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Merge pull request #279401 from yl3dy/gudhi_3_9_0
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2d41313f3e
@ -2,6 +2,7 @@
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, fetchFromGitHub
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, buildPythonPackage
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, cmake
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, setuptools
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, boost
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, eigen
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, gmp
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@ -19,37 +20,44 @@
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buildPythonPackage rec {
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pname = "gudhi";
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version = "3.8.0";
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format = "setuptools";
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version = "3.9.0";
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pyproject = true;
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src = fetchFromGitHub {
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owner = "GUDHI";
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repo = "gudhi-devel";
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rev = "tags/gudhi-release-${version}";
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fetchSubmodules = true;
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sha256 = "sha256-f2ajy4muG9vuf4JarGWZmdk/LF9OYd2KLSaGyY6BQrY=";
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hash = "sha256-VL6RIPe8a2/cUHnHOql9e9EUMBB9QU311kMCaMZTbGI=";
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};
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patches = [ ./remove_explicit_PYTHONPATH.patch ];
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nativeBuildInputs = [ cmake numpy cython pybind11 matplotlib ];
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nativeBuildInputs = [ cmake numpy cython pybind11 matplotlib setuptools ];
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buildInputs = [ boost eigen gmp cgal mpfr ]
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++ lib.optionals enableTBB [ tbb ];
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propagatedBuildInputs = [ numpy scipy ];
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nativeCheckInputs = [ pytest ];
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cmakeFlags = [
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"-DWITH_GUDHI_PYTHON=ON"
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"-DPython_ADDITIONAL_VERSIONS=3"
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(lib.cmakeBool "WITH_GUDHI_PYTHON" true)
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(lib.cmakeFeature "Python_ADDITIONAL_VERSIONS" "3")
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];
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prePatch = ''
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substituteInPlace src/python/CMakeLists.txt \
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--replace '"''${GUDHI_PYTHON_PATH_ENV}"' ""
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'';
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preBuild = ''
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cd src/python
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'';
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checkPhase = ''
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runHook preCheck
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rm -r gudhi
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${cmake}/bin/ctest --output-on-failure
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ctest --output-on-failure
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runHook postCheck
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'';
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pythonImportsCheck = [ "gudhi" "gudhi.hera" "gudhi.point_cloud" "gudhi.clustering" ];
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@ -1,195 +0,0 @@
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diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
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index 86a409b6..09544fb5 100644
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--- a/src/python/CMakeLists.txt
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+++ b/src/python/CMakeLists.txt
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@@ -329,15 +329,6 @@ if(PYTHONINTERP_FOUND)
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace")
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- add_custom_target(python ALL DEPENDS gudhi.so
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- COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
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-
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- # Path separator management for windows
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- if (WIN32)
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- set(GUDHI_PYTHON_PATH_ENV "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR};$ENV{PYTHONPATH}")
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- else(WIN32)
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- set(GUDHI_PYTHON_PATH_ENV "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}:$ENV{PYTHONPATH}")
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- endif(WIN32)
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# Documentation generation is available through sphinx - requires all modules
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# Make it first as sphinx test is by far the longest test which is nice when testing in parallel
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if(SPHINX_PATH)
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@@ -358,13 +349,13 @@ if(PYTHONINTERP_FOUND)
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# sphinx target requires gudhi.so, because conf.py reads gudhi version from it
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add_custom_target(sphinx
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WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
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DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
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COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
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add_test(NAME sphinx_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
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# Set missing or not modules
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set(GUDHI_MODULES ${GUDHI_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MODULES")
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@@ -408,13 +399,13 @@ if(PYTHONINTERP_FOUND)
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# Cubical
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add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
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--no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
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add_test(NAME random_cubical_complex_persistence_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
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10 10 10)
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@@ -426,7 +417,7 @@ if(PYTHONINTERP_FOUND)
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add_test(NAME cubical_complex_sklearn_itf_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/cubical_complex_sklearn_itf.py")
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endif()
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@@ -435,7 +426,7 @@ if(PYTHONINTERP_FOUND)
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# Bottleneck and Alpha
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add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
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-f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
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endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0)
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@@ -443,7 +434,7 @@ if(PYTHONINTERP_FOUND)
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# Tangential
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add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
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--no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
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@@ -452,13 +443,13 @@ if(PYTHONINTERP_FOUND)
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# Witness complex
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add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
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--no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
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add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
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--no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
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@@ -467,7 +458,7 @@ if(PYTHONINTERP_FOUND)
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# Bottleneck
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add_test(NAME bottleneck_basic_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
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add_gudhi_py_test(test_bottleneck_distance)
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@@ -479,26 +470,26 @@ if(PYTHONINTERP_FOUND)
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file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
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add_test(NAME cover_complex_nerve_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py"
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-f human.off -c 2 -r 10 -g 0.3)
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add_test(NAME cover_complex_coordinate_gic_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py"
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-f human.off -c 0 -v)
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add_test(NAME cover_complex_functional_gic_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py"
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-o lucky_cat.off
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-f lucky_cat_PCA1 -v)
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add_test(NAME cover_complex_voronoi_gic_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
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-f human.off -n 700 -v)
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@@ -506,15 +497,15 @@ if(PYTHONINTERP_FOUND)
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# Alpha
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add_test(NAME alpha_complex_from_points_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
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add_test(NAME alpha_complex_from_generated_points_on_sphere_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_generated_points_on_sphere_example.py")
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add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
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--no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
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add_gudhi_py_test(test_alpha_complex)
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@@ -532,19 +523,19 @@ if(PYTHONINTERP_FOUND)
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# Rips
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add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
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--no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -s , -e 12.0 -d 3)
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add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
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--no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3)
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add_test(NAME rips_complex_from_points_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
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add_gudhi_py_test(test_rips_complex)
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@@ -552,7 +543,7 @@ if(PYTHONINTERP_FOUND)
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# Simplex tree
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add_test(NAME simplex_tree_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
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add_gudhi_py_test(test_simplex_tree)
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@@ -565,7 +556,7 @@ if(PYTHONINTERP_FOUND)
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# Witness
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add_test(NAME witness_complex_from_nearest_landmark_table_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
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add_gudhi_py_test(test_witness_complex)
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