From 7be3bc8f1e1e0881d0a33931ff1123497b479739 Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Fri, 20 Jan 2023 17:03:14 +0100 Subject: Refresh patches, and add patch for Hera 1.0 compatibility --- ...le-tests-that-use-DFSG-deleted-data-files.patch | 101 ++++++++------------- debian/patches/0002-Use-system-MathJax.patch | 4 +- debian/patches/0003-Offline-header-for-docs.patch | 4 +- debian/patches/0005-Support-Hera-1.0.patch | 66 ++++++++++++++ debian/patches/0005-Support-QGLViewer-2.7.patch | 26 ------ debian/patches/series | 2 +- 6 files changed, 107 insertions(+), 96 deletions(-) create mode 100644 debian/patches/0005-Support-Hera-1.0.patch delete mode 100644 debian/patches/0005-Support-QGLViewer-2.7.patch 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 d451e683..af6b0afb 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 @@ -3,86 +3,57 @@ 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/python/CMakeLists.txt | 29 ----------------------------- - 3 files changed, 42 deletions(-) + src/Nerve_GIC/example/CMakeLists.txt | 6 ------ + src/Nerve_GIC/utilities/CMakeLists.txt | 7 ------- + src/python/CMakeLists.txt | 3 --- + 3 files changed, 16 deletions(-) diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt -index 4b0f467..110212d 100644 +index 9faf1f3..bbfa592 100644 --- a/src/Nerve_GIC/example/CMakeLists.txt +++ b/src/Nerve_GIC/example/CMakeLists.txt -@@ -12,14 +12,9 @@ if (NOT CGAL_VERSION VERSION_LESS 4.11.0) +@@ -10,12 +10,6 @@ endif() - # 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 ${CMAKE_CURRENT_BINARY_DIR}/) + # Copy files for not to pollute sources when testing + file(COPY "${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") - - endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) + 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") diff --git a/src/Nerve_GIC/utilities/CMakeLists.txt b/src/Nerve_GIC/utilities/CMakeLists.txt -index 65a08d9..3f16db9 100644 +index 4521a99..e28973f 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() +@@ -10,13 +10,6 @@ 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}/) + 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_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") - install(TARGETS Nerve DESTINATION bin) - install(TARGETS VoronoiGIC DESTINATION bin) + install(TARGETS Nerve DESTINATION bin) + install(TARGETS VoronoiGIC DESTINATION bin) diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt -index 5f32393..02082db 100644 +index 39e2acd..b3f2268 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt -@@ -432,35 +432,6 @@ 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 ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" -- ${PYTHON_EXECUTABLE} "${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 ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" -- ${PYTHON_EXECUTABLE} "${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 ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" -- ${PYTHON_EXECUTABLE} "${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 ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" -- ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py" -- -f human.off -n 700 -v) -- - add_gudhi_py_test(test_cover_complex) +@@ -435,9 +435,6 @@ if(PYTHONINTERP_FOUND) endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) + # 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 ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" diff --git a/debian/patches/0002-Use-system-MathJax.patch b/debian/patches/0002-Use-system-MathJax.patch index 4f8e143c..e5c328ee 100644 --- a/debian/patches/0002-Use-system-MathJax.patch +++ b/debian/patches/0002-Use-system-MathJax.patch @@ -7,10 +7,10 @@ Subject: Use system MathJax. 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Doxyfile.in b/src/Doxyfile.in -index 6e0e033..b2f44d5 100644 +index d5664a4..093aaa5 100644 --- a/src/Doxyfile.in +++ b/src/Doxyfile.in -@@ -1506,7 +1506,7 @@ MATHJAX_FORMAT = HTML-CSS +@@ -1499,7 +1499,7 @@ 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/0003-Offline-header-for-docs.patch b/debian/patches/0003-Offline-header-for-docs.patch index 2ba471d3..91cad23d 100644 --- a/debian/patches/0003-Offline-header-for-docs.patch +++ b/debian/patches/0003-Offline-header-for-docs.patch @@ -7,10 +7,10 @@ Subject: Offline header for docs. 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Doxyfile.in b/src/Doxyfile.in -index b2f44d5..c938635 100644 +index 093aaa5..152041e 100644 --- a/src/Doxyfile.in +++ b/src/Doxyfile.in -@@ -1096,7 +1096,7 @@ HTML_FILE_EXTENSION = .html +@@ -1095,7 +1095,7 @@ 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. diff --git a/debian/patches/0005-Support-Hera-1.0.patch b/debian/patches/0005-Support-Hera-1.0.patch new file mode 100644 index 00000000..de783cb4 --- /dev/null +++ b/debian/patches/0005-Support-Hera-1.0.patch @@ -0,0 +1,66 @@ +From: Gard Spreemann +Date: Fri, 20 Jan 2023 17:02:04 +0100 +Subject: Support Hera 1.0 + +Upstream GUDHI now expects Hera's headers to be organized as in Hera +2.0. This patch restores the old behavior until Hera 2.0 is available +in Debian. +--- + src/Nerve_GIC/include/gudhi/GIC.h | 4 ++-- + src/cmake/modules/GUDHI_submodules.cmake | 2 +- + src/python/gudhi/hera/bottleneck.cc | 2 +- + src/python/gudhi/hera/wasserstein.cc | 2 +- + 4 files changed, 5 insertions(+), 5 deletions(-) + +diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h +index 047fba6..560f7d6 100644 +--- a/src/Nerve_GIC/include/gudhi/GIC.h ++++ b/src/Nerve_GIC/include/gudhi/GIC.h +@@ -20,9 +20,9 @@ + #if __has_include() + # define GUDHI_GIC_USE_CGAL 1 + # include +-#elif __has_include() ++#elif __has_include() + # define GUDHI_GIC_USE_HERA 1 +-# include ++# include + #endif + + #include +diff --git a/src/cmake/modules/GUDHI_submodules.cmake b/src/cmake/modules/GUDHI_submodules.cmake +index 9ede852..cec9390 100644 +--- a/src/cmake/modules/GUDHI_submodules.cmake ++++ b/src/cmake/modules/GUDHI_submodules.cmake +@@ -2,4 +2,4 @@ + set(HERA_INTERNAL_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/include) + set(HERA_INCLUDE_DIR ${HERA_INTERNAL_INCLUDE_DIR} CACHE PATH "Directory where one can find hera/{wasserstein.h,bottleneck.h}") + # since everything is cleanly under include/hera/, there is no harm always including it +-include_directories(${HERA_INCLUDE_DIR}) ++include_directories(${HERA_INCLUDE_DIR}/bottleneck ${HERA_INCLUDE_DIR}/wasserstein) +diff --git a/src/python/gudhi/hera/bottleneck.cc b/src/python/gudhi/hera/bottleneck.cc +index ec461f7..0cb562c 100644 +--- a/src/python/gudhi/hera/bottleneck.cc ++++ b/src/python/gudhi/hera/bottleneck.cc +@@ -16,7 +16,7 @@ + using py::ssize_t; + #endif + +-#include // Hera ++#include // Hera + + double bottleneck_distance(Dgm d1, Dgm d2, double delta) + { +diff --git a/src/python/gudhi/hera/wasserstein.cc b/src/python/gudhi/hera/wasserstein.cc +index 3516352..e1bb1d7 100644 +--- a/src/python/gudhi/hera/wasserstein.cc ++++ b/src/python/gudhi/hera/wasserstein.cc +@@ -16,7 +16,7 @@ + using py::ssize_t; + #endif + +-#include // Hera ++#include // Hera + + double wasserstein_distance( + Dgm d1, Dgm d2, diff --git a/debian/patches/0005-Support-QGLViewer-2.7.patch b/debian/patches/0005-Support-QGLViewer-2.7.patch deleted file mode 100644 index 2f367d5f..00000000 --- a/debian/patches/0005-Support-QGLViewer-2.7.patch +++ /dev/null @@ -1,26 +0,0 @@ -From: Gard Spreemann -Date: Mon, 14 Nov 2022 17:28:23 +0100 -Subject: Support QGLViewer >=2.7 - -This is Marc Glisse's commit 1e71120bdacb6f5ec4c90fb4c1365f76ecea7ff9 -proposed upstream. ---- - src/GudhUI/view/Viewer.cpp | 4 ++++ - 1 file changed, 4 insertions(+) - -diff --git a/src/GudhUI/view/Viewer.cpp b/src/GudhUI/view/Viewer.cpp -index 6b17c83..2c00f86 100644 ---- a/src/GudhUI/view/Viewer.cpp -+++ b/src/GudhUI/view/Viewer.cpp -@@ -31,7 +31,11 @@ void Viewer::set_bounding_box(const Point_3 & lower_left, const Point_3 & upper_ - } - - void Viewer::update_GL() { -+#if QGLVIEWER_VERSION >= 0x020700 -+ this->update(); -+#else - this->updateGL(); -+#endif - } - - void Viewer::init_scene() { diff --git a/debian/patches/series b/debian/patches/series index 3f3da71a..0019c6f4 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -2,4 +2,4 @@ 0002-Use-system-MathJax.patch 0003-Offline-header-for-docs.patch 0004-Disable-Sphinx.patch -0005-Support-QGLViewer-2.7.patch +0005-Support-Hera-1.0.patch -- cgit v1.2.3