v10.1.0

Caution

Not recommended for use because certain artifacts were not built from the latest source files prior to release

Use version 10.1.2 instead.

What's Changed

As usual, this PR includes lots of changes to maintenance and QC code

The main changes to the schema itself are changes to the names and contents of enumerations and permissible values, and changes to descriptions and other textual annotations on other elements.

• remove legacy files from assets by @turbomam in #1718
• Try to ensure badge appears up-to-date by @eecavanna in #1732
• wipe all traces of "has unit" etc by @turbomam in #1733
• Alternatives for relationgraph, for generating materialized visualization by @turbomam in #1706
• 1731 update extract study command to search legacy ids by @mbthornton-lbl in #1737
• Update database tools add search for orphaned data objects by @mbthornton-lbl in #1699
• referential integrity checking of napa squads mongodb via sparql in fuseki by @turbomam in #1738
• better differentiation between pure-export and get-study-id-from-filename by @turbomam in #1746
• issue 598 add funding sources character limit by @brynnz22 in #1748
• 1767 map jgi template to nmdc slots add alias by @mslarae13 in #1768
• Rename enums per naming standards by @Shalsh23 in #1001
• Refrain from trying to read from non-existent collection by @eecavanna in #1785
• 1783 pyprojecttoml and projectmakefile entries for srcscriptsschema view relation graphpy by @turbomam in #1786
• rdf/owl targets by @turbomam in #1788
• 1747 improve logging for database tools extract-study warn for missing data objects by @mbthornton-lbl in #1770
• Add metagenomics_long_read PV to AnalysisTypeEnum by @pkalita-lbl in #1803
• Configure GHA to check docs for broken links by @eecavanna in #1796
• Update emsl_project_identifiers description by @mslarae13 in #1753
• add new MAGs workflow output files by @chienchi in #1791
• Update dna/rna plate position regex patterns to allow A10, A11, H10, H11 by @pkalita-lbl in #1766
• Update README.md by @cmungall in #1765
• added enum/pv tempalte and result by @turbomam in #1805
• Update EMSL sample type enum by @mslarae13 in #1799
• for v10.1 with generateds by @turbomam in #1810
• for v10.1 with generateds and updated version strings by @turbomam in #1811

New Contributors

• @chienchi made their first contribution in #1791

Full Changelog: v10.0.0...v10.1.0

v10.0.0

What's Changed

• Simplify migrator creation and usage by @eecavanna in #1457
• Indicate Apache Jena version number used by repo maintainer by @eecavanna in #1610
• Implement a container-based development environment for nmdc-schema by @eecavanna in #1605
• 1338 add slots infiltration 1 infiltration 2 infiltration notes by @bmeluch in #1483
• launching and config updates by @turbomam in #1615
• 1609 implement tool to extract all related entities for a study by @mbthornton-lbl in #1612
• Add boxes around notes using mkdocs material theme by @sujaypatil96 in #1631
• mkdocs need to look for javascripts/tablesort.js in docs/ directory by @sujaypatil96 in #1632
• Refactor to simplify API client and to use the nmdcschema GET endpoint by @mbthornton-lbl in #1630
• Add configuration parameters for Mermaid UML diagram inclusion/exclusion by @sujaypatil96 in #1625
• 1633 get study related records aka srcscripts nmdc_database_tools.py outputd path not working correctly by @mbthornton-lbl in #1641
• retrieve study and related records and then validate by @turbomam in #1645
• v7.8.0 is most appropriate for validating records in the napa mongodb by @turbomam in #1650
  • v8.0.0 understands the current prefix casing better
• Update extract-study to get schema version by @mbthornton-lbl in #1649
• Bump jinja2 from 3.1.2 to 3.1.3 by @dependabot in #1647
• no quick test; validate against v8.0.0 by @turbomam in #1653
• remove schema version from output and log file names by @mbthornton-lbl in #1654
• remove 404 style guide link by @turbomam in #1658
• filtered-status target by @turbomam in #1660
• tdb2.tdbloader and tdb2.tdbquery for get-study-related-records by @turbomam in #1662
• QC Report branch with test refinement by @turbomam in #1428
• Make FunctionalAnnotationAggMember slots required by @aclum in #1309
• Add note about host.docker.internal hostname by @eecavanna in #1622
• Add Fuseki to standard development environment (Docker Compose stack) by @eecavanna in #1686
• Delete quality_control_report field from Extraction in more circumstances by @eecavanna in #1682
• Fix issue where app container cannot run Java (in amd64 host environment) by @eecavanna in #1689
• highly automated fuseki load by @turbomam in #1692
• report for berkeley-schema-fy24 PR 66 by @turbomam in #1683
• Implement and integrate adapters for data migrations by @eecavanna in #1624
• move lists of yq commands from project.Makefile target into a separate files by @turbomam in #1696
• Update CODE_OF_CONDUCT.md regarding novelty by @turbomam in #1316
• Update CODE_OF_CONDUCT.md by @shreddd in #1698
• better-fuseki-comments-in-makefile by @turbomam in #1697
• Update migration_recursion script according to new Migrator design by @eecavanna in #1705
• in prep for next release by @turbomam in #1704
• pure-export migration-recursion and validation work by @turbomam in #1707
• remove legacy fuseki/tdb2 targets by @turbomam in #1712
• remove legacy build-datafile-from-api-requests targets by @turbomam in #1713
• remove experimental methods for getting Neon data from 3rd parties by @turbomam in #1714
• mixs.yaml regen requires curated assets/import_mixs_slots_regardless.tsv by @turbomam in #1716

Full Changelog: v9.3.2...v10.0.0

v9.3.2

This corrects the 9.3.1 release which was created without regenerating all artifacts.

• https://github.com/microbiomedata/nmdc-schema/releases/tag/v9.3.1
• https://github.com/microbiomedata/nmdc-schema/releases/tag/v9.3.0

v9.3.1

Forcing creation of PyPI artifact

otherwise see https://github.com/microbiomedata/nmdc-schema/releases/tag/v9.3.0

Full Changelog: v9.3.0...v9.3.1

v9.3.0

What's Changed

• 1432 expand raw data types to support emsl workflows by @aclum in #1479
• Update Extraction class and add valid data examples for review by @JamesTessmer in #1468
• Allow tables to be sorted in schema documentation by @sujaypatil96 in #1484
• problem examples become valid or invalid by @turbomam in #1452
• oaklib dependency OK now by @turbomam in #1486
• Update CONTRIBUTING.md by @cmungall in #1491
• create ChromatographicSeparationProcess class by @anastasiyaprymolenna in #1482
• Delete src/docs/nmdc-schema-style-and-collaboration-guide.md by @cmungall in #1497
• comments notes todos tidying by @turbomam in #1449
• obj prop domain assertions by @turbomam in #1500
• more free-standing modules by @turbomam in #1505
• commented out attribute defn and usages by @turbomam in #1504
• domains mostly ok by @turbomam in #1506
• re-scoped has_part back to pathways by @turbomam in #1507
• Add link to ADR by @cmungall in #1510
• 1130 emsl data object prefix by @aclum in #1509

New Contributors

• @anastasiyaprymolenna made their first contribution in #1482

Full Changelog: v9.2.0...v9.3.0

v9.2.0

PR #1400 introduces a breaking change requiring migration: websites values must not contain a DOI-like pattern. Migrator Migrator_from_9_1_to_9_2 is included in this release's project.Makefile

What's Changed

• Fix broken URI links on enum documentation pages by @sujaypatil96 in #1301
• Return the transformed study from the transformation function by @eecavanna in #1312
• add ORCID prefix expansion to nmdc.yaml by @turbomam in #1319
• Add OBI prefix expansions by @turbomam in #1318
• removed # comments and most deprecated elements by @turbomam in #1322
• null migration by @turbomam in #1323
• committed to emsl_project_identifiers by @turbomam in #1324
• has_part with NamedThing domain and range by @turbomam in #1345
• Refactor migrator classes into own modules and fix YAML file loading by @eecavanna in #1340
• added biosample prefix expansion by @turbomam in #1354
• Fix see_also link in external_identifier type by @sujaypatil96 in #1355
• Add doctests to example transformation function by @eecavanna in #1357
• add artifact upload to 'migration' action by @turbomam in #1363
• Refactor LabDevice, Instrument and InstrumentValue by @turbomam in #1332
• Add doctests to existing migration classes by @eecavanna in #1384
• linkml ^1.6.3 linkml-runtime ^1.6.2 by @turbomam in #1388
• update prov Activity description by @turbomam in #1390
• Add data_management_plan_doi enum by @brynnz22 in #1391
• include typecodes endpoint in static docs by @turbomam in #1392
• mkdocs.yml update after adding mention of typecode api by @turbomam in #1395
• Mark's update to mkdocs.yml by @turbomam in #1396
• Update make target to run all migrators' doctests (and fix bug in test) by @eecavanna in #1399
• don't use jsonschema library by @turbomam in #1401
• add element deprecation documentation by @brynnz22 in #1393
• add edi and zenodo permissible values by @brynnz22 in #1405
• Add FiltrationProcess class and supporting slots and enumerations by @JamesTessmer in #1326
• 1327 adding MixingProcess class for materialprocessing by @JamesTessmer in #1407
• Redirect /home to / on documentation website (mkdocs) by @eecavanna in #1410
• no special polymorphic dir or target by @turbomam in #1413
• Remove stray white space in MixingProcess description. by @JamesTessmer in #1416
• import host_disease_stat from MIxS by @turbomam in #1408
• Hyperlink all URLs that appear in in free text on documentation pages by @sujaypatil96 in #1417
• 1337 add slot bulk elect conductivity by @bmeluch in #1352
• host_disease_stat workarround plus PATO exp by @turbomam in #1425
• add regex pattern to websites slot: DOI-like values not allowed by @brynnz22 in #1400

New Contributors

• @bmeluch made their first contribution in #1352

Full Changelog: v9.1.0...v9.2.0

v9.1.0

What's Changed

• 487 Add slot description by @mbthornton-lbl in #1266
• Change name of invalid Study file to specify Database by @brynnz22 in #1286
• emsl: kept as is, UUID: -> emsl_uuid_like by @turbomam in #1292
• Fix issue where NMDC logo image would not appear on PyPI page and was distorted on GitHub by @eecavanna in #1294
• added terminal underscore to edam.data expansion by @turbomam in #1295
• include 'umbrella' in part_of Study slot usage definition for clarity by @brynnz22 in #1298
• allow slot insdc_bioproject_identifiers on class OmicsProcessing by @turbomam in #1296
• 1299 add ucd genome center to processinginstitutionenum by @aclum in #1300
• Update CODE_OF_CONDUCT.md by @shreddd in #1277
• Update CONTRIBUTING.md by @aclum in #1273
• version string updates for v9.1.0 by @turbomam in #1307

New Contributors

• @mbthornton-lbl made their first contribution in #1266
• @shreddd made their first contribution in #1277

Full Changelog: v9.0.4...v9.1.0

v9.0.4

What's Changed

Introduces a --migrator-name option for including multiple migrations in one migration-recursion session

Despite the PR title, @brynnz22's new DOI modeling does validate now!

see also

• https://github.com/microbiomedata/nmdc-schema/releases/tag/v9.0.0

• v9.0.2 really with version tag updates by @turbomam in #1265
• migration and validation OK, DOIs fail conversion by @turbomam in #1282

Full Changelog: v9.0.0...v9.0.4

v9.0.0

What's Changed

• Dois class by @brynnz22 in #1208

Full Changelog: v8.1.2...v9.0.0

v8.1.2

What's Changed

• for release v8.1.1 by @turbomam in #1260
• v8.1.2: forgot to include new version in pyproject.toml nmdc.yaml by @turbomam in #1261

Full Changelog: v8.1.1...v8.1.2