generate_version excludes bottleneck for version 1.2.0 - to be removed for 1.3.0

generate_version copies concept for doxygen purpose
Contact gudhi-users on skbl and contraction page
Doxygen warning fixes
Doxygen Software section



git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@871 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: bd7e252c2d0528f4bbc40c33a9221e1d6b386510

7 files changed, 68 insertions, 13 deletions

diff --git a/scripts/generate_version.sh b/scripts/generate_version.sh
index 43a54c1c..323396dc 100755
--- a/scripts/generate_version.sh
+++ b/scripts/generate_version.sh
@@ -61,12 +61,13 @@ cp $ROOT_DIR/GUDHIVersion.cmake.in $VERSION_DIR
 PACKAGE_INC_DIR="/include"
 #PACKAGE_SRC_DIR="/source"
 PACKAGE_EX_DIR="/example"
+PACKAGE_CONCEPT_DIR="/concept"
 PACKAGE_DOC_DIR="/doc"
 for package in `ls $ROOT_DIR/src/`
 do
-  echo $package
-  if [ -d "$ROOT_DIR/src/$package" ]
+  if [ -d "$ROOT_DIR/src/$package" ] && [ $package != "Bottleneck" ]
   then
+    echo $package
     if [ "$package" == "cmake" ]
     then
       # SPECIFIC FOR CMAKE MODULES
@@ -91,6 +92,11 @@ do
         mkdir -p $VERSION_DIR$PACKAGE_EX_DIR/$package
         cp -R $ROOT_DIR/src/$package$PACKAGE_EX_DIR/* $VERSION_DIR$PACKAGE_EX_DIR/$package
       fi
+      if [ -d "$ROOT_DIR/src/$package$PACKAGE_CONCEPT_DIR" ]
+      then
+        mkdir -p $VERSION_DIR$PACKAGE_CONCEPT_DIR/$package
+        cp -R $ROOT_DIR/src/$package$PACKAGE_CONCEPT_DIR/* $VERSION_DIR$PACKAGE_CONCEPT_DIR/$package
+      fi
       if [ -d "$ROOT_DIR/src/$package$PACKAGE_DOC_DIR" ]
       then
         mkdir -p $VERSION_DIR$PACKAGE_DOC_DIR/$package
diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h
index dfce8d1b..f3076057 100644
--- a/src/Contraction/include/gudhi/Edge_contraction.h
+++ b/src/Contraction/include/gudhi/Edge_contraction.h
@@ -226,7 +226,7 @@ Time to simplify and enumerate simplices:
 
 
 \copyright GNU General Public License v3.                         
-\verbatim  Contact: David Salinas,     david.salinas@inria.fr \endverbatim
+\verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
 */
 /** @} */  // end defgroup
 }  // namespace contraction
diff --git a/src/Doxyfile b/src/Doxyfile
index 85c496a8..084a9abb 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME           = "Gudhi"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = "1.1.0"
+PROJECT_NUMBER         = "1.2.0"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -1338,7 +1338,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-DISABLE_INDEX          = NO
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information. If the tag
@@ -1355,7 +1355,7 @@ DISABLE_INDEX          = NO
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-GENERATE_TREEVIEW      = NO
+GENERATE_TREEVIEW      = YES
 
 # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
 # doxygen will group on one line in the generated HTML documentation.
diff --git a/src/Simplex_tree/concept/SimplexTreeOptions.h b/src/Simplex_tree/concept/SimplexTreeOptions.h
index a50a2bf1..add3ebdd 100644
--- a/src/Simplex_tree/concept/SimplexTreeOptions.h
+++ b/src/Simplex_tree/concept/SimplexTreeOptions.h
@@ -34,8 +34,8 @@ struct SimplexTreeOptions {
   /// Must be a signed integer type.
   typedef SimplexKey Simplex_key;
   /// If true, each simplex has extra storage for one `Simplex_key`. Necessary for `Persistent_cohomology`.
-  static constexpr bool store_key;
-  /// If true, each simplex has extra storage for one `Filtration_value`, and this value is propagated by operations like `Gudhi::Simplex_tree<SimplexTreeOptions>::expansion`. Without it, `Persistent_cohomology` degenerates to computing usual (non-persistent) cohomology.
-  static constexpr bool store_filtration;
+  static const bool store_key;
+  /// If true, each simplex has extra storage for one `Filtration_value`, and this value is propagated by operations like `Gudhi::Simplex_tree::expansion`. Without it, `Persistent_cohomology` degenerates to computing usual (non-persistent) cohomology.
+  static const bool store_filtration;
 };
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
index 792a7994..3be480fd 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
@@ -241,7 +241,7 @@ their collaboration to write the two initial papers
 
 
 \copyright GNU General Public License v3.                         
-\verbatim  Contact: David Salinas,     david.salinas@inria.fr \endverbatim
+\verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
 */
 /** @} */  // end defgroup
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
index 07f371a2..d26d12b0 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
@@ -1018,7 +1018,7 @@ class Skeleton_blocker_complex {
   }
 
   //@}
-  /** @Simplification operations
+  /** @name Simplification operations
    */
   //@{
 
@@ -1131,7 +1131,7 @@ class Skeleton_blocker_complex {
   }
   //@}
 
-  /** @Edge contraction operations
+  /** @name Edge contraction operations
    */
   //@{
 
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 315aa0ac..d1060740 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -7,7 +7,7 @@ The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic C+
 topological analysis of high-dimensional data whose goal is to provide robust, efficient, flexible and easy to use 
 implementations of 
 state-of-the-art algorithms and data structures for computational topology.
-This library is part of the <a href="https://project.inria.fr/gudhi/">Gudhi project</a>.
+This library is part of the <a class="el" href="https://project.inria.fr/gudhi/">Gudhi project</a>.
 
 The current release of the library allows to use several data-structures for simplicial complexes :
 simplex tree, Hasse diagram or skeleton-blocker. Several  operations can then be done on top of these
@@ -70,3 +70,52 @@ make
 \verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
 
 */
+
+/*! \page Software Software
+ * \tableofcontents
+ * \section SoftwareIntroduction Introduction
+ * The GUDHI open source library will provide the central data structures and algorithms that underly applications in geometry understanding in higher dimensions. It is intended to both help the development of new algorithmic solutions inside and outside the project, and to facilitate the transfer of results in applied fields.
+ *
+ * The current release of the GUDHI library includes:
+ * 
+ * – Data structures to represent, construct and manipulate simplicial complexes.
+ * 
+ * – Algorithms to compute persistent homology and multi-field persistent homology.
+ * 
+ * – Simplification methods via implicit representations.
+ * 
+ *
+ * The library is available <a class="el" href="https://gforge.inria.fr/frs/?group_id=3865">here</a> and the documentation is
+ * available at this <a class="el" href="http://gudhi.gforge.inria.fr/doc/1.1.0/">webpage</a>.
+ * 
+ * \section ReleaseHistory Release history
+ *
+ * – ??-??-2015; release v.1.2.0, Skeleton-Blocker simplex insertion, GudhUI (Gudhi Qt demo), Simplex tree coface function, Clang build issue fix.
+ *
+ * – 12-18-2014; release v.1.1, Skeleton-Blocker data-structure, simplification package, additional examples for topological persistence.
+ *
+ * – 08-12-2014; release v. 1.0.2, initialize simplex keys in initialize_filtration in Simplex_tree
+ *
+ * – 07-11-2014: release v. 1.0.1, bug fix in summing columns in Persistent_cohomology
+ *
+ * – 06-23-2014: release v. 1.0
+ * 
+ * \section Citation How to cite Gudhi
+ * Each Gudhi <a class="el" href="modules.html">module</a> (either data structures or algorithms) has an author section.
+ * 
+ * Thank you to refer to this section, and to cite the author(s) of all the module you are using.
+ * 
+ * \section Soon Coming soon
+ *
+ * – Alpha complex.
+ *
+ * – Bottleneck distance.
+ *
+ * – Zig zag persistence.
+ *
+ * – Witness complex.
+ *
+ * – Tangential complex.
+ *
+ * – Hard clustering.
+*/