Unify

.github/workflows/main.yaml

@@ -3,7 +3,7 @@
 ---
 name: Build and test oscem_schemas
 
-on: [pull_request]
+on: [push, pull_request]
 
 jobs:
   test:
@@ -32,8 +32,5 @@ jobs:
       - name: Install project
         run: poetry install --no-interaction
 
-      - name: Run linter
-        run: make lint
-
       - name: Run test suite
         run: make test

.github/workflows/test_pages_build.yaml

@@ -6,6 +6,7 @@ on:
       - opened
       - reopened
       - synchronize
+      - edited
 
 concurrency: preview-${{ github.ref }}
 

.gitignore

@@ -2,6 +2,7 @@
 /project/docs/
 /tmp/
 /Testing
+/*_bak*
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

Makefile

@@ -8,21 +8,23 @@ SHELL := bash
 
 # environment variables
 .EXPORT_ALL_VARIABLES:
-ifdef LINKML_ENVIRONMENT_FILENAME
-include ${LINKML_ENVIRONMENT_FILENAME}
-else
 include config.public.mk
-endif
 
 RUN = poetry run
-SCHEMA_NAME = $(LINKML_SCHEMA_NAME)
-SOURCE_SCHEMA_PATH = $(LINKML_SCHEMA_SOURCE_PATH)
-SOURCE_SCHEMA_DIR = $(dir $(SOURCE_SCHEMA_PATH))
+
+# List all schema files matching oscem_schemas_*.yaml in the schema directory
+SCHEMA_FILES := $(wildcard src/oscem_schemas/schema/oscem_schemas_*.yaml)
+
+# Extract schema names without the directory and extension
+SCHEMA_NAMES := $(notdir $(basename $(SCHEMA_FILES)))
+SCHEMA_NAMES := $(patsubst oscem_schemas_%,%,$(SCHEMA_NAMES))
+
 SRC = src
 DEST = project
-PYMODEL = $(SRC)/$(SCHEMA_NAME)/datamodel
 DOCDIR = docs
 EXAMPLEDIR = examples
+SITE = site
+PERMDOCS = perm_docs
 
 CONFIG_YAML =
 ifdef LINKML_GENERATORS_CONFIG_YAML
@@ -34,24 +36,8 @@ ifdef LINKML_GENERATORS_DOC_ARGS
 GEN_DOC_ARGS = ${LINKML_GENERATORS_DOC_ARGS}
 endif
 
-GEN_OWL_ARGS =
-ifdef LINKML_GENERATORS_OWL_ARGS
-GEN_OWL_ARGS = ${LINKML_GENERATORS_OWL_ARGS}
-endif
-
-GEN_JAVA_ARGS =
-ifdef LINKML_GENERATORS_JAVA_ARGS
-GEN_JAVA_ARGS = ${LINKML_GENERATORS_JAVA_ARGS}
-endif
-
-GEN_TS_ARGS =
-ifdef LINKML_GENERATORS_TYPESCRIPT_ARGS
-GEN_TS_ARGS = ${LINKML_GENERATORS_TYPESCRIPT_ARGS}
-endif
-
-
 # basename of a YAML file in model/
-.PHONY: all clean setup gen-project gen-examples gendoc git-init-add git-init git-add git-commit git-status
+.PHONY:  setup gen-project git-init-add git-init git-add git-commit git-status
 
 # note: "help" MUST be the first target in the file,
 # when the user types "make" they should get help info
@@ -72,6 +58,13 @@ status: check-config
 	@echo "Project: $(SCHEMA_NAME)"
 	@echo "Source: $(SOURCE_SCHEMA_PATH)"
 
+check-config:
+ifndef LINKML_SCHEMA_NAME
+	$(error **Project not configured**:\n\n - See '.env.public'\n\n)
+else
+	$(info Ok)
+endif
+
 # generate products and add everything to github
 setup: check-config git-init install gen-project gen-examples gendoc git-add git-commit
 
@@ -99,104 +92,123 @@ update-template:
 update-linkml:
 	poetry add -D linkml@latest
 
-# EXPERIMENTAL
-create-data-harmonizer:
-	npm init data-harmonizer $(SOURCE_SCHEMA_PATH)
-
-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 -r src/data/examples/* $(EXAMPLEDIR)
-
-# generates all project files
-
-gen-project: $(PYMODEL)
-	$(RUN) gen-project ${CONFIG_YAML} -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
-
-
-# non-empty arg triggers owl (workaround https://github.com/linkml/linkml/issues/1453)
-ifneq ($(strip ${GEN_OWL_ARGS}),)
-	mkdir -p ${DEST}/owl || true
-	$(RUN) gen-owl ${GEN_OWL_ARGS} $(SOURCE_SCHEMA_PATH) >${DEST}/owl/${SCHEMA_NAME}.owl.ttl
-endif
-# non-empty arg triggers java
-ifneq ($(strip ${GEN_JAVA_ARGS}),)
-	$(RUN) gen-java ${GEN_JAVA_ARGS} --output-directory ${DEST}/java/ $(SOURCE_SCHEMA_PATH)
-endif
-# non-empty arg triggers typescript
-ifneq ($(strip ${GEN_TS_ARGS}),)
-	mkdir -p ${DEST}/typescript || true
-	$(RUN) gen-typescript ${GEN_TS_ARGS} $(SOURCE_SCHEMA_PATH) >${DEST}/typescript/${SCHEMA_NAME}.ts
-endif
-
-test: test-validate test-examples test-python
-.PHONY: test test-validate test-examples test-python
-
-test-schema:
-	$(RUN) gen-project ${CONFIG_YAML} -d tmp $(SOURCE_SCHEMA_PATH)
-
-test-python:
-	$(RUN) python -m unittest discover
-
-lint:
-	$(RUN) linkml-lint --validate --all --ignore-warnings $(SOURCE_SCHEMA_DIR)
-
-check-config:
-ifndef LINKML_SCHEMA_NAME
-	$(error **Project not configured**:\n\n - See '.env.public'\n\n)
-else
-	$(info Ok)
-endif
-
-test-validate:
-	$(RUN) linkml-validate -s $(SOURCE_SCHEMA_PATH) src/data/examples/*.yaml
-
-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/oscem_schemas/schema/oscem_schemas.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 \
-		--output-directory $@ \
-		--schema $< > $@/README.md
-
-# Test documentation locally
-serve: mkd-serve
-
-# Python datamodel
-$(PYMODEL):
-	mkdir -p $@
-
-
-$(DOCDIR):
-	mkdir -p $@
-
-gendoc: $(DOCDIR)
-	cp -rf $(SRC)/docs/files/* $(DOCDIR) ; \
-	$(RUN) gen-doc ${GEN_DOC_ARGS} -d $(DOCDIR) $(SOURCE_SCHEMA_PATH)
-
-testdoc: gendoc serve
+# Generate code for all schemas
+.PHONY: gen-project
+gen-project: $(SCHEMA_NAMES:%=gen-project-%)
+
+gen-project-%:
+	@echo "Generating code for schema $*"
+	mkdir -p $(DEST)/$*
+	$(RUN) gen-project $(CONFIG_YAML) -d $(DEST)/$* src/oscem_schemas/schema/oscem_schemas_$*.yaml
+
+# Generate documentation for all schemas
+.PHONY: gendoc
+gendoc: $(SCHEMA_NAMES:%=gendoc-%) 
+
+gendoc-%:
+	@echo "Generating documentation for schema $*"
+	mkdir -p $(DOCDIR)/$*
+	cp -rf $(SRC)/docs/files/* $(DOCDIR)/$*
+	$(RUN) gen-doc $(GEN_DOC_ARGS) -d $(DOCDIR)/$* src/oscem_schemas/schema/oscem_schemas_$*.yaml
+	cp $(PERMDOCS)/* $(DOCDIR)/
+
+
+
+# Generate examples for all schemas
+.PHONY: gen-examples
+gen-examples: $(SCHEMA_NAMES:%=gen-examples-%)
+
+gen-examples-%:
+	@echo "Copying examples for schema $*"
+	mkdir -p $(EXAMPLEDIR)
+	cp -r src/data/examples/example_valid_$*.yaml $(EXAMPLEDIR)/example_valid_$*.yaml 2>/dev/null || true
+
+# Run tests for all schemas
+test-python: $(SCHEMA_NAMES:%=test-%)
+test-lint: $(SCHEMA_NAMES:%=lint-%)
+test-examples: $(SCHEMA_NAMES:%=examples-%) 
+test: test-lint test-examples
+.PHONY: test test-lint test-examples
+
+test-%:
+	@echo "Running tests for schema $*"
+	@if [ -f tests/test_$*.py ]; then \
+		$(RUN) pytest tests/test_$*.py; \
+	else \
+		echo "No tests found for schema $*"; \
+	fi
+
+lint-%:
+	@echo "Running lint for schema $*" 
+	$(RUN) linkml-lint --validate --all --ignore-warnings src/oscem_schemas/schema/oscem_schemas_$*.yaml; \
+
+examples-%:
+	@echo "Validating examples against schema $*"	
+	@if [ -f src/data/examples/example_valid_$*.yaml ]; then \
+		$(RUN) linkml-validate -s src/oscem_schemas/schema/oscem_schemas_$*.yaml src/data/examples/example_valid_$*.yaml ; \
+	else \
+		echo "No example found"; \
+	fi
+
+##		 $(RUN) python -m unittest discover; \
+
+prepare-mkdocs: $(SCHEMA_NAMES:%=prepare-mkdocs-%)
+
+# two options, see which works better: 1 project/$*/$(DOCDIR) 2 $(DOCDIR)/$*
+prepare-mkdocs-%:
+	@echo "Preparing MkDocs configuration for schema $*"
+	@mkdir -p $(DOCDIR)/$*
+	@echo "site_name: 'OSC-EM_$*_Documentation'" > $(DOCDIR)/$*/mkdocs.yml
+	@echo "theme:" >> $(DOCDIR)/$*/mkdocs.yml
+	@echo "  name: material" >> $(DOCDIR)/$*/mkdocs.yml
+	@echo "  features:" >> $(DOCDIR)/$*/mkdocs.yml
+	@echo "    - content.tabs.link" >> $(DOCDIR)/$*/mkdocs.yml
+	@echo "plugins:" >> $(DOCDIR)/$*/mkdocs.yml
+	@echo "  - search" >> $(DOCDIR)/$*/mkdocs.yml
+	@echo "  - mermaid2" >> $(DOCDIR)/$*/mkdocs.yml
+	@echo "  - mermaid2:" >> $(DOCDIR)/$*/mkdocs.yml
+	@echo "       version: 10.9.0" >> $(DOCDIR)/$*/mkdocs.yml
+
+	@echo "docs_dir: '.'" >> $(DOCDIR)/$*/mkdocs.yml
+	@echo "site_dir: ../../$(SITE)/$*" >> $(DOCDIR)/$*/mkdocs.yml
+	@echo "nav:" >> $(DOCDIR)/$*/mkdocs.yml
+	@echo "  - Home: index.md" >> $(DOCDIR)/$*/mkdocs.yml
+
+
+	@echo "site_url: https://osc-em.github.io/OSCEM-schemas_$*" >> $(DOCDIR)/$*/mkdocs.yml
+	@echo "repo_url: https://github.com/osc-em/OSCEM_Schemas" >> $(DOCDIR)/$*/mkdocs.yml
+
+# Build Independent MkDocs Sites
+mkdocs-build: 
+	prepare-mkdocs $(SCHEMA_NAMES:%=build-%)
+
+build-test-%:
+	@echo "Building site for $*"
+	$(RUN) mkdocs build -f $(DOCDIR)/$*/mkdocs.yml
+# $(DOCDIR)/$*/
+#-d $(SITE)/$*
+build:
+	@echo "Building site for $*"
+	$(RUN) mkdocs build -f mkdocs.yml
+
+# Serve a Specific Schema Locally
+serve-test-%:
+	@echo "Serving site for $*"
+	$(RUN) mkdocs serve -f $(DOCDIR)/$*/mkdocs.yml -a 0.0.0.0:8000
+
+serve:
+	$(RUN) mkdocs serve -f mkdocs.yml -a 0.0.0.0:8000
+# Serve All Schemas Simultaneously
+serve-all: $(SCHEMA_NAMES:%=serve-%)
+
+
+
+.PHONY: serve prepare-mkdocs mkdocs-build serve-all serve-test build-test
 
 MKDOCS = $(RUN) mkdocs
 mkd-%:
 	$(MKDOCS) $*
+mkdocs-deploy: $(MKDOCS) gh-deploy
 
 git-init-add: git-init git-add git-commit git-status
 git-init:
@@ -208,15 +220,16 @@ git-commit:
 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 generated files
+.PHONY: clean
 clean:
-	rm -rf $(DEST)
-	rm -rf tmp
-	rm -fr docs/*
-	rm -fr $(PYMODEL)/*
-
-include project.Makefile
+	rm -rf $(DEST)/*
+	rm -rf $(DOCDIR)/* $(SITE)/*
+	rm -rf $(EXAMPLEDIR)/*
+#	rm -f mkdocs.yml
+
+# Default target
+.PHONY: all
+all: gen-project gen-examples gendoc test
+deploy: all mkdocs-deploy