pkgs/development/python-modules/gudhi/remove_explicit_PYTHONPATH.patch at litex · tjh.dev/nixpkgs

tjh.dev / nixpkgs
Clone of https://github.com/NixOS/nixpkgs.git (to stress-test knotserver)
nixpkgs / pkgs / development / python-modules / gudhi / remove_explicit_PYTHONPATH.patch
at litex 11 kB view raw
  1diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
  2index 5c1402a..48a1250 100644
  3--- a/src/python/CMakeLists.txt
  4+++ b/src/python/CMakeLists.txt
  5@@ -271,9 +271,6 @@ 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     install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install)")
 13 
 14   # Documentation generation is available through sphinx - requires all modules
 15@@ -295,14 +292,14 @@ if(PYTHONINTERP_FOUND)
 16                   # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
 17                   add_custom_target(sphinx
 18                       WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
 19-                      COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
 20+                      COMMAND ${CMAKE_COMMAND} -E env
 21                       ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
 22                       DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
 23                       COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
 24 
 25                   add_test(NAME sphinx_py_test
 26                            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 27-                           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
 28+                           COMMAND ${CMAKE_COMMAND} -E env
 29                            ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
 30 
 31                   # Set missing or not modules
 32@@ -346,13 +343,13 @@ if(PYTHONINTERP_FOUND)
 33       # Bottleneck and Alpha
 34       add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
 35                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 36-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
 37+               COMMAND ${CMAKE_COMMAND} -E env
 38                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
 39                -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
 40       # Tangential
 41       add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
 42                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 43-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
 44+               COMMAND ${CMAKE_COMMAND} -E env
 45                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
 46                --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
 47 
 48@@ -361,13 +358,13 @@ if(PYTHONINTERP_FOUND)
 49       # Witness complex
 50       add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
 51                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 52-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
 53+               COMMAND ${CMAKE_COMMAND} -E env
 54                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
 55                --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
 56 
 57       add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
 58                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 59-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
 60+               COMMAND ${CMAKE_COMMAND} -E env
 61                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
 62                --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
 63 
 64@@ -379,7 +376,7 @@ if(PYTHONINTERP_FOUND)
 65       # Bottleneck
 66       add_test(NAME bottleneck_basic_example_py_test
 67                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 68-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
 69+               COMMAND ${CMAKE_COMMAND} -E env
 70                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
 71 
 72       if (PYBIND11_FOUND)
 73@@ -392,26 +389,26 @@ if(PYTHONINTERP_FOUND)
 74       file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 75       add_test(NAME cover_complex_nerve_example_py_test
 76                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 77-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
 78+               COMMAND ${CMAKE_COMMAND} -E env
 79                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py"
 80                -f human.off -c 2 -r 10 -g 0.3)
 81 
 82       add_test(NAME cover_complex_coordinate_gic_example_py_test
 83                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 84-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
 85+               COMMAND ${CMAKE_COMMAND} -E env
 86                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py"
 87                -f human.off -c 0 -v)
 88 
 89       add_test(NAME cover_complex_functional_gic_example_py_test
 90                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 91-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
 92+               COMMAND ${CMAKE_COMMAND} -E env
 93                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py"
 94                -o lucky_cat.off
 95                -f lucky_cat_PCA1 -v)
 96 
 97       add_test(NAME cover_complex_voronoi_gic_example_py_test
 98                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 99-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
100+               COMMAND ${CMAKE_COMMAND} -E env
101                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
102                -f human.off -n 700 -v)
103 
104@@ -422,11 +419,11 @@ if(PYTHONINTERP_FOUND)
105       # Alpha
106       add_test(NAME alpha_complex_from_points_example_py_test
107                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
108-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
109+               COMMAND ${CMAKE_COMMAND} -E env
110                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
111       add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
112              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
113-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
114+             COMMAND ${CMAKE_COMMAND} -E env
115              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
116              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
117       add_gudhi_py_test(test_alpha_complex)
118@@ -441,13 +438,13 @@ if(PYTHONINTERP_FOUND)
119     # Cubical
120     add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
121              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
122-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
123+             COMMAND ${CMAKE_COMMAND} -E env
124              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
125              --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
126 
127     add_test(NAME random_cubical_complex_persistence_example_py_test
128              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
129-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
130+             COMMAND ${CMAKE_COMMAND} -E env
131              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
132              10 10 10)
133 
134@@ -456,19 +453,19 @@ if(PYTHONINTERP_FOUND)
135     # Rips
136     add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
137              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
138-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
139+             COMMAND ${CMAKE_COMMAND} -E env
140              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
141              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
142 
143     add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
144              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
145-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
146+             COMMAND ${CMAKE_COMMAND} -E env
147              ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
148              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
149 
150     add_test(NAME rips_complex_from_points_example_py_test
151              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
152-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
153+             COMMAND ${CMAKE_COMMAND} -E env
154              ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
155 
156     add_gudhi_py_test(test_rips_complex)
157@@ -476,7 +473,7 @@ if(PYTHONINTERP_FOUND)
158     # Simplex tree
159     add_test(NAME simplex_tree_example_py_test
160              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
161-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
162+             COMMAND ${CMAKE_COMMAND} -E env
163              ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
164 
165     add_gudhi_py_test(test_simplex_tree)
166@@ -485,7 +482,7 @@ if(PYTHONINTERP_FOUND)
167     # Witness
168     add_test(NAME witness_complex_from_nearest_landmark_table_py_test
169              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
170-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
171+             COMMAND ${CMAKE_COMMAND} -E env
172              ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
173 
174     add_gudhi_py_test(test_witness_complex)