v11.7.0

What's Changed

• Upgrade LinkML to version 1.9.1 by @turbomam in #2435
• Update DataObject.was_generated_by structured pattern to resolve validation error by @mbthornton-lbl in #2443
• Add new PVs for LC NOM workflow by @kheal in #2442
• Generate release artifacts for nmdc-schema version 11.7.0 by @eecavanna in #2449

Full Changelog: v11.6.1...v11.7.0

v11.6.1

What's Changed

• Ensure all CURIE prefixes make it into generated Python by @pkalita-lbl in #2428

see also the 11.6.0 release notes

Full Changelog: v11.6.0...v11.6.1

v11.6.0

What's Changed

• Add permissible values to support LCMS metabolomics by @kheal in #2370
• Adjust ranges to WorkflowExecution subclasses was_informed_by slots to match structured_pattern_syntax by @kheal in #2375
• Add structured_patten syntax to instrument_used slot by @kheal in #2376
• Add range to has_input and has_output slot usage on StorageProcess by @kheal in #2377
• Add range for WorkflowExecution's has_input and has_output slots by @kheal in #2378
• Add more range constraints to match range implied by structured_patterns. by @kheal in #2390
• update jinja2 for failing dependabot PR 2361 by @turbomam in #2411
• Add metatranscriptome raw read permissible values to FileTypeEnum by @pkalita-lbl in #2413
• eliminates lingering any_ofs and tests against future additions by @turbomam in #2420
• Deprecate sample_state_information slot by @mslarae13 in #2354
• add lipidomics to PV list by @mslarae13 in #2415
• Include inter-class relationship graph in schema documentation by @eecavanna in #2243
• audit/normalization of prefixes and comments by @turbomam in #2409
• ensure mixs_env_triad_field annotations plus deptry configuration by @turbomam in #2397
• Move development-only dependencies back to dev group by @pkalita-lbl in #2426

Full Changelog: v11.5.1...v11.6.0

v11.5.1

This release has the same content as v11.5.0, except that the derived files have been regenerated

What's Changed

• Add Illumina NovaSeq 600 to assets/misc/neon_sequencingMethod_to_nmdc_instrument_set.tsv by @sujaypatil96 in #2344
• dependency updates: linkml, linkml-runtime, jinja2 by @turbomam in #2350
• removed empty alternative_names from OntologyClass-chebi.yaml by @turbomam in #2351
• add env triad grouping slot by @aclum in #2347
• add extra metadata to ontology_class in order to capture obsolete and… by @sierra-moxon in #2360
• add NOM to extraction target enum by @mslarae13 in #2358
• Cleanup: Move ProtocolExecution and related slots to deprecated.yaml by @bmeluch in #2359

Full Changelog: v11.4.0...v11.5.0

v11.5.0

Note

When we created this release, we forgot to recompile the "derived files" in the repo from the latest source files. While that doesn't affect the PyPI package, it does affect the contents of the repo at this tag. We fixed this in release v11.5.1 and recommend you use that release instead.

What's Changed

• Add Illumina NovaSeq 600 to assets/misc/neon_sequencingMethod_to_nmdc_instrument_set.tsv by @sujaypatil96 in #2344
• dependency updates: linkml, linkml-runtime, jinja2 by @turbomam in #2350
• removed empty alternative_names from OntologyClass-chebi.yaml by @turbomam in #2351
• add env triad grouping slot by @aclum in #2347
• add extra metadata to ontology_class in order to capture obsolete and… by @sierra-moxon in #2360
• add NOM to extraction target enum by @mslarae13 in #2358
• Cleanup: Move ProtocolExecution and related slots to deprecated.yaml by @bmeluch in #2359

Full Changelog: v11.4.0...v11.5.0

v11.4.0

What's Changed

• Chemical entity deprecation, adding enumeration for limited set of chemicals needed (at the moment) in submissions by @sierra-moxon in #2324
• Ensure dependencies are correctly classified by @pkalita-lbl in #2328
• Add "Collection name(s)" column to typecode-to-class map table by @eecavanna in #2327
• Add slot and enumeration to MetabolomicsAnalysis and implements migrator by @kheal in #2332
• Add permissible value and example use for GC/MS raw data by @kheal in #2334
• Add BRC to BiosampleCategoryEnum by @mslarae13 in #2331
• Deprecate ProtocolExecution class and related slots by @bmeluch in #2338
• Generate release artifacts for nmdc-schema version v11.4.0 by @eecavanna in #2340

Full Changelog: v11.3.0...v11.4.0

v11.4.0rc1

What's Changed

• Chemical entity deprecation, adding enumeration for limited set of chemicals needed (at the moment) in submissions by @sierra-moxon in #2324
• Ensure dependencies are correctly classified by @pkalita-lbl in #2328
• Add "Collection name(s)" column to typecode-to-class map table by @eecavanna in #2327
• Add slot and enumeration to MetabolomicsAnalysis and implements migrator by @kheal in #2332

Full Changelog: v11.3.0...v11.4.0rc1

v11.3.0

What's Changed

• Document validation with linkml-validate and navigating the schema with schemaview by @sierra-moxon in #2281
• Remodeling of range for analyte_cateogry by @samobermiller in #2249
• Modify Mappings table to reduce redundancy by @sujaypatil96 in #2304
• Add NMDC instrument_set mapping value for GOLD Illumina MiSeq by @sujaypatil96 in #2309
• Update date and time examples to be strings by @pkalita-lbl in #2315
• Add permissible value to FileTypeEnum by @kheal in #2316
• Doc updates 2025 by @sierra-moxon in #2317
• Add docs page containing table that maps typecodes to schema classes by @eecavanna in #2319
• Add structured aliases for jat template keys by @aclum in #2321

Full Changelog: v11.2.1...v11.3.0

v11.3.0rc1

What's Changed

• Document validation with linkml-validate and navigating the schema with schemaview by @sierra-moxon in #2281
• Remodeling of range for analyte_cateogry by @samobermiller in #2249
• Modify Mappings table to reduce redundancy by @sujaypatil96 in #2304
• Add NMDC instrument_set mapping value for GOLD Illumina MiSeq by @sujaypatil96 in #2309
• Update date and time examples to be strings by @pkalita-lbl in #2315

Full Changelog: v11.2.1...v11.3.0rc1

v11.2.1

This release was created to synchronize the contents of the repository (specifically, the 5 files listed below) with the contents of the PyPI package. That synchronization was achieved by checking out v11.2.0, running $ make squeaky-clean all test, and committing the changed files to the repository.

nmdc.py
nmdc.schema.json
nmdc-pydantic.py
nmdc_materialized_patterns.schema.json
nmdc_materialized_patterns.yaml

In the previous release (v11.2.0 release), the two were not synchronized. Although the GitHub Actions workflow that builds and publishes the PyPI package runs $ make squeaky-clean all (no test), itself, it does not commit the result to the repository.

What's Changed

• Generate derivative JSON, YAML, and Python files from current source files by @eecavanna in #2301

Full Changelog: v11.2.0...v11.2.1