From 30a2d7854f5ef28e02d2b931b01255ea81cdebc6 Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Mon, 10 Sep 2018 05:25:43 +0200 Subject: Refresh patches. --- ...inx-test-since-we-re-not-currently-buildi.patch | 24 +++++++ ...hinx-test-since-we-re-not-currently-using.patch | 23 ------- ...le-tests-that-use-DFSG-deleted-data-files.patch | 79 ++++++++++++++++++++++ ...le-tests-that-use-DFSG-deleted-data-files.patch | 79 ---------------------- debian/patches/0003-Use-system-MathJax.patch | 21 ++++++ ...untime-library-dirs-for-Python-extensions.patch | 21 ++++++ debian/patches/0004-Use-system-MathJax.patch | 21 ------ ...untime-library-dirs-for-Python-extensions.patch | 21 ------ ...-Force-linking-of-Python-module-with-CGAL.patch | 21 ++++++ ...ng-against-libatomic-for-parts-that-use-T.patch | 21 ++++++ ...-Force-linking-of-Python-module-with-CGAL.patch | 21 ------ ...ng-against-libatomic-for-parts-that-use-T.patch | 21 ------ debian/patches/0007-Offline-header-for-docs.patch | 21 ++++++ ...der-to-avoid-loading-remote-resources-in-.patch | 21 ------ debian/patches/series | 14 ++-- 15 files changed, 215 insertions(+), 214 deletions(-) create mode 100644 debian/patches/0001-Disable-Sphinx-test-since-we-re-not-currently-buildi.patch delete mode 100644 debian/patches/0002-Disable-Sphinx-test-since-we-re-not-currently-using.patch create mode 100644 debian/patches/0002-Disable-tests-that-use-DFSG-deleted-data-files.patch delete mode 100644 debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch create mode 100644 debian/patches/0003-Use-system-MathJax.patch create mode 100644 debian/patches/0004-Don-t-set-runtime-library-dirs-for-Python-extensions.patch delete mode 100644 debian/patches/0004-Use-system-MathJax.patch delete mode 100644 debian/patches/0005-Don-t-set-runtime-library-dirs-for-Python-extensions.patch create mode 100644 debian/patches/0005-Force-linking-of-Python-module-with-CGAL.patch create mode 100644 debian/patches/0006-Force-linking-against-libatomic-for-parts-that-use-T.patch delete mode 100644 debian/patches/0006-Force-linking-of-Python-module-with-CGAL.patch delete mode 100644 debian/patches/0007-Force-linking-against-libatomic-for-parts-that-use-T.patch create mode 100644 debian/patches/0007-Offline-header-for-docs.patch delete mode 100644 debian/patches/0008-Offline-header-to-avoid-loading-remote-resources-in-.patch (limited to 'debian') diff --git a/debian/patches/0001-Disable-Sphinx-test-since-we-re-not-currently-buildi.patch b/debian/patches/0001-Disable-Sphinx-test-since-we-re-not-currently-buildi.patch new file mode 100644 index 00000000..d8bca9da --- /dev/null +++ b/debian/patches/0001-Disable-Sphinx-test-since-we-re-not-currently-buildi.patch @@ -0,0 +1,24 @@ +From: Gard Spreemann +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 09ea28f..829d53b 100644 +--- a/cython/CMakeLists.txt ++++ b/cython/CMakeLists.txt +@@ -396,10 +396,5 @@ 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 ${CMAKE_CURRENT_BINARY_DIR}/doctest) +- + endif() + endif(CYTHON_FOUND) diff --git a/debian/patches/0002-Disable-Sphinx-test-since-we-re-not-currently-using.patch b/debian/patches/0002-Disable-Sphinx-test-since-we-re-not-currently-using.patch deleted file mode 100644 index abf2a450..00000000 --- a/debian/patches/0002-Disable-Sphinx-test-since-we-re-not-currently-using.patch +++ /dev/null @@ -1,23 +0,0 @@ -From: Gard Spreemann -Date: Fri, 15 Jun 2018 13:18:26 +0200 -Subject: Disable Sphinx test since we're not currently using. - ---- - cython/CMakeLists.txt | 5 ----- - 1 file changed, 5 deletions(-) - -diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt -index 17d440e..9194e45 100644 ---- a/cython/CMakeLists.txt -+++ b/cython/CMakeLists.txt -@@ -280,10 +280,5 @@ if(CYTHON_FOUND) - DEPENDS "${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 ${CMAKE_CURRENT_BINARY_DIR}/doctest) -- - endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) - endif(CYTHON_FOUND) diff --git a/debian/patches/0002-Disable-tests-that-use-DFSG-deleted-data-files.patch b/debian/patches/0002-Disable-tests-that-use-DFSG-deleted-data-files.patch new file mode 100644 index 00000000..6dff318d --- /dev/null +++ b/debian/patches/0002-Disable-tests-that-use-DFSG-deleted-data-files.patch @@ -0,0 +1,79 @@ +From: Gard Spreemann +Date: Mon, 10 Sep 2018 05:17:29 +0200 +Subject: Disable tests that use DFSG-deleted data files. + +--- + example/Nerve_GIC/CMakeLists.txt | 6 ------ + example/Persistent_cohomology/CMakeLists.txt | 4 ---- + example/Simplex_tree/CMakeLists.txt | 2 -- + utilities/Nerve_GIC/CMakeLists.txt | 8 -------- + 4 files changed, 20 deletions(-) + +diff --git a/example/Nerve_GIC/CMakeLists.txt b/example/Nerve_GIC/CMakeLists.txt +index fdecf86..f63e08e 100644 +--- a/example/Nerve_GIC/CMakeLists.txt ++++ b/example/Nerve_GIC/CMakeLists.txt +@@ -12,16 +12,10 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + + # Copy files for not to pollute sources when testing + file(COPY "${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}/) + + add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $ + "${CMAKE_CURRENT_BINARY_DIR}/tore3D_1307.off" "0") + +- add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $ +- "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat.off" +- "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat_PCA1") +- + install(TARGETS CoordGIC DESTINATION bin) + install(TARGETS FuncGIC DESTINATION bin) + +diff --git a/example/Persistent_cohomology/CMakeLists.txt b/example/Persistent_cohomology/CMakeLists.txt +index 0f73151..4cac586 100644 +--- a/example/Persistent_cohomology/CMakeLists.txt ++++ b/example/Persistent_cohomology/CMakeLists.txt +@@ -28,10 +28,6 @@ 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 $ + "${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 $ +- "${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 $ +- "${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 857e851..48bb069 100644 +--- a/example/Simplex_tree/CMakeLists.txt ++++ b/example/Simplex_tree/CMakeLists.txt +@@ -29,8 +29,6 @@ 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 $ +- "${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off") + + install(TARGETS Simplex_tree_example_alpha_shapes_3_from_off DESTINATION bin) + +diff --git a/utilities/Nerve_GIC/CMakeLists.txt b/utilities/Nerve_GIC/CMakeLists.txt +index 215f9df..20aeb8e 100644 +--- a/utilities/Nerve_GIC/CMakeLists.txt ++++ b/utilities/Nerve_GIC/CMakeLists.txt +@@ -11,14 +11,6 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + endif() + + 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}/) +- +- add_test(NAME Nerve_GIC_utilities_nerve COMMAND $ +- "human.off" "2" "10" "0.3") +- +- add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $ +- "human.off" "100") + + install(TARGETS Nerve DESTINATION bin) + install(TARGETS VoronoiGIC DESTINATION bin) 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 d58b56a9..00000000 --- a/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch +++ /dev/null @@ -1,79 +0,0 @@ -From: Gard Spreemann -Date: Fri, 15 Jun 2018 13:19:42 +0200 -Subject: Disable tests that use DFSG-deleted data files. - ---- - example/Nerve_GIC/CMakeLists.txt | 6 ------ - example/Persistent_cohomology/CMakeLists.txt | 4 ---- - example/Simplex_tree/CMakeLists.txt | 2 -- - utilities/Nerve_GIC/CMakeLists.txt | 8 -------- - 4 files changed, 20 deletions(-) - -diff --git a/example/Nerve_GIC/CMakeLists.txt b/example/Nerve_GIC/CMakeLists.txt -index fdecf86..f63e08e 100644 ---- a/example/Nerve_GIC/CMakeLists.txt -+++ b/example/Nerve_GIC/CMakeLists.txt -@@ -12,16 +12,10 @@ 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}/) - - add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $ - "${CMAKE_CURRENT_BINARY_DIR}/tore3D_1307.off" "0") - -- add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $ -- "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat.off" -- "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat_PCA1") -- - install(TARGETS CoordGIC DESTINATION bin) - install(TARGETS FuncGIC DESTINATION bin) - -diff --git a/example/Persistent_cohomology/CMakeLists.txt b/example/Persistent_cohomology/CMakeLists.txt -index 0f73151..4cac586 100644 ---- a/example/Persistent_cohomology/CMakeLists.txt -+++ b/example/Persistent_cohomology/CMakeLists.txt -@@ -28,10 +28,6 @@ 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 $ - "${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 $ -- "${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 $ -- "${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 857e851..48bb069 100644 ---- a/example/Simplex_tree/CMakeLists.txt -+++ b/example/Simplex_tree/CMakeLists.txt -@@ -29,8 +29,6 @@ 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 $ -- "${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off") - - install(TARGETS Simplex_tree_example_alpha_shapes_3_from_off DESTINATION bin) - -diff --git a/utilities/Nerve_GIC/CMakeLists.txt b/utilities/Nerve_GIC/CMakeLists.txt -index 215f9df..20aeb8e 100644 ---- a/utilities/Nerve_GIC/CMakeLists.txt -+++ b/utilities/Nerve_GIC/CMakeLists.txt -@@ -11,14 +11,6 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1) - endif() - - 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}/) -- -- add_test(NAME Nerve_GIC_utilities_nerve COMMAND $ -- "human.off" "2" "10" "0.3") -- -- add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $ -- "human.off" "100") - - install(TARGETS Nerve DESTINATION bin) - install(TARGETS VoronoiGIC DESTINATION bin) diff --git a/debian/patches/0003-Use-system-MathJax.patch b/debian/patches/0003-Use-system-MathJax.patch new file mode 100644 index 00000000..4791b5d9 --- /dev/null +++ b/debian/patches/0003-Use-system-MathJax.patch @@ -0,0 +1,21 @@ +From: Gard Spreemann +Date: Mon, 10 Sep 2018 05:18:37 +0200 +Subject: Use system MathJax. + +--- + Doxyfile | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/Doxyfile b/Doxyfile +index a16431a..fb67087 100644 +--- a/Doxyfile ++++ b/Doxyfile +@@ -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. + +-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/0004-Don-t-set-runtime-library-dirs-for-Python-extensions.patch b/debian/patches/0004-Don-t-set-runtime-library-dirs-for-Python-extensions.patch new file mode 100644 index 00000000..b2b8c39c --- /dev/null +++ b/debian/patches/0004-Don-t-set-runtime-library-dirs-for-Python-extensions.patch @@ -0,0 +1,21 @@ +From: Gard Spreemann +Date: Mon, 10 Sep 2018 05:19:07 +0200 +Subject: Don't set runtime library dirs for Python extensions. + +--- + 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 4037aab..b0141aa 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/0004-Use-system-MathJax.patch b/debian/patches/0004-Use-system-MathJax.patch deleted file mode 100644 index ecd7b0d3..00000000 --- a/debian/patches/0004-Use-system-MathJax.patch +++ /dev/null @@ -1,21 +0,0 @@ -From: Gard Spreemann -Date: Fri, 15 Jun 2018 13:20:33 +0200 -Subject: Use system MathJax. - ---- - Doxyfile | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/Doxyfile b/Doxyfile -index 020667e..88ce932 100644 ---- a/Doxyfile -+++ b/Doxyfile -@@ -1454,7 +1454,7 @@ 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-Python-extensions.patch b/debian/patches/0005-Don-t-set-runtime-library-dirs-for-Python-extensions.patch deleted file mode 100644 index 5ab944f7..00000000 --- a/debian/patches/0005-Don-t-set-runtime-library-dirs-for-Python-extensions.patch +++ /dev/null @@ -1,21 +0,0 @@ -From: Gard Spreemann -Date: Fri, 15 Jun 2018 13:21:25 +0200 -Subject: Don't set runtime library dirs for Python extensions. - ---- - 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 ee381a1..3c8e0c4 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/0005-Force-linking-of-Python-module-with-CGAL.patch b/debian/patches/0005-Force-linking-of-Python-module-with-CGAL.patch new file mode 100644 index 00000000..52aa9737 --- /dev/null +++ b/debian/patches/0005-Force-linking-of-Python-module-with-CGAL.patch @@ -0,0 +1,21 @@ +From: Gard Spreemann +Date: Mon, 10 Sep 2018 05:20:33 +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 829d53b..b8004c5 100644 +--- a/cython/CMakeLists.txt ++++ b/cython/CMakeLists.txt +@@ -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_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, + if(CMAKE_BUILD_TYPE MATCHES Debug) diff --git a/debian/patches/0006-Force-linking-against-libatomic-for-parts-that-use-T.patch b/debian/patches/0006-Force-linking-against-libatomic-for-parts-that-use-T.patch new file mode 100644 index 00000000..b38232c8 --- /dev/null +++ b/debian/patches/0006-Force-linking-against-libatomic-for-parts-that-use-T.patch @@ -0,0 +1,21 @@ +From: Gard Spreemann +Date: Mon, 10 Sep 2018 05:20:57 +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 ${ALL_TBB_LIBRARIES} + CACHE PATH "TBB libraries" FORCE) + diff --git a/debian/patches/0006-Force-linking-of-Python-module-with-CGAL.patch b/debian/patches/0006-Force-linking-of-Python-module-with-CGAL.patch deleted file mode 100644 index cea5de9d..00000000 --- a/debian/patches/0006-Force-linking-of-Python-module-with-CGAL.patch +++ /dev/null @@ -1,21 +0,0 @@ -From: Gard Spreemann -Date: Fri, 15 Jun 2018 13:23:55 +0200 -Subject: Force linking of Python module with CGAL. - ---- - cython/CMakeLists.txt | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt -index 9194e45..90ca2b7 100644 ---- a/cython/CMakeLists.txt -+++ b/cython/CMakeLists.txt -@@ -78,7 +78,7 @@ if(CYTHON_FOUND) - if(CGAL_HEADER_ONLY) - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ") - else(CGAL_HEADER_ONLY) -- add_gudhi_cython_lib(${CGAL_LIBRARY}) -+ add_gudhi_cython_lib("${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}) diff --git a/debian/patches/0007-Force-linking-against-libatomic-for-parts-that-use-T.patch b/debian/patches/0007-Force-linking-against-libatomic-for-parts-that-use-T.patch deleted file mode 100644 index 7d69e5ce..00000000 --- a/debian/patches/0007-Force-linking-against-libatomic-for-parts-that-use-T.patch +++ /dev/null @@ -1,21 +0,0 @@ -From: Gard Spreemann -Date: Fri, 15 Jun 2018 13:25:37 +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/0007-Offline-header-for-docs.patch b/debian/patches/0007-Offline-header-for-docs.patch new file mode 100644 index 00000000..536227ad --- /dev/null +++ b/debian/patches/0007-Offline-header-for-docs.patch @@ -0,0 +1,21 @@ +From: Gard Spreemann +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 fb67087..a341cc6 100644 +--- a/Doxyfile ++++ b/Doxyfile +@@ -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. + +-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/0008-Offline-header-to-avoid-loading-remote-resources-in-.patch b/debian/patches/0008-Offline-header-to-avoid-loading-remote-resources-in-.patch deleted file mode 100644 index 3c93cecd..00000000 --- a/debian/patches/0008-Offline-header-to-avoid-loading-remote-resources-in-.patch +++ /dev/null @@ -1,21 +0,0 @@ -From: Gard Spreemann -Date: Fri, 15 Jun 2018 13:42:45 +0200 -Subject: Offline header to avoid loading remote resources in HTML docs. - ---- - Doxyfile | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/Doxyfile b/Doxyfile -index 88ce932..eb565bc 100644 ---- a/Doxyfile -+++ b/Doxyfile -@@ -1059,7 +1059,7 @@ 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 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 -- cgit v1.2.3