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diff --git a/cython/doc/installation.rst b/cython/doc/installation.rst deleted file mode 100644 index 43576ec9..00000000 --- a/cython/doc/installation.rst +++ /dev/null @@ -1,236 +0,0 @@ -: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. |