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

v10.7.0

What's Changed

• 2142 fileenumtype for indexed bam file by @aclum in #2143
• Delete queries for orphan functional_annotation_agg records and id non-conformaing Data Objects by @mbthornton-lbl in #2013

Full Changelog: v10.6.0...v10.7.0

v10.6.0

What's Changed

• Format Python source code (PR target: napa_compliance branch) by @eecavanna in #1382
• Convert insert_many_pymongo.py into click CLI command by @eecavanna in #1730
• Update connect_napa_mongo.py to output tsv with deleted record identifiers by @mbthornton-lbl in #1902
• napa_compliance branch: Update script to generate request bodies for /queries:run endpoint by @eecavanna in #1941
• Allow nmdc_data.py consumer to specify which variant of schema they want to access by @eecavanna in #2091
• Add PR template specific to the schema soft freeze (nmdc-schema) by @mslarae13 in #2105
• Use newer version of urllib3 to avoid moderate security bug by @turbomam in #2097
• manual poetry update for certifi warning by @turbomam in #2112
• Limit regex-anchoring carets (^) to LinkML settings, not structured_patterns by @turbomam in #2098
• Remove nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml and all references to it by @turbomam in #2094
• Remove nmdc_schema/nmdc_schema_merged.yaml along with all references to it by @turbomam in #2099
• Create DataObject_gen_by_omics.yaml by @aclum in #2118
• 1000 model rna library preparation by @aclum in #2113
• Modeling of workflow execution activities for metatranscriptomes by @aclum in #2117
• Napa compliance by @aclum in #1246
• Add tooltip annotation for gold_path_field by @aclum in #2120
• Adding metatranscriptome FileTypeEnum permissible values by @aclum in #2115
• Make it so PR template appears when people create PRs by @eecavanna in #2128
• 2129 update range and pattern on metagenome annotation id to allow metatranscriptome workflow activities by @aclum in #2130
• Add no-op migrators to versions 10.5.6 and 10.6.0 by @pkalita-lbl in #2135

Full Changelog: v10.5.6...v10.6.0