From e1138e5af8b13c2c543016df480d5d9db711e2ff Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Mon, 9 Oct 2017 11:47:26 +0200 Subject: Rebase patches. --- ...e-tests-that-uncleanly-write-outside-of-t.patch | 51 ------------------ ...ython-3-detection-to-avoid-mixing-2-and-3.patch | 36 +++++++++++++ ...le-tests-that-use-DFSG-deleted-data-files.patch | 61 --------------------- ...-Sphinx-test.-We-re-not-using-it-as-it-re.patch | 32 +++++++++++ ...le-tests-that-use-DFSG-deleted-data-files.patch | 63 ++++++++++++++++++++++ ...ython-3-detection-to-avoid-mixing-2-and-3.patch | 36 ------------- debian/patches/series | 6 +-- 7 files changed, 134 insertions(+), 151 deletions(-) delete mode 100644 debian/patches/0001-Disable-some-tests-that-uncleanly-write-outside-of-t.patch create mode 100644 debian/patches/0001-Force-Python-3-detection-to-avoid-mixing-2-and-3.patch delete mode 100644 debian/patches/0002-Disable-tests-that-use-DFSG-deleted-data-files.patch create mode 100644 debian/patches/0002-Disable-the-Sphinx-test.-We-re-not-using-it-as-it-re.patch create mode 100644 debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch delete mode 100644 debian/patches/0003-Force-Python-3-detection-to-avoid-mixing-2-and-3.patch (limited to 'debian') 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 -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 $ -- "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt") -+#add_test(NAME Bitmap_cubical_complex_example_persistence_one_sphere COMMAND $ -+# "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt") - --add_test(NAME Bitmap_cubical_complex_example_persistence_two_sphere COMMAND $ -- "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt") -+#add_test(NAME Bitmap_cubical_complex_example_persistence_two_sphere COMMAND $ -+# "${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 $ -- "${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt") -+#add_test(NAME Bitmap_cubical_complex_example_periodic_boundary_conditions_2d_torus -+# COMMAND $ -+# "${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt") - --add_test(NAME Bitmap_cubical_complex_example_periodic_boundary_conditions_3d_torus -- COMMAND $ -- "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt") -+#add_test(NAME Bitmap_cubical_complex_example_periodic_boundary_conditions_3d_torus -+# COMMAND $ -+# "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt") -+ --- -2.11.0 - diff --git a/debian/patches/0001-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 new file mode 100644 index 00000000..1b76f052 --- /dev/null +++ b/debian/patches/0001-Force-Python-3-detection-to-avoid-mixing-2-and-3.patch @@ -0,0 +1,36 @@ +From 3a8816f0a83e92307c39cd9cfa85ea6e67df48eb Mon Sep 17 00:00:00 2001 +From: Gard Spreemann +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 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/cmake/modules/FindCython.cmake b/cmake/modules/FindCython.cmake +index 04aed1f..f3a5b7b 100644 +--- a/cmake/modules/FindCython.cmake ++++ b/cmake/modules/FindCython.cmake +@@ -24,16 +24,16 @@ + + # Use the Cython executable that lives next to the Python executable + # if it is a local installation. +-find_package( PythonInterp ) ++find_package( PythonInterp 3 ) + if( PYTHONINTERP_FOUND ) + get_filename_component( _python_path ${PYTHON_EXECUTABLE} PATH ) + find_program( CYTHON_EXECUTABLE +- NAMES cython cython.bat cython3 ++ NAMES cython3 + HINTS ${_python_path} + ) + else() + find_program( CYTHON_EXECUTABLE +- NAMES cython cython.bat cython3 ++ NAMES cython3 + ) + endif() + +-- +2.11.0 + diff --git a/debian/patches/0002-Disable-tests-that-use-DFSG-deleted-data-files.patch b/debian/patches/0002-Disable-tests-that-use-DFSG-deleted-data-files.patch deleted file mode 100644 index 78a83a08..00000000 --- a/debian/patches/0002-Disable-tests-that-use-DFSG-deleted-data-files.patch +++ /dev/null @@ -1,61 +0,0 @@ -From d20e6c35c1365da5b13c771fd8bf2f3a9902391e Mon Sep 17 00:00:00 2001 -From: Gard Spreemann -Date: Wed, 26 Apr 2017 13:37:46 +0200 -Subject: [PATCH 2/2] Disable tests that use DFSG-deleted data files. - ---- - example/Persistent_cohomology/CMakeLists.txt | 8 ++++---- - example/Simplex_tree/CMakeLists.txt | 4 ++-- - example/common/CMakeLists.txt | 4 ++-- - 3 files changed, 8 insertions(+), 8 deletions(-) - -diff --git a/example/Persistent_cohomology/CMakeLists.txt b/example/Persistent_cohomology/CMakeLists.txt -index 3c45e79..abd71a5 100644 ---- a/example/Persistent_cohomology/CMakeLists.txt -+++ b/example/Persistent_cohomology/CMakeLists.txt -@@ -43,10 +43,10 @@ add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D CO - "${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 $ - "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100") --add_test(NAME Persistent_cohomology_example_from_file_3_2_0 COMMAND $ -- "${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 $ -- "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100") -+#add_test(NAME Persistent_cohomology_example_from_file_3_2_0 COMMAND $ -+# "${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 $ -+# "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100") - - if(GMP_FOUND) - if(GMPXX_FOUND) -diff --git a/example/Simplex_tree/CMakeLists.txt b/example/Simplex_tree/CMakeLists.txt -index b1ea98d..3acf6f0 100644 ---- a/example/Simplex_tree/CMakeLists.txt -+++ b/example/Simplex_tree/CMakeLists.txt -@@ -27,6 +27,6 @@ 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 $ -- "${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off") -+ #add_test(NAME Simplex_tree_example_alpha_shapes_3_from_off COMMAND $ -+ # "${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off") - endif() -diff --git a/example/common/CMakeLists.txt b/example/common/CMakeLists.txt -index d5311b1..91ab206 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}) --add_test(NAME Common_example_vector_double_off_reader COMMAND $ -- "${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off") -+#add_test(NAME Common_example_vector_double_off_reader COMMAND $ -+# "${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off") - - if(CGAL_FOUND) - add_executable ( cgal_3D_off_reader example_CGAL_3D_points_off_reader.cpp ) --- -2.11.0 - diff --git a/debian/patches/0002-Disable-the-Sphinx-test.-We-re-not-using-it-as-it-re.patch b/debian/patches/0002-Disable-the-Sphinx-test.-We-re-not-using-it-as-it-re.patch new file mode 100644 index 00000000..76bb686e --- /dev/null +++ b/debian/patches/0002-Disable-the-Sphinx-test.-We-re-not-using-it-as-it-re.patch @@ -0,0 +1,32 @@ +From c167dcc8b48db2670f132d579ca68984938c1d5a Mon Sep 17 00:00:00 2001 +From: Gard Spreemann +Date: Mon, 9 Oct 2017 12:05:01 +0200 +Subject: [PATCH 2/3] Disable the Sphinx test. We're not using it, as it + requires the Sphinx bibtex module (#800358). + +--- + cython/CMakeLists.txt | 8 ++++---- + 1 file changed, 4 insertions(+), 4 deletions(-) + +diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt +index afca9d6..ec3cb8f 100644 +--- a/cython/CMakeLists.txt ++++ b/cython/CMakeLists.txt +@@ -305,10 +305,10 @@ if(CYTHON_FOUND) + DEPENDS "${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 ${CMAKE_CURRENT_BINARY_DIR}/doctest) + + endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + endif(CYTHON_FOUND) +-- +2.11.0 + diff --git a/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch b/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch new file mode 100644 index 00000000..279c6091 --- /dev/null +++ b/debian/patches/0003-Disable-tests-that-use-DFSG-deleted-data-files.patch @@ -0,0 +1,63 @@ +From c80f7efa2fbdc3152fde015505be0e6b64074c49 Mon Sep 17 00:00:00 2001 +From: Gard Spreemann +Date: Mon, 9 Oct 2017 14:15:02 +0200 +Subject: [PATCH 3/3] Disable tests that use DFSG-deleted data files. + +--- + example/Persistent_cohomology/CMakeLists.txt | 8 ++++---- + example/Simplex_tree/CMakeLists.txt | 4 ++-- + example/common/CMakeLists.txt | 4 ++-- + 3 files changed, 8 insertions(+), 8 deletions(-) + +diff --git a/example/Persistent_cohomology/CMakeLists.txt b/example/Persistent_cohomology/CMakeLists.txt +index f47de4c..8f11ea0 100644 +--- a/example/Persistent_cohomology/CMakeLists.txt ++++ b/example/Persistent_cohomology/CMakeLists.txt +@@ -41,10 +41,10 @@ add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D CO + "${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 $ + "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100") +-add_test(NAME Persistent_cohomology_example_from_file_3_2_0 COMMAND $ +- "${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 $ +- "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100") ++#add_test(NAME Persistent_cohomology_example_from_file_3_2_0 COMMAND $ ++# "${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 $ ++# "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100") + + 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 e22cc92..99da80f 100644 +--- a/example/Simplex_tree/CMakeLists.txt ++++ b/example/Simplex_tree/CMakeLists.txt +@@ -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 $ +- "${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off") ++# add_test(NAME Simplex_tree_example_alpha_shapes_3_from_off COMMAND $ ++# "${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 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 ${CGAL_LIBRARY}) +-add_test(NAME Common_example_vector_double_off_reader COMMAND $ +- "${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off") ++#add_test(NAME Common_example_vector_double_off_reader COMMAND $ ++# "${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off") + + install(TARGETS vector_double_off_reader DESTINATION bin) + +-- +2.11.0 + diff --git a/debian/patches/0003-Force-Python-3-detection-to-avoid-mixing-2-and-3.patch b/debian/patches/0003-Force-Python-3-detection-to-avoid-mixing-2-and-3.patch deleted file mode 100644 index 431c6a5b..00000000 --- a/debian/patches/0003-Force-Python-3-detection-to-avoid-mixing-2-and-3.patch +++ /dev/null @@ -1,36 +0,0 @@ -From 719513ad96cf59e787b0d4eb96173feb527ea4ea Mon Sep 17 00:00:00 2001 -From: Gard Spreemann -Date: Thu, 27 Apr 2017 17:39:39 +0200 -Subject: [PATCH 3/3] Force Python 3 detection to avoid mixing 2 and 3. - ---- - cmake/modules/FindCython.cmake | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) - -diff --git a/cmake/modules/FindCython.cmake b/cmake/modules/FindCython.cmake -index 04aed1f..f3a5b7b 100644 ---- a/cmake/modules/FindCython.cmake -+++ b/cmake/modules/FindCython.cmake -@@ -24,16 +24,16 @@ - - # Use the Cython executable that lives next to the Python executable - # if it is a local installation. --find_package( PythonInterp ) -+find_package( PythonInterp 3 ) - if( PYTHONINTERP_FOUND ) - get_filename_component( _python_path ${PYTHON_EXECUTABLE} PATH ) - find_program( CYTHON_EXECUTABLE -- NAMES cython cython.bat cython3 -+ NAMES cython3 - HINTS ${_python_path} - ) - else() - find_program( CYTHON_EXECUTABLE -- NAMES cython cython.bat cython3 -+ NAMES cython3 - ) - endif() - --- -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 -- cgit v1.2.3