Merge pull request #307 from nschloe/meshio-bump

update for new meshio

.github/workflows/ci.yml

@@ -9,7 +9,7 @@ jobs:
     - uses: actions/setup-python@v1
       with:
         python-version: "3.x"
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v2
     - name: Lint with flake8
       run: |
         pip install flake8
@@ -28,7 +28,7 @@ jobs:
     - uses: actions/setup-python@v1
       with:
         python-version: "3.x"
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v2
     - run: sudo apt install -y python3-pip
     - name: Install gmsh from PPA
       run: |
@@ -50,5 +50,5 @@ jobs:
         gmsh --version
         pip install pytest pytest-cov
         cd test/ && pytest --cov pygmsh
-    - name: Submit to codecov
-      run: bash <(curl -s https://codecov.io/bash)
+    # - name: Submit to codecov
+    #   run: bash <(curl -s https://codecov.io/bash)

README.md

@@ -8,10 +8,11 @@
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg?style=flat-square)](https://github.com/psf/black)
 [![Documentation Status](https://readthedocs.org/projects/pygmsh/badge/?version=latest&style=flat-square)](https://pygmsh.readthedocs.org/en/latest/?badge=latest)
 [![PyPi Version](https://img.shields.io/pypi/v/pygmsh.svg?style=flat-square)](https://pypi.org/project/pygmsh)
+[![PyPI pyversions](https://img.shields.io/pypi/pyversions/pygmsh.svg?style=flat-square)](https://pypi.org/pypi/pygmsh/)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1173105.svg?style=flat-square)](https://doi.org/10.5281/zenodo.1173105)
 [![GitHub stars](https://img.shields.io/github/stars/nschloe/pygmsh.svg?style=flat-square&logo=github&label=Stars&logoColor=white)](https://github.com/nschloe/pygmsh)
 [![PyPi downloads](https://img.shields.io/pypi/dm/pygmsh.svg?style=flat-square)](https://pypistats.org/packages/pygmsh)
-[![Slack](https://img.shields.io/static/v1?logo=slack&label=slack&message=chat&color=4a154b&style=flat-square)](https://app.slack.com/client/TTL6Q54A3/CTLGZQFML/)
+[![Slack](https://img.shields.io/static/v1?logo=slack&label=chat&message=on%20slack&color=4a154b&style=flat-square)](https://app.slack.com/client/TTL6Q54A3/CTLGZQFML/)
 
 [Gmsh](https://gmsh.info/) is a powerful mesh generation tool with a scripting language
 that is notoriously hard to write.

pygmsh/__about__.py

@@ -1,4 +1,4 @@
-__version__ = "6.0.2"
+__version__ = "6.0.3"
 __author__ = "Nico Schlömer"
 __author_email__ = "[email protected]"
 __copyright__ = f"Copyright (c) 2013-2020, {__author__} <{__author_email__}>"

pygmsh/built_in/geometry.py

@@ -262,7 +262,7 @@ def set_recombined_surfaces(self, surfaces):
         for i, surface in enumerate(surfaces):
             assert isinstance(
                 surface, (PlaneSurface, Surface)
-            ), "item {} is not a surface".format(i)
+            ), f"item {i} is not a surface"
         code = "Recombine Surface {{{}}}".format(
             ", ".join([surface.id for surface in surfaces])
         )

pygmsh/helpers.py

@@ -144,8 +144,7 @@ def generate_mesh(  # noqa: C901
     mesh = meshio.read(msh_filename)
 
     if remove_faces:
-        # Only keep the cells of highest topological dimension; discard faces
-        # and such.
+        # Only keep the cells of highest topological dimension; discard faces and such.
         two_d_cells = {"triangle", "quad"}
         three_d_cells = {
             "tetra",
@@ -160,21 +159,26 @@ def generate_mesh(  # noqa: C901
         elif any(k in mesh.cells for k in two_d_cells):
             keep_keys = two_d_cells.intersection(mesh.cells.keys())
         else:
-            keep_keys = mesh.cells.keys()
+            keep_keys = set(cell_type for cell_type, _ in mesh.cells)
 
-        mesh.cells = {key: mesh.cells[key] for key in keep_keys}
-        mesh.cell_data = {key: mesh.cell_data[key] for key in keep_keys}
+        for key, val in mesh.cell_data.items():
+            mesh.cell_data[key] = [
+                d for d, c in zip(val, mesh.cells) if c[0] in keep_keys
+            ]
+        mesh.cells = [c for c in mesh.cells if c[0] in keep_keys]
 
     if prune_vertices:
         # Make sure to include only those vertices which belong to a cell.
-        ncells = numpy.concatenate([numpy.concatenate(c) for c in mesh.cells.values()])
+        ncells = numpy.concatenate([numpy.concatenate(c) for _, c in mesh.cells])
         uvertices, uidx = numpy.unique(ncells, return_inverse=True)
 
         k = 0
-        for key in mesh.cells.keys():
-            n = numpy.prod(mesh.cells[key].shape)
-            mesh.cells[key] = uidx[k : k + n].reshape(mesh.cells[key].shape)
+        cells = []
+        for key, cellblock in mesh.cells:
+            n = numpy.prod(cellblock.shape)
+            cells.append((key, uidx[k : k + n].reshape(cellblock.shape)))
             k += n
+        mesh.cells = cells
 
         mesh.points = mesh.points[uvertices]
         for key in mesh.point_data:

setup.py

@@ -1,4 +1,3 @@
-import codecs
 import os
 
 from setuptools import find_packages, setup
@@ -10,33 +9,34 @@
     exec(f.read(), about)
 
 
-def read(fname):
-    return codecs.open(os.path.join(base_dir, fname), encoding="utf-8").read()
-
-
 setup(
     name="pygmsh",
     version=about["__version__"],
     author=about["__author__"],
     author_email=about["__author_email__"],
     packages=find_packages(),
     description="Python frontend for Gmsh",
-    long_description=read("README.md"),
+    long_description=open("README.md").read(),
     long_description_content_type="text/markdown",
     url=about["__website__"],
-    project_urls={"Documentation": "https://pygmsh.readthedocs.org/en/latest"},
+    project_urls={
+        "Code": "https://github.com/nschloe/meshio",
+        "Documentation": "https://pygmsh.readthedocs.org/en/latest",
+        "Issue tracker": "https://github.com/nschloe/meshio/issues",
+    },
     license=about["__license__"],
     platforms="any",
-    install_requires=["meshio >=3.0, <4.0", "numpy >= 1.9"],
+    install_requires=["meshio >=4.0, <5.0", "numpy >= 1.9"],
     python_requires=">=3.6",
     keywords=["mesh", "gmsh", "mesh generation", "mathematics"],
     classifiers=[
         about["__status__"],
         about["__license__"],
         "Intended Audience :: Science/Research",
         "Operating System :: OS Independent",
-        "Programming Language :: Python",
-        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
         "Topic :: Scientific/Engineering :: Mathematics",
     ],
 )

test/helpers.py

@@ -42,29 +42,31 @@ def get_simplex_volumes(pts, cells):
 
 
 def compute_volume(mesh):
-    if "tetra" in mesh.cells:
+    if "tetra" in mesh.cells_dict:
         vol = math.fsum(
-            get_simplex_volumes(*prune_nodes(mesh.points, mesh.cells["tetra"]))
+            get_simplex_volumes(*prune_nodes(mesh.points, mesh.cells_dict["tetra"]))
         )
-    elif "triangle" in mesh.cells or "quad" in mesh.cells:
+    elif "triangle" in mesh.cells_dict or "quad" in mesh.cells_dict:
         vol = 0.0
-        if "triangle" in mesh.cells:
+        if "triangle" in mesh.cells_dict:
             # triangles
             vol += math.fsum(
-                get_triangle_volumes(*prune_nodes(mesh.points, mesh.cells["triangle"]))
+                get_triangle_volumes(
+                    *prune_nodes(mesh.points, mesh.cells_dict["triangle"])
+                )
             )
-        if "quad" in mesh.cells:
+        if "quad" in mesh.cells_dict:
             # quad: treat as two triangles
-            quads = mesh.cells["quad"].T
+            quads = mesh.cells_dict["quad"].T
             split_cells = numpy.column_stack(
                 [[quads[0], quads[1], quads[2]], [quads[0], quads[2], quads[3]]]
             ).T
             vol += math.fsum(
                 get_triangle_volumes(*prune_nodes(mesh.points, split_cells))
             )
     else:
-        assert "line" in mesh.cells
-        segs = numpy.diff(mesh.points[mesh.cells["line"]], axis=1).squeeze()
+        assert "line" in mesh.cells_dict
+        segs = numpy.diff(mesh.points[mesh.cells_dict["line"]], axis=1).squeeze()
         vol = numpy.sum(numpy.sqrt(numpy.einsum("...j, ...j", segs, segs)))
 
     return vol

test/test_booleans.py

@@ -105,13 +105,13 @@ def test_square_circle_slice():
     val = compute_volume(mesh)
     assert np.abs(val - ref) < 1e-3 * ref
 
-    outer_mask = np.where(mesh.cell_data["triangle"]["gmsh:geometrical"] == 13)[0]
+    outer_mask = np.where(mesh.cell_data["gmsh:geometrical"][2] == 13)[0]
     outer_cells = {}
-    outer_cells["triangle"] = mesh.cells["triangle"][outer_mask]
+    outer_cells["triangle"] = mesh.cells_dict["triangle"][outer_mask]
 
-    inner_mask = np.where(mesh.cell_data["triangle"]["gmsh:geometrical"] == 12)[0]
+    inner_mask = np.where(mesh.cell_data["gmsh:geometrical"][2] == 12)[0]
     inner_cells = {}
-    inner_cells["triangle"] = mesh.cells["triangle"][inner_mask]
+    inner_cells["triangle"] = mesh.cells_dict["triangle"][inner_mask]
 
     ref = 1 - 0.1 ** 2 * np.pi
     value = compute_volume(meshio.Mesh(mesh.points, outer_cells))
@@ -138,17 +138,16 @@ def test_fragments_diff_union():
     mesh = pygmsh.generate_mesh(geo_object)
     assert np.abs((compute_volume(mesh) - 1) / 1) < 1e-3
     surf = 1 - 0.1 ** 2 * np.pi
-    outer_mask = np.where(mesh.cell_data["triangle"]["gmsh:physical"] == 1)[0]
+    outer_mask = np.where(mesh.cell_data_dict["gmsh:physical"]["triangle"] == 1)[0]
     outer_cells = {}
-    outer_cells["triangle"] = mesh.cells["triangle"][outer_mask]
+    outer_cells["triangle"] = mesh.cells_dict["triangle"][outer_mask]
 
-    inner_mask = np.where(mesh.cell_data["triangle"]["gmsh:physical"] == 2)[0]
+    inner_mask = np.where(mesh.cell_data_dict["gmsh:physical"]["triangle"] == 2)[0]
     inner_cells = {}
-    inner_cells["triangle"] = mesh.cells["triangle"][inner_mask]
+    inner_cells["triangle"] = mesh.cells_dict["triangle"][inner_mask]
 
     value = compute_volume(meshio.Mesh(mesh.points, outer_cells))
     assert np.abs(value - surf) < 1e-2 * surf
-    return
 
 
 def test_diff_physical_assignment():
@@ -166,8 +165,8 @@ def test_diff_physical_assignment():
     geo_object2.boolean_difference([surf1], [surf2])
     mesh = pygmsh.generate_mesh(geo_object2)
     assert np.allclose(
-        mesh.cell_data["triangle"]["gmsh:physical"],
-        np.ones(mesh.cells["triangle"].shape[0]),
+        mesh.cell_data_dict["gmsh:physical"]["triangle"],
+        np.ones(mesh.cells_dict["triangle"].shape[0]),
     )
     surf = 1 - 0.1 ** 2 * np.pi
     assert np.abs((compute_volume(mesh) - surf) / surf) < 1e-3

test/test_hex.py

@@ -29,7 +29,8 @@ def test(lcar=1.0):
     # TODO compute hex volumes
     assert (
         abs(
-            compute_volume(meshio.Mesh(mesh.points, {"quad": mesh.cells["quad"]})) - ref
+            compute_volume(meshio.Mesh(mesh.points, {"quad": mesh.cells_dict["quad"]}))
+            - ref
         )
         < 1.0e-2 * ref
     )

test/test_opencascade_regular_extrusion.py

@@ -23,7 +23,7 @@ def test():
 
     # Each grid-cell from layered extrusion will result in 6 tetrahedrons.
     ref_tetras = 6 * x_layers * y_layers * z_layers
-    assert len(mesh.cells["tetra"]) == ref_tetras
+    assert len(mesh.cells_dict["tetra"]) == ref_tetras
 
     return mesh
 

test/test_recombine.py

@@ -1,6 +1,7 @@
-import pygmsh
 import numpy as np
 
+import pygmsh
+
 
 def test():
     geom = pygmsh.built_in.Geometry()
@@ -21,9 +22,9 @@ def test():
 
     mesh = pygmsh.generate_mesh(geom)
 
-    assert "quad" in mesh.cells.keys()
+    assert "quad" in mesh.cells_dict.keys()
     ref = np.array([[0, 4, 8, 7], [7, 8, 6, 2], [4, 1, 5, 8], [8, 5, 3, 6]])
-    assert np.array_equal(ref, mesh.cells["quad"])
+    assert np.array_equal(ref, mesh.cells_dict["quad"])
 
     return mesh
 

test/test_regular_extrusion.py

@@ -23,7 +23,7 @@ def test():
 
     # Each grid-cell from layered extrusion will result in 6 tetrahedrons.
     ref_tetras = 6 * x_layers * y_layers * z_layers
-    assert len(mesh.cells["tetra"]) == ref_tetras
+    assert len(mesh.cells_dict["tetra"]) == ref_tetras
 
     return mesh
 

test/test_transfinite.py

@@ -10,7 +10,7 @@ def test(lcar=1.0):
     geom.set_transfinite_surface(poly.surface, size=[11, 9])
 
     mesh = pygmsh.generate_mesh(geom, geo_filename="transfinite.geo")
-    assert len(mesh.cells["triangle"]) == 10 * 8 * 2
+    assert len(mesh.cells_dict["triangle"]) == 10 * 8 * 2
     return mesh