Updated information on bug reporting and references to the online res…

…ources to point to the correct pages for the NEST Initiative and the NEST simulator, respectively.

.gitignore

@@ -42,6 +42,7 @@ build/
 /sli/sli
 /testsuite/do_tests.sh
 /topology/setup.py
+/topology/doc/Topology_UserManual.out
 
 *.kdev4
 

INSTALL

@@ -1,6 +1,6 @@
 This file contains a brief summary or the steps needed to install NEST. More
-detailed information is available on the homepage of the NEST Initiative at
-http://www.nest-initiative.org/index.php/NEST_installation
+detailed information is available on the homepage of the NEST simulator at
+http://www.nest-simulator.org/installation
 
 Introduction
 ============

NEWS

@@ -1,2 +1 @@
-Please see http://nest-initiative.org/index.php/Software:Release_Notes
-for changes and improvements.
+Please see http://www.nest-simulator.org for release notes and news.

configure.ac

@@ -1154,8 +1154,8 @@ if test $SLI_distributed = set; then
   echo
 fi
 
-echo "If you experience problems with the installation or the use of"
-echo "NEST, please see http://nest-initiative.org/index.php/FAQ, or"
-echo "go to http://nest-initiative.org/index.php/Community to find out"
-echo "how to join the user mailing list."
+echo "If you experience problems with the installation or the use of NEST,"
+echo "please see http://www.nest-simulator.org/frequently_asked_questions"
+echo "or go to http://www.nest-simulator.org/community to find out how to"
+echo "join the user mailing list."
 echo

doc/index.html

@@ -47,14 +47,15 @@
     <center><div class="header">
       <h1>NEST HelpDesk</h1>
       <hr>
-      <h3><a href="http://www.nest-initiative.org/">http://www.nest-initiative.org/</a></h3>
-      <span><a href="http://www.nest-initiative.org/index.php/Software:Documentation">NEST Documentation index</a></span>
-      <hr>
       <span><a href="quickref.html">SLI command index by subject</a></span>
       <span><a href="help/helpindex.html">SLI command index by name</a></span>
-      <span><a href="http://www.nest-initiative.org/index.php/Software:Installation">Configuration and installation instructions</a> (ext.)</span>
-      <span><a href="http://www.nest-initiative.org/index.php/An_Introduction_to_SLI">Introduction to the simulation language SLI</a> (ext.)</span>
-      <span><a href="http://www.nest-initiative.org/index.php/PyNEST">Introduction to the Python bindings for NEST (PyNEST)</a> (ext.)</span>
+      <hr>
+      <span><a href="http://www.nest-simulator.org/documentation">NEST Documentation index</a> (ext.)</span>
+      <span><a href="http://www.nest-simulator.org/installation">Configuration and installation instructions</a> (ext.)</span>
+      <span><a href="http://www.nest-simulator.org/introduction-to-pynest">Introduction to the Python bindings for NEST (PyNEST)</a> (ext.)</span>
+      <span><a href="http://www.nest-simulator.org/an_introduction_to_sli">Introduction to the simulation language SLI</a> (ext.)</span>
+      <hr>
+      <span><a href="http://nest.github.io/nest-simulator">The NEST developer space</a> (ext.)</span>
       <span />
     </ul>
 

doc/quickref.html

@@ -3476,7 +3476,7 @@ <h2><a name="parallel">Parallel computing</a></h2>
 </table>
 
 <p style="text-align:center">
-  &copy; 2000-2010 <a href="http://www.nest-initiative.org">The NEST Initiative</a>
+  &copy; 2004 <a href="http://www.nest-initiative.org">The NEST Initiative</a>
 </p>
 
 </body>

examples/nest/Potjans_2014/README.txt

@@ -55,10 +55,9 @@ changed either.
 
 Instructions:
 
-1. Download NEST (http://www.nest-initiative.org/index.php/Software:Download)
+1. Download NEST (http://www.nest-simulator.org/download)
 
-2. Compile NEST according to the instructions on
-   http://www.nest-initiative.org/index.php/Software:Installation
+2. Compile NEST: http://www.nest-simulator.org/installation
    Use the --with-mpi flag to configure with MPI support
 
 3. In user_params.sli adjust output_dir, mpi_path, and nest_path to your system

extras/ConnPlotter/setup.py

@@ -28,7 +28,7 @@
       description = 'ConnPlotter is a tool to create connectivity pattern tables',
       author      = 'Hans Ekkehard Plesser (Idea: Eilen Nordlie)',
       author_email= 'hans.ekkehard.plesser@umb.no',
-      url         = 'http://www.nest-initiative.org',
+      url         = 'http://www.nest-simulator.org',
       license     = 'GNU Public License v2 or later',
       packages    = ['ConnPlotter', 'ConnPlotter.examples'],
       package_dir = {'ConnPlotter': ''}

lib/sli/helpinit.sli

@@ -575,7 +575,7 @@ SeeAlso: helpindex, help, makehelp, :makeallhelp
   </tr>
 </table>
 <p style="text-align:center">
-  &copy; 2000-2010 <a href="http://www.nest-initiative.org">The NEST Initiative</a>
+  &copy; 2004 <a href="http://www.nest-initiative.org">The NEST Initiative</a>
 </p>
 </body>\n</html>) <- endl closeostream
     } forall
@@ -742,7 +742,7 @@ SeeAlso: helpindex, help, makehelp, :makeallhelp
 </table>
 
 <p style="text-align:center">
-  &copy; 2000-2010 <a href="http://www.nest-initiative.org">The NEST Initiative</a>
+  &copy; 2004 <a href="http://www.nest-initiative.org">The NEST Initiative</a>
 </p>
 </body>\n</html>) <- endl ;
   end

lib/sli/regexp.sli

@@ -470,7 +470,7 @@ Examples:
 [(hello) (world)] (^hell)       grep -> [(hello)]
 [(hello) (world)] (not in here) grep -> []
 [(hello) (world)] ()            grep -> [(hello) (world)]
-statusdict /prgdocdir get (LICENSE) joinpath (http) grep -> [(or visit http://www.nest-initiative.org)]
+statusdict /prgdocdir get (LICENSE) joinpath (http) grep -> [(or visit http://www.nest-simulator.org)]
 
 Diagnostics:
 Raises /InvalidRegexError if the expression string is not a valid

lib/sli/sli-init.sli

@@ -1734,7 +1734,7 @@ systemdict /GNUreadline known
   (Type 'sysinfo' to see details on the system configuration.) =
   (Type 'authors' for information about the makers of NEST.) =
   (Type 'license' to display the license agreement that came with your copy of NEST.) =
-  (For more information visit http://www.nest-initiative.org.) =  
+  (For more information visit http://www.nest-simulator.org.) =
   (Type 'help' to see this text again.) =
   () =  
 } def
@@ -1789,8 +1789,7 @@ SeeAlso: nestrc
    warranty
 
    (Problems or suggestions?) =
-   (  Website     : http://www.nest-initiative.org) =
-   (  Mailing list: nest_user@nest-initiative.org) =
+   (  Visit http://www.nest-simulator.org) =
    () =
 
    (Type 'help' to get more information.) =
@@ -1832,15 +1831,8 @@ SeeAlso: nestrc
   cout endl
   (NEST has been created and is maintained by the ) <- 
   (members of the NEST Initiative:) <- endl endl
-  (  * Honda Research Institute Europe, Offenbach, Germany) <- endl
-  (  * Computational Neurophysics Research Unit,) <- endl
-  (    RIKEN Brain Science Institute, Wako City, Japan) <- endl
-  (  * Department of Mathematical Sciences & Technology,) <- endl
-  (    Norwegian University of Life Sciences, Aas, Norway) <- endl
-  (  * Neurobiology & Biophysics, Institute for Biology III,) <- endl
-  (    Albrecht-Ludwigs-Universitaet Freiburg, Germany) <- endl
-  ()   <- endl endl
-  (For the list of developers and more information visit us at http://www.nest-initiative.org.) <- endl endl ;  
+  (For a list of associated institutions and contributors,) <- endl
+  (visit us at http://www.nest-initiative.org.) <- endl endl ;
 
 } def
 

nestkernel/exceptions.cpp

@@ -251,8 +251,8 @@ nest::InvalidDefaultResolution::message()
   msg << "The default resolution of " << Time::get_resolution()
       << " is not consistent with the value " << val_ << " of property '" << prop_.toString()
       << "' in model " << model_ << ".\n"
-      << "This is an internal NEST error, please report to the "
-         "nest_user@nest-initiative.org mailing list!";
+      << "This is an internal NEST error, please report it at "
+         "https://github.com/nest/nest-simulator/issues";
   return msg.str();
 }
 
@@ -357,9 +357,7 @@ nest::GSLSolverFailure::message()
   msg << "In model " << model_ << ", the GSL solver "
       << "returned with exit status " << status_ << ".\n"
       << "Please make sure you have installed a recent "
-      << "GSL version (> gsl-1.10), or contact the "
-      << "nest_user@nest-initiative.org mailing list"
-      << "for further support.";
+      << "GSL version (> gsl-1.10).";
   return msg.str();
 }
 

nestkernel/nest.h

@@ -33,7 +33,7 @@
  * @mainpage NEST: Neural Simulation Tool
  *
  * The main resource on information about NEST is the homepage of the
- * NEST Initiative at http://www.nest-initiative.org
+ * NEST simulator at http://www.nest-simulator.org
  * <p>
  *
  * @see Diesmann, Markus and Gewaltig, Marc-Oliver (2002) NEST: An

nestkernel/nestmodule.cpp

@@ -1790,7 +1790,7 @@ NestModule::MPIAbort_iFunction::execute( SLIInterpreter* i ) const
    [1] Morrison A, Mehring C, Geisel T, Aertsen A, and Diesmann M (2005)
        Advancing the boundaries of high connectivity network simulation
        with distributed computing. Neural Computation 17(8):1776-1801
-       The article is available at www.nest-initiative.org
+       The article is available at www.nest-simulator.org
 
    Author: Tobias Potjans, Moritz Helias, Diesmann
    SeeAlso: GetGlobalRNG, RandomConvergentConnect
@@ -1841,7 +1841,7 @@ NestModule::GetVpRngFunction::execute( SLIInterpreter* i ) const
    [1] Morrison A, Mehring C, Geisel T, Aertsen A, and Diesmann M (2005)
        Advancing the boundaries of high connectivity network simulation
        with distributed computing. Neural Computation 17(8):1776-1801
-       The article is available at www.nest-initiative.org
+       The article is available at www.nest-simulator.org
 
    Author: Tobias Potjans, Moritz Helias, Diesmann
    SeeAlso: GetVpRNG, RandomDivergentConnect

pynest/nest/hl_api.py

@@ -77,7 +77,7 @@ def show_deprecation_warning(func_name, alt_func_name=None, text=None):
                        """\
                        {0} is deprecated and will be removed in a future version of NEST.
                        Please use {1} instead!
-                       For details, see the documentation at http://www.nest-simulator.org/connection_management\
+                       For details, see http://www.nest-simulator.org/connection_management\
                        """.format(func_name, alt_func_name)
                    )
 
@@ -303,7 +303,7 @@ def help(obj=None, pager="less"):
         print("Type 'nest.sysinfo()' to see details on the system configuration.")
         print("Type 'nest.version()' for information about the NEST version.")
         print()
-        print("For more information visit http://www.nest-initiative.org.")
+        print("For more information visit http://www.nest-simulator.org.")
 
 
 @check_stack

pynest/nest/pynest-init.sli

@@ -92,8 +92,7 @@ def
 
   cout
   (Problems or suggestions?) <- endl
-  (  Website     : http://www.nest-initiative.org) <- endl
-  (  Mailing list: nest_user@nest-initiative.org) <- endl
+  (  Visit http://www.nest-simulator.org) <- endl
 
   endl
   (Type 'nest.help()' to find out more about NEST.) <- endl ;

pynest/setup.py.in

@@ -26,8 +26,7 @@ setup(
     version='@SLI_VERSION@',
     description='PyNEST provides Python bindings for NEST',
     author='The NEST Initiative',
-    author_email='nest_user@nest-initiative.org',
-    url='http://www.nest-initiative.org',
+    url='http://www.nest-simulator.org',
     license='GPLv2+',
     packages=['nest', 'nest.tests'],
     package_dir={'nest': '@PKGSRCDIR@/pynest/nest'},

sli/slicontrol.cc

@@ -1943,10 +1943,9 @@ StartFunction::execute( SLIInterpreter* i ) const
     "Start",
     "Something went wrong "
     "during initialization of NEST or one of its modules. Probably "
-    "there is a bug in the startup scripts. Please send the output "
-    "of NEST to the nest_user@nest-initiative.org mailing list to help "
-    "us to diagnose the problem. You can try to find the bug by "
-    "re-starting NEST with the option: --debug" );
+    "there is a bug in the startup scripts. Please report the output "
+    "of NEST at https://github.com/nest/nest-simulator/issues . You "
+    "can try to find the bug by starting NEST with the option --debug" );
 }
 
 void

testsuite/do_tests.sh.in

@@ -79,15 +79,14 @@ bail_out ()
 ask_results ()
 {
     echo "***"
-    echo "*** Please send the archived content of these directories:"
+    echo "*** Please report the problem at"
+    echo "***     https://github.com/nest/nest-simulator/issues"
     echo "***"
+    echo "*** To help us diagnose the problem, please attach the archived content"
+    echo "*** of these directories to the issue:"
     echo "***     - '${TEST_OUTDIR}'"
     echo "***     - '${TEST_TMPDIR}'"
     echo "***"
-    echo "*** to the nest_user mailing list. Please find further information"
-    echo "*** about the mailing list at"
-    echo "***   http://www.nest-initiative.org/Software:Community"
-    echo "***"
     echo
 }
 

topology/doc/Topology_UserManual.tex

@@ -82,7 +82,7 @@
 \normalsize Department of Mathematical Sciences and Technology\\\normalsize Norwegian University of Life Sciences\\
 \normalsize 1432 Ås, Norway}
 \date{NEST 2.2, 2.4, and 2.6 (r9977 or later)\\[8cm]
-\centerline{\includegraphics{nest-initiative}}}
+\centerline{\includegraphics{nest-initiative.pdf}}}
 
 
 \begin{document}
@@ -124,7 +124,7 @@ \chapter{Introduction}\label{sec:intro}
 
 The Topology Module provides the NEST simulator\footnote{NEST is
   available under an open source license at
-\url{www.nest-initiative.org}.}
+\url{www.nest-simulator.org}.}
 \citep{Gewa:2007(1430)} with a convenient interface for creating
 layers of neurons placed in space and connecting neurons in such
 layers with probabilities and properties depending on the relative
@@ -1146,7 +1146,7 @@ \section{Query functions}\label{sec:queries}
   from NEST perspective. \\
   \lstinline!nest.GetConnections()! & Retrieve connections
   (all or for a given source or target); see also
-  \url{http://www.nest-initiative.org/index.php/Connection_Management}. \\
+  \url{http://www.nest-simulator.org/connection_management}. \\
   \lstinline!nest.GetNodes()! & Applied to a layer, returns GIDs of
   the layer elements. For simple layers, these are the actual model
   neurons,
@@ -1224,7 +1224,7 @@ \chapter{Adding topology kernels and masks}\label{ch:extending}
 programming language is needed for this. The functions will be added as a
 part of an extension module which is dynamically loaded into NEST. For more
 information on writing an extension module, see the section titled
-\href{http://www.nest-initiative.org/index.php/Writing_an_Extension_Module}{``Writing an Extension Module''}
+\href{http://nest.github.io/nest-simulator/extension_modules}{``Writing an Extension Module''}
 in the NEST Developer Manual. The basic steps required to get started are:
 \begin{enumerate}
 \item From the NEST source directory, copy directory examples/MyModule to

topology/setup.py.in

@@ -25,7 +25,7 @@ setup(name         = 'Topology',
       version      = '@SLI_VERSION@',
       description  = 'Python bindings for NEST Topology module',
       author       = 'The NEST Initiative',
-      url          = 'http://www.nest-initiative.org',     
+      url          = 'http://www.nest-simulator.org',
       packages     = ['nest.topology', 'nest.topology.tests'],
       package_dir  = {'nest.topology': '@PKGSRCDIR@/topology/pynest',
                       'nest.topology.tests': '@PKGSRCDIR@/topology/pynest/tests'})