Begin refreshing patches.

11 files changed, 0 insertions, 443 deletions

diff --git a/debian/patches/0001-Force-Python-3-detection-to-avoid-mixing-2-and-3.patch b/debian/patches/0001-Force-Python-3-detection-to-avoid-mixing-2-and-3.patch
deleted file mode 100644
index 12978cfe..00000000
--- a/debian/patches/0001-Force-Python-3-detection-to-avoid-mixing-2-and-3.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-From: Gard Spreemann <gspreemann@gmail.com>
-Date: Mon, 9 Oct 2017 11:46:06 +0200
-Subject: [PATCH 1/5] Force Python 3 detection to avoid mixing 2 and 3.
-
----
- cmake/modules/FindCython.cmake | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/cmake/modules/FindCython.cmake b/cmake/modules/FindCython.cmake
-index 04aed1f..f3a5b7b 100644
---- a/cmake/modules/FindCython.cmake
-+++ b/cmake/modules/FindCython.cmake
-@@ -24,16 +24,16 @@
- 
- # Use the Cython executable that lives next to the Python executable
- # if it is a local installation.
--find_package( PythonInterp )
-+find_package( PythonInterp 3 )
- if( PYTHONINTERP_FOUND )
-   get_filename_component( _python_path ${PYTHON_EXECUTABLE} PATH )
-   find_program( CYTHON_EXECUTABLE
--    NAMES cython cython.bat cython3
-+    NAMES cython3
-     HINTS ${_python_path}
-     )
- else()
-   find_program( CYTHON_EXECUTABLE
--    NAMES cython cython.bat cython3
-+    NAMES cython3
-     )
- endif()
- 
diff --git a/debian/patches/0002-Disable-the-Sphinx-test.-We-re-not-using-it-as-it-re.patch b/debian/patches/0002-Disable-the-Sphinx-test.-We-re-not-using-it-as-it-re.patch
deleted file mode 100644
index cd17e0f1..00000000
--- a/debian/patches/0002-Disable-the-Sphinx-test.-We-re-not-using-it-as-it-re.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-From: Gard Spreemann <gspreemann@gmail.com>
-Date: Mon, 9 Oct 2017 12:05:01 +0200
-Subject: [PATCH 2/5] Disable the Sphinx test. We're not using it,
- as it requires the Sphinx bibtex module (#800358).
-
----
- cython/CMakeLists.txt | 8 ++++----
- 1 file changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
-index afca9d6..ec3cb8f 100644
---- a/cython/CMakeLists.txt
-+++ b/cython/CMakeLists.txt
-@@ -305,10 +305,10 @@ if(CYTHON_FOUND)
-         DEPENDS "${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 ${CMAKE_CURRENT_BINARY_DIR}/doctest)
-+#    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 ${CMAKE_CURRENT_BINARY_DIR}/doctest)
- 
-   endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
- endif(CYTHON_FOUND)
diff --git a/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch b/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch
deleted file mode 100644
index 4edf1caa..00000000
--- a/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch
+++ /dev/null
@@ -1,107 +0,0 @@
-From: Gard Spreemann <gspreemann@gmail.com>
-Date: Mon, 5 Feb 2018 10:15:40 +0100
-Subject: [PATCH 3/5] Disable tests that use DFSG-deleted data files.
-
----
- example/Nerve_GIC/CMakeLists.txt             | 10 +++++-----
- example/Persistent_cohomology/CMakeLists.txt |  8 ++++----
- example/Simplex_tree/CMakeLists.txt          |  4 ++--
- example/common/CMakeLists.txt                |  4 ++--
- utilities/Nerve_GIC/CMakeLists.txt           | 10 +++++-----
- 5 files changed, 18 insertions(+), 18 deletions(-)
-
-diff --git a/example/Nerve_GIC/CMakeLists.txt b/example/Nerve_GIC/CMakeLists.txt
-index f262692..825974c 100644
---- a/example/Nerve_GIC/CMakeLists.txt
-+++ b/example/Nerve_GIC/CMakeLists.txt
-@@ -13,14 +13,14 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
- 
-   # Copy files for not to pollute sources when testing
-   file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
--  file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
--  file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-+  #file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-+  #file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
- 
-   add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $<TARGET_FILE:CoordGIC>
-       "tore3D_1307.off" "0")
- 
--  add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $<TARGET_FILE:FuncGIC>
--      "lucky_cat.off"
--      "lucky_cat_PCA1")
-+  #add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $<TARGET_FILE:FuncGIC>
-+  #    "lucky_cat.off"
-+  #    "lucky_cat_PCA1")
- 
- endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-diff --git a/example/Persistent_cohomology/CMakeLists.txt b/example/Persistent_cohomology/CMakeLists.txt
-index 18e2913..e2dca6d 100644
---- a/example/Persistent_cohomology/CMakeLists.txt
-+++ b/example/Persistent_cohomology/CMakeLists.txt
-@@ -29,10 +29,10 @@ add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D CO
-     "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3")
- add_test(NAME Persistent_cohomology_example_via_boundary_matrix COMMAND $<TARGET_FILE:rips_persistence_via_boundary_matrix>
-     "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100")
--add_test(NAME Persistent_cohomology_example_from_file_3_2_0 COMMAND $<TARGET_FILE:persistence_from_file>
--    "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "2" "-m" "0")
--add_test(NAME Persistent_cohomology_example_from_file_3_3_100 COMMAND $<TARGET_FILE:persistence_from_file>
--    "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100")
-+#add_test(NAME Persistent_cohomology_example_from_file_3_2_0 COMMAND $<TARGET_FILE:persistence_from_file>
-+#    "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "2" "-m" "0")
-+#add_test(NAME Persistent_cohomology_example_from_file_3_3_100 COMMAND $<TARGET_FILE:persistence_from_file>
-+#    "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100")
- 
- install(TARGETS plain_homology DESTINATION bin)
- install(TARGETS persistence_from_simple_simplex_tree DESTINATION bin)
-diff --git a/example/Simplex_tree/CMakeLists.txt b/example/Simplex_tree/CMakeLists.txt
-index b33b2d0..1cba524 100644
---- a/example/Simplex_tree/CMakeLists.txt
-+++ b/example/Simplex_tree/CMakeLists.txt
-@@ -30,8 +30,8 @@ if(GMP_FOUND AND CGAL_FOUND)
-   if (TBB_FOUND)
-     target_link_libraries(Simplex_tree_example_alpha_shapes_3_from_off ${TBB_LIBRARIES})
-   endif()
--  add_test(NAME Simplex_tree_example_alpha_shapes_3_from_off COMMAND $<TARGET_FILE:Simplex_tree_example_alpha_shapes_3_from_off>
--      "${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off")
-+#  add_test(NAME Simplex_tree_example_alpha_shapes_3_from_off COMMAND $<TARGET_FILE:Simplex_tree_example_alpha_shapes_3_from_off>
-+#      "${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off")
- 
-   install(TARGETS Simplex_tree_example_alpha_shapes_3_from_off DESTINATION bin)
- 
-diff --git a/example/common/CMakeLists.txt b/example/common/CMakeLists.txt
-index afe865d..2ad4a64 100644
---- a/example/common/CMakeLists.txt
-+++ b/example/common/CMakeLists.txt
-@@ -3,8 +3,8 @@ project(Common_examples)
- 
- add_executable ( vector_double_off_reader example_vector_double_points_off_reader.cpp )
- target_link_libraries(vector_double_off_reader ${CGAL_LIBRARY})
--add_test(NAME Common_example_vector_double_off_reader COMMAND $<TARGET_FILE:vector_double_off_reader>
--    "${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off")
-+#add_test(NAME Common_example_vector_double_off_reader COMMAND $<TARGET_FILE:vector_double_off_reader>
-+#    "${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off")
- 
- install(TARGETS vector_double_off_reader DESTINATION bin)
- 
-diff --git a/utilities/Nerve_GIC/CMakeLists.txt b/utilities/Nerve_GIC/CMakeLists.txt
-index 7762c8a..c41898b 100644
---- a/utilities/Nerve_GIC/CMakeLists.txt
-+++ b/utilities/Nerve_GIC/CMakeLists.txt
-@@ -13,12 +13,12 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
- 
-   file(COPY KeplerMapperVisuFromTxtFile.py km.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-   # Copy files for not to pollute sources when testing
--  file(COPY "${CMAKE_SOURCE_DIR}/data/points/human.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-+  #file(COPY "${CMAKE_SOURCE_DIR}/data/points/human.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
- 
--  add_test(NAME Nerve_GIC_utilities_nerve COMMAND $<TARGET_FILE:Nerve>
--      "human.off" "2" "10" "0.3")
-+  #add_test(NAME Nerve_GIC_utilities_nerve COMMAND $<TARGET_FILE:Nerve>
-+  #    "human.off" "2" "10" "0.3")
- 
--  add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC>
--      "human.off" "100")
-+  #add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC>
-+  #    "human.off" "100")
- 
- endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/debian/patches/0004-Use-system-MathJax.patch b/debian/patches/0004-Use-system-MathJax.patch
deleted file mode 100644
index c3346d1e..00000000
--- a/debian/patches/0004-Use-system-MathJax.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-From: Gard Spreemann <gspreemann@gmail.com>
-Date: Mon, 9 Oct 2017 16:06:36 +0200
-Subject: [PATCH 4/5] Use system MathJax.
-
----
- Doxyfile | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/Doxyfile b/Doxyfile
-index f1981e2..991645b 100644
---- a/Doxyfile
-+++ b/Doxyfile
-@@ -1453,7 +1453,7 @@ 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.
- 
--MATHJAX_RELPATH        = ../common
-+MATHJAX_RELPATH        = /usr/share/javascript/mathjax
- 
- # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
- # extension names that should be enabled during MathJax rendering. For example
diff --git a/debian/patches/0005-Don-t-set-runtime_library_dirs-for-the-Python-extens.patch b/debian/patches/0005-Don-t-set-runtime_library_dirs-for-the-Python-extens.patch
deleted file mode 100644
index 9f4c6412..00000000
--- a/debian/patches/0005-Don-t-set-runtime_library_dirs-for-the-Python-extens.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-From: Gard Spreemann <gspreemann@gmail.com>
-Date: Mon, 16 Oct 2017 13:46:22 +0200
-Subject: [PATCH 5/5] Don't set runtime_library_dirs for the Python extension.
- Avoid RPATH in the shared object.
-
----
- cython/setup.py.in | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/cython/setup.py.in b/cython/setup.py.in
-index c767e93..d00f65a 100644
---- a/cython/setup.py.in
-+++ b/cython/setup.py.in
-@@ -36,7 +36,7 @@ gudhi = Extension(
-     libraries=[@GUDHI_CYTHON_LIBRARIES@],
-     library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@],
-     include_dirs = [@GUDHI_CYTHON_INCLUDE_DIRS@],
--    runtime_library_dirs=[@GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS@],
-+    runtime_library_dirs=[],
- )
- 
- setup(
diff --git a/debian/patches/0007-CGAL-4.12-compatibility.patch b/debian/patches/0007-CGAL-4.12-compatibility.patch
deleted file mode 100644
index 604c40e7..00000000
--- a/debian/patches/0007-CGAL-4.12-compatibility.patch
+++ /dev/null
@@ -1,72 +0,0 @@
-From: Gard Spreemann <gspreemann@gmail.com>
-Date: Fri, 18 May 2018 19:13:09 +0200
-Subject: CGAL 4.12 compatibility.
-
----
- utilities/Alpha_complex/alpha_complex_3d_persistence.cpp                 | 1 +
- utilities/Alpha_complex/exact_alpha_complex_3d_persistence.cpp           | 1 +
- utilities/Alpha_complex/periodic_alpha_complex_3d_persistence.cpp        | 1 +
- utilities/Alpha_complex/weighted_alpha_complex_3d_persistence.cpp        | 1 +
- .../Alpha_complex/weighted_periodic_alpha_complex_3d_persistence.cpp     | 1 +
- 5 files changed, 5 insertions(+)
-
-diff --git a/utilities/Alpha_complex/alpha_complex_3d_persistence.cpp b/utilities/Alpha_complex/alpha_complex_3d_persistence.cpp
-index 8ef5ffb..6491dac 100644
---- a/utilities/Alpha_complex/alpha_complex_3d_persistence.cpp
-+++ b/utilities/Alpha_complex/alpha_complex_3d_persistence.cpp
-@@ -36,6 +36,7 @@
- #include <CGAL/Delaunay_triangulation_3.h>
- #include <CGAL/Alpha_shape_3.h>
- #include <CGAL/iterator.h>
-+#include <CGAL/Alpha_shape_vertex_base_3.h>
- 
- #include <fstream>
- #include <cmath>
-diff --git a/utilities/Alpha_complex/exact_alpha_complex_3d_persistence.cpp b/utilities/Alpha_complex/exact_alpha_complex_3d_persistence.cpp
-index cceac46..f762024 100644
---- a/utilities/Alpha_complex/exact_alpha_complex_3d_persistence.cpp
-+++ b/utilities/Alpha_complex/exact_alpha_complex_3d_persistence.cpp
-@@ -31,6 +31,7 @@
- #include <CGAL/Delaunay_triangulation_3.h>
- #include <CGAL/Alpha_shape_3.h>
- #include <CGAL/iterator.h>
-+#include <CGAL/Alpha_shape_vertex_base_3.h>
- 
- #include <fstream>
- #include <cmath>
-diff --git a/utilities/Alpha_complex/periodic_alpha_complex_3d_persistence.cpp b/utilities/Alpha_complex/periodic_alpha_complex_3d_persistence.cpp
-index 188cf60..a69ba9f 100644
---- a/utilities/Alpha_complex/periodic_alpha_complex_3d_persistence.cpp
-+++ b/utilities/Alpha_complex/periodic_alpha_complex_3d_persistence.cpp
-@@ -33,6 +33,7 @@
- #include <CGAL/Periodic_3_Delaunay_triangulation_3.h>
- #include <CGAL/Alpha_shape_3.h>
- #include <CGAL/iterator.h>
-+#include <CGAL/Alpha_shape_vertex_base_3.h>
- 
- #include <fstream>
- #include <cmath>
-diff --git a/utilities/Alpha_complex/weighted_alpha_complex_3d_persistence.cpp b/utilities/Alpha_complex/weighted_alpha_complex_3d_persistence.cpp
-index 93be8a0..b35ae31 100644
---- a/utilities/Alpha_complex/weighted_alpha_complex_3d_persistence.cpp
-+++ b/utilities/Alpha_complex/weighted_alpha_complex_3d_persistence.cpp
-@@ -32,6 +32,7 @@
- #include <CGAL/Regular_triangulation_3.h>
- #include <CGAL/Alpha_shape_3.h>
- #include <CGAL/iterator.h>
-+#include <CGAL/Alpha_shape_vertex_base_3.h>
- 
- // For CGAL < 4.11
- #if CGAL_VERSION_NR < 1041100000
-diff --git a/utilities/Alpha_complex/weighted_periodic_alpha_complex_3d_persistence.cpp b/utilities/Alpha_complex/weighted_periodic_alpha_complex_3d_persistence.cpp
-index 5321bb0..16864b5 100644
---- a/utilities/Alpha_complex/weighted_periodic_alpha_complex_3d_persistence.cpp
-+++ b/utilities/Alpha_complex/weighted_periodic_alpha_complex_3d_persistence.cpp
-@@ -32,6 +32,7 @@
- #include <CGAL/Periodic_3_regular_triangulation_3.h>
- #include <CGAL/Alpha_shape_3.h>
- #include <CGAL/iterator.h>
-+#include <CGAL/Alpha_shape_vertex_base_3.h>
- 
- #include <fstream>
- #include <cmath>
diff --git a/debian/patches/0008-Force-linking-of-Python-module-with-CGAL.patch b/debian/patches/0008-Force-linking-of-Python-module-with-CGAL.patch
deleted file mode 100644
index 2b3a91ba..00000000
--- a/debian/patches/0008-Force-linking-of-Python-module-with-CGAL.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-From: Gard Spreemann <gspreemann@gmail.com>
-Date: Thu, 24 May 2018 11:24:43 +0200
-Subject: Force linking of Python module with CGAL.
-
----
- cython/CMakeLists.txt | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
-index ec3cb8f..87b2846 100644
---- a/cython/CMakeLists.txt
-+++ b/cython/CMakeLists.txt
-@@ -103,7 +103,7 @@ if(CYTHON_FOUND)
-     if(CGAL_HEADER_ONLY)
-       set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
-     else(CGAL_HEADER_ONLY)
--      add_gudhi_cython_lib(${CGAL_LIBRARIES})
-+      add_gudhi_cython_lib("${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})
diff --git a/debian/patches/0009-Rounding-workaround-on-i686.patch b/debian/patches/0009-Rounding-workaround-on-i686.patch
deleted file mode 100644
index 39629fe1..00000000
--- a/debian/patches/0009-Rounding-workaround-on-i686.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-From: Gard Spreemann <gspreemann@gmail.com>
-Date: Mon, 11 Jun 2018 15:42:51 +0200
-Subject: Rounding workaround on i686.
-
----
- include/gudhi/Bottleneck.h | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/include/gudhi/Bottleneck.h b/include/gudhi/Bottleneck.h
-index 7aee07b..ffa87a8 100644
---- a/include/gudhi/Bottleneck.h
-+++ b/include/gudhi/Bottleneck.h
-@@ -42,7 +42,7 @@ double bottleneck_distance_approx(Persistence_graph& g, double e) {
-   Graph_matching m(g);
-   Graph_matching biggest_unperfect(g);
-   while (b_upper_bound - b_lower_bound > 2 * e) {
--    double step = b_lower_bound + (b_upper_bound - b_lower_bound) / alpha;
-+    volatile double step = b_lower_bound + (b_upper_bound - b_lower_bound) / alpha;
-     if (step <= b_lower_bound || step >= b_upper_bound)  // Avoid precision problem
-       break;
-     m.set_r(step);
diff --git a/debian/patches/0010-Force-linking-against-libatomic-for-parts-that-use-T.patch b/debian/patches/0010-Force-linking-against-libatomic-for-parts-that-use-T.patch
deleted file mode 100644
index cbf39039..00000000
--- a/debian/patches/0010-Force-linking-against-libatomic-for-parts-that-use-T.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-From: Gard Spreemann <gspreemann@gmail.com>
-Date: Tue, 12 Jun 2018 15:20:07 +0200
-Subject: Force linking against libatomic for parts that use TBB.
-
----
- cmake/modules/FindTBB.cmake | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/cmake/modules/FindTBB.cmake b/cmake/modules/FindTBB.cmake
-index 13f4d92..6baa8d7 100644
---- a/cmake/modules/FindTBB.cmake
-+++ b/cmake/modules/FindTBB.cmake
-@@ -375,6 +375,8 @@ if (TBB_INCLUDE_DIR)
-                 endif(NOT TBB_without_pthread)
-         endif(UNIX AND NOT APPLE)
- 
-+        list(APPEND ALL_TBB_LIBRARIES atomic)
-+        
-         set (TBB_LIBRARIES ${ALL_TBB_LIBRARIES}
-              CACHE PATH "TBB libraries" FORCE)
- 
diff --git a/debian/patches/no-external-doc-resources.patch b/debian/patches/no-external-doc-resources.patch
deleted file mode 100644
index 735ac63b..00000000
--- a/debian/patches/no-external-doc-resources.patch
+++ /dev/null
@@ -1,88 +0,0 @@
-From: Gard Spreemann <gspreemann@gmail.com>
-Date: Fri, 18 May 2018 19:09:11 +0200
-Subject: no-external-doc-resources
-
-Remove external resource references from Doxygen header. Later upstream
-versions will include an alternative header that does the job.
----
- doc/common/header.html | 60 --------------------------------------------------
- 1 file changed, 60 deletions(-)
-
-diff --git a/doc/common/header.html b/doc/common/header.html
-index 9c51438..6a02a89 100644
---- a/doc/common/header.html
-+++ b/doc/common/header.html
-@@ -8,8 +8,6 @@
- <meta name="generator" content="Doxygen $doxygenversion"/>
- <!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
- <!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
--<!-- GUDHI website css for header BEGIN -->
--<link rel="stylesheet" type="text/css" href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/gudhi-doc-2.0.0/assets/css/styles_feeling_responsive.css" />
- <!-- GUDHI website css for header END -->
- <link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/>
- <script type="text/javascript" src="$relpath^jquery.js"></script>
-@@ -22,64 +20,6 @@ $extrastylesheet
- </head>
- <body>
- 
--<!-- GUDHI website header BEGIN -->
--<div id="navigation" class="sticky">
--  <nav class="top-bar" role="navigation" data-topbar>
--    <ul class="title-area">
--      <li class="name">
--      <h1 class="show-for-small-only"><a href="http://gudhi.gforge.inria.fr" class="icon-tree"> GUDHI C++ library</a></h1>
--    </li>
--       <!-- Remove the class "menu-icon" to get rid of menu icon. Take out "Menu" to just have icon alone -->
--      <li class="toggle-topbar menu-icon"><a href="#"><span>Navigation</span></a></li>
--    </ul>
--    <section class="top-bar-section">
--      <ul class="right">
--              <li class="divider"></li>
--              <li><a href="http://gudhi.gforge.inria.fr/contact/">Contact</a></li>
--      </ul>
--      <ul class="left">
--              <li><a href="http://gudhi.gforge.inria.fr/"> <img src="http://gudhi.gforge.inria.fr/assets/img/home.png" alt="&nbsp;&nbsp;GUDHI">&nbsp;&nbsp;GUDHI </a></li>
--              <li class="divider"></li>
--              <li class="has-dropdown">
--                <a href="#">Project</a>
--                  <ul class="dropdown">
--                      <li><a href="http://gudhi.gforge.inria.fr/people/">People</a></li>
--                      <li><a href="http://gudhi.gforge.inria.fr/keepintouch/">Keep in touch</a></li>
--                      <li><a href="http://gudhi.gforge.inria.fr/partners/">Partners and Funding</a></li>
--                      <li><a href="http://gudhi.gforge.inria.fr/relatedprojects/">Related projects</a></li>
--                      <li><a href="http://gudhi.gforge.inria.fr/theyaretalkingaboutus/">They are talking about us</a></li>
--                  </ul>
--              </li>
--              <li class="divider"></li>
--              <li class="has-dropdown">
--                <a href="#">Download</a>
--                  <ul class="dropdown">
--                      <li><a href="http://gudhi.gforge.inria.fr/licensing/">Licensing</a></li>
--                      <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li>
--                      <li><a href="https://gforge.inria.fr/frs/download.php/file/37113/GUDHI_2.0.0_OSX_UTILS.beta.tar.gz" target="_blank">Utils for Mac OSx</a></li>
--                      <li><a href="https://gforge.inria.fr/frs/download.php/file/37112/GUDHI_2.0.0_WIN64_UTILS.beta.zip" target="_blank">Utils for Win x64</a></li>
--                  </ul>
--              </li>
--              <li class="divider"></li>
--              <li class="has-dropdown">
--                <a href="#">Documentation</a>
--                  <ul class="dropdown">
--                      <li><a href="http://gudhi.gforge.inria.fr/doc/latest/">C++ documentation</a></li>
--                      <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">C++ installation manual</a></li>
--                      <li><a href="http://gudhi.gforge.inria.fr/python/latest/">Python documentation</a></li>
--                      <li><a href="http://gudhi.gforge.inria.fr/python/latest/installation.html">Python installation manual</a></li>
--                      <li><a href="http://gudhi.gforge.inria.fr/utils/">Utilities</a></li>
--                      <li><a href="http://bertrand.michel.perso.math.cnrs.fr/Enseignements/TDA-Gudhi-Python.html" target="_blank">Tutorial</a></li>
--                  </ul>
--              </li>
--              <li class="divider"></li>
--              <li><a href="http://gudhi.gforge.inria.fr/interfaces/">Interfaces</a></li>
--              <li class="divider"></li>
--      </ul>
--    </section>
--  </nav>
--</div><!-- /#navigation -->
--<!-- GUDHI website header BEGIN -->
- 
- <div id="top"><!-- do not remove this div, it is closed by doxygen! -->
- 
diff --git a/debian/patches/series b/debian/patches/series
index d1e36399..e69de29b 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,10 +0,0 @@
-0001-Force-Python-3-detection-to-avoid-mixing-2-and-3.patch
-0002-Disable-the-Sphinx-test.-We-re-not-using-it-as-it-re.patch
-0003-Disable-tests-that-use-DFSG-deleted-data-files.patch
-0004-Use-system-MathJax.patch
-0005-Don-t-set-runtime_library_dirs-for-the-Python-extens.patch
-no-external-doc-resources.patch
-0007-CGAL-4.12-compatibility.patch
-0008-Force-linking-of-Python-module-with-CGAL.patch
-0009-Rounding-workaround-on-i686.patch
-0010-Force-linking-against-libatomic-for-parts-that-use-T.patch