more usability improvements

examples/scripts/_internal_data_demo.py

@@ -14,7 +14,7 @@
 # ## extract the vcell simulation dataset from the tarball (compressed to save space)
 
 
-test_data_dir = Path(os.getcwd()) / "solver_output"
+test_data_dir = Path(os.getcwd()).parent / "solver_output"
 
 
 # ## read vcell simulation results metadata

examples/scripts/fielddata_from_image_workflow.py

@@ -4,11 +4,9 @@
 
 import numpy as np
 
+import pyvcell.vcml as vc
 from pyvcell._internal.simdata.mesh import CartesianMesh
 from pyvcell.sim_results.var_types import NDArray3D, NDArray4D
-from pyvcell.vcml import VcmlReader
-from pyvcell.vcml.field import Field
-from pyvcell.vcml.vcml_simulation import VcmlSpatialSimulation as Solver
 
 
 def create_sinusoid(
@@ -34,7 +32,7 @@ def create_sinusoid(
 
     # ---- read in VCML file
     model_path = Path(os.getcwd()).parent / "models" / "SmallSpatialProject_3D.vcml"
-    bio_model = VcmlReader.biomodel_from_file(vcml_path=model_path)
+    bio_model = vc.load_vcml_file(model_path)
 
     # ---- get the species mappings for species "s0" and "s1"
     app = bio_model.applications[0]
@@ -46,7 +44,7 @@ def create_sinusoid(
     s1_mapping.init_conc = "vcField('checkerboard', 'v', 0.0, 'Volume')"
 
     sim = app.add_sim(name="new_sim", duration=10.0, output_time_step=0.1, mesh_size=(20, 20, 20))
-    fields = Field.create_fields(bio_model=bio_model, sim=sim)
+    fields = vc.Field.create_fields(bio_model=bio_model, sim=sim)
     print(fields)
 
     shape = fields[0].data_nD.shape
@@ -58,7 +56,7 @@ def create_sinusoid(
 
     # ---- add field data to the simulation
 
-    sim1_result = Solver(bio_model=bio_model, out_dir=sim_dir, fields=fields).run(sim.name)
+    sim1_result = vc.simulate(biomodel=bio_model, simulation=sim, fields=fields)
     print([c.label for c in sim1_result.channel_data])
     print(sim1_result.time_points[::11])
     sim1_result.plotter.plot_slice_3d(time_index=0, channel_id="s0")

examples/scripts/fielddata_from_sim_workflow.py

@@ -3,8 +3,7 @@
 import tempfile
 from pathlib import Path
 
-from pyvcell.vcml import VcmlReader
-from pyvcell.vcml.vcml_simulation import VcmlSpatialSimulation as Solver
+import pyvcell.vcml as vc
 
 with tempfile.TemporaryDirectory() as temp_dir_name, Path(temp_dir_name) as temp_dir:
     # ----- make a workspace
@@ -18,7 +17,7 @@
 
     # ---- read in VCML file
     model_fp = Path(os.getcwd()).parent / "models" / "SmallSpatialProject_3D.vcml"
-    bio_model1 = VcmlReader.biomodel_from_file(model_fp)
+    bio_model1 = vc.load_vcml_file(model_fp)
 
     # ---- get the application and the species mappings for species "s0" and "s1"
     app = bio_model1.applications[0]
@@ -34,19 +33,23 @@
 
     # ---- run simulation, store in sim1_dir, and plot results
     # >>>>> This forms the data for the "Field Data" identified by 'sim1_dir' <<<<<<
-    sim1_result = Solver(bio_model=bio_model1, out_dir=sim1_dir).run(sim.name)
+    sim1_result = vc.simulate(biomodel=bio_model1, simulation=sim.name)
     print([c.label for c in sim1_result.channel_data])
     print(sim1_result.time_points[::11])
     sim1_result.plotter.plot_slice_3d(time_index=0, channel_id="s0")
     sim1_result.plotter.plot_slice_3d(time_index=0, channel_id="s1")
     sim1_result.plotter.plot_concentrations()
+    sim1_result_dirname = sim1_result.solver_output_dir.name
 
     # ----- use field data from sim1_dir to set initial concentration of species "s0"
-    s0_mapping.init_conc = "vcField('sim1_dir','s0',0.0,'Volume') * vcField('sim1_dir','s1',0.0,'Volume')"
+    s0_mapping.init_conc = (
+        f"vcField('{sim1_result_dirname}','s0',0.0,'Volume') * vcField('{sim1_result_dirname}','s1',0.0,'Volume')"
+    )
     s1_mapping.init_conc = "5.0"
     # ---- re-run simulation and store in sim2_dir
     # note that the solution of s0 draws from the data from sim1_dir
-    sim2_result = Solver(bio_model=bio_model1, out_dir=sim2_dir).run(sim.name)
+    sim2_result = vc.simulate(biomodel=bio_model1, simulation=sim.name)
     sim2_result.plotter.plot_slice_3d(time_index=0, channel_id="s0")
     sim2_result.plotter.plot_slice_3d(time_index=0, channel_id="s1")
     sim2_result.plotter.plot_concentrations()
+    sim2_result.cleanup()

examples/scripts/sysbio_class.py

@@ -1,7 +1,6 @@
 from pathlib import Path
 
-import pyvcell.vcml as vcml
-from pyvcell.vcml.vcml_simulation import VcmlSpatialSimulation as VCSolver
+import pyvcell.vcml as vc
 
 WORKSPACE_DIR = Path(__file__).parent.resolve()
 
@@ -17,20 +16,21 @@
     A = 10
 """
 
-biomodel = vcml.load_antimony_str(antimony_str)
+biomodel = vc.load_antimony_str(antimony_str)
 
 # create a 3D geometry
-geo = vcml.Geometry(name="geo", origin=(0, 0, 0), extent=(10, 10, 10), dim=3)
+geo = vc.Geometry(name="geo", origin=(0, 0, 0), extent=(10, 10, 10), dim=3)
 # cell = geo.add_sphere(name="cell", radius=4, center=(5,5,5))
 medium = geo.add_background(name="background")
 
 # add an application to the biomodel
 app = biomodel.add_application("app1", geometry=geo)
 app.map_compartment(compartment=biomodel.model.get_compartment("cell"), domain=medium)  # type: ignore[union-attr]
 app.species_mappings = [
-    vcml.SpeciesMapping(species_name="A", init_conc="sin(x)"),
-    vcml.SpeciesMapping(species_name="B", init_conc="cos(x+y+z)"),
+    vc.SpeciesMapping(species_name="A", init_conc="sin(x)"),
+    vc.SpeciesMapping(species_name="B", init_conc="cos(x+y+z)"),
 ]
-sim = app.add_sim(name="sim1", duration=10.0, output_time_step=0.5, mesh_size=(50, 50, 50))
-results = VCSolver(bio_model=biomodel, out_dir=WORKSPACE_DIR / "sim1").run(simulation_name="sim1")
+sim = app.add_sim(name="sim1", duration=2.0, output_time_step=0.5, mesh_size=(50, 50, 50))
+results = vc.simulate(biomodel=biomodel, simulation="sim1")
 results.plotter.plot_concentrations()
+results.cleanup()

examples/scripts/vcml_bunny_workflow.py

@@ -1,20 +1,18 @@
 import os
 from pathlib import Path
 
-from pyvcell.vcml import VcmlReader
-from pyvcell.vcml.vcml_simulation import VcmlSpatialSimulation
+import pyvcell.vcml as vc
 
 model_fp = Path(os.getcwd()).parent / "models" / "Bunny.vcml"
 
-bio_model = VcmlReader.biomodel_from_file(model_fp)
+bio_model = vc.load_vcml_file(model_fp)
 sims = [sim for app in bio_model.applications for sim in app.simulations]
 
 # define editable spatial model and simulation instances
-simulation = VcmlSpatialSimulation(bio_model=bio_model)
-result = simulation.run(sims[0].name)
+result = vc.simulate(biomodel=bio_model, simulation=sims[0].name)
 
 print([c.label for c in result.channel_data])
 result.plotter.plot_slice_2d(time_index=3, channel_name="s_in", z_index=result.zarr_dataset.shape[3] // 2)
 result.plotter.plot_slice_3d(time_index=3, channel_id="s_in")
 result.plotter.plot_concentrations()
-simulation.cleanup()
+result.cleanup()