Use find_package(Python) instead of PythonInterp

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.1)
+cmake_minimum_required(VERSION 3.12)
 
 project(GUDHIdev)
 

src/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.1)
+cmake_minimum_required(VERSION 3.12)
 
 project(GUDHI)
 

src/cmake/modules/GUDHI_third_party_libraries.cmake

@@ -90,14 +90,14 @@ message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
 
 # Find the correct Python interpreter.
 # Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 or -DPython_ADDITIONAL_VERSIONS=3 for instance.
-find_package( PythonInterp )
+find_package( Python )
 
 # find_python_module tries to import module in Python interpreter and to retrieve its version number
 # returns ${PYTHON_MODULE_NAME_UP}_VERSION and ${PYTHON_MODULE_NAME_UP}_FOUND
 function( find_python_module PYTHON_MODULE_NAME )
   string(TOUPPER ${PYTHON_MODULE_NAME} PYTHON_MODULE_NAME_UP)
   execute_process(
-          COMMAND ${PYTHON_EXECUTABLE}  -c "import ${PYTHON_MODULE_NAME}; print(${PYTHON_MODULE_NAME}.__version__)"
+          COMMAND ${Python_EXECUTABLE}  -c "import ${PYTHON_MODULE_NAME}; print(${PYTHON_MODULE_NAME}.__version__)"
           RESULT_VARIABLE PYTHON_MODULE_RESULT
           OUTPUT_VARIABLE PYTHON_MODULE_VERSION
           ERROR_VARIABLE PYTHON_MODULE_ERROR)
@@ -118,7 +118,7 @@ function( find_python_module PYTHON_MODULE_NAME )
   endif()
 endfunction( find_python_module )
 
-if( PYTHONINTERP_FOUND )
+if( Python_Interpreter_FOUND )
   find_python_module("cython")
   find_python_module("pytest")
   find_python_module("matplotlib")
@@ -133,19 +133,19 @@ if(NOT GUDHI_PYTHON_PATH)
   message(FATAL_ERROR "ERROR: GUDHI_PYTHON_PATH is not valid.")
 endif(NOT GUDHI_PYTHON_PATH)
 
-option(WITH_GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS "Build with setting runtime_library_dirs. Usefull when setting rpath is not allowed" ON)
+option(WITH_GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS "Build with setting runtime_library_dirs. Useful when setting rpath is not allowed" ON)
 
-if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
+if(Python_Interpreter_FOUND AND CYTHON_FOUND)
   if(SPHINX_FOUND)
     # Documentation generation is available through sphinx
     find_program( SPHINX_PATH sphinx-build )
 
     if(NOT SPHINX_PATH)
-      if(PYTHON_VERSION_MAJOR EQUAL 3)
+      if(Python_VERSION_MAJOR EQUAL 3)
         # In Python3, just hack sphinx-build if it does not exist
-        set(SPHINX_PATH "${PYTHON_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/${GUDHI_PYTHON_PATH}/doc/python3-sphinx-build.py")
-      endif(PYTHON_VERSION_MAJOR EQUAL 3)
+        set(SPHINX_PATH "${Python_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/${GUDHI_PYTHON_PATH}/doc/python3-sphinx-build.py")
+      endif(Python_VERSION_MAJOR EQUAL 3)
     endif(NOT SPHINX_PATH)
   endif(SPHINX_FOUND)
-endif(PYTHONINTERP_FOUND AND CYTHON_FOUND)
+endif(Python_Interpreter_FOUND AND CYTHON_FOUND)
 

src/common/doc/installation.h

@@ -6,7 +6,7 @@
  * 
  * \section compiling Compiling
  * The library uses c++14 and requires <a target="_blank" href="http://www.boost.org/">Boost</a>  &ge; 1.56.0
- * and <a target="_blank" href="https://www.cmake.org/">CMake</a> &ge; 3.1.
+ * and <a target="_blank" href="https://www.cmake.org/">CMake</a> &ge; 3.12.
  * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015.
  * 
  * \subsection utilities Utilities and examples

src/python/CMakeLists.txt

@@ -17,11 +17,11 @@ endfunction( add_GUDHI_PYTHON_lib )
 # THE_TEST is the python test file name (without .py extension) containing tests functions
 function( add_gudhi_py_test THE_TEST )
   if(PYTEST_FOUND)
-    # use ${PYTHON_EXECUTABLE} -B, otherwise a __pycache__ directory is created in sources by python
+    # use ${Python_EXECUTABLE} -B, otherwise a __pycache__ directory is created in sources by python
     # use py.test no cache provider, otherwise a .cache file is created in sources by py.test
     add_test(NAME ${THE_TEST}_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} -B -m pytest -p no:cacheprovider ${CMAKE_CURRENT_SOURCE_DIR}/test/${THE_TEST}.py)
+             COMMAND ${Python_EXECUTABLE} -B -m pytest -p no:cacheprovider ${CMAKE_CURRENT_SOURCE_DIR}/test/${THE_TEST}.py)
   endif()
 endfunction( add_gudhi_py_test )
 
@@ -31,7 +31,7 @@ function( add_gudhi_debug_info DEBUG_INFO )
   set(GUDHI_PYTHON_DEBUG_INFO "${GUDHI_PYTHON_DEBUG_INFO}    \"${DEBUG_INFO}\\n\" \\\n" PARENT_SCOPE)
 endfunction( add_gudhi_debug_info )
 
-if(PYTHONINTERP_FOUND)
+if(Python_Interpreter_FOUND)
   if(CYTHON_FOUND)
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'off_reader', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'simplex_tree', ")
@@ -53,7 +53,7 @@ if(PYTHONINTERP_FOUND)
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'representations', ")
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'wasserstein', ")
 
-    add_gudhi_debug_info("Python version ${PYTHON_VERSION_STRING}")
+    add_gudhi_debug_info("Python version ${Python_VERSION}")
     add_gudhi_debug_info("Cython version ${CYTHON_VERSION}")
     if(PYTEST_FOUND)
       add_gudhi_debug_info("Pytest version ${PYTEST_VERSION}")
@@ -214,28 +214,28 @@ if(PYTHONINTERP_FOUND)
     add_custom_command(
         OUTPUT gudhi.so
         WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace")
+        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")
 
-    install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install)")
+    install(CODE "execute_process(COMMAND ${Python_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install)")
 
     # Test examples
     if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
       # 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}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
+               ${Python_EXECUTABLE} "${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)
 
       if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
         # Tangential
         add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
                  WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
                  COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
+                 ${Python_EXECUTABLE} "${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)
 
         add_gudhi_py_test(test_tangential_complex)
@@ -244,13 +244,13 @@ if(PYTHONINTERP_FOUND)
         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}"
-                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+                 ${Python_EXECUTABLE} "${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}"
-                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+                 ${Python_EXECUTABLE} "${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)
       endif()
 
@@ -263,7 +263,7 @@ if(PYTHONINTERP_FOUND)
       add_test(NAME bottleneck_basic_example_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
                COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
+               ${Python_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
 
       add_gudhi_py_test(test_bottleneck_distance)
 
@@ -274,26 +274,26 @@ if(PYTHONINTERP_FOUND)
       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}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py"
+               ${Python_EXECUTABLE} "${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}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py"
+               ${Python_EXECUTABLE} "${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}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py"
+               ${Python_EXECUTABLE} "${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}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
+               ${Python_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
                -f human.off -n 700 -v)
 
       add_gudhi_py_test(test_cover_complex)
@@ -304,13 +304,13 @@ if(PYTHONINTERP_FOUND)
       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}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
+               ${Python_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
 
       if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
         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}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
+               ${Python_EXECUTABLE} "${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)
       endif()
 
@@ -328,14 +328,14 @@ if(PYTHONINTERP_FOUND)
     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}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
+             ${Python_EXECUTABLE} "${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)
 
     if(NUMPY_FOUND)
       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}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
+               ${Python_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
                10 10 10)
     endif()
 
@@ -346,36 +346,36 @@ if(PYTHONINTERP_FOUND)
       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}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
+               ${Python_EXECUTABLE} "${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}"
-               ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
+               ${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)
     endif()
 
     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}"
-             ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
+             ${Python_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
 
     add_gudhi_py_test(test_rips_complex)
 
     # 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}"
-             ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
+             ${Python_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
 
     add_gudhi_py_test(test_simplex_tree)
 
     # 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}"
-             ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
+             ${Python_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
 
     add_gudhi_py_test(test_witness_complex)
 
@@ -457,7 +457,7 @@ if(PYTHONINTERP_FOUND)
     message("++ Python module will not be compiled because cython was not found")
     set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python" CACHE INTERNAL "GUDHI_MISSING_MODULES")
   endif(CYTHON_FOUND)
-else(PYTHONINTERP_FOUND)
+else(Python_Interpreter_FOUND)
   message("++ Python module will not be compiled because no Python interpreter was found")
   set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python" CACHE INTERNAL "GUDHI_MISSING_MODULES")
-endif(PYTHONINTERP_FOUND)
+endif(Python_Interpreter_FOUND)

src/python/doc/installation.rst

@@ -13,7 +13,7 @@ The easiest way to install the Python version of GUDHI is using
 Compiling
 *********
 The library uses c++14 and requires `Boost <https://www.boost.org/>`_ ≥ 1.56.0,
-`CMake <https://www.cmake.org/>`_ ≥ 3.1  to generate makefiles,
+`CMake <https://www.cmake.org/>`_ ≥ 3.12  to generate makefiles,
 `NumPy <http://numpy.org>`_ and `Cython <https://www.cython.org/>`_ to compile
 the GUDHI Python module.
 It is a multi-platform library and compiles on Linux, Mac OSX and Visual