Merge pull request #144 from KVSlab/hotfix-vtk

Hotfix for expat dependency (VTK)

.github/workflows/check_and_test_package.yml

@@ -15,7 +15,7 @@ on:
  - cron: "0 8 * * *"
 
 env:
- CACHE_NUMBER: 10 # Increase to reset cache
+ CACHE_NUMBER: 11 # Increase to reset cache
 
 jobs:
  check-code:

environment-test.yml

@@ -8,9 +8,11 @@ dependencies:
  - morphman
  - paramiko
  - pip
- - python >=3.8
  - git
+ - python >=3.8
+ - expat==2.5 # Hotfix for https://gitlab.archlinux.org/archlinux/packaging/packages/paraview/-/issues/4
  - pip:
+ - matplotlib
  - scipy
  - cppimport
  - git+https://github.com/KVSlab/OasisMove

environment.yml

@@ -8,8 +8,9 @@ dependencies:
  - morphman
  - paramiko
  - pip
- - python >=3.8
  - git
+ - python >=3.8
+ - expat==2.5 # Hotfix for https://gitlab.archlinux.org/archlinux/packaging/packages/paraview/-/issues/4
  - pip:
  - scipy
  - cppimport

src/vampy/automatedPreprocessing/automated_preprocessing.py

@@ -1,15 +1,17 @@
 import argparse
-import numpy as np
 import sys
-from morphman import get_uncapped_surface, write_polydata, get_parameters, vtk_clean_polydata, \
+from os import remove, path
+
+import numpy as np
+from morphman import get_uncapped_surface, write_polydata, read_polydata, get_parameters, vtk_clean_polydata, \
  vtk_triangulate_surface, write_parameters, vmtk_cap_polydata, compute_centerlines, get_centerline_tolerance, \
  get_vtk_point_locator, extract_single_line, vtk_merge_polydata, get_point_data_array, smooth_voronoi_diagram, \
  create_new_surface, compute_centers, vmtk_smooth_surface, str2bool, vmtk_compute_voronoi_diagram, \
  prepare_output_surface, vmtk_compute_geometric_features
-from os import remove, path
+
 # Local imports
 from vampy.automatedPreprocessing.moving_common import get_point_map, project_displacement, save_displacement
-from vampy.automatedPreprocessing.preprocessing_common import read_polydata, get_centers_for_meshing, \
+from vampy.automatedPreprocessing.preprocessing_common import get_centers_for_meshing, \
  dist_sphere_diam, dist_sphere_curvature, dist_sphere_constant, get_regions_to_refine, add_flow_extension, \
  write_mesh, mesh_alternative, generate_mesh, find_boundaries, compute_flow_rate, setup_model_network, \
  radiusArrayName, scale_surface, get_furtest_surface_point, check_if_closed_surface, remesh_surface

src/vampy/simulation/Probe.py

@@ -15,11 +15,12 @@
 ProbeObject = object
 
 try:
- probe11 = cppimport.imp('vampy.simulation.probe.probe11')
+ probe11 = cppimport.imp('probe.probe11')
  ProbeObject = probe11.Probes
  print("Successfully imported probe.probe11")
-except ImportError:
+except ImportError as e:
  print("Failed to import probe.probe11")
+ print(f"Error message: {e}")
 
 
 # Give the compiled classes some additional pythonic functionality