Merge branch 'fix-units-refactoring' into develop

src/sbmlsim/data.py

@@ -9,7 +9,7 @@
 
 from sbmlsim.combine import mathml
 from sbmlsim.result import XResult
-from sbmlsim.units import DimensionalityError, Quantity, UnitRegistry
+from sbmlsim.units import DimensionalityError, Quantity, UnitRegistry, UnitsInformation
 from sbmlsim.utils import deprecated
 
 
@@ -162,22 +162,22 @@ def get_data(self, to_units: str = None):
                 logger.error(error_msg)
                 raise KeyError(error_msg)
             try:
-                self.unit = dset.udict[uindex]
+                self.unit = dset.uinfo[uindex]
             except KeyError as err:
                 logger.error(
                     f"Units missing for key '{uindex}' in dataset: "
                     f"'{self.dset_id}'. Add missing units to dataset."
                 )
                 raise err
-            x = dset[self.index].values * dset.ureg(dset.udict[uindex])
+            x = dset[self.index].values * dset.uinfo.ureg(dset.uinfo[uindex])
 
         elif self.dtype == Data.Types.TASK:
             # read results of task
-            xres = self.experiment.results[self.task_id]  # type: XResult
+            xres: XResult = self.experiment.results[self.task_id]
             if not isinstance(xres, XResult):
                 raise ValueError("Only Result objects supported in task data.")
 
-            self.unit = xres.udict[self.index]
+            self.unit = xres.uinfo[self.index]
             # FIXME: complete data must be kept
             # print(xres)
             x = xres.dim_mean(self.index)
@@ -240,7 +240,7 @@ class DataSeries(pd.Series):
     """DataSet - a pd.Series with additional unit information."""
 
     # additional properties
-    _metadata = ["udict", "ureg"]
+    _metadata = ["uinfo"]
 
     @property
     def _constructor(self):
@@ -255,13 +255,11 @@ class DataSet(pd.DataFrame):
     """DataSet.
 
      pd.DataFrame with additional unit information in the form
-    of a unit dictionary 'udict' (Dict[str, str]) mapping column
-    keys to units. The UnitRegistry is the UnitRegistry conversions
-    are calculated on.
+    of UnitInformations.
     """
 
     # additional properties
-    _metadata = ["udict", "ureg"]
+    _metadata = ["uinfo", "Q_"]
 
     @property
     def _constructor(self):
@@ -276,10 +274,9 @@ def get_quantity(self, key: str):
 
         Requires using the numpy data instead of the series.
         """
-        return self.ureg.Quantity(
-            # downcasting !
+        return self.uinfo.ureg.Quantity(
             self[key].values,
-            self.udict[key],
+            self.uinfo[key],
         )
 
     def __repr__(self) -> str:
@@ -303,9 +300,9 @@ def from_df(
            'mean', 'value', 'sd' and 'se' columns
 
         :param df: pandas.DataFrame
-        :param udict: optional unit dictionary
-        :param ureg:
-        :return:
+        :param uinfo: optional units information
+
+        :return: dataset
         """
         if not isinstance(ureg, UnitRegistry):
             raise ValueError(
@@ -318,7 +315,7 @@ def from_df(
             udict = {}
 
         # all units from udict and DataFrame
-        all_udict = {}
+        all_udict: Dict[str, str] = {}
 
         for key in df.columns:
             # handle '*_unit columns'
@@ -381,11 +378,11 @@ def from_df(
                     setattr(df, f"{key}_unit", unit)
 
         dset = DataSet(df)
-        dset.udict = all_udict
-        dset.ureg = ureg
+        dset.uinfo = UnitsInformation(all_udict, ureg=ureg)
+        dset.Q_ = dset.uinfo.ureg.Quantity
         return dset
 
-    def unit_conversion(self, key, factor: Quantity, filter=None):
+    def unit_conversion(self, key, factor: Quantity):
         """Convert the units of the given key in the dataset.
 
         The quantity in the dataset is multiplied with the conversion factor.
@@ -407,14 +404,14 @@ def unit_conversion(self, key, factor: Quantity, filter=None):
         :return: None
         """
         if key in self.columns:
-            if key not in self.udict:
+            if key not in self.uinfo:
                 raise ValueError(
                     f"Unit conversion only possible on keys which have units! "
                     f"No unit defined for key '{key}'"
                 )
 
             # unit conversion and simplification
-            new_quantity = self.ureg.Quantity(self[key], self.udict[key]) * factor
+            new_quantity = self.uinfo.Q_(self[key], self.uinfo[key]) * factor
             new_quantity = new_quantity.to_base_units().to_reduced_units()
 
             # updated values
@@ -425,7 +422,7 @@ def unit_conversion(self, key, factor: Quantity, filter=None):
                 if err_key in self.columns:
                     # error keys not stored in udict, only the base quantity
                     new_err_quantity = (
-                        self.ureg.Quantity(self[err_key], self.udict[key]) * factor
+                        self.uinfo.Q_(self[err_key], self.uinfo[key]) * factor
                     )
                     new_err_quantity = (
                         new_err_quantity.to_base_units().to_reduced_units()
@@ -437,7 +434,7 @@ def unit_conversion(self, key, factor: Quantity, filter=None):
             new_units_str = (
                 str(new_units).replace("**", "^").replace(" ", "")
             )  # '{:~}'.format(new_units)
-            self.udict[key] = new_units_str
+            self.uinfo[key] = new_units_str
 
             if f"{key}_unit" in self.columns:
                 self[f"{key}_unit"] = new_units_str

src/sbmlsim/examples/example_parallel.py

@@ -17,7 +17,7 @@
     ray,
 )
 from sbmlsim.test import MODEL_GLCWB, MODEL_REPRESSILATOR
-from sbmlsim.units import Units
+from sbmlsim.units import Units, UnitsInformation
 
 
 def example_single_actor():
@@ -31,7 +31,7 @@ def example_single_actor():
     # create state file
     r = roadrunner.RoadRunner(str(MODEL_REPRESSILATOR))
     RoadrunnerSBMLModel.set_timecourse_selections(r)
-    udict, ureg = Units.get_units_from_sbml(str(MODEL_REPRESSILATOR))
+    uinfo = UnitsInformation.from_sbml_path(MODEL_REPRESSILATOR)
 
     f_state = tempfile.NamedTemporaryFile(suffix=".dat")
     r.saveState(f_state.name)
@@ -47,7 +47,7 @@ def example_single_actor():
         ]
     )
 
-    tcsim.normalize(udict=udict, ureg=ureg)
+    tcsim.normalize(uinfo=uinfo)
     tc_id = sa._timecourse.remote(tcsim)
     results = ray.get(tc_id)
     return results
@@ -61,7 +61,7 @@ def example_multiple_actors():
     # create state file
     r = roadrunner.RoadRunner(str(MODEL_REPRESSILATOR))
     RoadrunnerSBMLModel.set_timecourse_selections(r)
-    udict, ureg = Units.get_units_from_sbml(str(MODEL_REPRESSILATOR))
+    uinfo = UnitsInformation.from_sbml_path(MODEL_REPRESSILATOR)
 
     f_state = tempfile.NamedTemporaryFile(suffix=".dat")
     r.saveState(f_state.name)
@@ -76,7 +76,7 @@ def example_multiple_actors():
             Timecourse(start=0, end=100, steps=100, changes={"X": 10, "Y": 20}),
         ]
     )
-    tcsim.normalize(udict=udict, ureg=ureg)
+    tcsim.normalize(uinfo=uinfo)
 
     # run simulation on simulators
     tc_ids = [s._timecourse.remote(tcsim) for s in simulators]

src/sbmlsim/examples/example_scan.py

@@ -12,7 +12,7 @@
 def run_scan0d() -> XResult:
     """Perform a parameter 0D scan, i.e., simple simulation"""
     simulator = SimulatorSerial(model=MODEL_REPRESSILATOR)
-    Q_ = simulator.ureg.Quantity
+    Q_ = simulator.Q_
 
     scan0d = ScanSim(
         simulation=TimecourseSim(
@@ -37,7 +37,7 @@ def run_scan1d() -> XResult:
     Scanning a single parameter.
     """
     simulator = SimulatorSerial(model=MODEL_REPRESSILATOR)
-    Q_ = simulator.ureg.Quantity
+    Q_ = simulator.Q_
 
     scan1d = ScanSim(
         simulation=TimecourseSim(
@@ -67,7 +67,7 @@ def run_scan1d() -> XResult:
 def run_scan2d() -> XResult:
     """Perform a parameter scan"""
     simulator = SimulatorSerial(model=MODEL_REPRESSILATOR)
-    Q_ = simulator.ureg.Quantity
+    Q_ = simulator.Q_
 
     scan2d = ScanSim(
         simulation=TimecourseSim(
@@ -102,7 +102,7 @@ def run_scan2d() -> XResult:
 def run_scan1d_distribution() -> XResult:
     """Perform a parameter scan by sampling from a distribution"""
     simulator = SimulatorSerial(model=MODEL_REPRESSILATOR)
-    Q_ = simulator.ureg.Quantity
+    Q_ = simulator.Q_
 
     scan1d = ScanSim(
         simulation=TimecourseSim(

src/sbmlsim/examples/example_units.py

@@ -17,8 +17,7 @@ def run_demo_example():
     """ Run various timecourses. """
     simulator = Simulator(MODEL_DEMO)
     # build quantities using the unit registry for the model
-    Q_ = simulator.ureg.Quantity
-    pprint(simulator.udict)
+    Q_ = simulator.Q_
 
     # 1. simple timecourse simulation
     print("*** setting concentrations and amounts ***")

src/sbmlsim/examples/experiments/glucose/experiments/dose_response.py

@@ -13,6 +13,7 @@
 from sbmlsim.result import XResult
 from sbmlsim.simulation import Dimension, ScanSim, Timecourse, TimecourseSim
 from sbmlsim.task import Task
+from sbmlsim.units import UnitsInformation
 from sbmlsim.utils import timeit
 
 
@@ -98,7 +99,7 @@ def datasets(self) -> Dict[str, DataSet]:
                 "mean": df["unit"].unique()[0],
             }
             dsets[hormone_key.lower()] = DataSet.from_df(
-                df, udict=udict, ureg=self.ureg
+                df, ureg=self.ureg, udict=udict
             )
 
         return dsets
@@ -160,8 +161,7 @@ def figures(self) -> Dict[str, Figure]:
 
         dose_response["[glc_ext]"] = glc_vec
         df = pd.DataFrame(dose_response)
-        dset = DataSet.from_df(df, udict=model.udict, ureg=self.ureg)
-        print(dset)
+        dset = DataSet.from_df(df, udict=model.uinfo.udict, ureg=self.ureg)
 
         # plot scan results
         kwargs = {"linewidth": 2, "linestyle": "-", "marker": "None", "color": "black"}

src/sbmlsim/examples/experiments/glucose/results/DoseResponseExperiment/DoseResponseExperiment.html

@@ -77,6 +77,7 @@ <h2>Code</h2>
 from sbmlsim.result import XResult
 from sbmlsim.simulation import Dimension, ScanSim, Timecourse, TimecourseSim
 from sbmlsim.task import Task
+from sbmlsim.units import UnitsInformation
 from sbmlsim.utils import timeit
 
 
@@ -162,7 +163,7 @@ <h2>Code</h2>
                 "mean": df["unit"].unique()[0],
             }
             dsets[hormone_key.lower()] = DataSet.from_df(
-                df, udict=udict, ureg=self.ureg
+                df, ureg=self.ureg, udict=udict
             )
 
         return dsets
@@ -224,8 +225,7 @@ <h2>Code</h2>
 
         dose_response["[glc_ext]"] = glc_vec
         df = pd.DataFrame(dose_response)
-        dset = DataSet.from_df(df, udict=model.udict, ureg=self.ureg)
-        print(dset)
+        dset = DataSet.from_df(df, udict=model.uinfo.udict, ureg=self.ureg)
 
         # plot scan results
         kwargs = {"linewidth": 2, "linestyle": "-", "marker": "None", "color": "black"}

src/sbmlsim/experiment/experiment.py

@@ -398,17 +398,17 @@ def _run_tasks(self, simulator, reduced_selections: bool = True):
                 simulator.set_timecourse_selections(selections=None)
 
             # normalize model changes (these must be set in simulation!)
-            model.normalize(udict=simulator.udict, ureg=simulator.ureg)
+            model.normalize(uinfo=model.uinfo)
 
             for task_key in task_keys:  # type: str
                 task = self._tasks[task_key]
 
-                sim = self._simulations[
+                sim: Union[ScanSim, TimecourseSim] = self._simulations[
                     task.simulation_id
-                ]  # type: Union[ScanSim, TimecourseSim]
+                ]
 
                 # normalization before running to ensure correct serialization
-                sim.normalize(udict=simulator.udict, ureg=simulator.ureg)
+                sim.normalize(uinfo=simulator.uinfo)
 
                 # inject model changes (copy to create independent)
                 sim = deepcopy(sim)

src/sbmlsim/experiment/runner.py

@@ -15,7 +15,7 @@
 from sbmlsim.experiment import ExperimentResult, SimulationExperiment
 from sbmlsim.model import RoadrunnerSBMLModel
 from sbmlsim.simulator import SimulatorSerial
-from sbmlsim.units import UnitRegistry, Units
+from sbmlsim.units import UnitRegistry, Units, UnitsInformation
 from sbmlsim.utils import timeit
 
 
@@ -31,13 +31,13 @@ def __init__(
         base_path: Path,
         data_path: Path,
         simulator: SimulatorSerial = None,
-        ureg: UnitRegistry = None,
+        ureg: UnitRegistry = None,  # FIXME: is this needed on ExperimentRunner?
         **kwargs,
     ):
 
         # single UnitRegistry per runner
         if not ureg:
-            ureg = Units.default_ureg()
+            ureg = UnitsInformation._default_ureg()
         self.ureg = ureg
         self.Q_ = ureg.Quantity
 

src/sbmlsim/fit/optimization.py

@@ -310,9 +310,7 @@ def initialize(
 
                 task_id = mapping.observable.task_id
                 task = sim_experiment._tasks[task_id]
-                model = sim_experiment._models[
-                    task.model_id
-                ]  # type: RoadrunnerSBMLModel
+                model: RoadrunnerSBMLModel = sim_experiment._models[task.model_id]
                 simulation = sim_experiment._simulations[task.simulation_id]
 
                 if not isinstance(simulation, TimecourseSim):
@@ -323,8 +321,8 @@ def initialize(
                 # observable units
                 obs_xid = mapping.observable.x.index
                 obs_yid = mapping.observable.y.index
-                obs_x_unit = model.udict[obs_xid]
-                obs_y_unit = model.udict[obs_yid]
+                obs_x_unit = model.uinfo[obs_xid]
+                obs_y_unit = model.uinfo[obs_yid]
 
                 # prepare data
                 data_ref = mapping.reference.get_data()
@@ -683,8 +681,8 @@ def residuals(self, xlog: np.ndarray, complete_data=False):
             simulator.set_timecourse_selections(selections=self.selections[k])
 
             # FIXME: normalize simulations and parameters once outside of loop
-            simulation = self.simulations[k]  # type: TimecourseSim
-            simulation.normalize(udict=simulator.udict, ureg=simulator.ureg)
+            simulation: TimecourseSim = self.simulations[k]
+            simulation.normalize(uinfo=simulator.uinfo)
 
             # run simulation
             try:

src/sbmlsim/model/model.py

@@ -11,7 +11,7 @@
 from typing import Dict, List, Optional, Tuple, Union
 
 from sbmlsim.model.model_resources import Source
-from sbmlsim.units import Units
+from sbmlsim.units import Units, UnitsInformation
 
 
 logger = logging.getLogger(__name__)
@@ -83,9 +83,9 @@ def __init__(
 
         # normalize parameters at end of initialization
 
-    def normalize(self, udict, ureg):
+    def normalize(self, uinfo: UnitsInformation):
         """Normalize values to model units for all changes."""
-        self.changes = Units.normalize_changes(self.changes, udict=udict, ureg=ureg)
+        self.changes = UnitsInformation.normalize_changes(self.changes, uinfo=uinfo)
 
     def to_dict(self):
         """Convert to dictionary."""