pyrox.dev
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)