Update template & use hash-spec in actions

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/dalito/linkml-project-cookiecutter",
-  "commit": "d9b85bbbdcc49163416a3e3e18e23fe2ecce501b",
+  "commit": "21dc84dd378e7aade7affaa329956ce93d38202d",
   "checkout": null,
   "context": {
     "cookiecutter": {

.github/workflows/main.yaml

@@ -11,15 +11,15 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
 
       - name: Check out repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/pypi-publish.yaml

@@ -11,12 +11,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b
         with:
-          python-version: 3.9
+          python-version: 3.12
 
       - name: Install Poetry
         run: |
@@ -30,7 +30,7 @@ jobs:
         run: poetry build
 
       - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@v1.12.2
+        uses: pypa/gh-action-pypi-publish@fb13cb306901256ace3dab689990e13a5550ffaa
         with:
           user: __token__
           password: ${{ secrets.PYPI_PASSWORD }}

.gitignore

@@ -1,6 +1,7 @@
 /docs/
 /project/docs/
 /tmp/
+/local-js-pkgs
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

Makefile

@@ -11,7 +11,7 @@ SHELL := bash
 ifdef LINKML_ENVIRONMENT_FILENAME
 include ${LINKML_ENVIRONMENT_FILENAME}
 else
-include .env.public
+include config.public.mk
 endif
 
 RUN = poetry run
@@ -22,35 +22,37 @@ SRC = src
 DEST = project
 PYMODEL = $(SRC)/$(SCHEMA_NAME)/datamodel
 DOCDIR = docs
+DOCTEMPLATES = $(SRC)/docs/templates
 EXAMPLEDIR = examples
 SHEET_MODULE = personinfo_enums
 SHEET_ID = $(LINKML_SCHEMA_GOOGLE_SHEET_ID)
 SHEET_TABS = $(LINKML_SCHEMA_GOOGLE_SHEET_TABS)
 SHEET_MODULE_PATH = $(SOURCE_SCHEMA_DIR)/$(SHEET_MODULE).yaml
 
+# Use += to append variables from the variables file
 CONFIG_YAML =
 ifdef LINKML_GENERATORS_CONFIG_YAML
-CONFIG_YAML = ${LINKML_GENERATORS_CONFIG_YAML}
+CONFIG_YAML += ${LINKML_GENERATORS_CONFIG_YAML}
 endif
 
 GEN_DOC_ARGS =
 ifdef LINKML_GENERATORS_DOC_ARGS
-GEN_DOC_ARGS = ${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}
+GEN_OWL_ARGS += ${LINKML_GENERATORS_OWL_ARGS}
 endif
 
 GEN_JAVA_ARGS =
 ifdef LINKML_GENERATORS_JAVA_ARGS
-GEN_JAVA_ARGS = ${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}
+GEN_TS_ARGS += ${LINKML_GENERATORS_TYPESCRIPT_ARGS}
 endif
 
 
@@ -124,7 +126,7 @@ gen-examples:
 gen-project: $(PYMODEL)
 	$(RUN) gen-project ${CONFIG_YAML} -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
 	# addition vs. template
-	$(RUN) gen-pydantic --pydantic-version 2 $(SOURCE_SCHEMA_PATH) > $(PYMODEL)/pid4cat_model_pydantic.py
+	$(RUN) gen-pydantic $(SOURCE_SCHEMA_PATH) > $(PYMODEL)/pid4cat_model_pydantic.py
 
 # non-empty arg triggers owl (workaround https://github.com/linkml/linkml/issues/1453)
 ifneq ($(strip ${GEN_OWL_ARGS}),)
@@ -193,7 +195,7 @@ $(DOCDIR):
 	mkdir -p $@
 
 gendoc: $(DOCDIR)
-	cp -rf $(SRC)/docs/* $(DOCDIR) ; \
+	cp -rf $(SRC)/docs/files/* $(DOCDIR) ; \
 	$(RUN) gen-doc ${GEN_DOC_ARGS} -d $(DOCDIR) $(SOURCE_SCHEMA_PATH)
 
 testdoc: gendoc serve

config.public.mk

@@ -0,0 +1,32 @@
+# config.public.mk
+
+# This file is public in git. No sensitive info allowed.
+# These variables are sourced in Makefile, following make-file conventions.
+# Be aware that this file does not follow python or bash conventions, so may appear a little unfamiliar.
+
+###### schema definition variables, used by makefile
+
+# Note: makefile variables should not be quoted, as makefile handles quoting differently than bash
+LINKML_SCHEMA_NAME=pid4cat_model
+LINKML_SCHEMA_AUTHOR=David Linke <[email protected]>
+LINKML_SCHEMA_DESCRIPTION=LinkML model for handle-based PIDs for resources in catalysis (PID4Cat)
+LINKML_SCHEMA_SOURCE_PATH=src/pid4cat_model/schema/pid4cat_model.yaml
+LINKML_SCHEMA_GOOGLE_SHEET_ID=1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ
+LINKML_SCHEMA_GOOGLE_SHEET_TABS=personinfo enums
+
+###### linkml generator variables, used by makefile
+
+## gen-project configuration file
+LINKML_GENERATORS_CONFIG_YAML= --config-file config.yaml
+
+## pass args if gendoc ignores config.yaml (i.e. --no-mergeimports)
+LINKML_GENERATORS_DOC_ARGS=
+
+## pass args to workaround genowl rdfs config bug (linkml#1453)
+##   (i.e. --no-type-objects --no-metaclasses --metadata-profile rdfs)
+LINKML_GENERATORS_OWL_ARGS=
+
+## pass args to trigger experimental java/typescript generation
+LINKML_GENERATORS_JAVA_ARGS=
+LINKML_GENERATORS_TYPESCRIPT_ARGS=
+

mkdocs.yml

@@ -10,7 +10,9 @@ theme:
 plugins:
   - search
   - mermaid2:
-      version: 10.9.0
+      version: 11.4.1
+      # if you want/have to use a local copy of the mermaid.js library, uncomment the next line
+      #javascript: local-js-pkgs/mermaid.min.js
 nav:
   # - Home: home.md
   - Index: index.md

project/graphql/pid4cat_model.graphql

@@ -1,4 +1,76 @@
 # metamodel_version: 1.7.0
+enum ChangeLogField
+  {
+    STATUS
+    LANDING_PAGE
+    RESOURCE_INFO
+    RELATED_IDS
+    CONTACT
+    LICENSE
+  }
+
+enum PID4CatAgentRole
+  {
+    TRUSTEE
+    OWNER
+  }
+
+enum PID4CatStatus
+  {
+    SUBMITTED
+    REGISTERED
+    OBSOLETED
+    DEPRECATED
+  }
+
+enum RelationType
+  {
+    IS_CITED_BY
+    CITES
+    IS_SUPPLEMENT_TO
+    IS_SUPPLEMENTED_BY
+    IS_CONTINUED_BY
+    CONTINUES
+    HAS_METADATA
+    IS_METADATA_FOR
+    HAS_VERSION
+    IS_VERSION_OF
+    IS_NEW_VERSION_OF
+    IS_PREVIOUS_VERSION_OF
+    IS_PART_OF
+    HAS_PART
+    IS_DESCRIBED_BY
+    DESCRIBES
+    IS_PUBLISHED_IN
+    IS_REFERENCED_BY
+    REFERENCES
+    IS_DOCUMENTED_BY
+    DOCUMENTS
+    IS_COMPILED_BY
+    COMPILES
+    IS_VARIANT_FORM_OF
+    IS_ORIGINAL_FORM_OF
+    IS_IDENTICAL_TO
+    IS_DERIVED_FROM
+    IS_SOURCE_OF
+    IS_COLLECTED_BY
+    COLLECTS
+    IS_REQUIRED_BY
+    REQUIRES
+    IS_OBSOLETED_BY
+    OBSOLETES
+  }
+
+enum ResourceCategory
+  {
+    COLLECTION
+    SAMPLE
+    MATERIAL
+    DEVICE
+    DATA_OBJECT
+    DATA_SERVICE
+  }
+
 type Agent
   {
     name: String