regenerate registry from spreadsheet

Author: sierra-moxon

Makefile

@@ -6,7 +6,7 @@ SHELL := bash
 .SUFFIXES:
 .SECONDARY:
 
-RUN = poetry run
+RUN = uv run
 # get values from about.yaml file
 SCHEMA_NAME = $(shell ${SHELL} ./utils/get-value.sh name)
 SOURCE_SCHEMA_PATH = $(shell ${SHELL} ./utils/get-value.sh source_schema_path)
@@ -63,7 +63,7 @@ setup: install gen-project gen-examples gendoc git-init-add
 # install any dependencies required for building
 install:
 	git init
-	poetry install
+	uv install
 .PHONY: install
 
 # ---
@@ -83,7 +83,7 @@ update-template:
 
 # todo: consider pinning to template
 update-linkml:
-	poetry add -D linkml@latest
+	uv add -D linkml@latest
 
 # EXPERIMENTAL
 create-data-harmonizer:
@@ -170,7 +170,7 @@ git-init-add: git-init git-add git-commit git-status
 git-init:
 	git init
 git-add: .cruft.json
-	git add .gitignore .github .cruft.json Makefile LICENSE *.md examples utils about.yaml mkdocs.yml poetry.lock project.Makefile pyproject.toml src/linkml_common/schema/*yaml src/*/datamodel/*py src/data src/docs tests src/*/_version.py
+	git add .gitignore .github .cruft.json Makefile LICENSE *.md examples utils about.yaml mkdocs.yml uv.lock pyproject.toml src/*/datamodel/*py src/data src/docs tests src/*/_version.py
 	git add $(patsubst %, project/%, $(PROJECT_FOLDERS))
 git-commit:
 	git commit -m 'chore: initial commit' -a
@@ -188,4 +188,3 @@ clean:
 	rm -fr docs/*
 	rm -fr $(PYMODEL)/*
 
-include project.Makefile

docs/details/AGR.md

@@ -8,6 +8,7 @@ dynamic = [ "version" ]
 dependencies = [
     "fastmcp>=2.7.1",
     "jinja2>=3.1.6",
+    "linkml>=1.9.2",
     "mcp>=1.9.3",
     "pyyaml>=6.0.2",
     "requests>=2.32.4",

docs/details/Bridge2AI.md

@@ -26,22 +26,6 @@ public
 
 **Topics:** Schema
 
-## GenomicsStandardsConsortium/mixs
-
-
-
-**GitHub Organization:** https://github.com/GSC
-
-
-
-**License:** CC-0
-
-**Domain:** Duplicate
-
-
-
-**Topics:** Duplicate
-
 ## NeurodataWithoutBorders/nwb-schema
 
 exploratory
@@ -58,38 +42,6 @@ exploratory
 
 **Topics:** Schema Collection
 
-## alliance-genome/agr_curation_schema
-
-
-
-**GitHub Organization:** https://github.com/AGR
-
-
-
-**License:** CC-0
-
-**Domain:** Duplicate
-
-
-
-**Topics:** Duplicate
-
-## include-dcc/include-linkml
-
-
-
-**GitHub Organization:** https://github.com/INCLUDE
-
-
-
-**License:** CC-0
-
-**Domain:** Duplicate
-
-
-
-**Topics:** Duplicate
-
 ## bfurner/bdchm
 
 public
@@ -122,22 +74,6 @@ public
 
 **Topics:** Schema
 
-## monarch-initiative/babelon
-
-
-
-**GitHub Organization:** https://github.com/Monarch
-
-
-
-**License:** CC-0
-
-**Domain:** Duplicate
-
-
-
-**Topics:** Duplicate
-
 ## loinc/comp-loinc
 
 experimental?
@@ -186,22 +122,6 @@ public
 
 **Topics:** Schema Collection
 
-## bridge2ai/model-card-schema
-
-
-
-**GitHub Organization:** https://github.com/Bridge2AI
-
-
-
-**License:** CC-0
-
-**Domain:** Duplicate
-
-
-
-**Topics:** Duplicate
-
 ## DOE
 
 pre-alpha
@@ -650,22 +570,6 @@ public
 
 **Topics:** Schema Collection
 
-## sujaypatil96/ga4gh-va
-
-
-
-**GitHub Organization:** https://github.com/GA4GH
-
-
-
-**License:** CC-0
-
-**Domain:** Duplicate
-
-
-
-**Topics:** Duplicate
-
 ## clingen-data-model/variant-functional-assay
 
 
@@ -986,22 +890,6 @@ public
 
 **Topics:** Schema
 
-## loinc/comp-loinc
-
-
-
-**GitHub Organization:** https://github.com/LOINC
-
-
-
-**License:** CC-0
-
-**Domain:** Duplicate
-
-
-
-**Topics:** Duplicate
-
 ## lmodel/collections