linkml 1.9.2rc1__tar.gz → 1.9.3__tar.gz

{linkml-1.9.2rc1 → linkml-1.9.3}/LICENSE

@@ -10,4 +10,4 @@ Unless required by applicable law or agreed to in writing, software
 distributed under the License is distributed on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
-limitations under the License.
+limitations under the License.

{linkml-1.9.2rc1 → linkml-1.9.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: linkml
-Version: 1.9.2rc1
+Version: 1.9.3
 Summary: Linked Open Data Modeling Language
 License: Apache-2.0
 Keywords: schema,linked data,data modeling,rdf,owl,biolink
@@ -34,7 +34,7 @@ Requires-Dist: isodate (>=0.6.0)
 Requires-Dist: jinja2 (>=3.1.0)
 Requires-Dist: jsonasobj2 (>=1.0.3,<2.0.0)
 Requires-Dist: jsonschema[format] (>=4.0.0)
-Requires-Dist: linkml-runtime (>=1.9.2,<2.0.0)
+Requires-Dist: linkml-runtime (>=1.9.4,<2.0.0)
 Requires-Dist: numpydantic (>=1.6.1) ; extra == "numpydantic"
 Requires-Dist: numpydantic (>=1.6.1) ; extra == "tests"
 Requires-Dist: openpyxl

{linkml-1.9.2rc1 → linkml-1.9.3}/linkml/generators/PythonGenNotes.md

@@ -8,7 +8,7 @@ The elements that control the python for slot generation include
 * Whether `range` references an instance of a LinkML `type` or a LinkML `class`
 * If the slot range is a `class`:
     * Whether the class has a key (`key: <type>`), an identifier (`identifier: <type>`), or neither
-    * _If_ the class has a `key` or `identifier`, whether the instances are inlined as a dictionary (`inlined: true`), 
+    * _If_ the class has a `key` or `identifier`, whether the instances are inlined as a dictionary (`inlined: true`),
     inlined as a list (`inlined_as_list: true`) or are referenced elsewhere in the model (Default).
 * Whether the slot is or concrete (`abstract: false`) or abstract (`abstract: true` or `mixin: true`) (Default: `false`)
 * Whether a slot is required (`required: true`) or optional (`required: false`) (Default: `false`)
@@ -128,11 +128,11 @@ The python then emits a class definition for the `Integers` class, where we have
 
     * The type, `int`, is from the `base` attribute. The python generator does make use of strictly positional parameters,
     so all type declarations will have an appropriate default, which is `None` in this case:
-    
+
         `mand_integer: int = None`
-    
+
     * Check for the presence of the value itself:
-        ``` 
+        ```
         if self.mand_integer is None:
             raise ValueError("mand_integer must be supplied")
         ```
@@ -145,68 +145,68 @@ The python then emits a class definition for the `Integers` class, where we have
 2) `mand_multi_integer` - a mandatory list of integers
 
     * Accept _either_ a list of integers or a single integer, which will be converted to a list:
-    
-        `mand_multi_integer: Union[int, List[int]] = None` 
-    
+
+        `mand_multi_integer: Union[int, List[int]] = None`
+
     * Check that the value is present.  _Note:_ LinkML treats an empty list as the same as an absent value.
-     
+
         ```
             if self.mand_multi_integer is None:
                 raise ValueError("mand_multi_integer must be supplied")
         ```
     * Convert a non-list value into a list.  This allows constructors to be lazy when it comes to single valued entries.
-    Note, however, that this _does_ require that list-of-list constructs to be explicitly declared because, while the 
+    Note, however, that this _does_ require that list-of-list constructs to be explicitly declared because, while the
     code treats `x = C(1)` as the same as `x = C([1])` in the multivalued case, it does _not_ attempt to differentiate
     `x = C([1])` and `x = C([[1]])`. This could be done if there is a compelling reason to, however:
-    
-        ```        
+
+        ```
         elif not isinstance(self.mand_multi_integer, list):
             self.mand_multi_integer = [self.mand_multi_integer]
         ```
     *  Check that the mandatory list has at least one element (our definition of `mandatory list`:
-        ```        
+        ```
         elif len(self.mand_multi_integer) == 0:
             raise ValueError(f"mand_multi_integer must be a non-empty list")
         ```
     * Coerce all of the member of the list into the target type (`int`):
-    
+
         `self.mand_multi_integer = [v if isinstance(v, int) else int(v) for v in self.mand_multi_integer]`
-            
+
 3) `opt_integer` - Optional non-list.
     * Accept either an `int` or `None`, the latter being entailed in the `Optional` type:
         `opt_integer: Optional[int] = None`
-        
+
     * Coerce to an integer if the value is present, otherwise let it be:
-        ```        
+        ```
         if self.opt_integer is not None and not isinstance(self.opt_integer, int):
             self.opt_integer = int(self.opt_integer)
         ```
     * Type is `Optional[<type>]`
     * `__post_init__` adds type coercion if necessary
-    
+
 4) `opt_multi_integer`: list:
     * Accept one of `None`, `int`, list of `int`, or anything that can be coerced into `List[int]`:
-    
+
         `opt_multi_integer: Optional[Union[int, List[int]]] = empty_list()`
-        
+
     * The absence of a list property is always represented as an empty list:
-        ```        
+        ```
         if self.opt_multi_integer is None:
             self.opt_multi_integer = []
         ```
-      
+
     * Coerce any other non-list into a list:
-        ```        
+        ```
         if not isinstance(self.opt_multi_integer, list):
             self.opt_multi_integer = [self.opt_multi_integer]
         ```
-      
+
     * Coerce all the members of the list into the range type
-        ```        
+        ```
         self.opt_multi_integer = [v if isinstance(v, int) else int(v) for v in self.opt_multi_integer]
         ```
 
-    
+
 ### 2) Python generation for a Type defined in `metamodelcore.py` -- `XSDDate` in this example
 YAML:
 ```yaml
@@ -287,7 +287,7 @@ are the `Union` of the class representing the element and the `repr` element (e.
 `int` type:
 
         mand_multi_integer: Union[int, List[int]] = None
-        
+
 `XSDDate` type:
 
         mand_multi_date: Union[Union[str, XSDDate], List[Union[str, XSDDate]]] = None
@@ -375,15 +375,15 @@ The Python patterns for each of the inherited types (Inherited from basic (e.g.
 ### 2) Slot range is a LinkML `class` definition
 The previous section described the Python that was generated for slot ranges that reference LinkML **Type** definitions.
 This section addresses the second use case, where the slot range references another LinkML **Class**.  Classes are
-a more complex example, because, as opposed to types, classes can either be represented by _value_ or, if they have been 
+a more complex example, because, as opposed to types, classes can either be represented by _value_ or, if they have been
 declared to have unique identifiers, by _reference_.  In addition, classes that are represented by value can either be
-represented as lists of values or dictionaries. 
+represented as lists of values or dictionaries.
 
 The following attributes control how the python is generated for a LinkML `class` definition:
 * The slot `abstract` setting
 * The slot `required` setting
 * The slot `multivalued` setting
-* Whether a class includes a slot identified as a "key" (`"key": true`), an "identifier" (`"identifier": true`) or 
+* Whether a class includes a slot identified as a "key" (`"key": true`), an "identifier" (`"identifier": true`) or
 neither.  Note that at the moment, a class may have at most one key or identifier slot.  Two keys, two identifiers or
 a key and an identifier are all considered errors.  It is anticipated that a future version of LinkML will allow
 multiple key slots, directly implementing the notion of a "compound key".
@@ -438,16 +438,16 @@ An optional, single element class generates the following code:
         Range is a optional class that contains one non-key/non-identifier element
         """
         ...
-    
+
         v1: Optional[Union[dict, OneElementClass]] = None
-    
+
         def __post_init__(self, **kwargs: Dict[str, Any]):
             if self.v1 is not None and not isinstance(self.v1, OneElementClass):
                 self.v1 = OneElementClass(**self.v1)
-    
+
             super().__post_init__(**kwargs)
 ```
-`v1` can be one of: 
+`v1` can be one of:
 * `None` - as in indicated by the `Optional` type
 * any python `dict`, which is the type that underlies all class representations
 * an instance of `OneElementClass`
@@ -512,7 +512,7 @@ The code:
 
 In the final case, we've attempted to show both a) what a required inline list looks like and b) show that the target
 type is irrelevant as long as it is a LinkML `Class` and has no `key` or `identifier` slots
- 
+
 
 ```python
 @dataclass
@@ -542,7 +542,7 @@ The structural differences between the above class and its predecessor are:
 
 
 ### Keyed or Identified Classes
-When the range of a slot is a LinkML class that has a `key` or an `identifier`, additional options 
+When the range of a slot is a LinkML class that has a `key` or an `identifier`, additional options
 present themselves:
 1) Should elements be represented inline or as references?
 2) If inline, should the elements be represented as lists or as dictionaries, whose key is the `key` or `identifier`
@@ -776,7 +776,7 @@ The table below describes the various python generation options for single-value
 | 1.4 | false | - | Y | Y | slot value in of containing class (i.e. inline) |
 
 The YAML examples below the above options for both optional and required slots.
- 
+
  ```yaml
   OptionalThreeElementRange:
     description: Case 1.1(o) -- single values optional slot - range has no keys or identifiers
@@ -1135,7 +1135,7 @@ Starting with the signature:
 `v1: Optional[Union[Dict[Union[str, IdentifiedThreeElementClassName], Union[dict, IdentifiedThreeElementClass]], List[Union[dict, IdentifiedThreeElementClass]]]] = empty_list()`
 
 The outermost declaration: `Optional[...] = empty_list()` reflects:
-1) `v1` is not required: `None` is a valid value 
+1) `v1` is not required: `None` is a valid value
 2) the internal storage structure is going to be a list.  Note that None, [] and {} (Missing scalar, empty list and empty dictionary all indicate absence of a value)
 
 Moving inwards, `Union[Dict[...], List[...]]` means that the inputs can either be in the form of a dictionary or a list.
@@ -1172,12 +1172,12 @@ One can represent instances of `OptionalMultivaluedInlinedListIdentifiedThreeEle
 or in python as:
 ```python
 ktec_examples = OptionalMultivaluedInlinedListIdentifiedThreeElementRange(
-    { 
+    {
         element1: {value: 17, modifier: "2012-03-11"},
         KeyedThreeElementClassKey('element2'): {},
         element3: {name: 'element3', value: 42}
-    }   
-)  
+    }
+)
 ```
 Note that the following is not valid because, while the `name` attribute (the key) is not required, as it has already
 been established by the key, if present it _must_ match the key itself
@@ -1197,9 +1197,9 @@ ktec_examples: OptionalMultivaluedInlinedListIdentifiedThreeElementRange = {
 Would result in an error, as `itc.name` is an instance of `IdentifiedThreeElementClassKey` while `KeyedThreeElementClass` expects a `KeyedThreeElementClassKey`
 
 #### Input in the form of a list
-Starting with the skeleton we visited earlier, Moving inwards, `Union[Dict[...], List[...]]` the second option, 
+Starting with the skeleton we visited earlier, Moving inwards, `Union[Dict[...], List[...]]` the second option,
 `List[Union[dict, IdentifiedThreeElementClass]]` indicates that the input to the constructor can also be a _list_ of
-dictionaries that conform to the `IdentifiedThreeElementClass` model. Referencing the examples that we used above, 
+dictionaries that conform to the `IdentifiedThreeElementClass` model. Referencing the examples that we used above,
 we could also use:
 ```yaml
     - name: element1
@@ -1215,8 +1215,8 @@ ktec_examples = OptionalMultivaluedInlinedListIdentifiedThreeElementRange(
     [ {name: 'element1', value: 17, modifier: "2012-03-11"},
       {name: KeyedThreeElementClassKey('element2')},
       {name: 'element3', value: 42}
-    ]  
-)  
+    ]
+)
 ```
 We then move on to the generated code:
 ```python
@@ -1243,12 +1243,12 @@ The final line in the `__post_init__` section:
 ```python
     self._normalize_inlined_slot(slot_name="v1", slot_type=IdentifiedThreeElementClass, key_name="name", inlined_as_list=True, keyed=True)
 ```
-passes the remainder of the post initialization normalization to a function defined in `YAMLRoot`.  
+passes the remainder of the post initialization normalization to a function defined in `YAMLRoot`.
 
 
 The final case, Case 2.4 (Inlined as dictionary) is essentially the same, with the exception that the target type is
-a dictionary rather than a list.  
-  
+a dictionary rather than a list.
+
 ```yaml
 OptionalMultivaluedInlinedIdentifiedThreeElementRangeList:
     description: 2.4(o) Range is an optional identified three element class that is represented as an inlined dictionary
@@ -1321,7 +1321,7 @@ At the moment, the following code is emitted:
 # Slots
 class slots:
     pass
-    
+
     ...
 
 slots.RequiredInlinedKeyedTwoElementRange_v1 = Slot(uri=LISTS_AND_KEYS.v1, name="RequiredInlinedKeyedTwoElementRange_v1", curie=LISTS_AND_KEYS.curie('v1'),
@@ -1343,7 +1343,7 @@ a slot, you use `slots.RequiredInlinedTwoElementRange_v1` (which is the mangling
 At the _moment_, you have the following elements:
 
 * uri - the SLOT URI
-* name - the mangled name 
+* name - the mangled name
 * curie - the SLOT CURIE
 * model_uri - the slot URI where the base is the Model URI vs. one assigned via `slot_uri`
 * domain - the slot domain

{linkml-1.9.2rc1 → linkml-1.9.3}/linkml/generators/README.md

@@ -15,8 +15,8 @@
 |  gen-markdown   | [markdowngen.py](https://github.com/linkml/linkml/blob/main/linkml/generators/markdowngen.py) |    MarkdownGenerator | generate markdown documentation of the model  | [markdowngen help](../../tests/test_scripts/output/genmarkdown/help) |
 |  gen-namespaces | [namespacegen.py](https://github.com/linkml/linkml/blob/main/linkml/generators/namespacegen.py) | NamespaceGenerator | generate namespace manager for URI's in model | [namespacegen help](../../tests/test_scripts/output/gennamespace/help) |
 |  gen-owl   | [owlgen.py](https://github.com/linkml/linkml/blob/main/linkml/generators/owlgen.py) |    OwlSchemaGenerator | generate an OWL representation  | [owlgen help](../../tests/test_scripts/output/genowl/help) |
-|  gen-plantuml   | [plantumlgen.py](https://github.com/linkml/linkml/blob/main/linkml/generators/plantumlgen.py) |    PlantumlGenerator | generate PlantUML representation via [PlantUML](https://plantuml.com/)  | [plantumlgen help](../../tests/test_scripts/output/genuml/help) | 
+|  gen-plantuml   | [plantumlgen.py](https://github.com/linkml/linkml/blob/main/linkml/generators/plantumlgen.py) |    PlantumlGenerator | generate PlantUML representation via [PlantUML](https://plantuml.com/)  | [plantumlgen help](../../tests/test_scripts/output/genuml/help) |
 |  gen-python   | [pythongen.py](https://github.com/linkml/linkml/blob/main/linkml/generators/pythongen.py) | PythonGenerator | generate python classes for a model  | [pythongen help](../../tests/test_scripts/output/genpython/help) |
 |  gen-rdf | [rdfgen.py](https://github.com/linkml/linkml/blob/main/linkml/generators/rdfgen.py) | RDFGenerator | generate RDF representation of model | [rdfgen help](../../tests/test_scripts/output/genrdf/help) |
 |  gen-shex   | [shexgen.py](https://github.com/linkml/linkml/blob/main/linkml/generators/shexgen.py) |    ShExGenerator | generate a ShEx model representation  | [shexgen help](../../tests/test_scripts/output/genshex/help) |
-|  gen-yuml   | [yumlgen.py](https://github.com/linkml/linkml/blob/main/linkml/generators/yumlgen.py) |    YumlGenerator | generate YUML representation via [YUML](https://yuml.me/)  | [yumlgen help](../../tests/test_scripts/output/genuml/help) | 
+|  gen-yuml   | [yumlgen.py](https://github.com/linkml/linkml/blob/main/linkml/generators/yumlgen.py) |    YumlGenerator | generate YUML representation via [YUML](https://yuml.me/)  | [yumlgen help](../../tests/test_scripts/output/genuml/help) |

{linkml-1.9.2rc1 → linkml-1.9.3}/linkml/generators/dbmlgen.py

@@ -113,7 +113,6 @@ class DBMLGenerator(Generator):
 
                 # Check if the slot references another class
                 if slot.range in self.schemaview.all_classes():
-
                     # Find the identifier slot of the referenced class
                     identifier_slot_name = next(
                         (

{linkml-1.9.2rc1 → linkml-1.9.3}/linkml/generators/docgen/class.md.jinja2

@@ -21,13 +21,12 @@
     {%- endif -%}
 {% endmacro %}
 
-# Class: {{ title }} {% if element.deprecated %} <span style="color: red;"><strong> (DEPRECATED) </strong> {% endif %}
+# Class: {{ title }} {% if element.deprecated %} <span style="color: red;"><strong> (DEPRECATED) </strong></span> {% endif %}
 
 {%- if header -%}
-{{header}}
+{{ header }}
 {%- endif -%}
 
-
 {% if element.description %}
 {% set element_description_lines = element.description.split('\n') %}
 {% for element_description_line in element_description_lines %}
@@ -41,7 +40,6 @@ _{{ element_description_line }}_
 
 URI: {{ gen.uri_link(element) }}
 
-
 {% if diagram_type == "er_diagram" %}
 ```{{ gen.mermaid_directive() }}
 {{ gen.mermaid_diagram([element.name]) }}
@@ -93,7 +91,34 @@ URI: {{ gen.uri_link(element) }}
 | 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) }} |
+| {{ gen.link(usage.used_by) }} | {{ gen.link(usage.slot) }} | {{ usage.metaslot }} | {{ gen.link(usage.used) }} |
+{% endfor %}
+{% endif %}
+
+{% if element.rules %}
+## Rules
+
+{% for rule in gen.classrule_to_dict_view(element) %}
+### {{ rule.title }}
+
+| Rule Applied | Preconditions | Postconditions | Elseconditions |
+|--------------|---------------|----------------|----------------|
+{% for key in rule.preconditions -%}
+| {{ key }} |
+{%- if rule.preconditions[key] is defined -%}
+```{{ rule.preconditions[key] }}```
+{%- else -%}
+{% endif %} |
+{%- if rule.postconditions and rule.postconditions[key] is defined -%}
+```{{ rule.postconditions[key] }}```
+{%- else -%}
+{% endif %} |
+{%- if rule.elseconditions and rule.elseconditions[key] is defined -%}
+```{{ rule.elseconditions[key] }}```
+{%- else -%}
+{% endif %} |
+{% endfor %}
+
 {% endfor %}
 {% endif %}
 
@@ -102,7 +127,7 @@ URI: {{ gen.uri_link(element) }}
 {% if gen.example_object_blobs(element.name) -%}
 ## Examples
 {% for name, blob in gen.example_object_blobs(element.name) -%}
-### Example: {{name}}
+### Example: {{ name }}
 
 ```yaml
 {{ blob }}
@@ -110,7 +135,6 @@ URI: {{ gen.uri_link(element) }}
 {% endfor %}
 {% endif %}
 
-
 ## LinkML Source
 
 <!-- TODO: investigate https://stackoverflow.com/questions/37606292/how-to-create-tabbed-code-blocks-in-mkdocs-or-sphinx -->
@@ -119,7 +143,7 @@ URI: {{ gen.uri_link(element) }}
 
 <details>
 ```yaml
-{{gen.yaml(element)}}
+{{ gen.yaml(element) }}
 ```
 </details>
 
@@ -127,10 +151,10 @@ URI: {{ gen.uri_link(element) }}
 
 <details>
 ```yaml
-{{gen.yaml(element, inferred=True)}}
+{{ gen.yaml(element, inferred=True) }}
 ```
 </details>
 
 {%- if footer -%}
-{{footer}}
-{%- endif -%}
+{{ footer }}
+{%- endif -%}

{linkml-1.9.2rc1 → linkml-1.9.3}/linkml/generators/docgen/class_diagram.md.jinja2

@@ -3,7 +3,7 @@
         {% set range_element = gen.name(schemaview.get_element(slot.range)) %}
         {% set relation_label = gen.name(slot) %}
         {{ gen.name(element) }} --> "{{ gen.cardinality(slot) }}" {{ range_element }} : {{ relation_label }}
-        click {{ range_element }} href "../{{ range_element }}"
+        click {{ range_element }} href "{{ gen.link_mermaid(schemaview.get_element(slot.range)) }}"
     {% endif %}
 {% endmacro %}
 
@@ -11,19 +11,19 @@
 ```{{ gen.mermaid_directive() }}
  classDiagram
     class {{ gen.name(element) }}
-    click {{ gen.name(element) }} href "../{{gen.name(element)}}"
+    click {{ gen.name(element) }} href "{{ gen.link_mermaid(element) }}"
       {% for s in schemaview.class_parents(element.name)|sort(attribute='name') -%}
         {{ gen.name(schemaview.get_element(s)) }} <|-- {{ gen.name(element) }}
-        click {{ gen.name(schemaview.get_element(s)) }} href "../{{gen.name(schemaview.get_element(s))}}"
+        click {{ gen.name(schemaview.get_element(s)) }} href "{{ gen.link_mermaid(schemaview.get_element(s)) }}"
       {% endfor %}
 
       {% for s in schemaview.class_children(element.name)|sort(attribute='name') -%}
         {{ gen.name(element) }} <|-- {{ gen.name(schemaview.get_element(s)) }}
-        click {{ gen.name(schemaview.get_element(s)) }} href "../{{gen.name(schemaview.get_element(s))}}"
+        click {{ gen.name(schemaview.get_element(s)) }} href "{{ gen.link_mermaid(schemaview.get_element(s)) }}"
       {% endfor %}
-      
+
       {% for s in schemaview.class_induced_slots(element.name)|sort(attribute='name') -%}
-        {{ gen.name(element) }} : {{gen.name(s)}}
+        {{ gen.name(element) }} : {{ gen.name(s) }}
         {% if s.range is not none and s.range not in gen.all_type_object_names() %}
           {{ slot_relationship(element, s) }}
         {% endif %}
@@ -33,13 +33,13 @@
 ```{{ gen.mermaid_directive() }}
  classDiagram
     class {{ gen.name(element) }}
-    click {{ gen.name(element) }} href "../{{gen.name(element)}}"
+    click {{ gen.name(element) }} href "{{ gen.link_mermaid(element) }}"
       {% for s in schemaview.class_parents(element.name)|sort(attribute='name') -%}
         {{ gen.name(schemaview.get_element(s)) }} <|-- {{ gen.name(element) }}
-        click {{ gen.name(schemaview.get_element(s)) }} href "../{{gen.name(schemaview.get_element(s))}}"
+        click {{ gen.name(schemaview.get_element(s)) }} href "{{ gen.link_mermaid(schemaview.get_element(s)) }}"
       {% endfor %}
       {% for s in schemaview.class_induced_slots(element.name)|sort(attribute='name') -%}
-        {{ gen.name(element) }} : {{gen.name(s)}}
+        {{ gen.name(element) }} : {{ gen.name(s) }}
         {% if s.range is not none and s.range not in gen.all_type_object_names() %}
           {{ slot_relationship(element, s) }}
         {% endif %}
@@ -49,13 +49,13 @@
 ```{{ gen.mermaid_directive() }}
  classDiagram
     class {{ gen.name(element) }}
-    click {{ gen.name(element) }} href "../{{gen.name(element)}}"
+    click {{ gen.name(element) }} href "{{ gen.link_mermaid(element) }}"
       {% for s in schemaview.class_children(element.name)|sort(attribute='name') -%}
         {{ gen.name(element) }} <|-- {{ gen.name(schemaview.get_element(s)) }}
-        click {{ gen.name(schemaview.get_element(s)) }} href "../{{gen.name(schemaview.get_element(s))}}"
+        click {{ gen.name(schemaview.get_element(s)) }} href "{{ gen.link_mermaid(schemaview.get_element(s)) }}"
       {% endfor %}
       {% for s in schemaview.class_induced_slots(element.name)|sort(attribute='name') -%}
-        {{ gen.name(element) }} : {{gen.name(s)}}
+        {{ gen.name(element) }} : {{ gen.name(s) }}
         {% if s.range is not none and s.range not in gen.all_type_object_names() %}
           {{ slot_relationship(element, s) }}
         {% endif %}
@@ -65,12 +65,12 @@
 ```{{ gen.mermaid_directive() }}
  classDiagram
     class {{ gen.name(element) }}
-    click {{ gen.name(element) }} href "../{{gen.name(element)}}"
+    click {{ gen.name(element) }} href "{{ gen.link_mermaid(element) }}"
       {% for s in schemaview.class_induced_slots(element.name)|sort(attribute='name') -%}
-        {{ gen.name(element) }} : {{gen.name(s)}}
+        {{ gen.name(element) }} : {{ gen.name(s) }}
         {% if s.range is not none and s.range not in gen.all_type_object_names() %}
           {{ slot_relationship(element, s) }}
         {% endif %}
       {% endfor %}
 ```
-{% endif %}
+{% endif %}

{linkml-1.9.2rc1 → linkml-1.9.3}/linkml/generators/docgen/common_metadata.md.jinja2

@@ -6,7 +6,6 @@
 {%- endfor %}
 {% endif %}
 
-
 {% if element.examples %}
 ## Examples
 
@@ -21,7 +20,7 @@
 ## Comments
 
 {% for x in element.comments -%}
-* {{x}}
+* {{ x }}
 {% endfor %}
 {% endif -%}
 
@@ -29,7 +28,7 @@
 ## TODOs
 
 {% for x in element.todos -%}
-* {{x}}
+* {{ x }}
 {% endfor %}
 {% endif -%}
 
@@ -48,12 +47,11 @@
 
 Instances of this class *should* have identifiers with one of the following prefixes:
 {% for p in element.id_prefixes %}
-* {{p}}
+* {{ p }}
 {% endfor %}
 
 {% endif %}
 
-
 {% if element.annotations %}
 ### Annotations
 

{linkml-1.9.2rc1 → linkml-1.9.3}/linkml/generators/docgen/enum.md.jinja2

@@ -1,4 +1,4 @@
-# Enum: {{ gen.name(element) }} {% if element.deprecated %} <span style="color: red;"><strong> (DEPRECATED) </strong> {% endif %}
+# Enum: {{ gen.name(element) }} {% if element.deprecated %} <span style="color: red;"><strong> (DEPRECATED) </strong></span> {% endif %}
 
 {% if element.description %}
 {% set element_description_lines = element.description.split('\n') %}
@@ -7,7 +7,7 @@ _{{ element_description_line }}_
 {% endfor %}
 {% endif %}
 
-URI: {{ gen.link(element) }}
+URI: {{ gen.uri_link(element) }}
 
 {% if element.permissible_values -%}
 ## Permissible Values
@@ -15,7 +15,7 @@ URI: {{ gen.link(element) }}
 | Value | Meaning | Description |
 | --- | --- | --- |
 {% for pv in element.permissible_values.values() -%}
-| {{pv.text}} | {{pv.meaning}} | {{pv.description|enshorten}} |
+| {{ pv.text }} | {{ pv.meaning }} | {{ pv.description|enshorten }} |
 {% endfor %}
 {% else %}
 _This is a dynamic enum_
@@ -28,7 +28,7 @@ _This is a dynamic enum_
 | Name | Description |
 | ---  | --- |
 {% for s in schemaview.get_slots_by_enum(element.name) -%}
-| {{gen.link(s)}} | {{s.description|enshorten}} |
+| {{ gen.link(s) }} | {{ s.description|enshorten }} |
 {% endfor %}
 {% endif %}
 
@@ -38,7 +38,6 @@ _This is a dynamic enum_
 
 <details>
 ```yaml
-{{gen.yaml(element)}}
+{{ gen.yaml(element) }}
 ```
 </details>
-

{linkml-1.9.2rc1 → linkml-1.9.3}/linkml/generators/docgen/index.md.jinja2

@@ -25,7 +25,7 @@ Name: {{ schema.name }}
 {% endfor %}
 {% else -%}
 {% for c in gen.all_class_objects()|sort(attribute=sort_by) -%}
-| {{gen.link(c, True)}} | {{c.description|enshorten}} |
+| {{ gen.link(c, True) }} | {{ c.description|enshorten }} |
 {% endfor %}
 {% endif %}
 
@@ -34,7 +34,7 @@ Name: {{ schema.name }}
 | Slot | Description |
 | --- | --- |
 {% for s in gen.all_slot_objects()|sort(attribute=sort_by) -%}
-| {{gen.link(s, True)}} | {{s.description|enshorten}} |
+| {{ gen.link(s, True) }} | {{ s.description|enshorten }} |
 {% endfor %}
 
 ## Enumerations
@@ -42,7 +42,7 @@ Name: {{ schema.name }}
 | Enumeration | Description |
 | --- | --- |
 {% for e in gen.all_enum_objects()|sort(attribute=sort_by) -%}
-| {{gen.link(e, True)}} | {{e.description|enshorten}} |
+| {{ gen.link(e, True) }} | {{ e.description|enshorten }} |
 {% endfor %}
 
 ## Types
@@ -50,7 +50,7 @@ Name: {{ schema.name }}
 | Type | Description |
 | --- | --- |
 {% for t in gen.all_type_objects()|sort(attribute=sort_by) -%}
-| {{gen.link(t, True)}} | {{t.description|enshorten}} |
+| {{ gen.link(t, True) }} | {{ t.description|enshorten }} |
 {% endfor %}
 
 ## Subsets
@@ -58,5 +58,5 @@ Name: {{ schema.name }}
 | Subset | Description |
 | --- | --- |
 {% for ss in schemaview.all_subsets().values()|sort(attribute='name') -%}
-| {{gen.link(ss, True)}} | {{ss.description|enshorten}} |
+| {{ gen.link(ss, True) }} | {{ ss.description|enshorten }} |
 {% endfor %}

{linkml-1.9.2rc1 → linkml-1.9.3}/linkml/generators/docgen/index.tex.jinja2

@@ -1,7 +1,7 @@
 \documentclass{article}
 \usepackage[utf8]{inputenc}
 
-\title{ {{gen.latex(gen.schema_title())}} }
+\title{ {{ gen.latex(gen.schema_title()) }} }
 
 \begin{document}
 

{linkml-1.9.2rc1 → linkml-1.9.3}/linkml/generators/docgen/schema.md.jinja2

@@ -1,7 +1,5 @@
-# {{ schema.name }} {% if schema.deprecated %} <span style="color: red;"><strong> (DEPRECATED) </strong> {% endif %}
+# {{ schema.name }} {% if schema.deprecated %} <span style="color: red;"><strong> (DEPRECATED) </strong></span> {% endif %}
 
 {{ schema.description }}
 
 URI: {{ schema.id }}
-
-