diff --git a/.circleci/config.yml b/.circleci/config.yml index bcbca9d..89107ea 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -28,7 +28,8 @@ jobs: - run: apt-get install -y git python3-pip python3-vtk7 - run: pip3 install -U pytest pytest-cov excode - checkout - # install + # install; need a new pip + - run: pip3 install pip -U --force - run: pip3 install -r test_requirements.txt - run: pip3 install .[all] # The tests diff --git a/LICENSE b/LICENSE index 913b636..94a9ed0 100644 --- a/LICENSE +++ b/LICENSE @@ -1,21 +1,674 @@ -The MIT License (MIT) - -Copyright (c) 2017-2020 Nico Schlömer - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/Makefile b/Makefile index ca73ccd..bfbea3c 100644 --- a/Makefile +++ b/Makefile @@ -11,11 +11,12 @@ tag: # git push --tags curl -H "Authorization: token `cat $(HOME)/.github-access-token`" -d '{"tag_name": "v$(VERSION)"}' https://api.github.com/repos/nschloe/meshplex/releases -upload: setup.py +upload: @if [ "$(shell git rev-parse --abbrev-ref HEAD)" != "master" ]; then exit 1; fi rm -f dist/* - python3 setup.py sdist - python3 setup.py bdist_wheel + # python3 setup.py sdist bdist_wheel + # https://stackoverflow.com/a/58756491/353337 + python3 -m pep517.build --source --binary . twine upload dist/* publish: tag upload diff --git a/README.md b/README.md index 5342968..63050f3 100644 --- a/README.md +++ b/README.md @@ -138,5 +138,4 @@ pytest ``` ### License - -meshplex is published under the [MIT license](https://en.wikipedia.org/wiki/MIT_License). +This software is published under the [GPLv3 license](https://www.gnu.org/licenses/gpl-3.0.en.html). diff --git a/meshplex/base.py b/meshplex/base.py index 3758f9a..f7d597e 100644 --- a/meshplex/base.py +++ b/meshplex/base.py @@ -8,11 +8,16 @@ def compute_tri_areas(ei_dot_ej): - return 0.5 * numpy.sqrt( + vol2 = 0.25 * ( ei_dot_ej[2] * ei_dot_ej[0] + ei_dot_ej[0] * ei_dot_ej[1] + ei_dot_ej[1] * ei_dot_ej[2] ) + # vol2 is the squared volume, but can be slightly negative if it comes to round-off + # errors. Corrrect those. + assert numpy.all(vol2 > -1.0e-14) + vol2[vol2 < 0] = 0.0 + return numpy.sqrt(vol2) def compute_ce_ratios(ei_dot_ej, tri_areas): diff --git a/meshplex/mesh_tri.py b/meshplex/mesh_tri.py index 66aeb31..ae56669 100644 --- a/meshplex/mesh_tri.py +++ b/meshplex/mesh_tri.py @@ -141,6 +141,22 @@ def __repr__(self): # self.update_values() # return + @property + def euler_characteristic(self): + # number of vertices - number of edges + number of faces + if "edges" not in self.cells: + self.create_edges() + return ( + self.node_coords.shape[0] + - self.edges["nodes"].shape[0] + + self.cells["nodes"].shape[0] + ) + + @property + def genus(self): + # https://math.stackexchange.com/a/85164/36678 + return 1 - self.euler_characteristic / 2 + @property def ce_ratios(self): if self._ce_ratios is None: @@ -171,8 +187,8 @@ def update_values(self): if self.cell_volumes is not None or self.ce_ratios is not None: self.cell_volumes = compute_tri_areas(self.ei_dot_ej) - self._ce_ratios = compute_ce_ratios(self.ei_dot_ej, self.cell_volumes) + self._ce_ratios = None self._interior_edge_lengths = None self._cell_circumcenters = None self._interior_ce_ratios = None @@ -185,6 +201,51 @@ def update_values(self): self._cell_centroids = None return + def remove_degenerate_cells(self, threshold): + is_okay = self.cell_volumes > threshold + + self.cell_volumes = self.cell_volumes[is_okay] + self.cells["nodes"] = self.cells["nodes"][is_okay] + self.idx_hierarchy = self.idx_hierarchy[..., is_okay] + + if "edges" in self.cells: + self.cells["edges"] = self.cells["edges"][is_okay] + + if self._ce_ratios is not None: + self._ce_ratios = self._ce_ratios[is_okay] + + if self.half_edge_coords is not None: + self.half_edge_coords = self.half_edge_coords[:, is_okay] + + if self.ei_dot_ej is not None: + self.ei_dot_ej = self.ei_dot_ej[:, is_okay] + + if self.ei_dot_ei is not None: + self.ei_dot_ei = self.ei_dot_ei[:, is_okay] + + if self._cell_centroids is not None: + self._cell_centroids = self._cell_centroids[is_okay] + + if self._cell_circumcenters is not None: + self._cell_circumcenters = self._cell_circumcenters[is_okay] + + if self._cell_partitions is not None: + self._cell_partitions = self._cell_partitions[is_okay] + + self._interior_edge_lengths = None + self._interior_ce_ratios = None + self._control_volumes = None + self._cv_centroids = None + self._cvc_cell_mask = None + self._surface_areas = None + self._signed_cell_areas = None + self._is_boundary_node = None + self.is_boundary_edge = None + + self.create_edges() + + return numpy.sum(~is_okay) + @property def ce_ratios_per_interior_edge(self): """ @@ -757,7 +818,7 @@ def save(self, filename, *args, **kwargs): """Save the mesh to a file. """ _, file_extension = os.path.splitext(filename) - if file_extension in ".png": + if file_extension in [".png", ".svg"]: import matplotlib.pyplot as plt self.plot(*args, **kwargs) diff --git a/setup.cfg b/setup.cfg index 2143097..a1e4438 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = meshplex -version = 0.12.3 +version = 0.13.0 author = Nico Schlömer email = nico.schloemer@gmail.com description = Fast tools for simplex meshes, @@ -10,12 +10,12 @@ project_urls = Issues=https://github.com/nschloe/meshplex/issues long_description = file: README.md long_description_content_type = text/markdown -license = MIT +license = GPLv3 platforms = any classifiers = Development Status :: 4 - Beta Intended Audience :: Science/Research - License :: OSI Approved :: MIT License + License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+) Operating System :: OS Independent Programming Language :: Python Programming Language :: Python :: 3 diff --git a/setup.py b/setup.py deleted file mode 100644 index 7f1a176..0000000 --- a/setup.py +++ /dev/null @@ -1,4 +0,0 @@ -from setuptools import setup - -if __name__ == "__main__": - setup() diff --git a/test/mesh_tri_test.py b/test/mesh_tri_test.py index e66c9ab..347b0bf 100644 --- a/test/mesh_tri_test.py +++ b/test/mesh_tri_test.py @@ -52,6 +52,8 @@ def test_unit_triangle(): assert mesh.num_delaunay_violations() == 0 + assert mesh.genus == 0.5 + mesh.get_cell_mask() mesh.get_edge_mask() mesh.get_vertex_mask() @@ -74,8 +76,6 @@ def is_inside(self, X): mesh.save(filename) os.remove(filename) - return - def test_regular_tri_additional_points(): points = numpy.array( @@ -127,9 +127,7 @@ def test_regular_tri_additional_points(): [[0.25, 0.25, 0.0], [2.0 / 3.0, 1.0 / 6.0, 0.0], [1.0 / 6.0, 2.0 / 3.0, 0.0]], tol, ) - assert mesh.num_delaunay_violations() == 0 - return def test_regular_tri_order(): @@ -162,8 +160,6 @@ def test_regular_tri_order(): assert mesh.num_delaunay_violations() == 0 - return - @pytest.mark.parametrize("a", [1.0, 2.0]) def test_regular_tri2(a): @@ -197,8 +193,6 @@ def test_regular_tri2(a): # circumcenters assert near_equal(mesh.cell_circumcenters, [0.0, 0.0, 0.0], tol) - return - # def test_degenerate_small0(): # h = 1.0e-3 @@ -263,7 +257,6 @@ def test_regular_tri2(a): # self.assertAlmostEqual(mesh.centroids[2][2], 0.0, delta=tol) # self.assertEqual(mesh.num_delaunay_violations(), 0) -# return @pytest.mark.parametrize( @@ -299,7 +292,6 @@ def test_degenerate_small0b(h): assert near_equal(mesh.cell_circumcenters, [0.5, 0.375, 0.0], tol) assert mesh.num_delaunay_violations() == 0 - return # # TODO parametrize with flat boundary correction @@ -343,7 +335,6 @@ def test_degenerate_small0b(h): # assert near_equal(centroids[2], [0.5, gamma, 0.0], tol) # assert mesh.num_delaunay_violations() == 0 -# return @pytest.mark.parametrize("h, a", [(1.0e-3, 0.3)]) @@ -388,7 +379,6 @@ def test_degenerate_small1(h, a): # assert near_equal(mesh.surface_areas, [alpha0, alpha1, alpha2], tol) assert mesh.num_delaunay_violations() == 0 - return @pytest.mark.parametrize("h", [1.0e-2]) @@ -424,8 +414,6 @@ def test_degenerate_small2(h): assert mesh.num_delaunay_violations() == 1 - return - def test_rectanglesmall(): points = numpy.array( @@ -444,8 +432,6 @@ def test_rectanglesmall(): assert near_equal(mesh.cell_volumes, [5.0, 5.0], tol) assert mesh.num_delaunay_violations() == 0 - return - def test_pacman(): filename = download_mesh("pacman.vtk", "c621cb22f8b87cecd77724c2c0601c36") @@ -461,8 +447,6 @@ def test_pacman(): assert mesh.num_delaunay_violations() == 0 - return - def test_shell(): points = numpy.array( @@ -489,8 +473,6 @@ def test_shell(): assert mesh.num_delaunay_violations() == 0 - return - def test_sphere(): filename = download_mesh("sphere.vtk", "06b163871cc0f23344d71c990dffe577") @@ -502,9 +484,7 @@ def test_sphere(): [366.3982135866799, 1.7062353589387327], [0.72653362732751214, 0.05350373815413411], ) - # assertEqual(mesh.num_delaunay_violations(), 60) - return def test_signed_area(): @@ -517,7 +497,6 @@ def test_signed_area(): vols = mesh.signed_cell_areas assert numpy.all(abs(abs(vols) - mesh.cell_volumes) < 1.0e-12 * mesh.cell_volumes) - return def test_update_node_coordinates(): @@ -537,7 +516,6 @@ def test_update_node_coordinates(): tol = 1.0e-12 assert near_equal(mesh1.ei_dot_ej, mesh2.ei_dot_ej, tol) assert near_equal(mesh1.cell_volumes, mesh2.cell_volumes, tol) - return def test_flip_delaunay(): @@ -571,8 +549,6 @@ def test_flip_delaunay(): assert near_equal(mesh.cell_volumes, mesh2.cell_volumes, tol) assert near_equal(mesh.ei_dot_ej, mesh2.ei_dot_ej, tol) - return - def test_flip_delaunay_near_boundary(): points = numpy.array( @@ -591,7 +567,6 @@ def test_flip_delaunay_near_boundary(): assert mesh.num_delaunay_violations() == 0 assert numpy.array_equal(mesh.cells["nodes"], [[1, 3, 2], [1, 3, 0]]) assert numpy.array_equal(mesh.cells["edges"], [[4, 3, 1], [2, 0, 1]]) - return def test_flip_same_edge_twice(): @@ -623,8 +598,6 @@ def test_flip_same_edge_twice(): # mesh.show() mesh.plot() - return - def test_flip_two_edges(): alpha = numpy.array([1.0, 3.0, 5.0, 7.0, 9.0, 11.0]) / 6.0 * numpy.pi @@ -642,7 +615,6 @@ def test_flip_two_edges(): assert numpy.array_equal( mesh.cells["nodes"], [[5, 2, 3], [0, 2, 1], [5, 2, 0], [3, 4, 5]] ) - return def test_flip_delaunay_near_boundary_preserve_boundary_count(): @@ -671,7 +643,6 @@ def test_flip_delaunay_near_boundary_preserve_boundary_count(): mesh.mark_boundary() assert numpy.array_equal(mesh.is_boundary_node, is_boundary_node_ref) - return def test_inradius(): @@ -693,7 +664,6 @@ def test_inradius(): mesh = meshplex.MeshTri(points, cells) assert near_equal(mesh.cell_inradius, [a / 4 * (numpy.sqrt(3) - 1)], tol) - return def test_circumradius(): @@ -715,7 +685,6 @@ def test_circumradius(): mesh = meshplex.MeshTri(points, cells) assert near_equal(mesh.cell_circumradius, [a / 2], tol) - return def test_quality(): @@ -739,7 +708,6 @@ def test_quality(): q = mesh.cell_quality assert near_equal(q, 2 * mesh.cell_inradius / mesh.cell_circumradius, tol) - return def test_angles(): @@ -766,7 +734,6 @@ def test_angles(): ic = mesh.angles / numpy.pi * 180 assert near_equal(ic, [[90], [60], [30]], tol) - return # TODO reactivate @@ -828,7 +795,6 @@ def test_flat_boundary(): cv[i] += 0.25 * ce * numpy.dot(ei, ei) assert numpy.all(numpy.abs(cv - mesh.control_volumes) < 1.0e-12 * cv) - return def test_show_mesh(): @@ -838,7 +804,6 @@ def test_show_mesh(): # mesh.plot(show_axes=False) mesh.show(show_axes=False, cell_quality_coloring=("viridis", 0.0, 1.0, True)) # mesh.save("pacman.png", show_axes=False) - return def test_show_vertex(): @@ -846,7 +811,6 @@ def test_show_vertex(): mesh = meshplex.read(filename) # mesh.plot_vertex(125) mesh.show_vertex(125) - return if __name__ == "__main__":