Finished a new release: libDAI 0.2.7.

diff --git a/AUTHORS b/AUTHORS
index 95eadcd..f629134 100644 (file)
--- a/AUTHORS
+++ b/AUTHORS
@@ -1,21 +1,16 @@
-The following people have contributed to libDAI:
+libDAI was written by Joris M. Mooij with the help of the following people:
 
-Joris Mooij
-Martijn Leisink
-Frederik Eaton
-Charles Vaske
-Giuseppe Passino
-Bastian Wemmenhove
-Patrick Pletscher
-Christian Wojek
-Claudio Lima
-Jiuxiang Hu
-Peter Gober
-Sebastian Nowozin
-Alexander Schwing
-Ofer Meshi
-Alejandro Lage
-Peter Rockett
+Martijn Leisink (laid down the foundations for the library),
+Frederik Eaton (contributed the Gibbs sampler, conditioned BP, fractional BP and various other improvements),
+Charles Vaske (contributed the parameter learning algorithms),
+Giuseppe Passino (contributed the findMaximum function, and various other improvements),
+Bastian Wemmenhove (contributed the MR algorithm),
+Patrick Pletscher (contributed the SWIG interface).
+
+Smaller contributions (bug fixes and miscellaneous smaller patches) have been made by:
+Claudio Lima, Christian Wojek, Sebastian Nowozin, Stefano Pellegrini, Ofer Meshi,
+Dan Preston, Peter Gober, Jiuxiang Hu, Peter Rockett, Dhruv Batra, Alexander Schwing, 
+Alejandro Lage, Matt Dunham.
 
 Part of this work was part of the Interactive Collaborative Information Systems (ICIS) 
 project, supported by the Dutch Ministry of Economic Affairs, grant BSIK03024.

diff --git a/ChangeLog b/ChangeLog
index 89e978d..aa39936 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,5 +1,5 @@
-git master
-----------
+libDAI-0.2.7 (2010-08-19)
+-------------------------
 
 * Removed interfaces deprecated in 0.2.6.
 * Fixed a bug in JTree::findMaximum() (reported by zhengyun84 and Dhruv Batra):

diff --git a/Makefile b/Makefile
index 50fbf0f..29956c4 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -15,8 +15,8 @@ include Makefile.ALL
 include Makefile.conf
 
 # Set version and date
-DAI_VERSION="git master"
-DAI_DATE="August 11, 2010 (or later)"
+DAI_VERSION="0.2.7"
+DAI_DATE="August 19, 2010"
 
 # Directories of libDAI sources
 # Location of libDAI headers
@@ -120,6 +120,7 @@ MEX:=$(MEX) $(MEXINC) $(MEXFLAGS) $(WITHFLAGS) $(MEXLIB)
 ###############
 
 all : $(TARGETS)
+       @echo
        @echo libDAI built successfully!
 
 EXAMPLES=$(foreach name,example example_bipgraph example_varset example_permute example_sprinkler example_sprinkler_em,examples/$(name)$(EE))
@@ -134,7 +135,8 @@ examples : $(EXAMPLES)
 matlabs : matlab/dai$(ME) matlab/dai_readfg$(ME) matlab/dai_writefg$(ME) matlab/dai_potstrength$(ME)
 
 unittests : tests/unit/var_test$(EE) tests/unit/smallset_test$(EE) tests/unit/varset_test$(EE) tests/unit/graph_test$(EE) tests/unit/dag_test$(EE) tests/unit/bipgraph_test$(EE) tests/unit/weightedgraph_test$(EE) tests/unit/enum_test$(EE) tests/unit/enum_test$(EE) tests/unit/util_test$(EE) tests/unit/exceptions_test$(EE) tests/unit/properties_test$(EE) tests/unit/index_test$(EE) tests/unit/prob_test$(EE) tests/unit/factor_test$(EE) tests/unit/factorgraph_test$(EE) tests/unit/clustergraph_test$(EE) tests/unit/regiongraph_test$(EE) tests/unit/daialg_test$(EE) tests/unit/alldai_test$(EE)
-       echo Running unit tests...
+       @echo 'Running unit tests...(note: output containing "EXCEPTION" does not indicate an error)'
+       @echo
        tests/unit/var_test$(EE)
        tests/unit/smallset_test$(EE)
        tests/unit/varset_test$(EE)
@@ -154,6 +156,9 @@ unittests : tests/unit/var_test$(EE) tests/unit/smallset_test$(EE) tests/unit/va
        tests/unit/regiongraph_test$(EE)
        tests/unit/daialg_test$(EE)
        tests/unit/alldai_test$(EE)
+       @echo
+       @echo 'All unit tests completed successfully!'
+       @echo
 
 tests : tests/testdai$(EE) tests/testem/testem$(EE) tests/testbbp$(EE) $(unittests)
 

diff --git a/README b/README
index c3c674c..86261b6 100644 (file)
--- a/README
+++ b/README
@@ -2,8 +2,8 @@ libDAI  -  A free/open source C++ library for Discrete Approximate Inference
 
 -------------------------------------------------------------------------------
 
-Version:  git master
-Date:     August 11, 2010 (or later)
+Version:  0.2.7
+Date:     August 19, 2010
 See also: http://www.libdai.org
 
 -------------------------------------------------------------------------------
@@ -27,24 +27,23 @@ along with libDAI in the file COPYING. If not, see http://www.gnu.org/licenses/
 Citing libDAI
 
 If you write a scientific paper describing research that made substantive use
-of this program, please cite the software appropriately, by mentioning the
-fashion in which this software was used, including the version number.
+of this library, please cite the following paper describing libDAI:
 
-An appropriate citation would be:
+Joris M. Mooij;
+libDAI: A free & open source C++ library for Discrete Approximate Inference in
+graphical models;
+Journal of Machine Learning Research, in press, 2010.
 
-Joris M. Mooij et al. (2010) "libDAI 0.2.6: A free/open source C++ library for
-Discrete Approximate Inference", http://www.libdai.org
+In BiBTeX format (for your convenience):
 
-or in BiBTeX format:
-
-  @misc{mooij2010libdai,
-    author = "Joris M. Mooij et al.",
-    title = "lib{DAI} 0.2.6: A free/open source {C}++ library for {D}iscrete {A}pproximate {I}nference",
-    howpublished = "http://www.libdai.org/",
-    year = 2010
+  @article{mooij2010libDAI,
+    author  = {Joris M. Mooij},
+    title   = {lib{DAI}: A free & open source {C}++ Library for {D}iscrete {A}pproximate {I}nference in graphical models},
+    journal = {Journal of Machine Learning Research},
+    volume  = {in press},
+    year    = 2010
   }
 
-
 Moreover, as a personal note, I would appreciate it to be informed about any
 publications using libDAI at joris dot mooij at libdai dot org.
 
@@ -202,12 +201,16 @@ Building boost under Cygwin
 
         export PATH=$PATH:/boost_root/stage/lib
 
+
 Building libDAI
 
 To build the libDAI source, first copy a template Makefile.* to Makefile.conf
 (for example, copy Makefile.LINUX to Makefile.conf if you use GNU/Linux). Then,
-edit the Makefile.conf template to adapt it to your local setup. Especially
-directories may differ from system to system. Platform independent build
+edit the Makefile.conf template to adapt it to your local setup. In case you
+want to use Boost libraries which are installed in non-standard locations, you
+have to tell the compiler and linker about their locations (using the -I, -L
+flags for GCC; also you may need to set the LD_LIBRARY_PATH environment
+variable correctly before running libDAI binaries). Platform independent build
 options can be set in Makefile.ALL. Finally, run
 
   make
@@ -260,6 +263,7 @@ Because building boost under Windows is tricky, I provide some guidance here.
 
         bjam --with-graph --with-math --with-program_options --with-test link=static runtime-link=shared
 
+
 Building libDAI
 
 To build the source, copy Makefile.WINDOWS to Makefile.conf. Then, edit

diff --git a/include/dai/doc.h b/include/dai/doc.h
index 7ce2486..baeb332 100644 (file)
--- a/include/dai/doc.h
+++ b/include/dai/doc.h
@@ -35,8 +35,8 @@
 
 /** \mainpage Reference manual for libDAI - A free/open source C++ library for Discrete Approximate Inference methods
  *  \author Joris Mooij (with contributions of Frederik Eaton)
- *  \version git master
- *  \date August 11, 2010 (or later)
+ *  \version 0.2.7
+ *  \date August 19, 2010
  *
  *  <hr size="1">
  *  \section about About libDAI
@@ -165,24 +165,22 @@
  *  \section citations-citations Citing libDAI
  *
  *  If you write a scientific paper describing research that made substantive use
- *  of this program, please cite the software appropriately, by mentioning the 
- *  fashion in which this software was used, including the version number.
+ *  of this library, please cite the following paper describing libDAI:\n
  *
- *  An appropriate citation would be:\n
+ *  Joris M. Mooij;\n
+ *  libDAI: A free & open source C++ library for Discrete Approximate Inference in graphical models;\n
+ *  Journal of Machine Learning Research, in press, 2010.\n
  *
- *  Joris M. Mooij et al. (2010) "libDAI 0.2.6: A free/open source C++ library for Discrete 
- *  Approximate Inference", http://www.libdai.org
- *
- *  or in BiBTeX format:
+ *  In BiBTeX format (for your convenience):\n
  *  
  *  <pre>
- *  \@misc{mooij2010libdai,
- *    author = "Joris M. Mooij et al.",
- *    title = "lib{DAI} 0.2.6: A free/open source {C}++ library for {D}iscrete {A}pproximate {I}nference",
- *    howpublished = "http://www.libdai.org/",
- *    year = 2010
- *  }
- *  </pre>
+ *  \@article{mooij2010libDAI,
+ *    author  = {Joris M. Mooij},
+ *    title   = {lib{DAI}: A free \& open source {C}++ Library for {D}iscrete {A}pproximate {I}nference in graphical models},
+ *    journal = {Journal of Machine Learning Research},
+ *    volume  = {in press},
+ *    year    = 2010
+ *  }</pre>
  *
  *  Moreover, as a personal note, I would appreciate it to be informed about any
  *  publications using libDAI at joris dot mooij at libdai dot org.
@@ -242,9 +240,12 @@
  *
  *  To build the libDAI source, first copy a template Makefile.* to Makefile.conf
  *  (for example, copy Makefile.LINUX to Makefile.conf if you use GNU/Linux). 
- *  Then, edit the Makefile.conf template to adapt it to your local setup.
- *  Especially directories may differ from system to system. Platform independent
- *  build options can be set in Makefile.ALL. Finally, run
+ *  Then, edit the Makefile.conf template to adapt it to your local setup. In case
+ *  you want to use Boost libraries which are installed in non-standard locations,
+ *  you have to tell the compiler and linker about their locations (using the
+ *  -I, -L flags for GCC; also you may need to set the LD_LIBRARY_PATH environment 
+ *  variable correctly before running libDAI binaries). Platform independent build
+ *  options can be set in Makefile.ALL. Finally, run
  *  <pre>  make</pre>
  *  The build includes a regression test, which may take a while to complete.
  *