Refresh patches

6 files changed, 48 insertions, 87 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 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 <vincent.rouvreau@inria.fr>
 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<Edge_handle, Compare_cost, Undirected_edge_id> PQ;
--  typedef typename PQ::handle pq_handle;
-+#else
+ #else
+-  typedef CGAL::Modifiable_priority_queue<Edge_handle, Compare_cost, Undirected_edge_id, CGAL::CGAL_BOOST_PENDING_RELAXED_HEAP> PQ;
 +  typedef CGAL::Modifiable_priority_queue<Edge_handle, Compare_cost, Undirected_edge_id, CGAL::CGAL_BOOST_PAIRING_HEAP> 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;