From c15a3570fa54e837c27f0e5b862e7bb5c16302d7 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 7 Sep 2017 13:17:19 +0000 Subject: Python documentation is now built from sources to the build directory. Missing bibtex and images to be "as before" git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2649 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0deda91875e34ce534c88a601cfb167d9c7dfa01 --- src/cython/doc/Makefile.in | 44 ----------- src/cython/doc/alpha_complex_user.rst | 3 +- src/cython/doc/conf.py | 90 ++-------------------- src/cython/doc/cubical_complex_user.rst | 10 ++- src/cython/doc/examples.rst | 19 ++++- src/cython/doc/generate_examples.py | 43 ----------- src/cython/doc/make.bat.in | 67 ---------------- .../doc/persistence_graphical_tools_user.rst | 13 +++- src/cython/doc/pyplots/barcode_persistence.py | 3 +- src/cython/doc/pyplots/diagram_persistence.py | 3 +- src/cython/doc/rips_complex_user.rst | 6 +- src/cython/doc/tangential_complex_user.rst | 3 +- 12 files changed, 52 insertions(+), 252 deletions(-) delete mode 100644 src/cython/doc/Makefile.in delete mode 100755 src/cython/doc/generate_examples.py delete mode 100644 src/cython/doc/make.bat.in (limited to 'src/cython/doc') diff --git a/src/cython/doc/Makefile.in b/src/cython/doc/Makefile.in deleted file mode 100644 index 526350b3..00000000 --- a/src/cython/doc/Makefile.in +++ /dev/null @@ -1,44 +0,0 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = @SPHINX_PATH@ -PAPER = -BUILDDIR = _build - -# User-friendly check for sphinx-build -ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) -$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) -endif - -# Internal variables. -PAPEROPT_a4 = -D latex_paper_size=a4 -PAPEROPT_letter = -D latex_paper_size=letter -ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . -# the i18n builder cannot share the environment and doctrees with the others -I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . - -.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext - -help: - @echo "Please use \`make ' where is one of" - @echo " html to make standalone HTML files" - @echo " doctest to run all doctests embedded in the documentation (if enabled)" - -clean: - rm -f examples.inc - rm -rf $(BUILDDIR)/* - -# GUDHI specific : Examples.inc is generated with generate_examples.py (and deleted on clean) - -html: - ./generate_examples.py - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." - -doctest: - $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest - @echo "Testing of doctests in the sources finished, look at the " \ - "results in $(BUILDDIR)/doctest/output.txt." diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst index e8268ef1..e541e6d3 100644 --- a/src/cython/doc/alpha_complex_user.rst +++ b/src/cython/doc/alpha_complex_user.rst @@ -158,7 +158,8 @@ Then, it is asked to display information about the alpha complex: .. testcode:: import gudhi - alpha_complex = gudhi.AlphaComplex(off_file='alphacomplexdoc.off') + alpha_complex = gudhi.AlphaComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/alphacomplexdoc.off') simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=59.0) result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ repr(simplex_tree.num_simplices()) + ' simplices - ' + \ diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py index 072f7a94..19a880d4 100755 --- a/src/cython/doc/conf.py +++ b/src/cython/doc/conf.py @@ -21,7 +21,7 @@ import os #sys.path.insert(0, os.path.abspath('.')) # Path to Gudhi.so from source path -sys.path.insert(0, os.path.abspath('..')) +sys.path.insert(0, os.path.abspath('.')) # -- General configuration ------------------------------------------------ @@ -58,18 +58,20 @@ source_suffix = '.rst' # The master toctree document. master_doc = 'index' +import gudhi + # General information about the project. -project = u'GUDHI' -copyright = u'2016, GUDHI Editorial Board' +project = gudhi.__name__ +copyright = gudhi.__copyright__ # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. -version = '2.0' +version = gudhi.__version__ # The full version, including alpha/beta/rc tags. -release = '2.0.1-rc1' +#release = '2.0.1-rc1' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. @@ -198,81 +200,3 @@ html_static_path = ['_static'] # Output file base name for HTML help builder. htmlhelp_basename = 'GUDHIdoc' - -# -- Options for LaTeX output --------------------------------------------- - -latex_elements = { -# The paper size ('letterpaper' or 'a4paper'). -#'papersize': 'letterpaper', - -# The font size ('10pt', '11pt' or '12pt'). -#'pointsize': '10pt', - -# Additional stuff for the LaTeX preamble. -#'preamble': '', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - ('index', 'GUDHI.tex', u'GUDHI Documentation', - u'Vincent Rouvreau', 'manual'), -] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -#latex_logo = None - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -#latex_use_parts = False - -# If true, show page references after internal links. -#latex_show_pagerefs = False - -# If true, show URL addresses after external links. -#latex_show_urls = False - -# Documents to append as an appendix to all manuals. -#latex_appendices = [] - -# If false, no module index is generated. -#latex_domain_indices = True - - -# -- Options for manual page output --------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - ('index', 'gudhi', u'GUDHI Documentation', - [u'Vincent Rouvreau'], 1) -] - -# If true, show URL addresses after external links. -#man_show_urls = False - - -# -- Options for Texinfo output ------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - ('index', 'GUDHI', u'GUDHI Documentation', - u'Vincent Rouvreau', 'GUDHI', 'One line description of project.', - 'Miscellaneous'), -] - -# Documents to append as an appendix to all manuals. -#texinfo_appendices = [] - -# If false, no module index is generated. -#texinfo_domain_indices = True - -# How to display URL addresses: 'footnote', 'no', or 'inline'. -#texinfo_show_urls = 'footnote' - -# If true, do not generate a @detailmenu in the "Top" node's menu. -#texinfo_no_detailmenu = False diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst index 344b9554..8c9a3ed6 100644 --- a/src/cython/doc/cubical_complex_user.rst +++ b/src/cython/doc/cubical_complex_user.rst @@ -97,12 +97,13 @@ The input file for the following complex is: .. literalinclude:: cubicalcomplexdoc.txt -.. centered:: cubicalcomplexdoc.txt +.. centered:: data/bitmap/cubicalcomplexdoc.txt .. testcode:: import gudhi - cubical_complex = gudhi.CubicalComplex(perseus_file='cubicalcomplexdoc.txt') + cubical_complex = gudhi.CubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ + '/data/bitmap/cubicalcomplexdoc.txt') result_str = 'Cubical complex is of dimension ' + repr(cubical_complex.dimension()) + ' - ' + \ repr(cubical_complex.num_simplices()) + ' simplices.' print(result_str) @@ -129,14 +130,15 @@ For instance: .. literalinclude:: periodiccubicalcomplexdoc.txt -.. centered:: periodiccubicalcomplexdoc.txt +.. centered:: data/bitmap/periodiccubicalcomplexdoc.txt Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y. .. testcode:: import gudhi - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='periodiccubicalcomplexdoc.txt') + periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ + '/data/bitmap/periodiccubicalcomplexdoc.txt') result_str = 'Periodic cubical complex is of dimension ' + repr(periodic_cc.dimension()) + ' - ' + \ repr(periodic_cc.num_simplices()) + ' simplices.' print(result_str) diff --git a/src/cython/doc/examples.rst b/src/cython/doc/examples.rst index a89e0596..1e596e18 100644 --- a/src/cython/doc/examples.rst +++ b/src/cython/doc/examples.rst @@ -1,4 +1,21 @@ Examples ######## -.. include:: examples.inc +.. only:: builder_html + + * :download:`rips_complex_from_points_example.py <../example/rips_complex_from_points_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:`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>` + * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_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_persistence_diagram.py <../example/rips_persistence_diagram.py>` + * :download:`random_cubical_complex_persistence_example.py <../example/random_cubical_complex_persistence_example.py>` diff --git a/src/cython/doc/generate_examples.py b/src/cython/doc/generate_examples.py deleted file mode 100755 index d64d506c..00000000 --- a/src/cython/doc/generate_examples.py +++ /dev/null @@ -1,43 +0,0 @@ -#!/usr/bin/env python - -from os import listdir - -"""This file is part of the Gudhi Library. The Gudhi library - (Geometric Understanding in Higher Dimensions) is a generic C++ - library for computational topology. - - Author(s): Vincent Rouvreau - - Copyright (C) 2017 INRIA - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see . -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2017 INRIA" -__license__ = "GPL v3" - -""" -generate_examples.py generates examples.inc to be included in examples.rst. -Refer to Makefile and make.bat to see if it is correctly launched. -""" - -output_file = open('examples.inc','w') - -output_file.write('.. only:: builder_html\n\n') - -for file in listdir('../example/'): - output_file.write(" * :download:`" + file + " <../example/" + file + ">`\n") - -output_file.close() diff --git a/src/cython/doc/make.bat.in b/src/cython/doc/make.bat.in deleted file mode 100644 index ff1a6d56..00000000 --- a/src/cython/doc/make.bat.in +++ /dev/null @@ -1,67 +0,0 @@ -@ECHO OFF - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=@SPHINX_PATH@ -) -set BUILDDIR=_build -set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . -set I18NSPHINXOPTS=%SPHINXOPTS% . -if NOT "%PAPER%" == "" ( - set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% - set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% -) - -if "%1" == "" goto help - -if "%1" == "help" ( - :help - echo.Please use `make ^` where ^ is one of - echo. html to make standalone HTML files - echo. doctest to run all doctests embedded in the documentation if enabled - goto end -) - -if "%1" == "clean" ( - del examples.inc - for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i - del /q /s %BUILDDIR%\* - goto end -) - - -%SPHINXBUILD% 2> nul -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.http://sphinx-doc.org/ - exit /b 1 -) - -:: GUDHI specific : Examples.inc is generated with generate_examples.py (and deleted on clean) - -if "%1" == "html" ( - generate_examples.py - %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/html. - goto end -) - -if "%1" == "doctest" ( - %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest - if errorlevel 1 exit /b 1 - echo. - echo.Testing of doctests in the sources finished, look at the ^ -results in %BUILDDIR%/doctest/output.txt. - goto end -) - -:end diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index 13198162..9033331f 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -32,7 +32,8 @@ This function can display the persistence result as a barcode: import gudhi - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt') + 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() @@ -41,8 +42,10 @@ This function can display the persistence result as a barcode: import gudhi - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt') + periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ + '/data/bitmap/3d_torus.txt') diag = periodic_cc.persistence() + print("diag = ", diag) plt = gudhi.plot_persistence_barcode(diag) plt.show() @@ -55,7 +58,8 @@ This function can display the persistence result as a diagram: import gudhi - rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2) + rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/tore3D_1307.off', max_edge_length=0.2) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence() plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) @@ -65,7 +69,8 @@ This function can display the persistence result as a diagram: import gudhi - rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2) + rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/tore3D_1307.off', max_edge_length=0.2) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence() plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py index 9cd3149d..de33d506 100755 --- a/src/cython/doc/pyplots/barcode_persistence.py +++ b/src/cython/doc/pyplots/barcode_persistence.py @@ -1,6 +1,7 @@ import gudhi -periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt') +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 index 30661965..c2fbf801 100755 --- a/src/cython/doc/pyplots/diagram_persistence.py +++ b/src/cython/doc/pyplots/diagram_persistence.py @@ -1,6 +1,7 @@ import gudhi -rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2) +rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/tore3D_1307.off', max_edge_length=0.2) simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence() plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst index f9760976..6b48422b 100644 --- a/src/cython/doc/rips_complex_user.rst +++ b/src/cython/doc/rips_complex_user.rst @@ -101,7 +101,8 @@ Finally, it is asked to display information about the Rips complex. .. testcode:: import gudhi - rips_complex = gudhi.RipsComplex(off_file='alphacomplexdoc.off', max_edge_length=12.0) + rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/alphacomplexdoc.off', max_edge_length=12.0) simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ repr(simplex_tree.num_simplices()) + ' simplices - ' + \ @@ -205,7 +206,8 @@ Finally, it is asked to display information about the Rips complex. .. testcode:: import gudhi - rips_complex = gudhi.RipsComplex(csv_file='full_square_distance_matrix.csv', max_edge_length=12.0) + rips_complex = gudhi.RipsComplex(csv_file=gudhi.__root_source_dir__ + \ + '/data/distance_matrix/full_square_distance_matrix.csv', max_edge_length=12.0) simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ repr(simplex_tree.num_simplices()) + ' simplices - ' + \ diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst index 03f9fea6..d670cfdb 100644 --- a/src/cython/doc/tangential_complex_user.rst +++ b/src/cython/doc/tangential_complex_user.rst @@ -122,7 +122,8 @@ This example builds the Tangential complex of point set read in an OFF file. .. testcode:: import gudhi - tc = gudhi.TangentialComplex(off_file='alphacomplexdoc.off') + tc = gudhi.TangentialComplex(off_file=gudhi.__root_source_dir__ + \ + '/data/points/alphacomplexdoc.off') result_str = 'Tangential contains ' + repr(tc.num_simplices()) + \ ' simplices - ' + repr(tc.num_vertices()) + ' vertices.' print(result_str) -- cgit v1.2.3