Refresh patches.

5 files changed, 16 insertions, 16 deletions

diff --git a/debian/patches/0001-Disable-tests-that-use-DFSG-deleted-data-files.patch b/debian/patches/0001-Disable-tests-that-use-DFSG-deleted-data-files.patch
index 4c6e8d5d..f574ed63 100644
--- a/debian/patches/0001-Disable-tests-that-use-DFSG-deleted-data-files.patch
+++ b/debian/patches/0001-Disable-tests-that-use-DFSG-deleted-data-files.patch
@@ -50,7 +50,7 @@ index 65a08d9..3f16db9 100644
    install(TARGETS Nerve DESTINATION bin)
    install(TARGETS VoronoiGIC DESTINATION bin)
 diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
-index 94ec13c..4a48d21 100644
+index 4c08cd6..a7a7bcd 100644
 --- a/src/Persistent_cohomology/example/CMakeLists.txt
 +++ b/src/Persistent_cohomology/example/CMakeLists.txt
 @@ -28,10 +28,6 @@ add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D CO
@@ -65,10 +65,10 @@ index 94ec13c..4a48d21 100644
  install(TARGETS plain_homology DESTINATION bin)
  install(TARGETS persistence_from_simple_simplex_tree DESTINATION bin)
 diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt
-index f99b164..ae302dc 100644
+index a0aabee..5c572f8 100644
 --- a/src/Simplex_tree/example/CMakeLists.txt
 +++ b/src/Simplex_tree/example/CMakeLists.txt
-@@ -25,8 +25,6 @@ if(GMP_FOUND AND NOT CGAL_VERSION VERSION_LESS 4.11.0)
+@@ -28,8 +28,6 @@ if(GMP_FOUND AND NOT CGAL_VERSION VERSION_LESS 4.11.0)
    if (TBB_FOUND)
      target_link_libraries(Simplex_tree_example_alpha_shapes_3_from_off ${TBB_LIBRARIES})
    endif()
@@ -78,10 +78,10 @@ index f99b164..ae302dc 100644
  endif()
  
 diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
-index b558d4c..472993b 100644
+index ab08cd6..1a2f18b 100644
 --- a/src/python/CMakeLists.txt
 +++ b/src/python/CMakeLists.txt
-@@ -277,36 +277,7 @@ endif(CGAL_FOUND)
+@@ -355,36 +355,7 @@ if(PYTHONINTERP_FOUND)
  
        add_gudhi_py_test(test_bottleneck_distance)
  
diff --git a/debian/patches/0002-Use-system-MathJax.patch b/debian/patches/0002-Use-system-MathJax.patch
index b327c3cf..2985548e 100644
--- a/debian/patches/0002-Use-system-MathJax.patch
+++ b/debian/patches/0002-Use-system-MathJax.patch
@@ -7,10 +7,10 @@ Subject: Use system MathJax.
  1 file changed, 1 insertion(+), 1 deletion(-)
 
 diff --git a/src/Doxyfile.in b/src/Doxyfile.in
-index ec55188..e90d2fe 100644
+index 49e781b..52b8cbe 100644
 --- a/src/Doxyfile.in
 +++ b/src/Doxyfile.in
-@@ -1440,7 +1440,7 @@ MATHJAX_FORMAT         = HTML-CSS
+@@ -1441,7 +1441,7 @@ MATHJAX_FORMAT         = HTML-CSS
  # The default value is: http://cdn.mathjax.org/mathjax/latest.
  # This tag requires that the tag USE_MATHJAX is set to YES.
  
diff --git a/debian/patches/0004-Offline-header-for-docs.patch b/debian/patches/0004-Offline-header-for-docs.patch
index 70678963..b6dba1ab 100644
--- a/debian/patches/0004-Offline-header-for-docs.patch
+++ b/debian/patches/0004-Offline-header-for-docs.patch
@@ -7,10 +7,10 @@ Subject: Offline header for docs.
  1 file changed, 1 insertion(+), 1 deletion(-)
 
 diff --git a/src/Doxyfile.in b/src/Doxyfile.in
-index e90d2fe..f82baba 100644
+index 52b8cbe..f516ef7 100644
 --- a/src/Doxyfile.in
 +++ b/src/Doxyfile.in
-@@ -1045,7 +1045,7 @@ HTML_FILE_EXTENSION    = .html
+@@ -1046,7 +1046,7 @@ HTML_FILE_EXTENSION    = .html
  # of the possible markers and block names see the documentation.
  # This tag requires that the tag GENERATE_HTML is set to YES.
  
diff --git a/debian/patches/0005-Disable-Sphinx.patch b/debian/patches/0005-Disable-Sphinx.patch
index 69b76bc8..d741bb9f 100644
--- a/debian/patches/0005-Disable-Sphinx.patch
+++ b/debian/patches/0005-Disable-Sphinx.patch
@@ -7,14 +7,14 @@ Subject: Disable Sphinx.
  1 file changed, 1 deletion(-)
 
 diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
-index 24a3415..38484ba 100644
+index 0abe66b..7a418e4 100644
 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
 +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
-@@ -124,7 +124,6 @@ if( PYTHONINTERP_FOUND )
+@@ -175,7 +175,6 @@ if( PYTHONINTERP_FOUND )
    find_python_module("matplotlib")
    find_python_module("numpy")
    find_python_module("scipy")
 -  find_python_module("sphinx")
    find_python_module("sklearn")
    find_python_module("ot")
- endif()
+   find_python_module("pybind11")
diff --git a/debian/patches/0006-Install-Python-module-in-correct-location.patch b/debian/patches/0006-Install-Python-module-in-correct-location.patch
index 1e4310ee..e8c23fde 100644
--- a/debian/patches/0006-Install-Python-module-in-correct-location.patch
+++ b/debian/patches/0006-Install-Python-module-in-correct-location.patch
@@ -7,15 +7,15 @@ Subject: Install Python module in correct location.
  1 file changed, 1 insertion(+), 1 deletion(-)
 
 diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
-index 472993b..1dd3721 100644
+index 1a2f18b..94ef78b 100644
 --- a/src/python/CMakeLists.txt
 +++ b/src/python/CMakeLists.txt
-@@ -230,7 +230,7 @@ endif(CGAL_FOUND)
+@@ -243,7 +243,7 @@ if(PYTHONINTERP_FOUND)
      add_custom_target(python ALL DEPENDS gudhi.so
                        COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
  
 -    install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install)")
 +    install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} setup.py install --root=${CMAKE_SOURCE_DIR}/debian/tmp --single-version-externally-managed --install-layout=deb WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})")
  
-     # Test examples
-     if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
+   # Documentation generation is available through sphinx - requires all modules
+   # Make it first as sphinx test is by far the longest test which is nice when testing in parallel