labfreed 0.0.5__py3-none-any.whl → 0.2.0b0__py3-none-any.whl

labfreed/TREXExtension/uncertainty.py

@@ -1,32 +0,0 @@
-from math import floor, log10, pow
-
-def to_significant_digits_str(x:int|float, uncertainty:float|int) -> str:
-    if uncertainty == None:
-        if isinstance(x, float):
-            Warning(f'Uncertainty was given as none. Returning unrounded number')
-            return str(x)
-        else:
-            uncertainty = 1
-
-    
-    log_least_significant_digit = floor(log10(uncertainty))
-    digits = -log_least_significant_digit
-    
-    x_significant = round(x, digits)
-    
-    if digits <= 0:
-        return str(int(x_significant))
-    else:
-        return str(x_significant)
-        
-
-
-if __name__ == "__main__":
-    print(to_significant_digits_str(111111.1111111, 1000))
-    print(to_significant_digits_str(111111.1111111, 100))
-    print(to_significant_digits_str(111111.1111111, 10))
-    print(to_significant_digits_str(111111.1111111, 1))
-    print(to_significant_digits_str(111111.1111111, 0.1))
-    print(to_significant_digits_str(111111.1111111, 0.01))
-    print(to_significant_digits_str(111111.1111111, 0.001))
-    print(to_significant_digits_str(111111.1111111, 0.0001))

labfreed/TREXExtension/unit_utilities.py

@@ -1,143 +0,0 @@
-from typing import Tuple
-from typing_extensions import Annotated 
-from pydantic import BaseModel, AfterValidator
-import quantities as pq
-from quantities import Quantity, UnitQuantity, units, dimensionless
-from  .uncertainty import to_significant_digits_str
-            
-                
-
-def validate_unit(unit_name:str) -> str :
-    """
-    Pydantic validator function for the unit.
-    Checks if the unit is a valid unit.
-    
-
-    Args:
-        unit (str): unit symbol, e.g. 'kg'
-
-    Returns:
-        str: the input unit. 
-        
-    Errors:
-        raises an AssertionError if validation fails
-    """
-    if hasattr(pq, unit_name):
-        return unit_name
-    else:
-        assert False
-
-
-class PydanticUncertainQuantity(BaseModel):
-    data:int|float
-    unit_name: Annotated[str, AfterValidator(validate_unit)]
-    unit_symbol: str
-    uncertainty:float|None=None
-    
-    @property
-    def for_display(self):
-        return self.__str__()
-    
-    def as_strings(self):
-        unit_symbol = self.unit_symbol
-        if unit_symbol == "dimensionless":
-            unit_symbol = ""
-        s = ''
-
-        val_str = to_significant_digits_str(self.data, self.uncertainty)
-        return f"{val_str}", f"{unit_symbol}", f"{val_str} {unit_symbol}"
-        
-    
-    
-    def __str__(self):
-        unit_symbol = self.unit_symbol
-        if unit_symbol == "dimensionless":
-            unit_symbol = ""
-        
-        s = f"{to_significant_digits_str(self.data, self.uncertainty)} {unit_symbol}" 
-        return s
-    
-    
-unit_map = [
-    ('MGM', units.milligram),
-    ('GRM', units.gram),
-    ('KGM', units.kilogram),
-    
-    ('CEL', units.celsius),
-    
-    ('LTR', units.liter),
-    ('MLT', units.milliliter),
-
-    ('C34', units.mole),
-    ('D43',units.atomic_mass_unit),
-    
-    ('1', units.dimensionless),
-    ('C62', units.dimensionless),
-    
-    ('BAR',units.bar),
-    ('MBR',units.millibar),
-    ('KBA',units.kilobar),
-    
-    ('RPM', units.rpm),
-    
-    ('HTZ', units.hertz),
-    ('KHZ', units.kilohertz),
-    ('MHZ',units.megahertz),
-    
-    ('SEC', units.second),
-    ('MIN', units.minute),
-    ('HUR', units.hour),
-    
-    ('MTR', units.meter)
-    
-]      
-    
-    
-def quantity_from_UN_CEFACT(value:str, unit_UN_CEFACT) -> PydanticUncertainQuantity:
-    """ 
-    Maps units from https://unece.org/trade/documents/revision-17-annexes-i-iii
-    to an object of the quantities library https://python-quantities.readthedocs.io/en/latest/index.html 
-    """
-    # cast to numeric type. try int first, which will fail if string has no decimals.
-    # nothing to worry yet: try floast next. if that fails the input was not a str representation of a number
-    try:
-        value_out = int(value)
-    except ValueError:
-        try: 
-            value_out = float(value)
-        except ValueError as e:
-            raise Exception(f'Input {value} is not a str representation of a number') from e
-        
-    d = {um[0]: um[1] for um in unit_map}
-    
-    unit = d.get(unit_UN_CEFACT)
-    if not unit:
-        raise NotImplementedError(f"lookup for unit {unit} not implemented")
-    out = PydanticUncertainQuantity(data=value_out, unit_name=unit.name, unit_symbol=unit.symbol)
-
-    return out
-
-
-def quantity_to_UN_CEFACT(value:PydanticUncertainQuantity ) -> Tuple[int|float, str]:    
-    d = {um[1].symbol: um[0] for um in unit_map}
-    
-    unit_un_cefact = d.get(value.unit_symbol)
-    if not unit_un_cefact:
-        raise NotImplementedError(f"lookup for unit {value.unit_symbol} not implemented")
-    return value.data, unit_un_cefact
-    
-    
-    
-
-
-
-        
-        
-        
-if __name__ == "__main__":
-    pass
-                
-        
-        
-
-    

labfreed/validation.py

@@ -1,71 +0,0 @@
-from pydantic import BaseModel, Field, PrivateAttr
-from typing import List, Set, Tuple
-
-
-domain_name_pattern = r"(?!-)([A-Za-z0-9-]{1,63}(?<!-)\.)+[A-Za-z]{2,63}"
-hsegment_pattern = r"[A-Za-z0-9_\-\.~!$&'()+,:;=@]|%[0-9A-Fa-f]{2}"
-
-
-class ValidationWarning(BaseModel):
-    source:str 
-    type: str
-    problem_msg:str
-    recommendation_msg: str = ""
-    highlight:str = "" #this can be used to highlight problematic parts
-    highlight_sub:list[str] = Field(default_factory=list())
-    
-    
-
-
-class BaseModelWithWarnings(BaseModel):
-    """ Extension of Pydantic BaseModel, so that validator can issue warnings.
-    The purpose of that is to allow only minimal validation but on top check for stricter recommendations"""
-    _warnings: list[ValidationWarning] = PrivateAttr(default_factory=list)
-
-    def add_warning(self, *, msg: str, type:str, recommendation:str="", source:str="", highlight_pattern="", highlight_sub=None):
-        if not highlight_sub:
-            highlight_sub = []
-        w = ValidationWarning(problem_msg=msg, recommendation_msg=recommendation, source=source, type=type, highlight=highlight_pattern, highlight_sub=highlight_sub)
-        if not w in self._warnings:
-            self._warnings.append(w)
-
-    def get_warnings(self) -> list[ValidationWarning]:
-        return self._warnings
-
-    def clear_warnings(self):
-        self._warnings.clear()
-    
-    
-# Function to extract warnings from a model and its nested models
-def extract_warnings(model: BaseModelWithWarnings, parent_name: str = "", visited: Set[int] = None) -> List[ValidationWarning]:
-    """
-    Recursively extract warnings from a Pydantic model and its nested fields.
-    
-    :param model: The Pydantic model instance to inspect.
-    :param parent_name: The name of the parent model to track the path.
-    :return: List of tuples containing (model name, warning message).
-    """                   
-    if visited is None:
-        visited = set()
-
-    model_id = id(model)
-    if model_id in visited:
-        return []
-    visited.add(model_id)
-    
-    warnings_list = [(parent_name or model.__class__.__name__, model_id,  warning) for warning in model.get_warnings()]
-
-    for field_name, field in model.__fields__.items():
-        full_path = f"{parent_name}.{field_name}" if parent_name else field_name
-        value = getattr(model, field_name)
-
-        if isinstance(value, BaseModelWithWarnings):
-            warnings_list.extend(extract_warnings(value, full_path, visited))
-        elif isinstance(value, list):
-            for index, item in enumerate(value):
-                if isinstance(item, BaseModelWithWarnings):
-                    list_path = f"{full_path}[{index}]"
-                    warnings_list.extend(extract_warnings(item, list_path, visited))
-
-    return warnings_list
-

labfreed-0.0.5.dist-info/METADATA

@@ -1,34 +0,0 @@
-Metadata-Version: 2.4
-Name: labfreed
-Version: 0.0.5
-Summary: Python implementation of LabFREED building blocks
-Author-email: Reto Thürer <thuerer.r@buchi.com>
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown
-License-Expression: MIT
-Classifier: Programming Language :: Python :: 3
-Classifier: Operating System :: OS Independent
-License-File: LICENSE
-
-# LabFREED for Python
-
-A python implementation of [LabFREED](www.labfreed.com).
-
-
-
-# Examples:
-
-## Parse a PAC ID
-
-
-## Parse a PAC-ID with extensions
-
-
-
-## Create a PAC-ID
-
-## Create a PAC-ID and T-REX for a titration curve
-
-
-
-

labfreed-0.0.5.dist-info/RECORD

@@ -1,19 +0,0 @@
-labfreed/__init__.py,sha256=z3yAWKlMQqYGwnI20F528XNm0hlpE6qhvvfIkhRuSoI,87
-labfreed/validation.py,sha256=dG-SubAguub67RTvw51xlErkqXbzzq_5rwxJwWg6SfY,2869
-labfreed/DisplayNameExtension/DisplayNameExtension.py,sha256=FlT53u1EntpsLmho6GZtgIWBZBNWkl9STxzJBvojR6M,1033
-labfreed/DisplayNameExtension/base36.py,sha256=2lwmEMWm8qrFJkcrP-nMPwS0eCm2THhCJ3Vk-TdGQg0,2455
-labfreed/PAC_CAT/__init__.py,sha256=frcCV1k9oG9oKj3dpUqdJg1PxRT2RSN_XKdLCPjaYaY,2
-labfreed/PAC_CAT/data_model.py,sha256=hob-WNs2-633LmxQ7Ot3RBpcvStYFzdj20QDQZOQyqY,4306
-labfreed/PAC_ID/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-labfreed/PAC_ID/data_model.py,sha256=DKU9Rptl9DcxiUdFf28XMyy4YcGUG7-a1EWuEpIFXVc,7931
-labfreed/PAC_ID/parse.py,sha256=t38ABXZ0siUVDW5oEDmkF7uQ6iSX8Dbkeg-lWNlOgWA,5011
-labfreed/PAC_ID/serialize.py,sha256=0BhF7aXGlLpr312lkBvl1O5fXDFZeLLPgSBddO9Y86Q,1963
-labfreed/PAC_ID/well_known_segment_keys.py,sha256=zrzMvvS42urPpiwinI-IhHPgT3r86zEBl4TlEMOfzbU,338
-labfreed/TREXExtension/data_model.py,sha256=eT4KyQklTO6m-wA28KyJ8wzT8ONhG3fOB3JU6b19ScY,8011
-labfreed/TREXExtension/parse.py,sha256=Y04UK1KlMLG9tE_d7cQOiAJpm8Zh49UoJYjY7Lfqa4Y,1812
-labfreed/TREXExtension/uncertainty.py,sha256=l3WxrLnWTQYfX28gFisXwDcVPvT8bCAd4q6Xl02dRdE,1117
-labfreed/TREXExtension/unit_utilities.py,sha256=WzrC1CZMgBccxADXFP6nLkMWVDqCCkNb3trPyt3BvF8,3826
-labfreed-0.0.5.dist-info/licenses/LICENSE,sha256=gHFOv9FRKHxO8cInP3YXyPoJnuNeqrvcHjaE_wPSsQ8,1100
-labfreed-0.0.5.dist-info/WHEEL,sha256=_2ozNFCLWc93bK4WKHCO-eDUENDlo-dgc9cU3qokYO4,82
-labfreed-0.0.5.dist-info/METADATA,sha256=T_mGIHKlIMASuQnbuW_L4XXqUuxUc0DB6yGOcI-N-wE,594
-labfreed-0.0.5.dist-info/RECORD,,