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

12 files changed, 52 insertions, 252 deletions

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 <target>' where <target> 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 <http://www.gnu.org/licenses/>.
-"""
-
-__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 ^<target^>` where ^<target^> 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)