diff --git a/src/cript/nodes/primary_nodes/data.py b/src/cript/nodes/primary_nodes/data.py index 4fb61e0e3..acd2380ff 100644 --- a/src/cript/nodes/primary_nodes/data.py +++ b/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 ---------- diff --git a/src/cript/nodes/subobjects/citation.py b/src/cript/nodes/subobjects/citation.py index e3aae8bac..d574e630a 100644 --- a/src/cript/nodes/subobjects/citation.py +++ b/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 ---------- diff --git a/src/cript/nodes/subobjects/computational_forcefield.py b/src/cript/nodes/subobjects/computational_forcefield.py index 45416f0da..7f9993e8d 100644 --- a/src/cript/nodes/subobjects/computational_forcefield.py +++ b/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 diff --git a/src/cript/nodes/subobjects/condition.py b/src/cript/nodes/subobjects/condition.py index 27f6995cc..92bf513b1 100644 --- a/src/cript/nodes/subobjects/condition.py +++ b/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 diff --git a/src/cript/nodes/subobjects/equipment.py b/src/cript/nodes/subobjects/equipment.py index 625ae2648..a79aaa45a 100644 --- a/src/cript/nodes/subobjects/equipment.py +++ b/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 diff --git a/src/cript/nodes/subobjects/ingredient.py b/src/cript/nodes/subobjects/ingredient.py index b4f12020e..2e02ee82e 100644 --- a/src/cript/nodes/subobjects/ingredient.py +++ b/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 diff --git a/src/cript/nodes/subobjects/parameter.py b/src/cript/nodes/subobjects/parameter.py index 55726e7fd..10b28c6ea 100644 --- a/src/cript/nodes/subobjects/parameter.py +++ b/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 diff --git a/src/cript/nodes/subobjects/property.py b/src/cript/nodes/subobjects/property.py index e112a22f3..f6f137a4c 100644 --- a/src/cript/nodes/subobjects/property.py +++ b/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 diff --git a/src/cript/nodes/subobjects/quantity.py b/src/cript/nodes/subobjects/quantity.py index 1d9613f9d..4653215e1 100644 --- a/src/cript/nodes/subobjects/quantity.py +++ b/src/cript/nodes/subobjects/quantity.py @@ -69,7 +69,8 @@ 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 @@ -77,7 +78,8 @@ def __init__(self, key: str, value: Number, unit: str, uncertainty: Optional[Num 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 ------- diff --git a/src/cript/nodes/supporting_nodes/file.py b/src/cript/nodes/supporting_nodes/file.py index 2fbdc36ff..fccce85be 100644 --- a/src/cript/nodes/supporting_nodes/file.py +++ b/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