examples work or are commented out

Makefile

@@ -22,7 +22,7 @@ SRC = src
 DEST = project
 PYMODEL = $(SRC)/$(SCHEMA_NAME)/datamodel
 DOCDIR = docs
-EXAMPLEDIR = examples
+#EXAMPLEDIR = examples
 SHEET_MODULE = personinfo_enums
 SHEET_ID = $(LINKML_SCHEMA_GOOGLE_SHEET_ID)
 SHEET_TABS = $(LINKML_SCHEMA_GOOGLE_SHEET_TABS)
@@ -54,8 +54,9 @@ GEN_TS_ARGS = ${LINKML_GENERATORS_TYPESCRIPT_ARGS}
 endif
 
 
+# removed target gen-examples
 # 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: all clean setup gen-project gendoc 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
@@ -76,8 +77,9 @@ status: check-config
 	@echo "Project: $(SCHEMA_NAME)"
 	@echo "Source: $(SOURCE_SCHEMA_PATH)"
 
+# removed target gen-examples
 # generate products and add everything to github
-setup: check-config git-init install gen-project gen-examples gendoc git-add git-commit
+setup: check-config git-init install gen-project gendoc git-add git-commit
 
 # install any dependencies required for building
 install:
@@ -115,9 +117,9 @@ deploy: all mkd-gh-deploy
 compile-sheets:
 	$(RUN) sheets2linkml --gsheet-id $(SHEET_ID) $(SHEET_TABS) > $(SHEET_MODULE_PATH).tmp && mv $(SHEET_MODULE_PATH).tmp $(SHEET_MODULE_PATH)
 
-# In future this will be done by conversion
-gen-examples:
-	cp src/data/examples/* $(EXAMPLEDIR)
+## In future this will be done by conversion
+#gen-examples:
+#	cp src/data/examples/* $(EXAMPLEDIR)
 
 # generates all project files
 
@@ -140,7 +142,8 @@ ifneq ($(strip ${GEN_TS_ARGS}),)
 	$(RUN) gen-typescript ${GEN_TS_ARGS} $(SOURCE_SCHEMA_PATH) >${DEST}/typescript/${SCHEMA_NAME}.ts
 endif
 
-test: test-schema test-python test-examples
+# removed target test-examples
+test: test-schema test-python
 
 test-schema:
 	$(RUN) gen-project ${CONFIG_YAML} -d tmp $(SOURCE_SCHEMA_PATH)
@@ -158,17 +161,17 @@ else
 	$(info Ok)
 endif
 
-convert-examples-to-%:
-	$(patsubst %, $(RUN) linkml-convert  % -s $(SOURCE_SCHEMA_PATH) -C Person, $(shell ${SHELL} find src/data/examples -name "*.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/%.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/mixs_missing_value_sandbox/schema/mixs_missing_value_sandbox.yaml
 	mkdir -p $@

README.md

@@ -2,8 +2,6 @@
 
 experimentation with formal representations of missing data
 
-This repos starts off with a schema about people. It will be changed to a light subset of MIxS 6.2, with explicit handling of missing values.
-
 ## Website
 
 [https://GenomicsStandardsConsortium.github.io/mixs-missing-value-sandbox](https://GenomicsStandardsConsortium.github.io/mixs-missing-value-sandbox)
@@ -13,11 +11,11 @@ This repos starts off with a schema about people. It will be changed to a light
 * [examples/](examples/) - example data
 * [project/](project/) - project files (do not edit these)
 * [src/](src/) - source files (edit these)
-  * [mixs_missing_value_sandbox](src/mixs_missing_value_sandbox)
-    * [schema](src/mixs_missing_value_sandbox/schema) -- LinkML schema
-      (edit this)
-    * [datamodel](src/mixs_missing_value_sandbox/datamodel) -- generated
-      Python datamodel
+    * [mixs_missing_value_sandbox](src/mixs_missing_value_sandbox)
+        * [schema](src/mixs_missing_value_sandbox/schema) -- LinkML schema
+          (edit this)
+        * [datamodel](src/mixs_missing_value_sandbox/datamodel) -- generated
+          Python datamodel
 * [tests/](tests/) - Python tests
 
 ## Developer Documentation
@@ -27,6 +25,7 @@ Use the `make` command to generate project artefacts:
 
 * `make all`: make everything
 * `make deploy`: deploys site
+
 </details>
 
 ## Credits

project.Makefile

@@ -1,13 +1,13 @@
 RUN=poetry run
 
-src/data/valid/MixsCompliantData-001-report.txt: src/data/valid/MixsCompliantData-001.yaml \
+src/data/valid/MixsCompliantData-001-report.txt: src/data/examples/valid \
 src/mixs_missing_value_sandbox/schema/mixs_missing_value_sandbox.yaml
 	$(RUN) linkml-validate \
 		--schema $(word 2,$^) \
 		--target-class $(shell echo $(basename $(notdir $(word 1,$^))) | cut -d'-' -f1) \
 		$(word 1,$^) > $@
 
-src/data/valid/MixsCompliantData-001.tsv: src/data/valid/MixsCompliantData-001.yaml \
+src/data/valid/MixsCompliantData-001.tsv: src/data/examples/valid \
 src/mixs_missing_value_sandbox/schema/mixs_missing_value_sandbox.yaml
 	$(RUN) linkml-convert --schema $(word 2,$^) \
 		--output $@ \

src/data/examples/invalid/Soil-missing_sample_name.yaml

@@ -0,0 +1,4 @@
+depth: "123"
+elev: "123"
+project_name: abc
+