Refresh patches.

8 files changed, 30 insertions, 29 deletions

diff --git a/debian/patches/0002-Disable-Sphinx-test-since-we-re-not-currently-using.patch b/debian/patches/0001-Disable-Sphinx-test-since-we-re-not-currently-buildi.patch
index abf2a450..d8bca9da 100644
--- a/debian/patches/0002-Disable-Sphinx-test-since-we-re-not-currently-using.patch
+++ b/debian/patches/0001-Disable-Sphinx-test-since-we-re-not-currently-buildi.patch
@@ -1,16 +1,17 @@
 From: Gard Spreemann <gspreemann@gmail.com>
-Date: Fri, 15 Jun 2018 13:18:26 +0200
-Subject: Disable Sphinx test since we're not currently using.
+Date: Mon, 10 Sep 2018 05:16:45 +0200
+Subject: Disable Sphinx test since we're not currently building the Sphinx
+ docs.
 
 ---
  cython/CMakeLists.txt | 5 -----
  1 file changed, 5 deletions(-)
 
 diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
-index 17d440e..9194e45 100644
+index 09ea28f..829d53b 100644
 --- a/cython/CMakeLists.txt
 +++ b/cython/CMakeLists.txt
-@@ -280,10 +280,5 @@ if(CYTHON_FOUND)
+@@ -396,10 +396,5 @@ if(CYTHON_FOUND)
          DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
          COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
  
@@ -19,5 +20,5 @@ index 17d440e..9194e45 100644
 -             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
 -             ${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()
  endif(CYTHON_FOUND)
diff --git a/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch b/debian/patches/0002-Disable-tests-that-use-DFSG-deleted-data-files.patch
index d58b56a9..6dff318d 100644
--- a/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch
+++ b/debian/patches/0002-Disable-tests-that-use-DFSG-deleted-data-files.patch
@@ -1,5 +1,5 @@
 From: Gard Spreemann <gspreemann@gmail.com>
-Date: Fri, 15 Jun 2018 13:19:42 +0200
+Date: Mon, 10 Sep 2018 05:17:29 +0200
 Subject: Disable tests that use DFSG-deleted data files.
 
 ---
diff --git a/debian/patches/0004-Use-system-MathJax.patch b/debian/patches/0003-Use-system-MathJax.patch
index ecd7b0d3..4791b5d9 100644
--- a/debian/patches/0004-Use-system-MathJax.patch
+++ b/debian/patches/0003-Use-system-MathJax.patch
@@ -1,5 +1,5 @@
 From: Gard Spreemann <gspreemann@gmail.com>
-Date: Fri, 15 Jun 2018 13:20:33 +0200
+Date: Mon, 10 Sep 2018 05:18:37 +0200
 Subject: Use system MathJax.
 
 ---
@@ -7,10 +7,10 @@ Subject: Use system MathJax.
  1 file changed, 1 insertion(+), 1 deletion(-)
 
 diff --git a/Doxyfile b/Doxyfile
-index 020667e..88ce932 100644
+index a16431a..fb67087 100644
 --- a/Doxyfile
 +++ b/Doxyfile
-@@ -1454,7 +1454,7 @@ MATHJAX_FORMAT         = HTML-CSS
+@@ -1456,7 +1456,7 @@ 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/0005-Don-t-set-runtime-library-dirs-for-Python-extensions.patch b/debian/patches/0004-Don-t-set-runtime-library-dirs-for-Python-extensions.patch
index 5ab944f7..b2b8c39c 100644
--- a/debian/patches/0005-Don-t-set-runtime-library-dirs-for-Python-extensions.patch
+++ b/debian/patches/0004-Don-t-set-runtime-library-dirs-for-Python-extensions.patch
@@ -1,5 +1,5 @@
 From: Gard Spreemann <gspreemann@gmail.com>
-Date: Fri, 15 Jun 2018 13:21:25 +0200
+Date: Mon, 10 Sep 2018 05:19:07 +0200
 Subject: Don't set runtime library dirs for Python extensions.
 
 ---
@@ -7,7 +7,7 @@ Subject: Don't set runtime library dirs for Python extensions.
  1 file changed, 1 insertion(+), 1 deletion(-)
 
 diff --git a/cython/setup.py.in b/cython/setup.py.in
-index ee381a1..3c8e0c4 100644
+index 4037aab..b0141aa 100644
 --- a/cython/setup.py.in
 +++ b/cython/setup.py.in
 @@ -36,7 +36,7 @@ gudhi = Extension(
diff --git a/debian/patches/0006-Force-linking-of-Python-module-with-CGAL.patch b/debian/patches/0005-Force-linking-of-Python-module-with-CGAL.patch
index cea5de9d..52aa9737 100644
--- a/debian/patches/0006-Force-linking-of-Python-module-with-CGAL.patch
+++ b/debian/patches/0005-Force-linking-of-Python-module-with-CGAL.patch
@@ -1,5 +1,5 @@
 From: Gard Spreemann <gspreemann@gmail.com>
-Date: Fri, 15 Jun 2018 13:23:55 +0200
+Date: Mon, 10 Sep 2018 05:20:33 +0200
 Subject: Force linking of Python module with CGAL.
 
 ---
@@ -7,15 +7,15 @@ Subject: Force linking of Python module with CGAL.
  1 file changed, 1 insertion(+), 1 deletion(-)
 
 diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
-index 9194e45..90ca2b7 100644
+index 829d53b..b8004c5 100644
 --- a/cython/CMakeLists.txt
 +++ b/cython/CMakeLists.txt
-@@ -78,7 +78,7 @@ if(CYTHON_FOUND)
-     if(CGAL_HEADER_ONLY)
+@@ -143,7 +143,7 @@ if(CYTHON_FOUND)
        set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
      else(CGAL_HEADER_ONLY)
--      add_gudhi_cython_lib(${CGAL_LIBRARY})
+       add_gudhi_debug_info("CGAL version ${CGAL_VERSION}")
+-      add_gudhi_cython_lib("${CGAL_LIBRARY}")
 +      add_gudhi_cython_lib("${CGAL_LIBRARIES_DIR}/libCGAL.so")
        set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
        # If CGAL is not header only, CGAL library may link with boost system,
-       add_gudhi_cython_lib(${Boost_SYSTEM_LIBRARY})
+       if(CMAKE_BUILD_TYPE MATCHES Debug)
diff --git a/debian/patches/0007-Force-linking-against-libatomic-for-parts-that-use-T.patch b/debian/patches/0006-Force-linking-against-libatomic-for-parts-that-use-T.patch
index 7d69e5ce..b38232c8 100644
--- a/debian/patches/0007-Force-linking-against-libatomic-for-parts-that-use-T.patch
+++ b/debian/patches/0006-Force-linking-against-libatomic-for-parts-that-use-T.patch
@@ -1,5 +1,5 @@
 From: Gard Spreemann <gspreemann@gmail.com>
-Date: Fri, 15 Jun 2018 13:25:37 +0200
+Date: Mon, 10 Sep 2018 05:20:57 +0200
 Subject: Force linking against libatomic for parts that use TBB.
 
 ---
diff --git a/debian/patches/0008-Offline-header-to-avoid-loading-remote-resources-in-.patch b/debian/patches/0007-Offline-header-for-docs.patch
index 3c93cecd..536227ad 100644
--- a/debian/patches/0008-Offline-header-to-avoid-loading-remote-resources-in-.patch
+++ b/debian/patches/0007-Offline-header-for-docs.patch
@@ -1,16 +1,16 @@
 From: Gard Spreemann <gspreemann@gmail.com>
-Date: Fri, 15 Jun 2018 13:42:45 +0200
-Subject: Offline header to avoid loading remote resources in HTML docs.
+Date: Mon, 10 Sep 2018 05:22:06 +0200
+Subject: Offline header for docs.
 
 ---
  Doxyfile | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 
 diff --git a/Doxyfile b/Doxyfile
-index 88ce932..eb565bc 100644
+index fb67087..a341cc6 100644
 --- a/Doxyfile
 +++ b/Doxyfile
-@@ -1059,7 +1059,7 @@ HTML_FILE_EXTENSION    = .html
+@@ -1061,7 +1061,7 @@ 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/series b/debian/patches/series
index 81114a30..a3f89b1a 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,7 +1,7 @@
-0002-Disable-Sphinx-test-since-we-re-not-currently-using.patch
-0003-Disable-tests-that-use-DFSG-deleted-data-files.patch
-0004-Use-system-MathJax.patch
-0005-Don-t-set-runtime-library-dirs-for-Python-extensions.patch
-0006-Force-linking-of-Python-module-with-CGAL.patch
-0007-Force-linking-against-libatomic-for-parts-that-use-T.patch
-0008-Offline-header-to-avoid-loading-remote-resources-in-.patch
+0001-Disable-Sphinx-test-since-we-re-not-currently-buildi.patch
+0002-Disable-tests-that-use-DFSG-deleted-data-files.patch
+0003-Use-system-MathJax.patch
+0004-Don-t-set-runtime-library-dirs-for-Python-extensions.patch
+0005-Force-linking-of-Python-module-with-CGAL.patch
+0006-Force-linking-against-libatomic-for-parts-that-use-T.patch
+0007-Offline-header-for-docs.patch