Merge remote-tracking branch 'origin/master' into sparsev3

2 files changed, 50 insertions, 23 deletions

diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
index 040f6b4a..855dea44 100644
--- a/src/cython/doc/installation.rst
+++ b/src/cython/doc/installation.rst
@@ -7,24 +7,23 @@ Installation
 
 Compiling
 *********
-The library uses c++11 and requires `Boost <https://www.boost.org/>`_ ≥ 1.56.0
-and `CMake <https://www.cmake.org/>`_   ≥ 3.1.
+The library uses c++11 and requires `Boost <https://www.boost.org/>`_ ≥ 1.56.0,
+`CMake <https://www.cmake.org/>`_   ≥ 3.1  to generate makefiles, and
+`Cython <https://www.cython.org/>`_ to compile the GUDHI Python module.
 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
+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
-===================
+GUDHI Python module compilation
+===============================
 
-To build the GUDHI cython module, run the following commands in a terminal:
+To build the GUDHI Python module, run the following commands in a terminal:
 
 .. code-block:: bash
 
@@ -32,7 +31,28 @@ To build the GUDHI cython module, run the following commands in a terminal:
     mkdir build
     cd build/
     cmake ..
-    make cython
+    cd cython
+    make
+
+GUDHI Python module installation
+================================
+
+Once the compilation succeeds, one can add the GUDHI Python module path to the
+PYTHONPATH:
+
+.. code-block:: bash
+
+    # For windows, you have to set PYTHONPATH environment variable
+    export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/cython'
+
+Or install it definitely in your Python packages folder:
+
+.. code-block:: bash
+
+    cd /path-to-gudhi/build/cython
+    # May require sudo or administrator privileges
+    make install
+
 
 Test suites
 ===========
@@ -45,7 +65,7 @@ following command in a terminal:
     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
+    make test
 
 Debugging issues
 ================
@@ -54,7 +74,7 @@ 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:
+If :code:`import gudhi` succeeds, please have a look to debug information:
 
 .. code-block:: python
 
@@ -105,13 +125,17 @@ A complete configuration would be :
 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:
+To build the documentation, `sphinx-doc <http://www.sphinx-doc.org>`_ and
+`sphinxcontrib-bibtex <https://sphinxcontrib-bibtex.readthedocs.io>`_ are
+required. As the documentation is auto-tested, `CGAL`_, `Eigen3`_,
+`Matplotlib`_, `NumPy`_ and `SciPy`_ are also mandatory to build the
+documentation.
+
+Run the following commands in a terminal:
 
 .. code-block:: bash
 
+    cd /path-to-gudhi/build/cython
     make sphinx
 
 Optional third-party library
@@ -127,7 +151,7 @@ The :doc:`Alpha complex </alpha_complex_user>`,
 C++ library which provides easy access to efficient and reliable geometric
 algorithms.
 
-Having CGAL,  the Computational Geometry Algorithms Library, version 4.7.0 or
+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>`_.
diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst
index 5ce69e86..ebfe1e29 100644
--- a/src/cython/doc/tangential_complex_user.rst
+++ b/src/cython/doc/tangential_complex_user.rst
@@ -23,8 +23,10 @@ What is a Tangential Complex?
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Let us start with the description of the Tangential complex of a simple
-example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points
-:math:`P` located on a curve embedded in 2D.
+example, with :math:`k = 1` and :math:`d = 2`. The point set
+:math:`\mathscr P` is located on a closed curve embedded in 2D.
+Only 4 points will be displayed (more are required for PCA) to simplify the
+figures.
 
 .. figure:: ../../doc/Tangential_complex/tc_example_01.png
     :alt: The input
@@ -32,8 +34,7 @@ example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points
 
     The input
 
-For each point :math:`p`, estimate its tangent subspace :math:`T_p` (e.g.
-using PCA). 
+For each point :math:`P`, estimate its tangent subspace :math:`T_P` using PCA.
 
 .. figure:: ../../doc/Tangential_complex/tc_example_02.png
     :alt: The estimated normals
@@ -43,8 +44,8 @@ using PCA).
 
 
 Let us add the Voronoi diagram of the points in orange. For each point
-:math:`p`, construct its star in the Delaunay triangulation of :math:`P`
-restricted to :math:`T_p`.
+:math:`P`, construct its star in the Delaunay triangulation of
+:math:`\mathscr P` restricted to :math:`T_P`.
 
 .. figure:: ../../doc/Tangential_complex/tc_example_03.png
     :alt: The Voronoi diagram
@@ -72,7 +73,7 @@ Let us take the same example.
 
     Before
 
-Let us slightly move the tangent subspace :math:`T_q`
+Let us slightly move the tangent subspace :math:`T_Q`
 
 .. figure:: ../../doc/Tangential_complex/tc_example_07_after.png
     :alt: After
@@ -128,6 +129,7 @@ This example builds the Tangential complex of point set read in an OFF file.
     import gudhi
     tc = gudhi.TangentialComplex(intrisic_dim = 1,
         off_file=gudhi.__root_source_dir__ + '/data/points/alphacomplexdoc.off')
+    tc.compute_tangential_complex()
     result_str = 'Tangential contains ' + repr(tc.num_simplices()) + \
         ' simplices - ' + repr(tc.num_vertices()) + ' vertices.'
     print(result_str)
@@ -175,6 +177,7 @@ simplices.
    import gudhi
    tc = gudhi.TangentialComplex(intrisic_dim = 1,
        points=[[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]])
+   tc.compute_tangential_complex()
    result_str = 'Tangential contains ' + repr(tc.num_vertices()) + ' vertices.'
    print(result_str)