
• Add pre-commit config by @pkalita-lbl in https://github.com/linkml/linkml/pull/1537
• Fix broken links in docs by @rly in https://github.com/linkml/linkml/pull/1539
• allow both UML class and ER diagrams in docgen by @sujaypatil96 in https://github.com/linkml/linkml/pull/1541
• feat(validators): add option include descendants by @Silvanoc in https://github.com/linkml/linkml/pull/1543
• New cross-generator compliance test suite. by @cmungall in https://github.com/linkml/linkml/pull/1551
• Adding FAQ for JSON-LD by @cmungall in https://github.com/linkml/linkml/pull/1558
• fix unique_keys example by @saerdnaer in https://github.com/linkml/linkml/pull/1562
• Port tests/test_issues directory to pytest framework by @pkalita-lbl in https://github.com/linkml/linkml/pull/1563
• Generate permissible JSON schema for empty enum by @lkuchenb in https://github.com/linkml/linkml/pull/1559
• Add optimizations to reduce compliance test run time by @pkalita-lbl in https://github.com/linkml/linkml/pull/1566
• Fix issues identified by Ruff v0.0.284 by @pkalita-lbl in https://github.com/linkml/linkml/pull/1576
• Add option to generate Pydantic v2 by @glass-ships in https://github.com/linkml/linkml/pull/1575
• Update jinja template for subset documentation by @sujaypatil96 in https://github.com/linkml/linkml/pull/1564
• Pluggable validation module by @pkalita-lbl in https://github.com/linkml/linkml/pull/1517
• Update snapshots with changes from latest metamodel by @pkalita-lbl in https://github.com/linkml/linkml/pull/1587
• Convert tests/test_generators to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1586
• feat: add support for plantuml generated diagrams by @Silvanoc in https://github.com/linkml/linkml/pull/1509
• convert plantUML generator tests to pytest by @sujaypatil96 in https://github.com/linkml/linkml/pull/1591
• fix: check imported prefixes for default_prefix by @noelmcloughlin in https://github.com/linkml/linkml/pull/1505
• Update sqlalchemy.rst fix link to sqla site by @cmungall in https://github.com/linkml/linkml/pull/1599
• jsonschemagen includes descendants for range by default for type-designated classes. by @cmungall in https://github.com/linkml/linkml/pull/1613
• Adding presence_enum to jsonschemagen by @cmungall in https://github.com/linkml/linkml/pull/1616
• Make closed state configurable by @anjastrunk in https://github.com/linkml/linkml/pull/1593
• Add a schema transformer to make logical constraint models. by @cmungall in https://github.com/linkml/linkml/pull/1572
• Modified tutorial to make age explicitly a string in part1. by @cmungall in https://github.com/linkml/linkml/pull/1615
• Fixes #1162 by @cmungall in https://github.com/linkml/linkml/pull/1624
• Propagate pattern from type declarations fixes #1371 by @cmungall in https://github.com/linkml/linkml/pull/1623
• Fix some typos by @yarikoptic in https://github.com/linkml/linkml/pull/1631
• Add codecov config making coverage reports informational only by @pkalita-lbl in https://github.com/linkml/linkml/pull/1635
• fixing some small doc typos by @RichardBruskiewich in https://github.com/linkml/linkml/pull/1637
• allow polymorphism for dataclasses using type designators by @cmungall in https://github.com/linkml/linkml/pull/1617
• owlgen refactor v2 by @cmungall in https://github.com/linkml/linkml/pull/1646
• 1.6.0 release candidate by @cmungall in https://github.com/linkml/linkml/pull/1649

New Contributors

• @Silvanoc made their first contribution in https://github.com/linkml/linkml/pull/1351
• @jeff-cohere made their first contribution in https://github.com/linkml/linkml/pull/1418
• @nicholsn made their first contribution in https://github.com/linkml/linkml/pull/1425
• @rly made their first contribution in https://github.com/linkml/linkml/pull/1431
• @glass-ships made their first contribution in https://github.com/linkml/linkml/pull/1439
• @andrawaag made their first contribution in https://github.com/linkml/linkml/pull/1443
• @AlasdairGray made their first contribution in https://github.com/linkml/linkml/pull/1464
• @eecavanna made their first contribution in https://github.com/linkml/linkml/pull/1477
• @yarikoptic made their first contribution in https://github.com/linkml/linkml/pull/1491
• @anjastrunk made their first contribution in https://github.com/linkml/linkml/pull/1523
• @saerdnaer made their first contribution in https://github.com/linkml/linkml/pull/1562
• @lkuchenb made their first contribution in https://github.com/linkml/linkml/pull/1559

Full Changelog: https://github.com/linkml/linkml/compare/v1.5.0...v1.6.0

- Python
Published by cmungall over 2 years ago

linkml - v1.5.8

Highlights

Pluggable validation module

• https://github.com/linkml/linkml/pull/1517

Thanks to @pkalita-lbl for the implementation

Dataclasses now supports type designators

• https://github.com/linkml/linkml/pull/1617

Thanks to @kervel for the core implementation

This puts dataclasses on an equal footing with pydantic regarding type designators

Generation of PlantUML diagrams

• https://github.com/linkml/linkml/pull/1509

Thanks to @Silvanoc for the implementation

All changes

• Pluggable validation module by @pkalita-lbl in https://github.com/linkml/linkml/pull/1517
• Update snapshots with changes from latest metamodel by @pkalita-lbl in https://github.com/linkml/linkml/pull/1587
• Convert tests/test_generators to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1586
• feat: add support for plantuml generated diagrams by @Silvanoc in https://github.com/linkml/linkml/pull/1509
• convert plantUML generator tests to pytest by @sujaypatil96 in https://github.com/linkml/linkml/pull/1591
• fix: check imported prefixes for default_prefix by @noelmcloughlin in https://github.com/linkml/linkml/pull/1505
• Update sqlalchemy.rst fix link to sqla site by @cmungall in https://github.com/linkml/linkml/pull/1599
• jsonschemagen includes descendants for range by default for type-designated classes. by @cmungall in https://github.com/linkml/linkml/pull/1613
• Adding presence_enum to jsonschemagen by @cmungall in https://github.com/linkml/linkml/pull/1616
• Make closed state configurable by @anjastrunk in https://github.com/linkml/linkml/pull/1593
• Add a schema transformer to make logical constraint models. by @cmungall in https://github.com/linkml/linkml/pull/1572
• Modified tutorial to make age explicitly a string in part1. by @cmungall in https://github.com/linkml/linkml/pull/1615
• Fixes #1162 by @cmungall in https://github.com/linkml/linkml/pull/1624
• Propagate pattern from type declarations fixes #1371 by @cmungall in https://github.com/linkml/linkml/pull/1623
• Fix some typos by @yarikoptic in https://github.com/linkml/linkml/pull/1631
• Add codecov config making coverage reports informational only by @pkalita-lbl in https://github.com/linkml/linkml/pull/1635
• fixing some small doc typos by @RichardBruskiewich in https://github.com/linkml/linkml/pull/1637
• allow polymorphism for dataclasses using type designators by @kervel and @cmungall in https://github.com/linkml/linkml/pull/1617

Full Changelog: https://github.com/linkml/linkml/compare/v1.5.7...v1.5.8

- Python
Published by cmungall over 2 years ago

linkml - v1.5.8rc1

What's Changed

• Pluggable validation module by @pkalita-lbl in https://github.com/linkml/linkml/pull/1517
• Update snapshots with changes from latest metamodel by @pkalita-lbl in https://github.com/linkml/linkml/pull/1587
• Convert tests/test_generators to pytest by @pkalita-lbl in https://github.com/linkml/linkml/pull/1586
• feat: add support for plantuml generated diagrams by @Silvanoc in https://github.com/linkml/linkml/pull/1509
• convert plantUML generator tests to pytest by @sujaypatil96 in https://github.com/linkml/linkml/pull/1591
• fix: check imported prefixes for default_prefix by @noelmcloughlin in https://github.com/linkml/linkml/pull/1505
• Update sqlalchemy.rst fix link to sqla site by @cmungall in https://github.com/linkml/linkml/pull/1599
• jsonschemagen includes descendants for range by default for type-designated classes. by @cmungall in https://github.com/linkml/linkml/pull/1613
• Adding presence_enum to jsonschemagen by @cmungall in https://github.com/linkml/linkml/pull/1616
• Make closed state configurable by @anjastrunk in https://github.com/linkml/linkml/pull/1593
• Add a schema transformer to make logical constraint models. by @cmungall in https://github.com/linkml/linkml/pull/1572
• Modified tutorial to make age explicitly a string in part1. by @cmungall in https://github.com/linkml/linkml/pull/1615

Full Changelog: https://github.com/linkml/linkml/compare/v1.5.7...v1.5.8rc1

- Python
Published by cmungall almost 3 years ago

linkml - v1.5.7

What's Changed

• Add slot definitions for Tutorial 7 by @nicholsn in https://github.com/linkml/linkml/pull/1518
• Fix missing simple data types by @anjastrunk in https://github.com/linkml/linkml/pull/1523
• Include code quality checks in main workflow by @pkalita-lbl in https://github.com/linkml/linkml/pull/1520
• Fix shaclgen formatting by @pkalita-lbl in https://github.com/linkml/linkml/pull/1529
• update markdown generator documentation by @sujaypatil96 in https://github.com/linkml/linkml/pull/1528
• Documentation updates by @cmungall in https://github.com/linkml/linkml/pull/1527
• markdown documentation generation docs rst fixes by @sujaypatil96 in https://github.com/linkml/linkml/pull/1530
• Add pre-commit config by @pkalita-lbl in https://github.com/linkml/linkml/pull/1537
• Fix broken links in docs by @rly in https://github.com/linkml/linkml/pull/1539
• allow both UML class and ER diagrams in docgen by @sujaypatil96 in https://github.com/linkml/linkml/pull/1541
• feat(validators): add option include descendants by @Silvanoc in https://github.com/linkml/linkml/pull/1543
• New cross-generator compliance test suite. by @cmungall in https://github.com/linkml/linkml/pull/1551
• Adding FAQ for JSON-LD by @cmungall in https://github.com/linkml/linkml/pull/1558
• fix unique_keys example by @saerdnaer in https://github.com/linkml/linkml/pull/1562
• Port tests/test_issues directory to pytest framework by @pkalita-lbl in https://github.com/linkml/linkml/pull/1563
• Generate permissible JSON schema for empty enum by @lkuchenb in https://github.com/linkml/linkml/pull/1559
• Add optimizations to reduce compliance test run time by @pkalita-lbl in https://github.com/linkml/linkml/pull/1566
• Fix issues identified by Ruff v0.0.284 by @pkalita-lbl in https://github.com/linkml/linkml/pull/1576
• Add option to generate Pydantic v2 by @glass-ships in https://github.com/linkml/linkml/pull/1575
• Update jinja template for subset documentation by @sujaypatil96 in https://github.com/linkml/linkml/pull/1564

New Contributors

• @anjastrunk made their first contribution in https://github.com/linkml/linkml/pull/1523
• @saerdnaer made their first contribution in https://github.com/linkml/linkml/pull/1562
• @lkuchenb made their first contribution in https://github.com/linkml/linkml/pull/1559

Full Changelog: https://github.com/linkml/linkml/compare/v1.5.6...v1.5.7

- Python
Published by cmungall almost 3 years ago

linkml - v1.5.6

What's Changed

• fix #1472 by @nlharris in https://github.com/linkml/linkml/pull/1476
• Fix LinkML types appearing in generated JSON Schema by @pkalita-lbl in https://github.com/linkml/linkml/pull/1475
• Fix conversion to JSON-LD by @Silvanoc in https://github.com/linkml/linkml/pull/1482
• Delete [ character that was truncating hyperlink text (fixes #1473) by @eecavanna in https://github.com/linkml/linkml/pull/1477
• Add option to assert equivalentClass between a class and its class_uri by @deepakunni3 in https://github.com/linkml/linkml/pull/1484
• Various minor tune ups while going through the docs by @yarikoptic in https://github.com/linkml/linkml/pull/1491
• Codespell: config, workflog + some typos fixed by @yarikoptic in https://github.com/linkml/linkml/pull/1490
• Adding a how-to for combining LinkML and OpenAI 1499 by @cmungall in https://github.com/linkml/linkml/pull/1500
• Iterate over all errors found in JsonSchemaDataValidator by @pkalita-lbl in https://github.com/linkml/linkml/pull/1502
• More of codespell inspired fixes for some manually selected words by @yarikoptic in https://github.com/linkml/linkml/pull/1498
• Fix JsonSchemaDataValidator interaction with example runner by @pkalita-lbl in https://github.com/linkml/linkml/pull/1504
• Validation CLI improvements by @pkalita-lbl in https://github.com/linkml/linkml/pull/1510

New Contributors

• @eecavanna made their first contribution in https://github.com/linkml/linkml/pull/1477
• @yarikoptic made their first contribution in https://github.com/linkml/linkml/pull/1491

Full Changelog: https://github.com/linkml/linkml/compare/v1.5.5...v1.5.6

- Python
Published by pkalita-lbl almost 3 years ago

linkml - v1.5.5

What's Changed

• Fix owlgen bug where JsonObjs were being ommitted, 1463. by @cmungall in https://github.com/linkml/linkml/pull/1466
• moving some dependencies to dev dependencies. Fixes 1467 by @cmungall in https://github.com/linkml/linkml/pull/1468

Full Changelog: https://github.com/linkml/linkml/compare/v1.5.4...v1.5.5

- Python
Published by cmungall about 3 years ago

linkml - v1.5.4

What's Changed

• Make hierarchical indented rendering of class table default by @sujaypatil96 in https://github.com/linkml/linkml/pull/1458
• Correct gen-doc command by @AlasdairGray in https://github.com/linkml/linkml/pull/1464

New Contributors

• @AlasdairGray made their first contribution in https://github.com/linkml/linkml/pull/1464

Full Changelog: https://github.com/linkml/linkml/compare/v1.5.3...v1.5.4

- Python
Published by cmungall about 3 years ago

linkml - v1.5.3

What's Changed

• A first stab at a Golang generator by @jeff-cohere in https://github.com/linkml/linkml/pull/1418
• linkml-run-examples: validate from dict then try to instantiate by @cmungall in https://github.com/linkml/linkml/pull/1428
• Address linkml-convert issue in tutorial by @nicholsn in https://github.com/linkml/linkml/pull/1425
• Make Pydantic-generated required field have Field() not Field(None) by @rly in https://github.com/linkml/linkml/pull/1431
• regenerating test artefacts by @cmungall in https://github.com/linkml/linkml/pull/1437
• fixing spurious warnings by @cmungall in https://github.com/linkml/linkml/pull/1436
• Fix multivalued strings in typescriptgen by @kevinschaper in https://github.com/linkml/linkml/pull/1427
• Issue #1438 - required slots by @glass-ships in https://github.com/linkml/linkml/pull/1439
• Clean up print statements by @kevinschaper in https://github.com/linkml/linkml/pull/1442
• Fix erdiagramgen issue where mermaid output contains enum variable name by @nicholsn in https://github.com/linkml/linkml/pull/1433
• Adding compile_module to pydantic by @cmungall in https://github.com/linkml/linkml/pull/1377
• Update examples.ipynb by @andrawaag in https://github.com/linkml/linkml/pull/1443
• python 3.7 compatibility for pydanticgen by @kevinschaper in https://github.com/linkml/linkml/pull/1445
• Some workflow steps/jobs cannot run in forks by @Silvanoc in https://github.com/linkml/linkml/pull/1450
• add enum support to gen-typescript, fix it in gen-pydantic by @glass-ships in https://github.com/linkml/linkml/pull/1455
• Improve handling of range unions in jsonschemagen by @pkalita-lbl in https://github.com/linkml/linkml/pull/1461
• pydanticgen any_of conflict with default range by @kevinschaper in https://github.com/linkml/linkml/pull/1460

New Contributors

• @jeff-cohere made their first contribution in https://github.com/linkml/linkml/pull/1418
• @nicholsn made their first contribution in https://github.com/linkml/linkml/pull/1425
• @rly made their first contribution in https://github.com/linkml/linkml/pull/1431
• @glass-ships made their first contribution in https://github.com/linkml/linkml/pull/1439
• @andrawaag made their first contribution in https://github.com/linkml/linkml/pull/1443

Full Changelog: https://github.com/linkml/linkml/compare/v1.5.2...v1.5.3

- Python
Published by kevinschaper about 3 years ago

linkml - v1.5.2

What's Changed

• Fix pydanticgen/pythongen to prevent code injection attacks by @ialarmedalien in https://github.com/linkml/linkml/pull/1402
• Configure useenumvalues to True on pydanticgen BaseModel by @kevinschaper in https://github.com/linkml/linkml/pull/1288
• Un-break the build (pydanticgen template fix) by @kevinschaper in https://github.com/linkml/linkml/pull/1414
• Ensure rules are translated at class level and optionally at top level by @pkalita-lbl in https://github.com/linkml/linkml/pull/1415
• Support has_member and all_members in JSON Schema generator by @pkalita-lbl in https://github.com/linkml/linkml/pull/1411
• Add schema validation to linkml-lint command by @pkalita-lbl in https://github.com/linkml/linkml/pull/1410
• pydanticgen: Include keys when checking for inlining by @cmungall in https://github.com/linkml/linkml/pull/1416
• jsonschemavalidator caching keyed on schema and entry point by @sujaypatil96 in https://github.com/linkml/linkml/pull/1420

Full Changelog: https://github.com/linkml/linkml/compare/v1.5.1...v1.5.2

- Python
Published by sujaypatil96 about 3 years ago

linkml - v1.5.1

What's Changed

• fix(docgen): emphasizing multiline descriptions by @Silvanoc in https://github.com/linkml/linkml/pull/1351
• jsonschemavalidator should cache previous results of jsonschema generation by @cmungall in https://github.com/linkml/linkml/pull/1363
• Fix issue #1365 by @kervel in https://github.com/linkml/linkml/pull/1366
• logging in Excel generator by @sujaypatil96 in https://github.com/linkml/linkml/pull/1344
• Show min, max and pattern on slot pages by @sujaypatil96 in https://github.com/linkml/linkml/pull/1374
• notebook for Type Designators by @cmungall in https://github.com/linkml/linkml/pull/1378
• Add documentation about slot cardinality syntax by @sujaypatil96 in https://github.com/linkml/linkml/pull/1388
• howto docs for NDArray by @cmungall in https://github.com/linkml/linkml/pull/1376
• Fix issue with class specific slots not showing up in slot table on class doc pages by @sujaypatil96 in https://github.com/linkml/linkml/pull/1398
• Table showing classes that modify a slot by @amc-corey-cox in https://github.com/linkml/linkml/pull/1211

New Contributors

• @Silvanoc made their first contribution in https://github.com/linkml/linkml/pull/1351

Full Changelog: https://github.com/linkml/linkml/compare/v1.5.0...v1.5.1

- Python
Published by sujaypatil96 about 3 years ago

linkml - v1.5.0

LinkML Model 1.5.x series

See https://github.com/linkml/linkml-model/releases/tag/v1.5.0 for a summary of metamodel changes

What's Changed

• Fixing table in howto docs by @cmungall in https://github.com/linkml/linkml/pull/1193
• Use package name ("linkml") to look up version by @dalito in https://github.com/linkml/linkml/pull/1196
• Tests for schemas that have slots with leading digits. closes #1181 by @cmungall in https://github.com/linkml/linkml/pull/1182
• Add --validate command to pythongen. This will attempt to compile generated code by @cmungall in https://github.com/linkml/linkml/pull/1192
• Updating documentation and removing linkml-ws references fixes #1129, fixes #1183 by @sierra-moxon in https://github.com/linkml/linkml/pull/1201
• Improve clean-up of sqlAlchemy pools/sessions by @dalito in https://github.com/linkml/linkml/pull/1206
• Add a mermaid ERDiagram generator. by @cmungall in https://github.com/linkml/linkml/pull/1204
• Fix non-stopping CI on windows by @dalito in https://github.com/linkml/linkml/pull/1202
• Test case for pydantic inlining by @cmungall in https://github.com/linkml/linkml/pull/1199
• Fixes inheritance of range from slot_usage in docgen #1208 by @cmungall in https://github.com/linkml/linkml/pull/1209
• ensure mergeimports is being considered in linkmlgen by @sujaypatil96 in https://github.com/linkml/linkml/pull/1226
• Extend example runner and integrate into docgen, issue 1218 by @cmungall in https://github.com/linkml/linkml/pull/1222
• ensure example_runner initializes PythonGenerator safely. Fixes #1219 by @cmungall in https://github.com/linkml/linkml/pull/1230
• Add required annotations to generate not-NULL columns by @jankatins in https://github.com/linkml/linkml/pull/1233
• schema builder documentation by @cmungall in https://github.com/linkml/linkml/pull/1225
• Fix stacktrace setting to be localized to CLI. #1227 by @cmungall in https://github.com/linkml/linkml/pull/1229
• #1236 RUN expansion and test with poetry by @turbomam in https://github.com/linkml/linkml/pull/1237
• Let both sides of a linking tables include pk ids by @jankatins in https://github.com/linkml/linkml/pull/1232
• issue #1245 by @kervel in https://github.com/linkml/linkml/pull/1246
• Pydanticgen: support polymorphism using type designators by @sierra-moxon in https://github.com/linkml/linkml/pull/1224
• Fix shaclgen by making mixins and classes without parents not closed by @vemonet in https://github.com/linkml/linkml/pull/1264
• Pydantic: stop generating Unions with only one member by @kervel in https://github.com/linkml/linkml/pull/1265
• fix edge case with clashing injected PK name in relmodel_transformer. 1255 by @cmungall in https://github.com/linkml/linkml/pull/1256
• Add option for using type designators for example runner by @cmungall in https://github.com/linkml/linkml/pull/1274
• Implicitly apply value constrains to all elements of multivalued slots in JSON Schema by @pkalita-lbl in https://github.com/linkml/linkml/pull/1276
• Adding element name normalization to schema-fixer. Adding --expand-dicts option to example runner by @cmungall in https://github.com/linkml/linkml/pull/1284
• Added Slack link by @nlharris in https://github.com/linkml/linkml/pull/1289
• added link to FAQ: contributing by @nlharris in https://github.com/linkml/linkml/pull/1290
• yumlgen: use POST and add ability to name output file by @jankatins in https://github.com/linkml/linkml/pull/1293
• Support ifabsent in pydanticgen by @kevinschaper in https://github.com/linkml/linkml/pull/1252
• Pydantic gen: switch to external uri/curie by default, still accept native uri/curie. by @kervel in https://github.com/linkml/linkml/pull/1275
• Adding type-designator docs (not linked yet) by @cmungall in https://github.com/linkml/linkml/pull/1291
• Pydantic any_of range support by @kevinschaper in https://github.com/linkml/linkml/pull/1273
• replace pkg_resources methods with importlib methods by @sujaypatil96 in https://github.com/linkml/linkml/pull/1308
• Remove camelcasing of class name for type designator values by @kevinschaper in https://github.com/linkml/linkml/pull/1310
• fix mergeimports issue in docgen by @sujaypatil96 in https://github.com/linkml/linkml/pull/1309
• Handle local prefixes special when merging linkml files by @jankatins in https://github.com/linkml/linkml/pull/1295
• Add favicon to docs by @dalito in https://github.com/linkml/linkml/pull/1312
• Adding FAQ docs by @cmungall in https://github.com/linkml/linkml/pull/1321
• fix mergeimports handling in gendoc by @sujaypatil96 in https://github.com/linkml/linkml/pull/1313
• add dependency relationship between classes linked by a slot by @sujaypatil96 in https://github.com/linkml/linkml/pull/1316
• update poetry.lock file by @sujaypatil96 in https://github.com/linkml/linkml/pull/1323
• Fix errors in Actions by @sujaypatil96 in https://github.com/linkml/linkml/pull/1329
• fix class slot dependency relationships in mermaid diagram by @sujaypatil96 in https://github.com/linkml/linkml/pull/1327
• test case for ensuring domain_of for slot does not have dups by @sujaypatil96 in https://github.com/linkml/linkml/pull/1319
• owlgen - use either owl or OwlProfile as subset name (sync with linkml 1.6) by @cmungall in https://github.com/linkml/linkml/pull/1338
• First pass excelgen.py refactor with SchemaView by @sujaypatil96 in https://github.com/linkml/linkml/pull/1320
• Fix incorrect ifabsent generation. by @cmungall in https://github.com/linkml/linkml/pull/1335
• Trigger on push to main in addition to PR by @dalito in https://github.com/linkml/linkml/pull/1330
• Reverting to previous ifabsent behavior for default_ns. by @cmungall in https://github.com/linkml/linkml/pull/1343
• Adding FAQ entry on name clashes on imports by @cmungall in https://github.com/linkml/linkml/pull/1332
• jsonschemagen: use anyOf rather than oneOf for range class descendants by @kervel in https://github.com/linkml/linkml/pull/1342
• Set Poetry version to 1.3.2 in all workflows by @pkalita-lbl in https://github.com/linkml/linkml/pull/1358
• add test to ensure datetime validation works, fixes #606 by @cmungall in https://github.com/linkml/linkml/pull/1364
• 1.5 prerelease, redux by @cmungall in https://github.com/linkml/linkml/pull/1353

New Contributors

• @jankatins made their first contribution in https://github.com/linkml/linkml/pull/1233

Full Changelog: https://github.com/linkml/linkml/compare/v1.4.0...v1.5.0

- Python
Published by cmungall about 3 years ago

linkml - v1.5.0rc2

For model changes, see: https://github.com/linkml/linkml-model/releases/tag/v1.5.0rc1

What's Changed

• Fixing table in howto docs by @cmungall in https://github.com/linkml/linkml/pull/1193
• Use package name ("linkml") to look up version by @dalito in https://github.com/linkml/linkml/pull/1196
• Tests for schemas that have slots with leading digits. closes #1181 by @cmungall in https://github.com/linkml/linkml/pull/1182
• Add --validate command to pythongen. This will attempt to compile generated code by @cmungall in https://github.com/linkml/linkml/pull/1192
• Updating documentation and removing linkml-ws references fixes #1129, fixes #1183 by @sierra-moxon in https://github.com/linkml/linkml/pull/1201
• Improve clean-up of sqlAlchemy pools/sessions by @dalito in https://github.com/linkml/linkml/pull/1206
• Add a mermaid ERDiagram generator. by @cmungall in https://github.com/linkml/linkml/pull/1204
• Fix non-stopping CI on windows by @dalito in https://github.com/linkml/linkml/pull/1202
• Test case for pydantic inlining by @cmungall in https://github.com/linkml/linkml/pull/1199
• Fixes inheritance of range from slot_usage in docgen #1208 by @cmungall in https://github.com/linkml/linkml/pull/1209
• ensure mergeimports is being considered in linkmlgen by @sujaypatil96 in https://github.com/linkml/linkml/pull/1226
• Extend example runner and integrate into docgen, issue 1218 by @cmungall in https://github.com/linkml/linkml/pull/1222
• ensure example_runner initializes PythonGenerator safely. Fixes #1219 by @cmungall in https://github.com/linkml/linkml/pull/1230
• Add required annotations to generate not-NULL columns by @jankatins in https://github.com/linkml/linkml/pull/1233
• schema builder documentation by @cmungall in https://github.com/linkml/linkml/pull/1225
• Fix stacktrace setting to be localized to CLI. #1227 by @cmungall in https://github.com/linkml/linkml/pull/1229
• #1236 RUN expansion and test with poetry by @turbomam in https://github.com/linkml/linkml/pull/1237
• Let both sides of a linking tables include pk ids by @jankatins in https://github.com/linkml/linkml/pull/1232
• issue #1245 by @kervel in https://github.com/linkml/linkml/pull/1246
• Pydanticgen: support polymorphism using type designators by @sierra-moxon in https://github.com/linkml/linkml/pull/1224
• Fix shaclgen by making mixins and classes without parents not closed by @vemonet in https://github.com/linkml/linkml/pull/1264
• Pydantic: stop generating Unions with only one member by @kervel in https://github.com/linkml/linkml/pull/1265
• fix edge case with clashing injected PK name in relmodel_transformer. 1255 by @cmungall in https://github.com/linkml/linkml/pull/1256
• Add option for using type designators for example runner by @cmungall in https://github.com/linkml/linkml/pull/1274
• Implicitly apply value constrains to all elements of multivalued slots in JSON Schema by @pkalita-lbl in https://github.com/linkml/linkml/pull/1276
• Adding element name normalization to schema-fixer. Adding --expand-dicts option to example runner by @cmungall in https://github.com/linkml/linkml/pull/1284
• Added Slack link by @nlharris in https://github.com/linkml/linkml/pull/1289
• added link to FAQ: contributing by @nlharris in https://github.com/linkml/linkml/pull/1290
• yumlgen: use POST and add ability to name output file by @jankatins in https://github.com/linkml/linkml/pull/1293
• Support ifabsent in pydanticgen by @kevinschaper in https://github.com/linkml/linkml/pull/1252
• Pydantic gen: switch to external uri/curie by default, still accept native uri/curie. by @kervel in https://github.com/linkml/linkml/pull/1275
• Adding type-designator docs (not linked yet) by @cmungall in https://github.com/linkml/linkml/pull/1291
• Pydantic any_of range support by @kevinschaper in https://github.com/linkml/linkml/pull/1273
• replace pkg_resources methods with importlib methods by @sujaypatil96 in https://github.com/linkml/linkml/pull/1308
• Remove camelcasing of class name for type designator values by @kevinschaper in https://github.com/linkml/linkml/pull/1310
• fix mergeimports issue in docgen by @sujaypatil96 in https://github.com/linkml/linkml/pull/1309
• Handle local prefixes special when merging linkml files by @jankatins in https://github.com/linkml/linkml/pull/1295
• Add favicon to docs by @dalito in https://github.com/linkml/linkml/pull/1312
• Adding FAQ docs by @cmungall in https://github.com/linkml/linkml/pull/1321
• fix mergeimports handling in gendoc by @sujaypatil96 in https://github.com/linkml/linkml/pull/1313
• add dependency relationship between classes linked by a slot by @sujaypatil96 in https://github.com/linkml/linkml/pull/1316
• update poetry.lock file by @sujaypatil96 in https://github.com/linkml/linkml/pull/1323
• Fix errors in Actions by @sujaypatil96 in https://github.com/linkml/linkml/pull/1329
• fix class slot dependency relationships in mermaid diagram by @sujaypatil96 in https://github.com/linkml/linkml/pull/1327
• test case for ensuring domain_of for slot does not have dups by @sujaypatil96 in https://github.com/linkml/linkml/pull/1319
• owlgen - use either owl or OwlProfile as subset name (sync with linkml 1.6) by @cmungall in https://github.com/linkml/linkml/pull/1338
• First pass excelgen.py refactor with SchemaView by @sujaypatil96 in https://github.com/linkml/linkml/pull/1320
• Fix incorrect ifabsent generation. by @cmungall in https://github.com/linkml/linkml/pull/1335
• Trigger on push to main in addition to PR by @dalito in https://github.com/linkml/linkml/pull/1330
• Reverting to previous ifabsent behavior for default_ns. by @cmungall in https://github.com/linkml/linkml/pull/1343
• Adding FAQ entry on name clashes on imports by @cmungall in https://github.com/linkml/linkml/pull/1332
• jsonschemagen: use anyOf rather than oneOf for range class descendants by @kervel in https://github.com/linkml/linkml/pull/1342

New Contributors

• @jankatins made their first contribution in https://github.com/linkml/linkml/pull/1233

Full Changelog: https://github.com/linkml/linkml/compare/v1.4.0...v1.5.0rc2

- Python
Published by cmungall about 3 years ago

linkml - v1.4.11

What's Changed

• jsonschemagen: use anyOf rather than oneOf for range class descendants by @kervel in https://github.com/linkml/linkml/pull/1342

Full Changelog: https://github.com/linkml/linkml/compare/v1.4.10...v1.4.11

- Python
Published by cmungall about 3 years ago

linkml - v1.5.0rc1

For model changes, see: https://github.com/linkml/linkml-model/releases/tag/v1.5.0rc1

What's Changed

• Fixing table in howto docs by @cmungall in https://github.com/linkml/linkml/pull/1193
• Use package name ("linkml") to look up version by @dalito in https://github.com/linkml/linkml/pull/1196
• Tests for schemas that have slots with leading digits. closes #1181 by @cmungall in https://github.com/linkml/linkml/pull/1182
• Add --validate command to pythongen. This will attempt to compile generated code by @cmungall in https://github.com/linkml/linkml/pull/1192
• Updating documentation and removing linkml-ws references fixes #1129, fixes #1183 by @sierra-moxon in https://github.com/linkml/linkml/pull/1201
• Improve clean-up of sqlAlchemy pools/sessions by @dalito in https://github.com/linkml/linkml/pull/1206
• Add a mermaid ERDiagram generator. by @cmungall in https://github.com/linkml/linkml/pull/1204
• Fix non-stopping CI on windows by @dalito in https://github.com/linkml/linkml/pull/1202
• Test case for pydantic inlining by @cmungall in https://github.com/linkml/linkml/pull/1199
• Fixes inheritance of range from slot_usage in docgen #1208 by @cmungall in https://github.com/linkml/linkml/pull/1209
• ensure mergeimports is being considered in linkmlgen by @sujaypatil96 in https://github.com/linkml/linkml/pull/1226
• Extend example runner and integrate into docgen, issue 1218 by @cmungall in https://github.com/linkml/linkml/pull/1222
• ensure example_runner initializes PythonGenerator safely. Fixes #1219 by @cmungall in https://github.com/linkml/linkml/pull/1230
• Add required annotations to generate not-NULL columns by @jankatins in https://github.com/linkml/linkml/pull/1233
• schema builder documentation by @cmungall in https://github.com/linkml/linkml/pull/1225
• Fix stacktrace setting to be localized to CLI. #1227 by @cmungall in https://github.com/linkml/linkml/pull/1229
• #1236 RUN expansion and test with poetry by @turbomam in https://github.com/linkml/linkml/pull/1237
• Let both sides of a linking tables include pk ids by @jankatins in https://github.com/linkml/linkml/pull/1232
• issue #1245 by @kervel in https://github.com/linkml/linkml/pull/1246
• Pydanticgen: support polymorphism using type designators by @sierra-moxon in https://github.com/linkml/linkml/pull/1224
• Fix shaclgen by making mixins and classes without parents not closed by @vemonet in https://github.com/linkml/linkml/pull/1264
• Pydantic: stop generating Unions with only one member by @kervel in https://github.com/linkml/linkml/pull/1265
• fix edge case with clashing injected PK name in relmodel_transformer. 1255 by @cmungall in https://github.com/linkml/linkml/pull/1256
• Add option for using type designators for example runner by @cmungall in https://github.com/linkml/linkml/pull/1274
• Implicitly apply value constrains to all elements of multivalued slots in JSON Schema by @pkalita-lbl in https://github.com/linkml/linkml/pull/1276
• Adding element name normalization to schema-fixer. Adding --expand-dicts option to example runner by @cmungall in https://github.com/linkml/linkml/pull/1284
• Added Slack link by @nlharris in https://github.com/linkml/linkml/pull/1289
• added link to FAQ: contributing by @nlharris in https://github.com/linkml/linkml/pull/1290
• yumlgen: use POST and add ability to name output file by @jankatins in https://github.com/linkml/linkml/pull/1293
• Support ifabsent in pydanticgen by @kevinschaper in https://github.com/linkml/linkml/pull/1252
• Pydantic gen: switch to external uri/curie by default, still accept native uri/curie. by @kervel in https://github.com/linkml/linkml/pull/1275
• Adding type-designator docs (not linked yet) by @cmungall in https://github.com/linkml/linkml/pull/1291
• Pydantic any_of range support by @kevinschaper in https://github.com/linkml/linkml/pull/1273
• replace pkg_resources methods with importlib methods by @sujaypatil96 in https://github.com/linkml/linkml/pull/1308
• Remove camelcasing of class name for type designator values by @kevinschaper in https://github.com/linkml/linkml/pull/1310
• fix mergeimports issue in docgen by @sujaypatil96 in https://github.com/linkml/linkml/pull/1309
• Handle local prefixes special when merging linkml files by @jankatins in https://github.com/linkml/linkml/pull/1295
• Add favicon to docs by @dalito in https://github.com/linkml/linkml/pull/1312
• Adding FAQ docs by @cmungall in https://github.com/linkml/linkml/pull/1321
• fix mergeimports handling in gendoc by @sujaypatil96 in https://github.com/linkml/linkml/pull/1313
• add dependency relationship between classes linked by a slot by @sujaypatil96 in https://github.com/linkml/linkml/pull/1316
• update poetry.lock file by @sujaypatil96 in https://github.com/linkml/linkml/pull/1323
• Fix errors in Actions by @sujaypatil96 in https://github.com/linkml/linkml/pull/1329
• fix class slot dependency relationships in mermaid diagram by @sujaypatil96 in https://github.com/linkml/linkml/pull/1327
• test case for ensuring domain_of for slot does not have dups by @sujaypatil96 in https://github.com/linkml/linkml/pull/1319
• owlgen - use either owl or OwlProfile as subset name (sync with linkml 1.6) by @cmungall in https://github.com/linkml/linkml/pull/1338
• First pass excelgen.py refactor with SchemaView by @sujaypatil96 in https://github.com/linkml/linkml/pull/1320
• Fix incorrect ifabsent generation. by @cmungall in https://github.com/linkml/linkml/pull/1335
• Trigger on push to main in addition to PR by @dalito in https://github.com/linkml/linkml/pull/1330
• Reverting to previous ifabsent behavior for default_ns. by @cmungall in https://github.com/linkml/linkml/pull/1343
• Adding FAQ entry on name clashes on imports by @cmungall in https://github.com/linkml/linkml/pull/1332
• jsonschemagen: use anyOf rather than oneOf for range class descendants by @kervel in https://github.com/linkml/linkml/pull/1342

New Contributors

• @jankatins made their first contribution in https://github.com/linkml/linkml/pull/1233

Full Changelog: https://github.com/linkml/linkml/compare/v1.4.0...v1.5.0rc1

- Python
Published by cmungall about 3 years ago

linkml - v1.4.10

What's Changed

• Reverting to previous ifabsent behavior for default_ns. by @cmungall in https://github.com/linkml/linkml/pull/1343
• Adding FAQ entry on name clashes on imports by @cmungall and @noelmcloughlin in https://github.com/linkml/linkml/pull/1332

Full Changelog: https://github.com/linkml/linkml/compare/v1.4.9...v1.4.10

- Python
Published by cmungall over 3 years ago

linkml - v1.4.9

What's Changed

• Fix incorrect ifabsent generation. by @cmungall in https://github.com/linkml/linkml/pull/1335
• Trigger on push to main in addition to PR by @dalito in https://github.com/linkml/linkml/pull/1330

Full Changelog: https://github.com/linkml/linkml/compare/v1.4.8...v1.4.9

- Python
Published by cmungall over 3 years ago

linkml - v1.4.8

What's Changed

• Fix errors in Actions by @sujaypatil96 in https://github.com/linkml/linkml/pull/1329
• fix class slot dependency relationships in mermaid diagram by @sujaypatil96 in https://github.com/linkml/linkml/pull/1327
• test case for ensuring domain_of for slot does not have dups by @sujaypatil96 in https://github.com/linkml/linkml/pull/1319
• owlgen - use either owl or OwlProfile as subset name (sync with linkml 1.6) by @cmungall in https://github.com/linkml/linkml/pull/1338
• First pass excelgen.py refactor with SchemaView by @sujaypatil96 in https://github.com/linkml/linkml/pull/1320

Full Changelog: https://github.com/linkml/linkml/compare/v1.4.7...v1.4.8

- Python
Published by sujaypatil96 over 3 years ago

linkml - v1.4.7

What's Changed

• Add favicon to docs by @dalito in https://github.com/linkml/linkml/pull/1312
• Adding FAQ docs by @cmungall in https://github.com/linkml/linkml/pull/1321
• fix mergeimports handling in gendoc by @sujaypatil96 in https://github.com/linkml/linkml/pull/1313
• add dependency relationship between classes linked by a slot by @sujaypatil96 in https://github.com/linkml/linkml/pull/1316
• update poetry.lock file by @sujaypatil96 in https://github.com/linkml/linkml/pull/1323

Full Changelog: https://github.com/linkml/linkml/compare/v1.4.6...v1.4.7

- Python
Published by sujaypatil96 over 3 years ago

linkml - v1.4.6

What's Changed

• Adding type-designator docs (not linked yet) by @cmungall in https://github.com/linkml/linkml/pull/1291
• Pydantic any_of range support by @kevinschaper in https://github.com/linkml/linkml/pull/1273
• replace pkg_resources methods with importlib methods by @sujaypatil96 in https://github.com/linkml/linkml/pull/1308
• Remove camelcasing of class name for type designator values by @kevinschaper in https://github.com/linkml/linkml/pull/1310
• fix mergeimports issue in docgen by @sujaypatil96 in https://github.com/linkml/linkml/pull/1309
• Handle local prefixes special when merging linkml files by @jankatins in https://github.com/linkml/linkml/pull/1295

Full Changelog: https://github.com/linkml/linkml/compare/v1.4.5...v1.4.6

- Python
Published by cmungall over 3 years ago

linkml - v1.4.5

What's Changed

• Adding element name normalization to schema-fixer. Adding --expand-dicts option to example runner by @cmungall in https://github.com/linkml/linkml/pull/1284
• Added Slack link by @nlharris in https://github.com/linkml/linkml/pull/1289
• added link to FAQ: contributing by @nlharris in https://github.com/linkml/linkml/pull/1290
• yumlgen: use POST and add ability to name output file by @jankatins in https://github.com/linkml/linkml/pull/1293
• Support ifabsent in pydanticgen by @kevinschaper in https://github.com/linkml/linkml/pull/1252
• Pydantic gen: switch to external uri/curie by default, still accept native uri/curie. by @kervel in https://github.com/linkml/linkml/pull/1275

Full Changelog: https://github.com/linkml/linkml/compare/v1.4.4...v1.4.5

- Python
Published by cmungall over 3 years ago

linkml - v1.4.4

What's Changed

• Add option for using type designators for example runner by @cmungall in https://github.com/linkml/linkml/pull/1274
• Implicitly apply value constrains to all elements of multivalued slots in JSON Schema by @pkalita-lbl in https://github.com/linkml/linkml/pull/1276

Full Changelog: https://github.com/linkml/linkml/compare/v1.4.3...v1.4.4

- Python
Published by cmungall over 3 years ago

linkml - v1.4.3

What's Changed

• #1236 RUN expansion and test with poetry by @turbomam in https://github.com/linkml/linkml/pull/1237
• Let both sides of a linking tables include pk ids by @jankatins in https://github.com/linkml/linkml/pull/1232
• issue #1245 by @kervel in https://github.com/linkml/linkml/pull/1246
• Pydanticgen: support polymorphism using type designators by @sierra-moxon in https://github.com/linkml/linkml/pull/1224
• Fix shaclgen by making mixins and classes without parents not closed by @vemonet in https://github.com/linkml/linkml/pull/1264
• Pydantic: stop generating Unions with only one member by @kervel in https://github.com/linkml/linkml/pull/1265
• fix edge case with clashing injected PK name in relmodel_transformer. 1255 by @cmungall in https://github.com/linkml/linkml/pull/1256

Full Changelog: https://github.com/linkml/linkml/compare/v1.4.2...v1.4.3

- Python
Published by cmungall over 3 years ago

linkml - v1.4.2

What's Changed

• Fix non-stopping CI on windows by @dalito in https://github.com/linkml/linkml/pull/1202
• Test case for pydantic inlining by @cmungall in https://github.com/linkml/linkml/pull/1199
• Fixes inheritance of range from slot_usage in docgen #1208 by @cmungall in https://github.com/linkml/linkml/pull/1209
• ensure mergeimports is being considered in linkmlgen by @sujaypatil96 in https://github.com/linkml/linkml/pull/1226
• Extend example runner and integrate into docgen, issue 1218 by @cmungall in https://github.com/linkml/linkml/pull/1222
• ensure example_runner initializes PythonGenerator safely. Fixes #1219 by @cmungall in https://github.com/linkml/linkml/pull/1230
• Add required annotations to generate not-NULL columns by @jankatins in https://github.com/linkml/linkml/pull/1233
• schema builder documentation by @cmungall in https://github.com/linkml/linkml/pull/1225
• Fix stacktrace setting to be localized to CLI. #1227 by @cmungall in https://github.com/linkml/linkml/pull/1229

New Contributors

• @jankatins made their first contribution in https://github.com/linkml/linkml/pull/1233

Full Changelog: https://github.com/linkml/linkml/compare/v1.4.1...v1.4.2

- Python
Published by cmungall over 3 years ago

linkml - v1.4.1

Highlights

ER Diagrams (experimental)

You can now generate ER diagrams for a whole schema, or individual classes.

Example source:

```mermaid erDiagram Recipe { string label string description } Step {

} FoodItem { string id string label } Action { string id string label } Ingredient { string quantity } RecipeCategory { string id string label }

Recipe ||--}o RecipeCategory : "category" Recipe ||--}o Ingredient : "ingredients" Recipe ||--}o Step : "steps" Step ||--|o Action : "action" Step ||--}o FoodItem : "inputs" Step ||--}o FoodItem : "outputs" Ingredient ||--|o FoodItem : "food_item"

```

this will make an image:

Note for this to work with mkdocs, you need to make sure you are using the latest mermaid.js; add this to your mkdocs.yaml:

yaml plugins: - search - mermaid2: version: 9.3.0

What's Changed

• Fixing table in howto docs by @cmungall in https://github.com/linkml/linkml/pull/1193
• Use package name ("linkml") to look up version by @dalito in https://github.com/linkml/linkml/pull/1196
• Tests for schemas that have slots with leading digits. closes #1181 by @cmungall in https://github.com/linkml/linkml/pull/1182
• Add --validate command to pythongen. This will attempt to compile generated code by @cmungall in https://github.com/linkml/linkml/pull/1192
• Updating documentation and removing linkml-ws references fixes #1129, fixes #1183 by @sierra-moxon in https://github.com/linkml/linkml/pull/1201
• Improve clean-up of sqlAlchemy pools/sessions by @dalito in https://github.com/linkml/linkml/pull/1206
• Add a mermaid ERDiagram generator. by @cmungall in https://github.com/linkml/linkml/pull/1204

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.17...v1.4.1

- Python
Published by cmungall over 3 years ago

linkml - v1.4.0

1.4.0 release series

This release is to synchronize with the 1.4.0 runtime release

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.0...v1.4.0

- Python
Published by cmungall over 3 years ago

linkml - v1.3.17

What's Changed

• Inline dicts in pydanticgen by @kevinschaper in https://github.com/linkml/linkml/pull/1095
• Linkml runtime - allow to update to minor revision in downstream projects by @sierra-moxon in https://github.com/linkml/linkml/pull/1185
• Add indent option to gen-json-schema CLI by @pkalita-lbl in https://github.com/linkml/linkml/pull/1176
• New script: linkml-run-examples. See #501 by @cmungall in https://github.com/linkml/linkml/pull/1184
• Issue 675 by @hsolbrig in https://github.com/linkml/linkml/pull/1171

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.16...v1.3.17

- Python
Published by cmungall over 3 years ago

linkml - v1.3.16

What's Changed

• slots table breaking in few schemas by @sujaypatil96 in https://github.com/linkml/linkml/pull/1152
• Pass schemaview object to dumper while converting to JSONLD by @hrshdhgd in https://github.com/linkml/linkml/pull/1153
• Add support for multivalued slot constraints in JSON Schema generator by @pkalita-lbl in https://github.com/linkml/linkml/pull/1113

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.15...v1.3.16

- Python
Published by turbomam over 3 years ago

linkml - v1.3.15

What's Changed

• Fixes jinja template spacing for generating abstract java classes by @kevinschaper in https://github.com/linkml/linkml/pull/1118
• Add workflow for Docker build and publish by @pkalita-lbl in https://github.com/linkml/linkml/pull/1120
• improve contribution guidelines for writing unit tests by @sujaypatil96 in https://github.com/linkml/linkml/pull/1121
• Use cjmungall as Docker Hub username for publish by @pkalita-lbl in https://github.com/linkml/linkml/pull/1128
• Fix JSON Schema generation for boolean operations on value constraints by @pkalita-lbl in https://github.com/linkml/linkml/pull/1130
• Update to remove workflow warnings by @RichardBruskiewich in https://github.com/linkml/linkml/pull/1133
• Remove extra poetry install by @hrshdhgd in https://github.com/linkml/linkml/pull/1145
• @actions/core to 1.10.0 by @RichardBruskiewich in https://github.com/linkml/linkml/pull/1132

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.14...v1.3.15

- Python
Published by sierra-moxon over 3 years ago

linkml - v1.3.14

What's Changed

• Typescript template tweaks by @kevinschaper in https://github.com/linkml/linkml/pull/1093
• suggestion to include error message, if any, in bug report by @nlharris in https://github.com/linkml/linkml/pull/1106
• Add slots section to enum Jinja template and link to slots by @amc-corey-cox in https://github.com/linkml/linkml/pull/1092
• Rules support in JSON Schema generator by @pkalita-lbl in https://github.com/linkml/linkml/pull/1100
• Add stacktrace option w/ default no trace. by @hsolbrig in https://github.com/linkml/linkml/pull/1110
• Fixed: Could not determine join condition between parent/child tables in sqla (#1104) by @turbomam in https://github.com/linkml/linkml/pull/1105
• pattern property being set on structured_pattern expansion by @sujaypatil96 in https://github.com/linkml/linkml/pull/1115

New Contributors

• @amc-corey-cox made their first contribution in https://github.com/linkml/linkml/pull/1092

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.13...v1.3.14

- Python
Published by sujaypatil96 over 3 years ago

linkml - v1.3.13

What's Changed

• formatting fixes to docgen templates by @sujaypatil96 in https://github.com/linkml/linkml/pull/1096

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.12...v1.3.13

- Python
Published by sujaypatil96 over 3 years ago

linkml - v1.3.12

What's Changed

• docgen method to get class from which slot was inherited by @sujaypatil96 in https://github.com/linkml/linkml/pull/1049
• fixing typo in CHILD_OF mapping fixes #843 by @sierra-moxon in https://github.com/linkml/linkml/pull/1082
• Fix pypi publish pipeline, Follow-up to #1053 by @hrshdhgd in https://github.com/linkml/linkml/pull/1083
• move Aliases section into common metadata by @sujaypatil96 in https://github.com/linkml/linkml/pull/1084
• Docs workflow fix by @hrshdhgd in https://github.com/linkml/linkml/pull/1087
• Add See Also block to docgen templates by @sujaypatil96 in https://github.com/linkml/linkml/pull/1085
• mixin usage block on class and slot pages by @sujaypatil96 in https://github.com/linkml/linkml/pull/1086
• Refactor jsonschema generator to use schemaview by @pkalita-lbl in https://github.com/linkml/linkml/pull/1054

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.11...v1.3.12

- Python
Published by sujaypatil96 over 3 years ago

linkml - v1.3.12rc2

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.12rc1...v1.3.12rc2

- Python
Published by hrshdhgd over 3 years ago

linkml - v1.3.12rc1

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.11...v1.3.12rc1

- Python
Published by hrshdhgd over 3 years ago

linkml - v1.3.11

What's Changed

• fix the furo installation in docs workflow by @hrshdhgd in https://github.com/linkml/linkml/pull/1028
• Add dynamic versioning and --version command line option by @dalito in https://github.com/linkml/linkml/pull/1048
• Update oocodegen.map_type to use optional slot.required by @julesjacobsen in https://github.com/linkml/linkml/pull/1024
• Update pypi-publish.yaml for poetry-dynamic-versioning by @dalito in https://github.com/linkml/linkml/pull/1053
• Add -V / --version option to all remaining cmd scripts by @dalito in https://github.com/linkml/linkml/pull/1052

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.10...v1.3.11

- Python
Published by cmungall over 3 years ago

linkml - v1.3.10

What's Changed

• Moved furo under extras. by @hrshdhgd in https://github.com/linkml/linkml/pull/1027

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.9...v1.3.10

- Python
Published by hrshdhgd over 3 years ago

linkml - v1.3.9

What's Changed

• Switch to furo theme. by @cmungall in https://github.com/linkml/linkml/pull/1015
• Adding test for #349 by @cmungall in https://github.com/linkml/linkml/pull/1014
• Remove sphinxrtdtheme from extensions in docs config by @pkalita-lbl in https://github.com/linkml/linkml/pull/1020
• Fixing aliasing of rdf type. by @cmungall in https://github.com/linkml/linkml/pull/1022 fixes #1019

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.8...v1.3.9

- Python
Published by cmungall over 3 years ago

linkml - v1.3.8

What's Changed

• Distinguish between warnings and errors in linter exit code by @pkalita-lbl in https://github.com/linkml/linkml/pull/995
• Add verbose flag to linter CLI by @pkalita-lbl in https://github.com/linkml/linkml/pull/992
• support pydantic in SQLstore by @cmungall in https://github.com/linkml/linkml/pull/1001
• show label name in inheritance tree when use_slot_uris=True by @sujaypatil96 in https://github.com/linkml/linkml/pull/1010

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.7...v1.3.8

- Python
Published by sujaypatil96 over 3 years ago

linkml - v1.3.7

What's Changed

• docgen: fix inheritance column, add applicable classes [high priority fix] by @sujaypatil96 in https://github.com/linkml/linkml/pull/997

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.6...v1.3.7

- Python
Published by sujaypatil96 over 3 years ago

linkml - v1.3.6

What's Changed

• fix(datautils): support yml extension by @noelmcloughlin in https://github.com/linkml/linkml/pull/982
• Repair links in generator README table; clean up by @caufieldjh in https://github.com/linkml/linkml/pull/986
• Fix javagen to restore missing class vars by @ialarmedalien in https://github.com/linkml/linkml/pull/987
• Make element references in linter messages more consistent by @pkalita-lbl in https://github.com/linkml/linkml/pull/994
• unify template changes from MIxS and NMDC by @sujaypatil96 in https://github.com/linkml/linkml/pull/990
• regenerate PersonSchema artifacts by @sujaypatil96 in https://github.com/linkml/linkml/pull/996

New Contributors

• @caufieldjh made their first contribution in https://github.com/linkml/linkml/pull/986

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.5...v1.3.6

- Python
Published by sujaypatil96 over 3 years ago

linkml - v1.3.5

What's Changed

• Add documentation page for schema linter by @pkalita-lbl in https://github.com/linkml/linkml/pull/972
• Fixed gen-pydantic CLI bug. Fixes #976 by @cmungall in https://github.com/linkml/linkml/pull/977
• Use Python 3.8 compatible cache function by @pkalita-lbl in https://github.com/linkml/linkml/pull/980

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.4...v1.3.5

- Python
Published by cmungall over 3 years ago

linkml - v1.3.4

What's Changed

• Initialise config_file in linter cli by @ialarmedalien in https://github.com/linkml/linkml/pull/950
• Schema fixer de-redundancy: added test and large test schema by @turbomam in https://github.com/linkml/linkml/pull/955
• Adding more documentation by @cmungall in https://github.com/linkml/linkml/pull/956
• modify class jinja template for middle layer elements by @sujaypatil96 in https://github.com/linkml/linkml/pull/957
• hyperlinking of mixin elements in docgen inheritance tree by @sujaypatil96 in https://github.com/linkml/linkml/pull/958
• Removed unecesssary commas by @hrshdhgd in https://github.com/linkml/linkml/pull/960
• own and inherited attributes display functionality in docgen by @sujaypatil96 in https://github.com/linkml/linkml/pull/888
• Pin jinja2 to 3.x series by @cmungall in https://github.com/linkml/linkml/pull/967
• Add recommended linter rule set by @pkalita-lbl in https://github.com/linkml/linkml/pull/970

New Contributors

• @ialarmedalien made their first contribution in https://github.com/linkml/linkml/pull/950

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.3...v1.3.4

- Python
Published by cmungall over 3 years ago

linkml - v1.3.3

This release adds the linkml linter

To run:

linkml-lint --help

What's Changed

• Adding documentation on missing value inference by @cmungall in https://github.com/linkml/linkml/pull/904
• Linting using black and isort by @hrshdhgd in https://github.com/linkml/linkml/pull/902
• Adding how-to guide for modeling measurements/quantities by @cmungall in https://github.com/linkml/linkml/pull/914
• Adding support for enums in docgen. by @cmungall in https://github.com/linkml/linkml/pull/910
• Add linkml-lint command by @pkalita-lbl in https://github.com/linkml/linkml/pull/912
• WIP: refactoring generators to use dataclasses. Part 1 of #923 by @cmungall in https://github.com/linkml/linkml/pull/924
• remove unused dependency by @sierra-moxon in https://github.com/linkml/linkml/pull/929
• Adding option to materialize patterns from structured patterns by @cmungall in https://github.com/linkml/linkml/pull/935
• replaced by linkml-datalog by @cmungall in https://github.com/linkml/linkml/pull/937
• Ensure generators use local versioned copy of metamodel. by @cmungall in https://github.com/linkml/linkml/pull/940
• inheritance_tree() support for slot descendants by @sujaypatil96 in https://github.com/linkml/linkml/pull/942
• Add canonical_prefixes linter rule by @pkalita-lbl in https://github.com/linkml/linkml/pull/944
• show slot documentation pages with more detail by @sujaypatil96 in https://github.com/linkml/linkml/pull/949
• Fix 404 to the csvs.md page by @joshmoore in https://github.com/linkml/linkml/pull/946

New Contributors

• @joshmoore made their first contribution in https://github.com/linkml/linkml/pull/946

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.2...v1.3.3

- Python
Published by cmungall almost 4 years ago

linkml - v1.3.2

What's Changed

• Add note on how to clean up after running tests by @dalito in https://github.com/linkml/linkml/pull/879
• improved documentation by @cmungall in https://github.com/linkml/linkml/pull/881

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.1...v1.3.2

- Python
Published by sujaypatil96 almost 4 years ago

linkml - v1.3.1

What's Changed

• Update TYPEMAP in javagen.py to use xsd mappings by @julesjacobsen in https://github.com/linkml/linkml/pull/873
• Moving specification by @cmungall in https://github.com/linkml/linkml/pull/874
• Documentation updates by @cmungall in https://github.com/linkml/linkml/pull/876
• Adding sort-by option, allowing for sorting by rank by @cmungall in https://github.com/linkml/linkml/pull/877
• Dockerizing. See https://github.com/linkml/schema-automator/issues/76 by @cmungall in https://github.com/linkml/linkml/pull/857

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.0...v1.3.1

- Python
Published by cmungall almost 4 years ago

linkml - v1.3.0

The 1.3.0 release of the LinkML model includes

Support for Units

Main PR: https://github.com/linkml/linkml-model/pull/108

Dynamic Enums

Main PR: https://github.com/linkml/linkml-model/pull/106

Structured patterns

Main PR: https://github.com/linkml/linkml-model/pull/79

Full Changelog: https://github.com/linkml/linkml/compare/v1.2.2...v1.3.0

- Python
Published by cmungall almost 4 years ago

linkml - v1.3.0rc7

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.0rc5...v1.3.0rc7

- Python
Published by cmungall almost 4 years ago

linkml - v1.3.0rc5

Full Changelog: https://github.com/linkml/linkml/compare/v1.3.0rc3...v1.3.0rc5

- Python
Published by cmungall almost 4 years ago

linkml - v1.3.0rc3

preparing 1.3 release

- Python
Published by cmungall almost 4 years ago

linkml - v1.2.17

What's Changed

• Extend Pydantic from BaseModel by @kevinschaper in https://github.com/linkml/linkml/pull/838
• Adding SchemaFixer, this is a general purpose utility for enhancing schemas. Includes: by @cmungall in https://github.com/linkml/linkml/pull/854
• Bumping runtime version. Addresses #502 by @cmungall in https://github.com/linkml/linkml/pull/858
• Allow passing of csv-field-size-limit by @cmungall in https://github.com/linkml/linkml/pull/859

Full Changelog: https://github.com/linkml/linkml/compare/v1.2.15...v1.2.17

- Python
Published by cmungall almost 4 years ago

linkml - v1.2.16

What's Changed

• Extend Pydantic from BaseModel by @kevinschaper in https://github.com/linkml/linkml/pull/838
• Adding SchemaFixer, this is a general purpose utility for enhancing schemas. Includes: by @cmungall in https://github.com/linkml/linkml/pull/854
• Bumping runtime version. Addresses #502 by @cmungall in https://github.com/linkml/linkml/pull/858
• Allow passing of csv-field-size-limit by @cmungall in https://github.com/linkml/linkml/pull/859

Full Changelog: https://github.com/linkml/linkml/compare/v1.2.15...v1.2.16

- Python
Published by sierra-moxon almost 4 years ago

linkml - v1.2.15

What's Changed

• display classes in their hierarchical order from the schema by @sujaypatil96 in https://github.com/linkml/linkml/pull/842
• alphabetical ordering of classes in class_hierarchy_as_tuples() by @sujaypatil96 in https://github.com/linkml/linkml/pull/847
• Test latex template by @cmungall in https://github.com/linkml/linkml/pull/848
• Add capability for gen-doc to generate subset markdown by @sujaypatil96 in https://github.com/linkml/linkml/pull/849

Full Changelog: https://github.com/linkml/linkml/compare/v1.2.14...v1.2.15

- Python
Published by sujaypatil96 almost 4 years ago

linkml - v1.2.14

What's Changed

• Typo in docstring by @hrshdhgd in https://github.com/linkml/linkml/pull/821
• hyphen not underscore for unambiguous root cannot be inferred error msg by @turbomam in https://github.com/linkml/linkml/pull/823
• add utils method that materializes slot patterns based on structured patterns by @sujaypatil96 in https://github.com/linkml/linkml/pull/688
• Fix for enums stored in SqlAlchemy. Fixes #814 by @cmungall in https://github.com/linkml/linkml/pull/828
• remove generate_patterns() implementation from linkml core by @sujaypatil96 in https://github.com/linkml/linkml/pull/830
• Test for linkml:Any. Fixes #296 by @cmungall in https://github.com/linkml/linkml/pull/831
• codecov support for linkml by @sujaypatil96 in https://github.com/linkml/linkml/pull/832
• Adding a dialect option to gendocs and customizing mermaid output by @cmungall in https://github.com/linkml/linkml/pull/836

Full Changelog: https://github.com/linkml/linkml/compare/v1.2.13...v1.2.14

- Python
Published by cmungall about 4 years ago

linkml - v1.2.13

What's Changed

• Test for enums within list inlined objects, bump runtime version #817 by @cmungall in https://github.com/linkml/linkml/pull/818

Full Changelog: https://github.com/linkml/linkml/compare/v1.2.12...v1.2.13

- Python
Published by cmungall about 4 years ago