From ffa79d8f6a1e0ebdc6e6de362af7a4195a1b63a4 Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Wed, 16 Dec 2020 16:12:00 +0100 Subject: Refresh patches. --- ...le-tests-that-use-DFSG-deleted-data-files.patch | 47 +++++++++++++--------- debian/patches/0005-Disable-Sphinx.patch | 4 +- ...Install-Python-module-in-correct-location.patch | 4 +- .../0007-Move-towards-reproducible-builds.patch | 2 +- 4 files changed, 32 insertions(+), 25 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 index 4b4f24f3..6151ae79 100644 --- 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 @@ -5,16 +5,16 @@ 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/Persistent_cohomology/example/CMakeLists.txt | 12 --------- src/Simplex_tree/example/CMakeLists.txt | 2 -- src/python/CMakeLists.txt | 31 +----------------------- - 5 files changed, 1 insertion(+), 49 deletions(-) + 5 files changed, 1 insertion(+), 57 deletions(-) diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt -index 1667472..37c4759 100644 +index 4b0f467..110212d 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) +@@ -12,14 +12,9 @@ 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 ${CMAKE_CURRENT_BINARY_DIR}/) @@ -28,8 +28,7 @@ index 1667472..37c4759 100644 - "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat.off" - "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat_PCA1") - install(TARGETS CoordGIC DESTINATION bin) - install(TARGETS FuncGIC DESTINATION bin) + endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) diff --git a/src/Nerve_GIC/utilities/CMakeLists.txt b/src/Nerve_GIC/utilities/CMakeLists.txt index 65a08d9..3f16db9 100644 --- a/src/Nerve_GIC/utilities/CMakeLists.txt @@ -50,22 +49,30 @@ index 65a08d9..3f16db9 100644 install(TARGETS Nerve DESTINATION bin) install(TARGETS VoronoiGIC DESTINATION bin) diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt -index 4c08cd6..a7a7bcd 100644 +index c68c652..9a15a89 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt -@@ -28,10 +28,6 @@ add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D CO - "${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 $ - "${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 $ -- "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100") +@@ -33,18 +33,6 @@ if(TARGET Boost::program_options) + "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100") + endif() - install(TARGETS plain_homology DESTINATION bin) - install(TARGETS persistence_from_simple_simplex_tree DESTINATION bin) +-if(TARGET Boost::program_options) +- add_executable(persistence_from_file persistence_from_file.cpp) +- target_link_libraries(persistence_from_file Boost::program_options) +- if (TBB_FOUND) +- target_link_libraries(persistence_from_file ${TBB_LIBRARIES}) +- endif() +- 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") +-endif() +- + if(GMP_FOUND) + if(GMPXX_FOUND) + if(TARGET Boost::program_options) diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt -index a0aabee..5c572f8 100644 +index 73b2c6f..a6dd0b1 100644 --- a/src/Simplex_tree/example/CMakeLists.txt +++ b/src/Simplex_tree/example/CMakeLists.txt @@ -28,8 +28,6 @@ if(GMP_FOUND AND NOT CGAL_VERSION VERSION_LESS 4.11.0) @@ -78,10 +85,10 @@ index a0aabee..5c572f8 100644 endif() diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt -index 4f26481..99b648b 100644 +index 5c1402a..a45e13a 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt -@@ -381,36 +381,7 @@ if(PYTHONINTERP_FOUND) +@@ -386,36 +386,7 @@ if(PYTHONINTERP_FOUND) add_gudhi_py_test(test_bottleneck_distance) endif() diff --git a/debian/patches/0005-Disable-Sphinx.patch b/debian/patches/0005-Disable-Sphinx.patch index 0df79e58..2aee22ff 100644 --- a/debian/patches/0005-Disable-Sphinx.patch +++ b/debian/patches/0005-Disable-Sphinx.patch @@ -7,10 +7,10 @@ Subject: Disable Sphinx. 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 a56a275..11b5b20 100644 +index e156687..aa1c4bb 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake -@@ -178,7 +178,6 @@ if( PYTHONINTERP_FOUND ) +@@ -147,7 +147,6 @@ if( PYTHONINTERP_FOUND ) find_python_module("matplotlib") find_python_module("numpy") find_python_module("scipy") diff --git a/debian/patches/0006-Install-Python-module-in-correct-location.patch b/debian/patches/0006-Install-Python-module-in-correct-location.patch index 0b4a8f64..a395cdd8 100644 --- a/debian/patches/0006-Install-Python-module-in-correct-location.patch +++ b/debian/patches/0006-Install-Python-module-in-correct-location.patch @@ -7,10 +7,10 @@ Subject: Install Python module in correct location. 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt -index 99b648b..162bd27 100644 +index a45e13a..4d56f58 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt -@@ -267,7 +267,7 @@ if(PYTHONINTERP_FOUND) +@@ -274,7 +274,7 @@ 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") diff --git a/debian/patches/0007-Move-towards-reproducible-builds.patch b/debian/patches/0007-Move-towards-reproducible-builds.patch index 7e2f01db..7d6ae95d 100644 --- a/debian/patches/0007-Move-towards-reproducible-builds.patch +++ b/debian/patches/0007-Move-towards-reproducible-builds.patch @@ -9,7 +9,7 @@ but since we're not doing Sphinx stuff yet anyway, that is ok for now. 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/python/gudhi/__init__.py.in b/src/python/gudhi/__init__.py.in -index 79e12fb..991745a 100644 +index 3043201..ef6389e 100644 --- a/src/python/gudhi/__init__.py.in +++ b/src/python/gudhi/__init__.py.in @@ -15,7 +15,7 @@ __copyright__ = "Copyright (C) 2016 Inria" -- cgit v1.2.3