From 0c169783d8d637f9cfcdd4527de0d9d7563cf271 Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Mon, 5 Feb 2018 10:27:17 +0100 Subject: Refresh patches. --- ...ython-3-detection-to-avoid-mixing-2-and-3.patch | 4 +- ...-Sphinx-test.-We-re-not-using-it-as-it-re.patch | 4 +- ...le-tests-that-use-DFSG-deleted-data-files.patch | 68 ++++++++++++++++++---- debian/patches/0004-Use-system-MathJax.patch | 8 +-- ...untime_library_dirs-for-the-Python-extens.patch | 6 +- 5 files changed, 69 insertions(+), 21 deletions(-) (limited to 'debian/patches') 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 index b6e05ed7..ba76ed11 100644 --- 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 @@ -1,7 +1,7 @@ -From e92363ab8125cff24a9c2ef5eec159ff09afc381 Mon Sep 17 00:00:00 2001 +From 976e231e80eeb59c27f2389fb9ee70030c56cb44 Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Mon, 9 Oct 2017 11:46:06 +0200 -Subject: [PATCH 1/4] Force Python 3 detection to avoid mixing 2 and 3. +Subject: [PATCH 1/5] Force Python 3 detection to avoid mixing 2 and 3. --- cmake/modules/FindCython.cmake | 6 +++--- 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 index 2eb76f06..b532ab10 100644 --- 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 @@ -1,7 +1,7 @@ -From 2511e115a28311263e7ed85e98296c6af12ea960 Mon Sep 17 00:00:00 2001 +From 598ac8ccc13024583e51f25559cbe7eaf059188e Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Mon, 9 Oct 2017 12:05:01 +0200 -Subject: [PATCH 2/4] Disable the Sphinx test. We're not using it, as it +Subject: [PATCH 2/5] Disable the Sphinx test. We're not using it, as it requires the Sphinx bibtex module (#800358). --- 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 index eade3da7..54c13639 100644 --- 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 @@ -1,19 +1,45 @@ -From f31347031ea99c60d11064ec28bc27805b5c28b9 Mon Sep 17 00:00:00 2001 +From 9218bee33900e1e203991607e038f029a2216c3c Mon Sep 17 00:00:00 2001 From: Gard Spreemann -Date: Mon, 9 Oct 2017 14:15:02 +0200 -Subject: [PATCH 3/4] Disable tests that use DFSG-deleted data files. +Date: Mon, 5 Feb 2018 10:15:40 +0100 +Subject: [PATCH 3/5] 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(-) + example/Nerve_GIC/CMakeLists.txt | 10 +++++----- + example/Persistent_cohomology/CMakeLists.txt | 8 ++++---- + example/Simplex_tree/CMakeLists.txt | 4 ++-- + example/common/CMakeLists.txt | 4 ++-- + utilities/Nerve_GIC/CMakeLists.txt | 10 +++++----- + 5 files changed, 18 insertions(+), 18 deletions(-) +diff --git a/example/Nerve_GIC/CMakeLists.txt b/example/Nerve_GIC/CMakeLists.txt +index f262692..825974c 100644 +--- a/example/Nerve_GIC/CMakeLists.txt ++++ b/example/Nerve_GIC/CMakeLists.txt +@@ -13,14 +13,14 @@ 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 ${CMAKE_CURRENT_BINARY_DIR}/) ++ #file(COPY "${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 $ + "tore3D_1307.off" "0") + +- add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $ +- "lucky_cat.off" +- "lucky_cat_PCA1") ++ #add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $ ++ # "lucky_cat.off" ++ # "lucky_cat_PCA1") + + endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/example/Persistent_cohomology/CMakeLists.txt b/example/Persistent_cohomology/CMakeLists.txt -index f47de4c..8f11ea0 100644 +index 18e2913..e2dca6d 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 +@@ -29,10 +29,10 @@ 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 $ "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100") @@ -29,7 +55,7 @@ index f47de4c..8f11ea0 100644 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 +index b33b2d0..1cba524 100644 --- a/example/Simplex_tree/CMakeLists.txt +++ b/example/Simplex_tree/CMakeLists.txt @@ -30,8 +30,8 @@ if(GMP_FOUND AND CGAL_FOUND) @@ -58,6 +84,28 @@ index afe865d..2ad4a64 100644 install(TARGETS vector_double_off_reader DESTINATION bin) +diff --git a/utilities/Nerve_GIC/CMakeLists.txt b/utilities/Nerve_GIC/CMakeLists.txt +index 7762c8a..c41898b 100644 +--- a/utilities/Nerve_GIC/CMakeLists.txt ++++ b/utilities/Nerve_GIC/CMakeLists.txt +@@ -13,12 +13,12 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + + 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 ${CMAKE_CURRENT_BINARY_DIR}/) ++ #file(COPY "${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_nerve COMMAND $ ++ # "human.off" "2" "10" "0.3") + +- add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $ +- "human.off" "100") ++ #add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $ ++ # "human.off" "100") + + endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) -- 2.11.0 diff --git a/debian/patches/0004-Use-system-MathJax.patch b/debian/patches/0004-Use-system-MathJax.patch index 916d23b9..98510981 100644 --- a/debian/patches/0004-Use-system-MathJax.patch +++ b/debian/patches/0004-Use-system-MathJax.patch @@ -1,17 +1,17 @@ -From 46fdbaf1a91c320d7f731d061ef6d8d6da73232a Mon Sep 17 00:00:00 2001 +From 1228db48dd680c1baf20fdd9b5b99665adf8f212 Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Mon, 9 Oct 2017 16:06:36 +0200 -Subject: [PATCH 4/4] Use system MathJax. +Subject: [PATCH 4/5] Use system MathJax. --- Doxyfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Doxyfile b/Doxyfile -index 0ef81e5..51df82e 100644 +index f1981e2..991645b 100644 --- a/Doxyfile +++ b/Doxyfile -@@ -1450,7 +1450,7 @@ MATHJAX_FORMAT = HTML-CSS +@@ -1453,7 +1453,7 @@ 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. 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 index c5677149..ace45b46 100644 --- 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 @@ -1,7 +1,7 @@ -From 2dfc0e89fdf40fe474ef0ec2018fe06e5eb786d5 Mon Sep 17 00:00:00 2001 +From 8beaad20e6d61f9d2253ee1b679fe2feafff9bdc Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Mon, 16 Oct 2017 13:46:22 +0200 -Subject: [PATCH] Don't set runtime_library_dirs for the Python extension. +Subject: [PATCH 5/5] Don't set runtime_library_dirs for the Python extension. Avoid RPATH in the shared object. --- @@ -9,7 +9,7 @@ Subject: [PATCH] Don't set runtime_library_dirs for the Python extension. 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cython/setup.py.in b/cython/setup.py.in -index fefa36b..18d03ad 100644 +index c767e93..d00f65a 100644 --- a/cython/setup.py.in +++ b/cython/setup.py.in @@ -36,7 +36,7 @@ gudhi = Extension( -- cgit v1.2.3