Add explicit GPLv3 license to the files depending on pygmsh

LICENSE.md

@@ -1,4 +1,8 @@
-The main source code of scikit-fem is distributed with the following license.
+This document describes the licensing of Python source code in the [scikit-fem
+Github repository](https://github.com/kinnala/scikit-fem).
+
+The following license applies to all source code unless otherwise mentioned
+later in this document or at the beginning of the respective files.
 
 > Copyright 2018-2020 scikit-fem developers
 > 
@@ -27,29 +31,25 @@ The main source code of scikit-fem is distributed with the following license.
 > LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
 > OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-The above license applies to all files not included in the following list of
-exceptions.
+Some examples under `docs/examples/` are licensed differently.  In particular,
+they have a GPL-licensed dependency and, therefore, are also GPL-licensed.
+
+- docs/examples/ex{04,12,13,17,20,24,26,27,28,32,35}.py
 
-- skfem/zoo/tet_tensor.py
+> Copyright 2018-2020 scikit-fem developers
+> 
+> This program is free software: you can redistribute it and/or modify
+> it under the terms of the GNU General Public License as published by
+> the Free Software Foundation, either version 3 of the License, or
+> (at your option) any later version.
+> 
+> This program is distributed in the hope that it will be useful,
+> but WITHOUT ANY WARRANTY; without even the implied warranty of
+> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+> GNU General Public License for more details.
+> 
+> You should have received a copy of the GNU General Public License
+> along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
-> Copyright (c) 2016-2018 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. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
-> BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
-> ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-> CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-> THE SOFTWARE.
+The contents of `skfem/` are distributed via Python Package Index as the package
+`scikit-fem`.  This distribution contains only BSD-licensed source code.

README.md

@@ -104,6 +104,12 @@ demonstrate the use of other external packages; see our [CI job
 definition](https://github.com/kinnala/scikit-fem/blob/master/.travis.yml) for a
 full list of test dependencies.
 
+## Licensing
+
+The contents of `skfem/` and the PyPI package `scikit-fem` are licensed under
+the 3-clause BSD license.  Some examples under `docs/examples/` have a different
+license, see `LICENSE.md` for more information.
+
 ## Acknowledgements
 
 This project was started while working under a grant from the [Finnish Cultural Foundation](https://skr.fi/). The approach used in the finite element assembly has been inspired by the [work of A. Hannukainen and M. Juntunen](https://au.mathworks.com/matlabcentral/fileexchange/36108-hjfem_lite).

docs/examples/ex04.py

@@ -49,6 +49,24 @@
    candidate boundary :math:`\Gamma_C` until convergence.
    Extending this example should be straightforward.
 
+License
+-------
+
+Copyright 2018-2020 scikit-fem developers
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
 """
 
 from skfem import *

docs/examples/ex12.py

@@ -23,6 +23,24 @@
 0.07363) and circles (k' = 1/Pi/4) at the centre and so can be
 evaluated by interpolation.
 
+License
+-------
+
+Copyright 2018-2020 scikit-fem developers
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
 """
 
 from skfem import *

docs/examples/ex13.py

@@ -21,6 +21,24 @@
 so the conductance (for unit potential difference and conductivity) is
 :math:`\|\nabla u\|^2 = 2 \ln 2 / \pi`.
 
+License
+-------
+
+Copyright 2018-2020 scikit-fem developers
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
 """
 
 from skfem import *

docs/examples/ex17.py

@@ -26,6 +26,24 @@
 .. math::
    T(r=0) = \frac{A b^2}{4 k_0} \left( \frac{2k_0}{bh} + \frac{2 k_0}{k_1} \log \frac{b}{a} + 1\right).
 
+License
+-------
+
+Copyright 2018-2020 scikit-fem developers
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
 """
 from typing import Optional
 

docs/examples/ex20.py

@@ -28,6 +28,24 @@
 .. math::
     \psi = \left(1 - (x^2+y^2)/a^2\right)^2 / 64.
 
+License
+-------
+
+Copyright 2018-2020 scikit-fem developers
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
 """
 from skfem import *
 from skfem.io import from_meshio

docs/examples/ex24.py

@@ -12,6 +12,24 @@
 
 * Barkley, D., M. G. M. Gomes, & R. D. Henderson (2002). Three-dimensional instability in flow over a backward-facing step. Journal of Fluid Mechanics 473. pp. 167–190. `doi:10.1017/s002211200200232x <http://dx.doi.org/10.1017/s002211200200232x>`_
 
+License
+-------
+
+Copyright 2018-2020 scikit-fem developers
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
 """
 from itertools import cycle, islice
 

docs/examples/ex26.py

@@ -25,6 +25,24 @@
 The novelty here is that the temperature is defined as a finite element function
 throughout the mesh (:math:`r < b`) but only solved on a subdomain.
 
+License
+-------
+
+Copyright 2018-2020 scikit-fem developers
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
 """
 from skfem import *
 from skfem.models.poisson import laplace, unit_load

docs/examples/ex27.py

@@ -43,10 +43,25 @@
 .. math::
    -\mathrm{Re} \int_\Omega ((\nabla \delta \boldsymbol{u}) \boldsymbol{u} + (\nabla \boldsymbol{u}) \delta \boldsymbol{u}) \cdot \boldsymbol{v} \,\mathrm{d}x.
 
-The full source code of the example reads as follows:
+License
+-------
 
-.. literalinclude:: examples/ex27.py
-    :start-after: EOF"""
+Copyright 2018-2020 scikit-fem developers
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+"""
 from skfem import *
 from skfem.helpers import grad, dot
 from skfem.models.poisson import vector_laplace, laplace

docs/examples/ex28.py

@@ -54,6 +54,24 @@
   14th International Conference on Heat Transfer, Fluid Mechanics and
   Thermodynamics, Wicklow, Ireland.
 
+License
+-------
+
+Copyright 2018-2020 scikit-fem developers
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
 """
 from skfem import *
 from skfem.helpers import grad, dot

docs/examples/ex32.py

@@ -46,6 +46,24 @@
 
 .. [McBAIN] McBain, G. D. (2016). `Creeping convection in a horizontally heated ellipsoid <http://people.eng.unimelb.edu.au/imarusic/proceedings/20/548/%20Paper.pdf>`_. *Proceedings of the Twentieth Australasian Fluid Mechanics Conference*.
 
+License
+-------
+
+Copyright 2018-2020 scikit-fem developers
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
 """
 from typing import NamedTuple, Optional
 

docs/examples/ex35.py

@@ -221,6 +221,24 @@
 .. math::
    C = \\frac{2 E}{V^2}.
 
+License
+-------
+
+Copyright 2018-2020 scikit-fem developers
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
 """
 from skfem.mesh import MeshTri
 from skfem.assembly import InteriorBasis, FacetBasis

skfem/mesh/mesh2d/mesh_quad.py

@@ -119,18 +119,18 @@ def init_tensor(cls: Type[MeshType],
         nt = (npx - 1) * (npy - 1)
         t = np.zeros((4, nt))
         ix = ix.reshape(npy, npx, order='F').copy()
-        t[0, :] = (ix[0:(npy-1), 0:(npx-1)].reshape(nt, 1, order='F')
-                                           .copy()
-                                           .flatten())
-        t[1, :] = (ix[1:npy, 0:(npx-1)].reshape(nt, 1, order='F')
-                                       .copy()
-                                       .flatten())
-        t[2, :] = (ix[1:npy, 1:npx].reshape(nt, 1, order='F')
-                                   .copy()
-                                   .flatten())
-        t[3, :] = (ix[0:(npy-1), 1:npx].reshape(nt, 1, order='F')
-                                       .copy()
-                                       .flatten())
+        t[0] = (ix[0:(npy-1), 0:(npx-1)].reshape(nt, 1, order='F')
+                .copy()
+                .flatten())
+        t[1] = (ix[1:npy, 0:(npx-1)].reshape(nt, 1, order='F')
+                .copy()
+                .flatten())
+        t[2] = (ix[1:npy, 1:npx].reshape(nt, 1, order='F')
+                .copy()
+                .flatten())
+        t[3] = (ix[0:(npy-1), 1:npx].reshape(nt, 1, order='F')
+                .copy()
+                .flatten())
         return cls(p, t.astype(np.int64))
 
     @classmethod