refactor imports to prevent circular import

Author: jcschaff

examples/fv_solver_workflow.py

@@ -1,7 +1,8 @@
 import os
 from pathlib import Path
 
-from pyvcell.data_model import SbmlSpatialModel, SbmlSpatialSimulation
+from pyvcell.data_model.sbml_spatial_model import SbmlSpatialModel
+from pyvcell.data_model.simulation import SbmlSpatialSimulation
 
 model_fp = Path(os.getcwd()) / "solver_input" / "SmallSpacialProject_3D.xml"
 

pyvcell/data_model/__init__.py

@@ -1,22 +0,0 @@
-from pyvcell.data_model.plotter import Plotter
-from pyvcell.data_model.result import Result
-from pyvcell.data_model.sbml_spatial_model import SbmlSpatialModel
-from pyvcell.data_model.simulation import SbmlSpatialSimulation, VcmlSpatialSimulation
-from pyvcell.data_model.var_types import NDArray1D, NDArray2D, NDArray3D
-from pyvcell.data_model.vcml_spatial_model import VcmlSpatialModel
-from pyvcell.data_model.vtk_data import VtkData
-from pyvcell.data_model.zarr_types import Channel
-
-__all__ = [
-    "Plotter",
-    "Result",
-    "SbmlSpatialModel",
-    "SbmlSpatialSimulation",
-    "VcmlSpatialSimulation",
-    "VcmlSpatialModel",
-    "VtkData",
-    "Channel",
-    "NDArray1D",
-    "NDArray2D",
-    "NDArray3D",
-]

tests/data_model/test_model.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 
-from pyvcell.data_model import SbmlSpatialModel
+from pyvcell.data_model.sbml_spatial_model import SbmlSpatialModel
 
 
 def test_sbml_model_parse_1d(sbml_spatial_model_1d_path: Path) -> None:

tests/data_model/test_result.py

@@ -5,7 +5,8 @@
 import numpy as np
 import pytest
 
-from pyvcell.data_model import NDArray2D, Result
+from pyvcell.data_model.result import Result
+from pyvcell.data_model.var_types import NDArray2D
 
 IN_GITHUB_ACTIONS = os.getenv("GITHUB_ACTIONS") == "true"
 

tests/data_model/test_simulations.py

@@ -3,7 +3,10 @@
 import numpy as np
 
 import pyvcell.vcml as vc
-from pyvcell.data_model import Result, SbmlSpatialModel, SbmlSpatialSimulation, VcmlSpatialModel, VcmlSpatialSimulation
+from pyvcell.data_model.result import Result
+from pyvcell.data_model.sbml_spatial_model import SbmlSpatialModel
+from pyvcell.data_model.simulation import SbmlSpatialSimulation, VcmlSpatialSimulation
+from pyvcell.data_model.vcml_spatial_model import VcmlSpatialModel
 
 
 def test_sbml_model_parse_1d(sbml_spatial_model_1d_path: Path) -> None:

tests/simdata/test_vtk.py

@@ -4,7 +4,8 @@
 import pytest
 import pyvista
 
-from pyvcell.data_model import NDArray1D, Result
+from pyvcell.data_model.result import Result
+from pyvcell.data_model.var_types import NDArray1D
 from pyvcell.simdata.mesh import CartesianMesh
 from pyvcell.simdata.vtk.fv_mesh_mapping import from_mesh_data
 from pyvcell.simdata.vtk.vismesh import FiniteVolumeIndex, FiniteVolumeIndexData, VisMesh

tests/vcml/test_creation.py

@@ -1,7 +1,9 @@
 from pathlib import Path
 
 import pyvcell.vcml as vc
-from pyvcell.data_model import Result, VcmlSpatialModel, VcmlSpatialSimulation
+from pyvcell.data_model.result import Result
+from pyvcell.data_model.simulation import VcmlSpatialSimulation
+from pyvcell.data_model.vcml_spatial_model import VcmlSpatialModel
 
 
 def test_create() -> None: