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

v11.2.0

What's Changed

• Re-add prefixmaps generation to Makefile by @sierra-moxon in #2268
• Fix invalid or confusing examples by @pkalita-lbl in #2269
• Model amplicon data by @aclum in #2271
• Add pydantic version of ndmc-schema to repo and appropriate Makefile … by @sierra-moxon in #2273
• Move deprecated elements from previous release to deprecated yaml by @kheal in #2272
• Add pattern constraint to in_manifest on DataObject by @aclum in #2275
• OntologyClass metadata additions: alternative_names, alternative_identifiers, relations by @sierra-moxon in #2239
• Add slot and enumeration to MetaproteomicsAnalysis class and implement migrator. by @kheal in #2276
• Add mapping row for GOLD instrument Illumina NextSeq by @sujaypatil96 in #2277
• Add a Sample grouping class in order to remove any_of range constraints by @sierra-moxon in #2244
• Remove white-space in type names by @turbomam in #2288
• Render Mappings section generally on all element documentation pages by @sujaypatil96 in #2087
• Implement migrator that renames MassSpectrometry.has_calibration field by @eecavanna in #2292
• Delete assets/ files that are manually regenerated by @turbomam in #2296
• Remove nmdc_schema/nmdc_schema_accepting_legacy_ids.py by @turbomam in #2294
• Remove subsets by @turbomam in #2286
• Introduce generates_calibration and uses_calibration slots, examples, and migrator by @aclum in #2282

Full Changelog: v11.1.0...v11.2.0

v11.1.0

What's Changed

• Move valid src/data/invalid/DissolvingProcess-minimal-no-solvent.yaml to src/data/problem/invalid/DissolvingProcess-minimal-no-solvent.yaml by @turbomam in #2201
• Replace usages of api-berkeley in Makefiles and SPARQL with production API references by @turbomam in #2213
• No more scalar in_subsets by @turbomam in #2218
• Fix spelling errors in pyproject.toml by @turbomam in #2209
• Add custom jinja template for slot documentation pages by @sujaypatil96 in #2140
• Update comments about collection omission or modification in pure-export in project.Makefile by @turbomam in #2220
• Add figshare as a permissible value to doi provider enumeration by @aclum in #2210
• Add kegg module prefix by @aclum in #2211
• Resolve 634 azenta by @aclum in #2224
• Add genomad files to FileTypeEnum by @aclum in #2228
• Resolve 2182 add genomad file type enumerations by @aclum in #2229
• Make updates to MagsAnalysis slots by @aclum in #2225
• Write v10 vs v11/berkeley documentation by @turbomam in #2227
• Include inter-collection relationship graph in schema documentation by @eecavanna in #2241
• Move has_calibration from workflow_execution_set to data_generation_set by @brynnz22 in #2235
• Delete PR template by @mslarae13 in #2237
• Remove direct_infusion_category and DirectInfusionEnum by @samobermiller in #2248
• Add Manifest class by @kheal in #2230
• Update FunctionalAnnotationAggMember class for compatibility with MetaP Aggregation tables and implement migrator by @kheal in #2203
• Migrator: Update _from_version and _to_version to reflect role of migrator by @eecavanna in #2254
• Remove has_peptide_quantifications, deprecate associated classes and slots, and implement migrator by @kheal in #2251
• Migrations: Implement adapter method that copies values between two fields in all documents in a collection by @eecavanna in #2262
• Migrations: Implement adapter method that deletes field from all documents in collection by @eecavanna in #2263
• Migrations: Update migrator to run faster by delegating document iteration to MongoDB by @eecavanna in #2265
• Generate release artifacts for NMDC Schema version 11.1.0 by @eecavanna in #2266

New Contributors

• @samobermiller made their first contribution in #2248
• @kheal made their first contribution in #2230

Full Changelog: v11.0.3...v11.1.0

v11.0.3

Sets the multivalued attribute on the members_id slot, used by MagBin, to true

With this change, a MagBin can assert the mulitple contigs that it is constructed from

Changes from v11.0.2 to v11.0.3

• backported invalid data file from @bmeluch in 991d779
• regenerated files in nmdc_schema/

See

• #2222
• #2223

v11.0.2

Sets the multivalued attribute on the members_id slot, used by MagBin, to true

With this change, a MagBin can assert the mulitple contigs that it is constructed from

See

• #2222
• #2223

Full Changelog: v11.0.1...v11.0.2

v11.0.1

What's Changed

• Add bulk chemistry back to AnalysisTypeEnum by @pkalita-lbl in #2197

Full Changelog: v11.0.0...v11.0.1

v11.0.0

What's Changed

• Merge Berkeley schema (berkeley-schema-fy24/main) into Legacy schema (nmdc-schema/main) by @turbomam in #2195

Thanks to all of our internal and external contributors! 🎉

Narrative Changelog: https://microbiomedata.github.io/nmdc-schema/v10-vs-v11-retrospective/

Full (auto-generated) Changelog: v10.9.1...v11.0.0

v10.9.1

Full Changelog: v10.8.0...v10.9.1

regenerated derivative schema files

v10.9.0

What's Changed

• 2158 eukaryotic binning results modeling by @aclum in #2159
• Add pfam clan prefix by @aclum in #2163

Full Changelog: v10.7.0...v10.9.0

v10.8.0

What's Changed

• 2158 eukaryotic binning results modeling by @aclum in #2159
• Add pfam clan prefix by @aclum in #2163

Full Changelog: v10.7.0...v10.8.0