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What happens if I push all of nixpkgs
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123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txtindex 86a409b6..09544fb5 100644--- a/src/python/CMakeLists.txt+++ b/src/python/CMakeLists.txt@@ -329,15 +329,6 @@ if(PYTHONINTERP_FOUND) WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace") - add_custom_target(python ALL DEPENDS gudhi.so- COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")-- # Path separator management for windows- if (WIN32)- set(GUDHI_PYTHON_PATH_ENV "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR};$ENV{PYTHONPATH}")- else(WIN32)- set(GUDHI_PYTHON_PATH_ENV "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}:$ENV{PYTHONPATH}")- endif(WIN32) # Documentation generation is available through sphinx - requires all modules # Make it first as sphinx test is by far the longest test which is nice when testing in parallel if(SPHINX_PATH)@@ -358,13 +349,13 @@ if(PYTHONINTERP_FOUND) # sphinx target requires gudhi.so, because conf.py reads gudhi version from it add_custom_target(sphinx WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM) add_test(NAME sphinx_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest) # Set missing or not modules set(GUDHI_MODULES ${GUDHI_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MODULES")@@ -408,13 +399,13 @@ if(PYTHONINTERP_FOUND) # Cubical add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py" --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt) add_test(NAME random_cubical_complex_persistence_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py" 10 10 10) @@ -426,7 +417,7 @@ if(PYTHONINTERP_FOUND) add_test(NAME cubical_complex_sklearn_itf_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/cubical_complex_sklearn_itf.py") endif() @@ -435,7 +426,7 @@ if(PYTHONINTERP_FOUND) # Bottleneck and Alpha add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py" -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0)@@ -443,7 +434,7 @@ if(PYTHONINTERP_FOUND) # Tangential add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) @@ -452,13 +443,13 @@ if(PYTHONINTERP_FOUND) # Witness complex add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) @@ -467,7 +458,7 @@ if(PYTHONINTERP_FOUND) # Bottleneck add_test(NAME bottleneck_basic_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py") add_gudhi_py_test(test_bottleneck_distance)@@ -479,26 +470,26 @@ if(PYTHONINTERP_FOUND) 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}"+ COMMAND ${CMAKE_COMMAND} -E 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}"+ COMMAND ${CMAKE_COMMAND} -E 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}"+ COMMAND ${CMAKE_COMMAND} -E 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}"+ COMMAND ${CMAKE_COMMAND} -E env ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py" -f human.off -n 700 -v) @@ -506,15 +497,15 @@ if(PYTHONINTERP_FOUND) # Alpha add_test(NAME alpha_complex_from_points_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py") add_test(NAME alpha_complex_from_generated_points_on_sphere_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_generated_points_on_sphere_example.py") add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) add_gudhi_py_test(test_alpha_complex)@@ -532,19 +523,19 @@ if(PYTHONINTERP_FOUND) # Rips add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -s , -e 12.0 -d 3) add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3) add_test(NAME rips_complex_from_points_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py) add_gudhi_py_test(test_rips_complex)@@ -552,7 +543,7 @@ if(PYTHONINTERP_FOUND) # Simplex tree add_test(NAME simplex_tree_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py) add_gudhi_py_test(test_simplex_tree)@@ -565,7 +556,7 @@ if(PYTHONINTERP_FOUND) # Witness add_test(NAME witness_complex_from_nearest_landmark_table_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}- COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"+ COMMAND ${CMAKE_COMMAND} -E env ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py) add_gudhi_py_test(test_witness_complex)