#253

Makefile

@@ -72,7 +72,7 @@ install:
 .PHONY: install
 
 # ---
-# Project Syncronization
+# Project Synchronization
 # ---
 #
 # check we are up to date
@@ -95,7 +95,7 @@ site: clean schema-clean src/nmdc_submission_schema/schema/nmdc_submission_schem
 gen-project gendoc project/json/nmdc_submission_schema.json
 
 %.yaml: gen-project
-# make deploy has been depricated by an updated .github/workflows/deploy-docs.yaml
+# make deploy has been deprecated by an updated .github/workflows/deploy-docs.yaml
 #deploy: all mkd-gh-deploy
 
 # generates all project files

project.Makefile

@@ -25,11 +25,6 @@ schema-clean: modifications-clean sheets_and_friends-clean examples-clean post-c
 	cp placeholder.md local
 	mkdir -p examples/output
 
-# todo: fewer enums
-# todo: use booleans for yes/no enumerations
-# todo: some numbers appear as strings in the schema (just examples? check for minimum value etc)
-# todo maximum value for pH has to be an int?
-
 sheets_and_friends-clean:
 	rm -rf sheets_and_friends/yaml_out/with_shuttles.yaml
 
@@ -54,7 +49,6 @@ local/with_shuttles_yq.yaml: local/with_shuttles.yaml
 	# ControlledTermValue: what about multivalued CTVs? don't see any besides chem_administration above at this time
 	# for water, can depth be a point, a range, or both?
 
-
 # globally replace structured ranges with strings.
 # undoes some of the range alterations that nmdc-schema makes when importing MIxS terms
 # future versions of the nmdc-schema might just use strings, too
@@ -141,7 +135,6 @@ local/with_shuttles_yq.yaml: local/with_shuttles.yaml
 
 	yq -i 'del(.slots.[] | select(.name == "was_informed_by"))' $@
 
-
 modifications-clean:
 	rm -rf sheets_and_friends/yaml_out/with_modifications.yaml
 
@@ -230,8 +223,6 @@ examples-clean:
 examples/output/README.md: src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml \
 src/data/invalid src/data/valid
 	mkdir -p $(dir $@)
-	# RDF/TTL generation is failing
-	# https://github.com/microbiomedata/submission-schema/issues/13
 	$(RUN) linkml-run-examples \
 		--output-formats json \
 		--output-formats yaml \
@@ -256,20 +247,20 @@ dh-build: project/json/nmdc_submission_schema.json
 
 ###
 
-## todo frozen content in src/data/data_harmonizer_io has been removed
-## todo find a better home for the se scripts if they are still of any use
 #src/data/data_harmonizer_io/soil_data.json: src/data/data_harmonizer_io/soil_for_linkml.json
 #	$(RUN) linkml-json2dh \
 #		--input-file $< \
 #		--output-dir $(dir $@)
 
-local/usage_template.tsv: src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml
-	mkdir -p $(@D)
-	$(RUN) generate_and_populate_template \
-		 --base-class slot_definition \
-		 --columns-to-insert class \
-		 --columns-to-insert slot \
-		 --destination-template $@ \
-		 --meta-model-excel-file local/meta.xlsx \
-		 --meta-path https://raw.githubusercontent.com/linkml/linkml-model/main/linkml_model/model/schema/meta.yaml \
-		 --source-schema-path $<
+## depends on an old version of schemasheets?
+## could be replaced with https://github.com/linkml/schemasheets/blob/bdde85d74637ae116fb5fd64a2e47999a1aebdfb/pyproject.toml#L36C1-L36C20
+#local/usage_template.tsv: src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml
+#	mkdir -p $(@D)
+#	$(RUN) generate_and_populate_template \
+#		 --base-class slot_definition \
+#		 --columns-to-insert class \
+#		 --columns-to-insert slot \
+#		 --destination-template $@ \
+#		 --meta-model-excel-file local/meta.xlsx \
+#		 --meta-path https://raw.githubusercontent.com/linkml/linkml-model/main/linkml_model/model/schema/meta.yaml \
+#		 --source-schema-path $<

pyproject.toml

@@ -26,7 +26,7 @@ exhaustion-check = "^0.1.3"
 linkml = "^1.7.10"
 mkdocs-material = "^9.1.2"
 mkdocs-mermaid2-plugin = "^0.6.0"
-oaklib = "^0.5.28" # https://pypi.org/project/oaklib/0.5.6/
+oaklib = "^0.5.28"
 rdflib = "^6.2.0"
 sheets-and-friends = "^0.5.4"
 
@@ -53,12 +53,6 @@ patterns = [
     "(^version:\\s*['\\\"]?)[^'\\\"]*?(['\\\"]?)$"
 ]
 
-
-## /Users/MAM/Documents/gitrepos/sheets_and_friends
-## /home/mark/gitrepos/sheets_and_friends
-#sheets-and-friends = { path = "/home/mark/gitrepos/sheets_and_friends", develop = true }
-
-
 [build-system]
 requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
 build-backend = "poetry_dynamic_versioning.backend"