Added controlled vocab links to documentation for each node attribute…

…s where it was missing (#372)

* added vocabulary links to documentation where it was missing

src/cript/nodes/primary_nodes/data.py

@@ -214,7 +214,7 @@ def type(self) -> str:
     def type(self, new_data_type: str) -> None:
         """
         set the data type.
-        The data type must come from [CRIPT data type vocabulary]()
+        The data type must come from [CRIPT data type vocabulary](https://app.criptapp.org/vocab/data_type)
 
         Parameters
         ----------

src/cript/nodes/subobjects/citation.py

@@ -72,7 +72,7 @@ def __init__(self, type: str, reference: Reference, **kwargs):
         Parameters
         ----------
         type : citation type
-            citation type must come from [CRIPT Controlled Vocabulary]()
+            citation type must come from [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/citation_type)
         reference : Reference
             Reference node
 
@@ -134,9 +134,7 @@ def type(self) -> str:
     @beartype
     def type(self, new_type: str) -> None:
         """
-        set the citation subobject type
-
-        > Note: citation subobject must come from [CRIPT Controlled Vocabulary]()
+        set the citation sub-object type
 
         Parameters
         ----------

src/cript/nodes/subobjects/computational_forcefield.py

@@ -101,9 +101,11 @@ def __init__(self, key: str, building_block: str, coarse_grained_mapping: str =
         Parameters
         ----------
         key : str
-            type of forcefield key must come from [CRIPT Controlled Vocabulary]()
+            type of forcefield key must come from
+            [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/computational_forcefield_key)
         building_block : str
-            type of computational_forcefield building_block must come from [CRIPT Controlled Vocabulary]()
+            type of computational_forcefield building_block must come from
+            [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/building_block)
         coarse_grained_mapping : str, optional
             atom to beads mapping, by default ""
         implicit_solvent : str, optional

src/cript/nodes/subobjects/condition.py

@@ -195,8 +195,6 @@ def key(self, new_key: str) -> None:
         """
         set this Condition sub-object key
 
-        > Condition key must come from [CRIPT Controlled Vocabulary]()
-
         Parameters
         ----------
         new_key : str

src/cript/nodes/subobjects/equipment.py

@@ -67,7 +67,7 @@ def __init__(self, key: str, description: str = "", condition: Union[List[Condit
         Parameters
         ----------
         key : str
-            Equipment key must come from [CRIPT Controlled Vocabulary]()
+            Equipment key must come from [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/equipment_key)
         description : str, optional
             additional details about the equipment, by default ""
         condition : Union[List[Condition], None], optional
@@ -125,8 +125,6 @@ def key(self, new_key: str) -> None:
         """
         set the equipment key
 
-        > Equipment key must come from [CRIPT Controlled Vocabulary]()
-
         Parameters
         ----------
         new_key : str

src/cript/nodes/subobjects/ingredient.py

@@ -99,7 +99,8 @@ def __init__(self, material: Material, quantity: List[Quantity], keyword: Option
         quantity : List[Quantity]
             list of quantity sub-objects
         keyword : List[str], optional
-            ingredient keyword must come from [CRIPT Controlled Vocabulary](), by default ""
+            ingredient keyword must come from
+            [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/ingredient_keyword), by default ""
 
         Returns
         -------
@@ -206,8 +207,6 @@ def keyword(self, new_keyword: List[str]) -> None:
         """
         set new ingredient keyword to replace the current
 
-        ingredient keyword must come from the [CRIPT controlled vocabulary]()
-
         Parameters
         ----------
         new_keyword : str

src/cript/nodes/subobjects/parameter.py

@@ -75,7 +75,7 @@ def __init__(self, key: str, value: Number, unit: Optional[str] = None, **kwargs
         Parameters
         ----------
         key : str
-            Parameter key must come from [CRIPT Controlled Vocabulary]()
+            Parameter key must come from [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/parameter_key)
         value : Union[int, float]
             Parameter value
         unit : Union[str, None], optional
@@ -132,8 +132,6 @@ def key(self, new_key: str) -> None:
         """
         set new key for the Parameter sub-object
 
-        Parameter key must come from [CRIPT Controlled Vocabulary]()
-
         Parameters
         ----------
         new_key : str

src/cript/nodes/subobjects/property.py

@@ -113,9 +113,9 @@ def __init__(
         Parameters
         ----------
         key : str
-            type of property, Property key must come from the [CRIPT Controlled Vocabulary]()
+            type of property, Property key must come from the CRIPT Controlled Vocabulary
         type : str
-            type of value stored, Property type must come from the [CRIPT Controlled Vocabulary]()
+            type of value stored, Property type must come from the CRIPT Controlled Vocabulary
         value : Union[Number, None]
             value or quantity
         unit : str
@@ -477,8 +477,6 @@ def method(self, new_method: str) -> None:
         """
         set the Property method
 
-        Property method must come from [CRIPT Controlled Vocabulary]()
-
         Parameters
         ----------
         new_method : str

src/cript/nodes/subobjects/quantity.py

@@ -69,15 +69,17 @@ def __init__(self, key: str, value: Number, unit: str, uncertainty: Optional[Num
         Parameters
         ----------
         key : str
-            type of quantity. Quantity key must come from [CRIPT Controlled Vocabulary]()
+            type of quantity. Quantity key must come from
+            [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/quantity_key)
         value : Number
             amount of material
         unit : str
             unit for quantity
         uncertainty : Union[Number, None], optional
             uncertainty of value, by default None
         uncertainty_type : str, optional
-            type of uncertainty. Quantity uncertainty type must come from [CRIPT Controlled Vocabulary](), by default ""
+            type of uncertainty. Quantity uncertainty type must come from
+            [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/uncertainty_type), by default ""
 
         Examples
         --------
@@ -113,7 +115,7 @@ def set_key_unit(self, new_key: str, new_unit: str) -> None:
         """
         set the Quantity key and unit attributes
 
-        Quantity key must come from [CRIPT Controlled Vocabulary]()
+        Quantity key must come from [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/quantity_key)
 
         Examples
         --------
@@ -124,7 +126,8 @@ def set_key_unit(self, new_key: str, new_unit: str) -> None:
         Parameters
         ----------
         new_key : str
-            new Quantity key. Quantity key must come from [CRIPT Controlled Vocabulary]()
+            new Quantity key. Quantity key must come from
+            [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/quantity_key)
         new_unit : str
             new unit
 
@@ -235,7 +238,8 @@ def set_uncertainty(self, uncertainty: Optional[Number], type: str) -> None:
 
         Uncertainty and uncertainty type are set at the same time to keep the value and type in sync
 
-        `uncertainty_type` must come from [CRIPT Controlled Vocabulary]()
+        `uncertainty_type` must come from
+        [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/uncertainty_type)
 
         Examples
         --------
@@ -248,7 +252,8 @@ def set_uncertainty(self, uncertainty: Optional[Number], type: str) -> None:
         uncertainty : Number
             uncertainty value
         type : str
-            type of uncertainty, uncertainty_type must come from [CRIPT Controlled Vocabulary]()
+            type of uncertainty, uncertainty_type must come from
+            [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/uncertainty_type)
 
         Returns
         -------

src/cript/nodes/supporting_nodes/file.py

@@ -139,7 +139,8 @@ def __init__(self, name: str, source: str, type: str, extension: str, data_dicti
         source: str
             link or path to local file
         type: str
-            Pick a file type from CRIPT controlled vocabulary [File types]()
+            Pick a file type from CRIPT controlled vocabulary
+            [File types](https://app.criptapp.org/vocab/file_type)
         extension:str
             file extension
         data_dictionary:str
@@ -298,7 +299,7 @@ def type(self) -> str:
         Returns
         -------
         file type: str
-            file type must come from [CRIPT controlled vocabulary]()
+            file type must come from [CRIPT controlled vocabulary](https://app.criptapp.org/vocab/file_type)
         """
         return self._json_attrs.type