diff options
Diffstat (limited to 'src/python/doc')
| -rw-r--r-- | src/python/doc/_templates/layout.html | 53 | ||||
| -rw-r--r-- | src/python/doc/examples.rst | 33 | ||||
| -rw-r--r-- | src/python/doc/installation.rst | 29 | ||||
| -rw-r--r-- | src/python/doc/persistence_graphical_tools_user.rst | 11 |
4 files changed, 85 insertions, 41 deletions
diff --git a/src/python/doc/_templates/layout.html b/src/python/doc/_templates/layout.html index a672a281..cd40a51b 100644 --- a/src/python/doc/_templates/layout.html +++ b/src/python/doc/_templates/layout.html @@ -175,58 +175,59 @@ <h1 class="show-for-small-only"><a href="" class="icon-tree"> GUDHI library</a></h1> </li> <!-- Remove the class "menu-icon" to get rid of menu icon. Take out "Menu" to just have icon alone --> - <li class="toggle-topbar menu-icon"><a href="#"><span>Navigation</span></a></li> + <li class="toggle-topbar menu-icon"><a href="#"><span>Nav</span></a></li> </ul> <section class="top-bar-section"> <ul class="right"> <li class="divider"></li> - <li><a href="/contact/">Contact</a></li> + <li><a href="/contact/">Contact</a></li> </ul> <ul class="left"> - <li><a href="/"> <img src="/assets/img/home.png" alt=" GUDHI"> GUDHI </a></li> + <li><a href="/"> <img src="/assets/img/home.png" alt=" GUDHI"> GUDHI </a></li> <li class="divider"></li> <li class="has-dropdown"> - <a href="#">Project</a> + <a href="#">Project</a> <ul class="dropdown"> - <li><a href="/people/">People</a></li> - <li><a href="/keepintouch/">Keep in touch</a></li> - <li><a href="/partners/">Partners and Funding</a></li> - <li><a href="/relatedprojects/">Related projects</a></li> - <li><a href="/theyaretalkingaboutus/">They are talking about us</a></li> - <li><a href="/inaction/">GUDHI in action</a></li> + <li><a href="/people/">People</a></li> + <li><a href="/keepintouch/">Keep in touch</a></li> + <li><a href="/partners/">Partners and Funding</a></li> + <li><a href="/relatedprojects/">Related projects</a></li> + <li><a href="/theyaretalkingaboutus/">They are talking about us</a></li> + <li><a href="/inaction/">GUDHI in action</a></li> </ul> </li> <li class="divider"></li> <li class="has-dropdown"> - <a href="#">Download</a> + <a href="#">Download</a> <ul class="dropdown"> - <li><a href="/licensing/">Licensing</a></li> - <li><a href="https://github.com/GUDHI/gudhi-devel/releases/latest" target="_blank">Get the latest sources</a></li> - <li><a href="/conda/">Conda package</a></li> - <li><a href="/dockerfile/">Dockerfile</a></li> + <li><a href="/licensing/">Licensing</a></li> + <li><a href="https://github.com/GUDHI/gudhi-devel/releases/latest" target="_blank">Get the latest sources</a></li> + <li><a href="/conda/">Conda package</a></li> + <li><a href="https://pypi.org/project/gudhi/" target="_blank">Pip package</a></li> + <li><a href="/dockerfile/">Dockerfile</a></li> </ul> </li> <li class="divider"></li> <li class="has-dropdown"> - <a href="#">Documentation</a> + <a href="#">Documentation</a> <ul class="dropdown"> - <li><a href="/introduction/">Introduction</a></li> - <li><a href="https://gudhi.inria.fr/doc/latest/installation.html">C++ installation manual</a></li> - <li><a href="https://gudhi.inria.fr/doc/latest/">C++ documentation</a></li> - <li><a href="https://gudhi.inria.fr/python/latest/installation.html">Python installation manual</a></li> - <li><a href="https://gudhi.inria.fr/python/latest/">Python documentation</a></li> - <li><a href="/utils/">Utilities</a></li> - <li><a href="/tutorials/">Tutorials</a></li> + <li><a href="/introduction/">Introduction</a></li> + <li><a href="/doc/latest/installation.html">C++ installation manual</a></li> + <li><a href="/doc/latest/">C++ documentation</a></li> + <li><a href="/python/latest/installation.html">Python installation manual</a></li> + <li><a href="/python/latest/">Python documentation</a></li> + <li><a href="/utils/">Utilities</a></li> + <li><a href="/tutorials/">Tutorials</a></li> </ul> </li> <li class="divider"></li> - <li><a href="/interfaces/">Interfaces</a></li> + <li><a href="/interfaces/">Interfaces</a></li> <li class="divider"></li> </ul> </section> </nav> - </div><!-- /#navigation --> - <!-- GUDHI website header BEGIN --> + </div><!-- /#navigation --> + <!-- GUDHI website header END --> {%- block header %}{% endblock %} diff --git a/src/python/doc/examples.rst b/src/python/doc/examples.rst index a42227e3..76e5d4c7 100644 --- a/src/python/doc/examples.rst +++ b/src/python/doc/examples.rst @@ -7,27 +7,30 @@ Examples .. only:: builder_html - * :download:`rips_complex_from_points_example.py <../example/rips_complex_from_points_example.py>` + * :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:`simplex_tree_example.py <../example/simplex_tree_example.py>` * :download:`alpha_rips_persistence_bottleneck_distance.py <../example/alpha_rips_persistence_bottleneck_distance.py>` - * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>` - * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_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:`bottleneck_basic_example.py <../example/bottleneck_basic_example.py>` - * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_example.py>` - * :download:`plot_simplex_tree_dim012.py <../example/plot_simplex_tree_dim012.py>` - * :download:`plot_rips_complex.py <../example/plot_rips_complex.py>` - * :download:`plot_alpha_complex.py <../example/plot_alpha_complex.py>` - * :download:`witness_complex_from_nearest_landmark_table.py <../example/witness_complex_from_nearest_landmark_table.py>` + * :download:`coordinate_graph_induced_complex.py <../example/coordinate_graph_induced_complex.py>` + * :download:`diagram_vectorizations_distances_kernels.py <../example/diagram_vectorizations_distances_kernels.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>` - * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>` + * :download:`functional_graph_induced_complex.py <../example/functional_graph_induced_complex.py>` + * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_example.py>` + * :download:`nerve_of_a_covering.py <../example/nerve_of_a_covering.py>` + * :download:`periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>` + * :download:`plot_alpha_complex.py <../example/plot_alpha_complex.py>` + * :download:`plot_rips_complex.py <../example/plot_rips_complex.py>` + * :download:`plot_simplex_tree_dim012.py <../example/plot_simplex_tree_dim012.py>` + * :download:`random_cubical_complex_persistence_example.py <../example/random_cubical_complex_persistence_example.py>` + * :download:`rips_complex_diagram_persistence_from_correlation_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py>` * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_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_complex_edge_collapse_example.py <../example/rips_complex_edge_collapse_example.py>` + * :download:`rips_complex_from_points_example.py <../example/rips_complex_from_points_example.py>` * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>` + * :download:`simplex_tree_example.py <../example/simplex_tree_example.py>` * :download:`sparse_rips_persistence_diagram.py <../example/sparse_rips_persistence_diagram.py>` - * :download:`random_cubical_complex_persistence_example.py <../example/random_cubical_complex_persistence_example.py>` - * :download:`coordinate_graph_induced_complex.py <../example/coordinate_graph_induced_complex.py>` - * :download:`functional_graph_induced_complex.py <../example/functional_graph_induced_complex.py>` + * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>` * :download:`voronoi_graph_induced_complex.py <../example/voronoi_graph_induced_complex.py>` - * :download:`nerve_of_a_covering.py <../example/nerve_of_a_covering.py>` + * :download:`witness_complex_from_nearest_landmark_table.py <../example/witness_complex_from_nearest_landmark_table.py>` diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 525ca84e..78e1af73 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -323,6 +323,35 @@ The following examples require the `Matplotlib <http://matplotlib.org>`_: * :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>` +LaTeX +~~~~~ + +If a sufficiently complete LaTeX toolchain is available (including dvipng and ghostscript), the LaTeX option of +matplotlib is enabled for prettier captions (cf. +`matplotlib text rendering with LaTeX <https://matplotlib.org/3.3.0/tutorials/text/usetex.html>`_). +It also requires `type1cm` LaTeX package (not detected by matplotlib). + +If you are facing issues with LaTeX rendering, like this one: + +.. code-block:: none + + Traceback (most recent call last): + File "/usr/lib/python3/dist-packages/matplotlib/texmanager.py", line 302, in _run_checked_subprocess + report = subprocess.check_output(command, + ... + ! LaTeX Error: File `type1cm.sty' not found. + ... + +This is because the LaTeX package is not installed on your system. On Ubuntu systems you can install texlive-full +(for all LaTeX packages), or more specific packages like texlive-latex-extra, cm-super. + +You can still deactivate LaTeX rendering by saying: + +.. code-block:: python + + import gudhi + gudhi.persistence_graphical_tools._gudhi_matplotlib_use_tex=False + PyKeOps ------- diff --git a/src/python/doc/persistence_graphical_tools_user.rst b/src/python/doc/persistence_graphical_tools_user.rst index b5a38eb1..d95b9d2b 100644 --- a/src/python/doc/persistence_graphical_tools_user.rst +++ b/src/python/doc/persistence_graphical_tools_user.rst @@ -90,3 +90,14 @@ If you want more information on a specific dimension, for instance: gudhi.plot_persistence_density(persistence=pers_diag, dimension=1, legend=True, axes=axes[1]) plt.show() + +LaTeX support +------------- + +If you are facing issues with `LaTeX <installation.html#latex>`_ rendering, you can still deactivate LaTeX rendering by +saying: + +.. code-block:: python + + import gudhi + gudhi.persistence_graphical_tools._gudhi_matplotlib_use_tex=False |