Merge branch 'main' into update-publications-oct-2024

monarch-initiative · Oct 21, 2024 · ce09506 · ce09506
2 parents 660e2e5 + 226062c
commit ce09506
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Showing 69 changed files with 114,721 additions and 110,520 deletions.
diff --git a/Makefile b/Makefile
@@ -77,7 +77,7 @@ install-frontend:
 
 .PHONY: model
 model: install-backend	
-	$(RUN) gen-pydantic --pydantic-version 2 --extra-fields allow $(SCHEMADIR)/model.yaml > $(SCHEMADIR)/model.py
+	$(RUN) gen-pydantic --extra-fields allow $(SCHEMADIR)/model.yaml > $(SCHEMADIR)/model.py
 	$(RUN) gen-typescript $(SCHEMADIR)/model.yaml > frontend/src/api/model.ts
 	make format
 
@@ -108,7 +108,7 @@ data:
 	@echo "Generating frontpage metadata..."
 	$(RUN) python scripts/generate_fixtures.py --metadata
 	@echo "Generating publications data..."
-	$(RUN) python scripts/get_publications.py --update
+	$(RUN) python scripts/get_publications.py update --update-data
 	@echo "Generating resources data..."
 	wget https://raw.githubusercontent.com/monarch-initiative/monarch-documentation/main/src/docs/resources/monarch-app-resources.json -O frontend/src/pages/resources/resources.json
 	make format-frontend

diff --git a/backend/poetry.lock b/backend/poetry.lock
diff --git a/backend/pyproject.toml b/backend/pyproject.toml
@@ -17,7 +17,7 @@ packages = [{ include = "monarch_py", from = "src" }]
 python = "^3.9"
 pydantic = "^2"
 curies = "<1"
-linkml = "^1.7.10"
+linkml = "1.8.3"
 prefixmaps = "^0.2"
 bioregistry = "^0.10.57"
 oaklib = ">=0.6.6"