debian/0000755000000000000000000000000012235721435007172 5ustar debian/README.Debian0000644000000000000000000000112212005561705011224 0ustar For Debian, cnrun is configured --with-tools=no. These tools are: - varfold, a matrix convolution utility; - hh-latency-estimator, for measurement of first-spike latency in response to stimulation, and - spike2sdf, for estimation of a spike density function from a record of spike times. These utilities were used in the original experiment (http://johnhommer.com/academic/code/cnrun/ratiocoding), and hence not deemed of general purpose enough to be included in the Debian package. If you believe you have a particular need for any of them, feel free to build cnrun from source. debian/upstream0000644000000000000000000000076112007056040010747 0ustar Reference: Author: Zavada, A. and Buckley, C.L. and Martinez, D. and Rospars, J-P. and Nowotny, T. Title: Competition-based model of pheromone component ratio detection in the moth Journal: PLoS ONE Year: 2011 Volume: 6 Number: 2 Pages: e16308 DOI: 10.1371/journal.pone.0016308 PMID: 21373177 URL: http://johnhommer.com/academic/code/cnrun eprint: http://www.plosone.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0016308&representation=PDF debian/source/0000755000000000000000000000000011705656072010477 5ustar debian/source/format0000644000000000000000000000001411705656072011705 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000000241512005335275011125 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: cnrun Upstream-Contact: Andrei Zavada Source: http://johnhommer.com/academic/code/cnrun/source/ Files: * Copyright: 2008-2012 Andrei Zavada License: GPL-2+ Files: src/libcn/*.cc Copyright: 2008 Thomas Nowotny 2008-2012 Andrei Zavada License: GPL-2+ License: GPL-2+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the full text of the GNU General Public License version 2 can be found in the file `/usr/share/common-licenses/GPL-2'. debian/unwanted-files0000644000000000000000000000023111762733274012046 0ustar m4/* aclocal.m4 config.sub ltmain.sh depcomp install-sh autogen.sh configure config.guess Makefile.in src/Makefile.in src/*/Makefile.in doc/Makefile.in debian/changelog0000644000000000000000000000355212235721044011045 0ustar cnrun (1.1.14-1ubuntu1) trusty; urgency=low * Link libcn against required libraries. -- Dmitrijs Ledkovs Mon, 04 Nov 2013 13:33:12 +0000 cnrun (1.1.14-1) unstable; urgency=low * New upstream version (Closes: #722760). -- Andrei Zavada Sun, 22 sep 2013 15:37:56 +0200 cnrun (1.1.13-2) unstable; urgency=low * Update Vcs-* fields to point to git.debian.org/debian-med. -- Andrei Zavada Thu, 27 sep 2012 00:28:12 +0200 cnrun (1.1.13-1) unstable; urgency=low * More meaningful README.Debian. * Clean up build-depends. * Put all copyright info where it belongs. * Move examples into a dedicated doc/examples dir. * Initial Debian release (Closes: #682344) -- Andrei Zavada Thu, 04 Aug 2012 02:03:37 +0200 cnrun (1.1.12-1) UNRELEASED; urgency=low * Version bump. -- Andrei Zavada Sun, 22 Jul 2012 21:32:00 +0200 cnrun (1.1.11-1) UNRELEASED; urgency=low * Version bump. -- Andrei Zavada Thu, 26 Jan 2012 02:01:00 +0200 cnrun (1.1.10-1) UNRELEASED; urgency=low * Version bump. -- Andrei Zavada Sat, 21 Jan 2012 01:41:56 +0200 cnrun (1.1.8) UNRELEASED; urgency=low * Version bump. -- Andrei Zavada Wed, 22 Dec 2010 01:41:56 +0200 cnrun (1.1.6) UNRELEASED; urgency=low * Version bump. -- Andrei Zavada Sat, 22 May 2010 10:55:56 +0000 cnrun (1.1.5) UNRELEASED; urgency=low * Version bump. -- Andrei Zavada Wed, 28 Apr 2010 01:16:14 +0000 cnrun (1.1.4) UNRELEASED; urgency=low * Version bump. -- Andrei Zavada Tue, 16 Mar 2010 16:05:14 +0000 cnrun (1.1.2) UNRELEASED; urgency=low * Initial Release. -- Andrei Zavada Sun, 07 Mar 2010 16:05:14 +0000 debian/control0000644000000000000000000000233612235721047010600 0ustar Source: cnrun Section: science Priority: optional Maintainer: Ubuntu Developers XSBC-Original-Maintainer: Andrei Zavada Build-Depends: debhelper (>= 9), hardening-wrapper, hardening-includes, dh-autoreconf, autoconf-archive, libgomp1, libreadline6-dev, pkg-config, libgsl0-dev, libxml2-dev Standards-Version: 3.9.4 Homepage: http://johnhommer.com/academic/code/cnrun Vcs-Git: git://git.debian.org/git/debian-med/cnrun.git Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/cnrun.git;a=summary Package: cnrun Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: gnuplot Description: NeuroML-capable neuronal network simulator CNrun is a neuronal network model simulator, similar in purpose to NEURON except that individual neurons are not compartmentalised. It can read NeuroML files (e.g., as generated by neuroConstruct); provides a Hodgkin-Huxley neuron (plus some varieties), a Rall and Alpha-Beta synapses, Poisson, Van der Pol, Colpitts oscillators and regular pulse generator; external inputs and logging state variables. Uses a 6-5 Runge-Kutta integration method. Basic scripting and (if run interactively) context-aware autocompletion. debian/.backups/0000755000000000000000000000000012217630751010700 5ustar debian/cnrun.manpages0000644000000000000000000000001412006331161012014 0ustar man/cnrun.1 debian/rules0000755000000000000000000000127212005603446010250 0ustar #!/usr/bin/make -f # -*- makefile -*- # Sample debian/rules that uses debhelper. # This file was originally written by Joey Hess and Craig Small. # As a special exception, when this file is copied by dh-make into a # dh-make output file, you may use that output file without restriction. # This special exception was added by Craig Small in version 0.37 of dh-make. # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 export DEB_BUILD_HARDENING=1 include /usr/share/hardening-includes/hardening.make CXXFLAGS=$(shell dpkg-buildflags --get CFLAGS) LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS) CXXFLAGS+=$(HARDENING_CFLAGS) LDFLAGS+=$(HARDENING_LDFLAGS) %: dh $@ --with autoreconf debian/watch0000644000000000000000000000012311774421101010211 0ustar version=3 http://johnhommer.com/academic/code/cnrun/source/cnrun-([\d\.]+).tar.bz2 debian/patches/0000755000000000000000000000000012235721336010621 5ustar debian/patches/link-libs.patch0000644000000000000000000000052112235721336013524 0ustar Description: Link libcn against required libraries. Author: Dmitrijs Ledkovs --- cnrun-1.1.14.orig/src/libcn/Makefile.am +++ cnrun-1.1.14/src/libcn/Makefile.am @@ -30,6 +30,7 @@ libcn_la_LDFLAGS = \ -rpath $(libdir)/$(PACKAGE) \ -shared -module +libcn_la_LDFLAGS += $(LIBCN_LIBS) if DO_PCH BUILT_SOURCES = \ debian/patches/series0000644000000000000000000000002012235721113012017 0ustar link-libs.patch debian/compat0000644000000000000000000000000212005574312010363 0ustar 9