moosegui script.

debian/README.Debian

-moose for Debian
-----------------
-
-<possible notes regarding this package - if none, delete this file>
-
- -- Dilawar <dilawars@ncbs.res.in>  Thu, 24 Jul 2014 16:41:58 +0530

debian/changelog

-moose (3.0.2) unstable; urgency=low
-
-  * Initial release 
-  * Feature-freeze release.
-  * trunk series. Experimental branch.
-  * 3.0.2 relase.
-  * Just packed with SBML and GSL-1.6 support.
-
- -- Dilawar <dilawars@ncbs.res.in>  Sun, 05 July 2015 13:41:58 +0530

debian/compat

-9

debian/control

-Source: moose
-Section: science
-Priority: optional
-Maintainer: Dilawar Singh <dilawars@ncbs.res.in>
-Build-Depends: debhelper, cdbs, devscripts, cmake, python-setuptools, build-essential, doxygen, python-qt4, python-qt4-dev, libopenscenegraph-dev, python-sip-dev, libqt4-dev, libqt4-opengl-dev, libxml2-dev, libbz2-dev, python-dev, python-numpy, libhdf5-serial-dev, libgsl0-dev, python-qt4-gl
-Standards-Version: 3.9.5
-Homepage: http://moose.ncbs.res.in
-
-Package: moose-all
-Architecture: any
-Depends: moose-python, moose-gui, moose-moogli
-Description: MOOSE is the Multiscale Object-Oriented Simulation Environment
- It is the base and numerical core for large, detailed simulations including Computational Neuroscience and Systems Biology.
- .
- MOOSE spans the range from single molecules to subcellular networks, from
- single cells to neuronal networks, and to still larger systems.  MOOSE uses
- Python for scripting compatibility with a large range of software and
- analysis tools. It recognizes model definition standards including SBML,
- NeuroML, and GENESIS model file formatsGallery
- .
- MOOSE is open source software, licensed under the LGPL (Lesser GNU Public
- License). It has absolutely no warranty.
- .
- The MOOSE team is also participating in development of MOOGLI: a library and
- standalone application for displaying time-course of activity of detailed 3-D
- network models using OpenGL and also using OpenSceneGraph	
-
-
-Package: moose-core
-Architecture: any
-Depends: ${shlibs:Depends}
-Description: Core C++ part of MOOSE
- .
- Core MOOSE engine without any scripting support. For general use see moose-python, moose-gui packages. This is only useful on clusters.
-
-
-Package: moose-python
-Architecture: any
-Depends: ${shlibs:Depends}, python-numpy, python-matplotlib, python-nose, python-networkx, python-setuptools, python-suds
-Description: Python interface of MOOSE Simulator
- .
- This package installs python scripting interface.
-
-Package: moose-gui
-Architecture: any
-Depends: python-qt4, moose-python
-Description: GUI of moose
- .
- This package installs the GUI frontend of MOOSE neural simulator.
-
-Package: moose-moogli
-Architecture: any
-Depends: ${shlibs:Depends}, python-qt4-gl, python-sip, libqt4-gui, openscenegraph, moose-gui
-Suggests: moose-python
-Description: Visualizer for neural simulator
- .
- Moogli (a sister project of MOOSE) is a simulator independent openGL based
- visualization tool for neural simulations. Moogli can visualize morphology of
- single/multiple neurons or network of neurons, and can also visualize activity
- in these cells. 
-
-Package: moose-doc
-Architecture: any
-Description: User and developer documents of MOOSE neural simulator
- .
- This package installs user-manuals, tutorials, and developer document of MOOSE simulator.

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: moose
-Source: http://moose.ncbs.res.in
-
-Files: *
-Copyright: 2007-15 Upinder Bhalla 
-           2009-13 Subhasis Ray
-           2013-15 Dilawar Singh
-           2014-15 Aviral Goel
-
-License: LGPL-3.0+
-
-Files: debian/*
-Copyright: 2014 Dilawar Singh <dilawars@ncbs.res.in>
-License: LGPL-3.0+
-
-License: LGPL-3.0+
- This package is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public
- License as published by the Free Software Foundation; either
- version 3 of the License, or (at your option) any later version.
- .
- This package 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
- Lesser General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
- .
- On Debian systems, the full text of the GNU General Public
- License version 3 can be found in the file
- `/usr/share/common-licenses/GPL-3'.

debian/moose-core.install

-usr/bin/moose.bin
-usr/bin/moose

debian/moose-dev.install

-usr/bin/moose*
-usr/lib/libmoose*

debian/moose-gui.install

-usr/lib/moose/gui
-usr/bin/moosegui

debian/moose-moogli.install

-usr/share/moogli/moogli*.tar.gz

debian/moose-moogli.postinst

-#!/bin/sh
-# postinst script for moose
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# summary of how this script can be called:
-#        * <postinst> `configure' <most-recently-configured-version>
-#        * <old-postinst> `abort-upgrade' <new version>
-#        * <conflictor's-postinst> `abort-remove' `in-favour' <package>
-#          <new-version>
-#        * <postinst> `abort-remove'
-#        * <deconfigured's-postinst> `abort-deconfigure' `in-favour'
-#          <failed-install-package> <version> `removing'
-#          <conflicting-package> <version>
-# for details, see http://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-
-case "$1" in
-    configure)
-        mkdir -p /etc/moogli
-        cd /usr/share/moogli 
-        tar xzvf moogli-1.0.1.tar.gz
-        cd moogli-1.0.1
-        python setup-moogli.py install --install-layout=deb --record /etc/moogli/installed_files.txt
-    ;;
-
-    abort-upgrade|abort-remove|abort-deconfigure)
-    ;;
-
-    *)
-        echo "postinst called with unknown argument \`$1'" >&2
-        exit 1
-    ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0

debian/moose-moogli.prerm

-#!/bin/sh
-# prerm script for moose
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# summary of how this script can be called:
-#        * <prerm> `remove'
-#        * <old-prerm> `upgrade' <new-version>
-#        * <new-prerm> `failed-upgrade' <old-version>
-#        * <conflictor's-prerm> `remove' `in-favour' <package> <new-version>
-#        * <deconfigured's-prerm> `deconfigure' `in-favour'
-#          <package-being-installed> <version> `removing'
-#          <conflicting-package> <version>
-# for details, see http://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-
-case "$1" in
-    remove|upgrade|deconfigure)
-
-	if [ -d /usr/lib/moogli ]; then
-            rm -R /usr/lib/moogli
-	fi
-        if [ -d /etc/moogli ]; then
-            ( 
-            cd /etc/moogli
-            while read -r line
-            do
-                # get the egg directory and remove it.
-                dirname=`expr $line : '\(.*moogli-.*egg\)'`
-                if [ -d "$dirname" ]; then
-                    rm -rf $dirname
-                fi
-                # This line is usually redundant now.
-                if [ -f $line ]; then rm -f $line ; fi
-            done < installed_files.txt
-            )
-            rm -R /etc/moogli
-        fi
-    ;;
-
-    failed-upgrade)
-    ;;
-
-    *)
-        echo "prerm called with unknown argument \`$1'" >&2
-        exit 1
-    ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0

debian/moose-python.install

-usr/share/moose/moose*.tar.gz

debian/moose-python.postinst

-#!/bin/sh
-# postinst script for moose
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# summary of how this script can be called:
-#        * <postinst> `configure' <most-recently-configured-version>
-#        * <old-postinst> `abort-upgrade' <new version>
-#        * <conflictor's-postinst> `abort-remove' `in-favour' <package>
-#          <new-version>
-#        * <postinst> `abort-remove'
-#        * <deconfigured's-postinst> `abort-deconfigure' `in-favour'
-#          <failed-install-package> <version> `removing'
-#          <conflicting-package> <version>
-# for details, see http://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-
-case "$1" in
-    configure)
-        ( 
-        mkdir -p /etc/moose
-        cd /usr/share/moose 
-        tar xzvf moose-3.0.2.tar.gz
-        cd moose-3.0.2 
-        python setup-moose.py install --install-layout=deb --record /etc/moose/installed_files.txt
-        )
-    ;;
-
-    abort-upgrade|abort-remove|abort-deconfigure)
-    ;;
-
-    *)
-        echo "postinst called with unknown argument \`$1'" >&2
-        exit 1
-    ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0

debian/moose-python.prerm

-#!/bin/sh
-# prerm script for moose
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# summary of how this script can be called:
-#        * <prerm> `remove'
-#        * <old-prerm> `upgrade' <new-version>
-#        * <new-prerm> `failed-upgrade' <old-version>
-#        * <conflictor's-prerm> `remove' `in-favour' <package> <new-version>
-#        * <deconfigured's-prerm> `deconfigure' `in-favour'
-#          <package-being-installed> <version> `removing'
-#          <conflicting-package> <version>
-# for details, see http://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-case "$1" in
-    remove|upgrade|deconfigure)
-	if [ -d /etc/moose ]; then
-            (
-                cd /etc/moose 
-                while read -r line
-                do
-                    # get the egg directory and remove it.
-                    dirname=`expr $line : '\(.*moose-.*egg\)'`
-                    if [ -d "$dirname" ]; then
-                        rm -rf $dirname
-                    fi
-                    # This line is usually redundant now.
-                    if [ -f $line ]; then rm -f $line ; fi
-                done < installed_files.txt
-            )
-            rm -R /etc/moose
-	fi
-
-        if [ -d /usr/share/moose ]; then
-            rm -R /usr/share/moose
-        fi
-    ;;
-
-    failed-upgrade)
-    ;;
-
-    *)
-        echo "prerm called with unknown argument \`$1'" >&2
-        exit 1
-    ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0

debian/rules

-#!/usr/bin/make -f
-
-# export DH_VERBOSE=1
-export BUILD_DIR_MOOSE=_build
-NPROCS := 1
-OS := $(shell uname)
-ifeq ($J,)
-    ifeq ($(OS),Linux)
-    NPROCS := $(shell grep -c ^processor /proc/cpuinfo)
-else ifeq ($(OS),Darwin)
-    NPROCS := $(shell system_profiler | awk '/Number of CPUs/ {print $$4}{next;}')
-endif # $(OS)
-else
-    NPROCS := $J
-endif # $J
-
-MAKEFLAGS=-j$(NPROCS)
-
-export PYTHONPATH=$(shell pwd)/../debian/tmp/$(PYTHON_LIBS))
-
-## Here goes the debian make.
-
-%:
-	dh "$@" --parallel
-
-override_dh_auto_clean:
-	rm -rf $(BUILD_DIR_MOOSE)
-	dh_auto_clean --buildsystem=cmake
-
-# consider using -DUSE_VERSIONED_DIR=ON if backporting
-override_dh_auto_configure:
-	mkdir -p $(BUILD_DIR_MOOSE)
-	cd $(BUILD_DIR_MOOSE) && cmake -DDEBUG=OFF -DBUILD_MOOGLI=ON -DCMAKE_VERBOSE_MAKEFILE=OFF \
-	    -DCMAKE_INSTALL_PREFIX=../debian/tmp/usr ..
-
-override_dh_auto_build:
-	cd $(BUILD_DIR_MOOSE) && make VERBOSE=1 #-j${NPROCS}
-
-
-override_dh_auto_install:
-	# Distable python install
-	cd $(BUILD_DIR_MOOSE) && make install 
-
-override_dh_auto_test:
-	cd $(BUILD_DIR_MOOSE) && make test
-
-override_dh_shlibdeps:
-	dh_shlibdeps --dpkg-shlibdeps-params=--ignore-missing-info

packaging_scripts/build_debian_locally_on_ubuntu.sh

-#!/usr/bin/env bash
-(
-    cd ..
-    debuild -uc -us | tee $0.log
-)

packaging_scripts/build_debian_using_bzr.sh

-#!/usr/bin/env bash
-# This script is for launchpad.
-(
-set -e
-set -o xtrace
-cd ..
-cat > moose.recipe <<EOF
-# bzr-builder format 0.3 deb-version {debupstream}+{revno}
-lp:moose
-EOF
-# one can do nesting here.
-if [ $# -gt 0 ]; then
-    if [[ "$1" == "update" ]]; then
-        echo "Fetching repo and creating tar-ball"
-        bzr dailydeb --allow-fallback-to-native moose.recipe .. | tee $0.log
-    elif [[ "$1" == "pbuilder" ]]; then
-        bzr dailydeb --allow-fallback-to-native moose.recipe .. | tee $0.log
-        sudo -E pbuilder build ../*.dsc | tee $0.log
-        exit
-    fi
-fi
-
-tarFile=`find .. -type f -maxdepth 1 -name "moose_3.0*.tar.gz"`
-echo "Found tarfiles are $tarFile"
-if [[ ! $tarFile ]]; then
-    echo "I could not file a tar.gz file. Can't continue"
-    echo "++ Cleaning previous mess"
-    rm -rf ../moose_3.0* ../moose-{*
-    echo "++ Let me download a fresh one"
-    bzr dailydeb --allow-fallback-to-native moose.recipe .. | tee $0.log
-fi
-
-rm -f moose.recipe
-echo "Building debian package"
-bzr builddeb -- -uc -us | tee $0.log
-)

packaging_scripts/build_pypi.sh

-#!/bin/bash
-set -e
-# This creates a package for pip. For testing purpose
-moose_dir=moose-3.0
-( 
-    cd ..  
-    svn export --force . scripts/$moose_dir 
-)
-(
-    cp setup.py $moose_dir/
-    cd $moose_dir
-    echo "Creating new archive"
-    if [ -f dist/$moose_dir.tar.gz ]; then
-        rm -f dist/*.tar.gz
-    fi
-    python setup.py sdist -vv | tee $0.log
-    echo "Created new archive"
-    sudo pip install dist/*.tar.gz --no-clean | tee $0.log
-    echo "Do the rest in $moose_dir"
-)