From 3d092293bab8b5d9e866ac51283d95927f41c337 Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Wed, 25 Sep 2019 15:09:43 +0200 Subject: Prepare for refreshed patches. --- ...inx-test-since-we-re-not-currently-buildi.patch | 24 ---- ...le-tests-that-use-DFSG-deleted-data-files.patch | 121 --------------------- debian/patches/0003-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/0007-Offline-header-for-docs.patch | 21 ---- ...ate-CXXFLAGS-when-building-Python-modules.patch | 24 ---- debian/patches/series | 8 -- 9 files changed, 282 deletions(-) delete mode 100644 debian/patches/0001-Disable-Sphinx-test-since-we-re-not-currently-buildi.patch delete mode 100644 debian/patches/0002-Disable-tests-that-use-DFSG-deleted-data-files.patch delete mode 100644 debian/patches/0003-Use-system-MathJax.patch delete mode 100644 debian/patches/0004-Don-t-set-runtime-library-dirs-for-Python-extensions.patch delete mode 100644 debian/patches/0005-Force-linking-of-Python-module-with-CGAL.patch delete mode 100644 debian/patches/0006-Force-linking-against-libatomic-for-parts-that-use-T.patch delete mode 100644 debian/patches/0007-Offline-header-for-docs.patch delete mode 100644 debian/patches/0008-Propagate-CXXFLAGS-when-building-Python-modules.patch delete mode 100644 debian/patches/series (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 deleted file mode 100644 index d8bca9da..00000000 --- a/debian/patches/0001-Disable-Sphinx-test-since-we-re-not-currently-buildi.patch +++ /dev/null @@ -1,24 +0,0 @@ -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-tests-that-use-DFSG-deleted-data-files.patch b/debian/patches/0002-Disable-tests-that-use-DFSG-deleted-data-files.patch deleted file mode 100644 index e59a4f8b..00000000 --- a/debian/patches/0002-Disable-tests-that-use-DFSG-deleted-data-files.patch +++ /dev/null @@ -1,121 +0,0 @@ -From: Gard Spreemann -Date: Mon, 10 Sep 2018 05:17:29 +0200 -Subject: Disable tests that use DFSG-deleted data files. - ---- - cython/CMakeLists.txt | 30 ---------------------------- - example/Nerve_GIC/CMakeLists.txt | 6 ------ - example/Persistent_cohomology/CMakeLists.txt | 4 ---- - example/Simplex_tree/CMakeLists.txt | 2 -- - utilities/Nerve_GIC/CMakeLists.txt | 8 -------- - 5 files changed, 50 deletions(-) - -diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt -index 829d53b..219b99e 100644 ---- a/cython/CMakeLists.txt -+++ b/cython/CMakeLists.txt -@@ -265,36 +265,6 @@ if(CYTHON_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 4.8.1) - - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) -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 deleted file mode 100644 index 4791b5d9..00000000 --- a/debian/patches/0003-Use-system-MathJax.patch +++ /dev/null @@ -1,21 +0,0 @@ -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 deleted file mode 100644 index b2b8c39c..00000000 --- a/debian/patches/0004-Don-t-set-runtime-library-dirs-for-Python-extensions.patch +++ /dev/null @@ -1,21 +0,0 @@ -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/0005-Force-linking-of-Python-module-with-CGAL.patch b/debian/patches/0005-Force-linking-of-Python-module-with-CGAL.patch deleted file mode 100644 index d8ca0255..00000000 --- a/debian/patches/0005-Force-linking-of-Python-module-with-CGAL.patch +++ /dev/null @@ -1,21 +0,0 @@ -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 219b99e..7b8e38f 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 deleted file mode 100644 index b38232c8..00000000 --- a/debian/patches/0006-Force-linking-against-libatomic-for-parts-that-use-T.patch +++ /dev/null @@ -1,21 +0,0 @@ -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 ${ALL_TBB_LIBRARIES} - CACHE PATH "TBB libraries" FORCE) - diff --git a/debian/patches/0007-Offline-header-for-docs.patch b/debian/patches/0007-Offline-header-for-docs.patch deleted file mode 100644 index 536227ad..00000000 --- a/debian/patches/0007-Offline-header-for-docs.patch +++ /dev/null @@ -1,21 +0,0 @@ -From: Gard Spreemann -Date: Mon, 10 Sep 2018 05:22:06 +0200 -Subject: Offline header for docs. - ---- - Doxyfile | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/Doxyfile b/Doxyfile -index fb67087..a341cc6 100644 ---- a/Doxyfile -+++ b/Doxyfile -@@ -1061,7 +1061,7 @@ HTML_FILE_EXTENSION = .html - # of the possible markers and block names see the documentation. - # This tag requires that the tag GENERATE_HTML is set to YES. - --HTML_HEADER = doc/common/header.html -+HTML_HEADER = doc/common/offline_header.html - - # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each - # generated HTML page. If the tag is left blank doxygen will generate a standard diff --git a/debian/patches/0008-Propagate-CXXFLAGS-when-building-Python-modules.patch b/debian/patches/0008-Propagate-CXXFLAGS-when-building-Python-modules.patch deleted file mode 100644 index 03d4f63d..00000000 --- a/debian/patches/0008-Propagate-CXXFLAGS-when-building-Python-modules.patch +++ /dev/null @@ -1,24 +0,0 @@ -From: Gard Spreemann -Date: Fri, 5 Oct 2018 11:15:26 +0200 -Subject: Propagate CXXFLAGS when building Python modules. - ---- - cython/CMakeLists.txt | 5 +++++ - 1 file changed, 5 insertions(+) - -diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt -index 7b8e38f..6fdf343 100644 ---- a/cython/CMakeLists.txt -+++ b/cython/CMakeLists.txt -@@ -199,6 +199,11 @@ if(CYTHON_FOUND) - set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}") - endif(UNIX) - -+ string(REPLACE " " ";" TMP_FLAGS ${CMAKE_CXX_FLAGS}) -+ foreach(FLAG ${TMP_FLAGS}) -+ set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'${FLAG}', ") -+ endforeach() -+ - # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention - configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY) - # Generate gudhi.pyx - Gudhi cython file diff --git a/debian/patches/series b/debian/patches/series deleted file mode 100644 index 5f9ad2de..00000000 --- a/debian/patches/series +++ /dev/null @@ -1,8 +0,0 @@ -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 -0008-Propagate-CXXFLAGS-when-building-Python-modules.patch -- cgit v1.2.3