Fix all violations of code style

.github/actions/code_check/action.yml

@@ -9,5 +9,5 @@ runs:
         cd ${GITHUB_WORKSPACE}
         source python-testing-environment/bin/activate
         pip install -e .[CI-CD]
-        black . --check --exclude=python-testing-environment && exit 0
-        exit 1
+        pre-commit install --install-hooks
+        pre-commit run --all-files

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ repos:
     rev: v5.0.0
     hooks:
       - id: check-added-large-files
-        args: ['—-maxkb=1000']
+        args: [— maxkb=1000]
         name: Check for added large files
       - id: check-ast
         name: Check Python files for parse errors

meshpy/__init__.py

@@ -31,7 +31,6 @@
 """This module defines classes and functions to create and edit a 4C input
 file."""
 
-# Global configuration object.
 # Mesh items.
 from .base_mesh_item import BaseMeshItemString
 
@@ -45,13 +44,11 @@
 
 # Functions to set default header options.
 from .header_functions import (
-    get_comment,
-    get_yes_no,
     set_beam_to_solid_meshtying,
     set_header_static,
     set_runtime_output,
 )
-from .inputfile import InputFile, InputSection, InputSectionMultiKey
+from .inputfile import InputFile, InputSection
 from .material import (
     MaterialBeam,
     MaterialEulerBernoulli,
@@ -69,9 +66,6 @@
 # 3D rotations for nodes.
 from .rotation import Rotation
 
-# Utility functions.
-from .utility import clean_simulation_directory
-
 # Define the items that will be exported by default.
 __all__ = [
     # Option object.

meshpy/abaqus/__init__.py

@@ -31,8 +31,8 @@
 """This module defines classes and functions to create an Abaqus beam input
 file."""
 
-from .beam import AbaqusBeamMaterial, generate_abaqus_beam
-from .input_file import AbaqusBeamNormalDefinition, AbaqusInputFile
+from meshpy.abaqus.beam import AbaqusBeamMaterial, generate_abaqus_beam
+from meshpy.abaqus.input_file import AbaqusBeamNormalDefinition, AbaqusInputFile
 
 # Define the items that will be exported by default.
 __all__ = [

meshpy/abaqus/beam.py

@@ -31,10 +31,8 @@
 """This file provides functions to create Abaqus beam element classes to be
 used with MeshPy."""
 
-# Python modules
 import numpy as np
 
-# MeshPy modules
 from ..element_beam import Beam
 from ..material import MaterialBeam
 

meshpy/abaqus/input_file.py

@@ -31,12 +31,10 @@
 """This module defines the class that is used to create an input file for
 Abaqus."""
 
-# Python modules
 from enum import Enum, auto
 
 import numpy as np
 
-# MeshPy modules
 from ..conf import mpy
 from ..geometry_set import GeometrySet
 from ..mesh import Mesh
@@ -215,7 +213,7 @@ def get_nodes_lines(self):
         for coupling in self.mesh.boundary_conditions[
             mpy.bc.point_coupling, mpy.geo.point
         ]:
-            if not coupling.coupling_dof_type is mpy.coupling_dof.fix:
+            if coupling.coupling_dof_type is not mpy.coupling_dof.fix:
                 raise ValueError(
                     "Abaqus coupling is only implemented for rigid joints at the DOFs"
                 )

meshpy/boundary_condition.py

@@ -31,12 +31,9 @@
 """This module implements a class to handle boundary conditions in the input
 file."""
 
-# Python modules.
 import warnings
 
 from .base_mesh_item import BaseMeshItemFull
-
-# Meshpy modules.
 from .conf import mpy
 from .geometry_set import GeometrySet
 from .utility import find_close_nodes

meshpy/conf.py

@@ -31,7 +31,6 @@
 """This module defines a global object that manages all kind of stuff regarding
 meshpy."""
 
-# Python imports.
 from enum import Enum, auto
 
 

meshpy/coupling.py

@@ -30,12 +30,9 @@
 # -----------------------------------------------------------------------------
 """This module implements a class to couple geometry together."""
 
-# Python modules.
 import numpy as np
 
 from .boundary_condition import BoundaryConditionBase
-
-# Meshpy modules.
 from .conf import mpy
 from .geometry_set import GeometrySet, GeometrySetBase
 
@@ -154,7 +151,7 @@ def _get_dat(self):
             beam_four_c_type = type(nodes[0].element_link[0])
             for node in nodes:
                 for element in node.element_link:
-                    if not beam_four_c_type == type(element):
+                    if beam_four_c_type is not type(element):
                         raise ValueError(
                             "Coupling beams of different types is not yet possible!"
                         )

meshpy/element_beam.py

@@ -30,13 +30,12 @@
 # -----------------------------------------------------------------------------
 """This module implements beam elements for the mesh."""
 
-# Python modules.
 import warnings
+from typing import Any
 
 import numpy as np
 import vtk
 
-# Meshpy modules.
 from .conf import mpy
 from .element import Element
 from .material import (
@@ -57,14 +56,14 @@ class Beam(Element):
     #        [ xi, is_middle_node ], # fist node
     #        ...
     #        ]
-    nodes_create = []
+    nodes_create: Any = []
 
     # A list of valid material types for this element.
-    valid_material = []
+    valid_material: Any = []
 
     # Coupling strings.
-    coupling_fix_string = None
-    coupling_joint_string = None
+    coupling_fix_string = ""
+    coupling_joint_string = ""
 
     def __init__(self, material=None, nodes=None):
         super().__init__(nodes=nodes, material=material)

meshpy/element_volume.py

@@ -30,11 +30,11 @@
 # -----------------------------------------------------------------------------
 """This module implements volume elements for the mesh."""
 
-# Python modules.
+from typing import List, Optional
+
 import numpy as np
 import vtk
 
-# Meshpy modules.
 from .element import Element
 from .vtk_writer import add_point_data_node_sets
 
@@ -45,7 +45,7 @@ class VolumeElement(Element):
     # This class variables stores the information about the element shape in
     # vtk. And the connectivity to the nodes.
     vtk_cell_type = None
-    vtk_topology = None
+    vtk_topology: list = []
 
     def __init__(self, nodes=None, dat_pre_nodes="", dat_post_nodes="", **kwargs):
         super().__init__(nodes=nodes, material=None, **kwargs)

meshpy/four_c/beam_potential.py

@@ -31,10 +31,6 @@
 """This file includes functions to ease the creation of input files using beam
 interaction potentials."""
 
-# Python modules
-import numpy as np
-
-# MeshPy modules
 from ..boundary_condition import BoundaryCondition
 from ..header_functions import get_yes_no
 from ..inputfile import InputSection

meshpy/four_c/dbc_monitor.py

@@ -31,11 +31,9 @@
 """This function converts the DBC monitor log files to Neumann input
 sections."""
 
-# Python modules.
 import numpy as np
 
-# Meshpy stuff.
-from .. import BoundaryCondition, GeometrySet, mpy
+from meshpy import BoundaryCondition, GeometrySet, mpy
 
 
 def read_dbc_monitor_file(file_path):

meshpy/four_c/solid_shell_thickness_direction.py

@@ -207,7 +207,10 @@ def set_solid_shell_thickness_direction(
     for element in elements:
         is_hex8 = isinstance(element, VolumeHEX8)
         if is_hex8:
-            is_solid_shell = "SOLIDSH8" in element.dat_pre_nodes
+            is_solid_shell = (
+                hasattr(element, "dat_pre_nodes")
+                and "SOLIDSH8" in element.dat_pre_nodes
+            )
             if is_solid_shell:
                 # Get the element center and the Jacobian at the center
                 (

meshpy/function_utility.py

@@ -31,10 +31,8 @@
 """This module implements utility functions to create 4C space time
 function."""
 
-# Python modules
 import numpy as np
 
-# Meshpy modules
 from .function import Function
 
 

meshpy/geometric_search/__init__.py

@@ -29,12 +29,3 @@
 # SOFTWARE.
 # -----------------------------------------------------------------------------
 """This module defines geometric search functionality."""
-
-# Functions that should be used from the outside
-from .find_close_points import (
-    FindClosePointAlgorithm,
-    find_close_points,
-    partner_indices_to_point_partners,
-    point_partners_to_partner_indices,
-    point_partners_to_unique_indices,
-)

meshpy/geometric_search/find_close_points.py

@@ -31,20 +31,14 @@
 """Find unique points in a point cloud, i.e., points that are within a certain
 tolerance of each other will be considered as unique."""
 
-# Python modules
 from enum import Enum, auto
 
-# Cython modules
 from .geometric_search_cython import cython_available
-
-# Geometric search modules
-# SciPy
 from .geometric_search_scipy import find_close_points_scipy
 
 if cython_available:
     from .geometric_search_cython import find_close_points_brute_force_cython
 
-# ArborX
 from .geometric_search_arborx import arborx_available
 
 if arborx_available:

meshpy/geometric_search/geometric_search_arborx.py

@@ -31,7 +31,6 @@
 """This file defines the interface to the ArborX geometric search
 functionality."""
 
-# Python modules
 import os
 import sys
 
@@ -43,7 +42,7 @@
     import geometric_search_arborx_lib
 
     arborx_available = True
-except:
+except ImportError:
     arborx_available = False
 
 

meshpy/geometric_search/geometric_search_cython.py

@@ -44,7 +44,7 @@
     import geometric_search_cython_lib
 
     cython_available = True
-except:
+except ImportError:
     cython_available = False
 
 

meshpy/geometric_search/geometric_search_cython_lib.pyx

@@ -35,11 +35,9 @@ It uses cython to gain performance.
 """
 
 
-# Python imports.
 import numpy as np
 from libc.math cimport sqrt
 
-# Cython imports.
 cimport cython
 cimport numpy as np
 

meshpy/geometric_search/geometric_search_scipy.py

@@ -31,7 +31,6 @@
 """This file defines the interface to the Scipy spatial geometric search
 functionality."""
 
-import numpy as np
 from scipy.spatial import KDTree
 
 

meshpy/geometry_set.py

@@ -31,12 +31,9 @@
 """This module implements a basic class to manage geometry in the input
 file."""
 
-# Python modules.
 import numpy as np
 
 from .base_mesh_item import BaseMeshItemFull
-
-# Meshpy modules.
 from .conf import mpy
 from .element_beam import Beam
 from .node import Node

meshpy/header_functions.py

@@ -31,7 +31,6 @@
 """This module defines functions that can be used to add header information to
 an input file."""
 
-# Meshpy imports.
 from .conf import mpy
 from .inputfile import InputSection
 

meshpy/inputfile.py

@@ -31,16 +31,13 @@
 """This module defines the classes that are used to create an input file for
 4C."""
 
-# Python modules.
 import datetime
 import os
 import re
 import sys
 
 from .base_mesh_item import BaseMeshItemFull, BaseMeshItemString
 from .boundary_condition import BoundaryConditionBase
-
-# Meshpy modules.
 from .conf import mpy
 from .container import BoundaryConditionContainer, GeometrySetContainer
 from .element import Element
@@ -203,7 +200,7 @@ def add(self, data, **kwargs):
     def _add_data(self, option):
         """Add a InputLine object to the item."""
 
-        if (not option.get_key() in self.data.keys()) or option.overwrite:
+        if (option.get_key() not in self.data.keys()) or option.overwrite:
             self.data[option.get_key()] = option
         else:
             raise KeyError(f"Key {option.get_key()} is already set!")

meshpy/material.py

@@ -31,10 +31,8 @@
 """This module implements a basic class to manage materials in the 4C input
 file."""
 
-# Python modules.
 import numpy as np
 
-# Meshpy modules.
 from .base_mesh_item import BaseMeshItemFull