Fix issue #4 : [CMake - global] List all that is missing

          #21 : [python - global] Additional information on how GUDHI was compiled could help to debug users problems



git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ninja_cmake_warning_fix_vincent@3751 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ded8b49b7e282dbf262df5695f2b5285a9907551

5 files changed, 147 insertions, 54 deletions

diff --git a/src/cmake/modules/FindCython.cmake b/src/cmake/modules/FindCython.cmake
deleted file mode 100644
index 04aed1f8..00000000
--- a/src/cmake/modules/FindCython.cmake
+++ /dev/null
@@ -1,44 +0,0 @@
-# Find the Cython compiler.
-#
-# This code sets the following variables:
-#
-#  CYTHON_EXECUTABLE
-#
-# See also UseCython.cmake
-
-#=============================================================================
-# Copyright 2011 Kitware, Inc.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#=============================================================================
-
-# Use the Cython executable that lives next to the Python executable
-# if it is a local installation.
-find_package( PythonInterp )
-if( PYTHONINTERP_FOUND )
-  get_filename_component( _python_path ${PYTHON_EXECUTABLE} PATH )
-  find_program( CYTHON_EXECUTABLE
-    NAMES cython cython.bat cython3
-    HINTS ${_python_path}
-    )
-else()
-  find_program( CYTHON_EXECUTABLE
-    NAMES cython cython.bat cython3
-    )
-endif()
-
-
-include( FindPackageHandleStandardArgs )
-FIND_PACKAGE_HANDLE_STANDARD_ARGS( Cython REQUIRED_VARS CYTHON_EXECUTABLE )
-
-mark_as_advanced( CYTHON_EXECUTABLE )
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 7433f2f3..abee8f80 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -8,11 +8,9 @@ endif(NOT Boost_FOUND)
 
 find_package(GMP)
 if(GMP_FOUND)
-  message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}")
   INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
   find_package(GMPXX)
   if(GMPXX_FOUND)
-    message(STATUS "GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
     INCLUDE_DIRECTORIES(${GMPXX_INCLUDE_DIR})
   endif()
 endif()
@@ -79,7 +77,6 @@ endif(WITH_GUDHI_USE_TBB)
 set(CGAL_WITH_EIGEN3_VERSION 0.0.0)
 find_package(Eigen3 3.1.0)
 if (EIGEN3_FOUND)
-  message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
   include( ${EIGEN3_USE_FILE} )
   set(CGAL_WITH_EIGEN3_VERSION ${CGAL_VERSION})
 endif (EIGEN3_FOUND)
@@ -119,7 +116,33 @@ 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(Cython)
+find_package( PythonInterp )
+
+# 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__)"
+          RESULT_VARIABLE PYTHON_MODULE_RESULT
+          OUTPUT_VARIABLE PYTHON_MODULE_VERSION)
+  if(PYTHON_MODULE_RESULT EQUAL 0)
+    # Remove carriage return
+    string(STRIP ${PYTHON_MODULE_VERSION} PYTHON_MODULE_VERSION)
+    set(${PYTHON_MODULE_NAME_UP}_VERSION ${PYTHON_MODULE_VERSION} PARENT_SCOPE)
+    set(${PYTHON_MODULE_NAME_UP}_FOUND TRUE PARENT_SCOPE)
+  else()
+    unset(${PYTHON_MODULE_NAME_UP}_VERSION PARENT_SCOPE)
+    set(${PYTHON_MODULE_NAME_UP}_FOUND FALSE PARENT_SCOPE)
+  endif()
+endfunction( find_python_module )
+
+if( PYTHONINTERP_FOUND )
+  find_python_module("cython")
+  find_python_module("pytest")
+  find_python_module("matplotlib")
+  find_python_module("numpy")
+endif()
 
 if(NOT GUDHI_CYTHON_PATH)
   message(FATAL_ERROR "ERROR: GUDHI_CYTHON_PATH is not valid.")
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 8f1dec76..8b5d231a 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -23,10 +23,42 @@ function( add_gudhi_py_test THE_TEST )
            COMMAND ${PYTHON_EXECUTABLE} -B -m pytest -p no:cacheprovider ${CMAKE_CURRENT_SOURCE_DIR}/test/${THE_TEST}.py)
 endfunction( add_gudhi_py_test )
 
+# Set gudhi.__debug_info__
+# WARNING : to be done before gudhi.pyx.in configure_file
+function( add_gudhi_debug_info DEBUG_INFO )
+  set(GUDHI_CYTHON_DEBUG_INFO "${GUDHI_CYTHON_DEBUG_INFO}    \"${DEBUG_INFO}\\n\" \\\n" PARENT_SCOPE)
+endfunction( add_gudhi_debug_info )
+
 
 if(CYTHON_FOUND)
-  message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - Sphinx is ${SPHINX_PATH}")
+  set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}off_reader;")
+  set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}simplex_tree;")
+  set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}rips_complex;")
+  set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}cubical_complex;")
+  set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}periodic_cubical_complex;")
+  set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
+  set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}reader_utils;")
+  set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}witness_complex;")
+  set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}strong_witness_complex;")
+
+  add_gudhi_debug_info("Python version ${PYTHON_VERSION_STRING}")
+  add_gudhi_debug_info("Cython version ${CYTHON_VERSION}")
+  if(PYTEST_FOUND)
+    add_gudhi_debug_info("Pytest version ${PYTEST_VERSION}")
+  endif()
+  if(MATPLOTLIB_FOUND)
+  add_gudhi_debug_info("Matplotlib version ${MATPLOTLIB_VERSION}")
+  endif()
+  if(NUMPY_FOUND)
+  add_gudhi_debug_info("Numpy version ${NUMPY_VERSION}")
+  endif()
+  if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
+  else()
+      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
+  endif()
 
+  message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_VERSION} - Sphinx is ${SPHINX_PATH}")
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ")
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ")
@@ -49,25 +81,49 @@ if(CYTHON_FOUND)
   endif()
 
   if (EIGEN3_FOUND)
+    add_gudhi_debug_info("Eigen3 version ${EIGEN3_VERSION}")
     # No problem, even if no CGAL found
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
   endif (EIGEN3_FOUND)
 
   if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
     set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}bottleneck_distance;")
     set(GUDHI_CYTHON_NERVE_GIC "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/nerve_gic.pyx'")
-  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}nerve_gic;")
+  else()
+    set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}bottleneck_distance;")
+    set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}nerve_gic;")
+  endif ()
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
     set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}subsampling;")
     set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}tangential_complex;")
+  else()
+    set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}subsampling;")
+    set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}tangential_complex;")
+  endif ()
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
     set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}alpha_complex;")
+  else()
+    set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}alpha_complex;")
+  endif ()
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
     set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX
         "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n")
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}euclidean_witness_complex;")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}euclidean_strong_witness_complex;")
+  else()
+    set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}euclidean_witness_complex;")
+    set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}euclidean_strong_witness_complex;")
+  endif ()
+
+  add_gudhi_debug_info("Installed modules are: ${GUDHI_CYTHON_MODULES}")
+  if(GUDHI_CYTHON_MISSING_MODULES)
+    add_gudhi_debug_info("Missing modules are: ${GUDHI_CYTHON_MISSING_MODULES}")
+  endif()
 
   if(CGAL_FOUND)
     can_cgal_use_cxx11_thread_local()
@@ -77,8 +133,10 @@ if(CYTHON_FOUND)
     endif()
     # Add CGAL compilation args
     if(CGAL_HEADER_ONLY)
+      add_gudhi_debug_info("CGAL header only version ${CGAL_VERSION}")
       set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
     else(CGAL_HEADER_ONLY)
+      add_gudhi_debug_info("CGAL version ${CGAL_VERSION}")
       add_gudhi_cython_lib(${CGAL_LIBRARY})
       set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
       # If CGAL is not header only, CGAL library may link with boost system,
@@ -87,10 +145,12 @@ if(CYTHON_FOUND)
     endif(CGAL_HEADER_ONLY)
     # GMP and GMPXX are not required, but if present, CGAL will link with them.
     if(GMP_FOUND)
+      add_gudhi_debug_info("GMP_LIBRARIES = ${GMP_LIBRARIES}")
       set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
       add_gudhi_cython_lib(${GMP_LIBRARIES})
       set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
       if(GMPXX_FOUND)
+        add_gudhi_debug_info("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
         set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ")
         add_gudhi_cython_lib(${GMPXX_LIBRARIES})
         set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ")
@@ -112,6 +172,7 @@ if(CYTHON_FOUND)
   set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ")
 
   if (TBB_FOUND AND WITH_GUDHI_USE_TBB)
+    add_gudhi_debug_info("TBB version ${TBB_INTERFACE_VERSION} found and used")
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ")
     add_gudhi_cython_lib(${TBB_RELEASE_LIBRARY})
     add_gudhi_cython_lib(${TBB_MALLOC_RELEASE_LIBRARY})
diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
index 43ff85c5..43576ec9 100644
--- a/src/cython/doc/installation.rst
+++ b/src/cython/doc/installation.rst
@@ -47,9 +47,61 @@ following command in a terminal:
     export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/cython'
     ctest -R py_test
 
-If tests fail, please try to :code:`import gudhi` and check the errors.
+Debugging issues
+================
+
+If tests fail, please check your PYTHONPATH and try to :code:`import gudhi`
+and check the errors.
 The problem can come from a third-party library bad link or installation.
 
+If :code:`import gudhi` succeeds, please have a look to debug informations:
+
+.. code-block:: python
+
+    import gudhi
+    print(gudhi.__debug_info__)
+
+You shall have something like:
+
+.. code-block:: none
+
+    Python version 2.7.15
+    Cython version 0.26.1
+    Eigen3 version 3.1.1
+    Installed modules are: off_reader;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex;
+        persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex;alpha_complex;
+        euclidean_witness_complex;euclidean_strong_witness_complex;
+    Missing modules are: bottleneck_distance;nerve_gic;subsampling;tangential_complex;persistence_graphical_tools;
+    CGAL version 4.7.1000
+    GMP_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmp.so
+    GMPXX_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmpxx.so
+    TBB version 9107 found and used
+
+Here, you can see that bottleneck_distance, nerve_gic, subsampling and
+tangential_complex are missing because of the CGAL version.
+persistence_graphical_tools is not available as numpy and matplotlib are not
+available.
+Unitary tests cannot be run as pytest is missing.
+
+A complete configuration would be :
+
+.. code-block:: none
+
+    Python version 3.6.5
+    Cython version 0.28.2
+    Pytest version 3.3.2
+    Matplotlib version 2.2.2
+    Numpy version 1.14.5
+    Eigen3 version 3.3.4
+    Installed modules are: off_reader;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex;
+        persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex;persistence_graphical_tools;
+        bottleneck_distance;nerve_gic;subsampling;tangential_complex;alpha_complex;euclidean_witness_complex;
+        euclidean_strong_witness_complex;
+    CGAL header only version 4.11.0
+    GMP_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmp.so
+    GMPXX_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmpxx.so
+    TBB version 9107 found and used
+
 Documentation
 =============
 
diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in
index 56a72b04..0d4b966b 100644
--- a/src/cython/gudhi.pyx.in
+++ b/src/cython/gudhi.pyx.in
@@ -26,6 +26,7 @@ __license__ = "GPL v3"
 __version__ = "@GUDHI_VERSION@"
 # This variable is used by doctest to find files
 __root_source_dir__ = "@CMAKE_SOURCE_DIR@"
+__debug_info__ = @GUDHI_CYTHON_DEBUG_INFO@
 
 include '@CMAKE_CURRENT_SOURCE_DIR@/cython/off_reader.pyx'
 include '@CMAKE_CURRENT_SOURCE_DIR@/cython/simplex_tree.pyx'