String units (#34)

* Remove ontomaps.toml and refactor unit definitions in predefined.py to use string representations instead of UnitDefinition instances. This simplifies the unit handling and eliminates the need for the deleted units.py file.

* Refactor unit handling across readers and models to use string representations instead of UnitDefinition instances. This change enhances clarity and consistency in unit management, while also updating related tests and example data for improved accuracy.

* Update version number in pyproject.toml to 0.9.18

Author: haeussma

chromatopy/ioutils/enzymeml.py

@@ -2,6 +2,7 @@
 from enum import Enum
 
 from calipytion.tools.calibrator import Calibrator
+from mdmodels.units.annotation import UnitDefinitionAnnot
 from pyenzyme import (
     DataTypes,
     EnzymeMLDocument,
@@ -10,10 +11,8 @@
     SmallMolecule,
 )
 from pyenzyme import Measurement as EnzymeMLMeasurement
-from pyenzyme import UnitDefinition as EnzymeMLUnitDefinition
 
 from ..model import Chromatogram, Measurement
-from ..model import UnitDefinition as UnitDefinition
 from ..tools.analyzer import ChromAnalyzer
 from ..tools.internal_standard import InternalStandard
 from ..tools.molecule import Molecule
@@ -168,13 +167,13 @@ def create_enzymeml(
 
     species_data = list(measurement_data_instances.values())
     for species in species_data:
-        species.time_unit = EnzymeMLUnitDefinition(**time_unit.model_dump())
+        species.time_unit = time_unit.name
 
     enzml_measurement = EnzymeMLMeasurement(
         id=measurement_id,
         name=measurement_id,
         temperature=temp,
-        temperature_unit=EnzymeMLUnitDefinition(**temp_unit.model_dump()),
+        temperature_unit=temp_unit.name,
         ph=ph,
         species_data=list(measurement_data_instances.values()),
     )
@@ -250,10 +249,11 @@ def create_MeasurementData_instances(
         A MeasurementData instance for molecule {species.name} already exists.
         """)
 
-    assert isinstance(species.conc_unit, UnitDefinition), f"""
-    The concentration unit of the molecule {species.name} needs to be defined.
-    Please specify the `conc_unit` attribute of {species.name}.
-    """
+    if not species.conc_unit:
+        raise ValueError(f"""
+        The concentration unit of the molecule {species.name} needs to be defined.
+        Please specify the `conc_unit` attribute of {species.name}.
+        """)
 
     # Determine the data type based on the species type
     if isinstance(species, ChromProtein):
@@ -263,7 +263,7 @@ def create_MeasurementData_instances(
             species_id=species.id,
             initial=species.init_conc,
             prepared=species.init_conc,
-            data_unit=EnzymeMLUnitDefinition(**species.conc_unit.model_dump()),
+            data_unit=species.conc_unit.name,
             data_type=data_type,
         )
     elif isinstance(species, Molecule):
@@ -272,7 +272,7 @@ def create_MeasurementData_instances(
             species_id=species.id,
             initial=species.init_conc,
             prepared=species.init_conc,
-            data_unit=EnzymeMLUnitDefinition(**species.conc_unit.model_dump()),
+            data_unit=species.conc_unit.name,
             data_type=data_type,
         )
 
@@ -311,29 +311,38 @@ def add_measurements_to_enzymeml(
     ph, temp, time_unit, temp_unit = extract_measurement_conditions(new_measurements)
 
     # Create MeasurementData instances for existing molecules
-    measurement_data_instances = {
-        mol.id: MeasurementData(
+    measurement_data_instances: dict[str, MeasurementData] = {}
+    for mol in molecules:
+        if mol.internal_standard:
+            continue
+        if not mol.conc_unit:
+            raise ValueError(
+                f"Concentration unit is not defined for molecule {mol.name}."
+            )
+
+        measurement_data_instances[mol.id] = MeasurementData(
             species_id=mol.id,
             initial=mol.init_conc,
             prepared=mol.init_conc,
-            data_unit=EnzymeMLUnitDefinition(**mol.conc_unit.model_dump()),  # type: ignore
+            data_unit=mol.conc_unit.name,
             data_type=DataTypes.PEAK_AREA,
-            time_unit=EnzymeMLUnitDefinition(**time_unit.model_dump()),
+            time_unit=time_unit.name,
         )
-        for mol in molecules
-        if not mol.internal_standard
-    }
 
     # Add MeasurementData instances for proteins
     for protein in proteins:
+        if not protein.conc_unit:
+            raise ValueError(
+                f"Concentration unit is not defined for protein {protein.name}."
+            )
         if protein.id not in measurement_data_instances:
             measurement_data_instances[protein.id] = MeasurementData(
                 species_id=protein.id,
                 initial=protein.init_conc,
                 prepared=protein.init_conc,
-                data_unit=EnzymeMLUnitDefinition(**protein.conc_unit.model_dump()),  # type: ignore
+                data_unit=protein.conc_unit.name,
                 data_type=DataTypes.CONCENTRATION,
-                time_unit=EnzymeMLUnitDefinition(**time_unit.model_dump()),
+                time_unit=time_unit.name,
             )
 
     # Convert new measurements to MeasurementData instances
@@ -351,7 +360,7 @@ def add_measurements_to_enzymeml(
         id=measurement_id,
         name=measurement_id,
         temperature=temp,
-        temperature_unit=EnzymeMLUnitDefinition(**temp_unit.model_dump()),
+        temperature_unit=temp_unit.name,
         ph=ph,
         species_data=list(measurement_data_instances.values()),
     )
@@ -431,6 +440,12 @@ def add_measurement_to_MeasurementData(
         if species_id in measured_once:
             # Handle molecules with peaks
             for measurement in measurements:
+                dilution_factor = (
+                    measurement.dilution_factor
+                    if measurement.dilution_factor is not None
+                    else 1.0
+                )
+
                 for chrom in measurement.chromatograms:
                     add_data(
                         measurement_data=meas_data,
@@ -439,7 +454,7 @@ def add_measurement_to_MeasurementData(
                         calibrators=calibrators,
                         calibrator_type=strategy,
                         extrapolate=extrapolate,
-                        dilution_factor=measurement.dilution_factor,
+                        dilution_factor=dilution_factor,
                     )
         else:
             # Handle proteins or molecules without peaks - add zero values for molecules with retention times
@@ -626,7 +641,7 @@ def setup_internal_calibrators(
                 standard_molecule_id=internal_standard.id,
                 molecule_init_conc=molecule.init_conc,
                 standard_init_conc=internal_standard.init_conc,
-                molecule_conc_unit=molecule.conc_unit,
+                molecule_conc_unit=molecule.conc_unit.name,
                 molecule_t0_signal=peak_analyte.area,
                 standard_t0_signal=peak_internal_standard.area,
             )
@@ -636,7 +651,7 @@ def setup_internal_calibrators(
 
 def extract_measurement_conditions(
     measurements: list[Measurement],
-) -> tuple[float, float, UnitDefinition, UnitDefinition]:
+) -> tuple[float, float, UnitDefinitionAnnot, UnitDefinitionAnnot]:
     """Asserts and extracts the measurement conditions from a list of Measurement instances.
 
     Args: