added MFEM 3D export feature

.github/pull_request_template.md

@@ -0,0 +1,24 @@
+# Overview
+
+Description
+
+## Addressed issues
+
+*  Issues addressed
+
+## Showcase
+
+A short / one-liner example to highlight the (new) feature
+
+```python
+import gustaf
+
+...
+```
+
+## Checklists
+
+* [ ] Set target branch to develop
+* [ ] Documentations are up-to-date.
+* [ ] Added example(s)
+* [ ] Added test(s)

.github/workflows/tests.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
-        os: [ubuntu-latest, macos-13, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
       - uses: actions/checkout@v4

.pre-commit-config.yaml

@@ -7,6 +7,7 @@
 # use default options for ci
 ci:
   autoupdate_schedule: "weekly"
+  autoupdate_branch: 'develop'
   submodules: false
 
 repos:
@@ -21,25 +22,21 @@ repos:
   - id: check-toml
   - id: check-yaml
   - id: debug-statements
-  - id: end-of-file-fixer
   - id: mixed-line-ending
   - id: requirements-txt-fixer
   - id: trailing-whitespace
 
-- repo: https://github.com/psf/black
-  rev: "25.1.0"
-  hooks:
-  - id: black
-    args: [--line-length=79]
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   rev: v0.12.12
   hooks:
+    # Run the linter.
     - id: ruff-check
-      args: [
-        --fix,
-        --exit-non-zero-on-fix,
-      ]
+      types_or: [python, pyi]
+      args: [--fix, --exit-non-zero-on-fix]
+    # Run the formatter.
+    - id: ruff-format
+      types_or: [python, pyi]
 
 - repo: https://github.com/codespell-project/codespell
   rev: v2.4.1
@@ -48,9 +45,3 @@ repos:
     additional_dependencies:
       - tomli
     args: [-w]
-
-- repo: https://github.com/keewis/blackdoc
-  rev: v0.4.1
-  hooks:
-  - id: blackdoc
-    args: [--line-length=75]

gustaf/create/faces.py

@@ -125,7 +125,7 @@ def to_simplex(quad, alternate=False):
     else:
         tri = quad
         utils.log.debug(
-            "Non quadrilateral mesh provided, return original" " mesh."
+            "Non quadrilateral mesh provided, return original mesh."
         )
 
     return tri

gustaf/io/mfem.py

@@ -107,97 +107,176 @@ def extract_values(fname, start_index, n_lines, total_lines, dtype):
         return mesh
 
 
+def format_array(array):
+    """Format NumPy array into string. Each entry in a row is separated by
+    a blank space and every row is separated by a new line.
+
+    Parameters
+    ------------
+    array: NumPy array
+
+    Returns
+    ------------
+    str
+    """
+    row_strings = [" ".join(map(str, row)) for row in array]
+    return "\n".join(row_strings)
+
+
 def export(fname, mesh):
     """Export mesh in MFEM format. Supports 2D triangle and quadrilateral
-    meshes. Does not support different element attributes or difference in
-    vertex dimension and mesh dimension.
+    meshes as well as 3D tetrahedral and hexahedral meshes. Also extracts
+    boundary information from the GustafObject.BC variable. Does not
+    support different element attributes or difference in vertex dimension
+    and mesh dimension.
 
     Parameters
     ------------
     fname: str
-    mesh: Faces
+    mesh: Faces, Volumes
 
     Returns
     ------------
     None
     """
-    # Basic infos
-    nvertices, dim = mesh.vertices.shape
+    # Get dimension info based on vertices and choose corresponding export
+    dim = mesh.vertices.shape[1]
+
+    if dim == 2:
+        elements_string, boundary_string, vertices_string = _export_2d(mesh)
+    elif dim == 3:
+        elements_string, boundary_string, vertices_string = _export_3d(mesh)
+    else:
+        raise NotImplementedError(
+            f"Sorry, we cannot export meshes of dimension {dim}."
+        )
 
-    def format_array(array):
-        """Format NumPy array into string. Each entry in a row is separated by
-        a blank space and every row is separated by a new line.
+    with open(fname, "w") as f:
+        f.write("MFEM mesh v1.0\n\n")
+        f.write(f"dimension\n{dim}\n\n")
+        f.write(elements_string)
+        f.write(boundary_string)
+        f.write(vertices_string)
 
-        Parameters
-        ------------
-        array: NumPy array
 
-        Returns
-        ------------
-        str
-        """
-        row_strings = [" ".join(map(str, row)) for row in array]
-        return "\n".join(row_strings)
+def _export_2d(mesh):
+    """Internal function to export 2D meshes.
 
-    # Export 2D mesh
-    if dim == 2:
-        # Elements
-        element_attribute = 1  # Other numbers not yet supported
-        elements = mesh.elements
-        n_elements, n_element_vertices = elements.shape
-        if n_element_vertices == 3:
-            geometry_type = geometry_types["TRIANGLE"]
-        elif n_element_vertices == 4:
-            geometry_type = geometry_types["SQUARE"]
-        else:
-            raise NotImplementedError(
-                "Sorry, we cannot export mesh with elements "
-                f"with {n_element_vertices} vertices."
-            )
-        e = np.ones((n_elements, 1), dtype=settings.INT_DTYPE)
-        elements_array = np.hstack(
-            (element_attribute * e, geometry_type * e, elements)
+    Parameters
+    ------------
+    mesh: Faces
+
+    Returns
+    ------------
+    elements_string, boundary_string, vertices_string
+    """
+    element_attribute = 1  # Other numbers not yet supported
+    elements = mesh.elements
+    n_elements = elements.shape[0]
+    if mesh.whatami == "tri":
+        geometry_type = geometry_types["TRIANGLE"]
+    elif mesh.whatami == "quad":
+        geometry_type = geometry_types["SQUARE"]
+    else:
+        raise NotImplementedError(
+            f"Sorry, we cannot export 2D meshes of type {mesh.whatami}."
         )
-        elements_array_string = format_array(elements_array)
-        elements_string = f"elements\n{n_elements}\n"
-        elements_string += f"{elements_array_string}\n\n"
-
-        # Boundary
-        edges = mesh.edges()
-        nboundary_edges = sum(map(len, mesh.BC.values()))
-        boundary_array = np.empty(
-            (nboundary_edges, 4), dtype=settings.INT_DTYPE
+    e = np.ones((n_elements, 1), dtype=settings.INT_DTYPE)
+    elements_array = np.hstack(
+        (element_attribute * e, geometry_type * e, elements)
+    )
+    elements_array_string = format_array(elements_array)
+    elements_string = f"elements\n{n_elements}\n"
+    elements_string += f"{elements_array_string}\n\n"
+
+    # Boundary
+    edges = mesh.edges()
+    nboundary_edges = sum(map(len, mesh.BC.values()))
+    boundary_array = np.empty((nboundary_edges, 4), dtype=settings.INT_DTYPE)
+    startrow = 0
+    # Add boundary one by one as SEGMENTs
+    for bid, edgeids in mesh.BC.items():
+        nedges = len(edgeids)
+        e = np.ones(nedges).reshape(-1, 1)
+        vertex_list = edges[edgeids, :]
+        boundary_array[startrow : (startrow + nedges), :] = np.hstack(
+            (int(bid) * e, geometry_types["SEGMENT"] * e, vertex_list)
         )
-        startrow = 0
-        # Add boundary one by one as SEGMENTs
-        for bid, edgeids in mesh.BC.items():
-            nedges = len(edgeids)
-            e = np.ones(nedges).reshape(-1, 1)
-            vertex_list = edges[edgeids, :]
-            boundary_array[startrow : (startrow + nedges), :] = np.hstack(
-                (int(bid) * e, geometry_types["SEGMENT"] * e, vertex_list)
-            )
-            startrow += nedges
-
-        boundary_array_string = format_array(boundary_array)
-        boundary_string = f"boundary\n{nboundary_edges}\n"
-        boundary_string += f"{boundary_array_string}\n\n"
-
-        # Vertices
-        vdim = 2  # Currently only option
-        vertices_array_string = format_array(mesh.vertices)
-        vertices_string = f"vertices\n{nvertices}\n{vdim}\n"
-        vertices_string += f"{vertices_array_string}"
-
-        with open(fname, "w") as f:
-            f.write("MFEM mesh v1.0\n\n")
-            f.write(f"dimension\n{dim}\n\n")
-            f.write(elements_string)
-            f.write(boundary_string)
-            f.write(vertices_string)
-
-    # Export 3D mesh
+        startrow += nedges
+
+    boundary_array_string = format_array(boundary_array)
+    boundary_string = f"boundary\n{nboundary_edges}\n"
+    boundary_string += f"{boundary_array_string}\n\n"
+
+    # Vertices
+    vdim = 2  # Currently only option
+    vertices_array_string = format_array(mesh.vertices)
+    nvertices = mesh.vertices.shape[0]
+    vertices_string = f"vertices\n{nvertices}\n{vdim}\n"
+    vertices_string += f"{vertices_array_string}"
+    return elements_string, boundary_string, vertices_string
+
+
+def _export_3d(mesh):
+    """Internal function to export 3D meshes.
+
+    Parameters
+    ------------
+    mesh: Volumes
+
+    Returns
+    ------------
+    elements_string, boundary_string, vertices_string
+    """
+    element_attribute = 1  # Other numbers not yet supported
+    elements = mesh.elements
+    n_elements = elements.shape[0]
+    if mesh.whatami == "tet":
+        body_geometry_type = geometry_types["TETRAHEDRON"]
+        face_geometry_type = geometry_types["TRIANGLE"]
+        n_face_vertices = 3
+    elif mesh.whatami == "hexa":
+        body_geometry_type = geometry_types["CUBE"]
+        face_geometry_type = geometry_types["SQUARE"]
+        n_face_vertices = 4
     else:
         raise NotImplementedError(
-            f"Sorry, we cannot export mesh of dimension {dim}."
+            f"Sorry, we cannot export 3D meshes of type {mesh.whatami}."
         )
+    e = np.ones((n_elements, 1), dtype=settings.INT_DTYPE)
+    elements_array = np.hstack(
+        (element_attribute * e, body_geometry_type * e, elements)
+    )
+    elements_array_string = format_array(elements_array)
+    elements_string = f"elements\n{n_elements}\n"
+    elements_string += f"{elements_array_string}\n\n"
+
+    # Boundary
+    faces = mesh.faces()
+
+    nboundary_faces = sum(map(len, mesh.BC.values()))
+    boundary_array = np.empty(
+        (nboundary_faces, n_face_vertices + 2), dtype=settings.INT_DTYPE
+    )
+    startrow = 0
+    # Add boundary one by one as TRIANGLEs
+    for bid, faceids in mesh.BC.items():
+        nfaces = len(faceids)
+        e = np.ones(nfaces).reshape(-1, 1)
+        vertex_list = faces[faceids, :]
+        boundary_array[startrow : (startrow + nfaces), :] = np.hstack(
+            (int(bid) * e, face_geometry_type * e, vertex_list)
+        )
+        startrow += nfaces
+
+    boundary_array_string = format_array(boundary_array)
+    boundary_string = f"boundary\n{nboundary_faces}\n"
+    boundary_string += f"{boundary_array_string}\n\n"
+
+    # Vertices
+    vdim = 3  # Currently only option
+    vertices_array_string = format_array(mesh.vertices)
+    nvertices = mesh.vertices.shape[0]
+    vertices_string = f"vertices\n{nvertices}\n{vdim}\n"
+    vertices_string += f"{vertices_array_string}"
+    return elements_string, boundary_string, vertices_string

gustaf/utils/tictoc.py

@@ -88,7 +88,7 @@ def summary(self, log=True, print_=False):
            times for each lap from the timer start (cumulative time).
         """
         start = self._laps[0]
-        cumulative = [f"{lap-start:.10f}" for lap in self._laps[1:]]
+        cumulative = [f"{lap - start:.10f}" for lap in self._laps[1:]]
 
         if log or print_:
             message = [f"\n+++ {self._title} - time logs +++\n"]

pyproject.toml

@@ -52,16 +52,16 @@ test = [
     "napf>=0.0.5",
 ]
 dev = [
-    "pytest",
-    "funi",
-    "napf",
+    "pre-commit",
     "vedo>=2023.5.0",
     "scipy",
     "meshio",
+    "napf>=0.0.5",
+    "funi>=0.0.1",
     "requests",
-    "pre-commit",
     "ipywidgets",
     "k3d",
+    "pytest",
 ]
 
 [tool.setuptools]
@@ -82,7 +82,8 @@ version = {attr = "gustaf._version.version"}
 
 [tool.ruff]
 line-length = 79
-target-version = "py38"
+target-version = "py39"
+exclude = ["tests/data"]
 
 [tool.ruff.lint]
 select = [