From 7441f013f50f613b1a9c0e7a9bff697df442a78e Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Fri, 15 Jun 2018 13:38:49 +0200 Subject: Refresh patches. The i686 rounding workaround and CGAL 4.12 compatibility patches dropped. --- debian/patches/0001-Force-Python-3-detection.patch | 32 +++++++++ ...hinx-test-since-we-re-not-currently-using.patch | 23 +++++++ ...le-tests-that-use-DFSG-deleted-data-files.patch | 77 ++++++++++++++++++++++ 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 ++++++ debian/patches/series | 7 ++ 8 files changed, 223 insertions(+) create mode 100644 debian/patches/0001-Force-Python-3-detection.patch create mode 100644 debian/patches/0002-Disable-Sphinx-test-since-we-re-not-currently-using.patch create mode 100644 debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch create mode 100644 debian/patches/0004-Use-system-MathJax.patch create mode 100644 debian/patches/0005-Don-t-set-runtime-library-dirs-for-Python-extensions.patch create mode 100644 debian/patches/0006-Force-linking-of-Python-module-with-CGAL.patch create mode 100644 debian/patches/0007-Force-linking-against-libatomic-for-parts-that-use-T.patch (limited to 'debian/patches') diff --git a/debian/patches/0001-Force-Python-3-detection.patch b/debian/patches/0001-Force-Python-3-detection.patch new file mode 100644 index 00000000..828025a6 --- /dev/null +++ b/debian/patches/0001-Force-Python-3-detection.patch @@ -0,0 +1,32 @@ +From: Gard Spreemann +Date: Fri, 15 Jun 2018 13:17:30 +0200 +Subject: Force Python 3 detection. + +--- + 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 ${_python_path} + ) + else() + find_program( CYTHON_EXECUTABLE +- NAMES cython cython.bat cython3 ++ NAMES cython3 + ) + endif() + diff --git a/debian/patches/0002-Disable-Sphinx-test-since-we-re-not-currently-using.patch b/debian/patches/0002-Disable-Sphinx-test-since-we-re-not-currently-using.patch new file mode 100644 index 00000000..abf2a450 --- /dev/null +++ b/debian/patches/0002-Disable-Sphinx-test-since-we-re-not-currently-using.patch @@ -0,0 +1,23 @@ +From: Gard Spreemann +Date: Fri, 15 Jun 2018 13:18:26 +0200 +Subject: Disable Sphinx test since we're not currently using. + +--- + cython/CMakeLists.txt | 5 ----- + 1 file changed, 5 deletions(-) + +diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt +index 17d440e..9194e45 100644 +--- a/cython/CMakeLists.txt ++++ b/cython/CMakeLists.txt +@@ -280,10 +280,5 @@ if(CYTHON_FOUND) + DEPENDS "${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 ${CMAKE_CURRENT_BINARY_DIR}/doctest) +- + endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + endif(CYTHON_FOUND) diff --git a/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch b/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch new file mode 100644 index 00000000..3f5fb5bb --- /dev/null +++ b/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch @@ -0,0 +1,77 @@ +From: Gard Spreemann +Date: Fri, 15 Jun 2018 13:19:42 +0200 +Subject: Disable tests that use DFSG-deleted data files. + +--- + example/Nerve_GIC/CMakeLists.txt | 6 ------ + example/Persistent_cohomology/CMakeLists.txt | 4 ---- + example/Simplex_tree/CMakeLists.txt | 2 -- + utilities/Nerve_GIC/CMakeLists.txt | 6 ------ + 4 files changed, 18 deletions(-) + +diff --git a/example/Nerve_GIC/CMakeLists.txt b/example/Nerve_GIC/CMakeLists.txt +index fdecf86..f63e08e 100644 +--- a/example/Nerve_GIC/CMakeLists.txt ++++ b/example/Nerve_GIC/CMakeLists.txt +@@ -12,16 +12,10 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + + # Copy files for not to pollute sources when testing + file(COPY "${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 $ +- "${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off") + + install(TARGETS Simplex_tree_example_alpha_shapes_3_from_off DESTINATION bin) + +diff --git a/utilities/Nerve_GIC/CMakeLists.txt b/utilities/Nerve_GIC/CMakeLists.txt +index 215f9df..266171d 100644 +--- a/utilities/Nerve_GIC/CMakeLists.txt ++++ b/utilities/Nerve_GIC/CMakeLists.txt +@@ -14,12 +14,6 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + # Copy files for not to pollute sources when testing + file(COPY "${CMAKE_SOURCE_DIR}/data/points/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) + install(FILES KeplerMapperVisuFromTxtFile.py km.py km.py.COPYRIGHT DESTINATION bin) diff --git a/debian/patches/0004-Use-system-MathJax.patch b/debian/patches/0004-Use-system-MathJax.patch new file mode 100644 index 00000000..ecd7b0d3 --- /dev/null +++ b/debian/patches/0004-Use-system-MathJax.patch @@ -0,0 +1,21 @@ +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 new file mode 100644 index 00000000..5ab944f7 --- /dev/null +++ b/debian/patches/0005-Don-t-set-runtime-library-dirs-for-Python-extensions.patch @@ -0,0 +1,21 @@ +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/0006-Force-linking-of-Python-module-with-CGAL.patch b/debian/patches/0006-Force-linking-of-Python-module-with-CGAL.patch new file mode 100644 index 00000000..cea5de9d --- /dev/null +++ b/debian/patches/0006-Force-linking-of-Python-module-with-CGAL.patch @@ -0,0 +1,21 @@ +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 new file mode 100644 index 00000000..7d69e5ce --- /dev/null +++ b/debian/patches/0007-Force-linking-against-libatomic-for-parts-that-use-T.patch @@ -0,0 +1,21 @@ +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/series b/debian/patches/series index e69de29b..efd45f90 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -0,0 +1,7 @@ +0001-Force-Python-3-detection.patch +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 -- cgit v1.2.3