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:orphan:
.. To get rid of WARNING: document isn't included in any toctree
Installation
############
Compiling
*********
The library uses c++11 and requires `Boost <https://www.boost.org/>`_ ≥ 1.48.0
and `CMake <https://www.cmake.org/>`_ ≥ 3.1.
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
Debugging issues
================
If tests fail, please check your PYTHONPATH and try to :code:`import gudhi`
and check the errors.
The problem can come from a third-party library bad link or installation.
If :code:`import gudhi` succeeds, please have a look to debug informations:
.. code-block:: python
import gudhi
print(gudhi.__debug_info__)
You shall have something like:
.. code-block:: none
Python version 2.7.15
Cython version 0.26.1
Eigen3 version 3.1.1
Installed modules are: off_reader;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex;
persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex;alpha_complex;
euclidean_witness_complex;euclidean_strong_witness_complex;
Missing modules are: bottleneck_distance;nerve_gic;subsampling;tangential_complex;persistence_graphical_tools;
CGAL version 4.7.1000
GMP_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmp.so
GMPXX_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmpxx.so
TBB version 9107 found and used
Here, you can see that bottleneck_distance, nerve_gic, subsampling and
tangential_complex are missing because of the CGAL version.
persistence_graphical_tools is not available as numpy and matplotlib are not
available.
Unitary tests cannot be run as pytest is missing.
A complete configuration would be :
.. code-block:: none
Python version 3.6.5
Cython version 0.28.2
Pytest version 3.3.2
Matplotlib version 2.2.2
Numpy version 1.14.5
Eigen3 version 3.3.4
Installed modules are: off_reader;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex;
persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex;persistence_graphical_tools;
bottleneck_distance;nerve_gic;subsampling;tangential_complex;alpha_complex;euclidean_witness_complex;
euclidean_strong_witness_complex;
CGAL header only version 4.11.0
GMP_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmp.so
GMPXX_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmpxx.so
TBB version 9107 found and used
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, the Computational Geometry Algorithms Library, version 4.7.0 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 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 examples 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>`
The following examples requires CGAL version ≥ 4.8.1:
.. 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>`
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.
|
