Merge pull request #20 from FAIRChemistry/dev

Dev

.gitignore

@@ -25,6 +25,7 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
+.pyrightconfig.json
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

MTPHandler/core/blankstate.py

@@ -41,7 +41,7 @@ class BlankState(
         default="https://github.com/FAIRChemistry/MTPHandler"
     )
     _commit: Optional[str] = PrivateAttr(
-        default="862fbd059c9b36c968c7988ff728719b3737ac24"
+        default="b67724f080afb13c3b78cd2a559646f8b3f2e6e7"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

MTPHandler/core/initcondition.py

@@ -45,7 +45,7 @@ class InitCondition(
         default="https://github.com/FAIRChemistry/MTPHandler"
     )
     _commit: Optional[str] = PrivateAttr(
-        default="862fbd059c9b36c968c7988ff728719b3737ac24"
+        default="b67724f080afb13c3b78cd2a559646f8b3f2e6e7"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

MTPHandler/core/photometricmeasurement.py

@@ -77,7 +77,7 @@ class PhotometricMeasurement(
         default="https://github.com/FAIRChemistry/MTPHandler"
     )
     _commit: Optional[str] = PrivateAttr(
-        default="862fbd059c9b36c968c7988ff728719b3737ac24"
+        default="b67724f080afb13c3b78cd2a559646f8b3f2e6e7"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

MTPHandler/core/plate.py

@@ -20,6 +20,7 @@
 from plotly.subplots import make_subplots
 from pydantic import PrivateAttr, model_validator
 from pydantic_xml import attr, element
+from rich.jupyter import print
 from sdRDM.base.datatypes import Identifier, Unit
 from sdRDM.base.listplus import ListPlus
 from sdRDM.tools.utils import elem2dict
@@ -123,7 +124,7 @@ class Plate(
         default="https://github.com/FAIRChemistry/MTPHandler"
     )
     _commit: Optional[str] = PrivateAttr(
-        default="862fbd059c9b36c968c7988ff728719b3737ac24"
+        default="b67724f080afb13c3b78cd2a559646f8b3f2e6e7"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
@@ -343,7 +344,7 @@ def add_species(
 
         if not id:
             warnings.warn(
-                """No ID provided for species. This might cause issues when referencing the species. 
+                """No ID provided for species. This might cause issues when referencing the species.
                 Consider providing an ID which references the species such as a Chebi ID."""
             )
 
@@ -475,8 +476,8 @@ def assign_species_to_all(
             )
 
         print(
-            f"Assigned {species.name} ({species.id}) with {init_conc} {conc_unit} to"
-            " all wells."
+            f"Assigned [bold magenta]{species.name}[/] ({species.id}) with"
+            f" {init_conc} {conc_unit} to all wells."
         )
 
     def assign_species_to_columns(
@@ -511,7 +512,7 @@ def assign_species_to_columns(
             assert len(init_concs) == len(
                 wells
             ), f"""
-            Number of initial concentrations ({len(init_concs)}) does not match number 
+            Number of initial concentrations ({len(init_concs)}) does not match number
             of wells ({len(wells)}) in columns ({column_ids}).
             """
 
@@ -527,8 +528,8 @@ def assign_species_to_columns(
                 )
 
         print(
-            f"Assigned {species.name} ({species.id}) with concentrations of"
-            f" {init_concs} {conc_unit} to columns {column_ids}."
+            f"Assigned [bold magenta]{species.name}[/] ({species.id}) with"
+            f" concentrations of {init_concs} {conc_unit} to columns {column_ids}."
         )
 
     def assign_species_to_rows(
@@ -557,7 +558,7 @@ def assign_species_to_rows(
             assert len(init_concs) == len(
                 wells
             ), f"""
-            Number of initial concentrations ({len(init_concs)}) does not match number 
+            Number of initial concentrations ({len(init_concs)}) does not match number
             of wells ({len(wells)}) in rows ({row_ids}).
             """
 
@@ -573,8 +574,8 @@ def assign_species_to_rows(
                 )
 
         print(
-            f"Assigned {species.name} ({species.id}) with {init_conc} {conc_unit}"
-            f" to rows {row_ids}."
+            f"Assigned [bold magenta]{species.name}[/] ({species.id}) with"
+            f" {init_conc} {conc_unit} to rows {row_ids}."
         )
 
     @staticmethod
@@ -598,56 +599,6 @@ def _handle_blank_status(
                 contributes_to_signal=contributes,
             )
 
-    def _handle_wavelength(self) -> float:
-        if len(self.measured_wavelengths) == 1:
-            return self.measured_wavelengths[0]
-
-        else:
-            raise AttributeError(
-                "Argument 'wavelength' must be provided. Measured wavelengths are:"
-                f" {self.measured_wavelengths}"
-            )
-
-    def get_wells(
-        self,
-        wavelength: int = None,
-    ) -> List[Well]:
-        if not wavelength:
-            wavelength = self._handle_wavelength()
-
-    def get_well_by_id(self, _id: str) -> Well:
-        for well in self.wells:
-            if well.id == _id.upper():
-                return well
-
-        raise ValueError(f"No well found with id {_id}")
-
-    def _get_wells_by_column_id(self, column_id: int, wavelength: int) -> Well:
-        x_pos = column_id - 1
-        y_positions = [
-            well.y_pos
-            for well in self.wells
-            if well.x_pos == x_pos and well.wavelength == wavelength
-        ]
-
-        return [self._get_well_by_xy(x_pos, y_pos, wavelength) for y_pos in y_positions]
-
-    def _get_wells_by_row_id(self, row_id: str) -> List[Well]:
-        return [well for well in self.wells if row_id in well.id and well.measurements]
-
-    def _get_well_by_xy(self, x_pos: int, y_pos: int, wavelength: int) -> Well:
-        for well in self.wells:
-            if (
-                well.x_pos == x_pos
-                and well.y_pos == y_pos
-                and well.wavelength == wavelength
-            ):
-                return well
-
-        raise ValueError(
-            f"No well found with x position {x_pos} and y position {y_pos}"
-        )
-
     def assign_species_to_all_except(
         self,
         well_ids: List[str],
@@ -672,8 +623,8 @@ def assign_species_to_all_except(
             )
 
         print(
-            f"Assigned {species.name} ({species.id}) with {init_conc} {conc_unit}"
-            f" to all wells except {well_ids}."
+            f"Assigned [bold magenta]{species.name}[/] ({species.id}) with"
+            f" {init_conc} {conc_unit} to all wells except {well_ids}."
         )
 
     def assign_species_from_spreadsheet(
@@ -730,8 +681,8 @@ def assign_species_from_spreadsheet(
             )
 
         print(
-            f"Assigned initial concentrations from {path} to"
-            f" {species.name} ({species.id})."
+            f"Assigned initial concentrations for [bold magenta]{species.name}[/]"
+            f" ({species.id}) from {path}."
         )
 
     def get_well(self, _id: str) -> Well:
@@ -804,7 +755,7 @@ def blank_species(
         if len(wells) == 0:
             print(
                 f"{species.name} ({species.id}) at {wavelength} nm does not contribute"
-                " to signal."
+                " to signal. Is the specified wavelength correct?print"
             )
 
         if len(blanking_wells) == 0:
@@ -815,7 +766,7 @@ def blank_species(
 
         # get mapping of concentration to blank wells
         conc_blank_mapping = self._get_conc_blank_mapping(
-            wells=blanking_wells, species_id=species, wavelength=wavelength
+            wells=blanking_wells, species=species, wavelength=wavelength
         )
 
         # apply to wells where species is present in respective concentration
@@ -846,14 +797,14 @@ def blank_species(
 
         print(f"Blanked {len(blanked_wells)} wells containing {species.name}.\n")
 
-    def visualize(self, zoom: bool = False, wavelengths: float = None):
+    def visualize(self, zoom: bool = False, wavelengths: list[float] = []):
         if zoom:
             shared_yaxes = False
         else:
             shared_yaxes = True
 
         if not wavelengths:
-            wavelengths = self.wells[0].measurements[0].wavelength
+            wavelengths = [self.wells[0].measurements[0].wavelength]
 
         if not isinstance(wavelengths, list):
             wavelengths = [wavelengths]
@@ -893,7 +844,7 @@ def visualize(self, zoom: bool = False, wavelengths: float = None):
             plot_bgcolor="white",
             hovermode="x",
             title=dict(
-                text=f"{self.temperatures[0]} °{self.temperature_unit.name}",
+                text=f"{self.temperatures[0]} {self.temperature_unit.name}",
             ),
             margin=dict(l=20, r=20, t=100, b=20),
         )
@@ -926,7 +877,7 @@ def _get_conc_blank_mapping(
     ) -> Dict[float, List[Well]]:
         blank_measurement_mapping = defaultdict(list)
         for well in wells:
-            condition = well._get_species_condition(species)
+            condition = well._get_species_condition(species.id)
 
             blank_measurement_mapping[condition.init_conc].append(
                 well.get_measurement(wavelength).absorption
@@ -935,10 +886,13 @@ def _get_conc_blank_mapping(
         conc_mean_blank_mapping = {}
         for conc, absorptions in blank_measurement_mapping.items():
             mean_absorption = np.nanmean(absorptions)
+            std_absorption = np.nanstd(absorptions)
+            std_perc = abs(std_absorption / mean_absorption) * 100
             print(
-                f"Mean absorption of {species.name} ({species.id}) at"
-                f" {conc} {condition.conc_unit.name}: {mean_absorption:.4f} calculated"
-                f" based on wells {[well.id for well in wells]}."
+                f"Mean absorption of [bold magenta]{species.name}[/] ({species.id}) at"
+                f" {conc} {condition.conc_unit.name}: {mean_absorption:.4f} ±"
+                f" {std_perc:.0f}%  calculated based on wells"
+                f" {[well.id for well in wells]}."
             )
             conc_mean_blank_mapping[conc] = mean_absorption
 

MTPHandler/core/protein.py

@@ -49,7 +49,7 @@ class Protein(
         default="https://github.com/FAIRChemistry/MTPHandler"
     )
     _commit: Optional[str] = PrivateAttr(
-        default="862fbd059c9b36c968c7988ff728719b3737ac24"
+        default="b67724f080afb13c3b78cd2a559646f8b3f2e6e7"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

MTPHandler/core/species.py

@@ -43,7 +43,7 @@ class Species(
         default="https://github.com/FAIRChemistry/MTPHandler"
     )
     _commit: Optional[str] = PrivateAttr(
-        default="862fbd059c9b36c968c7988ff728719b3737ac24"
+        default="b67724f080afb13c3b78cd2a559646f8b3f2e6e7"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

MTPHandler/core/well.py

@@ -82,7 +82,7 @@ class Well(
         default="https://github.com/FAIRChemistry/MTPHandler"
     )
     _commit: Optional[str] = PrivateAttr(
-        default="862fbd059c9b36c968c7988ff728719b3737ac24"
+        default="b67724f080afb13c3b78cd2a559646f8b3f2e6e7"
     )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)

MTPHandler/readers/factory.py

@@ -21,6 +21,7 @@ def read(
         from MTPHandler.readers.megellan_parser import read_magellan
         from MTPHandler.readers.multiskan_spectrum_parser import read_multiskan_spectrum
         from MTPHandler.readers.spectramax_parser import read_spectramax
+        from MTPHandler.readers.tekan_spark_parser import read_tekan_spark
 
         try:
             return read_magellan(
@@ -42,7 +43,7 @@ def read(
                 temperature=temperature,
                 temperature_unit=temperature_unit,
             )
-        except ValueError:
+        except Exception:
             pass
 
         try:
@@ -52,7 +53,16 @@ def read(
                 ph=ph,
                 time_unit=time_unit,
             )
-        except ValueError:
+        except Exception:
+            pass
+
+        try:
+            return read_tekan_spark(
+                cls=cls,
+                path=path,
+                ph=ph,
+            )
+        except Exception:
             pass
 
         raise ValueError("Could not read file with implemented readers.")