Refresh patches, and add patch for Hera 1.0 compatibility

1 files changed, 36 insertions, 65 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 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 $<TARGET_FILE:CoordGIC>
-       "${CMAKE_CURRENT_BINARY_DIR}/tore3D_1307.off" "0")
- 
--  add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $<TARGET_FILE:FuncGIC>
--      "${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 $<TARGET_FILE:CoordGIC>
+     "${CMAKE_CURRENT_BINARY_DIR}/tore3D_1307.off" "0")
+-
+-add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $<TARGET_FILE:FuncGIC>
+-    "${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 $<TARGET_FILE:Nerve>
--      "human.off" "2" "10" "0.3")
+-add_test(NAME Nerve_GIC_utilities_nerve COMMAND $<TARGET_FILE:Nerve>
+-    "human.off" "2" "10" "0.3")
 -
--  add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC>
--      "human.off" "100")
+-add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC>
+-    "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}"