Rebase patches

1 files changed, 13 insertions, 53 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 6151ae79..82abd0ed 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
@@ -3,12 +3,10 @@ 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/Persistent_cohomology/example/CMakeLists.txt | 12 ---------
- src/Simplex_tree/example/CMakeLists.txt          |  2 --
- src/python/CMakeLists.txt                        | 31 +-----------------------
- 5 files changed, 1 insertion(+), 57 deletions(-)
+ src/Nerve_GIC/example/CMakeLists.txt   |  5 -----
+ src/Nerve_GIC/utilities/CMakeLists.txt |  8 --------
+ src/python/CMakeLists.txt              | 29 -----------------------------
+ 3 files changed, 42 deletions(-)
 
 diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt
 index 4b0f467..110212d 100644
@@ -48,49 +46,13 @@ index 65a08d9..3f16db9 100644
  
    install(TARGETS Nerve DESTINATION bin)
    install(TARGETS VoronoiGIC DESTINATION bin)
-diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
-index c68c652..9a15a89 100644
---- a/src/Persistent_cohomology/example/CMakeLists.txt
-+++ b/src/Persistent_cohomology/example/CMakeLists.txt
-@@ -33,18 +33,6 @@ if(TARGET Boost::program_options)
-       "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100")
- endif()
- 
--if(TARGET Boost::program_options)
--  add_executable(persistence_from_file persistence_from_file.cpp)
--  target_link_libraries(persistence_from_file Boost::program_options)
--  if (TBB_FOUND)
--    target_link_libraries(persistence_from_file ${TBB_LIBRARIES})
--  endif()
--  add_test(NAME Persistent_cohomology_example_from_file_3_2_0 COMMAND $<TARGET_FILE:persistence_from_file>
--      "${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")
--endif()
--
- if(GMP_FOUND)
-   if(GMPXX_FOUND)
-     if(TARGET Boost::program_options)
-diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt
-index 73b2c6f..a6dd0b1 100644
---- a/src/Simplex_tree/example/CMakeLists.txt
-+++ b/src/Simplex_tree/example/CMakeLists.txt
-@@ -28,8 +28,6 @@ if(GMP_FOUND AND NOT CGAL_VERSION VERSION_LESS 4.11.0)
-   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")
- 
- endif()
- 
 diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
-index 5c1402a..a45e13a 100644
+index 1314b44..7edac67 100644
 --- a/src/python/CMakeLists.txt
 +++ b/src/python/CMakeLists.txt
-@@ -386,36 +386,7 @@ if(PYTHONINTERP_FOUND)
-         add_gudhi_py_test(test_bottleneck_distance)
-       endif()
+@@ -414,35 +414,6 @@ 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}/)
@@ -98,31 +60,29 @@ index 5c1402a..a45e13a 100644
 -      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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${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)
-+      
+       add_gudhi_py_test(test_cover_complex)
      endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
  
-     if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)