Available/missing python modules are now managed by the __init__.py

3 files changed, 66 insertions, 42 deletions

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 509a122e..b69b2c7d 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -33,15 +33,23 @@ endfunction( add_gudhi_debug_info )
 
 if(PYTHONINTERP_FOUND)
   if(CYTHON_FOUND)
-    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 "${GUDHI_CYTHON_MODULES}strong_witness_complex;")
+    set(GUDHI_CYTHON_MODULES "${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', ")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'persistence_graphical_tools' ")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'bottleneck_distance', ")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'nerve_gic', ")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'subsampling', ")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'tangential_complex', ")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'alpha_complex', ")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'euclidean_witness_complex', ")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'euclidean_strong_witness_complex', ")
 
     add_gudhi_debug_info("Python version ${PYTHON_VERSION_STRING}")
     add_gudhi_debug_info("Cython version ${CYTHON_VERSION}")
@@ -57,11 +65,6 @@ if(PYTHONINTERP_FOUND)
     if(SCIPY_FOUND)
       add_gudhi_debug_info("Scipy version ${SCIPY_VERSION}")
     endif()
-    if(MATPLOTLIB_FOUND AND NUMPY_FOUND AND SCIPY_FOUND)
-      set(GUDHI_CYTHON_MODULES "${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', ")
@@ -93,43 +96,20 @@ if(PYTHONINTERP_FOUND)
 
     if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
       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 '${CMAKE_CURRENT_SOURCE_DIR}/cython/nerve_gic.pyx'")
-      set(GUDHI_CYTHON_MODULES "${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 4.11.0)
       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 '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
-      set(GUDHI_CYTHON_MODULES "${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 4.11.0)
       set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
-      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}alpha_complex;")
-    else()
-      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}alpha_complex;")
     endif ()
     if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
       set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX
           "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n")
-      set(GUDHI_CYTHON_MODULES "${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: ${GUDHI_CYTHON_MISSING_MODULES}")
-    endif()
-
     if(CGAL_FOUND)
       can_cgal_use_cxx11_thread_local()
       if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
@@ -213,6 +193,10 @@ if(PYTHONINTERP_FOUND)
     # Generate gudhi.pyx - Gudhi cython file
     configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY)
 
+    # Generate gudhi/__init__.py
+    file(MAKE_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
+    configure_file(__init__.py.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi/__init__.py" @ONLY)
+
     add_custom_command(
         OUTPUT gudhi.so
         WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
diff --git a/src/cython/__init__.py.in b/src/cython/__init__.py.in
new file mode 100644
index 00000000..60ad7865
--- /dev/null
+++ b/src/cython/__init__.py.in
@@ -0,0 +1,40 @@
+from importlib import import_module
+
+"""This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+    Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2016  Inria
+
+   Modification(s):
+     - YYYY/MM Author: Description of the modification
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 Inria"
+__license__ = "https://gudhi.inria.fr/licensing/"
+__version__ = "@GUDHI_VERSION@"
+# This variable is used by doctest to find files
+__root_source_dir__ = "@CMAKE_SOURCE_DIR@"
+__debug_info__ = @GUDHI_CYTHON_DEBUG_INFO@
+
+from sys import exc_info
+from importlib import import_module
+
+__all__ = [@GUDHI_CYTHON_MODULES@]
+
+__available_modules__ = ''
+__missing_modules__ = ''
+
+# try to import * from gudhi.__module_name__
+for __module_name__ in __all__:
+    try:
+        __module__ = import_module('gudhi.' + __module_name__)
+        try:
+            __to_import__ = __module__.__all__
+        except AttributeError:
+            __to_import__ = [name for name in __module__.__dict__ if not name.startswith('_')]
+        globals().update({name: __module__.__dict__[name] for name in __to_import__})
+        __available_modules__ += __module_name__ + ";"
+    except:
+        __missing_modules__ += __module_name__ + ";"
diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in
index 70c85852..454be9af 100644
--- a/src/cython/setup.py.in
+++ b/src/cython/setup.py.in
@@ -14,11 +14,11 @@ from numpy import get_include as numpy_get_include
 
 __author__ = "GUDHI Editorial Board"
 __copyright__ = "Copyright (C) 2016  Inria"
-__license__ = "GPL v3"
+__license__ = "MIT"
 
-gudhi = Extension(
-    "gudhi",
-    sources = ['@CMAKE_CURRENT_BINARY_DIR@/gudhi.pyx',],
+simplextree = Extension(
+    "gudhi.simplextree",
+    sources = ['@CMAKE_CURRENT_SOURCE_DIR@/cython/simplex_tree.pyx',],
     language = 'c++',
     extra_compile_args=[@GUDHI_CYTHON_EXTRA_COMPILE_ARGS@],
     extra_link_args=[@GUDHI_CYTHON_EXTRA_LINK_ARGS@],
@@ -34,7 +34,7 @@ setup(
     author_email='gudhi-contact@lists.gforge.inria.fr',
     version='@GUDHI_VERSION@',
     url='http://gudhi.gforge.inria.fr/',
-    ext_modules = cythonize(gudhi),
+    ext_modules = cythonize(simplextree),
     install_requires = ['cython','numpy >= 1.9',],
     setup_requires = ['numpy >= 1.9',],
 )