fixing imports

Author: matthiaskoenig

src/sbmlsim/TODO.md

@@ -1,8 +1,9 @@
 """DataGenerator."""
+
 from typing import Dict
 
 from sbmlsim.data import DataSet
-from sbmlsim.xresult import XResult
+from sbmlsim.result import XResult
 
 
 class DataGeneratorFunction:

src/sbmlsim/combine/datagenerator.py

@@ -2,11 +2,11 @@
 
 Using sympy to evaluate the expressions.
 """
-from typing import Any, Dict, Set, Tuple
+
+from typing import Any, Dict, Set
 from pymetadata import log
 import libsedml
-from sbmlutils import log
-from sympy import Symbol, lambdify, sympify
+from sympy import lambdify, sympify
 
 
 logger = log.get_logger(__name__)
@@ -172,7 +172,6 @@ def replace_piecewise(formula):
 
 
 if __name__ == "__main__":
-
     # Piecewise in sympy
     # https://docs.sympy.org/latest/modules/functions/elementary.html#piecewise
     # Piecewise((expr, cond), (expr, cond), … )

src/sbmlsim/combine/mathml.py

@@ -78,6 +78,7 @@
 import re
 import shutil
 import warnings
+import roadrunner
 from collections import defaultdict
 from enum import Enum
 from pathlib import Path
@@ -98,7 +99,6 @@
 from sbmlsim.fit import FitData, FitExperiment, FitMapping, FitParameter
 from sbmlsim.model import RoadrunnerSBMLModel
 from sbmlsim.model.model import AbstractModel
-from sbmlsim.model.rr_model import roadrunner
 from sbmlsim.plot import Axis, Curve, Figure, Plot
 from sbmlsim.plot.plotting import (
     AbstractCurve,

src/sbmlsim/combine/sedml/parser.py

@@ -1,16 +1,18 @@
 """Example for DataGenerator functionality."""
+
 import numpy as np
+from matplotlib import pyplot as plt
 
 from sbmlsim.combine.datagenerator import DataGeneratorIndexingFunction
 from sbmlsim.resources import MIDAZOLAM_SBML
 from sbmlsim.simulation import Dimension, ScanSim, Timecourse, TimecourseSim
 from sbmlsim.simulator.simulation_serial import SimulatorSerial
-from sbmlsim.test import MODEL_MIDAZOLAM
+from sbmlsim.result import XResult
 
 
 def example_scan() -> XResult:
     """Run scan and return results."""
-    simulator = SimulatorSerial(model=MODEL_MIDAZOLAM)
+    simulator = SimulatorSerial(model=MIDAZOLAM_SBML)
     Q_ = simulator.Q_
 
     scan = ScanSim(
@@ -50,9 +52,6 @@ def datagenerator_example() -> None:
 
     res_first = dgen_first(xresults={"res1": xres})
     res_last = dgen_last(xresults={"res1": xres})
-    xres1 = res_first["res1"]
-
-    from matplotlib import pyplot as plt
 
     x = (res_first["res1"]["IVDOSE_mid"]).mean(dim="dim_bw")
     y = (res_last["res1"]["[Cve_mid]"]).mean(dim="dim_bw")

src/sbmlsim/examples/datagenerator_example.py

@@ -3,14 +3,15 @@
 
 For instance clamping species to given formulas.
 """
+
 import pandas as pd
 
 from sbmlsim.model import ModelChange, RoadrunnerSBMLModel
 from sbmlsim.plot.serialization_matplotlib import plt
 from sbmlsim.resources import REPRESSILATOR_SBML
 from sbmlsim.simulation import Timecourse, TimecourseSim
 from sbmlsim.simulator.rr_simulator_serial import SimulatorSerialRR
-from sbmlsim.xresult import XResult
+from sbmlsim.result import XResult
 
 
 def run_model_change_example1():

src/sbmlsim/examples/example_model_change.py

@@ -1,16 +1,16 @@
-"""Example shows basic model simulations and plotting with scan.
-"""
+"""Example shows basic model simulations and plotting with scan."""
+
 import numpy as np
 
 from sbmlsim.resources import REPRESSILATOR_SBML
 from sbmlsim.simulation import Dimension, ScanSim, Timecourse, TimecourseSim
-from sbmlsim.simulator import SimulatorSerialRR
-from sbmlsim.xresult import XResult
+from sbmlsim.simulator import SimulatorSerial
+from sbmlsim.result import XResult
 
 
 def run_scan0d() -> XResult:
     """Perform a parameter 0D scan, i.e., simple simulation"""
-    simulator = SimulatorSerialRR.from_sbml(sbml_path=REPRESSILATOR_SBML)
+    simulator = SimulatorSerial.from_sbml(sbml_path=REPRESSILATOR_SBML)
 
     scan0d = ScanSim(
         simulation=TimecourseSim(
@@ -30,7 +30,7 @@ def run_scan1d() -> XResult:
 
     Scanning a single parameter.
     """
-    simulator = SimulatorSerialRR.from_sbml(sbml_path=REPRESSILATOR_SBML)
+    simulator = SimulatorSerial.from_sbml(sbml_path=REPRESSILATOR_SBML)
 
     scan1d = ScanSim(
         simulation=TimecourseSim(
@@ -55,7 +55,7 @@ def run_scan1d() -> XResult:
 
 def run_scan2d() -> XResult:
     """Perform a parameter scan"""
-    simulator = SimulatorSerialRR.from_sbml(sbml_path=REPRESSILATOR_SBML)
+    simulator = SimulatorSerial.from_sbml(sbml_path=REPRESSILATOR_SBML)
 
     scan2d = ScanSim(
         simulation=TimecourseSim(
@@ -85,7 +85,7 @@ def run_scan2d() -> XResult:
 
 def run_scan1d_distribution() -> XResult:
     """Perform a parameter scan by sampling from a distribution"""
-    simulator = SimulatorSerialRR.from_sbml(sbml_path=REPRESSILATOR_SBML)
+    simulator = SimulatorSerial.from_sbml(sbml_path=REPRESSILATOR_SBML)
 
     scan1d = ScanSim(
         simulation=TimecourseSim(

src/sbmlsim/examples/example_scan.py

@@ -2,13 +2,13 @@
 Example shows basic model simulations and plotting.
 """
 
-from sbmlsim.model.rr_model import roadrunner
+import roadrunner
 from sbmlsim.plot.serialization_matplotlib import plt
 from sbmlsim.resources import REPRESSILATOR_SBML
 from sbmlsim.simulation import Timecourse, TimecourseSim
 from sbmlsim.simulation.sensitivity import ModelSensitivity
-from sbmlsim.simulator import SimulatorSerialRR
-from sbmlsim.xresult import XResult
+from sbmlsim.simulator import SimulatorSerial
+from sbmlsim.result import XResult
 
 
 def plot_results(xres: XResult):
@@ -61,7 +61,7 @@ def run_sensitivity():
 
     :return:
     """
-    simulator = SimulatorSerialRR.from_sbml(REPRESSILATOR_SBML)
+    simulator = SimulatorSerial.from_sbml(REPRESSILATOR_SBML)
 
     # parameter sensitivity
     tcsim = TimecourseSim(

src/sbmlsim/examples/example_sensitivity.py

@@ -10,7 +10,7 @@
 from sbmlsim.simulation import Dimension, ScanSim, Timecourse, TimecourseSim
 from sbmlsim.simulator.rr_simulator_serial import SimulatorSerialRR
 from sbmlsim.units import UnitsInformation
-from sbmlsim.xresult import XResult
+from sbmlsim.result import XResult
 
 
 def run_demo_example():

src/sbmlsim/examples/example_units.py

@@ -6,16 +6,17 @@
 import xarray as xr
 from matplotlib.pyplot import Figure
 
+from build.lib.sbmlsim.plot.plotting_deprecated_matplotlib import add_data
 from sbmlsim.data import Data, DataSet, load_pkdb_dataframe
 from sbmlsim.experiment import SimulationExperiment
 from sbmlsim.model import AbstractModel
+
 # from sbmlsim.plot.plotting_deprecated_matplotlib import add_data
 from sbmlsim.plot.serialization_matplotlib import plt
 from sbmlsim.simulation import Dimension, ScanSim, Timecourse, TimecourseSim
 from sbmlsim.task import Task
-from sbmlsim.units import UnitsInformation
 from sbmlsim.utils import timeit
-from sbmlsim.xresult import XResult
+from sbmlsim.result import XResult
 
 
 class DoseResponseExperiment(SimulationExperiment):