Run cruft update

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/linkml/linkml-project-cookiecutter",
-  "commit": "b801ab6c7e44c46db15905bf440aa573a8f1b3b2",
+  "commit": "ef7ff16925321a2abdbaa5a2ba5db8aa83ebf24f",
   "checkout": null,
   "context": {
     "cookiecutter": {

.github/workflows/deploy-docs.yaml

@@ -9,12 +9,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@main
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0  # otherwise, you will failed to push refs to dest repo
 
       - name: Set up Python 3.
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
 
@@ -28,6 +28,14 @@ jobs:
         run: |
           mkdir -p docs
           touch docs/.nojekyll
+<<<<<<< ours
           cp src/docs/*md docs
           poetry run gen-doc -d docs src/mifc/schema/mifc.yaml
           poetry run mkdocs gh-deploy
+=======
+          make gendoc
+          ([ ! -f docs/about.md ] && cp src/docs/about.md docs/) || true
+          make mkd-gh-deploy
+
+...
+>>>>>>> theirs

.github/workflows/main.yaml

@@ -17,10 +17,10 @@ jobs:
     steps:
 
       - name: Check out repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/pypi-publish.yaml

@@ -11,10 +11,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v2.2.2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
 

Makefile

@@ -22,14 +22,16 @@ SHEET_TABS = $(shell ${SHELL} ./utils/get-value.sh google_sheet_tabs)
 SHEET_MODULE_PATH = $(SOURCE_SCHEMA_DIR)/$(SHEET_MODULE).yaml
 
 # environment variables
+include config.env
+
 GEN_PARGS =
-ifdef LINKML_COOKIECUTTER_GEN_PROJECT_ARGS
-GEN_PARGS = ${LINKML_COOKIECUTTER_GEN_PROJECT_ARGS}
+ifdef LINKML_GENERATORS_PROJECT_ARGS
+GEN_PARGS = ${LINKML_GENERATORS_PROJECT_ARGS}
 endif
 
 GEN_DARGS =
-ifdef LINKML_COOKIECUTTER_GEN_DOC_ARGS
-GEN_DARGS = ${LINKML_COOKIECUTTER_GEN_DOC_ARGS}
+ifdef LINKML_GENERATORS_MARKDOWN_ARGS
+GEN_DARGS = ${LINKML_GENERATORS_MARKDOWN_ARGS}
 endif
 
 
@@ -44,7 +46,7 @@ help: status
 	@echo "make site -- makes site locally"
 	@echo "make install -- install dependencies"
 	@echo "make test -- runs tests"
-	@echo "make lint -- perfom linting"
+	@echo "make lint -- perform linting"
 	@echo "make testdoc -- builds docs and runs local test server"
 	@echo "make deploy -- deploys site"
 	@echo "make update -- updates linkml version"
@@ -60,12 +62,12 @@ setup: install gen-project gen-examples gendoc git-init-add
 
 # install any dependencies required for building
 install:
-	git init     # issues/33
+	git init
 	poetry install
 .PHONY: install
 
 # ---
-# Project Syncronization
+# Project Synchronization
 # ---
 #
 # check we are up to date
@@ -183,5 +185,6 @@ clean:
 	rm -rf $(DEST)
 	rm -rf tmp
 	rm -fr docs/*
+	rm -fr $(PYMODEL)/*
 
 include project.Makefile

config.env

@@ -0,0 +1,8 @@
+LINKML_GENERATORS_PROJECT_ARGS=--config-file config.yaml
+
+### Extra layer of configuration for Makefile beyond
+### what 'gen-project --config-file config.yaml' provides.
+### Uncomment and set environment variables as needed.
+
+# LINKML_GENERATORS_MARKDOWN_ARGS=--no-mergeimports
+

config.yaml

@@ -0,0 +1,41 @@
+# Configuration of generators (defaults illustrated)
+---
+generator_args:
+  excel:
+    mergeimports: true
+  owl:
+    mergeimports: true
+    metaclasses: true
+    type_objects: true
+    # throws 'Cannot handle metadata profile: rdfs'
+    # metadata_profile: rdfs
+  markdown:
+    mergeimports: true
+  graphql:
+    mergeimports: true
+  java:
+    mergeimports: true
+    metadata: true
+  jsonld:
+    mergeimports: true
+  jsonschema:
+    mergeimports: true
+  jsonldcontext:
+    mergeimports: true
+  python:
+    mergeimports: true
+  prefixmap:
+    mergeimports: true
+  proto:
+    mergeimports: true
+  shacl:
+    mergeimports: true
+  shex:
+    mergeimports: true
+  sqlddl:
+    mergeimports: true
+  typescript:
+    mergeimports: true
+    metadata: true
+
+...

project/jsonld/mifc.jsonld

@@ -238,7 +238,7 @@
       "definition_uri": "https://w3id.org/linkml/Objectidentifier",
       "description": "A URI or CURIE that represents an object in the model.",
       "comments": [
-        "Used for inheritence and type checking"
+        "Used for inheritance and type checking"
       ],
       "from_schema": "https://w3id.org/linkml/types",
       "imported_from": "linkml:types",

src/data/examples/Food-001.yaml

@@ -1,6 +1,7 @@
 # Example data object
 ---
-id: example:Food001
-name: foo bar
-primary_email: foo.bar@example.com
-age_in_years: 33
+entries:
+  - id: example:Food001
+    name: foo bar
+    primary_email: foo.bar@example.com
+    age_in_years: 33