reorg makefile into modules

biolink · Oct 4, 2024 · e81cd85 · e81cd85
1 parent 6585de1
commit e81cd85
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Showing 11 changed files with 155 additions and 246 deletions.
diff --git a/Makefile b/Makefile
@@ -8,221 +8,45 @@ SHELL := bash
 
 RUN = poetry 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)
-SOURCE_SCHEMA_DIR = $(dir $(SOURCE_SCHEMA_PATH))
-SRC = src
-DEST = project
-PYMODEL = $(SRC)/information_resource_registry/datamodel
-DOCDIR = docs
-EXAMPLEDIR = examples
-TEMPLATEDIR = doc-templates
-
-# environment variables
-include config.env
-
-GEN_PARGS =
-ifdef LINKML_GENERATORS_PROJECT_ARGS
-GEN_PARGS = ${LINKML_GENERATORS_PROJECT_ARGS}
-endif
-
-GEN_DARGS =
-ifdef LINKML_GENERATORS_MARKDOWN_ARGS
-GEN_DARGS = ${LINKML_GENERATORS_MARKDOWN_ARGS}
-endif
-
 
 # basename of a YAML file in model/
 .PHONY: all clean
 
+include relation_map.Makefile
+include validation.Makefile
+include documentation.Makefile
+include linkml.Makefile
+
 # note: "help" MUST be the first target in the file,
 # when the user types "make" they should get help info
-help: status
+help:
 	@echo ""
-	@echo "make site -- makes site locally"
 	@echo "make install -- install dependencies"
-	@echo "make test -- runs tests"
-	@echo "make lint -- perform linting"
+	@echo "make test -- runs tests including spelling checks and linting checks"
+	@echo "make lint -- perform schema linting"
 	@echo "make testdoc -- builds docs and runs local test server"
-	@echo "make deploy -- deploys site"
-	@echo "make update -- updates linkml version"
 	@echo "make help -- show this help"
 	@echo ""
 
-status: check-config
-	@echo "Project: $(SCHEMA_NAME)"
-	@echo "Source: $(SOURCE_SCHEMA_PATH)"
-
-# generate products and add everything to github
-setup: install gen-project gen-examples gendoc git-init-add
-
 # install any dependencies required for building
 install:
 	git init
 	poetry install
 .PHONY: install
 
-# ---
-# Project Synchronization
-# ---
-#
-# check we are up to date
-check: cruft-check
-cruft-check:
-	cruft check
-cruft-diff:
-	cruft diff
-
-update: update-template update-linkml
-update-template:
-	cruft update
-
-# todo: consider pinning to template
-update-linkml:
-	poetry add -D linkml@latest
-
 all: site
 site: gen-project gendoc
-%.yaml: gen-project
-deploy: all mkd-gh-deploy
 
-# In future this will be done by conversion
-gen-examples:
-	cp src/data/examples/* $(EXAMPLEDIR)
-
-infores:
-	$(RUN) gen-python src/information_resource_registry/schema/information_resource_registry.yaml > src/information_resource_registry/datamodel/information_resource_registry.py
-
-validate_infores:
-	$(RUN) python src/information_resource_registry/validation/verify_infores.py
-
-spell:
-	poetry run codespell
-
-# generates all project files
-
-gen-project: $(PYMODEL)
-	# keep these in sync between PROJECT_FOLDERS and the includes/excludes for gen-project and test-schema
-	$(RUN) gen-project \
-		--exclude excel \
-		--include graphql \
-		--include jsonld \
-		--exclude markdown \
-		--include prefixmap \
-		--include proto \
-		--include shacl \
-		--include shex \
-		--exclude sqlddl \
-		--include jsonldcontext \
-		--include jsonschema \
-		--exclude owl \
-		--include python \
-		--include rdf \
-		-d $(DEST) $(SOURCE_SCHEMA_PATH)
-	$(RUN) gen-pydantic --pydantic-version 2 src/information_resource_registry/schema/information_resource_registry.yaml > $(PYMODEL)/pydanticmodel_v2.py
-	$(RUN) gen-owl --mergeimports --no-metaclasses --no-type-objects --add-root-classes --mixins-as-expressions src/information_resource_registry/schema/information_resource_registry.yaml > $(DEST)/owl/information_resource.owl.ttl
-	$(MAKE) infores
-
-tests:
+test: test-schema lint spell
 	$(RUN) python -m unittest discover -p 'test_*.py'
 	$(RUN) codespell
 	$(RUN) yamllint -c .yamllint-config src/information_resource_registry.yaml
 	$(RUN) yamllint -c .yamllint-config infores_catalog.yaml
 	$(RUN) python validation/verify_infores.py
 
-test: test-schema test-python test-examples lint spell tests
-
-test-schema: gen-project
-
-test-python:
-	$(RUN) python -m unittest discover -p 'test_*.py'
-
-lint:
-	$(RUN) linkml-lint $(SOURCE_SCHEMA_PATH)
-
-convert-examples-to-%:
-	$(patsubst %, $(RUN) linkml-convert  % -s $(SOURCE_SCHEMA_PATH) -C Person, $(shell ${SHELL} find src/data/examples -name "*.yaml"))
-
-examples/%.yaml: src/data/examples/%.yaml
-	$(RUN) linkml-convert -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@
-examples/%.json: src/data/examples/%.yaml
-	$(RUN) linkml-convert -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@
-examples/%.ttl: src/data/examples/%.yaml
-	$(RUN) linkml-convert -P EXAMPLE=http://example.org/ -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@
-
-test-examples: examples/output
-
-examples/output: src/information_resource_registry/schema/information_resource_registry.yaml
-	mkdir -p $@
-	$(RUN) linkml-run-examples \
-		--output-formats json \
-		--output-formats yaml \
-		--counter-example-input-directory src/data/examples/invalid \
-		--input-directory src/data/examples/valid \
-		--output-directory $@ \
-		--schema $< > $@/README.md
-
-# Test documentation locally
-serve: mkd-serve
-
-# Python datamodel
-$(PYMODEL):
-	mkdir -p $@
-
-
-$(DOCDIR):
-	mkdir -p $@
-
-gen-viz:
-	$(RUN) generate_viz_json
-
-gendoc: $(DOCDIR)
-	# DO NOT REMOVE: these cp statements are crucial to maintain the w3 ids for the model artifacts
-	cp $(DEST)/owl/information_resource_registry.owl.ttl $(DOCDIR)/information_resource_registry.owl.ttl ; \
-	cp $(DEST)/jsonld/information_resource_registry.context.jsonld $(DOCDIR)/information_resource_registry.context.jsonld ; \
-	cp $(DEST)/jsonld/information_resource_registry.context.jsonld $(DOCDIR)/context.jsonld ; \
-	cp $(DEST)/jsonld/information_resource_registry.jsonld $(DOCDIR)/information_resource_registry.jsonld ; \
-	cp $(DEST)/jsonschema/information_resource_registry.schema.json $(DOCDIR)/information_resource_registry.json ; \
-	cp $(DEST)/graphql/information_resource_registry.graphql $(DOCDIR)/information_resource_registry.graphql ; \
-	cp $(DEST)/shex/information_resource_registry.shex $(DOCDIR)/information_resource_registryn.shex ; \
-	cp $(DEST)/shacl/information_resource_registry.shacl.ttl $(DOCDIR)/information_resource_registry.shacl.ttl ; \
-	cp infores_catalog.yaml $(DOCDIR) ; \
-	cp $(SRC)/information_resource_registry/schema/information_resource_registry.yaml $(DOCDIR) ; \
-	cp $(SRC)/docs/*md $(DOCDIR) ; \
-	cp -r $(SRC)/docs/images $(DOCDIR)/images ; \
-	# the .json cp here is the data required for the d3 visualizations
-	# this supports the display of our d3 visualizations
-	cp $(SRC)/docs/*.css $(DOCDIR) ; \
-	$(RUN) gen-doc -d $(DOCDIR) --template-directory $(SRC)/$(TEMPLATEDIR) $(SOURCE_SCHEMA_PATH)
-
-
-testdoc: gendoc serve
-
-MKDOCS = $(RUN) mkdocs
-mkd-%:
-	$(MKDOCS) $*
-
-PROJECT_FOLDERS = sqlschema shex shacl protobuf prefixmap owl jsonschema jsonld graphql excel
-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/information_resource_registry/schema/*yaml 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
-git-status:
-	git status
-
-# only necessary if setting up via cookiecutter
-.cruft.json:
-	echo "creating a stub for .cruft.json. IMPORTANT: setup via cruft not cookiecutter recommended!" ; \
-	touch $@
-
 clean:
 	rm -rf $(DEST)
 	rm -rf tmp
 	rm -fr docs/*
 	rm -fr $(PYMODEL)/*
 
-include project.Makefile
diff --git a/documentation.Makefile b/documentation.Makefile
@@ -0,0 +1,25 @@
+RUN = poetry run
+
+# Test documentation locally
+serve: mkd-serve
+
+gendoc: $(DOCDIR)
+	# DO NOT REMOVE: these cp statements are crucial to maintain the w3 ids for the model artifacts
+	cp $(DEST)/owl/information_resource_registry.owl.ttl $(DOCDIR)/information_resource_registry.owl.ttl ; \
+	cp $(DEST)/jsonld/information_resource_registry.context.jsonld $(DOCDIR)/information_resource_registry.context.jsonld ; \
+	cp $(DEST)/jsonld/information_resource_registry.context.jsonld $(DOCDIR)/context.jsonld ; \
+	cp $(DEST)/jsonld/information_resource_registry.jsonld $(DOCDIR)/information_resource_registry.jsonld ; \
+	cp $(DEST)/jsonschema/information_resource_registry.schema.json $(DOCDIR)/information_resource_registry.json ; \
+	cp $(DEST)/graphql/information_resource_registry.graphql $(DOCDIR)/information_resource_registry.graphql ; \
+	cp $(DEST)/shex/information_resource_registry.shex $(DOCDIR)/information_resource_registryn.shex ; \
+	cp $(DEST)/shacl/information_resource_registry.shacl.ttl $(DOCDIR)/information_resource_registry.shacl.ttl ; \
+	cp infores_catalog.yaml $(DOCDIR) ; \
+	cp $(SRC)/information_resource_registry/schema/information_resource_registry.yaml $(DOCDIR) ; \
+	cp $(SRC)/docs/*md $(DOCDIR) ; \
+	cp -r $(SRC)/docs/images $(DOCDIR)/images ; \
+	# the .json cp here is the data required for the d3 visualizations
+	# this supports the display of our d3 visualizations
+	cp $(SRC)/docs/*.css $(DOCDIR) ; \
+	$(RUN) gen-doc -d $(DOCDIR) --template-directory $(SRC)/$(TEMPLATEDIR) $(SOURCE_SCHEMA_PATH)
+
+testdoc: gendoc serve
diff --git a/linkml.Makefile b/linkml.Makefile
@@ -0,0 +1,50 @@
+SCHEMA_NAME = $(shell ${SHELL} ./utils/get-value.sh name)
+SOURCE_SCHEMA_PATH = $(shell ${SHELL} ./utils/get-value.sh source_schema_path)
+SOURCE_SCHEMA_DIR = $(dir $(SOURCE_SCHEMA_PATH))
+SRC = src
+DEST = project
+PYMODEL = $(SRC)/information_resource_registry/datamodel
+DOCDIR = docs
+EXAMPLEDIR = examples
+TEMPLATEDIR = doc-templates
+
+# environment variables
+include config.env
+
+GEN_PARGS =
+ifdef LINKML_GENERATORS_PROJECT_ARGS
+GEN_PARGS = ${LINKML_GENERATORS_PROJECT_ARGS}
+endif
+
+GEN_DARGS =
+ifdef LINKML_GENERATORS_MARKDOWN_ARGS
+GEN_DARGS = ${LINKML_GENERATORS_MARKDOWN_ARGS}
+endif
+
+test-schema: gen-project
+
+infores:
+	$(RUN) gen-python src/information_resource_registry/schema/information_resource_registry.yaml > src/information_resource_registry/datamodel/information_resource_registry.py
+# generates all project files
+
+gen-project: $(PYMODEL)
+	# keep these in sync between PROJECT_FOLDERS and the includes/excludes for gen-project and test-schema
+	$(RUN) gen-project \
+		--exclude excel \
+		--include graphql \
+		--include jsonld \
+		--exclude markdown \
+		--include prefixmap \
+		--include proto \
+		--include shacl \
+		--include shex \
+		--exclude sqlddl \
+		--include jsonldcontext \
+		--include jsonschema \
+		--exclude owl \
+		--include python \
+		--include rdf \
+		-d $(DEST) $(SOURCE_SCHEMA_PATH)
+	$(RUN) gen-pydantic --pydantic-version 2 src/information_resource_registry/schema/information_resource_registry.yaml > $(PYMODEL)/pydanticmodel_v2.py
+	$(RUN) gen-owl --mergeimports --no-metaclasses --no-type-objects --add-root-classes --mixins-as-expressions src/information_resource_registry/schema/information_resource_registry.yaml > $(DEST)/owl/information_resource.owl.ttl
+	$(MAKE) infores
diff --git a/project/information_resource_registry.py b/project/information_resource_registry.py
@@ -1,5 +1,5 @@
 # Auto generated from information_resource_registry.yaml by pythongen.py version: 0.0.1
-# Generation date: 2024-10-01T23:33:32
+# Generation date: 2024-10-04T11:56:48
 # Schema: Information-Resource-Registry-Schema
 #
 # id: https://w3id.org/biolink/information_resource_registry.yaml

diff --git a/project/jsonld/information_resource_registry.context.jsonld b/project/jsonld/information_resource_registry.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-10-01T23:33:31",
+      "generation_date": "2024-10-04T11:56:46",
       "source": "information_resource_registry.yaml"
    },
    "@context": {

diff --git a/project/jsonld/information_resource_registry.jsonld b/project/jsonld/information_resource_registry.jsonld
@@ -647,9 +647,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "information_resource_registry.yaml",
-  "source_file_date": "2024-10-01T23:32:49",
+  "source_file_date": "2024-09-18T16:41:40",
   "source_file_size": 11239,
-  "generation_date": "2024-10-01T23:33:31",
+  "generation_date": "2024-10-04T11:56:46",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/information_resource_registry.context.jsonld",