v11.14.0

What's Changed

• Update makefile to use pytest so test_nmdc_schema_validation_plugin is used by @samobermiller in #2709
• Add storage_units annotations for 7 slots reviewed in PR #2653 by @turbomam in #2689
• Fix bug where link checker GHA workflow failed to install Python dependencies by @eecavanna in #2708
• Update submission status enum to reflect applied functionality by @samobermiller in #2720
• 2710 add slot to biosample to track metadata origin by @aclum in #2711
• Start improving slots that had units excuses by @turbomam in #2690
• Remove note on biosample definitions in core.yaml by @aclum in #2722
• Clean up commented status values in StatusEnum by @aclum in #2721
• Add LinkML metamodel validation to build process by @turbomam in #2727
• Update to latest linkml 1.9.6 and linkml-runtime 1.9.5 by @turbomam in #2732
• Add LinkML linting for source schema modules by @turbomam in #2734
• Modeling updates to ecosystem_path_id by @aclum in #2723
• Add editor and office temporary files to .gitignore by @turbomam in #2741
• Quote ecosystem_path_id example value as string by @turbomam in #2746
• Add check-dependencies to make test target by @turbomam in #2743
• 2747 gh actions cleanup by @turbomam in #2748
• GitHub Actions cleanup and documentation workflow optimization by @turbomam in #2752
• Add test to prevent new units_alignment_excuse annotations by @turbomam in #2753
• Test docs generation with test_slot_delete_me by @turbomam in #2755
• Remove test_slot_delete_me (docs test complete) by @turbomam in #2756
• Separate deptry from make test, break out CI steps by @turbomam in #2757
• Remove gen-linkml-schema-files target (redundant with linting) by @turbomam in #2759
• 2716 remove cli aliases for scripts not in package by @turbomam in #2763
• Fix ncbi_nmdc_exact_term_matching.py: replace OmicsProcessing with DataGeneration by @turbomam in #2765
• Fix ncbi_nmdc_exact_term_matching.py: replace OmicsProcessing with DataGeneration by @turbomam in #2767
• Update urllib3 to 2.6.0 (security fix) by @turbomam in #2770

Full Changelog: v11.13.0...v11.14.0

v11.14.0-rc.1

What's Changed

• Update makefile to use pytest so test_nmdc_schema_validation_plugin is used by @samobermiller in #2709
• Add storage_units annotations for 7 slots reviewed in PR #2653 by @turbomam in #2689
• Fix bug where link checker GHA workflow failed to install Python dependencies by @eecavanna in #2708
• Update submission status enum to reflect applied functionality by @samobermiller in #2720

Full Changelog: v11.13.0...v11.14.0-rc.1

v11.13.0

What's Changed

• Deprecate class ChemicalEntity by @aclum in #2667
• Update title description by @aclum in #2672
• Change casing of GOLD structured alias for Illumina MiSeq by @aclum in #2670
• Update amplicon example valid data by @aclum in #2668
• Raise minimum Python version to 3.10 by @pkalita-lbl in #2675
• Fix order of poetry installation; use pipx for install by @pkalita-lbl in #2676
• Use run instead of use in GHA workflows to install pipx by @pkalita-lbl in #2677
• Add workflow_dispatch trigger to deploy-docs.yaml by @turbomam in #2680
• Change deployment command to use mkdocs with --force by @turbomam in #2683
• Add slot to capture long read sequencing DNA extraction method by @mslarae13 in #2662
• Add troubleshooting section for documentation deployment by @turbomam in #2685
• Add pattern constraint to igsn_biosample_identifiers by @aclum in #2669
• Add SingleM FileTypeEnum permissible values and example data by @aclum in #2694
• Enforce ExternalIdentifier range for external identifier mixins by @aclum in #2671
• Add orbitrap_exploris_120 as permissible value to InstrumentModelEnum by @kheal in #2700
• Dematerialize mixs.yaml generation: remove verbosity from induced schema by @turbomam in #2696
• Remove examples from sample_shipped description by @mslarae13 in #2684
• Add slot to WorkflowExecution and DataObject classes to point to newer versions of associated WorkflowExecution by @kheal in #2695
• Generate release artifacts for nmdc-schema version 11.13.0 by @eecavanna in #2703

Full Changelog: v11.12.1...v11.13.0

v11.12.1

What's Changed

• Fix NmdcSchemaValidationPlugin import by @pkalita-lbl in #2666

Full Changelog: v11.12.0...v11.12.1

v11.12.0

What's Changed

• Fix typo in API_DEV_URL in project makefile by @kheal in #2639
• Connecting units to slots with annotations by @turbomam in #2599
• units readmes cleanup by @turbomam in #2647
• Ensure in-schema examples align with storage_units annotations by @pkalita-lbl in #2649
• add mg/L as a unit for final_concentration by @samobermiller in #2656
• add misc_param structure change by @mslarae13 in #2634
• Add unique_keys and and update description for Instrument for make:model restructuring by @kheal in #2659
• Add protocol_for and analysis_type slots to Protocol by @pkalita-lbl in #2665
• Migrator assuring unit compliance with annotations and UnitEnum by @samobermiller in #2648

Full Changelog: v11.11.1...v11.12.0

v11.12.0-rc.2

What's Changed

• Ensure in-schema examples align with storage_units annotations by @pkalita-lbl in #2649

Full Changelog: v11.12.0-rc.1...v11.12.0-rc.2

v11.12.0-rc.1

What's Changed

• Fix typo in API_DEV_URL in project makefile by @kheal in #2639
• Connecting units to slots with annotations by @turbomam in #2599
• units readmes cleanup by @turbomam in #2647

Full Changelog: v11.11.1...v11.12.0-rc.1

v11.11.1

What's Changed

• Fix kwarg-related issue preventing partial migrator from being run by @eecavanna in #2643

Full Changelog: v11.11.0...v11.11.1

v11.11.0

What's Changed

• Add description slot to Protocol class by @kheal in #2627
• Fix bug in downloading nmdc_materialized_patterns.yaml from GitHub within project.Makefile by @hesspnnl in #2612
• Add structured aliases to InstrumentModelEnum permissible values by @aclum in #2620
• Remove unused JGI-only slots from Biosample Class by @mslarae13 in #2607
• Finalize deprecation of some FileTypeEnum permissible values by @aclum in #2617
• Bump lycheeverse/lychee-action to v2 and bump actions/checkout to v5 by @dependabot[bot] in #2628
• Generate release artifacts for nmdc-schema version 11.11.0 by @eecavanna in #2638

Full Changelog: v11.10.0...v11.11.0

v11.10.0

What's Changed

• Add link to nmdc-schema PyPI project page by @eecavanna in #2568
• Refactor to separate out AttributeValue classes and slots by @aclum in #2578
• Add descriptions to classes and slots pertaining to functional annotation aggregated results by @aclum in #2575
• Delete accidentally committed swap file by @aclum in #2574
• Add meanings to InstrumentModelEnum permissible values by @aclum in #2576
• Generate JSON formatted schema definition by @pkalita-lbl in #2582
• Complete Phase 2 of Deprecation for MetagenomeSequencing class by @hesspnnl in #2579
• Modeling updates to execution_resource and processing_institution for WorkflowExecution by @aclum in #2583
• Make has_unit required and range of UnitEnum, add migrator, add reporting and transaction framework for mongodb adapters. by @sierra-moxon in #2523
• Add permissible value to InstrumentModelEnum by @kheal in #2589
• Add syntax constraint to gene_function_id for class FunctionalAnnotationAggMember by @aclum in #2590
• add wrapper migrator for partials associated with 11_9_0 to 11_10_0 by @sierra-moxon in #2592
• Pass commit flag as parameter on init to MigratorBase so that scripts can be run from notebooks in runtime and commit changes. by @sierra-moxon in #2595
• Separate concerns between processing_institution and execution_resource by @aclum in #2585
• Update method signature to comply with base class by @eecavanna in #2597
• Add instrument_instance_specifier slot to DataGeneration by @kheal in #2587
• Move slots from NucleotideSequencing class to LibraryPreparation class by @aclum in #2594
• Add PVs to ChemicalEntityEnum and StationaryPhaseEnum for EMP500 mass spec material processing modeling by @samobermiller in #2600

Full Changelog: v11.9.1...v11.10.0