diff options
author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-06-06 09:32:46 +0000 |
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committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-06-06 09:32:46 +0000 |
commit | a47b6aad7563e729635705ed3b7668194d3e2d24 (patch) | |
tree | 9d10f800c1deeaf5a85e947399aa7a9f805a73ea /src | |
parent | dde12ef73a36913c06d33ff3f5c2df43dd209930 (diff) | |
parent | f7e559c5eca0ad23bb293a8b57a9db6cb124420c (diff) |
Merge of branch python_2.1.0_vincent branch to fix sphinx warnings and issue with new version of sphinx
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3545 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 1bae865ddef6b92c5c3426bbbb8172e876b6d8d2
Diffstat (limited to 'src')
41 files changed, 155 insertions, 69 deletions
diff --git a/src/cython/doc/_templates/layout.html b/src/cython/doc/_templates/layout.html index 613d7d06..081d2dda 100644 --- a/src/cython/doc/_templates/layout.html +++ b/src/cython/doc/_templates/layout.html @@ -56,6 +56,12 @@ </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> {%- if sidebars != None %} {#- new style sidebar: explicitly include/exclude templates #} {%- for sidebartemplate in sidebars %} @@ -64,13 +70,6 @@ {%- else %} {#- old style sidebars: using blocks -- should be deprecated #} {%- block sidebartoc %} -<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> - {%- include "localtoc.html" %} {%- endblock %} {%- block sidebarrel %} diff --git a/src/cython/doc/alpha_complex_ref.rst b/src/cython/doc/alpha_complex_ref.rst index 6a122b09..7da79543 100644 --- a/src/cython/doc/alpha_complex_ref.rst +++ b/src/cython/doc/alpha_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ============================== Alpha complex reference manual ============================== diff --git a/src/cython/doc/alpha_complex_sum.rst b/src/cython/doc/alpha_complex_sum.inc index 1680a712..1680a712 100644 --- a/src/cython/doc/alpha_complex_sum.rst +++ b/src/cython/doc/alpha_complex_sum.inc diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst index db7edd6f..d1e9c7cd 100644 --- a/src/cython/doc/alpha_complex_user.rst +++ b/src/cython/doc/alpha_complex_user.rst @@ -1,11 +1,15 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Alpha complex user manual ========================= Definition ---------- -.. include:: alpha_complex_sum.rst +.. include:: alpha_complex_sum.inc -Alpha_complex is constructing a :doc:`Simplex_tree <simplex_tree_sum>` using +Alpha_complex is constructing a :doc:`Simplex_tree <simplex_tree_ref>` using `Delaunay Triangulation <http://doc.cgal.org/latest/Triangulation/index.html#Chapter_Triangulations>`_ :cite:`cgal:hdj-t-15b` from `CGAL <http://www.cgal.org/>`_ (the Computational Geometry Algorithms Library :cite:`cgal:eb-15b`). @@ -99,9 +103,9 @@ Filtration value computation algorithm **end for** **end for** **end for** - + make_filtration_non_decreasing() - + prune_above_filtration() Dimension 2 diff --git a/src/cython/doc/bottleneck_distance_sum.rst b/src/cython/doc/bottleneck_distance_sum.inc index 030fad9e..030fad9e 100644 --- a/src/cython/doc/bottleneck_distance_sum.rst +++ b/src/cython/doc/bottleneck_distance_sum.inc diff --git a/src/cython/doc/bottleneck_distance_user.rst b/src/cython/doc/bottleneck_distance_user.rst index 7692dce2..605db022 100644 --- a/src/cython/doc/bottleneck_distance_user.rst +++ b/src/cython/doc/bottleneck_distance_user.rst @@ -1,9 +1,13 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Bottleneck distance user manual =============================== Definition ---------- -.. include:: bottleneck_distance_sum.rst +.. include:: bottleneck_distance_sum.inc Function -------- diff --git a/src/cython/doc/citation.rst b/src/cython/doc/citation.rst index f4fdf83b..117eb9dd 100644 --- a/src/cython/doc/citation.rst +++ b/src/cython/doc/citation.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Acknowledging the GUDHI library ############################### diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py index a13c9751..4a54d4fd 100755 --- a/src/cython/doc/conf.py +++ b/src/cython/doc/conf.py @@ -85,7 +85,7 @@ version = gudhi.__version__ # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. -exclude_patterns = ['_build'] +exclude_patterns = ['_build', '*.inc'] # The reST default role (used for this markup: `text`) to use for all # documents. @@ -125,6 +125,7 @@ html_theme_options = { "sidebarbgcolor": "#A1ADCD", "sidebartextcolor": "black", "sidebarlinkcolor": "#334D5C", + "body_max_width": "1200px", } # Add any paths that contain custom themes here, relative to this directory. diff --git a/src/cython/doc/cubical_complex_ref.rst b/src/cython/doc/cubical_complex_ref.rst index 84aa4223..1fe9d5fb 100644 --- a/src/cython/doc/cubical_complex_ref.rst +++ b/src/cython/doc/cubical_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Cubical complex reference manual ################################ diff --git a/src/cython/doc/cubical_complex_sum.rst b/src/cython/doc/cubical_complex_sum.inc index 280ad0e0..280ad0e0 100644 --- a/src/cython/doc/cubical_complex_sum.rst +++ b/src/cython/doc/cubical_complex_sum.inc diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst index dd82ad93..320bd79b 100644 --- a/src/cython/doc/cubical_complex_user.rst +++ b/src/cython/doc/cubical_complex_user.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Cubical complex user manual =========================== Definition @@ -144,6 +148,7 @@ the program output is: .. testoutput:: Periodic cubical complex is of dimension 2 - 42 simplices. + Examples. --------- diff --git a/src/cython/doc/euclidean_strong_witness_complex_ref.rst b/src/cython/doc/euclidean_strong_witness_complex_ref.rst index bebf0f9a..1a602cd5 100644 --- a/src/cython/doc/euclidean_strong_witness_complex_ref.rst +++ b/src/cython/doc/euclidean_strong_witness_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ================================================= Euclidean strong witness complex reference manual ================================================= diff --git a/src/cython/doc/euclidean_witness_complex_ref.rst b/src/cython/doc/euclidean_witness_complex_ref.rst index 29b8806f..28daf965 100644 --- a/src/cython/doc/euclidean_witness_complex_ref.rst +++ b/src/cython/doc/euclidean_witness_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ========================================== Euclidean witness complex reference manual ========================================== diff --git a/src/cython/doc/examples.rst b/src/cython/doc/examples.rst index 1e596e18..d42f5a92 100644 --- a/src/cython/doc/examples.rst +++ b/src/cython/doc/examples.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Examples ######## diff --git a/src/cython/doc/fileformats.rst b/src/cython/doc/fileformats.rst index 4f0b6f6d..ff20f26e 100644 --- a/src/cython/doc/fileformats.rst +++ b/src/cython/doc/fileformats.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + File formats ############ diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst index 3945d72a..4e444fb0 100644 --- a/src/cython/doc/index.rst +++ b/src/cython/doc/index.rst @@ -34,32 +34,32 @@ Data structures Alpha complex ============= -.. include:: alpha_complex_sum.rst +.. include:: alpha_complex_sum.inc Cubical complex =============== -.. include:: cubical_complex_sum.rst +.. include:: cubical_complex_sum.inc Rips complex ============ -.. include:: rips_complex_sum.rst +.. include:: rips_complex_sum.inc Simplex tree ============ -.. include:: simplex_tree_sum.rst +.. include:: simplex_tree_sum.inc Tangential complex ================== -.. include:: tangential_complex_sum.rst +.. include:: tangential_complex_sum.inc Witness complex =============== -.. include:: witness_complex_sum.rst +.. include:: witness_complex_sum.inc Toolbox @@ -68,17 +68,17 @@ Toolbox Bottleneck distance =================== -.. include:: bottleneck_distance_sum.rst +.. include:: bottleneck_distance_sum.inc Persistence cohomology ====================== -.. include:: persistent_cohomology_sum.rst +.. include:: persistent_cohomology_sum.inc Persistence graphical tools =========================== -.. include:: persistence_graphical_tools_sum.rst +.. include:: persistence_graphical_tools_sum.inc Bibliography ************ diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst index b0bc5f38..43ff85c5 100644 --- a/src/cython/doc/installation.rst +++ b/src/cython/doc/installation.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Installation ############ diff --git a/src/cython/doc/periodic_cubical_complex_ref.rst b/src/cython/doc/periodic_cubical_complex_ref.rst index c6190a1b..4b831647 100644 --- a/src/cython/doc/periodic_cubical_complex_ref.rst +++ b/src/cython/doc/periodic_cubical_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Periodic cubical complex reference manual ######################################### diff --git a/src/cython/doc/persistence_graphical_tools_ref.rst b/src/cython/doc/persistence_graphical_tools_ref.rst index a69c8ba2..a2c6bcef 100644 --- a/src/cython/doc/persistence_graphical_tools_ref.rst +++ b/src/cython/doc/persistence_graphical_tools_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ============================================ Persistence graphical tools reference manual ============================================ diff --git a/src/cython/doc/persistence_graphical_tools_sum.rst b/src/cython/doc/persistence_graphical_tools_sum.inc index d602daa7..d602daa7 100644 --- a/src/cython/doc/persistence_graphical_tools_sum.rst +++ b/src/cython/doc/persistence_graphical_tools_sum.inc diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index 46f871c7..292915eb 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -1,8 +1,12 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Persistence graphical tools user manual ======================================= Definition ---------- -.. include:: persistence_graphical_tools_sum.rst +.. include:: persistence_graphical_tools_sum.inc Show persistence as a barcode @@ -10,22 +14,13 @@ Show persistence as a barcode This function can display the persistence result as a barcode: -.. testcode:: - - import gudhi - - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ - '/data/bitmap/3d_torus.txt') - diag = periodic_cc.persistence() - plt = gudhi.plot_persistence_barcode(diag) - plt.show() - .. plot:: + :include-source: import gudhi - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ - '/data/bitmap/3d_torus.txt') + perseus_file = gudhi.__root_source_dir__ + '/data/bitmap/3d_torus.txt' + periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=perseus_file) diag = periodic_cc.persistence() print("diag = ", diag) plt = gudhi.plot_persistence_barcode(diag) @@ -36,24 +31,32 @@ Show persistence as a diagram This function can display the persistence result as a diagram: -.. testcode:: +.. plot:: + :include-source: import gudhi - - point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + '/data/points/tore3D_1307.off') - rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.3) - simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) - diag = simplex_tree.persistence() - plt = gudhi.plot_persistence_diagram(diag) + + # 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, + legend=True) plt.show() +If you want more information on a specific dimension, for instance: + .. plot:: + :include-source: import gudhi - point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + '/data/points/tore3D_1307.off') - rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.3) - simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) - diag = simplex_tree.persistence() - plt = gudhi.plot_persistence_diagram(diag) + persistence_file=gudhi.__root_source_dir__ + \ + '/data/persistence_diagram/rips_on_tore3D_1307.pers' + diag = \ + gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file=\ + persistence_file) + dim = 1 + # Display all points with some transparency + plt = gudhi.plot_persistence_diagram([(dim,interval) for interval in diag[dim]], + max_plots=0, alpha=0.1) plt.show() diff --git a/src/cython/doc/persistent_cohomology_sum.rst b/src/cython/doc/persistent_cohomology_sum.inc index a26df1dc..a26df1dc 100644 --- a/src/cython/doc/persistent_cohomology_sum.rst +++ b/src/cython/doc/persistent_cohomology_sum.inc diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst index bf90c163..ce7fc685 100644 --- a/src/cython/doc/persistent_cohomology_user.rst +++ b/src/cython/doc/persistent_cohomology_user.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Persistent cohomology user manual ================================= Definition diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py deleted file mode 100755 index de33d506..00000000 --- a/src/cython/doc/pyplots/barcode_persistence.py +++ /dev/null @@ -1,7 +0,0 @@ -import gudhi - -periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ - '/data/bitmap/3d_torus.txt') -diag = periodic_cc.persistence() -plt = gudhi.plot_persistence_barcode(diag) -plt.show() diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py deleted file mode 100755 index 3bab0ca1..00000000 --- a/src/cython/doc/pyplots/diagram_persistence.py +++ /dev/null @@ -1,9 +0,0 @@ -import gudhi - -point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + \ - '/data/points/tore3D_1307.off') -rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.3) -simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) -diag = simplex_tree.persistence() -plt = gudhi.plot_persistence_diagram(diag) -plt.show() diff --git a/src/cython/doc/reader_utils_ref.rst b/src/cython/doc/reader_utils_ref.rst index 9c1ea6fc..f3ecebad 100644 --- a/src/cython/doc/reader_utils_ref.rst +++ b/src/cython/doc/reader_utils_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ============================= Reader utils reference manual ============================= diff --git a/src/cython/doc/rips_complex_ref.rst b/src/cython/doc/rips_complex_ref.rst index b17dc4e0..22b5616c 100644 --- a/src/cython/doc/rips_complex_ref.rst +++ b/src/cython/doc/rips_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ============================= Rips complex reference manual ============================= diff --git a/src/cython/doc/rips_complex_sum.rst b/src/cython/doc/rips_complex_sum.inc index 5616bfa9..5616bfa9 100644 --- a/src/cython/doc/rips_complex_sum.rst +++ b/src/cython/doc/rips_complex_sum.inc diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst index 7738aef0..a8c06cf9 100644 --- a/src/cython/doc/rips_complex_user.rst +++ b/src/cython/doc/rips_complex_user.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Rips complex user manual ========================= Definition @@ -243,7 +247,7 @@ the program output is: [3, 6] -> 11.00 Correlation matrix ---------------- +------------------ Example from a correlation matrix ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/src/cython/doc/simplex_tree_ref.rst b/src/cython/doc/simplex_tree_ref.rst index 6d196843..9eb8c199 100644 --- a/src/cython/doc/simplex_tree_ref.rst +++ b/src/cython/doc/simplex_tree_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ============================= Simplex tree reference manual ============================= diff --git a/src/cython/doc/simplex_tree_sum.rst b/src/cython/doc/simplex_tree_sum.inc index fb0e54c1..fb0e54c1 100644 --- a/src/cython/doc/simplex_tree_sum.rst +++ b/src/cython/doc/simplex_tree_sum.inc diff --git a/src/cython/doc/simplex_tree_user.rst b/src/cython/doc/simplex_tree_user.rst index 4b1dde19..aebeb29f 100644 --- a/src/cython/doc/simplex_tree_user.rst +++ b/src/cython/doc/simplex_tree_user.rst @@ -1,9 +1,13 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Simplex tree user manual ======================== Definition ---------- -.. include:: simplex_tree_sum.rst +.. include:: simplex_tree_sum.inc A simplicial complex :math:`\mathbf{K}` on a set of vertices :math:`V = \{1, \cdots ,|V|\}` is a collection of simplices :math:`\{\sigma\}`, :math:`\sigma \subseteq V` such that diff --git a/src/cython/doc/strong_witness_complex_ref.rst b/src/cython/doc/strong_witness_complex_ref.rst index 4ed4fe46..d624d711 100644 --- a/src/cython/doc/strong_witness_complex_ref.rst +++ b/src/cython/doc/strong_witness_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ======================================= Strong witness complex reference manual ======================================= diff --git a/src/cython/doc/tangential_complex_ref.rst b/src/cython/doc/tangential_complex_ref.rst index 35589475..cdfda082 100644 --- a/src/cython/doc/tangential_complex_ref.rst +++ b/src/cython/doc/tangential_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + =================================== Tangential complex reference manual =================================== diff --git a/src/cython/doc/tangential_complex_sum.rst b/src/cython/doc/tangential_complex_sum.inc index 72b4d7ba..72b4d7ba 100644 --- a/src/cython/doc/tangential_complex_sum.rst +++ b/src/cython/doc/tangential_complex_sum.inc diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst index fafb3193..5ce69e86 100644 --- a/src/cython/doc/tangential_complex_user.rst +++ b/src/cython/doc/tangential_complex_user.rst @@ -1,6 +1,10 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Tangential complex user manual ============================== -.. include:: tangential_complex_sum.rst +.. include:: tangential_complex_sum.inc Definition ---------- diff --git a/src/cython/doc/todos.rst b/src/cython/doc/todos.rst index 78972a4c..ca274ced 100644 --- a/src/cython/doc/todos.rst +++ b/src/cython/doc/todos.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ========== To be done ========== diff --git a/src/cython/doc/witness_complex_ref.rst b/src/cython/doc/witness_complex_ref.rst index c78760cb..9987d3fd 100644 --- a/src/cython/doc/witness_complex_ref.rst +++ b/src/cython/doc/witness_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ================================ Witness complex reference manual ================================ diff --git a/src/cython/doc/witness_complex_sum.rst b/src/cython/doc/witness_complex_sum.inc index a8a126a0..a8a126a0 100644 --- a/src/cython/doc/witness_complex_sum.rst +++ b/src/cython/doc/witness_complex_sum.inc diff --git a/src/cython/doc/witness_complex_user.rst b/src/cython/doc/witness_complex_user.rst index 99be5185..40e94134 100644 --- a/src/cython/doc/witness_complex_user.rst +++ b/src/cython/doc/witness_complex_user.rst @@ -1,7 +1,11 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Witness complex user manual =========================== -.. include:: witness_complex_sum.rst +.. include:: witness_complex_sum.inc Definitions ----------- diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in index a798717d..ee381a1b 100644 --- a/src/cython/setup.py.in +++ b/src/cython/setup.py.in @@ -46,8 +46,6 @@ setup( version='@GUDHI_VERSION@', url='http://gudhi.gforge.inria.fr/', ext_modules = cythonize(gudhi), - - #install_requires = required, install_requires = [ "matplotlib", "numpy", |