mesh_doctor installation via pip

geosx_mesh_doctor/mesh_doctor.py → geosx_mesh_doctor/mesh_doctor/main.py

@@ -9,10 +9,9 @@
 
 import logging
 
-from parsing import CheckHelper
-from parsing.cli_parsing import parse_and_set_verbosity
-import register
-
+from mesh_doctor.parsing import CheckHelper
+from mesh_doctor.parsing.cli_parsing import parse_and_set_verbosity
+from mesh_doctor import register as register
 
 def main():
     logging.basicConfig( format='[%(asctime)s][%(levelname)s] %(message)s' )

geosx_mesh_doctor/parsing/cli_parsing.py → geosx_mesh_doctor/mesh_doctor/parsing/cli_parsing.py

@@ -48,7 +48,7 @@ def init_parser() -> argparse.ArgumentParser:
         Increase verbosity (-{__VERBOSITY_FLAG}, -{__VERBOSITY_FLAG * 2}) to get full information.
         """
     formatter = lambda prog: argparse.RawTextHelpFormatter( prog, max_help_position=8 )
-    parser = argparse.ArgumentParser( description='Inspects meshes for GEOSX.',
+    parser = argparse.ArgumentParser( description='Inspects meshes for GEOS.',
                                       epilog=textwrap.dedent( epilog_msg ),
                                       formatter_class=formatter )
     # Nothing will be done with this verbosity/quiet input.

geosx_mesh_doctor/parsing/collocated_nodes_parsing.py → geosx_mesh_doctor/mesh_doctor/parsing/collocated_nodes_parsing.py

@@ -5,7 +5,7 @@
     List,
 )
 
-from checks.collocated_nodes import Options, Result
+from ..checks.collocated_nodes import Options, Result
 
 from . import COLLOCATES_NODES
 

geosx_mesh_doctor/parsing/element_volumes_parsing.py → geosx_mesh_doctor/mesh_doctor/parsing/element_volumes_parsing.py

@@ -1,6 +1,6 @@
 import logging
 
-from checks.element_volumes import Options, Result
+from ..checks.element_volumes import Options, Result
 
 from . import ELEMENT_VOLUMES
 

geosx_mesh_doctor/parsing/fix_elements_orderings_parsing.py → geosx_mesh_doctor/mesh_doctor/parsing/fix_elements_orderings_parsing.py

@@ -11,7 +11,7 @@
     VTK_WEDGE,
 )
 
-from checks.fix_elements_orderings import Options, Result
+from ..checks.fix_elements_orderings import Options, Result
 
 from . import vtk_output_parsing, FIX_ELEMENTS_ORDERINGS
 

geosx_mesh_doctor/parsing/generate_cube_parsing.py → geosx_mesh_doctor/mesh_doctor/parsing/generate_cube_parsing.py

@@ -1,6 +1,6 @@
 import logging
 
-from checks.generate_cube import Options, Result, FieldInfo
+from ..checks.generate_cube import Options, Result, FieldInfo
 
 from . import vtk_output_parsing, generate_global_ids_parsing, GENERATE_CUBE
 from .generate_global_ids_parsing import GlobalIdsInfo

geosx_mesh_doctor/parsing/generate_fractures_parsing.py → geosx_mesh_doctor/mesh_doctor/parsing/generate_fractures_parsing.py

@@ -1,6 +1,6 @@
 import logging
 
-from checks.generate_fractures import Options, Result, FracturePolicy
+from ..checks.generate_fractures import Options, Result, FracturePolicy
 
 from . import vtk_output_parsing, GENERATE_FRACTURES
 

geosx_mesh_doctor/parsing/generate_global_ids_parsing.py → geosx_mesh_doctor/mesh_doctor/parsing/generate_global_ids_parsing.py

@@ -1,7 +1,7 @@
 from dataclasses import dataclass
 import logging
 
-from checks.generate_global_ids import Options, Result
+from ..checks.generate_global_ids import Options, Result
 
 from . import vtk_output_parsing, GENERATE_GLOBAL_IDS
 

geosx_mesh_doctor/parsing/non_conformal_parsing.py → geosx_mesh_doctor/mesh_doctor/parsing/non_conformal_parsing.py

@@ -5,7 +5,7 @@
     List,
 )
 
-from checks.non_conformal import Options, Result
+from ..checks.non_conformal import Options, Result
 
 from . import NON_CONFORMAL
 

geosx_mesh_doctor/parsing/self_intersecting_elements_parsing.py → geosx_mesh_doctor/mesh_doctor/parsing/self_intersecting_elements_parsing.py

@@ -2,7 +2,7 @@
 
 import numpy
 
-from checks.self_intersecting_elements import Options, Result
+from ..checks.self_intersecting_elements import Options, Result
 
 from . import SELF_INTERSECTING_ELEMENTS
 

geosx_mesh_doctor/parsing/supported_elements_parsing.py → geosx_mesh_doctor/mesh_doctor/parsing/supported_elements_parsing.py

@@ -1,7 +1,7 @@
 import logging
 import multiprocessing
 
-from checks.supported_elements import Options, Result
+from ..checks.supported_elements import Options, Result
 
 from . import SUPPORTED_ELEMENTS
 

geosx_mesh_doctor/parsing/vtk_output_parsing.py → geosx_mesh_doctor/mesh_doctor/parsing/vtk_output_parsing.py

@@ -2,7 +2,7 @@
 import logging
 import textwrap
 
-from checks.vtk_utils import VtkOutput
+from ..checks.vtk_utils import VtkOutput
 
 __OUTPUT_FILE = "output"
 __OUTPUT_BINARY_MODE = "data-mode"

geosx_mesh_doctor/register.py → geosx_mesh_doctor/mesh_doctor/register.py

@@ -3,20 +3,20 @@
 import logging
 from typing import Dict, Callable, Any, Tuple
 
-import parsing
-from parsing import CheckHelper, cli_parsing
+import mesh_doctor.parsing as parsing
+from .parsing import CheckHelper, cli_parsing
 
 __HELPERS: Dict[ str, Callable[ [ None ], CheckHelper ] ] = dict()
 __CHECKS: Dict[ str, Callable[ [ None ], Any ] ] = dict()
 
 
 def __load_module_check( module_name: str, check_fct="check" ):
-    module = importlib.import_module( "checks." + module_name )
+    module = importlib.import_module( "mesh_doctor.checks." + module_name )
     return getattr( module, check_fct )
 
 
 def __load_module_check_helper( module_name: str, parsing_fct_suffix="_parsing" ):
-    module = importlib.import_module( "parsing." + module_name + parsing_fct_suffix )
+    module = importlib.import_module( "mesh_doctor.parsing." + module_name + parsing_fct_suffix )
     return CheckHelper( fill_subparser=module.fill_subparser,
                         convert=module.convert,
                         display_results=module.display_results )

geosx_mesh_doctor/tests/test_cli_parsing.py → geosx_mesh_doctor/mesh_doctor/tests/test_cli_parsing.py

@@ -8,10 +8,10 @@
 
 import pytest
 
-from checks.vtk_utils import (
+from ..checks.vtk_utils import (
     VtkOutput, )
 
-from checks.generate_fractures import (
+from ..checks.generate_fractures import (
     FracturePolicy,
     Options,
 )

geosx_mesh_doctor/tests/test_collocated_nodes.py → geosx_mesh_doctor/mesh_doctor/tests/test_collocated_nodes.py

@@ -11,7 +11,7 @@
     vtkUnstructuredGrid,
 )
 
-from checks.collocated_nodes import Options, __check
+from ..checks.collocated_nodes import Options, __check
 
 
 def get_points() -> Iterator[ Tuple[ vtkPoints, int ] ]:

geosx_mesh_doctor/tests/test_element_volumes.py → geosx_mesh_doctor/mesh_doctor/tests/test_element_volumes.py

@@ -9,7 +9,7 @@
     vtkUnstructuredGrid,
 )
 
-from checks.element_volumes import Options, __check
+from ..checks.element_volumes import Options, __check
 
 
 def test_simple_tet():

geosx_mesh_doctor/tests/test_generate_cube.py → geosx_mesh_doctor/mesh_doctor/tests/test_generate_cube.py

@@ -1,4 +1,4 @@
-from checks.generate_cube import __build, Options, FieldInfo
+from ..checks.generate_cube import __build, Options, FieldInfo
 
 
 def test_generate_cube():

geosx_mesh_doctor/tests/test_generate_fractures.py → geosx_mesh_doctor/mesh_doctor/tests/test_generate_fractures.py

@@ -20,12 +20,12 @@
 from vtkmodules.util.numpy_support import (
     numpy_to_vtk, )
 
-from checks.vtk_utils import (
+from ..checks.vtk_utils import (
     to_vtk_id_list, )
 
-from checks.check_fractures import format_collocated_nodes
-from checks.generate_cube import build_rectilinear_blocks_mesh, XYZ
-from checks.generate_fractures import __split_mesh_on_fracture, Options, FracturePolicy
+from ..checks.check_fractures import format_collocated_nodes
+from ..checks.generate_cube import build_rectilinear_blocks_mesh, XYZ
+from ..checks.generate_fractures import __split_mesh_on_fracture, Options, FracturePolicy
 
 
 @dataclass( frozen=True )

geosx_mesh_doctor/tests/test_generate_global_ids.py → geosx_mesh_doctor/mesh_doctor/tests/test_generate_global_ids.py

@@ -7,7 +7,7 @@
     vtkVertex,
 )
 
-from checks.generate_global_ids import __build_global_ids
+from ..checks.generate_global_ids import __build_global_ids
 
 
 def test_generate_global_ids():

geosx_mesh_doctor/tests/test_non_conformal.py → geosx_mesh_doctor/mesh_doctor/tests/test_non_conformal.py

@@ -1,7 +1,7 @@
 import numpy
 
-from checks.non_conformal import Options, __check
-from checks.generate_cube import (
+from ..checks.non_conformal import Options, __check
+from ..checks.generate_cube import (
     build_rectilinear_blocks_mesh,
     XYZ,
 )

geosx_mesh_doctor/tests/test_reorient_mesh.py → geosx_mesh_doctor/mesh_doctor/tests/test_reorient_mesh.py

@@ -14,9 +14,9 @@
 
 import numpy
 
-from checks.reorient_mesh import reorient_mesh
-from checks.vtk_polyhedron import FaceStream
-from checks.vtk_utils import (
+from ..checks.reorient_mesh import reorient_mesh
+from ..checks.vtk_polyhedron import FaceStream
+from ..checks.vtk_utils import (
     to_vtk_id_list,
     vtk_iter,
 )

geosx_mesh_doctor/tests/test_self_intersecting_elements.py → geosx_mesh_doctor/mesh_doctor/tests/test_self_intersecting_elements.py

@@ -7,7 +7,7 @@
     vtkUnstructuredGrid,
 )
 
-from checks.self_intersecting_elements import Options, __check
+from ..checks.self_intersecting_elements import Options, __check
 
 
 def test_jumbled_hex():

geosx_mesh_doctor/tests/test_supported_elements.py → geosx_mesh_doctor/mesh_doctor/tests/test_supported_elements.py

@@ -12,9 +12,9 @@
     vtkUnstructuredGrid,
 )
 
-from checks.supported_elements import Options, check, __check
-from checks.vtk_polyhedron import parse_face_stream, build_face_to_face_connectivity_through_edges, FaceStream
-from checks.vtk_utils import (
+from ..checks.supported_elements import Options, check, __check
+from ..checks.vtk_polyhedron import parse_face_stream, build_face_to_face_connectivity_through_edges, FaceStream
+from ..checks.vtk_utils import (
     to_vtk_id_list, )
 
 

geosx_mesh_doctor/tests/test_triangle_distance.py → geosx_mesh_doctor/mesh_doctor/tests/test_triangle_distance.py

@@ -4,7 +4,7 @@
 from numpy.linalg import norm
 import pytest
 
-from checks.triangle_distance import distance_between_two_segments, distance_between_two_triangles
+from ..checks.triangle_distance import distance_between_two_segments, distance_between_two_triangles
 
 
 @dataclass( frozen=True )

geosx_mesh_doctor/setup.cfg

@@ -0,0 +1,24 @@
+[metadata]
+name = mesh_doctor
+version = 0.1.0
+description = Mesh doctor
+author = Gazzolab
+author_email = [email protected]
+license = LGPL-2.1
+
+[options]
+packages =
+    mesh_doctor
+    mesh_doctor.checks
+    mesh_doctor.parsing
+    mesh_doctor.tests
+install_requires =
+    vtk >= 9.1
+    networkx >= 2.4
+    tqdm
+    numpy
+python_requires = >=3.7
+
+[options.entry_points]
+console_scripts =
+    mesh_doctor = mesh_doctor.main:main