starting simulator update

setup.cfg

@@ -46,15 +46,15 @@ keywords =
 
 [options]
 zip_safe = True
-python_requires = >=3.9
+python_requires = >=3.11
 install_requires =
     sbmlutils>=0.8.7
-    numpy==1.21.3         # see https://github.com/sys-bio/roadrunner/issues/963
-    libroadrunner==2.1.3  # see https://github.com/sys-bio/roadrunner/issues/963
-    scipy==1.10.1
-    pint==0.19.2
+    numpy>=1.26.4
+    libroadrunner>=2.6.0
+    scipy>=1.12.0
+    pint>=0.23
 
-    # -> sbmlutils (no version pin)
+    # from sbmlutils (no version pin)
     python-libsbml
     rich
     depinfo
@@ -66,28 +66,22 @@ install_requires =
     matplotlib
 
     # dependencies
-    petab>=0.1.25
-    # fix for windows access violations
-	ray[default]>=2.9.3
-    grpcio==1.49.1
-    pydantic>=2.6.3
-	tables>=3.8.0
-	xarray>=2023.6.0
-	bottleneck>=1.3.4
+    petab>=0.2.9
+    pydantic>=2.6.4
+	tables>=3.9.2
+	xarray>=2024.3.0
+	bottleneck>=1.3.8
+	psutil>=5.9.8
+	setproctitle>=1.3.3
+
+	plotly>=5.20.0
+	altair>=5.3.0
+	seaborn>=0.13.2
+    xmltodict>=0.13.0
+	pyDOE>=0.3.8
 
 	python-libsedml>=2.0.32
 	python-libnuml>=1.1.6
-    # biosimulators-utils>=0.1.171
-
-	psutil>=5.9.0
-	setproctitle>=1.2.2
-
-	plotly>=5.6.0
-	altair>=4.2.0
-	seaborn>=0.11.2
-
-    xmltodict>=0.12.0
-	pyDOE>=0.3.8
 tests_require =
 	tox>=3.24.3
 	pytest>=7.0.1

src/sbmlsim/combine/sedml/runner.py

@@ -10,7 +10,6 @@
 from sbmlsim.combine.sedml.parser import SEDMLParser
 from sbmlsim.experiment import ExperimentRunner, SimulationExperiment
 from sbmlsim.simulator import SimulatorSerial
-from sbmlsim.simulator.simulation_ray import SimulatorParallel
 
 
 def sedmltojson(sedml_path: Path) -> None:

src/sbmlsim/examples/datagenerator_example.py

@@ -4,13 +4,13 @@
 from sbmlsim.result import XResult
 from sbmlsim.result.datagenerator import DataGeneratorIndexingFunction
 from sbmlsim.simulation import Dimension, ScanSim, Timecourse, TimecourseSim
-from sbmlsim.simulator.simulation_ray import SimulatorParallel
+from sbmlsim.simulator.simulation_serial import SimulatorSerial
 from sbmlsim.test import MODEL_MIDAZOLAM
 
 
 def example_scan() -> XResult:
     """Run scan and return results."""
-    simulator = SimulatorParallel(model=MODEL_MIDAZOLAM)
+    simulator = SimulatorSerial(model=MODEL_MIDAZOLAM)
     Q_ = simulator.Q_
 
     scan = ScanSim(

src/sbmlsim/examples/experiments/covid/simulate.py

@@ -24,7 +24,6 @@ def run_covid_examples(output_path: Path) -> None:
         output_path=output_path / "sbmlsim",
         data_path=output_path,
         base_path=output_path,
-        parallel=True,
     )
 
     for experiment in experiments:

src/sbmlsim/examples/experiments/curve_types/experiment.py

@@ -10,7 +10,7 @@
 from sbmlsim.plot import Axis, Figure, Plot
 from sbmlsim.result.report import Report
 from sbmlsim.simulation import AbstractSim, Timecourse, TimecourseSim
-from sbmlsim.simulator.simulation_ray import SimulatorParallel, SimulatorSerial
+from sbmlsim.simulator.simulation_serial import SimulatorSerial
 from sbmlsim.task import Task
 from sbmlsim.test import MODEL_REPRESSILATOR
 
@@ -95,7 +95,7 @@ def run_curve_types_experiments(output_path: Path) -> Path:
 
     runner = ExperimentRunner(
         CurveTypesExperiment,
-        simulator=SimulatorParallel(),
+        simulator=SimulatorSerial(),
         data_path=data_path,
         base_path=base_path,
     )

src/sbmlsim/examples/experiments/demo/demo.py

@@ -20,7 +20,7 @@
     TimecourseSim,
 )
 from sbmlsim.simulation.sensitivity import ModelSensitivity, SensitivityType
-from sbmlsim.simulator.simulation_ray import SimulatorParallel, SimulatorSerial
+from sbmlsim.simulator.simulation_serial import SimulatorSerial
 from sbmlsim.task import Task
 from sbmlsim.test import MODEL_DEMO
 
@@ -106,7 +106,7 @@ def run_demo_experiments(output_path: Path) -> None:
 
     runner = ExperimentRunner(
         DemoExperiment,
-        simulator=SimulatorParallel(),
+        simulator=SimulatorSerial(),
         data_path=data_path,
         base_path=base_path,
     )

src/sbmlsim/examples/experiments/initial_assignment/initial_assignment.py

@@ -8,7 +8,7 @@
 from sbmlsim.model import AbstractModel, RoadrunnerSBMLModel
 from sbmlsim.plot import Axis, Figure
 from sbmlsim.simulation import AbstractSim, Timecourse, TimecourseSim
-from sbmlsim.simulator.simulation_ray import SimulatorParallel
+from sbmlsim.simulator.simulation_serial import SimulatorSerial
 from sbmlsim.task import Task
 
 
@@ -119,7 +119,7 @@ def run(output_path):
 
     runner = ExperimentRunner(
         AssignmentExperiment,
-        simulator=SimulatorParallel(),
+        simulator=SimulatorSerial(),
         base_path=base_path,
         data_path=base_path,
     )

src/sbmlsim/examples/experiments/midazolam/simulate.py

@@ -12,7 +12,7 @@
 from sbmlsim.examples.experiments.midazolam.experiments.mandema1992 import Mandema1992
 from sbmlsim.experiment import ExperimentRunner, SimulationExperiment
 from sbmlsim.report.experiment_report import ExperimentReport, ReportResults
-from sbmlsim.simulator.simulation_ray import SimulatorParallel
+from sbmlsim.simulator.simulation_serial import SimulatorSerial
 
 
 def run_midazolam_experiments(output_path: Path) -> None:
@@ -23,7 +23,7 @@ def run_midazolam_experiments(output_path: Path) -> None:
             Mandema1992,
             Kupferschmidt1995,
         ],
-        simulator=SimulatorParallel(),
+        simulator=SimulatorSerial(),
         base_path=base_path,
         data_path=base_path / "data",
     )

src/sbmlsim/examples/experiments/repressilator/repressilator_scans.py

@@ -17,7 +17,7 @@
     Timecourse,
     TimecourseSim,
 )
-from sbmlsim.simulator.simulation_ray import SimulatorParallel, SimulatorSerial
+from sbmlsim.simulator.simulation_serial import SimulatorSerial
 from sbmlsim.task import Task
 from sbmlsim.test import MODEL_REPRESSILATOR
 
@@ -219,7 +219,7 @@ def run_repressilator_experiments(output_path: Path) -> Path:
     base_path = Path(__file__).parent
     data_path = base_path
 
-    for simulator in [SimulatorSerial(), SimulatorParallel()]:
+    for simulator in [SimulatorSerial()]:
         runner = ExperimentRunner(
             [RepressilatorScanExperiment],
             simulator=simulator,