Merge pull request #146 from KVSlab/update-imports

Update imports

.github/workflows/check_and_test_package.yml

@@ -97,8 +97,6 @@ jobs:
 
  - name: Run tests
  run: python3 -m pytest tests
- env:
- OASIS_MODE: TESTING
 
  - name: Upload coverage report to codecov
  if: matrix.os == 'ubuntu-latest'

src/vampy/simulation/Artery.py

@@ -1,22 +1,31 @@
+import importlib.util
 import json
-import os
 import pickle
 from pprint import pprint
-import numpy as np
-from dolfin import set_log_level
 
-if os.environ.get('OASIS_MODE') == 'TESTING':
- from oasismove.problems.NSfracStep import *
-else:
- from oasis.problems.NSfracStep import *
+import numpy as np
+from dolfin import set_log_level, MPI
 
 from vampy.simulation.Probe import Probes # type: ignore
 from vampy.simulation.Womersley import make_womersley_bcs, compute_boundary_geometry_acrn
 from vampy.simulation.simulation_common import get_file_paths, store_u_mean, print_mesh_information, \
  store_velocity_and_pressure_h5, dump_probes
 
+# Check for oasis and oasismove
+package_name_oasis = 'oasis'
+package_name_oasismove = 'oasismove'
+oasis_exists = importlib.util.find_spec(package_name_oasis)
+oasismove_exists = importlib.util.find_spec(package_name_oasismove)
+if oasismove_exists:
+ from oasismove.problems.NSfracStep import *
+elif oasis_exists:
+ from oasis.problems.NSfracStep import *
+else:
+ print("Neither oasis nor oasismove is installed. Exiting simulation..")
+
 # FEniCS specific command to control the desired level of logging, here set to critical errors
 set_log_level(50)
+comm = MPI.comm_world
 
 
 def problem_parameters(commandline_kwargs, NS_parameters, NS_expressions, **NS_namespace):
@@ -75,7 +84,7 @@ def problem_parameters(commandline_kwargs, NS_parameters, NS_expressions, **NS_n
  case_name = mesh_file.split(".")[0]
  NS_parameters["folder"] = path.join(NS_parameters["folder"], case_name)
 
- if MPI.rank(MPI.comm_world) == 0:
+ if MPI.rank(comm) == 0:
  print("=== Starting simulation for case: {} ===".format(case_name))
  print("Running with the following parameters:")
  pprint(NS_parameters)
@@ -131,7 +140,7 @@ def create_bcs(t, NS_expressions, V, Q, area_ratio, area_inlet, mesh, mesh_path,
  area_out.append(assemble(Constant(1.0) * dsi))
 
  bc_p = []
- if MPI.rank(MPI.comm_world) == 0:
+ if MPI.rank(comm) == 0:
  print("=== Initial pressure and area fraction ===")
 
  for i, ID in enumerate(id_out):
@@ -140,7 +149,7 @@ def create_bcs(t, NS_expressions, V, Q, area_ratio, area_inlet, mesh, mesh_path,
  bc = DirichletBC(Q, outflow, boundary, ID)
  bc_p.append(bc)
  NS_expressions[ID] = outflow
- if MPI.rank(MPI.comm_world) == 0:
+ if MPI.rank(comm) == 0:
  print(f"Boundary ID={ID}, pressure: {p_initial:.5f}, area fraction: {area_ratio[i]:0.5f}")
 
  # No slip condition at wall
@@ -171,7 +180,7 @@ def pre_solve_hook(mesh, V, Q, newfolder, mesh_path, restart_folder, velocity_de
  probe_points = np.array(json.load(infile))
 
  # Store points file in checkpoint
- if MPI.rank(MPI.comm_world) == 0:
+ if MPI.rank(comm) == 0:
  probe_points.dump(path.join(newfolder, "Checkpoint", "points"))
 
  eval_dict["centerline_u_x_probes"] = Probes(probe_points.flatten(), V)
@@ -187,7 +196,7 @@ def pre_solve_hook(mesh, V, Q, newfolder, mesh_path, restart_folder, velocity_de
  files = NS_namespace["files"]
 
  # Save mesh as HDF5 file for post-processing
- with HDF5File(MPI.comm_world, files["mesh"], "w") as mesh_file:
+ with HDF5File(comm, files["mesh"], "w") as mesh_file:
  mesh_file.write(mesh, "mesh")
 
  # Create vector function for storing velocity
@@ -219,7 +228,7 @@ def temporal_hook(u_, p_, mesh, tstep, dump_probe_frequency, eval_dict, newfolde
  tstep, u_)
 
  # Compute flow rates and updated pressure at outlets, and mean velocity and Reynolds number at inlet
- if MPI.rank(MPI.comm_world) == 0 and tstep % 10 == 0:
+ if MPI.rank(comm) == 0 and tstep % 10 == 0:
  U_mean = Q_in / area_inlet[0]
  diam_inlet = np.sqrt(4 * area_inlet[0] / np.pi)
  Re = U_mean * diam_inlet / nu

src/vampy/simulation/Atrium.py

@@ -1,19 +1,28 @@
+import importlib.util
 import json
-import os
 import pickle
 from pprint import pprint
-from dolfin import set_log_level, MPI
 
-if os.environ.get('OASIS_MODE') == 'TESTING':
- from oasismove.problems.NSfracStep import *
-else:
- from oasis.problems.NSfracStep import *
+import numpy as np
+from dolfin import set_log_level, MPI
 
 from vampy.simulation.Probe import Probes # type: ignore
 from vampy.simulation.Womersley import make_womersley_bcs, compute_boundary_geometry_acrn
 from vampy.simulation.simulation_common import store_u_mean, get_file_paths, print_mesh_information, \
  store_velocity_and_pressure_h5, dump_probes
 
+# Check for oasis and oasismove
+package_name_oasis = 'oasis'
+package_name_oasismove = 'oasismove'
+oasis_exists = importlib.util.find_spec(package_name_oasis)
+oasismove_exists = importlib.util.find_spec(package_name_oasismove)
+if oasismove_exists:
+ from oasismove.problems.NSfracStep import *
+elif oasis_exists:
+ from oasis.problems.NSfracStep import *
+else:
+ print("Neither oasis nor oasismove is installed. Exiting simulation..")
+
 # FEniCS specific command to control the desired level of logging, here set to critical errors
 set_log_level(50)
 comm = MPI.comm_world
@@ -74,7 +83,7 @@ def problem_parameters(commandline_kwargs, NS_parameters, scalar_components, Sch
  case_name = mesh_file.split(".")[0]
  NS_parameters["folder"] = path.join(NS_parameters["folder"], case_name)
 
- if MPI.rank(MPI.comm_world) == 0:
+ if MPI.rank(comm) == 0:
  print("=== Starting simulation for Atrium.py ===")
  print("Running with the following parameters:")
  pprint(NS_parameters)
@@ -165,7 +174,7 @@ def pre_solve_hook(V, Q, cardiac_cycle, dt, save_solution_after_cycle, mesh_path
  probe_points = np.array(json.load(infile))
 
  # Store points file in checkpoint
- if MPI.rank(MPI.comm_world) == 0:
+ if MPI.rank(comm) == 0:
  probe_points.dump(path.join(newfolder, "Checkpoint", "points"))
 
  eval_dict["centerline_u_x_probes"] = Probes(probe_points.flatten(), V)
@@ -181,7 +190,7 @@ def pre_solve_hook(V, Q, cardiac_cycle, dt, save_solution_after_cycle, mesh_path
  files = NS_namespace["files"]
 
  # Save mesh as HDF5 file for post-processing
- with HDF5File(MPI.comm_world, files["mesh"], "w") as mesh_file:
+ with HDF5File(comm, files["mesh"], "w") as mesh_file:
  mesh_file.write(mesh, "mesh")
 
  # Create vector function for storing velocity
@@ -221,7 +230,7 @@ def temporal_hook(mesh, dt, t, save_solution_frequency, u_, NS_expressions, id_i
  U_mean = comm.gather(local_U_mean, 0)
  U_max = comm.gather(local_U_max, 0)
 
- if MPI.rank(MPI.comm_world) == 0:
+ if MPI.rank(comm) == 0:
  u_mean = np.mean(U_mean)
  u_max = max(U_max)