working on updates

Author: matthiaskoenig

src/sbmlsim/combine/sedml/parser.py

@@ -98,7 +98,7 @@
 from sbmlsim.fit import FitData, FitExperiment, FitMapping, FitParameter
 from sbmlsim.model import RoadrunnerSBMLModel
 from sbmlsim.model.model import AbstractModel
-from sbmlsim.model.model_roadrunner import roadrunner
+from sbmlsim.model.rr_model import roadrunner
 from sbmlsim.plot import Axis, Curve, Figure, Plot
 from sbmlsim.plot.plotting import (
     AbstractCurve,

src/sbmlsim/examples/example_sensitivity.py

@@ -2,7 +2,7 @@
 Example shows basic model simulations and plotting.
 """
 
-from sbmlsim.model.model_roadrunner import roadrunner
+from sbmlsim.model.rr_model import roadrunner
 from sbmlsim.plot.serialization_matplotlib import plt
 from sbmlsim.resources import REPRESSILATOR_SBML
 from sbmlsim.simulation import Timecourse, TimecourseSim

src/sbmlsim/fit/objects.py

@@ -1,15 +1,15 @@
 """Definition of Objects used in FitProblems and optimization."""
+
 from __future__ import annotations
 import json
 import math
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Any, Callable, Dict, Iterable, List, Optional, Sized, Union
+from typing import Any, Callable, Dict, Iterable, List, Optional, Union
 
 import numpy as np
 import pandas as pd
 from pymetadata import log
-from pymetadata.console import console
 
 from sbmlsim.data import Data
 from sbmlsim.serialization import to_json
@@ -90,7 +90,7 @@ def weights(self, weights: Union[float, List[float]] = None) -> None:
                 weights_processed = weights
 
             # all weights have to be None, i.e [None, ..., None].
-            # the weights are calculated dynamically by evalutating the fit mappings.
+            # the weights are calculated dynamically by evaluating the fit mappings.
             if weights_processed != mapping_weights:
                 logger.error(
                     f"Either 'weights' can be set on a FitExperiment or the weight of "

src/sbmlsim/fit/optimization.py

@@ -5,7 +5,7 @@
 from copy import deepcopy
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Any, Callable, Collection, Dict, List, Optional, Set, Tuple, Union
+from typing import Any, Dict, List, Optional, Set, Tuple, Union
 
 import numpy as np
 import pandas as pd
@@ -14,7 +14,6 @@
 from pymetadata.console import console
 from scipy import interpolate, optimize
 
-from sbmlsim.data import Data
 from sbmlsim.experiment import ExperimentRunner
 from sbmlsim.fit.objects import FitExperiment, FitMapping, FitParameter
 from sbmlsim.fit.options import (
@@ -28,7 +27,7 @@
 from sbmlsim.model import RoadrunnerSBMLModel
 from sbmlsim.serialization import ObjectJSONEncoder, to_json
 from sbmlsim.simulation import TimecourseSim
-from sbmlsim.simulator import SimulatorSerialRR
+from sbmlsim.simulator import SimulatorSerial
 from sbmlsim.units import DimensionalityError
 from sbmlsim.utils import timeit
 
@@ -243,9 +242,8 @@ def initialize(
         )
 
         # Collect information for simulations
-        fit_exp: Callable
+        # fit_exp: Callable
         for fit_experiment in self.fit_experiments:
-
             # get simulation experiment
             sid = fit_experiment.experiment_class.__name__
             sim_experiment = self.runner.experiments[sid]
@@ -671,7 +669,7 @@ def residuals(self, xlog: np.ndarray, complete_data=False):
             residual_data = defaultdict(list)
 
         # simulate all mappings for all experiments
-        simulator: SimulatorSerialRR = self.runner.simulator
+        simulator: SimulatorSerial = self.runner.simulator
         Q_ = self.runner.Q_
 
         for k, _ in enumerate(self.mapping_keys):
@@ -701,15 +699,7 @@ def residuals(self, xlog: np.ndarray, complete_data=False):
                     copy=False,
                     assume_sorted=True,
                 )
-                try:
-                    y_obsip = f(self.x_references[k])
-                except ValueError as err:
-                    logger.error(
-                        f"x data outside of interpolation range, increase simulation "
-                        f"times in mapping `{self.mapping_keys[k]}` in "
-                        f"{self.experiment_keys[k]}."
-                    )
-                    raise err
+                y_obsip = f(self.x_references[k])
 
                 if self.residual in {
                     ResidualType.ABSOLUTE_TO_BASELINE,

src/sbmlsim/simulation/sensitivity.py

@@ -11,7 +11,7 @@
 from pymetadata import log
 from pymetadata.console import console
 
-from sbmlsim.model.model_roadrunner import roadrunner
+from sbmlsim.model.rr_model import roadrunner
 from sbmlsim.simulation import Dimension, ScanSim, TimecourseSim
 
 

src/sbmlsim/simulator/rr_simulator_ray.py

@@ -10,7 +10,7 @@
 import ray
 from sbmlutils import log
 
-from sbmlsim.model.model_roadrunner import roadrunner
+from sbmlsim.model.rr_model import roadrunner
 from sbmlsim.simulation import TimecourseSim
 from sbmlsim.simulator.rr_simulator_abstract import SimulatorAbstractRR
 from sbmlsim.simulator.rr_worker import SimulationWorkerRR

src/sbmlsim/simulator/rr_simulator_serial.py

@@ -10,7 +10,7 @@
 import pandas as pd
 from sbmlutils import log
 
-from sbmlsim.model.model_roadrunner import roadrunner
+from sbmlsim.model.rr_model import roadrunner
 from sbmlsim.simulation import TimecourseSim
 from sbmlsim.simulator.rr_simulator_abstract import SimulatorAbstractRR
 from sbmlsim.simulator.rr_worker import SimulationWorkerRR

src/sbmlsim/simulator/rr_worker.py

@@ -6,7 +6,7 @@
 from sbmlutils import log
 
 from sbmlsim.model import ModelChange
-from sbmlsim.model.model_roadrunner import IntegratorSettingKeys, roadrunner
+from sbmlsim.model.rr_model import IntegratorSettingKeys, roadrunner
 from sbmlsim.simulation import Timecourse, TimecourseSim
 
 

tests/conftest.py

@@ -4,7 +4,7 @@
 
 import pytest
 
-from sbmlsim.model.model_roadrunner import roadrunner
+from sbmlsim.model.rr_model import roadrunner
 from sbmlsim.resources import DEMO_SBML, REPRESSILATOR_SBML