What's Changed

• refactor: move converter from utils by @Silvanoc in #2716
• Rustgen: ability to generate rust packages with ergonomic python bindings by @kervel in #2916
• Feature: Extend YARRRML generator with CSV/TSV source support by @lapkinvladimir in #2937
• fix compile errors in rust crate generated from tfliss toy schema by @kervel in #2930
• rustgen: minor cleanups by @kervel in #2919
• docs: Add how-to guide for implementing skip logic by @cmungall in #2918
• Enhance OWL enum/permissible value handling and add comprehensive test coverage by @cmungall in #2950

Full Changelog: v1.9.5-rc1...v1.9.5-rc2

What's Changed

• permissible values: more compliance tests, fixing owlgen to properly encode all PVs by @cmungall in #2869
• Convert test_cli to pytest by @vladistan in #2855
• Bump actions/download-artifact from 4.3.0 to 5.0.0 by @dependabot[bot] in #2885
• Bump codecov/codecov-action from 5.4.3 to 5.5.0 by @dependabot[bot] in #2887
• Use full versions specs for all github actions by @vladistan in #2890
• Fix GraphQL generated scalars by @Silvanoc in #2707
• chore: add test dependencies to developer setup by @Silvanoc in #2906
• Pydantic fixes by @vladistan in #2829
• Report inconsistencies and fixed issues related to inlining in loader by @Silvanoc in #2819
• Rust generator for LinkML by @kervel in #2889
• fix: Handle special characters in slot names by @emmanuel-ferdman in #2908
• Feature: JSON-LD framing support by @lapkinvladimir in #2912
• fix(rdfgen): binary-safe output with -o by @lapkinvladimir in #2894
• 2776 Pandera support for inlined slots by @tfliss in #2803
• Add preserve_names option to documentation and JSON Schema generators by @saibalmars in #2881
• Respect include_null option for multivalued slots by @hugh-emerson in #2878
• Mask keywords by @EOltmanns in #2862
• Make optional lists empty instead of none (closes #2876) by @EOltmanns in #2877
• Remove erroneous @click.option definition (closes #2871) by @EOltmanns in #2872
• Bump pypa/gh-action-pypi-publish from 1.12.4 to 1.13.0 by @dependabot[bot] in #2922
• Bump docker/login-action from 3.5.0 to 3.6.0 by @dependabot[bot] in #2925
• Bump codecov/codecov-action from 5.4.3 to 5.5.1 by @dependabot[bot] in #2924
• Bump actions/setup-python from 5.6.0 to 6.0.0 by @dependabot[bot] in #2923
• OnePerClass linter rules for identifier and key attributes by @ialarmedalien in #2921
• Feature: YARRRML generator with CLI by @lapkinvladimir in #2934
• Update link to "intro to LinkML" slides by @nlharris in #2932
• Feature: JSON-LD framing with embedded context by @lapkinvladimir in #2931
• Addressing issues with the index CLI by @VictoriaSavage1NNL in #2904
• don't run the slow tests in the non-slow tests by @sneakers-the-rat in #2941
• Correct misconception about use of @type in JSON-LD @context by @Silvanoc in #2900

New Contributors

• @emmanuel-ferdman made their first contribution in #2908
• @lapkinvladimir made their first contribution in #2912
• @saibalmars made their first contribution in #2881
• @hugh-emerson made their first contribution in #2878
• @VictoriaSavage1NNL made their first contribution in #2904

Full Changelog: v1.9.4...v1.9.5-rc1

What's Changed

• update linkml-runtime dependency by @sierra-moxon in #2870

Full Changelog: v1.9.4-rc1...v1.9.4-rc2

What's Changed

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

New Contributors

• @EOltmanns made their first contribution in #2865

Full Changelog: v1.9.3...v1.9.4-rc1

What's Changed

• Allow excluding abstract classes from ERD Diagram by @vladistan in #2840
• Sort output of ErdDiagram for repeatable output by @vladistan in #2846
• exclude entities from standard naming linter rule by @turbomam in #2793
• migrate to uv by @iQuxLE in #2779
• Update person schema by @vladistan in #2848
• Bump actions/checkout to v5 in github workflows (closes #2864) by @EOltmanns in #2865
• Update contributing.md by @cmungall in #2859
• Enabling some disabled schemaloader tests for improved test coverage by @ialarmedalien in #2834
• refactor: move cli utils by @Silvanoc in #2715
• Add tests to ensure that class_uri becomes exactMatch in JSON-LD and RDF by @Silvanoc in #2692
• update linkml-runtime dependency by @sierra-moxon in #2870

New Contributors

• @EOltmanns made their first contribution in #2865

Full Changelog: v1.9.3...v1.9.4

What's Changed

• update to linkml-runtime 1.9.4 by @sierra-moxon in #2839
• Fix doc generation to add PURL URIs for enums by @dalito in #2711

Full Changelog: v1.9.3-rc2...v1.9.3-rc3

What's Changed

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

New Contributors

• @kimrutherford made their first contribution in #2784

Full Changelog: v1.9.2...v1.9.3

What's Changed

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

New Contributors

• @kimrutherford made their first contribution in #2784

Full Changelog: v1.9.3-rc1...v1.9.3-rc2

What's Changed

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

Full Changelog: v1.9.2...v1.9.3-rc1

What's Changed

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

New Contributors

• @clevinson made their first contribution in #2629
• @VictoriaSavageNNL made their first contribution in #2612
• @dependabot made their first contribution in #2657
• @iQuxLE made their first contribution in #2618

Full Changelog: v1.9.1...v1.9.2-rc1