diff options
Diffstat (limited to 'debian/patches')
8 files changed, 256 insertions, 0 deletions
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..82a72911 --- /dev/null +++ b/debian/patches/0001-Disable-tests-that-use-DFSG-deleted-data-files.patch @@ -0,0 +1,121 @@ +From: Gard Spreemann <gspr@nonempty.org> +Date: Wed, 25 Sep 2019 15:12:45 +0200 +Subject: Disable tests that use DFSG-deleted data files. + +--- + src/Nerve_GIC/example/CMakeLists.txt | 5 ---- + src/Nerve_GIC/utilities/CMakeLists.txt | 8 ------ + src/Persistent_cohomology/example/CMakeLists.txt | 4 --- + src/Simplex_tree/example/CMakeLists.txt | 2 -- + src/python/CMakeLists.txt | 31 +----------------------- + 5 files changed, 1 insertion(+), 49 deletions(-) + +diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt +index 1667472..37c4759 100644 +--- a/src/Nerve_GIC/example/CMakeLists.txt ++++ b/src/Nerve_GIC/example/CMakeLists.txt +@@ -12,15 +12,10 @@ if (NOT CGAL_VERSION VERSION_LESS 4.11.0) + + # 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 $<TARGET_FILE:CoordGIC> + "${CMAKE_CURRENT_BINARY_DIR}/tore3D_1307.off" "0") + +- add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $<TARGET_FILE:FuncGIC> +- "${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/src/Nerve_GIC/utilities/CMakeLists.txt b/src/Nerve_GIC/utilities/CMakeLists.txt +index 65a08d9..3f16db9 100644 +--- a/src/Nerve_GIC/utilities/CMakeLists.txt ++++ b/src/Nerve_GIC/utilities/CMakeLists.txt +@@ -11,14 +11,6 @@ if (NOT CGAL_VERSION VERSION_LESS 4.11.0) + 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 $<TARGET_FILE:Nerve> +- "human.off" "2" "10" "0.3") +- +- add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC> +- "human.off" "100") + + install(TARGETS Nerve DESTINATION bin) + install(TARGETS VoronoiGIC DESTINATION bin) +diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt +index 94ec13c..4a48d21 100644 +--- a/src/Persistent_cohomology/example/CMakeLists.txt ++++ b/src/Persistent_cohomology/example/CMakeLists.txt +@@ -28,10 +28,6 @@ add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D CO + "${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 $<TARGET_FILE:rips_persistence_via_boundary_matrix> + "${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") + + install(TARGETS plain_homology DESTINATION bin) + install(TARGETS persistence_from_simple_simplex_tree DESTINATION bin) +diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt +index f99b164..ae302dc 100644 +--- a/src/Simplex_tree/example/CMakeLists.txt ++++ b/src/Simplex_tree/example/CMakeLists.txt +@@ -25,8 +25,6 @@ if(GMP_FOUND AND NOT CGAL_VERSION VERSION_LESS 4.11.0) + 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") + + endif() + +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 <gspr@nonempty.org> +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-Force-linking-against-libatomic-for-parts-that-use-T.patch b/debian/patches/0003-Force-linking-against-libatomic-for-parts-that-use-T.patch new file mode 100644 index 00000000..0a20ce1e --- /dev/null +++ b/debian/patches/0003-Force-linking-against-libatomic-for-parts-that-use-T.patch @@ -0,0 +1,21 @@ +From: Gard Spreemann <gspr@nonempty.org> +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/0004-Offline-header-for-docs.patch b/debian/patches/0004-Offline-header-for-docs.patch new file mode 100644 index 00000000..232d7e53 --- /dev/null +++ b/debian/patches/0004-Offline-header-for-docs.patch @@ -0,0 +1,21 @@ +From: Gard Spreemann <gspr@nonempty.org> +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/0005-Disable-Sphinx.patch b/debian/patches/0005-Disable-Sphinx.patch new file mode 100644 index 00000000..e3f42382 --- /dev/null +++ b/debian/patches/0005-Disable-Sphinx.patch @@ -0,0 +1,20 @@ +From: Gard Spreemann <gspr@nonempty.org> +Date: Wed, 25 Sep 2019 15:28:15 +0200 +Subject: Disable Sphinx. + +--- + src/cmake/modules/GUDHI_third_party_libraries.cmake | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake +index 360a230..bffd2ee 100644 +--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake ++++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake +@@ -124,7 +124,6 @@ if( PYTHONINTERP_FOUND ) + find_python_module("matplotlib") + find_python_module("numpy") + find_python_module("scipy") +- find_python_module("sphinx") + endif() + + if(NOT GUDHI_PYTHON_PATH) diff --git a/debian/patches/0006-Install-Python-module-in-correct-location.patch b/debian/patches/0006-Install-Python-module-in-correct-location.patch new file mode 100644 index 00000000..67999267 --- /dev/null +++ b/debian/patches/0006-Install-Python-module-in-correct-location.patch @@ -0,0 +1,21 @@ +From: Gard Spreemann <gspr@nonempty.org> +Date: Thu, 26 Sep 2019 13:26:22 +0200 +Subject: Install Python module in correct location. + +--- + 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..a999cea 100644 +--- a/src/python/CMakeLists.txt ++++ b/src/python/CMakeLists.txt +@@ -208,7 +208,7 @@ if(PYTHONINTERP_FOUND) + add_custom_target(python ALL DEPENDS gudhi.so + COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests") + +- install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install)") ++ install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} setup.py install --root=${CMAKE_SOURCE_DIR}/debian/tmp --single-version-externally-managed --install-layout=deb WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})") + + # Test examples + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/debian/patches/0007-Move-towards-reproducible-builds.patch b/debian/patches/0007-Move-towards-reproducible-builds.patch new file mode 100644 index 00000000..4c487bab --- /dev/null +++ b/debian/patches/0007-Move-towards-reproducible-builds.patch @@ -0,0 +1,24 @@ +From: Gard Spreemann <gspr@nonempty.org> +Date: Tue, 10 Dec 2019 14:31:47 +0100 +Subject: Move towards reproducible builds. + +This probably does not take us all the way there, and probably breaks +doctest, but since we're not doing sphinx stuff yet anyway, that is ok +for now. +--- + src/python/gudhi/__init__.py.in | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/python/gudhi/__init__.py.in b/src/python/gudhi/__init__.py.in +index 28bab0e..e22dde4 100644 +--- a/src/python/gudhi/__init__.py.in ++++ b/src/python/gudhi/__init__.py.in +@@ -15,7 +15,7 @@ __copyright__ = "Copyright (C) 2016 Inria" + __license__ = "https://gudhi.inria.fr/licensing/" + __version__ = "@GUDHI_VERSION@" + # This variable is used by doctest to find files +-__root_source_dir__ = "@CMAKE_SOURCE_DIR@" ++__root_source_dir__ = "." + __debug_info__ = @GUDHI_PYTHON_DEBUG_INFO@ + + from sys import exc_info diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 00000000..adeb35f7 --- /dev/null +++ b/debian/patches/series @@ -0,0 +1,7 @@ +0001-Disable-tests-that-use-DFSG-deleted-data-files.patch +0002-Use-system-MathJax.patch +0003-Force-linking-against-libatomic-for-parts-that-use-T.patch +0004-Offline-header-for-docs.patch +0005-Disable-Sphinx.patch +0006-Install-Python-module-in-correct-location.patch +0007-Move-towards-reproducible-builds.patch |