Merge pull request #14 from EDG-Acoustics/update_ci_cd_actions

Update ci cd actions

Author: apalha

.github/workflows/cffconvert.yml

@@ -4,9 +4,11 @@ on:
   push:
     branches:
     - main
+    - development
   pull_request:
     branches:
     - main
+    - development
 
 jobs:
 

.github/workflows/documentation.yml

@@ -4,9 +4,11 @@ on:
   push:
     branches:
     - main
+    - development
   pull_request:
     branches:
     - main
+    - development
 
 jobs:
   build-documentation:
@@ -30,7 +32,7 @@ jobs:
           python3 -m pip install --upgrade pip setuptools
           python3 -m pip install .[dev,publishing]
       - name: Install pandoc using apt
-        run: sudo apt install pandoc        
+        run: sudo apt install pandoc
       - name: Build documentation
         run: make coverage doctest html
-        working-directory: docs
+        working-directory: docs

.github/workflows/markdown-link-check.yml

@@ -4,9 +4,11 @@ on:
   push:
     branches:
     - main
+    - development
   pull_request:
     branches:
     - main
+    - development
 
 jobs:
 

.prospector.yml

@@ -17,6 +17,13 @@ pyroma:
 
 pycodestyle:
     full: true
+    options:
+      max-line-length: 300
+
+pylint:
+  disable:
+    - line-too-long  # Already checked by pycodestyle
+    - import-self  # Giving error on __init__ importing mesh.py
 
 pydocstyle:
     disable: [
@@ -27,3 +34,7 @@ pydocstyle:
         D213,  # Multi-line docstring summary should start at the second line
         D404,  # First word of the docstring should not be This
     ]
+
+pyflakes:
+  disable:
+    - F401  # Temporarily disabled since it was raising errors in __init__

data/tests/mesh/Coarse_mesh_object.dat

@@ -1,12 +1,10 @@
 """Documentation about edg_acoustics"""
 import logging
-
 from .mesh import *
 
+
 logging.getLogger(__name__).addHandler(logging.NullHandler())
 
 __author__ = "Huiqing Wang"
 __email__ = "[email protected]"
 __version__ = "0.1.0"
-
-

edg_acoustics/__init__.py

@@ -21,9 +21,9 @@
    Mesh
 """
 from __future__ import annotations
+import meshio
 import numpy
 
-import meshio
 
 __all__ = ['Mesh']
 
@@ -68,29 +68,31 @@ class Mesh:
         N_BC_triangles (dict[str, int]): the number of triangles on the boundary of the domain associated to each
             boundary label in self.BC_labels. For example self.N_BC_triangles['my_label'] returns the number of boundary
             triangles associated to lable 'my_label'. 'my_label' must be a key of self.BC_labels.
-        vertices (numpy.ndarray): An (self.N_vertices x M) array containing the M coordinates of the self.N_vertices vertices that make up
-            the mesh. M specifies the geometric dimension of the mesh, such that the mesh describes an M-dimensional
-            domain.
+        vertices (numpy.ndarray): An (self.N_vertices x M) array containing the M coordinates of the self.N_vertices
+            vertices that make up the mesh. M specifies the geometric dimension of the mesh, such that the mesh
+            describes an M-dimensional domain.
         tets (numpy.ndarray): An (self.N_tets x 4) array containing the 4 indices of the vertices of the self.N_tets
                tetrahedra that make up the mesh.
         BC_triangles (dict[str, numpy.ndarray]):
 
     Example:
         An element of this class can be initialized in the following way
 
-            >>> import edg_acoustics
-            >>> BC_labels = {'CNRBC': 12, 'slip': 11, 'impedance': 33}
-            >>> filename = "path_to_my_mesh_file/mesh_filename.msh"
-            >>> mesh = edg_acoustics.Mesh(filename, BC_labels)
+        >>> import edg_acoustics
+        >>> BC_labels = {'slip': 11, 'impedance1': 13, 'impedance2': 14, 'impedance3': 15}
+        >>> filename = "../data/tests/mesh/CoarseMesh.msh"
+        >>> mesh = edg_acoustics.Mesh(filename, BC_labels)
+        <BLANKLINE>
+        >>> mesh.N_BC_triangles
+        {'slip': 5347, 'impedance1': 400, 'impedance2': 3576, 'impedance3': 3294}
+
     """
 
     def __init__(self, filename: str, BC_labels: dict[str, int]):
         # Init from file
         self.__init_from_file(filename, BC_labels)
 
     def __init_from_file(self, filename: str, BC_labels: dict[str, int]):
-        print("Init from filename")
-
         # Load mesh data from mesh file
         mesh_data = meshio.read(filename)
 
@@ -101,16 +103,16 @@ def __init_from_file(self, filename: str, BC_labels: dict[str, int]):
         self.vertices = mesh_data.points
 
         # Check if all labels provided as input exist in the mesh data and vice versa, if not, raise error
-        BC_labels_in_mesh = sorted(numpy.unique(mesh_data.cell_data_dict['gmsh:physical']['triangle']))  # get all labels in the mesh, sort for faster comparison below
+        BC_labels_in_mesh = sorted(numpy.unique(mesh_data.cell_data_dict['gmsh:physical']['triangle']))  # get labels in the mesh, sort for faster comparison below
         BC_labels_in_input = sorted(BC_labels.values())  # get all labels specified in input
         if not BC_labels_in_input == BC_labels_in_mesh:
             raise ValueError(
                 "[edg_acoustics.Mesh] All BC labels must be present in the mesh and all labels in the mesh must be "
                 "present in BC_labels.")
 
         # Read the boundary triangles and their definitions separating them into the different boundary condition labels
-        self.N_BC_triangles = dict()
-        self.BC_triangles = dict()
+        self.N_BC_triangles = {}
+        self.BC_triangles = {}
         for BC_label in BC_labels:
             triangles_have_label = (mesh_data.cell_data_dict['gmsh:physical']['triangle'] == BC_labels[BC_label])  # array with bools specifying if triangle has BC_label or not
             self.N_BC_triangles[BC_label] = triangles_have_label.sum()  # number of triangles with label BC_label
@@ -123,6 +125,23 @@ def __init_from_file(self, filename: str, BC_labels: dict[str, int]):
         # Compute the mesh connectivity
         self.EToE, self.EToF = self.__compute_element_connectivity(self.tets)
 
+    # Operators --------------------------------------------------------------------------------------------------------
+    def __eq__(self, other):
+        if isinstance(other, type(self)):
+            # If self and other are mesh objects then check if all properties contain the same data
+            are_equal = (self.N_vertices == other.N_vertices
+                         and self.N_tets == other.N_tets
+                         and self.N_BC_triangles == other.N_BC_triangles
+                         and numpy.array_equal(self.vertices, other.vertices)
+                         and numpy.array_equal(self.tets, other.tets)
+                         and all(numpy.array_equal(item, other.BC_triangles[key]) for key, item in self.BC_triangles.items()))
+        else:
+            # If they are of different types, then they are not the same
+            are_equal = False
+
+        return are_equal
+
+    # ------------------------------------------------------------------------------------------------------------------
 
     # Static methods ---------------------------------------------------------------------------------------------------
     @staticmethod
@@ -156,7 +175,7 @@ def __compute_element_connectivity(tets: numpy.ndarray):
         # Get information on the number of faces, tets, and vertices
         N_faces_per_tet = 4  # number of faces per element
         N_tets = tets.shape[0]  # number of elements in the mesh
-        N_vertices = tets.max() + 1  # number of vertices in the mesh, +1 because indexing starts at 0
+        # N_vertices = tets.max() + 1  # number of vertices in the mesh, +1 because indexing starts at 0
 
         # Create a unique identifier for each face based on the vertices that make up the face
         # the order of the vertices does not matter.
@@ -201,10 +220,8 @@ def __compute_element_connectivity(tets: numpy.ndarray):
         # We now sort the face_ids so that we have the identical faces next to each other
         face_ids_sort_indices = numpy.argsort(face_ids)  # get the ordering that sorts the face_ids
         face_ids = face_ids[face_ids_sort_indices]  # sort the face ids
-        face_vertices = face_vertices[face_ids_sort_indices, :]  # reorder the faces so that their corresponding
-                                                                 # face_ids are sorted
-        face_vertices_idx = face_vertices_idx[face_ids_sort_indices]  # reorder the face indices so that their
-                                                                      # corresponding face_ids are sorted
+        face_vertices = face_vertices[face_ids_sort_indices, :]     # reorder the faces so that their corresponding face_ids are sorted
+        face_vertices_idx = face_vertices_idx[face_ids_sort_indices]  # reorder the face indices so that their corresponding face_ids are sorted
 
         # Find the indices of face_ids of all interior faces, i.e., that are shared by two elements
         # i.e., faces that appear twice (one time for each element)
@@ -257,5 +274,3 @@ def EToV(self):
                tetrahedra that make up the mesh. It returns the value in self.tets, since it is the same data."""
         return self.tets
     # ------------------------------------------------------------------------------------------------------------------
-
-

edg_acoustics/mesh.py

@@ -2,6 +2,7 @@
 """
 import pytest
 import numpy
+import pickle
 
 import edg_acoustics
 
@@ -11,7 +12,7 @@ def mesh_file_data_valid():
     """Define valid file input data for mesh generation.
     """
     # The valid filename with mesh data
-    filename = "../data/tests/mesh/CoarseMesh.msh"
+    filename = "data/tests/mesh/CoarseMesh.msh"
 
     return filename
 
@@ -56,20 +57,28 @@ def BC_labels_data_missing_invalid():
 
 
 def test_mesh_file_data_valid_input(mesh_file_data_valid, BC_labels_data_valid):
+    # Load reference mesh from file
+    with open('data/tests/mesh/Coarse_mesh_object.dat', 'rb') as mesh_file:
+        mesh_ref = pickle.load(mesh_file)
+
+    # Load mesh data from gmsh file
     mesh = edg_acoustics.Mesh(mesh_file_data_valid, BC_labels_data_valid)
 
+    # Compare mesh to reference data
+    assert (mesh == mesh_ref)
+
 
 def test_mesh_file_extra_label_invalid_input(mesh_file_data_valid, BC_labels_data_extra_invalid):
     with pytest.raises(ValueError) as excinfo:
-        mesh = edg_acoustics.Mesh(mesh_file_data_valid, BC_labels_data_extra_invalid)
+        _ = edg_acoustics.Mesh(mesh_file_data_valid, BC_labels_data_extra_invalid)
 
     assert "[edg_acoustics.Mesh] All BC labels must be present in the mesh and all labels in the mesh must be " \
                 "present in BC_labels." in str(excinfo.value)
 
 
 def test_mesh_file_missing_label_invalid_input(mesh_file_data_valid, BC_labels_data_missing_invalid):
     with pytest.raises(ValueError) as excinfo:
-        mesh = edg_acoustics.Mesh(mesh_file_data_valid, BC_labels_data_missing_invalid)
+        _ = edg_acoustics.Mesh(mesh_file_data_valid, BC_labels_data_missing_invalid)
 
     assert "[edg_acoustics.Mesh] All BC labels must be present in the mesh and all labels in the mesh must be " \
                 "present in BC_labels." in str(excinfo.value)
@@ -79,7 +88,7 @@ def test_mesh_connectivity(mesh_file_data_valid, BC_labels_data_valid):
     mesh = edg_acoustics.Mesh(mesh_file_data_valid, BC_labels_data_valid)
 
     # Load the reference data
-    reference_data = numpy.load('../data/tests/mesh/CoarseMesh_connectivity.npz')
+    reference_data = numpy.load('data/tests/mesh/CoarseMesh_connectivity.npz')
 
     # Check if mesh.EToV was correctly generated
     assert numpy.abs(mesh.EToV - reference_data['EToV']).sum() == 0