From 94bf43f9d92f546837f5120379ffdc08bf274302 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 5 Sep 2017 15:47:24 +0000
Subject: Tests and compilation are now from sources (even if doc and examples
 are copied) This modification does not fix it for the doc

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2645 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0fa4850747d3f18cd54e0622ef1831d5d5c5a0df
---
 src/cython/CMakeLists.txt | 123 ++++++++++++++++++++++++++++++++++------------
 src/cython/gudhi.pyx.in   |  18 +++----
 src/cython/setup.py.in    |   2 +-
 3 files changed, 102 insertions(+), 41 deletions(-)

(limited to 'src')

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index ab5ea9ef..a12b6029 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -73,13 +73,11 @@ if(CYTHON_FOUND)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
   endif (EIGEN3_FOUND)
 
-  # Copy recursively include, cython, example, doc and test repositories before packages finding
+  # Copy recursively example and doc repositories before packages finding
   # Some tests and doc files are removed in case some packages are not found
-  file(COPY include DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  file(COPY cython DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
   file(COPY example DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  file(COPY test DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
   file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
   # Developper version for doc images
   file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png")
   file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
@@ -104,9 +102,9 @@ if(CYTHON_FOUND)
 
   if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
     # If CGAL_VERSION >= 4.8.1, include subsampling
-    set(GUDHI_CYTHON_SUBSAMPLING "include 'cython/subsampling.pyx'")
-    set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include 'cython/tangential_complex.pyx'")
-    set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include 'cython/bottleneck_distance.pyx'")
+    set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
+    set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
+    set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
   else (NOT CGAL_VERSION VERSION_LESS 4.8.1)
     # Remove subsampling unitary tests
     file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_subsampling.py)
@@ -125,7 +123,7 @@ if(CYTHON_FOUND)
   endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
     # If CGAL_VERSION >= 4.7.0, include alpha
-    set(GUDHI_CYTHON_ALPHA_COMPLEX "include 'cython/alpha_complex.pyx'")
+    set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
   else (NOT CGAL_VERSION VERSION_LESS 4.7.0)
     # Remove alpha complex unitary tests
     file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py)
@@ -136,9 +134,9 @@ if(CYTHON_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
     # If CGAL_VERSION >= 4.6.0, include euclidean versions of witness complex
     set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX
-        "include 'cython/euclidean_witness_complex.pyx'\ninclude 'cython/euclidean_strong_witness_complex.pyx'\n")
+        "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n")
   else (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    # Remove alpha complex unitary tests
+    # Remove euclidean witness complex unitary tests
     file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_euclidean_witness_complex.py)
     file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_witness_complex_ref.rst")
     file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_strong_witness_complex_ref.rst")
@@ -177,6 +175,7 @@ if(CYTHON_FOUND)
   # Loop on INCLUDE_DIRECTORIES PROPERTY
   get_property(GUDHI_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES)
   foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
+    message("  ---  ${GUDHI_INCLUDE_DIRECTORY} ---")
     set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ")
   endforeach()
   set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ")
@@ -220,97 +219,159 @@ if(CYTHON_FOUND)
 
   # Test examples
   if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+    # Bottleneck
     add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
+             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
              -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
     set_tests_properties(alpha_rips_persistence_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
     add_test(NAME bottleneck_basic_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/bottleneck_basic_example.py")
+             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
     set_tests_properties(bottleneck_basic_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
+    add_test(
+        NAME test_bottleneck_distance_py_test
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py)
+    set_tests_properties(test_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+    # Tangential
     add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
+             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
     set_tests_properties(tangential_complex_plain_homology_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
+    add_test(
+        NAME test_tangential_complex_py_test
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_tangential_complex.py)
+    set_tests_properties(test_tangential_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+    # Euclidean witness
     add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
     set_tests_properties(euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
     add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
     set_tests_properties(euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+    add_test(
+        NAME test_euclidean_witness_complex_py_test
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py)
+    set_tests_properties(test_euclidean_witness_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
   endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
 
   if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+    # Alpha
     add_test(NAME alpha_complex_from_points_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_from_points_example.py")
+             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
     set_tests_properties(alpha_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
     add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
+             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
     set_tests_properties(alpha_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
-  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
 
-  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-  endif (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+    add_test(
+        NAME test_alpha_complex_py_test
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_alpha_complex.py)
+    set_tests_properties(test_alpha_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
 
+  # Cubical
   add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
+           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
            --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
   set_tests_properties(periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   add_test(NAME random_cubical_complex_persistence_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/random_cubical_complex_persistence_example.py"
+           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
            10 10 10)
   set_tests_properties(random_cubical_complex_persistence_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
+  add_test(
+      NAME test_cubical_complex_py_test
+      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_cubical_complex.py)
+  set_tests_properties(test_cubical_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  # Rips
   add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
+           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
            --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
   set_tests_properties(rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
+           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
            --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
   set_tests_properties(rips_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   add_test(NAME rips_complex_from_points_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_from_points_example.py)
+           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
   set_tests_properties(rips_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
+  add_test(
+      NAME test_rips_complex_py_test
+      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_rips_complex.py)
+  set_tests_properties(test_rips_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  # Simplex tree
   add_test(NAME simplex_tree_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/simplex_tree_example.py)
+           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
   set_tests_properties(simplex_tree_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
+  add_test(
+      NAME test_simplex_tree_py_test
+      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_simplex_tree.py)
+  set_tests_properties(test_simplex_tree_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  # Witness
   add_test(NAME witness_complex_from_nearest_landmark_table_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/witness_complex_from_nearest_landmark_table.py)
+           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
   set_tests_properties(witness_complex_from_nearest_landmark_table_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
-  # Unitary tests are available through py.test
   add_test(
-      NAME gudhi_cython_py_test
+      NAME test_witness_complex_py_test
+      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_witness_complex.py)
+  set_tests_properties(test_witness_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  # Reader utils
+  add_test(
+      NAME test_reader_utils_py_test
+      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_reader_utils.py)
+  set_tests_properties(test_reader_utils_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  # Subsampling
+  add_test(
+      NAME test_subsampling_py_test
       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} -m pytest)
-  set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py)
+  set_tests_properties(test_subsampling_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   # Documentation generation is available through sphinx
   if(SPHINX_PATH)
diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in
index ed2d28cc..1141673a 100644
--- a/src/cython/gudhi.pyx.in
+++ b/src/cython/gudhi.pyx.in
@@ -24,15 +24,15 @@ __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016  INRIA"
 __license__ = "GPL v3"
 
-include "cython/off_reader.pyx"
-include "cython/simplex_tree.pyx"
-include "cython/rips_complex.pyx"
-include "cython/cubical_complex.pyx"
-include "cython/periodic_cubical_complex.pyx"
-include "cython/persistence_graphical_tools.py"
-include "cython/reader_utils.pyx"
-include "cython/witness_complex.pyx"
-include "cython/strong_witness_complex.pyx"
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/off_reader.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/simplex_tree.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/rips_complex.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/cubical_complex.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/periodic_cubical_complex.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/persistence_graphical_tools.py'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/reader_utils.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/witness_complex.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/strong_witness_complex.pyx'
 @GUDHI_CYTHON_ALPHA_COMPLEX@
 @GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX@
 @GUDHI_CYTHON_SUBSAMPLING@
diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in
index c1a1717a..fefa36bb 100644
--- a/src/cython/setup.py.in
+++ b/src/cython/setup.py.in
@@ -29,7 +29,7 @@ __license__ = "GPL v3"
 
 gudhi = Extension(
     "gudhi",
-    sources = ['gudhi.pyx',],
+    sources = ['@CMAKE_CURRENT_BINARY_DIR@/gudhi.pyx',],
     language = 'c++',
     extra_compile_args=[@GUDHI_CYTHON_EXTRA_COMPILE_ARGS@],
     extra_link_args=[@GUDHI_CYTHON_EXTRA_LINK_ARGS@],
-- 
cgit v1.2.3


From c15a3570fa54e837c27f0e5b862e7bb5c16302d7 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
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/CMakeLists.txt                          | 200 ++++++++-------------
 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 +-
 src/cython/gudhi.pyx.in                            |   3 +
 14 files changed, 131 insertions(+), 376 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')

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index a12b6029..6c8232ea 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -73,33 +73,6 @@ if(CYTHON_FOUND)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
   endif (EIGEN3_FOUND)
 
-  # Copy recursively example and doc repositories before packages finding
-  # Some tests and doc files are removed in case some packages are not found
-  file(COPY example DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-
-  # Developper version for doc images
-  file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png")
-  file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
-  file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.svg")
-  file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
-  # User version for doc images
-  file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.png")
-  file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
-  file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.svg")
-  file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
-  # Biblio
-  file(GLOB GUDHI_BIB_FILES "${CMAKE_SOURCE_DIR}/biblio/*.bib")
-  file(COPY ${GUDHI_BIB_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/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/")
-  file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-  file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-  # Persistence graphical tools examples
-  file(COPY "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-  file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-
   if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
     # If CGAL_VERSION >= 4.8.1, include subsampling
     set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
@@ -192,11 +165,6 @@ if(CYTHON_FOUND)
     set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}")
   endif(UNIX)
 
-  # set sphinx-build in make files
-  configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY)
-  configure_file(doc/Makefile.in "${CMAKE_CURRENT_BINARY_DIR}/doc/Makefile" @ONLY)
-  configure_file(doc/make.bat.in "${CMAKE_CURRENT_BINARY_DIR}/doc/make.bat" @ONLY)
-
   # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention
   configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY)
   # Generate gudhi.pyx - Gudhi cython file
@@ -222,52 +190,46 @@ if(CYTHON_FOUND)
     # Bottleneck
     add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
              -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
-    set_tests_properties(alpha_rips_persistence_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
     add_test(NAME bottleneck_basic_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
-    set_tests_properties(bottleneck_basic_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
 
-    add_test(
-        NAME test_bottleneck_distance_py_test
-        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py)
-    set_tests_properties(test_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+    add_test(NAME test_bottleneck_distance_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py)
 
     # Tangential
     add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
-    set_tests_properties(tangential_complex_plain_homology_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
-    add_test(
-        NAME test_tangential_complex_py_test
-        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_tangential_complex.py)
-    set_tests_properties(test_tangential_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+    add_test(NAME test_tangential_complex_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_tangential_complex.py)
 
     # Euclidean witness
     add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-    set_tests_properties(euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
     add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-    set_tests_properties(euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
-    add_test(
-        NAME test_euclidean_witness_complex_py_test
-        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py)
-    set_tests_properties(test_euclidean_witness_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+    add_test(NAME test_euclidean_witness_complex_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py)
 
   endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
 
@@ -275,115 +237,105 @@ if(CYTHON_FOUND)
     # Alpha
     add_test(NAME alpha_complex_from_points_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
-    set_tests_properties(alpha_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
 
     add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
-    set_tests_properties(alpha_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
-    add_test(
-        NAME test_alpha_complex_py_test
-        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_alpha_complex.py)
-    set_tests_properties(test_alpha_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+    add_test(NAME test_alpha_complex_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_alpha_complex.py)
 
   endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
 
   # Cubical
   add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
            --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
-  set_tests_properties(periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   add_test(NAME random_cubical_complex_persistence_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
            10 10 10)
-  set_tests_properties(random_cubical_complex_persistence_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
-  add_test(
-      NAME test_cubical_complex_py_test
-      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_cubical_complex.py)
-  set_tests_properties(test_cubical_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+  add_test(NAME test_cubical_complex_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_cubical_complex.py)
 
   # Rips
   add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
            --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
-  set_tests_properties(rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
            --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
-  set_tests_properties(rips_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   add_test(NAME rips_complex_from_points_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
-  set_tests_properties(rips_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
 
-  add_test(
-      NAME test_rips_complex_py_test
-      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_rips_complex.py)
-  set_tests_properties(test_rips_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+  add_test(NAME test_rips_complex_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_rips_complex.py)
 
   # Simplex tree
   add_test(NAME simplex_tree_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
-  set_tests_properties(simplex_tree_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
 
-  add_test(
-      NAME test_simplex_tree_py_test
-      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_simplex_tree.py)
-  set_tests_properties(test_simplex_tree_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+  add_test(NAME test_simplex_tree_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_simplex_tree.py)
 
   # Witness
   add_test(NAME witness_complex_from_nearest_landmark_table_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
-  set_tests_properties(witness_complex_from_nearest_landmark_table_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
 
-  add_test(
-      NAME test_witness_complex_py_test
-      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_witness_complex.py)
-  set_tests_properties(test_witness_complex_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+  add_test(NAME test_witness_complex_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_witness_complex.py)
 
   # Reader utils
-  add_test(
-      NAME test_reader_utils_py_test
-      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_reader_utils.py)
-  set_tests_properties(test_reader_utils_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+  add_test(NAME test_reader_utils_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_reader_utils.py)
 
   # Subsampling
-  add_test(
-      NAME test_subsampling_py_test
-      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py)
-  set_tests_properties(test_subsampling_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
-
-  # Documentation generation is available through sphinx
-  if(SPHINX_PATH)
-    if (UNIX)
-      add_custom_target(sphinx
-          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
-          DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
-          COMMAND make html doctest)
-    else (UNIX)
-      add_custom_target(sphinx
-          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
-          COMMAND make.bat html doctest)
-    endif (UNIX)
-  endif(SPHINX_PATH)
+  add_test(NAME test_subsampling_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py)
+
+  # Documentation generation is available through sphinx - requires all modules
+  if(SPHINX_PATH AND NOT CGAL_VERSION VERSION_LESS 4.8.1)
+    # set sphinx-build in make files
+    configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY)
+
+    add_custom_target(sphinx
+        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
+        COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+        ${SPHINX_PATH} -b html . "${CMAKE_CURRENT_BINARY_DIR}/sphinx"
+        DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so")
+
+    add_test(NAME sphinx_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc "${CMAKE_CURRENT_BINARY_DIR}/sphinx")
+
+  endif(SPHINX_PATH AND NOT CGAL_VERSION VERSION_LESS 4.8.1)
 endif(CYTHON_FOUND)
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)
diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in
index 1141673a..a8dd9f80 100644
--- a/src/cython/gudhi.pyx.in
+++ b/src/cython/gudhi.pyx.in
@@ -23,6 +23,9 @@
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016  INRIA"
 __license__ = "GPL v3"
+__version__ = "@GUDHI_VERSION@"
+# This variable is used by doctest to find files
+__root_source_dir__ = "@CMAKE_SOURCE_DIR@"
 
 include '@CMAKE_CURRENT_SOURCE_DIR@/cython/off_reader.pyx'
 include '@CMAKE_CURRENT_SOURCE_DIR@/cython/simplex_tree.pyx'
-- 
cgit v1.2.3


From ef8a5bca22be47df00f61d660e84948f1f45f9ba Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 7 Sep 2017 16:07:41 +0000
Subject: Fix doc for user_version

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2650 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 18aebd67968fd48ccfcfcfbff75c614496f4424e
---
 src/cython/doc/alpha_complex_sum.rst          |  2 +-
 src/cython/doc/alpha_complex_user.rst         |  6 +++---
 src/cython/doc/bottleneck_distance_sum.rst    |  2 +-
 src/cython/doc/cubical_complex_sum.rst        | 22 +++++++++++-----------
 src/cython/doc/cubical_complex_user.rst       |  2 +-
 src/cython/doc/index.rst                      |  8 +++++---
 src/cython/doc/persistent_cohomology_sum.rst  |  2 +-
 src/cython/doc/persistent_cohomology_user.rst |  2 +-
 src/cython/doc/rips_complex_sum.rst           |  2 +-
 src/cython/doc/rips_complex_user.rst          |  2 +-
 src/cython/doc/simplex_tree_sum.rst           |  2 +-
 src/cython/doc/tangential_complex_sum.rst     |  4 ++--
 src/cython/doc/tangential_complex_user.rst    | 14 +++++++-------
 src/cython/doc/witness_complex_sum.rst        | 26 ++++++++++++++------------
 src/cython/doc/witness_complex_user.rst       |  4 ++--
 15 files changed, 52 insertions(+), 48 deletions(-)

(limited to 'src')

diff --git a/src/cython/doc/alpha_complex_sum.rst b/src/cython/doc/alpha_complex_sum.rst
index a5f6420a..1680a712 100644
--- a/src/cython/doc/alpha_complex_sum.rst
+++ b/src/cython/doc/alpha_complex_sum.rst
@@ -5,7 +5,7 @@
 
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | .. figure::                                                    | Alpha_complex is a simplicial complex constructed from the finite      |
-|      img/alpha_complex_representation.png                      | cells of a Delaunay Triangulation.                                     |
+|      ../../doc/Alpha_complex/alpha_complex_representation.png  | cells of a Delaunay Triangulation.                                     |
 |      :alt: Alpha complex representation                        |                                                                        |
 |      :figclass: align-center                                   | The filtration value of each simplex is computed as the square of the  |
 |                                                                | circumradius of the simplex if the circumsphere is empty (the simplex  |
diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst
index e541e6d3..c3a13bef 100644
--- a/src/cython/doc/alpha_complex_user.rst
+++ b/src/cython/doc/alpha_complex_user.rst
@@ -75,7 +75,7 @@ In order to build the alpha complex, first, a Simplex tree is built from the cel
 (The filtration value is set to NaN, which stands for unknown value):
 
 .. figure::
-    img/alpha_complex_doc.png
+    ../../doc/Alpha_complex/alpha_complex_doc.png
     :figclass: align-center
     :alt: Simplex tree structure construction example
 
@@ -112,7 +112,7 @@ computes the filtration value of the triangle, and then propagates the filtratio
 here:
 
 .. figure::
-    img/alpha_complex_doc_420.png
+    ../../doc/Alpha_complex/alpha_complex_doc_420.png
     :figclass: align-center
     :alt: Filtration value propagation example
 
@@ -201,6 +201,6 @@ the program output is:
 CGAL citations
 ==============
 
-.. bibliography:: how_to_cite_cgal.bib
+.. bibliography:: ../../biblio/how_to_cite_cgal.bib
    :filter: docnames
    :style: unsrt
diff --git a/src/cython/doc/bottleneck_distance_sum.rst b/src/cython/doc/bottleneck_distance_sum.rst
index 5c475d0d..030fad9e 100644
--- a/src/cython/doc/bottleneck_distance_sum.rst
+++ b/src/cython/doc/bottleneck_distance_sum.rst
@@ -5,7 +5,7 @@
 
 +-----------------------------------------------------------------+----------------------------------------------------------------------+
 | .. figure::                                                     | Bottleneck distance measures the similarity between two persistence  |
-|      img/perturb_pd.png                                         | diagrams. It's the shortest distance b for which there exists a      |
+|      ../../doc/Bottleneck_distance/perturb_pd.png               | diagrams. It's the shortest distance b for which there exists a      |
 |      :figclass: align-center                                    | perfect matching between the points of the two diagrams (+ all the   |
 |                                                                 | diagonal points) such that any couple of matched points are at       |
 |      Bottleneck distance is the length of                       | distance at most b.                                                  |
diff --git a/src/cython/doc/cubical_complex_sum.rst b/src/cython/doc/cubical_complex_sum.rst
index 3ddf6375..280ad0e0 100644
--- a/src/cython/doc/cubical_complex_sum.rst
+++ b/src/cython/doc/cubical_complex_sum.rst
@@ -2,14 +2,14 @@
 :Author: Pawel Dlotko                                              :Introduced in: GUDHI 2.0.0          :Copyright: GPL v3
 =================================================================  ===================================  ===================================
 
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| .. figure::                                                     | The cubical complex is an example of a structured complex useful in  |
-|      img/Cubical_complex_representation.png                     | computational mathematics (specially rigorous numerics) and image    |
-|      :alt: Cubical complex representation                       | analysis.                                                            |
-|      :figclass: align-center                                    |                                                                      |
-|                                                                 |                                                                      |
-|      Cubical complex representation                             |                                                                      |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| :doc:`cubical_complex_user`                                     | * :doc:`cubical_complex_ref`                                         |
-|                                                                 | * :doc:`periodic_cubical_complex_ref`                                |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
++--------------------------------------------------------------------------+----------------------------------------------------------------------+
+| .. figure::                                                              | The cubical complex is an example of a structured complex useful in  |
+|      ../../doc/Bitmap_cubical_complex/Cubical_complex_representation.png | computational mathematics (specially rigorous numerics) and image    |
+|      :alt: Cubical complex representation                                | analysis.                                                            |
+|      :figclass: align-center                                             |                                                                      |
+|                                                                          |                                                                      |
+|      Cubical complex representation                                      |                                                                      |
++--------------------------------------------------------------------------+----------------------------------------------------------------------+
+| :doc:`cubical_complex_user`                                              | * :doc:`cubical_complex_ref`                                         |
+|                                                                          | * :doc:`periodic_cubical_complex_ref`                                |
++--------------------------------------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst
index 8c9a3ed6..36fa3ba9 100644
--- a/src/cython/doc/cubical_complex_user.rst
+++ b/src/cython/doc/cubical_complex_user.rst
@@ -157,6 +157,6 @@ End user programs are available in cython/example/ folder.
 Bibliography
 ============
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst
index f6d10567..3945d72a 100644
--- a/src/cython/doc/index.rst
+++ b/src/cython/doc/index.rst
@@ -1,8 +1,10 @@
 GUDHI Python module documentation
 #################################
 
-.. image:: img/Gudhi_banner.png
-   :align: center
+.. figure::
+     ../../doc/common/Gudhi_banner.png
+     :alt: Gudhi banner
+     :figclass: align-center
 
 Introduction
 ************
@@ -81,6 +83,6 @@ Persistence graphical tools
 Bibliography
 ************
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../biblio/bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/src/cython/doc/persistent_cohomology_sum.rst b/src/cython/doc/persistent_cohomology_sum.rst
index d1f79cb4..a26df1dc 100644
--- a/src/cython/doc/persistent_cohomology_sum.rst
+++ b/src/cython/doc/persistent_cohomology_sum.rst
@@ -4,7 +4,7 @@
 
 +-----------------------------------------------------------------+-----------------------------------------------------------------------+
 | .. figure::                                                     | The theory of homology consists in attaching to a topological space   |
-|      img/3DTorus_poch.png                                       | a sequence of (homology) groups, capturing global topological         |
+|      ../../doc/Persistent_cohomology/3DTorus_poch.png           | a sequence of (homology) groups, capturing global topological         |
 |      :figclass: align-center                                    | features like connected components, holes, cavities, etc. Persistent  |
 |                                                                 | homology studies the evolution -- birth, life and death -- of these   |
 |      Rips Persistent Cohomology on a 3D                         | features when the topological space is changing. Consequently, the    |
diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst
index 72f1a7f7..bf90c163 100644
--- a/src/cython/doc/persistent_cohomology_user.rst
+++ b/src/cython/doc/persistent_cohomology_user.rst
@@ -109,6 +109,6 @@ We provide several example files: run these examples with -h for details on thei
 Bibliography
 ============
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../biblio/bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/src/cython/doc/rips_complex_sum.rst b/src/cython/doc/rips_complex_sum.rst
index 2b65fc19..5616bfa9 100644
--- a/src/cython/doc/rips_complex_sum.rst
+++ b/src/cython/doc/rips_complex_sum.rst
@@ -4,7 +4,7 @@
 
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | .. figure::                                                    | Rips complex is a simplicial complex constructed from a one skeleton   |
-|      img/rips_complex_representation.png                       | graph.                                                                 |
+|      ../../doc/Rips_complex/rips_complex_representation.png    | graph.                                                                 |
 |      :figclass: align-center                                   |                                                                        |
 |                                                                | The filtration value of each edge is computed from a user-given        |
 |      Rips complex representation                               | distance function and is inserted until a user-given threshold         |
diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst
index 6b48422b..96ba9944 100644
--- a/src/cython/doc/rips_complex_user.rst
+++ b/src/cython/doc/rips_complex_user.rst
@@ -26,7 +26,7 @@ structure, and then expands the simplicial complex when required.
 Vertex name correspond to the index of the point in the given range (aka. the point cloud).
 
 .. figure::
-    img/rips_complex_representation.png
+    ../../doc/Rips_complex/rips_complex_representation.png
     :align: center
 
     Rips-complex one skeleton graph representation
diff --git a/src/cython/doc/simplex_tree_sum.rst b/src/cython/doc/simplex_tree_sum.rst
index 3174fb62..fb0e54c1 100644
--- a/src/cython/doc/simplex_tree_sum.rst
+++ b/src/cython/doc/simplex_tree_sum.rst
@@ -4,7 +4,7 @@
 
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | .. figure::                                                    | The simplex tree is an efficient and flexible data structure for       |
-|      img/Simplex_tree_representation.png                       | representing general (filtered) simplicial complexes.                  |
+|      ../../doc/Simplex_tree/Simplex_tree_representation.png    | representing general (filtered) simplicial complexes.                  |
 |      :alt: Simplex tree representation                         |                                                                        |
 |      :figclass: align-center                                   | The data structure is described in                                     |
 |                                                                | :cite:`boissonnatmariasimplextreealgorithmica`                         |
diff --git a/src/cython/doc/tangential_complex_sum.rst b/src/cython/doc/tangential_complex_sum.rst
index 2b05bc10..72b4d7ba 100644
--- a/src/cython/doc/tangential_complex_sum.rst
+++ b/src/cython/doc/tangential_complex_sum.rst
@@ -5,10 +5,10 @@
 
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | .. figure::                                                    | A Tangential Delaunay complex is a simplicial complex designed to      |
-|      img/tc_examples.png                                       | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`-    |
+|      ../../doc/Tangential_complex/tc_examples.png              | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`-    |
 |      :figclass: align-center                                   | dimensional Euclidean space. The input is a point sample coming from   |
 |                                                                | an unknown manifold. The running time depends only linearly on the     |
-|      **Tangential complex representation**                     | extrinsic dimension :math:`d` and exponentially on the intrinsic       |
+|      Tangential complex representation                         | extrinsic dimension :math:`d` and exponentially on the intrinsic       |
 |                                                                | dimension :math:`k`.                                                   |
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | :doc:`tangential_complex_user`                                 | :doc:`tangential_complex_ref`                                          |
diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst
index d670cfdb..efa6d7ce 100644
--- a/src/cython/doc/tangential_complex_user.rst
+++ b/src/cython/doc/tangential_complex_user.rst
@@ -22,7 +22,7 @@ Let us start with the description of the Tangential complex of a simple
 example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points
 :math:`P` located on a curve embedded in 2D.
 
-.. figure:: img/tc_example_01.png
+.. figure:: ../../doc/Tangential_complex/tc_example_01.png
     :alt: The input
     :figclass: align-center
 
@@ -31,7 +31,7 @@ example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points
 For each point :math:`p`, estimate its tangent subspace :math:`T_p` (e.g.
 using PCA). 
 
-.. figure:: img/tc_example_02.png
+.. figure:: ../../doc/Tangential_complex/tc_example_02.png
     :alt: The estimated normals
     :figclass: align-center
 
@@ -42,7 +42,7 @@ Let us add the Voronoi diagram of the points in orange. For each point
 :math:`p`, construct its star in the Delaunay triangulation of :math:`P`
 restricted to :math:`T_p`.
 
-.. figure:: img/tc_example_03.png
+.. figure:: ../../doc/Tangential_complex/tc_example_03.png
     :alt: The Voronoi diagram
     :figclass: align-center
 
@@ -62,7 +62,7 @@ simplex is not in the star of all its vertices.
 
 Let us take the same example.
 
-.. figure:: img/tc_example_07_before.png
+.. figure:: ../../doc/Tangential_complex/tc_example_07_before.png
     :alt: Before
     :figclass: align-center
 
@@ -70,7 +70,7 @@ Let us take the same example.
 
 Let us slightly move the tangent subspace :math:`T_q`
 
-.. figure:: img/tc_example_07_after.png
+.. figure:: ../../doc/Tangential_complex/tc_example_07_after.png
     :alt: After
     :figclass: align-center
 
@@ -79,7 +79,7 @@ Let us slightly move the tangent subspace :math:`T_q`
 Now, the star of :math:`Q` contains :math:`QP`, but the star of :math:`P` does
 not contain :math:`QP`. We have an inconsistency.
 
-.. figure:: img/tc_example_08.png
+.. figure:: ../../doc/Tangential_complex/tc_example_08.png
     :alt: After
     :figclass: align-center
 
@@ -191,6 +191,6 @@ The output is:
 Bibliography
 ============
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../biblio/bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/src/cython/doc/witness_complex_sum.rst b/src/cython/doc/witness_complex_sum.rst
index b65522ba..a8a126a0 100644
--- a/src/cython/doc/witness_complex_sum.rst
+++ b/src/cython/doc/witness_complex_sum.rst
@@ -3,15 +3,17 @@
 :Euclidean version requires: CGAL :math:`\geq` 4.6.0               Eigen3
 =================================================================  ===================================  ===================================
 
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| .. image::                                                      | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on  |
-|      img/Witness_complex_representation.png                     | two sets of points in :math:`\mathbb{R}^D`.                          |
-|                                                                 |                                                                      |
-|                                                                 | The data structure is described in                                   |
-|                                                                 | :cite:`boissonnatmariasimplextreealgorithmica`.                      |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| :doc:`witness_complex_user`                                     | * :doc:`witness_complex_ref`                                         |
-|                                                                 | * :doc:`strong_witness_complex_ref`                                  |
-|                                                                 | * :doc:`euclidean_witness_complex_ref`                               |
-|                                                                 | * :doc:`euclidean_strong_witness_complex_ref`                        |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
++-------------------------------------------------------------------+----------------------------------------------------------------------+
+| .. figure::                                                       | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on  |
+|      ../../doc/Witness_complex/Witness_complex_representation.png | two sets of points in :math:`\mathbb{R}^D`.                          |
+|      :alt: Witness complex representation                         |                                                                      |
+|      :figclass: align-center                                      | The data structure is described in                                   |
+|                                                                   | :cite:`boissonnatmariasimplextreealgorithmica`.                      |
+|                                                                   |                                                                      |
+|      Witness complex representation                               |                                                                      |
++-------------------------------------------------------------------+----------------------------------------------------------------------+
+| :doc:`witness_complex_user`                                       | * :doc:`witness_complex_ref`                                         |
+|                                                                   | * :doc:`strong_witness_complex_ref`                                  |
+|                                                                   | * :doc:`euclidean_witness_complex_ref`                               |
+|                                                                   | * :doc:`euclidean_strong_witness_complex_ref`                        |
++-------------------------------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/witness_complex_user.rst b/src/cython/doc/witness_complex_user.rst
index aa9cbb2c..29413269 100644
--- a/src/cython/doc/witness_complex_user.rst
+++ b/src/cython/doc/witness_complex_user.rst
@@ -33,7 +33,7 @@ Both definitions can be relaxed by a real value :math:`\alpha`:
 which leads to definitions of **weak relaxed witness complex** (or just relaxed witness complex for short) and
 **strong relaxed witness complex** respectively.
 
-.. figure:: img/swit.svg
+.. figure:: ../../doc/Witness_complex/swit.svg
     :alt: Strongly witnessed simplex
     :figclass: align-center
 
@@ -126,6 +126,6 @@ Here is an example of constructing a strong witness complex filtration and compu
 Bibliography
 ============
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../biblio/bibliography.bib
    :filter: docnames
    :style: unsrt
-- 
cgit v1.2.3


From df9030e6c1df5fb735914eadd44cf27b86fce239 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 11 Sep 2017 15:12:01 +0000
Subject: Add comment for the dependency

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2655 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ab03b16bc884fe3291e3308e4a975b7c6232a861
---
 src/cython/CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

(limited to 'src')

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 6c8232ea..ea6e840a 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -326,6 +326,7 @@ if(CYTHON_FOUND)
     # set sphinx-build in make files
     configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY)
 
+    # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
     add_custom_target(sphinx
         WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
         COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-- 
cgit v1.2.3


From 03bb8ee15f7c8b71fd922a27ed02bca4c98825d9 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 11 Sep 2017 15:16:39 +0000
Subject: remove debug traces

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2656 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 4ea039d0564268458ca64950113fbffdc86c10b3
---
 src/cython/CMakeLists.txt | 1 -
 1 file changed, 1 deletion(-)

(limited to 'src')

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index ea6e840a..7cf31a03 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -148,7 +148,6 @@ if(CYTHON_FOUND)
   # Loop on INCLUDE_DIRECTORIES PROPERTY
   get_property(GUDHI_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES)
   foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
-    message("  ---  ${GUDHI_INCLUDE_DIRECTORY} ---")
     set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ")
   endforeach()
   set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ")
-- 
cgit v1.2.3


From 04fe614e8a859257b57aadfdb5aa14fc3d78babb Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 12 Sep 2017 08:30:31 +0000
Subject: Euclidean witness requires CGAL 4.6.0 Subsampling requires CGAL 4.8.1
 All modules requiring CGAL requires also Eigen3

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2662 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: df4c03882b8c5eb91f12939b460b3c9b85cbb870
---
 src/cython/CMakeLists.txt | 96 +++++++++++++++++------------------------------
 1 file changed, 35 insertions(+), 61 deletions(-)

(limited to 'src')

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 7cf31a03..db23d42b 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -73,47 +73,18 @@ if(CYTHON_FOUND)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
   endif (EIGEN3_FOUND)
 
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    # If CGAL_VERSION >= 4.8.1, include subsampling
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
     set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
     set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
     set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
-  else (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    # Remove subsampling unitary tests
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_subsampling.py)
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_sum.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_user.rst")
-    # Remove tangential complex and bottleneck unitary tests
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_tangential_complex.py)
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_bottleneck_distance.py)
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_sum.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_user.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_sum.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_user.rst")
-  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-    # If CGAL_VERSION >= 4.7.0, include alpha
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
     set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
-  else (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-    # Remove alpha complex unitary tests
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py)
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_sum.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_user.rst")
-  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    # If CGAL_VERSION >= 4.6.0, include euclidean versions of witness complex
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
     set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX
         "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n")
-  else (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    # Remove euclidean witness complex unitary tests
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_euclidean_witness_complex.py)
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_witness_complex_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_strong_witness_complex_ref.rst")
-  endif (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
 
   if(CGAL_FOUND)
     # Add CGAL compilation args
@@ -185,7 +156,7 @@ if(CYTHON_FOUND)
       PATTERN "*.pyd")
 
   # Test examples
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
     # Bottleneck
     add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
@@ -213,26 +184,14 @@ if(CYTHON_FOUND)
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_tangential_complex.py)
 
-    # Euclidean witness
-    add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-
-    add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-
-    add_test(NAME test_euclidean_witness_complex_py_test
+    # Subsampling
+    add_test(NAME test_subsampling_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py)
+             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py)
 
-  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
 
-  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
     # Alpha
     add_test(NAME alpha_complex_from_points_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
@@ -249,7 +208,27 @@ if(CYTHON_FOUND)
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_alpha_complex.py)
 
-  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+    # Euclidean witness
+    add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+
+    add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+
+    add_test(NAME test_euclidean_witness_complex_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py)
+
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
 
   # Cubical
   add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
@@ -315,13 +294,8 @@ if(CYTHON_FOUND)
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
            COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_reader_utils.py)
 
-  # Subsampling
-  add_test(NAME test_subsampling_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py)
-
   # Documentation generation is available through sphinx - requires all modules
-  if(SPHINX_PATH AND NOT CGAL_VERSION VERSION_LESS 4.8.1)
+  if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
     # set sphinx-build in make files
     configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY)
 
@@ -337,5 +311,5 @@ if(CYTHON_FOUND)
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
              ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc "${CMAKE_CURRENT_BINARY_DIR}/sphinx")
 
-  endif(SPHINX_PATH AND NOT CGAL_VERSION VERSION_LESS 4.8.1)
+  endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
 endif(CYTHON_FOUND)
-- 
cgit v1.2.3


From 5470c3565cfb4b9e3827a42bfdc3fbec461638a5 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 12 Sep 2017 10:05:46 +0000
Subject: Fix in Python3 if sphinx is not installed

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2663 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0005d7fe2e7e8513a276543295c02351456595cc
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

(limited to 'src')

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index dbf2106a..4cf2f445 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -122,8 +122,12 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
     # Documentation generation is available through sphinx
     find_program( SPHINX_PATH sphinx-build )
   elseif(PYTHON_VERSION_MAJOR EQUAL 3)
-    # No sphinx-build in Pyton3, just hack it
-    set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
+    execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "from sphinx import main"
+                    RESULT_VARIABLE SPHINX_MODULE_IS_INSTALLED)
+    if(SPHINX_MODULE_IS_INSTALLED)
+      # No sphinx-build in Pyton3, just hack it
+      set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
+    endif(SPHINX_MODULE_IS_INSTALLED)
   else()
     message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.")
   endif(PYTHON_VERSION_MAJOR EQUAL 2)
-- 
cgit v1.2.3


From 3dd4db9ad872eecae58e6edf3c16915ca1ec7ccc Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 12 Sep 2017 11:26:30 +0000
Subject: Add debug traces

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2664 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: e4c572d98f4628e7f9b36fd9925ba7ce68e3cf81
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 1 +
 1 file changed, 1 insertion(+)

(limited to 'src')

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 4cf2f445..799d28b6 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -124,6 +124,7 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
   elseif(PYTHON_VERSION_MAJOR EQUAL 3)
     execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "from sphinx import main"
                     RESULT_VARIABLE SPHINX_MODULE_IS_INSTALLED)
+    message("  --- SPHINX_MODULE_IS_INSTALLED --- ${SPHINX_MODULE_IS_INSTALLED}")
     if(SPHINX_MODULE_IS_INSTALLED)
       # No sphinx-build in Pyton3, just hack it
       set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
-- 
cgit v1.2.3


From 90f4783f287e266d3d8787d0d18b84d27f8b96b6 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 12 Sep 2017 12:45:20 +0000
Subject: Modification rollback

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2665 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 2f977f8b93c6104d2b7c8f16c13da974b36f1535
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

(limited to 'src')

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 799d28b6..dbf2106a 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -122,13 +122,8 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
     # Documentation generation is available through sphinx
     find_program( SPHINX_PATH sphinx-build )
   elseif(PYTHON_VERSION_MAJOR EQUAL 3)
-    execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "from sphinx import main"
-                    RESULT_VARIABLE SPHINX_MODULE_IS_INSTALLED)
-    message("  --- SPHINX_MODULE_IS_INSTALLED --- ${SPHINX_MODULE_IS_INSTALLED}")
-    if(SPHINX_MODULE_IS_INSTALLED)
-      # No sphinx-build in Pyton3, just hack it
-      set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
-    endif(SPHINX_MODULE_IS_INSTALLED)
+    # No sphinx-build in Pyton3, just hack it
+    set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
   else()
     message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.")
   endif(PYTHON_VERSION_MAJOR EQUAL 2)
-- 
cgit v1.2.3


From 9a3df180af4976242fb45d7dcd49c3632e65f04c Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 12 Sep 2017 20:36:58 +0000
Subject: Bottleneck does not require Eigen3 (C++ and Python) Doc issue about
 examples requiring Eigen3

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2666 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5e127d4e8137a44ee3bd688c32653acfb4a55007
---
 src/Bottleneck_distance/benchmark/CMakeLists.txt |  4 ++--
 src/Bottleneck_distance/example/CMakeLists.txt   | 26 ++++++++++++++++--------
 src/Bottleneck_distance/test/CMakeLists.txt      |  4 ++--
 src/common/doc/main_page.h                       | 20 ++++++++++++++++--
 src/cython/CMakeLists.txt                        | 26 ++++++++++++++----------
 5 files changed, 54 insertions(+), 26 deletions(-)

(limited to 'src')

diff --git a/src/Bottleneck_distance/benchmark/CMakeLists.txt b/src/Bottleneck_distance/benchmark/CMakeLists.txt
index 170081ce..20a4e47b 100644
--- a/src/Bottleneck_distance/benchmark/CMakeLists.txt
+++ b/src/Bottleneck_distance/benchmark/CMakeLists.txt
@@ -1,9 +1,9 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_benchmark)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   add_executable ( bottleneck_chrono bottleneck_chrono.cpp )
   if (TBB_FOUND)
     target_link_libraries(bottleneck_chrono ${TBB_LIBRARIES})
   endif(TBB_FOUND)
-endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+endif(NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index dc1da31c..eac617db 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -1,30 +1,38 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_examples)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp)
   add_executable (bottleneck_basic_example bottleneck_basic_example.cpp)
 
-  add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
-  target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(bottleneck_read_file_example ${TBB_LIBRARIES})
     target_link_libraries(bottleneck_basic_example ${TBB_LIBRARIES})
-    target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
   endif(TBB_FOUND)
 
   add_test(NAME Bottleneck_distance_example_basic COMMAND $<TARGET_FILE:bottleneck_basic_example>)
 
-  add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck
-      COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance>
-      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3")
-
   add_test(NAME Bottleneck_read_file_example
       COMMAND $<TARGET_FILE:bottleneck_read_file_example>
       "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers")
 
   install(TARGETS bottleneck_read_file_example DESTINATION bin)
   install(TARGETS bottleneck_basic_example DESTINATION bin)
-  install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin)
 
+endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+
+# Eigen3 and CGAL > 4.7.0 is required for alpha complex
+# CGAL > 4.8.1 is required for bottleneck distance =>
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
+  target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+  add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck
+           COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance>
+           "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3")
+
+  install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin)
+  if (TBB_FOUND)
+    target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt
index a165d472..2676b82c 100644
--- a/src/Bottleneck_distance/test/CMakeLists.txt
+++ b/src/Bottleneck_distance/test/CMakeLists.txt
@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_tests)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   include(GUDHI_test_coverage)
 
   add_executable ( Bottleneck_distance_test_unit bottleneck_unit_test.cpp )
@@ -12,4 +12,4 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
 
   gudhi_add_coverage_test(Bottleneck_distance_test_unit)
 
-endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index bd4615f5..1a7994a5 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -160,7 +160,7 @@
       <b>Author:</b> Fran&ccedil;ois Godi<br>
       <b>Introduced in:</b> GUDHI 2.0.0<br>
       <b>Copyright:</b> GPL v3<br>
-      <b>Requires:</b> \ref cgal &ge; 4.8.1 and \ref eigen3
+      <b>Requires:</b> \ref cgal &ge; 4.8.1
     </td>
     <td width="75%">
     Bottleneck distance measures the similarity between two persistence diagrams. 
@@ -329,13 +329,29 @@ make doxygen
  * Alpha_complex/Alpha_complex_from_off.cpp</a>
  * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
  * Alpha_complex/Alpha_complex_from_points.cpp</a>
+ * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
+ * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a>
  * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
  * Persistent_cohomology/alpha_complex_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
  * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
  * Persistent_cohomology/custom_persistence_sort.cpp</a>
- * 
+ * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html">
+ * Spatial_searching/example_spatial_searching.cpp</a>
+ * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html">
+ * Subsampling/example_choose_n_farthest_points.cpp</a>
+ * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html">
+ * Subsampling/example_custom_kernel.cpp</a>
+ * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html">
+ * Subsampling/example_pick_n_random_points.cpp</a>
+ * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html">
+ * Subsampling/example_sparsify_point_set.cpp</a>
+ * \li <a href="_tangential_complex_2example_basic_8cpp-example.html">
+ * Tangential_complex/example_basic.cpp</a>
+ * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html">
+ * Tangential_complex/example_with_perturb.cpp</a>
+ *
  * \subsection tbb Threading Building Blocks
  * <a target="_blank" href="https://www.threadingbuildingblocks.org/">Intel&reg; TBB</a> lets you easily write parallel
  * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index db23d42b..baeeb203 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -73,10 +73,12 @@ if(CYTHON_FOUND)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
   endif (EIGEN3_FOUND)
 
+  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+    set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
     set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
     set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
-    set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
     set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
@@ -157,22 +159,13 @@ if(CYTHON_FOUND)
 
   # Test examples
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-    # Bottleneck
+    # Bottleneck and Alpha
     add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
              -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
 
-    add_test(NAME bottleneck_basic_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
-
-    add_test(NAME test_bottleneck_distance_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py)
-
     # Tangential
     add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
@@ -190,6 +183,17 @@ if(CYTHON_FOUND)
              COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py)
 
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+    # Bottleneck
+    add_test(NAME bottleneck_basic_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
+
+    add_test(NAME test_bottleneck_distance_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py)
+  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
 
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
     # Alpha
-- 
cgit v1.2.3


From 8a22b7c6111b41e91766cdd53c0116b845e068b5 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 12 Sep 2017 21:47:19 +0000
Subject: Fix sphinx build for python3 on Ubuntu

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2667 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c720b8be2919344e06f3d71cefdd7693439f63f0
---
 src/cmake/modules/GUDHI_third_party_libraries.cmake |  2 +-
 src/cython/CMakeLists.txt                           |  9 +++------
 src/cython/doc/python3-sphinx-build.in              | 11 -----------
 src/cython/doc/python3-sphinx-build.py              | 11 +++++++++++
 4 files changed, 15 insertions(+), 18 deletions(-)
 delete mode 100755 src/cython/doc/python3-sphinx-build.in
 create mode 100755 src/cython/doc/python3-sphinx-build.py

(limited to 'src')

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index dbf2106a..f2bbafdc 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -123,7 +123,7 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
     find_program( SPHINX_PATH sphinx-build )
   elseif(PYTHON_VERSION_MAJOR EQUAL 3)
     # No sphinx-build in Pyton3, just hack it
-    set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
+    set(SPHINX_PATH "${PYTHON_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build.py")
   else()
     message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.")
   endif(PYTHON_VERSION_MAJOR EQUAL 2)
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index baeeb203..d1761f47 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -75,7 +75,7 @@ if(CYTHON_FOUND)
 
   if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
     set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
     set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
     set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
@@ -300,20 +300,17 @@ if(CYTHON_FOUND)
 
   # Documentation generation is available through sphinx - requires all modules
   if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-    # set sphinx-build in make files
-    configure_file(doc/python3-sphinx-build.in "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build" @ONLY)
-
     # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
     add_custom_target(sphinx
         WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
         COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-        ${SPHINX_PATH} -b html . "${CMAKE_CURRENT_BINARY_DIR}/sphinx"
+        ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc sphinx
         DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so")
 
     add_test(NAME sphinx_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc "${CMAKE_CURRENT_BINARY_DIR}/sphinx")
+             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc doctest)
 
   endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
 endif(CYTHON_FOUND)
diff --git a/src/cython/doc/python3-sphinx-build.in b/src/cython/doc/python3-sphinx-build.in
deleted file mode 100755
index c97965f5..00000000
--- a/src/cython/doc/python3-sphinx-build.in
+++ /dev/null
@@ -1,11 +0,0 @@
-#!@PYTHON_EXECUTABLE@
-
-"""
-Emulate sphinx-build for python3
-"""
-
-from sys import exit, argv
-from sphinx import main
-
-if __name__ == '__main__':
-    exit(main(argv))
diff --git a/src/cython/doc/python3-sphinx-build.py b/src/cython/doc/python3-sphinx-build.py
new file mode 100755
index 00000000..44b94169
--- /dev/null
+++ b/src/cython/doc/python3-sphinx-build.py
@@ -0,0 +1,11 @@
+#!/usr/bin/python3
+
+"""
+Emulate sphinx-build for python3
+"""
+
+from sys import exit, argv
+from sphinx import main
+
+if __name__ == '__main__':
+    exit(main(argv))
-- 
cgit v1.2.3


From bc62d9afbb151279a9da1e082a53788d3fd0d242 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 18 Sep 2017 09:37:20 +0000
Subject: Add warning for developper version that sphinx is configured for user
 version Removes GudhUI ERROR mesages (just warnings

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2677 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0111272d9f6d6dc10e370360b2242eff4828611b
---
 src/GudhUI/CMakeLists.txt | 34 +++-------------------------------
 src/cython/CMakeLists.txt | 13 ++++++++++---
 2 files changed, 13 insertions(+), 34 deletions(-)

(limited to 'src')

diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index 57861946..374195d0 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -5,28 +5,6 @@ find_package(Qt5 COMPONENTS Widgets Xml OpenGL)
 find_package(QGLViewer)
 find_package(OpenGL)
 
-if (CGAL_VERSION VERSION_EQUAL 4.8.0)
-  message(ERROR " GudhUI does not compile with CGAL 4.8.0. 4.8.1, 4.8.2 and 4.9 are OK.")
-endif()
-
-if (NOT CGAL_FOUND)
-  message(ERROR " GudhUI requires CGAL and will not be compiled.")
-endif()
-
-if (NOT Qt5_FOUND)
-  message(ERROR " GudhUI requires Qt5 and will not be compiled.")
-endif()
-
-if (NOT OPENGL_FOUND)
-  message(ERROR " GudhUI requires OpenGL and will not be compiled.")
-endif()
-
-if (NOT QGLVIEWER_FOUND)
-  message(ERROR " GudhUI requires QGLViewer and will not be compiled.")
-endif()
-
-
-
 if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND AND NOT CGAL_VERSION VERSION_EQUAL 4.8.0)
 
   set(CMAKE_AUTOMOC ON)
@@ -37,8 +15,6 @@ if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND AND NOT CGAL_
   SET(Boost_USE_MULTITHREAD OFF)
   include_directories (${QGLVIEWER_INCLUDE_DIR})
  
-  #####################################################################
-
   add_executable  ( GudhUI 
     gui/gudhui.cpp
     gui/MainWindow.cpp
@@ -52,14 +28,10 @@ if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND AND NOT CGAL_
   target_link_libraries( GudhUI Qt5::Widgets Qt5::Xml Qt5::OpenGL )
   target_link_libraries( GudhUI ${QGLVIEWER_LIBRARIES} )
   target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} )	
-if (TBB_FOUND)
-  target_link_libraries( GudhUI ${TBB_LIBRARIES})
-endif()
+  if (TBB_FOUND)
+    target_link_libraries( GudhUI ${TBB_LIBRARIES})
+  endif()
 
   install(TARGETS GudhUI DESTINATION bin)
 
-###############################################################################
-
-else()
-  message(STATUS "NOTICE: GudhUI requires CGAL, the QGLViewer, OpenGL and Qt5, and will not be compiled.")
 endif()
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index d1761f47..ed0aace1 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -300,17 +300,24 @@ if(CYTHON_FOUND)
 
   # Documentation generation is available through sphinx - requires all modules
   if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+    set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
+    # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
+    # Images and biblio warnings because not found on developper version
+    if (GUDHI_CYTHON_PATH STREQUAL "src/cython")
+      set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss")
+    endif()
     # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
     add_custom_target(sphinx
         WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
         COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-        ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc sphinx
-        DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so")
+        ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
+        DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+        COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
 
     add_test(NAME sphinx_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc doctest)
+             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
 
   endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
 endif(CYTHON_FOUND)
-- 
cgit v1.2.3


From 7f7aac2010f5cda05dfd1057827d8deaea186cf5 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 18 Sep 2017 12:58:10 +0000
Subject: Add a function to launch py.test as required for no cache files in
 sources

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2678 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 92ca1aabcbe276198fa29ea75f763fb0aa3c504f
---
 src/cython/CMakeLists.txt | 50 +++++++++++++++++++----------------------------
 1 file changed, 20 insertions(+), 30 deletions(-)

(limited to 'src')

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index ed0aace1..ec8589f0 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -15,6 +15,16 @@ function( add_gudhi_cython_lib THE_LIB )
   endif(EXISTS ${THE_LIB})
 endfunction( add_gudhi_cython_lib )
 
+# THE_TEST is the python test file name (without .py extension) containing tests functions
+function( add_gudhi_py_test THE_TEST )
+  # use ${PYTHON_EXECUTABLE} -B, otherwise a __pycache__ directory is created in sources by python
+  # use py.test no cache provider, otherwise a .cache file is created in sources by py.test
+  add_test(NAME ${THE_TEST}_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} -B -m pytest -p no:cacheprovider ${CMAKE_CURRENT_SOURCE_DIR}/test/${THE_TEST}.py)
+endfunction( add_gudhi_py_test )
+
+
 if(CYTHON_FOUND)
   message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - Sphinx is ${SPHINX_PATH}")
 
@@ -173,14 +183,10 @@ if(CYTHON_FOUND)
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
 
-    add_test(NAME test_tangential_complex_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_tangential_complex.py)
+    add_gudhi_py_test(test_tangential_complex)
 
     # Subsampling
-    add_test(NAME test_subsampling_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py)
+    add_gudhi_py_test(test_subsampling)
 
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
@@ -190,9 +196,7 @@ if(CYTHON_FOUND)
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
 
-    add_test(NAME test_bottleneck_distance_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py)
+    add_gudhi_py_test(test_bottleneck_distance)
   endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
 
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
@@ -208,9 +212,7 @@ if(CYTHON_FOUND)
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
 
-    add_test(NAME test_alpha_complex_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_alpha_complex.py)
+    add_gudhi_py_test(test_alpha_complex)
 
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
 
@@ -228,9 +230,7 @@ if(CYTHON_FOUND)
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
 
-    add_test(NAME test_euclidean_witness_complex_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_euclidean_witness_complex.py)
+    add_gudhi_py_test(test_euclidean_witness_complex)
 
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
 
@@ -247,9 +247,7 @@ if(CYTHON_FOUND)
            ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
            10 10 10)
 
-  add_test(NAME test_cubical_complex_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_cubical_complex.py)
+  add_gudhi_py_test(test_cubical_complex)
 
   # Rips
   add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
@@ -269,9 +267,7 @@ if(CYTHON_FOUND)
            COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
            ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
 
-  add_test(NAME test_rips_complex_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_rips_complex.py)
+  add_gudhi_py_test(test_rips_complex)
 
   # Simplex tree
   add_test(NAME simplex_tree_example_py_test
@@ -279,9 +275,7 @@ if(CYTHON_FOUND)
            COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
            ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
 
-  add_test(NAME test_simplex_tree_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_simplex_tree.py)
+  add_gudhi_py_test(test_simplex_tree)
 
   # Witness
   add_test(NAME witness_complex_from_nearest_landmark_table_py_test
@@ -289,14 +283,10 @@ if(CYTHON_FOUND)
            COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
            ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
 
-  add_test(NAME test_witness_complex_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_witness_complex.py)
+  add_gudhi_py_test(test_witness_complex)
 
   # Reader utils
-  add_test(NAME test_reader_utils_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_reader_utils.py)
+  add_gudhi_py_test(test_reader_utils)
 
   # Documentation generation is available through sphinx - requires all modules
   if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-- 
cgit v1.2.3