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https://github.com/nomad-coe/pyzeo

Python interface for the zeo++ package
https://github.com/nomad-coe/pyzeo

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Python interface for the zeo++ package

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README 

        
# pyzeo



Python wrapper for the [Zeo++ library](http://zeoplusplus.org). Based on the latest released version 0.3.



## Installation



We provide pre-built wheels for several platforms (including Apple Silicon). So in most cases you will want to install the package with `pip`:



```sh

pip install pyzeo

```



### Installing from source



If you wish to install the package directly from the source code, you can do so with:



```sh

git clone https://github.com/nomad-coe/pyzeo

cd pyzeo

pip install .

```



Note that this type of installation will require a separate, platfrom-dependent

compilation step. These are some common problems you may encounter in the compilation step:



- **fatal error: Python.h: No such file or directory**: The package depends on

   C/C++ extensions that are compiled during the setup. For the compilation to

   work you will need to install the *pythonX.X-dev*-package, where X.X is the

   python version you use. E.g. for python 3.9 on Ubuntu this package could be

   installed with:



   .. code-block:: sh



       sudo apt install python3.9-dev



 - **Installation errors on MacOS**: The package depends on C++ extensions that

   are compiled during the setup. If experiencing problems with setup on MacOS,

   you may need to install the Xcode Command Line tools package. This can be

   done with:



   .. code-block:: sh



       xcode-select --install



### Cython



By default the package comes with pre-built Cython binding code. The cython

wrapper definitions live inside src/pyzeo. These bindings can be recreated

by first setting `USE_CYTHON=True` in setup.py, and then recreating the bindings

with:



```sh

python setup.py build_ext --inplace --force

```



Remember to disable cython afterwards by setting `USE_CYTHON=False` in setup.py.



### License



The python wrapper code is licensed under Apache 2.0. [Zeo++

library](http://zeoplusplus.org) and [Voro++

library](https://math.lbl.gov/voro++/) which are included in the source code

have the following license:



#### Zeo++



> Zeo++ Copyright (c) 2011, The Regents of the University

> of California, through Lawrence Berkeley National Laboratory (subject

> to receipt of any required approvals from the U.S. Dept. of Energy).

> All rights reserved.



> Redistribution and use in source and binary forms, with or without

> modification, are permitted provided that the following conditions are

> met:



> (1) Redistributions of source code must retain the above copyright

> notice, this list of conditions and the following disclaimer.



> (2) Redistributions in binary form must reproduce the above copyright

> notice, this list of conditions and the following disclaimer in the

> documentation and/or other materials provided with the distribution.



> (3) Neither the name of the University of California, Lawrence

> Berkeley National Laboratory, U.S. Dept. of Energy nor the names of

> its contributors may be used to endorse or promote products derived

> from this software without specific prior written permission.



> THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS

> "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT

> LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR

> A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT

> OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,

> SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT

> LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,

> DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY

> THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT 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.



> You are under no obligation whatsoever to provide any bug fixes,

> patches, or upgrades to the features, functionality or performance of

> the source code ("Enhancements") to anyone; however, if you choose to

> make your Enhancements available either publicly, or directly to

> Lawrence Berkeley National Laboratory, without imposing a separate

> written license agreement for such Enhancements, then you hereby grant

> the following license: a  non-exclusive, royalty-free perpetual

> license to install, use, modify, prepare derivative works, incorporate

> into other computer software, distribute, and sublicense such

> enhancements or derivative works thereof, in binary and source code

> form.



#### Voro++



> Voro++ Copyright (c) 2008, The Regents of the University of California, through

> Lawrence Berkeley National Laboratory (subject to receipt of any required

> approvals from the U.S. Dept. of Energy). All rights reserved.



> Redistribution and use in source and binary forms, with or without

> modification, are permitted provided that the following conditions are met: 



> (1) Redistributions of source code must retain the above copyright notice, this

> list of conditions and the following disclaimer. 



> (2) Redistributions in binary form must reproduce the above copyright notice,

> this list of conditions and the following disclaimer in the documentation

> and/or other materials provided with the distribution. 



> (3) Neither the name of the University of California, Lawrence Berkeley

> National Laboratory, U.S. Dept. of Energy nor the names of its contributors may

> be used to endorse or promote products derived from this software without

> specific prior written permission. 



> THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND

> ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED

> WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE

> DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR

> ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES

> (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;

> LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON

> ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT 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. 



> You are under no obligation whatsoever to provide any bug fixes, patches, or

> upgrades to the features, functionality or performance of the source code

> ("Enhancements") to anyone; however, if you choose to make your Enhancements

> available either publicly, or directly to Lawrence Berkeley National

> Laboratory, without imposing a separate written license agreement for such

> Enhancements, then you hereby grant the following license: a  non-exclusive,

> royalty-free perpetual license to install, use, modify, prepare derivative

> works, incorporate into other computer software, distribute, and sublicense

> such enhancements or derivative works thereof, in binary and source code form.