diff --git a/packaging_scripts/moosegui b/data/moosegui similarity index 100% rename from packaging_scripts/moosegui rename to data/moosegui diff --git a/debian/README.Debian b/debian/README.Debian deleted file mode 100644 index 989036c43affbbb8e847362757dcb2130944f3bc..0000000000000000000000000000000000000000 --- a/debian/README.Debian +++ /dev/null @@ -1,6 +0,0 @@ -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 diff --git a/debian/changelog b/debian/changelog deleted file mode 100644 index 8e3e68294ddb44a0e37a3ea237c4b9ebaf2f717c..0000000000000000000000000000000000000000 --- a/debian/changelog +++ /dev/null @@ -1,9 +0,0 @@ -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 diff --git a/debian/compat b/debian/compat deleted file mode 100644 index ec635144f60048986bc560c5576355344005e6e7..0000000000000000000000000000000000000000 --- a/debian/compat +++ /dev/null @@ -1 +0,0 @@ -9 diff --git a/debian/control b/debian/control deleted file mode 100644 index 9c0ebf67027b27a3d75ee38a71eaba5d6711dd61..0000000000000000000000000000000000000000 --- a/debian/control +++ /dev/null @@ -1,66 +0,0 @@ -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. diff --git a/debian/copyright b/debian/copyright deleted file mode 100644 index 48013513002090668cef809b58cc390ab46cab7e..0000000000000000000000000000000000000000 --- a/debian/copyright +++ /dev/null @@ -1,33 +0,0 @@ -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'. diff --git a/debian/moose-core.install b/debian/moose-core.install deleted file mode 100644 index 1cb4958509f4be898e9dd542539aa860c3b8cd09..0000000000000000000000000000000000000000 --- a/debian/moose-core.install +++ /dev/null @@ -1,2 +0,0 @@ -usr/bin/moose.bin -usr/bin/moose diff --git a/debian/moose-dev.install b/debian/moose-dev.install deleted file mode 100644 index 34534c3611780be8dfcac26ef0d97d341f30788a..0000000000000000000000000000000000000000 --- a/debian/moose-dev.install +++ /dev/null @@ -1,2 +0,0 @@ -usr/bin/moose* -usr/lib/libmoose* diff --git a/debian/moose-doc.install b/debian/moose-doc.install deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/debian/moose-gui.install b/debian/moose-gui.install deleted file mode 100644 index ba3a0386847a58124fac20f217bcb5dd1240c9a4..0000000000000000000000000000000000000000 --- a/debian/moose-gui.install +++ /dev/null @@ -1,2 +0,0 @@ -usr/lib/moose/gui -usr/bin/moosegui diff --git a/debian/moose-moogli.install b/debian/moose-moogli.install deleted file mode 100644 index 2fc6202aa0181b611f4f7f354526ab1ff76a2218..0000000000000000000000000000000000000000 --- a/debian/moose-moogli.install +++ /dev/null @@ -1 +0,0 @@ -usr/share/moogli/moogli*.tar.gz diff --git a/debian/moose-moogli.postinst b/debian/moose-moogli.postinst deleted file mode 100755 index 0624d9c3d828965fc4241d27ed6ea14ebef9cb0b..0000000000000000000000000000000000000000 --- a/debian/moose-moogli.postinst +++ /dev/null @@ -1,44 +0,0 @@ -#!/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 diff --git a/debian/moose-moogli.prerm b/debian/moose-moogli.prerm deleted file mode 100755 index 5bbe65c6aa7eb6e97324a277c2e0a750734df6ad..0000000000000000000000000000000000000000 --- a/debian/moose-moogli.prerm +++ /dev/null @@ -1,58 +0,0 @@ -#!/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 diff --git a/debian/moose-python.install b/debian/moose-python.install deleted file mode 100644 index 0043ee3c07f5dbc67a1751b90e4487ed01406355..0000000000000000000000000000000000000000 --- a/debian/moose-python.install +++ /dev/null @@ -1 +0,0 @@ -usr/share/moose/moose*.tar.gz diff --git a/debian/moose-python.postinst b/debian/moose-python.postinst deleted file mode 100755 index 43a7ebefdca53afd387f101ec93f2a2eadfdb788..0000000000000000000000000000000000000000 --- a/debian/moose-python.postinst +++ /dev/null @@ -1,46 +0,0 @@ -#!/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 diff --git a/debian/moose-python.prerm b/debian/moose-python.prerm deleted file mode 100755 index fb54a154655945f4026006062c6762bb7f107b6a..0000000000000000000000000000000000000000 --- a/debian/moose-python.prerm +++ /dev/null @@ -1,57 +0,0 @@ -#!/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 diff --git a/debian/rules b/debian/rules deleted file mode 100755 index 50a253efb155aeb23b03ff63177bc01459c03fe2..0000000000000000000000000000000000000000 --- a/debian/rules +++ /dev/null @@ -1,48 +0,0 @@ -#!/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 diff --git a/packaging_scripts/build_debian_locally_on_ubuntu.sh b/packaging_scripts/build_debian_locally_on_ubuntu.sh deleted file mode 100755 index 4cebfaa8b70bfe916688580efe08bf50f5b9d025..0000000000000000000000000000000000000000 --- a/packaging_scripts/build_debian_locally_on_ubuntu.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/usr/bin/env bash -( - cd .. - debuild -uc -us | tee $0.log -) diff --git a/packaging_scripts/build_debian_using_bzr.sh b/packaging_scripts/build_debian_using_bzr.sh deleted file mode 100755 index fecfe77292219d9d17c2da00ccfb9918774adc8b..0000000000000000000000000000000000000000 --- a/packaging_scripts/build_debian_using_bzr.sh +++ /dev/null @@ -1,36 +0,0 @@ -#!/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 $0.log -) diff --git a/packaging_scripts/build_pypi.sh b/packaging_scripts/build_pypi.sh deleted file mode 100755 index 9071bfefe14835f165cfe5d9eb6b6e9ea21782cb..0000000000000000000000000000000000000000 --- a/packaging_scripts/build_pypi.sh +++ /dev/null @@ -1,20 +0,0 @@ -#!/bin/bash -set -e -# This creates a package for pip. For testing purpose -moose_dir=moose-3.0 -( - cd .. - svn export --force . scripts/$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" -) diff --git a/packaging_scripts/cmake_sanity_check.py b/packaging_scripts/cmake_sanity_check.py deleted file mode 100755 index e39e6d8ae18c19932b043fa02a78175ce7a80f70..0000000000000000000000000000000000000000 --- a/packaging_scripts/cmake_sanity_check.py +++ /dev/null @@ -1,87 +0,0 @@ -#!/usr/bin/env python -"""cmake_sanity_check.py: Check if Cmake files are ok. - -Last modified: Sat Jan 18, 2014 05:01PM - -""" - -__author__ = "Dilawar Singh" -__copyright__ = "Copyright 2013, Dilawar Singh and NCBS Bangalore" -__credits__ = ["NCBS Bangalore"] -__license__ = "GNU GPL" -__version__ = "1.0.0" -__maintainer__ = "Dilawar Singh" -__email__ = "dilawars@ncbs.res.in" -__status__ = "Development" - -import sys -import os -import re -from collections import defaultdict - -makefiles = {} -cmakefiles = {} -makedirs = set() -cmakedirs = set() - -def check(d): - searchMakefiles(d) - checkMissingCMake() - checkSrcs() - -def checkMissingCMake(): - if (makedirs - cmakedirs): - print("[Failed] Test 1") - print("Following directories have Makefile but not a CMakeFiles.txt file.") - print("%s" % "\t\n".join(makedirs - cmakedirs)) - -def searchMakefiles(d): - for d, subd, fs in os.walk(d): - if "CMakeLists.txt" in fs: - cmakedirs.add(d) - cmakefiles[d] = fs - if "Makefile" in fs: - makedirs.add(d) - makefiles[d] = fs - else: pass - -def checkSrcs(): - objPat = re.compile(r"\w+\.o") - srcPat = re.compile(r"\w+\.cpp") - srcs = [] - csrcs = [] - for d in makefiles: - with open(os.path.join(d, "Makefile"), "r") as f: - txt = f.read() - srcs = objPat.findall(txt) - try: - with open(os.path.join(d, "CMakeLists.txt"), "r") as f: - txt = f.read() - csrcs = srcPat.findall(txt) - except: - print("Dir {} does not have CMakeLists.txt".format(d)) - csrcs = [] - #print("[TEST 2] Checking if CMake is creating extra objects") - for csr in csrcs: - objName = csr.replace(".cpp", ".o") - if objName in srcs: - pass - else: - #print(" Failed: In dir {}, CMake is creating extra object {}".format(d, objName)) - - pass - print("[TEST 3] Checking if CMake is missing some objects") - for obj in srcs: - srcName = obj.replace(".o", ".cpp") - if srcName in csrcs: pass - else: - print(" Failed: In dir {}, CMake is missing object {}".format(d, - srcName)) - -def main(): - dir = sys.argv[1] - check(dir) - - -if __name__ == '__main__': - main() diff --git a/packaging_scripts/packages_local_using_cmake.sh b/packaging_scripts/packages_local_using_cmake.sh deleted file mode 100755 index 3504983ad78ee515eaf2a0e1158d0c7fd84c795a..0000000000000000000000000000000000000000 --- a/packaging_scripts/packages_local_using_cmake.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/bash -set -e -set -x -( -cd .. -mkdir -p _build -cd _build -cmake .. -make | tee $0.log -cpack -G DEB -sudo dpkg -i moose*.deb -moosegui -) diff --git a/packaging_scripts/pbuilder_debian.sh b/packaging_scripts/pbuilder_debian.sh deleted file mode 100755 index fecfe77292219d9d17c2da00ccfb9918774adc8b..0000000000000000000000000000000000000000 --- a/packaging_scripts/pbuilder_debian.sh +++ /dev/null @@ -1,36 +0,0 @@ -#!/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 -)