Refreshed patches.

7 files changed, 161 insertions, 0 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
new file mode 100644
index 00000000..973adfc3
--- /dev/null
+++ b/debian/patches/0001-Disable-tests-that-use-DFSG-deleted-data-files.patch
@@ -0,0 +1,50 @@
+From: Gard Spreemann <gspr@nonempty.org>
+Date: Wed, 25 Sep 2019 15:12:45 +0200
+Subject: Disable tests that use DFSG-deleted data files.
+
+---
+ src/python/CMakeLists.txt | 31 +------------------------------
+ 1 file changed, 1 insertion(+), 30 deletions(-)
+
+diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
+index 5508cbc..1778290 100644
+--- a/src/python/CMakeLists.txt
++++ b/src/python/CMakeLists.txt
+@@ -256,36 +256,7 @@ if(PYTHONINTERP_FOUND)
+ 
+       add_gudhi_py_test(test_bottleneck_distance)
+ 
+-      # Cover complex
+-      file(COPY ${CMAKE_SOURCE_DIR}/data/points/human.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}/)
+-      add_test(NAME cover_complex_nerve_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/nerve_of_a_covering.py"
+-               -f human.off -c 2 -r 10 -g 0.3)
+-
+-      add_test(NAME cover_complex_coordinate_gic_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/coordinate_graph_induced_complex.py"
+-               -f human.off -c 0 -v)
+-
+-      add_test(NAME cover_complex_functional_gic_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/functional_graph_induced_complex.py"
+-               -o lucky_cat.off
+-               -f lucky_cat_PCA1 -v)
+-
+-      add_test(NAME cover_complex_voronoi_gic_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/voronoi_graph_induced_complex.py"
+-               -f human.off -n 700 -v)
+-
+-      add_gudhi_py_test(test_cover_complex)
++      
+     endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
+ 
+     if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
diff --git a/debian/patches/0002-Use-system-MathJax.patch b/debian/patches/0002-Use-system-MathJax.patch
new file mode 100644
index 00000000..fd6288ba
--- /dev/null
+++ b/debian/patches/0002-Use-system-MathJax.patch
@@ -0,0 +1,21 @@
+From: Gard Spreemann <gspr@nonempty.org>
+Date: Wed, 25 Sep 2019 15:14:13 +0200
+Subject: Use system MathJax.
+
+---
+ src/Doxyfile.in | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/Doxyfile.in b/src/Doxyfile.in
+index 5777549..de452c9 100644
+--- a/src/Doxyfile.in
++++ b/src/Doxyfile.in
+@@ -1440,7 +1440,7 @@ 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        = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2
++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/0003-Don-t-set-runtime-library-dirs-for-Python-extensions.patch b/debian/patches/0003-Don-t-set-runtime-library-dirs-for-Python-extensions.patch
new file mode 100644
index 00000000..f5c6e30d
--- /dev/null
+++ b/debian/patches/0003-Don-t-set-runtime-library-dirs-for-Python-extensions.patch
@@ -0,0 +1,21 @@
+From: Gard Spreemann <gspr@nonempty.org>
+Date: Wed, 25 Sep 2019 15:14:52 +0200
+Subject: Don't set runtime library dirs for Python extensions.
+
+---
+ src/python/setup.py.in | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/python/setup.py.in b/src/python/setup.py.in
+index 3f1d442..1011f38 100644
+--- a/src/python/setup.py.in
++++ b/src/python/setup.py.in
+@@ -24,7 +24,7 @@ extra_link_args=[@GUDHI_PYTHON_EXTRA_LINK_ARGS@]
+ libraries=[@GUDHI_PYTHON_LIBRARIES@]
+ library_dirs=[@GUDHI_PYTHON_LIBRARY_DIRS@]
+ include_dirs = [numpy_get_include(), '@CMAKE_CURRENT_SOURCE_DIR@/gudhi/', @GUDHI_PYTHON_INCLUDE_DIRS@]
+-runtime_library_dirs=[@GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS@]
++runtime_library_dirs=[]
+ 
+ # Create ext_modules list from module list
+ ext_modules = []
diff --git a/debian/patches/0004-Force-linking-of-Python-module-with-CGAL.patch b/debian/patches/0004-Force-linking-of-Python-module-with-CGAL.patch
new file mode 100644
index 00000000..75c516cb
--- /dev/null
+++ b/debian/patches/0004-Force-linking-of-Python-module-with-CGAL.patch
@@ -0,0 +1,21 @@
+From: Gard Spreemann <gspr@nonempty.org>
+Date: Wed, 25 Sep 2019 15:16:27 +0200
+Subject: Force linking of Python module with CGAL.
+
+---
+ src/python/CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
+index 1778290..4c6840f 100644
+--- a/src/python/CMakeLists.txt
++++ b/src/python/CMakeLists.txt
+@@ -129,7 +129,7 @@ if(PYTHONINTERP_FOUND)
+         set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
+       else(CGAL_HEADER_ONLY)
+         add_gudhi_debug_info("CGAL version ${CGAL_VERSION}")
+-        add_GUDHI_PYTHON_lib("${CGAL_LIBRARY}")
++        add_GUDHI_PYTHON_lib("${CGAL_LIBRARIES_DIR}/libCGAL.so")
+         set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
+         message("** Add CGAL ${CGAL_LIBRARIES_DIR}")
+         # If CGAL is not header only, CGAL library may link with boost system,
diff --git a/debian/patches/0005-Force-linking-against-libatomic-for-parts-that-use-T.patch b/debian/patches/0005-Force-linking-against-libatomic-for-parts-that-use-T.patch
new file mode 100644
index 00000000..0a20ce1e
--- /dev/null
+++ b/debian/patches/0005-Force-linking-against-libatomic-for-parts-that-use-T.patch
@@ -0,0 +1,21 @@
+From: Gard Spreemann <gspr@nonempty.org>
+Date: Wed, 25 Sep 2019 15:18:08 +0200
+Subject: Force linking against libatomic for parts that use TBB.
+
+---
+ src/cmake/modules/FindTBB.cmake | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/src/cmake/modules/FindTBB.cmake b/src/cmake/modules/FindTBB.cmake
+index 13f4d92..6baa8d7 100644
+--- a/src/cmake/modules/FindTBB.cmake
++++ b/src/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/0006-Offline-header-for-docs.patch b/debian/patches/0006-Offline-header-for-docs.patch
new file mode 100644
index 00000000..232d7e53
--- /dev/null
+++ b/debian/patches/0006-Offline-header-for-docs.patch
@@ -0,0 +1,21 @@
+From: Gard Spreemann <gspr@nonempty.org>
+Date: Wed, 25 Sep 2019 15:19:14 +0200
+Subject: Offline header for docs.
+
+---
+ src/Doxyfile.in | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/Doxyfile.in b/src/Doxyfile.in
+index de452c9..98d8b96 100644
+--- a/src/Doxyfile.in
++++ b/src/Doxyfile.in
+@@ -1045,7 +1045,7 @@ 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.
+ 
+-HTML_HEADER            = doc/common/header.html
++HTML_HEADER            = doc/common/offline_header.html
+ 
+ # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+ # generated HTML page. If the tag is left blank doxygen will generate a standard
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 00000000..827de801
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,6 @@
+0001-Disable-tests-that-use-DFSG-deleted-data-files.patch
+0002-Use-system-MathJax.patch
+0003-Don-t-set-runtime-library-dirs-for-Python-extensions.patch
+0004-Force-linking-of-Python-module-with-CGAL.patch
+0005-Force-linking-against-libatomic-for-parts-that-use-T.patch
+0006-Offline-header-for-docs.patch