diff --git a/.github/workflows/check_and_test_package.yml b/.github/workflows/check_and_test_package.yml index ebf7359c..bf15459b 100644 --- a/.github/workflows/check_and_test_package.yml +++ b/.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: diff --git a/environment-test.yml b/environment-test.yml index 214d94d5..743e46a6 100644 --- a/environment-test.yml +++ b/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 diff --git a/environment.yml b/environment.yml index 0c97cb9b..c6eb7fb7 100644 --- a/environment.yml +++ b/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 diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 47eb2953..00000000 --- a/requirements.txt +++ /dev/null @@ -1,6 +0,0 @@ -jupyter-book -matplotlib -numpy -ghp-import -cppimport -scipy \ No newline at end of file diff --git a/src/vampy/automatedPreprocessing/automated_preprocessing.py b/src/vampy/automatedPreprocessing/automated_preprocessing.py index 8c76e4fc..87f04a66 100644 --- a/src/vampy/automatedPreprocessing/automated_preprocessing.py +++ b/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 diff --git a/src/vampy/simulation/Probe.py b/src/vampy/simulation/Probe.py index b4e46d4b..8c1c9332 100644 --- a/src/vampy/simulation/Probe.py +++ b/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