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nixpkgs/pkgs/development/python-modules/gudhi/remove_explicit_PYTHONPATH.patch
George Macon 33c54f6afb python3Packages.gudhi: 3.4.1 -> 3.8.0
2023-06-09 10:50:52 -04:00

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diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 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)
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