From eebfa6562adc8b910611261ba3163a45b1b66216 Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Wed, 17 Aug 2022 15:15:22 +0200 Subject: Refresh patches --- ...le-tests-that-use-DFSG-deleted-data-files.patch | 4 +- debian/patches/0002-Use-system-MathJax.patch | 6 +- debian/patches/0003-Offline-header-for-docs.patch | 4 +- debian/patches/0004-Disable-Sphinx.patch | 39 ++++++++--- ...ocess-the-entire-source-tree-with-Doxygen.patch | 4 +- debian/patches/0006-CGAL-5.5-compatibility.patch | 78 +++------------------- 6 files changed, 48 insertions(+), 87 deletions(-) (limited to 'debian') 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 82abd0ed..d451e683 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 @@ -47,10 +47,10 @@ index 65a08d9..3f16db9 100644 install(TARGETS Nerve DESTINATION bin) install(TARGETS VoronoiGIC DESTINATION bin) diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt -index 1314b44..7edac67 100644 +index 5f32393..02082db 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt -@@ -414,35 +414,6 @@ if(PYTHONINTERP_FOUND) +@@ -432,35 +432,6 @@ if(PYTHONINTERP_FOUND) add_gudhi_py_test(test_bottleneck_distance) diff --git a/debian/patches/0002-Use-system-MathJax.patch b/debian/patches/0002-Use-system-MathJax.patch index 8123a42d..4f8e143c 100644 --- a/debian/patches/0002-Use-system-MathJax.patch +++ b/debian/patches/0002-Use-system-MathJax.patch @@ -7,14 +7,14 @@ Subject: Use system MathJax. 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Doxyfile.in b/src/Doxyfile.in -index ae8db1a..9f697a5 100644 +index 6e0e033..b2f44d5 100644 --- a/src/Doxyfile.in +++ b/src/Doxyfile.in -@@ -1526,7 +1526,7 @@ MATHJAX_FORMAT = HTML-CSS +@@ -1506,7 +1506,7 @@ 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 = +MATHJAX_RELPATH = /usr/share/javascript/mathjax # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax diff --git a/debian/patches/0003-Offline-header-for-docs.patch b/debian/patches/0003-Offline-header-for-docs.patch index 01b58c29..2ba471d3 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 9f697a5..4b6d792 100644 +index b2f44d5..c938635 100644 --- a/src/Doxyfile.in +++ b/src/Doxyfile.in -@@ -1127,7 +1127,7 @@ HTML_FILE_EXTENSION = .html +@@ -1096,7 +1096,7 @@ 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/0004-Disable-Sphinx.patch b/debian/patches/0004-Disable-Sphinx.patch index de66bbfb..9d22ec9d 100644 --- a/debian/patches/0004-Disable-Sphinx.patch +++ b/debian/patches/0004-Disable-Sphinx.patch @@ -3,18 +3,35 @@ Date: Tue, 21 Jan 2020 10:36:48 +0100 Subject: Disable Sphinx. --- - src/cmake/modules/GUDHI_third_party_libraries.cmake | 1 - - 1 file changed, 1 deletion(-) + src/cmake/modules/GUDHI_third_party_libraries.cmake | 12 ------------ + 1 file changed, 12 deletions(-) diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake -index 21c9d47..d22697c 100644 +index 2cf6787..e36e22b 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake -@@ -148,7 +148,6 @@ if( PYTHONINTERP_FOUND ) - find_python_module("matplotlib") - find_python_module("numpy") - find_python_module("scipy") -- find_python_module("sphinx") - find_python_module("sklearn") - find_python_module("ot") - find_python_module("pybind11") +@@ -151,7 +151,6 @@ if (WITH_GUDHI_PYTHON) + find_python_module("matplotlib") + find_python_module("numpy") + find_python_module("scipy") +- find_python_module("sphinx") + find_python_module("sklearn") + find_python_module("ot") + find_python_module("pybind11") +@@ -171,16 +170,5 @@ if (WITH_GUDHI_PYTHON) + option(WITH_GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS "Build with setting runtime_library_dirs. Useful when setting rpath is not allowed" ON) + + if(PYTHONINTERP_FOUND AND CYTHON_FOUND) +- if(SPHINX_FOUND) +- # Documentation generation is available through sphinx +- find_program( SPHINX_PATH sphinx-build ) +- +- if(NOT SPHINX_PATH) +- if(PYTHON_VERSION_MAJOR EQUAL 3) +- # In Python3, just hack sphinx-build if it does not exist +- set(SPHINX_PATH "${PYTHON_EXECUTABLE}" "-m" "sphinx.cmd.build") +- endif(PYTHON_VERSION_MAJOR EQUAL 3) +- endif(NOT SPHINX_PATH) +- endif(SPHINX_FOUND) + endif(PYTHONINTERP_FOUND AND CYTHON_FOUND) + endif (WITH_GUDHI_PYTHON) diff --git a/debian/patches/0005-Don-t-process-the-entire-source-tree-with-Doxygen.patch b/debian/patches/0005-Don-t-process-the-entire-source-tree-with-Doxygen.patch index bb9c622d..4e15991b 100644 --- a/debian/patches/0005-Don-t-process-the-entire-source-tree-with-Doxygen.patch +++ b/debian/patches/0005-Don-t-process-the-entire-source-tree-with-Doxygen.patch @@ -7,10 +7,10 @@ Subject: Don't process the entire source tree with Doxygen 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Doxyfile.in b/src/Doxyfile.in -index 4b6d792..8b38967 100644 +index c938635..f5b3555 100644 --- a/src/Doxyfile.in +++ b/src/Doxyfile.in -@@ -783,7 +783,7 @@ WARN_LOGFILE = +@@ -778,7 +778,7 @@ WARN_LOGFILE = doxygen.log # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING # Note: If this tag is empty the current directory is searched. diff --git a/debian/patches/0006-CGAL-5.5-compatibility.patch b/debian/patches/0006-CGAL-5.5-compatibility.patch index a5d28944..949b5e4d 100644 --- a/debian/patches/0006-CGAL-5.5-compatibility.patch +++ b/debian/patches/0006-CGAL-5.5-compatibility.patch @@ -2,77 +2,21 @@ From: Vincent Rouvreau Date: Tue, 9 Aug 2022 16:06:06 +0200 Subject: CGAL 5.5 compatibility -Based on upstream commits - - dc7a0aed53d7b74580ed5625293e27cacd452c34 - 71cbf8f35814d247fe7421c079a6ea78da2282f4 - -with modifications from discussion in - - https://github.com/CGAL/cgal/issues/6799 +Based on discussion in https://github.com/CGAL/cgal/issues/6799 --- - .../include/gudhi/Skeleton_blocker_contractor.h | 21 ++++++++++++++++----- - 1 file changed, 16 insertions(+), 5 deletions(-) + src/Contraction/include/gudhi/Skeleton_blocker_contractor.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h -index a0d9f2b..d510043 100644 +index 6911ca2..7910e7b 100644 --- a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h +++ b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h -@@ -171,8 +171,13 @@ typename GeometricSimplifiableComplex::Vertex_handle> { - Self const* algorithm_; - }; - -+#if CGAL_VERSION_NR < 1050500000 +@@ -174,7 +174,7 @@ typename GeometricSimplifiableComplex::Vertex_handle> { + #if CGAL_VERSION_NR < 1050500000 typedef CGAL::Modifiable_priority_queue PQ; -- typedef typename PQ::handle pq_handle; -+#else + #else +- typedef CGAL::Modifiable_priority_queue PQ; + typedef CGAL::Modifiable_priority_queue PQ; -+#endif -+ -+ typedef bool pq_handle; - - - // An Edge_data is associated with EVERY edge in the complex (collapsible or not). -@@ -196,7 +201,7 @@ typename GeometricSimplifiableComplex::Vertex_handle> { - } - - bool is_in_PQ() const { -- return PQHandle_ != PQ::null_handle(); -+ return PQHandle_ != false; - } - - void set_PQ_handle(pq_handle h) { -@@ -204,7 +209,7 @@ typename GeometricSimplifiableComplex::Vertex_handle> { - } - - void reset_PQ_handle() { -- PQHandle_ = PQ::null_handle(); -+ PQHandle_ = false; - } - - private: -@@ -238,16 +243,22 @@ typename GeometricSimplifiableComplex::Vertex_handle> { - } - - void insert_in_PQ(Edge_handle edge, Edge_data& data) { -- data.set_PQ_handle(heap_PQ_->push(edge)); -+ heap_PQ_->push(edge); -+ data.set_PQ_handle(true); - ++current_num_edges_heap_; - } - - void update_in_PQ(Edge_handle edge, Edge_data& data) { -+#if CGAL_VERSION_NR < 1050500000 - data.set_PQ_handle(heap_PQ_->update(edge, data.PQ_handle())); -+#else -+ heap_PQ_->update(edge); -+#endif - } - - void remove_from_PQ(Edge_handle edge, Edge_data& data) { -- data.set_PQ_handle(heap_PQ_->erase(edge, data.PQ_handle())); -+ heap_PQ_->erase(edge); -+ data.set_PQ_handle(false); - --current_num_edges_heap_; - } - + #endif + + typedef bool pq_handle; -- cgit v1.2.3