Rename namespaces according to convention

+ Missing Boost_THREAD_LIBRARY
+ Useless typename
+ Use TBB_LIBRARIES

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/fix_naming@1274 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5c02ec481b62ef52b40d849e76e3d333e2ca4e7c

11 files changed, 34 insertions, 24 deletions

diff --git a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
index 550e90b9..4c9c04d9 100644
--- a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
+++ b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
@@ -26,7 +26,7 @@
 
 namespace Gudhi {
 
-namespace Cubical_complex {
+namespace cubical_complex {
 
 /**  \defgroup cubical_complex Cubical complex
  *
@@ -150,7 +150,9 @@ namespace Cubical_complex {
  */
 /** @} */  // end defgroup cubical_complex
 
-}  // namespace Cubical_complex
+}  // namespace cubical_complex
+
+namespace Cubical_complex = cubical_complex;
 
 }  // namespace Gudhi
 
diff --git a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp
index 7c7e8ac5..e6bc6648 100644
--- a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp
+++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp
@@ -47,8 +47,8 @@ int main(int argc, char** argv) {
     return 1;
   }
 
-  typedef Gudhi::Cubical_complex::Bitmap_cubical_complex_base<double> Bitmap_cubical_complex_base;
-  typedef Gudhi::Cubical_complex::Bitmap_cubical_complex<Bitmap_cubical_complex_base> Bitmap_cubical_complex;
+  typedef Gudhi::cubical_complex::Bitmap_cubical_complex_base<double> Bitmap_cubical_complex_base;
+  typedef Gudhi::cubical_complex::Bitmap_cubical_complex<Bitmap_cubical_complex_base> Bitmap_cubical_complex;
   typedef Gudhi::persistent_cohomology::Field_Zp Field_Zp;
   typedef Gudhi::persistent_cohomology::Persistent_cohomology<Bitmap_cubical_complex, Field_Zp> Persistent_cohomology;
 
diff --git a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
index 2c5d7fd3..839a4c89 100644
--- a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
+++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
@@ -49,8 +49,8 @@ int main(int argc, char** argv) {
     return 1;
   }
 
-  typedef Gudhi::Cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double> Bitmap_base;
-  typedef Gudhi::Cubical_complex::Bitmap_cubical_complex< Bitmap_base > Bitmap_cubical_complex;
+  typedef Gudhi::cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double> Bitmap_base;
+  typedef Gudhi::cubical_complex::Bitmap_cubical_complex< Bitmap_base > Bitmap_cubical_complex;
 
   Bitmap_cubical_complex b(argv[1]);
 
diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt
index b26999d0..2fddc514 100644
--- a/src/Bitmap_cubical_complex/example/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt
@@ -4,7 +4,7 @@ project(Bitmap_cubical_complex_examples)
 add_executable ( Bitmap_cubical_complex Bitmap_cubical_complex.cpp )
 target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})
 if (TBB_FOUND)
-  target_link_libraries(Bitmap_cubical_complex ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(Bitmap_cubical_complex ${TBB_LIBRARIES})
 endif()
 add_test(Bitmap_cubical_complex_one_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt)
 add_test(Bitmap_cubical_complex_two_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
@@ -12,14 +12,14 @@ add_test(Bitmap_cubical_complex_two_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cu
 add_executable ( Random_bitmap_cubical_complex Random_bitmap_cubical_complex.cpp )
 target_link_libraries(Random_bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})
 if (TBB_FOUND)
-  target_link_libraries(Random_bitmap_cubical_complex ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(Random_bitmap_cubical_complex ${TBB_LIBRARIES})
 endif()
 add_test(Random_bitmap_cubical_complex ${CMAKE_CURRENT_BINARY_DIR}/Random_bitmap_cubical_complex 2 100 100)
 
 add_executable ( Bitmap_cubical_complex_periodic_boundary_conditions Bitmap_cubical_complex_periodic_boundary_conditions.cpp )
 target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${Boost_SYSTEM_LIBRARY})
 if (TBB_FOUND)
-  target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${TBB_LIBRARIES})
 endif()
 add_test(Bitmap_cubical_complex_periodic_2d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt)
 add_test(Bitmap_cubical_complex_periodic_3d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt)
diff --git a/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp
index 416ad8f2..16ad65a0 100644
--- a/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp
+++ b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp
@@ -61,8 +61,8 @@ int main(int argc, char** argv) {
     data.push_back(rand() / static_cast<double>(RAND_MAX));
   }
 
-  typedef Gudhi::Cubical_complex::Bitmap_cubical_complex_base<double> Bitmap_cubical_complex_base;
-  typedef Gudhi::Cubical_complex::Bitmap_cubical_complex<Bitmap_cubical_complex_base> Bitmap_cubical_complex;
+  typedef Gudhi::cubical_complex::Bitmap_cubical_complex_base<double> Bitmap_cubical_complex_base;
+  typedef Gudhi::cubical_complex::Bitmap_cubical_complex<Bitmap_cubical_complex_base> Bitmap_cubical_complex;
   Bitmap_cubical_complex b(sizes, data);
 
   // Compute the persistence diagram of the complex
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
index 56fa297c..5a87b9b8 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
@@ -38,7 +38,7 @@
 
 namespace Gudhi {
 
-namespace Cubical_complex {
+namespace cubical_complex {
 
 // global variable, was used just for debugging.
 const bool globalDbg = false;
@@ -586,7 +586,9 @@ class is_before_in_filtration {
   Bitmap_cubical_complex<T>* CC_;
 };
 
-}  // namespace Cubical_complex
+}  // namespace cubical_complex
+
+namespace Cubical_complex = cubical_complex;
 
 }  // namespace Gudhi
 
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h
index 3a8c3988..4b072f10 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h
@@ -28,7 +28,7 @@
 
 namespace Gudhi {
 
-namespace Cubical_complex {
+namespace cubical_complex {
 
 /**
  * @brief This is an implementation of a counter being a vector of integers. 
@@ -135,7 +135,9 @@ class counter {
   std::vector< unsigned > current;
 };
 
-}  // namespace Cubical_complex
+}  // namespace cubical_complex
+
+namespace Cubical_complex = cubical_complex;
 
 }  // namespace Gudhi
 
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
index 2f74ba9e..0442ac34 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
@@ -36,7 +36,7 @@
 
 namespace Gudhi {
 
-namespace Cubical_complex {
+namespace cubical_complex {
 
 /**
  * @brief Cubical complex represented as a bitmap, class with basic implementation.
@@ -808,7 +808,9 @@ bool compareFirstElementsOfTuples(const std::pair< std::pair< T, size_t >, char
   }
 }
 
-}  // namespace Cubical_complex
+}  // namespace cubical_complex
+
+namespace Cubical_complex = cubical_complex;
 
 }  // namespace Gudhi
 
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h
index 0d0f2f84..c3cc93dd 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h
@@ -31,7 +31,7 @@
 
 namespace Gudhi {
 
-namespace Cubical_complex {
+namespace cubical_complex {
 
 // in this class, we are storing all the elements which are in normal bitmap (i.e. the bitmap without the periodic
 // boundary conditions). But, we set up the iterators and the procedures to compute boundary and coboundary in the way
@@ -299,7 +299,9 @@ std::vector< size_t > Bitmap_cubical_complex_periodic_boundary_conditions_base<T
   return coboundary_elements;
 }
 
-}  // namespace Cubical_complex
+}  // namespace cubical_complex
+
+namespace Cubical_complex = cubical_complex;
 
 }  // namespace Gudhi
 
diff --git a/src/Bitmap_cubical_complex/test/Bitmap_test.cpp b/src/Bitmap_cubical_complex/test/Bitmap_test.cpp
index a9162cee..db90eb94 100644
--- a/src/Bitmap_cubical_complex/test/Bitmap_test.cpp
+++ b/src/Bitmap_cubical_complex/test/Bitmap_test.cpp
@@ -34,12 +34,12 @@
 #include <vector>
 
 
-typedef Gudhi::Cubical_complex::Bitmap_cubical_complex_base<double> Bitmap_cubical_complex_base;
-typedef Gudhi::Cubical_complex::Bitmap_cubical_complex<Bitmap_cubical_complex_base> Bitmap_cubical_complex;
+typedef Gudhi::cubical_complex::Bitmap_cubical_complex_base<double> Bitmap_cubical_complex_base;
+typedef Gudhi::cubical_complex::Bitmap_cubical_complex<Bitmap_cubical_complex_base> Bitmap_cubical_complex;
 
-typedef Gudhi::Cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double>
+typedef Gudhi::cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double>
 Bitmap_cubical_complex_periodic_boundary_conditions_base;
-typedef Gudhi::Cubical_complex::Bitmap_cubical_complex<Bitmap_cubical_complex_periodic_boundary_conditions_base>
+typedef Gudhi::cubical_complex::Bitmap_cubical_complex<Bitmap_cubical_complex_periodic_boundary_conditions_base>
 Bitmap_cubical_complex_periodic_boundary_conditions;
 
 BOOST_AUTO_TEST_CASE(check_dimension) {
diff --git a/src/Bitmap_cubical_complex/test/CMakeLists.txt b/src/Bitmap_cubical_complex/test/CMakeLists.txt
index e98251c2..daf0e14f 100644
--- a/src/Bitmap_cubical_complex/test/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/test/CMakeLists.txt
@@ -13,7 +13,7 @@ endif()
 add_executable ( BitmapCCUT Bitmap_test.cpp )
 target_link_libraries(BitmapCCUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 if (TBB_FOUND)
-  target_link_libraries(BitmapCCUT ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(BitmapCCUT ${TBB_LIBRARIES})
 endif()
 
 # Unitary tests