Rebase patches.

5 files changed, 57 insertions, 74 deletions

diff --git a/debian/patches/0001-Disable-some-tests-that-uncleanly-write-outside-of-t.patch b/debian/patches/0001-Disable-some-tests-that-uncleanly-write-outside-of-t.patch
deleted file mode 100644
index c4b39f01..00000000
--- a/debian/patches/0001-Disable-some-tests-that-uncleanly-write-outside-of-t.patch
+++ /dev/null
@@ -1,51 +0,0 @@
-From d453ab3742d87c3c1e985db3899f1085cd57829a Mon Sep 17 00:00:00 2001
-From: Gard Spreemann <gspreemann@gmail.com>
-Date: Fri, 21 Apr 2017 11:55:21 +0200
-Subject: [PATCH 1/2] Disable some tests that uncleanly write outside of the
- build directory.
-
----
- example/Bitmap_cubical_complex/CMakeLists.txt | 21 +++++++++++----------
- 1 file changed, 11 insertions(+), 10 deletions(-)
-
-diff --git a/example/Bitmap_cubical_complex/CMakeLists.txt b/example/Bitmap_cubical_complex/CMakeLists.txt
-index 241a11e..82fd911 100644
---- a/example/Bitmap_cubical_complex/CMakeLists.txt
-+++ b/example/Bitmap_cubical_complex/CMakeLists.txt
-@@ -7,11 +7,11 @@ if (TBB_FOUND)
-   target_link_libraries(Bitmap_cubical_complex ${TBB_LIBRARIES})
- endif()
- 
--add_test(NAME Bitmap_cubical_complex_example_persistence_one_sphere COMMAND $<TARGET_FILE:Bitmap_cubical_complex>
--    "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt")
-+#add_test(NAME Bitmap_cubical_complex_example_persistence_one_sphere COMMAND $<TARGET_FILE:Bitmap_cubical_complex>
-+#    "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt")
- 
--add_test(NAME Bitmap_cubical_complex_example_persistence_two_sphere COMMAND $<TARGET_FILE:Bitmap_cubical_complex>
--    "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt")
-+#add_test(NAME Bitmap_cubical_complex_example_persistence_two_sphere COMMAND $<TARGET_FILE:Bitmap_cubical_complex>
-+#    "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt")
- 
- add_executable ( Random_bitmap_cubical_complex Random_bitmap_cubical_complex.cpp )
- target_link_libraries(Random_bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})
-@@ -27,10 +27,11 @@ if (TBB_FOUND)
-   target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${TBB_LIBRARIES})
- endif()
- 
--add_test(NAME Bitmap_cubical_complex_example_periodic_boundary_conditions_2d_torus
--    COMMAND $<TARGET_FILE:Bitmap_cubical_complex_periodic_boundary_conditions>
--    "${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt")
-+#add_test(NAME Bitmap_cubical_complex_example_periodic_boundary_conditions_2d_torus
-+#    COMMAND $<TARGET_FILE:Bitmap_cubical_complex_periodic_boundary_conditions>
-+#    "${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt")
- 
--add_test(NAME Bitmap_cubical_complex_example_periodic_boundary_conditions_3d_torus
--    COMMAND $<TARGET_FILE:Bitmap_cubical_complex_periodic_boundary_conditions>
--    "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt")
-+#add_test(NAME Bitmap_cubical_complex_example_periodic_boundary_conditions_3d_torus
-+#    COMMAND $<TARGET_FILE:Bitmap_cubical_complex_periodic_boundary_conditions>
-+#    "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt")
-+ 
--- 
-2.11.0
-
diff --git a/debian/patches/0003-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 431c6a5b..1b76f052 100644
--- a/debian/patches/0003-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 719513ad96cf59e787b0d4eb96173feb527ea4ea Mon Sep 17 00:00:00 2001
+From 3a8816f0a83e92307c39cd9cfa85ea6e67df48eb Mon Sep 17 00:00:00 2001
 From: Gard Spreemann <gspreemann@gmail.com>
-Date: Thu, 27 Apr 2017 17:39:39 +0200
-Subject: [PATCH 3/3] Force Python 3 detection to avoid mixing 2 and 3.
+Date: Mon, 9 Oct 2017 11:46:06 +0200
+Subject: [PATCH 1/3] 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
new file mode 100644
index 00000000..76bb686e
--- /dev/null
+++ b/debian/patches/0002-Disable-the-Sphinx-test.-We-re-not-using-it-as-it-re.patch
@@ -0,0 +1,32 @@
+From c167dcc8b48db2670f132d579ca68984938c1d5a Mon Sep 17 00:00:00 2001
+From: Gard Spreemann <gspreemann@gmail.com>
+Date: Mon, 9 Oct 2017 12:05:01 +0200
+Subject: [PATCH 2/3] Disable the Sphinx test. We're not using it, as it
+ requires the Sphinx bibtex module (#800358).
+
+---
+ cython/CMakeLists.txt | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
+index afca9d6..ec3cb8f 100644
+--- a/cython/CMakeLists.txt
++++ b/cython/CMakeLists.txt
+@@ -305,10 +305,10 @@ if(CYTHON_FOUND)
+         DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+         COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
+ 
+-    add_test(NAME sphinx_py_test
+-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+-             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
++#    add_test(NAME sphinx_py_test
++#             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
++#             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
++#             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
+ 
+   endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+ endif(CYTHON_FOUND)
+-- 
+2.11.0
+
diff --git a/debian/patches/0002-Disable-tests-that-use-DFSG-deleted-data-files.patch b/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch
index 78a83a08..279c6091 100644
--- a/debian/patches/0002-Disable-tests-that-use-DFSG-deleted-data-files.patch
+++ b/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch
@@ -1,7 +1,7 @@
-From d20e6c35c1365da5b13c771fd8bf2f3a9902391e Mon Sep 17 00:00:00 2001
+From c80f7efa2fbdc3152fde015505be0e6b64074c49 Mon Sep 17 00:00:00 2001
 From: Gard Spreemann <gspreemann@gmail.com>
-Date: Wed, 26 Apr 2017 13:37:46 +0200
-Subject: [PATCH 2/2] Disable tests that use DFSG-deleted data files.
+Date: Mon, 9 Oct 2017 14:15:02 +0200
+Subject: [PATCH 3/3] Disable tests that use DFSG-deleted data files.
 
 ---
  example/Persistent_cohomology/CMakeLists.txt | 8 ++++----
@@ -10,10 +10,10 @@ Subject: [PATCH 2/2] Disable tests that use DFSG-deleted data files.
  3 files changed, 8 insertions(+), 8 deletions(-)
 
 diff --git a/example/Persistent_cohomology/CMakeLists.txt b/example/Persistent_cohomology/CMakeLists.txt
-index 3c45e79..abd71a5 100644
+index f47de4c..8f11ea0 100644
 --- a/example/Persistent_cohomology/CMakeLists.txt
 +++ b/example/Persistent_cohomology/CMakeLists.txt
-@@ -43,10 +43,10 @@ add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D CO
+@@ -41,10 +41,10 @@ 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 $<TARGET_FILE:rips_persistence_via_boundary_matrix>
      "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100")
@@ -25,37 +25,39 @@ index 3c45e79..abd71a5 100644
 +#    "${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 $<TARGET_FILE:persistence_from_file>
 +#    "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100")
-    
- if(GMP_FOUND)
-    if(GMPXX_FOUND)
+ 
+ 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 b1ea98d..3acf6f0 100644
+index e22cc92..99da80f 100644
 --- a/example/Simplex_tree/CMakeLists.txt
 +++ b/example/Simplex_tree/CMakeLists.txt
-@@ -27,6 +27,6 @@ if(GMP_FOUND AND CGAL_FOUND)
+@@ -30,8 +30,8 @@ if(GMP_FOUND AND CGAL_FOUND)
    if (TBB_FOUND)
      target_link_libraries(Simplex_tree_example_alpha_shapes_3_from_off ${TBB_LIBRARIES})
    endif()
 -  add_test(NAME Simplex_tree_example_alpha_shapes_3_from_off COMMAND $<TARGET_FILE:Simplex_tree_example_alpha_shapes_3_from_off>
 -      "${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off")
-+  #add_test(NAME Simplex_tree_example_alpha_shapes_3_from_off COMMAND $<TARGET_FILE:Simplex_tree_example_alpha_shapes_3_from_off>
-+  #    "${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off")
- endif()
++#  add_test(NAME Simplex_tree_example_alpha_shapes_3_from_off COMMAND $<TARGET_FILE:Simplex_tree_example_alpha_shapes_3_from_off>
++#      "${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off")
+ 
+   install(TARGETS Simplex_tree_example_alpha_shapes_3_from_off DESTINATION bin)
+ 
 diff --git a/example/common/CMakeLists.txt b/example/common/CMakeLists.txt
-index d5311b1..91ab206 100644
+index afe865d..2ad4a64 100644
 --- a/example/common/CMakeLists.txt
 +++ b/example/common/CMakeLists.txt
 @@ -3,8 +3,8 @@ project(Common_examples)
  
  add_executable ( vector_double_off_reader example_vector_double_points_off_reader.cpp )
- target_link_libraries(vector_double_off_reader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+ target_link_libraries(vector_double_off_reader ${CGAL_LIBRARY})
 -add_test(NAME Common_example_vector_double_off_reader COMMAND $<TARGET_FILE:vector_double_off_reader>
 -    "${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off")
 +#add_test(NAME Common_example_vector_double_off_reader COMMAND $<TARGET_FILE:vector_double_off_reader>
 +#    "${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off")
  
- if(CGAL_FOUND)
-   add_executable ( cgal_3D_off_reader example_CGAL_3D_points_off_reader.cpp )
+ install(TARGETS vector_double_off_reader DESTINATION bin)
+ 
 -- 
 2.11.0
 
diff --git a/debian/patches/series b/debian/patches/series
index d0f9780d..e40c26b6 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,3 @@
-0001-Disable-some-tests-that-uncleanly-write-outside-of-t.patch
-0002-Disable-tests-that-use-DFSG-deleted-data-files.patch
-0003-Force-Python-3-detection-to-avoid-mixing-2-and-3.patch
+0001-Force-Python-3-detection-to-avoid-mixing-2-and-3.patch
+0002-Disable-the-Sphinx-test.-We-re-not-using-it-as-it-re.patch
+0003-Disable-tests-that-use-DFSG-deleted-data-files.patch