diff options
Diffstat (limited to 'debian/patches')
6 files changed, 187 insertions, 0 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 new file mode 100644 index 00000000..b6e05ed7 --- /dev/null +++ b/debian/patches/0001-Force-Python-3-detection-to-avoid-mixing-2-and-3.patch @@ -0,0 +1,36 @@ +From e92363ab8125cff24a9c2ef5eec159ff09afc381 Mon Sep 17 00:00:00 2001 +From: Gard Spreemann <gspreemann@gmail.com> +Date: Mon, 9 Oct 2017 11:46:06 +0200 +Subject: [PATCH 1/4] 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 ${_python_path} + ) + else() + find_program( CYTHON_EXECUTABLE +- NAMES cython cython.bat cython3 ++ NAMES cython3 + ) + endif() + +-- +2.11.0 + diff --git a/debian/patches/0002-Disable-the-Sphinx-test.-We-re-not-using-it-as-it-re.patch b/debian/patches/0002-Disable-the-Sphinx-test.-We-re-not-using-it-as-it-re.patch new file mode 100644 index 00000000..2eb76f06 --- /dev/null +++ b/debian/patches/0002-Disable-the-Sphinx-test.-We-re-not-using-it-as-it-re.patch @@ -0,0 +1,32 @@ +From 2511e115a28311263e7ed85e98296c6af12ea960 Mon Sep 17 00:00:00 2001 +From: Gard Spreemann <gspreemann@gmail.com> +Date: Mon, 9 Oct 2017 12:05:01 +0200 +Subject: [PATCH 2/4] Disable the Sphinx test. We're not using it, as it + requires the Sphinx bibtex module (#800358). + +--- + cython/CMakeLists.txt | 8 ++++---- + 1 file changed, 4 insertions(+), 4 deletions(-) + +diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt +index afca9d6..ec3cb8f 100644 +--- a/cython/CMakeLists.txt ++++ b/cython/CMakeLists.txt +@@ -305,10 +305,10 @@ if(CYTHON_FOUND) + DEPENDS "${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 ${CMAKE_CURRENT_BINARY_DIR}/doctest) + + endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + endif(CYTHON_FOUND) +-- +2.11.0 + diff --git a/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch b/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch new file mode 100644 index 00000000..eade3da7 --- /dev/null +++ b/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch @@ -0,0 +1,63 @@ +From f31347031ea99c60d11064ec28bc27805b5c28b9 Mon Sep 17 00:00:00 2001 +From: Gard Spreemann <gspreemann@gmail.com> +Date: Mon, 9 Oct 2017 14:15:02 +0200 +Subject: [PATCH 3/4] Disable tests that use DFSG-deleted data files. + +--- + example/Persistent_cohomology/CMakeLists.txt | 8 ++++---- + example/Simplex_tree/CMakeLists.txt | 4 ++-- + example/common/CMakeLists.txt | 4 ++-- + 3 files changed, 8 insertions(+), 8 deletions(-) + +diff --git a/example/Persistent_cohomology/CMakeLists.txt b/example/Persistent_cohomology/CMakeLists.txt +index f47de4c..8f11ea0 100644 +--- a/example/Persistent_cohomology/CMakeLists.txt ++++ b/example/Persistent_cohomology/CMakeLists.txt +@@ -41,10 +41,10 @@ add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D CO + "${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 e22cc92..99da80f 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) + +-- +2.11.0 + diff --git a/debian/patches/0004-Use-system-MathJax.patch b/debian/patches/0004-Use-system-MathJax.patch new file mode 100644 index 00000000..916d23b9 --- /dev/null +++ b/debian/patches/0004-Use-system-MathJax.patch @@ -0,0 +1,25 @@ +From 46fdbaf1a91c320d7f731d061ef6d8d6da73232a Mon Sep 17 00:00:00 2001 +From: Gard Spreemann <gspreemann@gmail.com> +Date: Mon, 9 Oct 2017 16:06:36 +0200 +Subject: [PATCH 4/4] Use system MathJax. + +--- + Doxyfile | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/Doxyfile b/Doxyfile +index 0ef81e5..51df82e 100644 +--- a/Doxyfile ++++ b/Doxyfile +@@ -1450,7 +1450,7 @@ 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 +-- +2.11.0 + 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 new file mode 100644 index 00000000..c5677149 --- /dev/null +++ b/debian/patches/0005-Don-t-set-runtime_library_dirs-for-the-Python-extens.patch @@ -0,0 +1,26 @@ +From 2dfc0e89fdf40fe474ef0ec2018fe06e5eb786d5 Mon Sep 17 00:00:00 2001 +From: Gard Spreemann <gspreemann@gmail.com> +Date: Mon, 16 Oct 2017 13:46:22 +0200 +Subject: [PATCH] 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 fefa36b..18d03ad 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( +-- +2.11.0 + diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 00000000..cd9fa866 --- /dev/null +++ b/debian/patches/series @@ -0,0 +1,5 @@ +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 |