Major refactor for first stable release (#21)

* added example and parser

* fixed stash error

* API update

* fixed test

* API update

* fixed parser

* API update

* functionality now in PlateManager class

* Refactor import statements for PlateManager class

* Refactor import statements for PlateManager class

---------

Co-authored-by: sdRDM Bot <sdRDM@bot.com>

.github/workflows/mkdocs.yml

@@ -21,5 +21,5 @@ jobs:
         with:
           path: .cache
           key: ${{ github.ref }}
-      - run: pip install mkdocs-material
+      - run: pip install mkdocs-material mkdocs-plotly-plugin mkdocstrings-python
       - run: mkdocs gh-deploy --force

.github/workflows/tests.yml

@@ -9,7 +9,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
@@ -27,4 +27,4 @@ jobs:
 
       - name: Run tests with pytest
         run: |
-          poetry run pytest
+          poetry run pytest

.gitignore

@@ -110,6 +110,9 @@ poetry.lock
 #   https://pdm.fming.dev/#use-with-ide
 .pdm.toml
 
+# DS_Store files
+.DS_Store
+
 # PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
 __pypackages__/
 

MTPHandler/__init__.py

@@ -1,10 +1,3 @@
 import os
 
-from .core.blankstate import BlankState
-from .core.initcondition import InitCondition
-from .core.photometricmeasurement import PhotometricMeasurement
-from .core.plate import Plate
-from .core.protein import Protein
-from .core.reactant import Reactant
-from .core.species import Species
-from .core.well import Well
+from MTPHandler.plate_manager import PlateManager

MTPHandler/ioutils/calipytion.py

@@ -1,46 +1,42 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, List, Union
+from typing import List, Optional
 
 import numpy as np
-from calipytion.core import Sample, SignalType, Standard
+from calipytion.model import Sample, SignalType, Standard, UnitDefinition
 from calipytion.tools.calibrator import Calibrator
 
-from MTPHandler.core.well import Well
-
-if TYPE_CHECKING:
-    from MTPHandler.core import Plate, Protein, Reactant
+from MTPHandler.model import Molecule, Plate, Protein, Species, Well
+from MTPHandler.tools import (
+    get_measurement,
+    get_species_condition,
+    measurement_is_blanked_for,
+    well_contains_species,
+)
 
 
 def _get_standard_wells(
     plate: Plate,
-    species: Union[Protein, Reactant],
-    wavelength: int,
+    species: Species | Molecule | Protein,
+    wavelength: float,
 ) -> List[Well]:
-    # handel wavelength
-    if not wavelength:
-        if len(plate.measured_wavelengths) == 1:
-            wavelength = plate.measured_wavelengths[0]
-        else:
-            raise AttributeError(
-                f"Argument 'wavelength' must be provided. Measured wavelengths are: {plate.measured_wavelengths}"
-            )
-
     # Subset of wells, that contain specified species, do not contain a protein, and are blanked
     protein_ids = [
         species.id for species in plate.species if isinstance(species, Protein)
     ]
 
     standard_wells = []
     for well in plate.wells:
-        if not well._contains_species(species.id):
+        if not well_contains_species(well, species.id):
             continue
 
-        if any([well._contains_species(catalyst_id) for catalyst_id in protein_ids]):
+        if any(
+            [well_contains_species(well, catalyst_id) for catalyst_id in protein_ids]
+        ):
             continue
 
-        measurement = well.get_measurement(wavelength)
-        if measurement.is_blanked_for(species.id):
+        measurement = get_measurement(well, wavelength)
+        if measurement_is_blanked_for(measurement, species.id):
             standard_wells.append(well)
 
         # Add wells with zero concentration to standard wells
@@ -57,9 +53,9 @@ def _get_standard_wells(
 
 def map_to_standard(
     plate: Plate,
-    species: Union[Protein, Reactant],
-    wavelength: int = None,
-    signal_type: str = "abs",
+    species: Species | Molecule | Protein,
+    wavelength: float,
+    signal_type: SignalType = SignalType.ABSORBANCE,
 ) -> Standard:
     standard_wells = _get_standard_wells(
         plate=plate,
@@ -71,14 +67,15 @@ def map_to_standard(
     samples = []
     phs = []
     for well in standard_wells:
-        condition = well._get_species_condition(species.id)
-        measurement = well.get_measurement(wavelength)
+        condition = get_species_condition(well, species.id)
+        measurement = get_measurement(well, wavelength)
+
         samples.append(
             Sample(
-                id=well.id,
+                # id=well.id,
                 concentration=condition.init_conc,
-                conc_unit=condition.conc_unit,
-                signal=float(np.nanmean(measurement.absorptions)),
+                conc_unit=UnitDefinition(**condition.conc_unit.model_dump()),
+                signal=float(np.nanmean(measurement.absorption)),
             )
         )
         phs.append(well.ph)
@@ -90,27 +87,54 @@ def map_to_standard(
         )
     ph = phs[0]
 
+    if species.ld_id:
+        species_id = species.ld_id
+    else:
+        species_id = species.id
+
+    temp_unit = UnitDefinition(**plate.temperature_unit.model_dump())
+
     # Create standard
     return Standard(
-        species_id=species.id,
-        name=species.name,
+        molecule_id=species_id,
+        molecule_symbol=species.id,
+        molecule_name=species.name,
         wavelength=wavelength,
         signal_type=signal_type,
         samples=samples,
         ph=ph,
         temperature=plate.temperatures[0],
-        temperature_unit=plate.temperature_unit,
-        created=plate.date_measured,
+        temp_unit=temp_unit,
     )
 
 
 def initialize_calibrator(
-    plate: "Plate",
-    species: Union[Protein, Reactant],
-    wavelength: int = None,
+    plate: Plate,
+    wavelength: float,
+    species: Species | Molecule | Protein,
     signal_type: SignalType = SignalType.ABSORBANCE,
-    cutoff: float = None,
+    cutoff: Optional[float] = None,
 ) -> Calibrator:
+    """
+    Initialize a calibrator for a given species.
+
+    Parameters
+    ----------
+    plate : Plate
+        The plate containing the wells.
+    wavelength : float
+        The wavelength of the measurements.
+    species : Species | Molecule | Protein
+        The species to calibrate.
+    signal_type : SignalType, optional
+        The type of signal to calibrate, by default SignalType.ABSORBANCE.
+
+    Returns
+    -------
+    Calibrator
+        The initialized calibrator for creating a calibration curve.
+
+    """
     standard = map_to_standard(
         plate=plate,
         species=species,