diff options
Diffstat (limited to 'src/python/doc')
| -rw-r--r-- | src/python/doc/_templates/layout.html | 16 | ||||
| -rw-r--r-- | src/python/doc/examples.rst | 3 | ||||
| -rw-r--r-- | src/python/doc/index.rst | 4 | ||||
| -rw-r--r-- | src/python/doc/installation.rst | 25 | ||||
| -rw-r--r-- | src/python/doc/persistence_graphical_tools_user.rst | 13 |
5 files changed, 48 insertions, 13 deletions
diff --git a/src/python/doc/_templates/layout.html b/src/python/doc/_templates/layout.html index fe64fb3d..2f2d9c72 100644 --- a/src/python/doc/_templates/layout.html +++ b/src/python/doc/_templates/layout.html @@ -56,12 +56,16 @@ </a></p> {%- endif %} {%- endblock %} - <h2><a href="index.html">GUDHI</a></h2> - <h2><a href="fileformats.html">File formats</a></h2> - <h2><a href="installation.html">GUDHI installation</a></h2> - <h2><a href="citation.html">Acknowledging the GUDHI library</a></h2> - <h2><a href="genindex.html">Index</a></h2> - <h2><a href="examples.html">Examples</a></h2> + <b> + <ul style="list-style-type:circle;"> + <li><a href="index.html">Modules</a></li> + <li><a href="installation.html">Installation</a></li> + <li><a href="examples.html">Examples</a></li> + <li><a href="fileformats.html">File formats</a></li> + <li><a href="citation.html">Acknowledging</a></li> + <li><a href="genindex.html">Index</a></li> + </ul> + </b> {%- if sidebars != None %} {#- new style sidebar: explicitly include/exclude templates #} {%- for sidebartemplate in sidebars %} diff --git a/src/python/doc/examples.rst b/src/python/doc/examples.rst index edbc2f72..a42227e3 100644 --- a/src/python/doc/examples.rst +++ b/src/python/doc/examples.rst @@ -16,6 +16,9 @@ Examples * :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:`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>` diff --git a/src/python/doc/index.rst b/src/python/doc/index.rst index 1ef08096..c36a578f 100644 --- a/src/python/doc/index.rst +++ b/src/python/doc/index.rst @@ -1,5 +1,5 @@ -GUDHI Python module documentation -################################# +GUDHI Python modules documentation +################################## .. figure:: ../../doc/common/Gudhi_banner.png diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 7699a5bb..54504413 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -40,6 +40,20 @@ To build the GUDHI Python module, run the following commands in a terminal: cd python make +.. note:: + + :code:`make python` (or :code:`make` in python directory) is only a + `CMake custom targets <https://cmake.org/cmake/help/latest/command/add_custom_target.html>`_ + to shortcut :code:`python setup.py build_ext --inplace` command. + No specific other options (:code:`-j8` for parallel, or even :code:`make clean`, ...) are + available. + But one can use :code:`python setup.py ...` specific options in the python directory: + +.. code-block:: bash + + python setup.py clean --all # Clean former compilation + python setup.py build_ext -j 8 --inplace # Build in parallel + GUDHI Python module installation ================================ @@ -59,6 +73,17 @@ Or install it definitely in your Python packages folder: # May require sudo or administrator privileges make install +.. note:: + + :code:`make install` is only a + `CMake custom targets <https://cmake.org/cmake/help/latest/command/add_custom_target.html>`_ + to shortcut :code:`python setup.py install` command. + It does not take into account :code:`CMAKE_INSTALL_PREFIX`. + But one can use :code:`python setup.py install ...` specific options in the python directory: + +.. code-block:: bash + + python setup.py install --prefix /home/gudhi # Install in /home/gudhi directory Test suites =========== diff --git a/src/python/doc/persistence_graphical_tools_user.rst b/src/python/doc/persistence_graphical_tools_user.rst index b2124fdd..2de99252 100644 --- a/src/python/doc/persistence_graphical_tools_user.rst +++ b/src/python/doc/persistence_graphical_tools_user.rst @@ -20,6 +20,7 @@ This function can display the persistence result as a barcode: .. plot:: :include-source: + import matplotlib.pyplot as plot import gudhi off_file = gudhi.__root_source_dir__ + '/data/points/tore3D_300.off' @@ -29,7 +30,7 @@ This function can display the persistence result as a barcode: simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence(min_persistence=0.4) - plot = gudhi.plot_persistence_barcode(diag) + gudhi.plot_persistence_barcode(diag) plot.show() Show persistence as a diagram @@ -43,14 +44,15 @@ This function can display the persistence result as a diagram: .. plot:: :include-source: + import matplotlib.pyplot as plot import gudhi # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method persistence_file=gudhi.__root_source_dir__ + \ '/data/persistence_diagram/rips_on_tore3D_1307.pers' - plt = gudhi.plot_persistence_diagram(persistence_file=persistence_file, + gudhi.plot_persistence_diagram(persistence_file=persistence_file, legend=True) - plt.show() + plot.show() Persistence density ------------------- @@ -63,11 +65,12 @@ If you want more information on a specific dimension, for instance: .. plot:: :include-source: + import matplotlib.pyplot as plot import gudhi # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method persistence_file=gudhi.__root_source_dir__ + \ '/data/persistence_diagram/rips_on_tore3D_1307.pers' - plt = gudhi.plot_persistence_density(persistence_file=persistence_file, + gudhi.plot_persistence_density(persistence_file=persistence_file, max_intervals=0, dimension=1, legend=True) - plt.show() + plot.show() |