v6.3.0

What's Changed

• Fix strange characters and typos in slot descriptions by @turbomam in #1109
• Fix broken links in CONTRIBUTING.md by @turbomam in #1108
• add MISIP-MIMS checklist by @mslarae13 in #1002
• Release v6.3.0 by @github-actions[bot] in #1123

Full Changelog: v6.2.3...v6.3.0

v6.2.3

What's Changed

• Bump urllib3 from 2.6.0 to 2.6.3 by @dependabot[bot] in #1092
• example & constraint alignment by @turbomam in #1095
• Bump pyasn1 from 0.6.1 to 0.6.2 by @dependabot[bot] in #1093
• v6.2.3 release, fixing minor syntactic conflicts between some term patterns/constraints and the in-line schema examples by @turbomam in #1101
• Release v6.2.3 by @github-actions[bot] in #1103

Full Changelog: v6.2.2...v6.2.3

v6.2.2

What's Changed

MIxS now has a GitHub action for generating releases like this, with documentation pending in docs/edit_workflow.md in PR #1090

• generated class/slot schemasheet by @turbomam in #662
• Fix composition section on combination pages by @sujaypatil96 in #674
• Update term-request.md - change package to extension by @cmungall in #668
• new mixs.yaml with CamelCase EnumNames by @turbomam in #691
• Replace enumerations section on index/landing page with enumerations page by @sujaypatil96 in #687
• Enumeration URIs redirect to resolvable pages not 404 by @sujaypatil96 in #688
• Remove redundant sections on subset pages by @sujaypatil96 in #690
• Do not display _data slots in full term table by @sujaypatil96 in #694
• Subset URI links currently broken/404, link it out properly by @sujaypatil96 in #697
• Make links in schema text/content clickable by @sujaypatil96 in #702
• Improve site search by including parentheses as word-splitting characters by @sujaypatil96 in #710
• Enable prebuild_index option using mkdocs by @sujaypatil96 in #712
• Add mkdocs search suggestions to site search by @sujaypatil96 in #718
• Apply --use-class-uris option from linkml v1.6.5 to MIxS schema by @sujaypatil96 in #727
• Modification of class documentation pages jinja in support of --use-class-uris by @sujaypatil96 in #728
• Addition of Excel data collection templates back into the repo by @sujaypatil96 in #733
• Add missing checklist only data collection templates by @sujaypatil96 in #734
• scripted removal of unhelpful slot_usages; manually assert dense dict forms by @turbomam in #753
• Bump jinja2 from 3.1.2 to 3.1.3 by @dependabot[bot] in #749
• extension dendrogram with code by @turbomam in #767
• Add Applicable checklists and extensions section into MIxS docs by @sujaypatil96 in #778
• Bump black from 23.12.1 to 24.3.0 by @dependabot[bot] in #780
• add descriptions and other annotations to extensions by @turbomam in #769
• Slot report for sharing in LLMs by @turbomam in #757
• Replace > with >- in Extensions descriptions by @sujaypatil96 in #783
• Rename folders in mixs-templates/ by @sujaypatil96 in #785
• Reformat term list table to Title (Name) by @sujaypatil96 in #784
• Bump pillow from 10.2.0 to 10.3.0 by @dependabot[bot] in #787
• Update assembly_qual description by @cmungall in #671
• addition of an extension update ticket template by @only1chunts in #609
• Add schema description to src/mixs/schema/mixs.yaml by @sujaypatil96 in #788
• remove example from description pcr_cond by @mslarae13 in #750
• Bump tqdm from 4.66.2 to 4.66.3 by @dependabot[bot] in #793
• Bump jinja2 from 3.1.3 to 3.1.4 by @dependabot[bot] in #794
• Bump requests from 2.31.0 to 2.32.0 by @dependabot[bot] in #798
• Bump urllib3 from 2.2.1 to 2.2.2 by @dependabot[bot] in #803
• Linting of LinkML YAML schema files by @sujaypatil96 in #808
• Bump certifi from 2024.6.2 to 2024.7.4 by @dependabot[bot] in #816
• add deprecation protocol for GSC by @mslarae13 in #805
• Fix make gendoc target by @sujaypatil96 in #822
• Add document start to src/mixs/schema/mixs.yaml by @sujaypatil96 in #821
• Marker Sequences, not Marker Specimens by @turbomam in #817
• Organization of generated TSV files by @sujaypatil96 in #833
• updated fao_class description link and permissible values by @mslarae13 in #726
• global update for idna ; removed pydantic 1 constraint by @turbomam in #864
• add --- document separator to beginning of deprecated.yaml file by @turbomam in #852
• add enums to replace some string_syntaxes with complex patterns by @turbomam in #840
• Add report of slots shared between two extensions in src/scripts/extension_slot_diffrences.py by @turbomam in #831
• Add user-specific and developer-specific documentation (in GitHub README files, website) by @sujaypatil96 in #810
• script to describe enums by slots using by @turbomam in #866
• mixs-schema-formatting-variants by @turbomam in #865
• correct description of size_frac_low and size_frac_up by @mslarae13 in #825
• src/scripts documentation as Markdown files by @turbomam in #869
• TSV representations of MIxS classes (and ChatGPT based documentation of Python code in of src/scripts/*.py) by @turbomam in #812
• isolate inactive scripts by @turbomam in #868
• Update mixs-templates/README.md by @turbomam in #786
• Python for generating class model tsvs by @turbomam in #870
• with enum descriptions then normalized by @turbomam in #872
• add readme documentation & directory to releases by @mslarae13 in #850
• Change term request issue to GitHub form by @jfy133 in #876
• add soil_conductivity slot descriptions by @mslarae13 in #826
• deprecate climate_environment by @mslarae13 in #820
• Bump jinja2 from 3.1.4 to 3.1.5 by @dependabot[bot] in #884
• Remove duplicate titles appearing on Enum documentation pages by @sujaypatil96 in #894
• Add automatic LinkML linting of schema on each PR changing schema by @jfy133 in #896
• Automated linkml linter run by @sujaypatil96 in #898
• Replace misrepresented string_serialization with structured_pattern – batch 1 by @sujaypatil96 in #902
• Example added to air temperature by @jjkoehorst in #885
• 606 mixs editing workflow and policy by @cmungall in #789
• Bump jinja2 from 3.1.5 to 3.1.6 by @dependabot[bot] in #906
• generated files including converted examples, especially OWL for Bioportal by @turbomam in #911
• project generation configuration for owl with better hierarchy by @turbomam in #920
• cleanup phase 1 by @turbomam in #922
• update and deprecate nose_mouth_teeth_throat_disord [MIXS:0000283] by @mslarae13 in https://github.com/GenomicsStandard...

v6.2.0

New source of truth: https://github.com/GenomicsStandardsConsortium/mixs/blob/main/src/mixs/schema/mixs.yaml

New directory layout: https://github.com/linkml/linkml-project-cookiecutter

New release naming style, inspired by https://semver.org/

It's easy to view previous releases: https://github.com/GenomicsStandardsConsortium/mixs/releases

There are many contributors who made this possible in addition to those credited for pull request merges below.

What's Changed

• overwrite MIxS 6.1 main branch with MIxS 6.2.0 by @turbomam in #611
• Update README.md by @ramonawalls in #613
• remove mentions of mixs 6.2 by @turbomam in #620
• Update README.md by @turbomam in #641
• removed generation-time from_schema annotations by @turbomam in #647
• only define required prefixes by @turbomam in #650
• removed name text and tag assertions by @turbomam in #652
• don't assert false values by @turbomam in #654
• Term pages should resolve based on ids by @sujaypatil96 in #638
• Tailor MIXS docs pages based on feedback - part 1 by @sujaypatil96 in #660

Full Changelog: mixs6.1.1...v6.2.0

mixs6.1.1

What's Changed

• MIxS term documentation accessible through term id by @sujaypatil96 in #503
• slot documentation page title display by @sujaypatil96 in #504
• slot page web docs remove redundancy by @sujaypatil96 in #505
• updates to documentation templates by @sujaypatil96 in #509
• Bump certifi from 2022.9.24 to 2022.12.7 by @dependabot in #519
• remove empty additional properties section in docs by @sujaypatil96 in #526
• GitHub Action for autopublishing documentation by @sujaypatil96 in #527
• Bump ipython from 8.9.0 to 8.10.0 by @dependabot in #532
• Updated prefixes by @turbomam in #531
• Turbomam patch 1 by @turbomam in #536
• Revert "Turbomam patch 1" by @turbomam in #538
• upgrade to latest version of linkml by @sujaypatil96 in #544

Full Changelog: mixs6.0.0...mixs6.1.1

mixs6.1.0

The primary change for this release is to change the name of the release directory to "mixs" instead of release.

Excel files to describe checklists, which were missing from the 6.0.0 release, have been added.

This release includes several updates to the LinkML code used to generate artifacts and the web pages.

mixs6.0.0

This is the first official release of MIxS 6 using LinkML. See the change log for a description of the changes to terms since MIxS 5.

The path to the last major release, as a source file, is https://github.com/GenomicsStandardsConsortium/mixs/blob/mixs6.0.0/model/schema/mixs.yaml

https://github.com/GenomicsStandardsConsortium/mixs/blob/main/release/excel/mixs_v6.xlsx

MIxS5

This a release to preserve the directory structure that was in place for MIxS5, before the release of MIxS 6. A release was never made for MIxS 5, and some interm files were added to the repository that need to be preserved, under In progress and Published packages.

With the release of MIxS6, these files will be removed.

In the future, any in progress files should go in a branch. Any published files will be part of a release. See issue #332.