forked from mirrors/nixpkgs
python3Packages.gudhi: init at 3.4.1
This commit is contained in:
Alexander Kiselyov
parent
db40f88157
commit
9f5d822ef0
61
pkgs/development/python-modules/gudhi/default.nix
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61
pkgs/development/python-modules/gudhi/default.nix
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@ -0,0 +1,61 @@
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{ lib
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, fetchFromGitHub
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, buildPythonPackage
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, cmake
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, boost
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, eigen
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, gmp
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, cgal_5 # see https://github.com/NixOS/nixpkgs/pull/94875 about cgal
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, mpfr
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, tbb
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, numpy
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, cython
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, pybind11
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, matplotlib
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, scipy
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, pytest
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, enableTBB ? false
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}:
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buildPythonPackage rec {
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pname = "gudhi";
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version = "3.4.1";
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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-${version}";
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fetchSubmodules = true;
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sha256 = "1m03qazzfraxn62l1cb11icjz4x8q2sg9c2k3syw5v0yv9ndgx1v";
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};
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patches = [ ./remove_explicit_PYTHONPATH.patch ];
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nativeBuildInputs = [ cmake numpy cython pybind11 matplotlib ];
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buildInputs = [ boost eigen gmp cgal_5 mpfr ]
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++ lib.optionals enableTBB [ tbb ];
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propagatedBuildInputs = [ numpy scipy ];
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checkInputs = [ pytest ];
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enableParallelBuilding = true;
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cmakeFlags = "-DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3";
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preBuild = ''
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cd src/python
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'';
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checkPhase = ''
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rm -r gudhi
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${cmake}/bin/ctest --output-on-failure
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'';
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pythonImportsCheck = [ "gudhi" "gudhi.hera" "gudhi.point_cloud" "gudhi.clustering" ];
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meta = {
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description = "Library for Computational Topology and Topological Data Analysis (TDA)";
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homepage = "https://gudhi.inria.fr/python/3.4.1/";
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downloadPage = "https://github.com/GUDHI/gudhi-devel";
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license = with lib.licenses; [ mit gpl3 ];
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maintainers = with lib.maintainers; [ yl3dy ];
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};
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}
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@ -0,0 +1,174 @@
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diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
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index 5c1402a..48a1250 100644
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--- a/src/python/CMakeLists.txt
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+++ b/src/python/CMakeLists.txt
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@@ -271,9 +271,6 @@ 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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install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install)")
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# Documentation generation is available through sphinx - requires all modules
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@@ -295,14 +292,14 @@ 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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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@@ -346,13 +343,13 @@ 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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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# 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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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@@ -361,13 +358,13 @@ 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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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@@ -379,7 +376,7 @@ 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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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if (PYBIND11_FOUND)
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@@ -392,26 +389,26 @@ 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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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@@ -422,11 +419,11 @@ 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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_diagram_persistence_from_off_file_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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 -a 0.6)
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add_gudhi_py_test(test_alpha_complex)
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@@ -441,13 +438,13 @@ 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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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@@ -456,19 +453,19 @@ 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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 -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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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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@@ -476,7 +473,7 @@ 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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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@@ -485,7 +482,7 @@ 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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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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@ -3206,6 +3206,8 @@ in {
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guestfs = callPackage ../development/python-modules/guestfs { };
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gudhi = callPackage ../development/python-modules/gudhi { };
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gumath = callPackage ../development/python-modules/gumath { };
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gunicorn = callPackage ../development/python-modules/gunicorn { };
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