From 6233293ba27c017be71175ec5db98872262aa12a Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Wed, 25 Sep 2019 15:20:22 +0200 Subject: Refreshed patches. --- ...le-tests-that-use-DFSG-deleted-data-files.patch | 50 ++++++++++++++++++++++ debian/patches/0002-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 +++++++++ debian/patches/0006-Offline-header-for-docs.patch | 21 +++++++++ debian/patches/series | 6 +++ 7 files changed, 161 insertions(+) create mode 100644 debian/patches/0001-Disable-tests-that-use-DFSG-deleted-data-files.patch create mode 100644 debian/patches/0002-Use-system-MathJax.patch create mode 100644 debian/patches/0003-Don-t-set-runtime-library-dirs-for-Python-extensions.patch create mode 100644 debian/patches/0004-Force-linking-of-Python-module-with-CGAL.patch create mode 100644 debian/patches/0005-Force-linking-against-libatomic-for-parts-that-use-T.patch create mode 100644 debian/patches/0006-Offline-header-for-docs.patch create mode 100644 debian/patches/series (limited to 'debian') 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 +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 +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 +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 +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 +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 +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 -- cgit v1.2.3