pymor 0.2.0rc2-15-g22475c4

License

Copyright (c) 2013, Felix Albrecht, Rene Milk, Stephan Rave All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

• 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.

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 HOLDER 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.

Installation

We recommend the following way to install pyMOR with all its dependencies.

This procedure has been tested on the following platforms:

Ubuntu 12.04, Ubuntu 13.04, Arch Linux

1. Open a terminal and make sure you have git and python installed on your computer. (On Debian based linux distributions (e.g. Ubunutu) use sudo apt-get install git python2.7 to install both git and python.)

2. Clone the pyMOR main repository using

   git clone https://github.com/pymor/pymor.git

   This will create a directory named pymor in your current working directory. Change into this directory using

   cd pymor

3. Excecute the provided installation script

   ./install.py

   The installation script will ensure that all necessary system libraries and development headers are installed, create a new python virtual environment (virtualenv, see www.virtualenv.org), install all necessary python packages into this virtualenv, and finally install pyMOR itself.

   The installation process can be customized using various command-line arguments. (See ./install.py –help.) Most notable, the path of the virtualenv can be configured using the –virtualenv-dir option. Moreover, if you intend to work directly inside the pyMOR source tree, use

   ./install.py –only-deps

   to prevent the installation of pyMOR itself into the site-packages directory of the virtualenv. In this case, the installation script will add the pyMOR source tree to the PYTHONPATH of the virtualenv, so pyMOR will always be importable inside the virtualenv. (This can be prevented by adding the –without-python-path option.) Moreover

   python setup.py build_ext –inplace

   will be automatically called, to build pyMOR’s Cython extensions modules.

4. Activate the new virtualenv. If you did not change the default path of the virtualenv, this can be done by executing

   source $HOME/virtualenv/pymor/bin/activate

5. Try out one of the provided demos, e.g. call

   cd src/pymordemos ./thermalblock.py -ep –plot-solutions 2 2 3 16

Documentation

To build the documentation execute

make doc

inside the root directory of the pyMOR source tree. This will generate HTML documentation in ‘docs/_build/html’. The documentation is also available online on Read the Docs.

Cython extension modules

pyMOR uses Cython extension modules to speed up numerical algorithms which cannot be efficiently expressed using NumPy idioms. To benefit from these optimizations, the modules’ source files (currently pymor/tools/inplace.pyx and pymor/tools/realations.pyx) have to be processed by Cython into a .c-file which then must be compiled into a shared object. These .so-files then take precedence over the non-optimized pure python modules. This whole build process is handeled automatically by setup.py which is internally called by the install.py script.

If you want to develop Cython extensions modules for pyMOR yourself, you should add your module to the ext_modules list defined in the _setup method of setup.py. Calling

python setup.py build_ext –inplace

will then build the extension module and place it into your pyMOR source tree.

Tests

pyMOR uses pytest for unit testing. To run the test suite, simply execute make test in the base directory of the pyMOR repository. This will also create a test coverage report which can be found in the htmlcov directory. Alternatively, you can run make full-test which will also enable pyflakes and pep8 checks.

All tests are contained within the src/pymortests directory and can be run individually by executing py.test src/pymortests/the_module.py.

Contact

Should you have any questions regarding pyMOR or wish to contribute, do not hestitate to contact us via our development mailing list:

http://listserv.uni-muenster.de/mailman/listinfo/pymor-dev