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

v10.5.6

Bugfix release due to a migrator lacking some essential functionality.

What's Changed

• Update migrator to keep DataObject.was_generated_by in sync with updated id by @eecavanna in #2088

Full Changelog: v10.5.5...v10.5.6

v10.5.5

Bugfix release due to issues integrating v10.5.4 into nmdc-runtime.

What's Changed

• Remove activity_set slot from Database class by @aclum in #2082
• Use --include-range-class-descendants flag in JSON Schema generator calls by @pkalita-lbl in #2083
• 2084 tighter pattern constraint on was_generated_by by @aclum in #2085

Full Changelog: v10.5.4...v10.5.5

v10.5.4

nmdc-schema is frozen until further notice

• Development of PRs is still allowed.
• PRs can be brought up for team review in regularly scheduled Monday and Wednesday schema/metadata meetings if the PR does not
  • change the expressiveness of the schema
  • make previously valid data invalid
  • make previously invalid data valid
• Please ask the rollout task leaders for review in advance.
  • see the Berkeley-Schema-Refactor-RollOutNotes
• We anticipate merging berkeley-schema-fy24 into this repo in October 2024, at which time the freeze will be lifted.

What's Changed

• GitHub workflow to preview documentation changes/builds with example changes by @sujaypatil96 in #2057
• Add migrator for nom_analysis_activity ID by @JamesTessmer in #2059
• Implement a "no op" migrator from v10.4.0 to v10.5.4 by @eecavanna in #2071

Full Changelog: v10.5.3...v10.5.4

v10.5.3

What's Changed

• Poetry linkml-runtime dependency version update by @sujaypatil96 in #2041
• add metagnome input id pattern constraint by @turbomam in #2044

Full Changelog: v10.5.2...v10.5.3

v10.5.2

What's Changed

• don't pin pymongo in pyproject.toml by @turbomam in #2039
• regenerated poetry.lock by @turbomam in #2040

Full Changelog: v10.5.1...v10.5.2

v10.5.1

Freeze exemption: this had been reviewed by multiple team members and was intended for inclusion in v10.5.0.

What's Changed

• Restore adapter method lost during PR #2009 merge: do_for_each_document by @eecavanna in #2032

Full Changelog: v10.5.0...v10.5.1

v10.5.0

nmdc-schema soft freeze begins now

What's Changed

• Manual addition of structured_pattern constraints on class mentioning slots, plus... by @turbomam in #1994
• remove-keep-keep-paths by @turbomam in #2026
• Identify redundant EMP500 records and generate queries:run delete commands by @aclum in #2012
• tooltips not alt descriptions or display hints by @turbomam in #2029
• degenerate metagenome sequencing by @turbomam in #2030

Full Changelog: v10.4.0...v10.5.0

v10.4.0

The nmdc-schema is approaching a freeze at the end of May.

After that point, efforts will focus on merging in berkeley-schema-fy24.

berkeley-schema-fy24 GH releases appear in their own repo, but the PyPI packages are being published as nmdc-schema, with 11.x.x release candidate versions.

This freeze is expected to last until roughly October 2024

What's Changed

• Bump requests from 2.31.0 to 2.32.0 by @dependabot in #1991
• Restore dump_single_modality version of pure-export by @turbomam in #1985
• Updates to syntax for nmdc identifiers by @aclum in #1989
• Report slots, as used by some class, that have another class in their range, when that range class has a strcutred pattern by @turbomam in #1990
• 1846 incorrect range for was informed by by @aclum in #1968
• 1992 add alternative identifiers to WorkflowExeuctionActivity by @aclum in #1993
• Migrations: Implement do_for_each_document adapter method by @eecavanna in #2006
• Migrations: Update create_migrator.py to use template file and omit leading/trailing newlines by @eecavanna in #2015
• Migrations: Implement set_field_of_each_document adapter method by @eecavanna in #2009

Full Changelog: v10.3.0...v10.4.0