diff options
Diffstat (limited to 'cython/doc/installation.rst')
| -rw-r--r-- | cython/doc/installation.rst | 176 |
1 files changed, 176 insertions, 0 deletions
diff --git a/cython/doc/installation.rst b/cython/doc/installation.rst new file mode 100644 index 00000000..f98a5039 --- /dev/null +++ b/cython/doc/installation.rst @@ -0,0 +1,176 @@ +Installation +############ + +Compiling +********* + +The library uses c++11 and requires `Boost <http://www.boost.org/>`_ with +version 1.48.0 or more recent. It is a multi-platform library and compiles on +Linux, Mac OSX and Visual Studio 2015. +It also requires cmake to generate makefiles, and cython to compile the +library. + +On `Windows <https://wiki.python.org/moin/WindowsCompilers>`_ , only Python +3.5 and 3.6 are available because of the required Visual Studio version. + +On other systems, if you have several Python/cython installed, the version 2.X +will be used by default, but you can force it by adding +:code:`-DPython_ADDITIONAL_VERSIONS=3` to the cmake command. + +GUDHI Cythonization +=================== + +To build the GUDHI cython module, run the following commands in a terminal: + +.. code-block:: bash + + cd /path-to-gudhi/ + mkdir build + cd build/ + cmake .. + make cython + +Test suites +=========== + +To test your build, `py.test <http://doc.pytest.org>`_ is optional. Run the +following command in a terminal: + +.. code-block:: bash + + cd /path-to-gudhi/build/cython + # For windows, you have to set PYTHONPATH environment variable + export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/cython' + ctest -R py_test + +Documentation +============= + +To build the documentation, `sphinx-doc <http://http://www.sphinx-doc.org>`_ is +required. Please refer to *conf.py* file to see which +`sphinx-doc <http://http://www.sphinx-doc.org>`_ modules are required to +generate the documentation. Run the following commands in a terminal: + +.. code-block:: bash + + make sphinx + +Optional third-party library +**************************** + +CGAL +==== + +The :doc:`Alpha complex </alpha_complex_user>`, +:doc:`Tangential complex </tangential_complex_user>` and +:doc:`Witness complex </witness_complex_user>` data structures, and +:doc:`Bottleneck distance </bottleneck_distance_user>` requires CGAL, which is a +C++ library which provides easy access to efficient and reliable geometric +algorithms. + +Having CGAL version 4.6.0 or higher installed is recommended. The procedure to +install this library according to your operating system is detailed +`here <http://doc.cgal.org/latest/Manual/installation.html>`_. + +The following examples require the Computational Geometry Algorithms Library: + +.. only:: builder_html + + * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` + * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>` + +The following example requires CGAL version ≥ 4.7.0: + +.. only:: builder_html + + * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>` + * :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>` + +The following example requires CGAL version ≥ 4.8.0: + +.. only:: builder_html + + * :download:`bottleneck_basic_example.py <../example/bottleneck_basic_example.py>` + * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>` + +Eigen3 +====== + +The :doc:`Alpha complex </alpha_complex_user>`, +:doc:`Tangential complex </tangential_complex_user>` and +:doc:`Witness complex </witness_complex_user>` data structures and few +examples requires `Eigen3 <http://eigen.tuxfamily.org/>`_, a C++ template +library for linear algebra: matrices, vectors, numerical solvers, and related +algorithms. + +The following examples require the `Eigen3 <http://eigen.tuxfamily.org/>`_: + +.. only:: builder_html + + * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>` + * :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>` + * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>` + * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` + * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>` + +Matplotlib +========== + +The :doc:`persistence graphical tools </persistence_graphical_tools_user>` +module requires `Matplotlib <http://matplotlib.org>`_, a Python 2D plotting +library which produces publication quality figures in a variety of hardcopy +formats and interactive environments across platforms. + +The following examples require the `Matplotlib <http://matplotlib.org>`_: + +.. only:: builder_html + + * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>` + * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_example.py>` + * :download:`periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>` + * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>` + * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>` + * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>` + * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>` + * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` + * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>` + +Numpy +===== + +The :doc:`persistence graphical tools </persistence_graphical_tools_user>` +module requires `NumPy <http://numpy.org>`_, a fundamental package for +scientific computing with Python. + +The following examples require the `NumPy <http://numpy.org>`_: + +.. only:: builder_html + + * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>` + * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_example.py>` + * :download:`periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>` + * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>` + * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>` + * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>` + * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>` + * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` + * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>` + +Threading Building Blocks +========================= + +`Intel® TBB <https://www.threadingbuildingblocks.org/>`_ lets you easily write +parallel C++ programs that take full advantage of multicore performance, that +are portable and composable, and that have future-proof scalability. + +Having Intel® TBB installed is recommended to parallelize and accelerate some +GUDHI computations. + +Bug reports and contributions +***************************** + +Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: + + Contact: gudhi-users@lists.gforge.inria.fr + +GUDHI is open to external contributions. If you want to join our development team, please contact us. |