pkgs/development/python-modules/gudhi/remove_explicit_PYTHONPATH.patch

   1 diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
   2 index 86a409b6..09544fb5 100644
   3 --- a/src/python/CMakeLists.txt
   4 +++ b/src/python/CMakeLists.txt
   5 @@ -329,15 +329,6 @@ if(PYTHONINTERP_FOUND)
   6          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
   7          COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace")
   8
   9 -    add_custom_target(python ALL DEPENDS gudhi.so
  10 -                      COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
  11 -
  12 -    # Path separator management for windows
  13 -    if (WIN32)
  14 -      set(GUDHI_PYTHON_PATH_ENV "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR};$ENV{PYTHONPATH}")
  15 -    else(WIN32)
  16 -      set(GUDHI_PYTHON_PATH_ENV "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}:$ENV{PYTHONPATH}")
  17 -    endif(WIN32)
  18      # Documentation generation is available through sphinx - requires all modules
  19      # Make it first as sphinx test is by far the longest test which is nice when testing in parallel
  20      if(SPHINX_PATH)
  21 @@ -358,13 +349,13 @@ if(PYTHONINTERP_FOUND)
  22                        # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
  23                        add_custom_target(sphinx
  24                            WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
  25 -                          COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
  26 +                          COMMAND ${CMAKE_COMMAND} -E env
  27                            ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
  28                            DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
  29                            COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
  30                        add_test(NAME sphinx_py_test
  31                                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
  32 -                               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
  33 +                               COMMAND ${CMAKE_COMMAND} -E env
  34                                 ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
  35                        # Set missing or not modules
  36                        set(GUDHI_MODULES ${GUDHI_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MODULES")
  37 @@ -408,13 +399,13 @@ if(PYTHONINTERP_FOUND)
  38      # Cubical
  39      add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
  40               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
  41 -             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
  42 +             COMMAND ${CMAKE_COMMAND} -E env
  43               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
  44               --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
  45
  46      add_test(NAME random_cubical_complex_persistence_example_py_test
  47               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
  48 -             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
  49 +             COMMAND ${CMAKE_COMMAND} -E env
  50               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
  51               10 10 10)
  52
  53 @@ -426,7 +417,7 @@ if(PYTHONINTERP_FOUND)
  54
  55        add_test(NAME cubical_complex_sklearn_itf_py_test
  56                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
  57 -               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
  58 +               COMMAND ${CMAKE_COMMAND} -E env
  59                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/cubical_complex_sklearn_itf.py")
  60      endif()
  61
  62 @@ -435,7 +426,7 @@ if(PYTHONINTERP_FOUND)
  63        # Bottleneck and Alpha
  64        add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
  65                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
  66 -               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
  67 +               COMMAND ${CMAKE_COMMAND} -E env
  68                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
  69                 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
  70      endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0)
  71 @@ -443,7 +434,7 @@ if(PYTHONINTERP_FOUND)
  72        # Tangential
  73        add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
  74                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
  75 -               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
  76 +               COMMAND ${CMAKE_COMMAND} -E env
  77                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
  78                 --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
  79
  80 @@ -452,13 +443,13 @@ if(PYTHONINTERP_FOUND)
  81        # Witness complex
  82        add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
  83                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
  84 -               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
  85 +               COMMAND ${CMAKE_COMMAND} -E env
  86                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
  87                 --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
  88
  89        add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
  90                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
  91 -               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
  92 +               COMMAND ${CMAKE_COMMAND} -E env
  93                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
  94                 --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
  95
  96 @@ -467,7 +458,7 @@ if(PYTHONINTERP_FOUND)
  97        # Bottleneck
  98        add_test(NAME bottleneck_basic_example_py_test
  99                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 100 -               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
 101 +               COMMAND ${CMAKE_COMMAND} -E env
 102                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
 103
 104        add_gudhi_py_test(test_bottleneck_distance)
 105 @@ -479,26 +470,26 @@ if(PYTHONINTERP_FOUND)
 106      file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 107      add_test(NAME cover_complex_nerve_example_py_test
 108               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 109 -             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
 110 +             COMMAND ${CMAKE_COMMAND} -E env
 111               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py"
 112               -f human.off -c 2 -r 10 -g 0.3)
 113
 114      add_test(NAME cover_complex_coordinate_gic_example_py_test
 115               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 116 -             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
 117 +             COMMAND ${CMAKE_COMMAND} -E env
 118               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py"
 119               -f human.off -c 0 -v)
 120
 121      add_test(NAME cover_complex_functional_gic_example_py_test
 122               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 123 -             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
 124 +             COMMAND ${CMAKE_COMMAND} -E env
 125               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py"
 126               -o lucky_cat.off
 127               -f lucky_cat_PCA1 -v)
 128
 129      add_test(NAME cover_complex_voronoi_gic_example_py_test
 130               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 131 -             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
 132 +             COMMAND ${CMAKE_COMMAND} -E env
 133               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
 134               -f human.off -n 700 -v)
 135
 136 @@ -506,15 +497,15 @@ if(PYTHONINTERP_FOUND)
 137        # Alpha
 138        add_test(NAME alpha_complex_from_points_example_py_test
 139                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 140 -               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
 141 +               COMMAND ${CMAKE_COMMAND} -E env
 142                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
 143        add_test(NAME alpha_complex_from_generated_points_on_sphere_example_py_test
 144                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 145 -               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
 146 +               COMMAND ${CMAKE_COMMAND} -E env
 147                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_generated_points_on_sphere_example.py")
 148        add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
 149               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 150 -             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
 151 +             COMMAND ${CMAKE_COMMAND} -E env
 152               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
 153               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
 154        add_gudhi_py_test(test_alpha_complex)
 155 @@ -532,19 +523,19 @@ if(PYTHONINTERP_FOUND)
 156      # Rips
 157      add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
 158               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 159 -             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
 160 +             COMMAND ${CMAKE_COMMAND} -E env
 161               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
 162               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -s , -e 12.0 -d 3)
 163
 164      add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
 165               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 166 -             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
 167 +             COMMAND ${CMAKE_COMMAND} -E env
 168               ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
 169               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
 170
 171      add_test(NAME rips_complex_from_points_example_py_test
 172               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 173 -             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
 174 +             COMMAND ${CMAKE_COMMAND} -E env
 175               ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
 176
 177      add_gudhi_py_test(test_rips_complex)
 178 @@ -552,7 +543,7 @@ if(PYTHONINTERP_FOUND)
 179      # Simplex tree
 180      add_test(NAME simplex_tree_example_py_test
 181               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 182 -             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
 183 +             COMMAND ${CMAKE_COMMAND} -E env
 184               ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
 185
 186      add_gudhi_py_test(test_simplex_tree)
 187 @@ -565,7 +556,7 @@ if(PYTHONINTERP_FOUND)
 188      # Witness
 189      add_test(NAME witness_complex_from_nearest_landmark_table_py_test
 190               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 191 -             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
 192 +             COMMAND ${CMAKE_COMMAND} -E env
 193               ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
 194
 195      add_gudhi_py_test(test_witness_complex)