Merge branch 'master' into cthoyt-patch-1

.github/workflows/deploy_documentation.yml

@@ -71,6 +71,6 @@ jobs:
       run: |
         mkdir docs
         touch docs/.nojekyll
-        cp -r src/docs/* docs/
-        poetry run gen-doc -d docs src/sssom_schema/schema/sssom_schema.yaml
-        poetry run mkdocs gh-deploy
+        make gendoc
+        ([ ! -f docs/about.md ] && cp src/docs/about.md docs/) || true
+        make mkd-gh-deploy

Makefile

@@ -14,6 +14,7 @@ SRC = src
 DEST = project
 PYMODEL = $(SRC)/$(SCHEMA_NAME)/datamodel
 DOCDIR = docs
+TEMPLATE_DIR = $(SRC)/doc-templates
 
 # basename of a YAML file in model/
 .PHONY: all clean
@@ -46,10 +47,14 @@ deploy: all mkd-gh-deploy
 
 # generates all project files
 gen-project: $(PYMODEL)
-	$(RUN) gen-project -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
+	$(RUN) gen-project \
+		--exclude owl \
+		-d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
 
 test:
-	$(RUN) gen-project -d tmp $(SOURCE_SCHEMA_PATH) 
+	$(RUN) gen-project \
+		--exclude owl \
+		-d tmp $(SOURCE_SCHEMA_PATH) 
 
 check-config:
 	@(grep my-datamodel about.yaml > /dev/null && printf "\n**Project not configured**:\n\n  - Remember to edit 'about.yaml'\n\n" || exit 0)
@@ -83,8 +88,8 @@ $(DOCDIR):
 	mkdir -p $@
 
 gendoc: $(DOCDIR)
-	cp $(SRC)/docs/*md $(DOCDIR) ; \
-	$(RUN) gen-doc -d $(DOCDIR) $(SOURCE_SCHEMA_PATH)
+	cp -rf $(SRC)/docs/* $(DOCDIR) ; \
+	$(RUN) gen-doc -d $(DOCDIR) $(SOURCE_SCHEMA_PATH) --template-directory $(TEMPLATE_DIR)
 
 testdoc: gendoc serve
 

pyproject.toml

@@ -10,12 +10,12 @@ authors = [
 license = "MIT"
 
 [tool.poetry.dependencies]
-python = "^3.7.6"
+python = "^3.8"
 linkml-runtime = "*"
 mkdocs-mermaid2-plugin = "^0.6.0"
 
 [tool.poetry.dev-dependencies]
-linkml = "^1.2.17"
+linkml = "^1.6.2"
 mkdocs-material = "^8.2.8"
 
 [build-system]

src/doc-templates/class.md.jinja2

@@ -0,0 +1,123 @@
+# Class: {{ gen.name(element) }}
+
+{%- if header -%}
+{{header}}
+{%- endif -%}
+
+
+{% if element.description %}
+{% set element_description_lines = element.description.split('\n') %}
+{% for element_description_line in element_description_lines %}
+_{{ element_description_line }}_
+{% endfor %}
+{% endif %}
+
+{% if element.abstract %}
+* __NOTE__: this is an abstract class and should not be instantiated directly
+{% endif %}
+
+URI: {{ gen.uri_link(element) }}
+
+
+{% if diagram_type == "er_diagram" %}
+```{{ gen.mermaid_directive() }}
+{{ gen.mermaid_diagram([element.name]) }}
+```
+{% else %}
+{% include "class_diagram.md.jinja2" %}
+{% endif %}
+
+{% if schemaview.class_parents(element.name) or schemaview.class_children(element.name, mixins=False) %}
+
+## Inheritance
+{{ gen.inheritance_tree(element, mixins=True) }}
+{% else %}
+<!-- no inheritance hierarchy -->
+{% endif %}
+
+## Slots
+
+| Name | Cardinality and Range | Description | Inheritance |
+| ---  | --- | --- | --- |
+{% if gen.get_direct_slots(element)|length > 0 %}
+{%- for slot in gen.get_direct_slots(element) -%}
+| {{ gen.link(slot) }} | {{ gen.cardinality(slot) }} <br/> {{ gen.link(slot.range) }} | {{ slot.description|enshorten }} | direct |
+{% endfor -%}
+{% endif -%}
+{% if gen.get_indirect_slots(element)|length > 0 %}
+{%- for slot in gen.get_indirect_slots(element) -%}
+| {{ gen.link(slot) }} | {{ gen.cardinality(slot) }} <br/> {{ gen.link(slot.range) }} | {{ slot.description|enshorten }} | {{ gen.links(gen.get_slot_inherited_from(element.name, slot.name))|join(', ') }} |
+{% endfor -%}
+{% endif %}
+
+{% if schemaview.is_mixin(element.name) %}
+## Mixin Usage
+
+| mixed into | description |
+| --- | --- |
+{% for c in schemaview.class_children(element.name, is_a=False) -%}
+| {{ gen.link(c) }} | {{ schemaview.get_class(c).description|enshorten }} |
+{% endfor %}
+{% endif %}
+
+{% if schemaview.usage_index().get(element.name) %}
+## Usages
+
+| used by | used in | type | used |
+| ---  | --- | --- | --- |
+{% for usage in schemaview.usage_index().get(element.name) -%}
+| {{gen.link(usage.used_by)}} | {{gen.link(usage.slot)}} | {{usage.metaslot}} | {{ gen.link(usage.used) }} |
+{% endfor %}
+{% endif %}
+
+{% include "common_metadata.md.jinja2" %}
+
+
+{% if schemaview.get_mappings(element.name).items() -%}
+## Mappings
+
+| Mapping Type | Mapped Value |
+| ---  | ---  |
+{% for m, mt in schemaview.get_mappings(element.name).items() -%}
+{% if mt|length > 0 -%}
+| {{ m }} | {{ mt|join(', ') }} |
+{% endif -%}
+{% endfor %}
+
+{% endif -%}
+
+{% if gen.example_object_blobs(element.name) -%}
+## Examples
+{% for name, blob in gen.example_object_blobs(element.name) -%}
+### Example: {{name}}
+
+```yaml
+{{ blob }}
+```
+{% endfor %}
+{% endif %}
+
+
+## LinkML Source
+
+<!-- TODO: investigate https://stackoverflow.com/questions/37606292/how-to-create-tabbed-code-blocks-in-mkdocs-or-sphinx -->
+
+### Direct
+
+<details>
+```yaml
+{{gen.yaml(element)}}
+```
+</details>
+
+### Induced
+
+<details>
+```yaml
+{{gen.yaml(element, inferred=True)}}
+```
+</details>
+
+{%- if footer -%}
+{{footer}}
+{%- endif -%}

src/doc-templates/class_diagram.md.jinja2

@@ -0,0 +1,59 @@
+{% if schemaview.class_parents(element.name) and schemaview.class_children(element.name) %}
+```{{ gen.mermaid_directive() }}
+ classDiagram
+    class {{ gen.name(element) }}
+      {% for s in schemaview.class_parents(element.name)|sort(attribute='name') -%}
+        {{ gen.name(schemaview.get_element(s)) }} <|-- {{ gen.name(element) }}
+      {% endfor %}
+
+      {% for s in schemaview.class_children(element.name)|sort(attribute='name') -%}
+        {{ gen.name(element) }} <|-- {{ gen.name(schemaview.get_element(s)) }}
+      {% endfor %}
+
+      {% for s in schemaview.class_induced_slots(element.name)|sort(attribute='name') -%}
+        {{ gen.name(element) }} : {{gen.name(s)}}
+        {% if s.range not in gen.all_type_object_names() %}
+          {{ gen.name(element) }} --|> {{ s.range }} : {{ gen.name(s) }}
+        {% endif %}
+      {% endfor %}
+```
+{% elif schemaview.class_parents(element.name) %}
+```{{ gen.mermaid_directive() }}
+ classDiagram
+    class {{ gen.name(element) }}
+      {% for s in schemaview.class_parents(element.name)|sort(attribute='name') -%}
+        {{ gen.name(schemaview.get_element(s)) }} <|-- {{ gen.name(element) }}
+      {% endfor %}
+      {% for s in schemaview.class_induced_slots(element.name)|sort(attribute='name') -%}
+        {{ gen.name(element) }} : {{gen.name(s)}}
+        {% if s.range not in gen.all_type_object_names() %}
+          {{ gen.name(element) }} --|> {{ s.range }} : {{ gen.name(s) }}
+        {% endif %}
+      {% endfor %}
+```
+{% elif schemaview.class_children(element.name)  %}
+```{{ gen.mermaid_directive() }}
+ classDiagram
+    class {{ gen.name(element) }}
+      {% for s in schemaview.class_children(element.name)|sort(attribute='name') -%}
+        {{ gen.name(element) }} <|-- {{ gen.name(schemaview.get_element(s)) }}
+      {% endfor %}
+      {% for s in schemaview.class_induced_slots(element.name)|sort(attribute='name') -%}
+        {{ gen.name(element) }} : {{gen.name(s)}}
+        {% if s.range not in gen.all_type_object_names() %}
+          {{ gen.name(element) }} --|> {{ s.range }} : {{ gen.name(s) }}
+        {% endif %}
+      {% endfor %}
+```
+{% else %}
+```{{ gen.mermaid_directive() }}
+ classDiagram
+    class {{ gen.name(element) }}
+      {% for s in schemaview.class_induced_slots(element.name)|sort(attribute='name') -%}
+        {{ gen.name(element) }} : {{gen.name(s)}}
+        {% if s.range not in gen.all_type_object_names() %}
+          {{ gen.name(element) }} --|> {{ s.range }} : {{ gen.name(s) }}
+        {% endif %}
+      {% endfor %}
+```
+{% endif %}

src/doc-templates/common_metadata.md.jinja2

@@ -0,0 +1,78 @@
+{% if element.aliases %}
+## Aliases
+
+{% for alias in element.aliases %}
+* {{ alias }}
+{%- endfor %}
+{% endif %}
+
+
+{% if element.examples %}
+## Examples
+
+| Value |
+| --- |
+{% for x in element.examples -%}
+| {{ x.value }} |
+{% endfor %}
+{% endif -%}
+
+{% if element.comments -%}
+## Comments
+
+{% for x in element.comments -%}
+* {{x}}
+{% endfor %}
+{% endif -%}
+
+{% if element.todos -%}
+## TODOs
+
+{% for x in element.todos -%}
+* {{x}}
+{% endfor %}
+{% endif -%}
+
+{% if element.see_also -%}
+## See Also
+
+{% for x in element.see_also -%}
+* {{ gen.uri_link(x) }}
+{% endfor %}
+{% endif -%}
+
+## Identifier and Mapping Information
+
+{% if element.id_prefixes %}
+### Valid ID Prefixes
+
+Instances of this class *should* have identifiers with one of the following prefixes:
+{% for p in element.id_prefixes %}
+* {{p}}
+{% endfor %}
+
+{% endif %}
+
+
+{% if element.annotations %}
+### Annotations
+
+| property | value |
+| --- | --- |
+{% for a in element.annotations -%}
+{%- if a|string|first != '_' -%}
+| {{ a }} | {{ element.annotations[a].value }} |
+{%- endif -%}
+{% endfor %}
+{% endif %}
+
+{% if element.from_schema or element.imported_from %}
+### Schema Source
+
+{% if element.from_schema %}
+* from schema: {{ element.from_schema }}
+{% endif %}
+{% if element.imported_from %}
+* imported from: {{ element.imported_from }}
+{% endif %}
+{% endif %}

src/doc-templates/index.md.jinja2

@@ -0,0 +1,62 @@
+# {% if schema.title %}{{ schema.title }}{% else %}{{ schema.name }}{% endif %}
+
+{% if schema.description %}{{ schema.description }}{% endif %}
+
+URI: {{ schema.id }}
+
+Name: {{ schema.name }}
+
+{% if include_top_level_diagram %}
+
+## Schema Diagram
+
+```{{ gen.mermaid_directive() }}
+{{ gen.mermaid_diagram() }}
+```
+{% endif %}
+
+## Classes
+
+| Class | Description |
+| --- | --- |
+{% if gen.hierarchical_class_view -%}
+{% for u, v in gen.class_hierarchy_as_tuples() -%}
+| {{ " "|safe*u*8 }}{{ gen.link(schemaview.get_class(v)) }} | {{ schemaview.get_class(v).description }} |
+{% endfor %}
+{% else -%}
+{% for c in gen.all_class_objects()|sort(attribute=sort_by) -%}
+| {{gen.link(c)}} | {{c.description|enshorten}} |
+{% endfor %}
+{% endif %}
+
+## Slots
+
+| Slot | Description |
+| --- | --- |
+{% for s in gen.all_slot_objects()|sort(attribute=sort_by) -%}
+| {{gen.link(s)}} | {{s.description|enshorten}} |
+{% endfor %}
+
+## Enumerations
+
+| Enumeration | Description |
+| --- | --- |
+{% for e in gen.all_enum_objects()|sort(attribute=sort_by) -%}
+| {{gen.link(e)}} | {{e.description|enshorten}} |
+{% endfor %}
+
+## Types
+
+| Type | Description |
+| --- | --- |
+{% for t in gen.all_type_objects()|sort(attribute=sort_by) -%}
+| {{gen.link(t)}} | {{t.description|enshorten}} |
+{% endfor %}
+
+## Subsets
+
+| Subset | Description |
+| --- | --- |
+{% for ss in schemaview.all_subsets().values()|sort(attribute='name') -%}
+| {{gen.link(ss)}} | {{ss.description|enshorten}} |
+{% endfor %}