fixing merge

.travis.yml

@@ -27,17 +27,17 @@ notifications:
 env:
   - CONFIG="Debug,Magick,GMP,ITK"
   - CONFIG="Debug,Cairo,QGLviewer,HDF5"
-  - CONFIG="Documentation,Debug,Cairo,GMP"
+  - CONFIG="Documentation"
   - CONFIG="DGtalTools"
 
 matrix:
   fast_finish: true
   exclude:
     - os: osx
-      env: CONFIG="Documentation,Debug,Cairo,GMP"
+      env: CONFIG="Documentation"
     - compiler: gcc
       os: linux
-      env: CONFIG="Documentation,Debug,Cairo,GMP"
+      env: CONFIG="Documentation"
     - compiler: gcc
       env: CONFIG="DGtalTools"
     - os: osx
@@ -70,15 +70,17 @@ addons:
 
 before_install:
   - if [ $CXX == "g++" ]; then CCOMPILER="gcc-4.8"; CXXCOMPILER="g++-4.8"; fi
-  - DOC="false"
+  - BUILD_DOC="false"
+  - UPLOAD_DOC="false"
   - NEEDCORE="true";
   - NEEDEXAMPLESANDTESTS="true";
-  - if [ $CONFIG == "Documentation,Debug,Cairo,GMP" ]; then NEEDEXAMPLESANDTESTS="false"; NEEDCORE="false"; if [ $OriginalRepo == "true" ];  then if [ $TRAVIS_PULL_REQUEST == "false" ]; then DOC="true"; fi; fi; fi
+  - if [ $CONFIG == "Documentation" ]; then NEEDEXAMPLESANDTESTS="false"; NEEDCORE="false"; BUILD_DOC="true"; if [ $OriginalRepo == "true" ];  then if [ $TRAVIS_PULL_REQUEST == "false" ]; then UPLOAD_DOC="true"; fi; fi; fi
   - if [ $CONFIG == "Debug,Magick,GMP,ITK" ]; then BTYPE="-DCMAKE_BUILD_TYPE=Debug  -DWITH_MAGICK=true -DWITH_GMP=true  -DBUILD_TESTING=ON  -DWARNING_AS_ERROR=ON";  fi
   - if [ $CONFIG == "Debug,Cairo,QGLviewer,HDF5" ]; then BTYPE="-DCMAKE_BUILD_TYPE=Debug -DWITH_HDF5=true -DWITH_CAIRO=true -DWITH_QGLVIEWER=true -DBUILD_TESTING=ON -DWARNING_AS_ERROR=OFF";   fi
-  - if [ $DOC == "true" ]; then  .travis/install_doxygen.sh;  BTYPE="-DDOXYGEN_EXECUTABLE=$HOME/doxygen/doxygen-1.8.10/bin/doxygen -DCMAKE_BUILD_TYPE=Debug -DWITH_CAIRO=true  -DWITH_GMP=true"; DOC="true"; openssl aes-256-cbc -K $encrypted_47769ec71275_key -iv $encrypted_47769ec71275_iv -in .travis/dgtal_rsa.enc -out .travis/dgtal_rsa -d; chmod 600 .travis/dgtal_rsa; DOC="true"; fi
   - if [ $CONFIG == "DGtalTools" ]; then NEEDEXAMPLESANDTESTS="false"; BTYPE="-DCMAKE_BUILD_TYPE=Debug  -DWITH_MAGICK=true -DWITH_GMP=true -DWITH_HDF5=true -DWITH_CAIRO=true -DWITH_QGLVIEWER=true -DBUILD_TESTING=OFF -DBUILD_EXAMPLES=off";  fi
-  - if [ $DOC == "true"]; then wget http://dgtal.org/doc/tags/DGtalTools-tagfile; fi 
+  - if [ $UPLOAD_DOC == "true" ]; then openssl aes-256-cbc -K $encrypted_47769ec71275_key -iv $encrypted_47769ec71275_iv -in .travis/dgtal_rsa.enc -out .travis/dgtal_rsa -d; chmod 600 .travis/dgtal_rsa; BUILD_DOC="true"; fi
+  - if [ $BUILD_DOC == "true" ]; then wget http://dgtal.org/doc/tags/DGtalTools-tagfile; fi
+  - if [ $BUILD_DOC == "true" ]; then .travis/install_doxygen.sh;  BTYPE="-DDOXYGEN_EXECUTABLE=$HOME/doxygen/doxygen-1.8.10/bin/doxygen"; fi
 
 ########
 # Deps.
@@ -93,23 +95,24 @@ before_script:
 ############
 script:
   - cmake . $BTYPE -DCMAKE_CXX_COMPILER=$CXXCOMPILER -DCMAKE_C_COMPILER=$CCOMPILER
-  - echo $DOC
+  - echo $BUILD_DOC
+  - echo $UPLOAD_DOC
   - echo $BTYPE
   - if [ $NEEDCORE == "true" ]; then  make -j 3 DGtal && make -j 3 DGtalIO; fi
   - if [ $NEEDEXAMPLESANDTESTS == "true" ]; then  cd examples && make  -j 3 ; fi
   - if [ $NEEDEXAMPLESANDTESTS == "true" ]; then  cd ../tests &&  make -j 3 &&  cd .. ; fi
   - if [ $NEEDEXAMPLESANDTESTS == "true" ]; then  make test ARGS=--output-on-failure ; fi
   - if [ $CONFIG == "DGtalTools" ]; then pwd ; .travis/getAndCheckDGtalTools.sh ; fi
-
+  - if [ $BUILD_DOC == "true" ]; then make doc; fi
+  - if [ $CONFIG == "Documentation" ]; then ./.travis/checkDoxygenDocumentation.sh; fi
 
 
 ###########
 ## Building the documentation
 ###########
 after_success:
-  - if [ $DOC == "true" ]; then  make doc; fi
-  - if [ $DOC == "true" ]; then rsync -azv --delete --delete-after -e 'ssh -oStrictHostKeyChecking=no -i  .travis/dgtal_rsa' html/ [email protected]:/home/dgtal/public_html/doc/nightly/;  fi
-  - if [ $DOC == "true" ]; then cd html; make ; wget http://dgtal.org/doc/docset/template.tgz ; tar zxvf template.tgz ; mv template/* org.dgtal.docset ; tar zcvf DGtal-devel.tgz org.dgtal.docset ; cd .. ;rsync  -azv --delete --delete-after -e 'ssh -oStrictHostKeyChecking=no -i  .travis/dgtal_rsa' html/DGtal-devel.tgz [email protected]:/home/dgtal/public_html/doc/docset ;   fi
+  - if [ $UPLOAD_DOC == "true" ]; then rsync -azv --delete --delete-after -e 'ssh -oStrictHostKeyChecking=no -i  .travis/dgtal_rsa' html/ [email protected]:/home/dgtal/public_html/doc/nightly/;  fi
+  - if [ $UPLOAD_DOC == "true" ]; then cd html; make ; wget http://dgtal.org/doc/docset/template.tgz ; tar zxvf template.tgz ; mv template/* org.dgtal.docset ; tar zcvf DGtal-devel.tgz org.dgtal.docset ; cd .. ;rsync  -azv --delete --delete-after -e 'ssh -oStrictHostKeyChecking=no -i  .travis/dgtal_rsa' html/DGtal-devel.tgz [email protected]:/home/dgtal/public_html/doc/docset ;   fi
     ## We publish the DGtalTools tags
-  - if [ $DOC == "true" ]; then scp -i  .travis/dgtal_rsa  DGtal-tagfile [email protected]:/home/dgtal/public_html/doc/tags/;scp -i  .travis/dgtal_rsa  Board-tagfile [email protected]:/home/dgtal/public_html/doc/tags/; fi
+  - if [ $UPLOAD_DOC == "true" ]; then scp -i  .travis/dgtal_rsa  DGtal-tagfile [email protected]:/home/dgtal/public_html/doc/tags/;scp -i  .travis/dgtal_rsa  Board-tagfile [email protected]:/home/dgtal/public_html/doc/tags/; fi
   - echo "All done..."

.travis/checkDoxygenDocumentation.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+
+return_code=0
+return_code2=0
+return_code3=0
+HOMEPATH=$PWD
+
+
+## We first check that the doxygen.log is empty
+if [[ -s doxygen.log ]]
+then
+    return_code=1
+    echo "Doxygen log file not empty !"
+    echo "====================================="
+    cat doxygen.log
+    echo "====================================="
+else
+    return_code=0
+fi
+
+## We check src code consitency
+cd src/
+$HOMEPATH/.travis/check_src_file_tag.sh
+if [[ $? -ne 0 ]]
+then
+    return_code2=1;
+fi
+cd ..
+
+## We check examples consistency
+#
+# TODO
+# 
+
+return_code=$((return_code + return_code2 + return_code3))
+exit $return_code

.travis/check_examples_file_tag.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+return_code=0
+
+# Checking that examples has proper @file tag
+for file in `find * -type f \( -name \*.c -o -name \*.cpp -o -name \*.cxx -o -name \*.h -o -name \*.hpp -o -name \*.hxx \)`
+do
+  expected_name=$file
+  if ! $(grep -aqE "^\s*(\**|//[/!]|/\*[\*!])\s*?[@\\\\]example(\s+${expected_name})?\s*$" $file)
+  then
+    echo -E "Error in file $file:"
+    echo -E "  expecting \" * @example ${expected_name}\""
+    echo -E "  but found \"$(grep -m 1 -aP '[@\\](example|file)' $file)\""
+    echo
+
+    return_code=1
+  fi
+done
+
+exit $return_code

.travis/check_src_file_tag.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+return_code=0
+
+# Checking that source code has proper @file tag
+for file in `find * -type f \( -name \*.cpp -o -name \*.h -o -name \*.ih \)`
+do
+  expected_name=$(basename $file)
+  if ! $(grep -aqE "^\s*(\**|//[/!]|/\*[\*!])\s*?[@\\\\]file(\s+${expected_name})?\s*$" $file)
+  then
+    echo -E "Error in file $file:"
+    echo -E "  expecting \" * @file ${expected_name}\""
+    echo -E "  or simply \" * @file\""
+    echo -E "  but found \"$(grep -m 1 -aP '[@\\]file' $file)\""
+    echo
+
+    return_code=1
+  fi
+done
+
+exit $return_code

ChangeLog.md

@@ -3,6 +3,8 @@
 ## New Features / Critical Changes
 
 - *Documentation*
+ - Fixing all doxygen warnings.
+   (Roland Denis, [#1182](https://github.com/DGtal-team/DGtal/pull/1182))
  - New "@seeDGtalTools" doxygen command to cite a DGtalTools tool in
    DGtal documentation (David Coeurjolly,
    [#1179](https://github.com/DGtal-team/DGtal/pull/1179))
@@ -12,8 +14,21 @@
    voting (Boulc'h & Marlet, SGP 2012).
    (David Coeurjolly, [#1149](https://github.com/DGtal-team/DGtal/pull/1149))
 
+- *Topology Package*
+ - Adding periodic closure for KhalimskySpaceND and per-dimension closure
+   specification.
+   (Roland Denis, [#1086](https://github.com/DGtal-team/DGtal/pull/1086))
+ - Adding CPreCellularGridSpaceND concept and KhalimskyPreSpaceND model
+   to manipulate unbounded Khalimsky space and cells.
+   KhalimskySpaceND now checks that all given cells are within the bounds.
+   (Roland Denis, [#1086](https://github.com/DGtal-team/DGtal/pull/1086))
+
 ## Changes
 - *Configuration/General*
+ - Travis Continuous integration will check that doxygen raises no warnings
+   and that the documented file names are valid.
+   (David Coeurjolly, Roland Denis,
+        [#1182](https://github.com/DGtal-team/DGtal/pull/1182))
  - Cleaning remaining preprocessor directives related to C++11 features.
    (Roland Denis, [#1141](https://github.com/DGtal-team/DGtal/pull/1141))
  - Travis Continuous integration will check that DGtalTools still compiles with
@@ -24,7 +39,9 @@
    [#1155](https://github.com/DGtal-team/DGtal/pull/1155))
  - Documentation graphs are now in SVG instead of PNG. (David Coeurjolly,
    [#1192](https://github.com/DGtal-team/DGtal/pull/1192))
-
+ - Check and add all DGtal examples in the Examples listing section.
+   (Bertrand Kerautret,[#1166](https://github.com/DGtal-team/DGtal/pull/1166))))
+
 - *Base Package*
  - Alias and ConstAlias now raise compilation error when using invalid
    constructor, like from a rvalue reference. Adding ConstAlias in many classes
@@ -37,6 +54,9 @@
    (https://github.com/DGtal-team/DGtal/pull/1164))
 
 - *IO Package*
+ - Viewer3D: improvement of the viewer state record by saving the rendering 
+   mode. A new setter was also added to desable/enable double face rendering.
+   (Bertrand Kerautret [#1166](https://github.com/DGtal-team/DGtal/pull/1162))
  - Viewer3D: add a mode to display ball primitive with OpenGL point instead of
    quadrangulated mesh.
    (Bertrand Kerautret [#1162](https://github.com/DGtal-team/DGtal/pull/1162))
@@ -71,6 +91,8 @@
    when displaying a small segment. Fix a non initialized attribute with
    some improvements on bounding box computation with orientation check.
    (B. Kerautret, [#1123](https://github.com/DGtal-team/DGtal/pull/1123))
+ - Frechet Shortcut: fix implicit rounding.
+   (I. Sivignon, [#1180](https://github.com/DGtal-team/DGtal/pull/1180))
 
 - *Image Package*
  - Fixing issue [#779](https://github.com/DGtal-team/DGtal/issues/779) by

README.md

@@ -26,13 +26,16 @@ Quick Install
 
 * Linux: [Binary packages](https://software.opensuse.org/download.html?project=home%3Acopyme%3ADGtal&package=DGtal) (Arch, CentOS, Fedora, openSUSE, RHEL, SL)
 * MacOS (using [homebrew](http://brew.sh)):
-        brew install dgtal
+
+       ```brew install dgtal```
+
+
 (```brew options dgtal``` to enable optional features)
 
 * Windows: no binary package, please compile the library.
 
 
-Additional instructions are availalbe in the
+Additional instructions are available in the
 [documentation](http://dgtal.org/doc/nightly/moduleBuildDGtal.html).
 
 Quick Build Instructions

doc/doxy.config.Board.in

@@ -759,7 +759,7 @@ WARN_FORMAT            = "$file:$line: $text"
 # messages should be written. If left blank the output is written to standard
 # error (stderr).
 
-WARN_LOGFILE           =
+WARN_LOGFILE           = @top_bindir@/doxygen.Board.log
 
 #---------------------------------------------------------------------------
 # Configuration options related to the input files
@@ -800,6 +800,7 @@ FILE_PATTERNS          = *.cpp \
                          *.hpp \
                          *.cxx \
                          *.h \
+                         *.ih \
                          *.dox
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
@@ -848,7 +849,7 @@ EXCLUDE_SYMBOLS        =
 # that contain example code fragments that are included (see the \include
 # command).
 
-EXAMPLE_PATH           = html
+EXAMPLE_PATH           =
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and

doc/doxy.config.dox.in

@@ -761,7 +761,7 @@ WARN_FORMAT            = "$file:$line: $text"
 # messages should be written. If left blank the output is written to standard
 # error (stderr).
 
-WARN_LOGFILE           =
+WARN_LOGFILE           = @top_bindir@/doxygen.dox.log
 
 #---------------------------------------------------------------------------
 # Configuration options related to the input files

doc/doxy.config.in

@@ -161,7 +161,7 @@ STRIP_FROM_PATH        =
 # specify the list of include paths that are normally passed to the compiler
 # using the -I flag.
 
-STRIP_FROM_INC_PATH    = @top_srcdir@/src/DGtal/
+STRIP_FROM_INC_PATH    = @top_srcdir@/src/
 
 # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
 # less readable) file names. This can be useful is your file systems doesn't
@@ -763,7 +763,7 @@ WARN_FORMAT            = "$file:$line: $text"
 # messages should be written. If left blank the output is written to standard
 # error (stderr).
 
-WARN_LOGFILE           =
+WARN_LOGFILE           = @top_bindir@/doxygen.log
 
 #---------------------------------------------------------------------------
 # Configuration options related to the input files
@@ -881,7 +881,6 @@ EXAMPLE_RECURSIVE      = YES
 
 IMAGE_PATH             = @top_srcdir@/src/DGtal/doc/images \
                          @top_srcdir@/src/DGtal/doc/tutorials/images \
-                         @top_srcdir@/src/DGtal/base/doc/images \
                          @top_srcdir@/src/DGtal/kernel/doc/images \
                          @top_srcdir@/src/DGtal/graph/doc/images \
                          @top_srcdir@/src/DGtal/dec/doc/images \
@@ -891,8 +890,7 @@ IMAGE_PATH             = @top_srcdir@/src/DGtal/doc/images \
                          @top_srcdir@/src/DGtal/math/doc/images \
                          @top_srcdir@/src/DGtal/geometry/doc/images \
                          @top_srcdir@/src/DGtal/topology/doc/images \
-                         @top_srcdir@/src/DGtal/shapes/doc/images \
-                         @top_srcdir@/src/DGtal/helpers/doc/images
+                         @top_srcdir@/src/DGtal/shapes/doc/images
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program
@@ -2007,15 +2005,15 @@ ENABLE_PREPROCESSING   = YES
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-MACRO_EXPANSION        = NO
+MACRO_EXPANSION        = YES
 
 # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
 # the macro expansion is limited to the macros specified with the PREDEFINED and
 # EXPAND_AS_DEFINED tags.
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-EXPAND_ONLY_PREDEF     = NO
+EXPAND_ONLY_PREDEF     = YES
 
 # If the SEARCH_INCLUDES tag is set to YES, the include files in the
 # INCLUDE_PATH will be searched if a #include is found.
@@ -2047,7 +2045,17 @@ INCLUDE_FILE_PATTERNS  =
 # recursively expanded use the := operator instead of the = operator.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-PREDEFINED             =
+PREDEFINED             = "BOOST_FUSION_ADAPT_STRUCT(x,y)=" \
+                         "WITH_GMP=" \
+                         "WITH_CAIRO=" \
+                         "WITH_CGAL=" \
+                         "WITH_EIGEN=" \
+                         "WITH_HDF5=" \
+                         "WITH_ITK=" \
+                         "WITH_MAGICK=" \
+                         "WITH_PATATE=" \
+                         "WITH_QGLVIEWER="
+
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
 # tag can be used to specify a list of macro names that should be expanded. The
@@ -2085,8 +2093,7 @@ SKIP_FUNCTION_MACROS   = YES
 # the path). If a tag file is not located in the directory in which doxygen is
 # run, you must also specify the path to the tagfile here.
 
-TAGFILES               = "DGtalTools-tagfile=http://dgtal.org/doc/tools/nightly/" \
-                         "Board-tagfile=http://dgtal.org/doc/nightly/"
+TAGFILES               = "DGtalTools-tagfile=http://dgtal.org/doc/tools/nightly/"
 
 # When a file name is specified after GENERATE_TAGFILE, doxygen will create a
 # tag file that is based on the input files it reads. See section "Linking to

examples/arithmetic/approximation.cpp

@@ -1,5 +1,5 @@
 /**
- * @file approximation.cpp
+ * @file arithmetic/approximation.cpp
  * @ingroup Examples
  * @author Jacques-Olivier Lachaud (\c [email protected] )
  * Laboratory of Mathematics (CNRS, UMR 5127), University of Savoie, France

examples/arithmetic/convergents-biginteger.cpp

@@ -1,5 +1,5 @@
 /**
- * @file convergents-biginteger.cpp
+ * @file arithmetic/convergents-biginteger.cpp
  * @ingroup Examples
  * @author Jacques-Olivier Lachaud (\c [email protected] )
  * Laboratory of Mathematics (CNRS, UMR 5127), University of Savoie, France

examples/arithmetic/convergents.cpp

@@ -1,5 +1,5 @@
 /**
- * @file convergents.cpp
+ * @file arithmetic/convergents.cpp
  * @ingroup Examples
  * @author Jacques-Olivier Lachaud (\c [email protected] )
  * Laboratory of Mathematics (CNRS, UMR 5127), University of Savoie, France

examples/arithmetic/extended-euclid.cpp

@@ -1,5 +1,5 @@
 /**
- * @file extended-euclid.cpp
+ * @file arithmetic/extended-euclid.cpp
  * @ingroup Examples
  * @author Jacques-Olivier Lachaud (\c [email protected] )
  * Laboratory of Mathematics (CNRS, UMR 5127), University of Savoie, France

examples/arithmetic/fraction.cpp

@@ -1,5 +1,5 @@
 /**
- * @file fraction.cpp
+ * @file arithmetic/fraction.cpp
  * @ingroup Examples
  * @author Jacques-Olivier Lachaud (\c [email protected] )
  * Laboratory of Mathematics (CNRS, UMR 5127), University of Savoie, France

examples/arithmetic/lower-integer-convex-hull.cpp

@@ -1,5 +1,5 @@
 /**
- * @file lower-integer-convex-hull.cpp
+ * @file arithmetic/lower-integer-convex-hull.cpp
  * @ingroup Examples
  * @author Jacques-Olivier Lachaud (\c [email protected] )
  * Laboratory of Mathematics (CNRS, UMR 5127), University of Savoie, France