add doc-templates folder for jinja templates

{{cookiecutter.project_name}}/Makefile

@@ -15,6 +15,7 @@ SRC = src
 DEST = project
 PYMODEL = $(SRC)/$(SCHEMA_NAME)/datamodel
 DOCDIR = docs
+DOCTEMPLATESDIR = doc-templates
 EXAMPLEDIR = examples
 SHEET_MODULE = {{cookiecutter.__google_sheet_module}}
 SHEET_ID = $(shell sh ./utils/get-value.sh google_sheet_id)
@@ -126,9 +127,9 @@ $(PYMODEL):
 $(DOCDIR):
 	mkdir -p $@
 
-gendoc: $(DOCDIR)
+gendoc: $(DOCDIR) $(DOCTEMPLATESDIR)
 	cp $(SRC)/docs/*md $(DOCDIR) ; \
-	$(RUN) gen-doc -d $(DOCDIR) $(SOURCE_SCHEMA_PATH)
+	$(RUN) gen-doc -d $(DOCDIR) $(SOURCE_SCHEMA_PATH) --template-directory $(DOCTEMPLATESDIR)
 
 testdoc: gendoc serve
 

{{cookiecutter.project_name}}/src/doc-templates/class.md.jinja2

@@ -0,0 +1,145 @@
+# Class: {{ gen.name(element) }}
+
+{%- if header -%}
+{{header}}
+{%- endif -%}
+
+
+{% if element.description %}
+_{{ element.description }}_
+{% endif %}
+
+{% if element.abstract %}
+* __NOTE__: this is an abstract class and should not be instantiated directly
+{% endif %}
+{% if element.mixin %}
+* __NOTE__: this is a mixin class intended to be used in combination with other classes, and not used directly
+{% endif %}
+
+URI: {{ gen.uri_link(element) }}
+
+
+
+{% 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_induced_slots(element.name)|sort(attribute='name') -%}
+        {{ gen.name(element) }} : {{gen.name(s)}}
+      {% 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)}}
+      {% 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)}}
+      {% 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)}}
+      {% 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)}}
+      {% endfor %}
+```
+{% 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  |
+| ---  | ---  | --- |
+{% for s in schemaview.class_induced_slots(element.name) -%}
+| {{gen.link(s)}} | {{ gen.cardinality(s) }} <br/> {{gen.link(s.range)}}  | {{s.description|enshorten}}  |
+{% endfor %}
+
+## Usages
+
+{% if schemaview.usage_index().get(element.name) %}
+| 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}} | {{usage.used }} |
+{% endfor %}
+{% endif %}
+
+{% include "common_metadata.md.jinja2" %}
+
+
+{% if element.rules or element.classification_rules %}
+
+## Rules
+
+{% endif %}
+
+{% 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 }} |
+{% endif -%}
+{% endfor %}
+
+{% endif -%}
+
+
+## LinkML Specification
+
+<!-- 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 -%}

{{cookiecutter.project_name}}/src/doc-templates/common_metadata.md.jinja2

@@ -0,0 +1,49 @@
+{% if element.comments -%}
+## Comments
+
+{% for x in element.comments -%}
+* {{x}}
+{% endfor %}
+{% endif -%}
+
+{% if element.todos -%}
+## TODOs
+
+{% for x in element.todos -%}
+* {{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 -%}
+| {{a}} | {{ element.annotations[a].value }} |
+{% 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 %}

{{cookiecutter.project_name}}/src/doc-templates/enum.md.jinja2

@@ -0,0 +1,28 @@
+# {{ gen.name(element) }}
+
+{{ element.description }}
+
+URI: {{ gen.uri(element) }}
+
+{% if element.permissible_values -%}
+## Permissible Values
+
+| Value | Meaning | Description | Info |
+| --- | --- | --- | --- |
+{% for pv in element.permissible_values.values() -%}
+| {{pv.text}} | {{pv.meaning}} | {{pv.description|enshorten}} | |
+{% endfor %}
+{% else %}
+_This is a dynamic enum_
+{% endif %}
+
+{% include "common_metadata.md.jinja2" %}
+
+## Schema
+
+<details>
+```yaml
+{{gen.yaml(element)}}
+```
+</details>
+

{{cookiecutter.project_name}}/src/doc-templates/index.md.jinja2

@@ -0,0 +1,46 @@
+# {% if schema.title %}{{ schema.title }}{% else %}{{ schema.name }}{% endif %}
+
+{{ schema.description }}
+
+URI: {{ schema.id }}
+Name: {{ schema.name }}
+
+## Classes
+
+| Class | Description |
+| --- | --- |
+{% for c in gen.all_class_objects()|sort(attribute=sort_by) -%}
+| {{gen.link(c)}} | {{c.description|enshorten}} |
+{% endfor %}
+
+## 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 %}

{{cookiecutter.project_name}}/src/doc-templates/index.tex.jinja2

@@ -0,0 +1,26 @@
+\documentclass{article}
+\usepackage[utf8]{inputenc}
+
+\title{ {{gen.latex(gen.schema_title())}} }
+
+\begin{document}
+
+{{ schema.description }}
+
+URI: {{ gen.latex(schema.id) }}
+Name: {{ gen.latex(schema.name) }}
+
+\subsection{Classes}\label{classes}
+
+\begin{tabular}{ |c|c| }
+ \hline
+ Class & Description \\\\
+ \hline
+
+{% for c in schemaview.all_classes().values()|sort(attribute='name') -%}
+{{ gen.latex(c.name) }} & {{ gen.latex(c.description) }} \\\\
+{% endfor %}
+ \hline
+\end{tabular}
+
+\end{document}

{{cookiecutter.project_name}}/src/doc-templates/schema.md.jinja2

@@ -0,0 +1,7 @@
+# {{ schema.name }}
+
+{{ schema.description }}
+
+URI: {{ schema.id }}
+
+