diff options
-rw-r--r-- | src/cython/CMakeLists.txt | 14 | ||||
-rw-r--r-- | src/cython/src/doc/Makefile | 177 | ||||
-rw-r--r-- | src/cython/src/doc/alpha_complex_ref.rst (renamed from src/cython/doc/source/alpha_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/cython/src/doc/alpha_complex_sum.rst (renamed from src/cython/doc/source/alpha_complex_sum.rst) | 0 | ||||
-rw-r--r-- | src/cython/src/doc/alpha_complex_user.rst (renamed from src/cython/doc/source/alpha_complex_user.rst) | 2 | ||||
-rw-r--r-- | src/cython/src/doc/biblio.rst (renamed from src/cython/doc/source/biblio.rst) | 0 | ||||
-rw-r--r-- | src/cython/src/doc/cgal_citation.rst (renamed from src/cython/doc/source/cgal_citation.rst) | 0 | ||||
-rwxr-xr-x | src/cython/src/doc/conf.py | 271 | ||||
-rw-r--r-- | src/cython/src/doc/cubical_complex_ref.rst (renamed from src/cython/doc/source/cubical_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/cython/src/doc/cubical_complex_sum.rst (renamed from src/cython/doc/source/cubical_complex_sum.rst) | 0 | ||||
-rw-r--r-- | src/cython/src/doc/cubical_complex_user.rst (renamed from src/cython/doc/source/cubical_complex_user.rst) | 4 | ||||
-rw-r--r-- | src/cython/src/doc/index.rst | 63 | ||||
-rw-r--r-- | src/cython/src/doc/make.bat | 242 | ||||
-rw-r--r-- | src/cython/src/doc/periodic_cubical_complex_ref.rst (renamed from src/cython/doc/source/periodic_cubical_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/cython/src/doc/persistent_cohomology_sum.rst (renamed from src/cython/doc/source/persistent_cohomology_sum.rst) | 0 | ||||
-rw-r--r-- | src/cython/src/doc/persistent_cohomology_user.rst (renamed from src/cython/doc/source/persistent_cohomology_user.rst) | 0 | ||||
-rw-r--r-- | src/cython/src/doc/simplex_tree_ref.rst (renamed from src/cython/doc/source/simplex_tree_ref.rst) | 0 | ||||
-rw-r--r-- | src/cython/src/doc/simplex_tree_sum.rst (renamed from src/cython/doc/source/simplex_tree_sum.rst) | 0 | ||||
-rw-r--r-- | src/cython/src/doc/simplex_tree_user.rst (renamed from src/cython/doc/source/simplex_tree_user.rst) | 0 | ||||
-rw-r--r-- | src/cython/src/doc/witness_complex_ref.rst (renamed from src/cython/doc/source/witness_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/cython/src/doc/witness_complex_sum.rst (renamed from src/cython/doc/source/witness_complex_sum.rst) | 0 | ||||
-rw-r--r-- | src/cython/src/doc/witness_complex_user.rst (renamed from src/cython/doc/source/witness_complex_user.rst) | 0 |
22 files changed, 763 insertions, 10 deletions
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index b5ed37a6..8012b592 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -91,24 +91,24 @@ if(PYTHON_PATH AND CYTHON_PATH) file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) # Developper version file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png") - file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/source/img") + file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/src/doc/img") # User version file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.png") - file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/source/img") + file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/src/doc/img") # Biblio file(GLOB GUDHI_BIB_FILES "${CMAKE_SOURCE_DIR}/biblio/*.bib") - file(COPY ${GUDHI_BIB_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/source/") + file(COPY ${GUDHI_BIB_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/src/doc/") # Cubical complex perseus doc example file(GLOB GUDHI_CUBICAL_PERSEUS_FILES "${CMAKE_SOURCE_DIR}/data/bitmap/*cubicalcomplexdoc.txt") - file(COPY ${GUDHI_CUBICAL_PERSEUS_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/source/") - file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/source/") + file(COPY ${GUDHI_CUBICAL_PERSEUS_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/src/doc/") + file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/src/doc/") if (UNIX) add_custom_target(html - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/src/doc COMMAND make html && make doctest) else (UNIX) add_custom_target(html - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/src/doc COMMAND make.bat html) endif (UNIX) endif(SPHINX_PATH) diff --git a/src/cython/src/doc/Makefile b/src/cython/src/doc/Makefile new file mode 100644 index 00000000..fc353a37 --- /dev/null +++ b/src/cython/src/doc/Makefile @@ -0,0 +1,177 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = _build + +# User-friendly check for sphinx-build +ifeq ($(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 <target>' where <target> is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " xml to make Docutils-native XML files" + @echo " pseudoxml to make pseudoxml-XML files for display purposes" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/pouet.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pouet.qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/pouet" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pouet" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +latexpdfja: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through platex and dvipdfmx..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +texinfo: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo + @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." + @echo "Run \`make' in that directory to run these through makeinfo" \ + "(use \`make info' here to do that automatically)." + +info: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo "Running Texinfo files through makeinfo..." + make -C $(BUILDDIR)/texinfo info + @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." + +gettext: + $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale + @echo + @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." + +xml: + $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml + @echo + @echo "Build finished. The XML files are in $(BUILDDIR)/xml." + +pseudoxml: + $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml + @echo + @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." diff --git a/src/cython/doc/source/alpha_complex_ref.rst b/src/cython/src/doc/alpha_complex_ref.rst index 6a122b09..6a122b09 100644 --- a/src/cython/doc/source/alpha_complex_ref.rst +++ b/src/cython/src/doc/alpha_complex_ref.rst diff --git a/src/cython/doc/source/alpha_complex_sum.rst b/src/cython/src/doc/alpha_complex_sum.rst index b608050e..b608050e 100644 --- a/src/cython/doc/source/alpha_complex_sum.rst +++ b/src/cython/src/doc/alpha_complex_sum.rst diff --git a/src/cython/doc/source/alpha_complex_user.rst b/src/cython/src/doc/alpha_complex_user.rst index 07bfcabf..b6b6e550 100644 --- a/src/cython/doc/source/alpha_complex_user.rst +++ b/src/cython/src/doc/alpha_complex_user.rst @@ -153,7 +153,7 @@ Then, it is asked to display information about the alpha complex: .. testcode:: import gudhi - alpha_complex = gudhi.AlphaComplex(off_file='source/alphacomplexdoc.off', + alpha_complex = gudhi.AlphaComplex(off_file='alphacomplexdoc.off', max_alpha_square=59.0) result_str = 'Alpha complex is of dimension ' + repr(alpha_complex.dimension()) + ' - ' + \ repr(alpha_complex.num_simplices()) + ' simplices - ' + \ diff --git a/src/cython/doc/source/biblio.rst b/src/cython/src/doc/biblio.rst index b8e733ed..b8e733ed 100644 --- a/src/cython/doc/source/biblio.rst +++ b/src/cython/src/doc/biblio.rst diff --git a/src/cython/doc/source/cgal_citation.rst b/src/cython/src/doc/cgal_citation.rst index bbc4ef9e..bbc4ef9e 100644 --- a/src/cython/doc/source/cgal_citation.rst +++ b/src/cython/src/doc/cgal_citation.rst diff --git a/src/cython/src/doc/conf.py b/src/cython/src/doc/conf.py new file mode 100755 index 00000000..bc138025 --- /dev/null +++ b/src/cython/src/doc/conf.py @@ -0,0 +1,271 @@ +# -*- coding: utf-8 -*- +# +# GUDHI documentation build configuration file, created by +# sphinx-quickstart on Thu Jun 30 09:55:51 2016. +# +# This file is execfile()d with the current directory set to its +# containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import sys +import os + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +#sys.path.insert(0, os.path.abspath('.')) + +# Path to Gudhi.so from source path +sys.path.insert(0, os.path.abspath('../..')) + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +#needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + 'sphinx.ext.autodoc', + 'sphinx.ext.doctest', + 'sphinx.ext.todo', + 'sphinx.ext.coverage', + 'sphinx.ext.mathjax', + 'sphinx.ext.ifconfig', + 'sphinx.ext.viewcode', + 'sphinxcontrib.bibtex', +] + +todo_include_todos = True +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix of source filenames. +source_suffix = '.rst' + +# The encoding of source files. +#source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'GUDHI' +copyright = u'2016, Vincent Rouvreau' + +# 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 = '1.3.1' +# The full version, including alpha/beta/rc tags. +release = '1.3.1' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +#language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +#today = '' +# Else, today_fmt is used as the format for a strftime call. +#today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ['_build'] + +# The reST default role (used for this markup: `text`) to use for all +# documents. +#default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +#add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +#add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +#show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +#modindex_common_prefix = [] + +# If true, keep warnings as "system message" paragraphs in the built documents. +#keep_warnings = False + + +# -- Options for HTML output ---------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = 'default' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +#html_theme_options = {} + +# Add any paths that contain custom themes here, relative to this directory. +#html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# "<project> v<release> documentation". +#html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +#html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +#html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +#html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +# Add any extra paths that contain custom files (such as robots.txt or +# .htaccess) here, relative to this directory. These files are copied +# directly to the root of the documentation. +#html_extra_path = [] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +#html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +#html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +#html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +#html_additional_pages = {} + +# If false, no module index is generated. +#html_domain_indices = True + +# If false, no index is generated. +#html_use_index = True + +# If true, the index is split into individual pages for each letter. +#html_split_index = False + +# If true, links to the reST sources are added to the pages. +#html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +#html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +#html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a <link> tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +#html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +#html_file_suffix = None + +# 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/source/cubical_complex_ref.rst b/src/cython/src/doc/cubical_complex_ref.rst index 84aa4223..84aa4223 100644 --- a/src/cython/doc/source/cubical_complex_ref.rst +++ b/src/cython/src/doc/cubical_complex_ref.rst diff --git a/src/cython/doc/source/cubical_complex_sum.rst b/src/cython/src/doc/cubical_complex_sum.rst index 4008a1fd..4008a1fd 100644 --- a/src/cython/doc/source/cubical_complex_sum.rst +++ b/src/cython/src/doc/cubical_complex_sum.rst diff --git a/src/cython/doc/source/cubical_complex_user.rst b/src/cython/src/doc/cubical_complex_user.rst index 38ff978c..2cd85c0a 100644 --- a/src/cython/doc/source/cubical_complex_user.rst +++ b/src/cython/src/doc/cubical_complex_user.rst @@ -99,7 +99,7 @@ The input file for the following complex is: .. testcode:: import gudhi - cubical_complex = gudhi.CubicalComplex(perseus_file='source/cubicalcomplexdoc.txt') + cubical_complex = gudhi.CubicalComplex(perseus_file='cubicalcomplexdoc.txt') result_str = 'Cubical complex is of dimension ' + repr(cubical_complex.dimension()) + ' - ' + \ repr(cubical_complex.num_simplices()) + ' simplices.' print(result_str) @@ -133,7 +133,7 @@ Indicate that we have imposed periodic boundary conditions in the direction x, b .. testcode:: import gudhi - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='source/periodiccubicalcomplexdoc.txt') + periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='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/src/doc/index.rst b/src/cython/src/doc/index.rst new file mode 100644 index 00000000..5245d69d --- /dev/null +++ b/src/cython/src/doc/index.rst @@ -0,0 +1,63 @@ +.. GUDHI documentation master file, created by + sphinx-quickstart on Thu Jun 30 09:55:51 2016. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +GUDHI's documentation +##################### + +.. image:: img/Gudhi_banner.png + :align: center + +Introduction +************ + +The Gudhi library (Geometry Understanding in Higher Dimensions) is a generic +open source C++ library for Computational Topology and Topological Data +Analysis (`TDA <https://en.wikipedia.org/wiki/Topological_data_analysis>`_). +The GUDHI library intends to help the development of new algorithmic solutions +in TDA and their transfer to applications. It provides robust, efficient, +flexible and easy to use implementations of state-of-the-art algorithms and +data structures. + +The current release of the GUDHI library includes: + +* Data structures to represent, construct and manipulate simplicial complexes. +* Algorithms to compute persistent homology and multi-field persistent homology. +* Simplication of simplicial complexes by edge contraction. + +All data-structures are generic and several of their aspects can be +parameterized via template classes. We refer to :cite:`gudhilibrary_ICMS14` +for a detailed description of the design of the library. + +Data structures +*************** + +Alpha complex +============= + +.. include:: alpha_complex_sum.rst + +Cubical complex +=============== + +.. include:: cubical_complex_sum.rst + +Simplex tree +============ + +.. include:: simplex_tree_sum.rst + +Witness complex +=============== + +.. include:: witness_complex_sum.rst + + +Toolbox +******* + +Persistence cohomology +====================== + +.. include:: persistent_cohomology_sum.rst diff --git a/src/cython/src/doc/make.bat b/src/cython/src/doc/make.bat new file mode 100644 index 00000000..656c0105 --- /dev/null +++ b/src/cython/src/doc/make.bat @@ -0,0 +1,242 @@ +@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+ set SPHINXBUILD=sphinx-build
+)
+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 ^<target^>` where ^<target^> is one of
+ echo. html to make standalone HTML files
+ echo. dirhtml to make HTML files named index.html in directories
+ echo. singlehtml to make a single large HTML file
+ echo. pickle to make pickle files
+ echo. json to make JSON files
+ echo. htmlhelp to make HTML files and a HTML help project
+ echo. qthelp to make HTML files and a qthelp project
+ echo. devhelp to make HTML files and a Devhelp project
+ echo. epub to make an epub
+ echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+ echo. text to make text files
+ echo. man to make manual pages
+ echo. texinfo to make Texinfo files
+ echo. gettext to make PO message catalogs
+ echo. changes to make an overview over all changed/added/deprecated items
+ echo. xml to make Docutils-native XML files
+ echo. pseudoxml to make pseudoxml-XML files for display purposes
+ echo. linkcheck to check all external links for integrity
+ echo. doctest to run all doctests embedded in the documentation if enabled
+ goto end
+)
+
+if "%1" == "clean" (
+ 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
+)
+
+if "%1" == "html" (
+ %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" == "dirhtml" (
+ %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
+ goto end
+)
+
+if "%1" == "singlehtml" (
+ %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
+ goto end
+)
+
+if "%1" == "pickle" (
+ %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can process the pickle files.
+ goto end
+)
+
+if "%1" == "json" (
+ %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can process the JSON files.
+ goto end
+)
+
+if "%1" == "htmlhelp" (
+ %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in %BUILDDIR%/htmlhelp.
+ goto end
+)
+
+if "%1" == "qthelp" (
+ %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in %BUILDDIR%/qthelp, like this:
+ echo.^> qcollectiongenerator %BUILDDIR%\qthelp\pouet.qhcp
+ echo.To view the help file:
+ echo.^> assistant -collectionFile %BUILDDIR%\qthelp\pouet.ghc
+ goto end
+)
+
+if "%1" == "devhelp" (
+ %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished.
+ goto end
+)
+
+if "%1" == "epub" (
+ %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The epub file is in %BUILDDIR%/epub.
+ goto end
+)
+
+if "%1" == "latex" (
+ %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
+ goto end
+)
+
+if "%1" == "latexpdf" (
+ %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+ cd %BUILDDIR%/latex
+ make all-pdf
+ cd %BUILDDIR%/..
+ echo.
+ echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+ goto end
+)
+
+if "%1" == "latexpdfja" (
+ %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+ cd %BUILDDIR%/latex
+ make all-pdf-ja
+ cd %BUILDDIR%/..
+ echo.
+ echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+ goto end
+)
+
+if "%1" == "text" (
+ %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The text files are in %BUILDDIR%/text.
+ goto end
+)
+
+if "%1" == "man" (
+ %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The manual pages are in %BUILDDIR%/man.
+ goto end
+)
+
+if "%1" == "texinfo" (
+ %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
+ goto end
+)
+
+if "%1" == "gettext" (
+ %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
+ goto end
+)
+
+if "%1" == "changes" (
+ %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.The overview file is in %BUILDDIR%/changes.
+ goto end
+)
+
+if "%1" == "linkcheck" (
+ %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Link check complete; look for any errors in the above output ^
+or in %BUILDDIR%/linkcheck/output.txt.
+ 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
+)
+
+if "%1" == "xml" (
+ %SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The XML files are in %BUILDDIR%/xml.
+ goto end
+)
+
+if "%1" == "pseudoxml" (
+ %SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
+ goto end
+)
+
+:end
diff --git a/src/cython/doc/source/periodic_cubical_complex_ref.rst b/src/cython/src/doc/periodic_cubical_complex_ref.rst index c6190a1b..c6190a1b 100644 --- a/src/cython/doc/source/periodic_cubical_complex_ref.rst +++ b/src/cython/src/doc/periodic_cubical_complex_ref.rst diff --git a/src/cython/doc/source/persistent_cohomology_sum.rst b/src/cython/src/doc/persistent_cohomology_sum.rst index 081399a5..081399a5 100644 --- a/src/cython/doc/source/persistent_cohomology_sum.rst +++ b/src/cython/src/doc/persistent_cohomology_sum.rst diff --git a/src/cython/doc/source/persistent_cohomology_user.rst b/src/cython/src/doc/persistent_cohomology_user.rst index 33b19ce2..33b19ce2 100644 --- a/src/cython/doc/source/persistent_cohomology_user.rst +++ b/src/cython/src/doc/persistent_cohomology_user.rst diff --git a/src/cython/doc/source/simplex_tree_ref.rst b/src/cython/src/doc/simplex_tree_ref.rst index 6d196843..6d196843 100644 --- a/src/cython/doc/source/simplex_tree_ref.rst +++ b/src/cython/src/doc/simplex_tree_ref.rst diff --git a/src/cython/doc/source/simplex_tree_sum.rst b/src/cython/src/doc/simplex_tree_sum.rst index ffdb2cf4..ffdb2cf4 100644 --- a/src/cython/doc/source/simplex_tree_sum.rst +++ b/src/cython/src/doc/simplex_tree_sum.rst diff --git a/src/cython/doc/source/simplex_tree_user.rst b/src/cython/src/doc/simplex_tree_user.rst index 3a00f1ac..3a00f1ac 100644 --- a/src/cython/doc/source/simplex_tree_user.rst +++ b/src/cython/src/doc/simplex_tree_user.rst diff --git a/src/cython/doc/source/witness_complex_ref.rst b/src/cython/src/doc/witness_complex_ref.rst index c78760cb..c78760cb 100644 --- a/src/cython/doc/source/witness_complex_ref.rst +++ b/src/cython/src/doc/witness_complex_ref.rst diff --git a/src/cython/doc/source/witness_complex_sum.rst b/src/cython/src/doc/witness_complex_sum.rst index 0d65d420..0d65d420 100644 --- a/src/cython/doc/source/witness_complex_sum.rst +++ b/src/cython/src/doc/witness_complex_sum.rst diff --git a/src/cython/doc/source/witness_complex_user.rst b/src/cython/src/doc/witness_complex_user.rst index 604c7357..604c7357 100644 --- a/src/cython/doc/source/witness_complex_user.rst +++ b/src/cython/src/doc/witness_complex_user.rst |