Merge branch 'master' into python_weighted_alpha_complex

3 files changed, 34 insertions, 34 deletions

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 5c1402a6..73303a24 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -276,6 +276,7 @@ if(PYTHONINTERP_FOUND)
 
     install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install)")
 
+  set(GUDHI_PYTHON_PATH_ENV "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}:$ENV{PYTHONPATH}")
   # 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)
@@ -295,14 +296,14 @@ 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                      COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                           COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
                            ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
 
                   # Set missing or not modules
@@ -346,13 +347,13 @@ if(PYTHONINTERP_FOUND)
       # Bottleneck and Alpha
       add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_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)
       # Tangential
       add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_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)
 
@@ -361,13 +362,13 @@ 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_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)
 
@@ -379,7 +380,7 @@ if(PYTHONINTERP_FOUND)
       # Bottleneck
       add_test(NAME bottleneck_basic_example_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
 
       if (PYBIND11_FOUND)
@@ -392,26 +393,26 @@ 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
                -f human.off -n 700 -v)
 
@@ -422,13 +423,13 @@ if(PYTHONINTERP_FOUND)
       # Alpha
       add_test(NAME alpha_complex_from_points_example_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
       add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_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 -a 0.6)
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
       add_gudhi_py_test(test_alpha_complex)
     endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
 
@@ -441,13 +442,13 @@ 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
              10 10 10)
 
@@ -456,19 +457,19 @@ 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_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 -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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
              ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
 
     add_gudhi_py_test(test_rips_complex)
@@ -476,7 +477,7 @@ if(PYTHONINTERP_FOUND)
     # Simplex tree
     add_test(NAME simplex_tree_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
              ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
 
     add_gudhi_py_test(test_simplex_tree)
@@ -485,7 +486,7 @@ if(PYTHONINTERP_FOUND)
     # Witness
     add_test(NAME witness_complex_from_nearest_landmark_table_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
              ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
 
     add_gudhi_py_test(test_witness_complex)
diff --git a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
index 1e0273b3..fe03be31 100755
--- a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
@@ -25,12 +25,12 @@ parser = argparse.ArgumentParser(
     description="AlphaComplex creation from " "points read in a OFF file.",
     epilog="Example: "
     "example/alpha_complex_diagram_persistence_from_off_file_example.py "
-    "-f ../data/points/tore3D_300.off -a 0.6"
+    "-f ../data/points/tore3D_300.off"
     "- Constructs a alpha complex with the "
     "points from the given OFF file.",
 )
 parser.add_argument("-f", "--file", type=str, required=True)
-parser.add_argument("-a", "--max_alpha_square", type=float, default=0.5)
+parser.add_argument("-a", "--max_alpha_square", type=float, required=False)
 parser.add_argument("-b", "--band", type=float, default=0.0)
 parser.add_argument(
     "--no-diagram",
@@ -47,21 +47,20 @@ with open(args.file, "r") as f:
         print("##############################################################")
         print("AlphaComplex creation from points read in a OFF file")
 
-        message = "AlphaComplex with max_edge_length=" + repr(args.max_alpha_square)
-        print(message)
-
         alpha_complex = gudhi.AlphaComplex(off_file=args.file)
-        simplex_tree = alpha_complex.create_simplex_tree(
-            max_alpha_square=args.max_alpha_square
-        )
+        if args.max_alpha_square is not None:
+            print("with max_edge_length=", args.max_alpha_square)
+            simplex_tree = alpha_complex.create_simplex_tree(
+                max_alpha_square=args.max_alpha_square
+            )
+        else:
+            simplex_tree = alpha_complex.create_simplex_tree()
 
-        message = "Number of simplices=" + repr(simplex_tree.num_simplices())
-        print(message)
+        print("Number of simplices=", simplex_tree.num_simplices())
 
         diag = simplex_tree.persistence()
 
-        print("betti_numbers()=")
-        print(simplex_tree.betti_numbers())
+        print("betti_numbers()=", simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
             import matplotlib.pyplot as plot
diff --git a/src/python/example/alpha_complex_from_points_example.py b/src/python/example/alpha_complex_from_points_example.py
index 465632eb..5d5ca66a 100755
--- a/src/python/example/alpha_complex_from_points_example.py
+++ b/src/python/example/alpha_complex_from_points_example.py
@@ -19,7 +19,7 @@ __license__ = "MIT"
 print("#####################################################################")
 print("AlphaComplex creation from points")
 alpha_complex = AlphaComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]])
-simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=60.0)
+simplex_tree = alpha_complex.create_simplex_tree()
 
 if simplex_tree.find([0, 1]):
     print("[0, 1] Found !!")