diff --git a/.travis.yml b/.travis.yml
index 1a6d6efdb4424b0f968eec02155ea2adb15f7178..2f51ab7adc2766858e3019cd18ab902e1b066dee 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,23 +1,19 @@
-sudo : required
-
+sudo: required
+dist: trusty
+language: cpp
compiler:
- gcc
- clang
+
os:
- linux
- - osx
-
-allow_failure:
- - osx
-
-osx_image : xcode8
branches:
only:
- master
+ - chamcham
- chennapoda
-
notifications:
email:
recipients:
@@ -31,11 +27,27 @@ notifications:
env:
- CTEST_MODEL=Nightly
+cache: apt
before_script:
- - if [ "$TRAVIS_OS_NAME" == "linux" ]; then ./_travis/prepare_linux.sh ; fi
- - if [ "$TRAVIS_OS_NAME" == "osx" ]; then ./_travis/prepare_osx.sh ; fi
-
+ - sudo apt-get update -qq
+ - sudo apt-get install libxml2-dev libbz2-dev wget
+ - sudo apt-get install libhdf5-serial-dev
+ - sudo apt-get install python-numpy python-setuptools python-networkx python-pip
+ - sudo apt-get install cmake cdbs
+ - sudo apt-get install python-suds python-matplotlib python-nose
+ - sudo apt-get install python-qt4-dev python-qt4-gl python-sip-dev libqt4-dev libopenscenegraph-dev
+ - sudo apt-get install doxygen python-sphinx python-lxml
+ - sudo apt-get install git-buildpackage
+
+install:
+ - wget http://ftp.debian.org/debian/pool/main/g/gsl/libgsl0ldbl_1.16+dfsg-2_amd64.deb -O gsl_1.16.deb
+ - sudo dpkg -i gsl_1.16.deb
+ - wget http://ftp.debian.org/debian/pool/main/g/gsl/libgsl0-dev_1.16+dfsg-2_amd64.deb -O gsl_1.16-dev.deb
+ - sudo dpkg -i gsl_1.16-dev.deb
+ - sudo apt-get install -f
+ - sudo ldconfig /usr/lib64
script:
- - if [ "$TRAVIS_OS_NAME" == "linux" ]; then ./_travis/build_on_linux.sh ; fi
- - if [ "$TRAVIS_OS_NAME" == "osx" ]; then ./_travis/build_on_osx.sh ; fi
+ - ./.travis_build.sh
+ - sudo dpkg -i ../moose*.deb
+ - python -c 'import moose;print(moose.version());print(moose.__file__)'
diff --git a/.travis_build.sh b/.travis_build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..8d92cd1fa250ecd35699aa86aef02bfce8b72c54
--- /dev/null
+++ b/.travis_build.sh
@@ -0,0 +1,24 @@
+#!/bin/bash -
+#===============================================================================
+#
+# FILE: .travis_build.sh
+#
+# USAGE: ./.travis_build.sh
+#
+# DESCRIPTION:
+#
+# OPTIONS: ---
+# REQUIREMENTS: ---
+# BUGS: ---
+# NOTES: ---
+# AUTHOR: Dilawar Singh (), dilawars@ncbs.res.in
+# ORGANIZATION: NCBS Bangalore
+# CREATED: 03/05/2018 03:49:35 PM
+# REVISION: ---
+#===============================================================================
+
+set -o nounset # Treat unset variables as an error
+set -e -x
+PATH=/usr/bin:/usr/local/bin:$PATH
+gbp buildpackage --git-ignore-branch --git-ignore-new -uc -us -d | tee _gbp.log
+pwd
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 6968c32f41fe9b6cad0f3944aba695070c6cf49b..def09d5795c9e91ed37c5084f890366326d77604 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,7 +1,6 @@
-CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+cmake_minimum_required(VERSION 2.8)
project(moose)
-
if(POLICY CMP0048)
cmake_policy(SET CMP0048 OLD )
endif(POLICY CMP0048)
@@ -10,15 +9,21 @@ endif(POLICY CMP0048)
# version file. If GIT fails, use the previous known version.
find_program(GIT_EXEC "git")
message( STATUS "Looking for git ${GIT_EXEC}" )
-if( (NOT MOOSE_VERSION) AND GIT_EXEC)
+if(VERSION_MOOSE)
+ message( STATUS "MOOSE version is set to ${VERSION_MOOSE} at build time" )
+elseif(GIT_EXEC)
+ message( STATUS "Getting version by reading git tags" )
execute_process(
COMMAND ${GIT_EXEC} describe --tags --long
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
- OUTPUT_VARIABLE MOOSE_VERSION
+ OUTPUT_VARIABLE VERSION_MOOSE
OUTPUT_STRIP_TRAILING_WHITESPACE
)
endif( )
-message( STATUS "Building version ${MOOSE_VERSION}" )
+message( STATUS "Building version ${VERSION_MOOSE}" )
+
+# Prefix
+message( STATUS "CMAKE_INSTALL_PREFIX= ${CMAKE_INSTALL_PREFIX}" )
# Options to pass down to moose-core
option(WITH_DOC "Build documentation" OFF)
@@ -28,46 +33,20 @@ option(WITH_CUDA "Use CUDA/GPU" OFF)
option(WITH_MPI "Use MPI (experimental)" OFF)
option(WITH_GUI "Install moose-gui. Works only with python2." ON )
-
-# On python3. Do not install GUI.
+# Required packages.
find_package(PythonInterp REQUIRED)
if(PYTHON_VERSION_MAJOR VERSION_EQUAL 3)
- message(STATUS "moose-gui does not support python3 yet. Disabling" )
set(WITH_GUI OFF)
endif( )
-# On debian or ubuntu, --install-layout=deb needs to be passed.
-if(UNIX AND NOT APPLE)
- find_program(LSB_RELEASE lsb_release)
- if(LSB_RELEASE)
- execute_process(COMMAND ${LSB_RELEASE} -is
- OUTPUT_VARIABLE LSB_RELEASE_ID_SHORT
- OUTPUT_STRIP_TRAILING_WHITESPACE
- )
- if(${LSB_RELEASE_ID_SHORT} STREQUAL "Ubuntu"
- OR ${LSB_RELEASE_ID_SHORT} STREQUAL "Debian" )
- message(STATUS "Debian based LINUX: ${LSB_RELEASE_ID_SHORT}" )
- set(CMAKE_PYMOOSE_ARGS "-DDISTUTILS_EXTRA_ARGS=\"--install-layout=deb\"" )
- endif( )
- endif( )
-endif( )
-
-
add_custom_target(moose ALL)
-
+## intialize paths
set(PYMOOSE_SOURCE_DIR "${CMAKE_SOURCE_DIR}/moose-core")
set(PYMOOSE_BUILD_DIR ${CMAKE_BINARY_DIR}/__moose-core_build)
-
-# NOTE: new setuptools does not install python module to this directory unless
-# installing into user_specified path, set PYTHONPATH to this directory. We now
-# create a bdist to this directory.
set(PYMOOSE_INSTALL_DIR ${CMAKE_BINARY_DIR}/__moose-core_install)
file(MAKE_DIRECTORY ${PYMOOSE_INSTALL_DIR})
-set(PYMOOSE_BDIST_DIR ${PYMOOSE_BUILD_DIR})
-message( STATUS "bdist directory PYMOOSE_BDIST_DIR ${PYMOOSE_BDIST_DIR}" )
-
if(WITH_GUI)
set(MOOSE_GUI_DIR ${CMAKE_SOURCE_DIR}/moose-gui)
set(MOOSE_GUI_INSTALL_DIR ${CMAKE_BINARY_DIR}/__moose-gui_install)
@@ -82,23 +61,19 @@ file(MAKE_DIRECTORY ${PYMOOSE_BUILD_DIR})
# different platform.
set(OUTPUT_MOOSEBIN ${PYMOOSE_BUILD_DIR}/moose.bin)
-configure_file( ${CMAKE_SOURCE_DIR}/cmake/build_moose-core.sh.in
- ${CMAKE_BINARY_DIR}/build_moose-core.sh )
+configure_file(
+ ${CMAKE_SOURCE_DIR}/cmake/build_moose-core.sh.in
+ ${PYMOOSE_BUILD_DIR}/build_moose-core.sh
+ )
# Build pymoose module.
-add_custom_target( moose-core ALL DEPENDS ${OUTPUT_MOOSEBIN} )
-
+add_custom_target( moose-core DEPENDS ${OUTPUT_MOOSEBIN} )
add_custom_command( OUTPUT ${OUTPUT_MOOSEBIN}
- COMMAND MAKE=$(MAKE) bash -c ${CMAKE_BINARY_DIR}/build_moose-core.sh
- # Note that this command requires us to be in the same directory where we
- # want to extract the tar file.
- COMMAND ${CMAKE_COMMAND} -E chdir ${PYMOOSE_INSTALL_DIR}
- tar xvf ${PYMOOSE_BUILD_DIR}/pymoose-${MOOSE_VERSION}.*.tar.gz
- COMMENT "Building bdist and unarchiving it"
- # VERBATIM ## WARN: Don't use VERBATIM here. The glob * in tar xvf will not
- # work
+ COMMAND ${PYMOOSE_BUILD_DIR}/build_moose-core.sh
+ WORKING_DIRECTORY ${PYMOOSE_BUILD_DIR}
+ COMMENT "Building pymoose in ${PYMOOSE_BUILD_DIR}"
+ VERBATIM
)
-add_dependencies(moose moose-core)
if(WITH_GUI)
# Now build moose-gui and moose-examples.
@@ -115,17 +90,17 @@ if(WITH_GUI)
COMMAND ${PYTHON_EXECUTABLE} -m compileall -q ${MOOSE_EXAMPLE_INSTALL_DIR}
VERBATIM
)
+endif()
+
+add_dependencies(moose moose-core)
+
+if(WITH_GUI)
add_dependencies(moose gui examples)
add_dependencies(examples gui)
endif()
-# moose-gui
-# TODO: moose-gui should be a python module.
-set(MOOSE_GUI_DIR ${CMAKE_SOURCE_DIR}/moose-gui)
-# Install pymoose. Use tar.gz in PYMOOSE_BUILD_DIR and unarchive it.
-# /usr is prefixed by bdist so we need to replace it.
install(DIRECTORY ${PYMOOSE_INSTALL_DIR}/usr/
DESTINATION ${CMAKE_INSTALL_PREFIX}
PATTERN ".git" EXCLUDE
@@ -133,6 +108,8 @@ install(DIRECTORY ${PYMOOSE_INSTALL_DIR}/usr/
)
if(WITH_GUI)
+ # moose-gui
+ set(MOOSE_GUI_DIR ${CMAKE_SOURCE_DIR}/moose-gui)
install(DIRECTORY ${MOOSE_GUI_INSTALL_DIR}/
DESTINATION lib/moose/gui
PATTERN ".git*" EXCLUDE
@@ -146,49 +123,48 @@ if(WITH_GUI)
PATTERN ".travis*" EXCLUDE
PATTERN "*.pyc" EXCLUDE
)
+
+ configure_file( ${CMAKE_SOURCE_DIR}/cmake/moose.in
+ ${CMAKE_BINARY_DIR}/moosegui )
+ install(PROGRAMS ${CMAKE_BINARY_DIR}/moosegui DESTINATION bin)
endif()
-configure_file(
- ${CMAKE_SOURCE_DIR}/cmake/moosegui.in
- ${CMAKE_BINARY_DIR}/moosegui
- )
-install(PROGRAMS ${CMAKE_BINARY_DIR}/moosegui DESTINATION bin)
+## UNINSTALL
+add_custom_target(uninstall DEPENDS __uninstall_moose-core__ )
-# UNINSTALL
add_custom_command(OUTPUT __uninstall_moose-core__
COMMAND xargs rm -rf < install_manifest.txt
COMMAND pip uninstall -y moose
COMMAND ${CMAKE_COMMAND} -E remove ${CMAKE_INSTALL_PREFIX}/bin/moose.bin
)
-add_custom_target(uninstall DEPENDS __uninstall_moose-core__ )
if(WITH_GUI)
- add_custom_command(OUTPUT __uninstall_moose-gui__
+ add_custom_target( __uninstall_moose-gui__ )
+ add_custom_command(TARGET __uninstall_moose-gui__
COMMAND ${CMAKE_COMMAND} -E remove_directory
${CMAKE_INSTALL_PREFIX}/lib/moose/gui
- COMMAND ${CMAKE_COMMAND} -E remove ${CMAKE_INSTALL_PREFIX}/bin/moose
+ COMMAND ${CMAKE_COMMAND} -E remove ${CMAKE_INSTALL_PREFIX}/bin/moosegui
)
- #add_dependencies( uninstall __uninstall_moose-gui__ )
+ add_dependencies( uninstall __uninstall_moose-gui__ )
endif()
################################################################################
# CTEST
#################################################################################
-enable_testing( )
-add_test( NAME test_pymoose_sanity
- COMMAND ${PYTHON_EXECUTABLE} -c "import moose"
- )
-
-set_tests_properties( test_pymoose_sanity
- PROPERTIES ENVIRONMENT "PYTHONPATH=${PYMOOSE_BUILD_DIR}/python"
- )
+if("${CMAKE_BUILD_TYPE}" EQUAL "DEBUG")
+ enable_testing( )
+ add_test( NAME test_pymoose_sanity
+ COMMAND ${PYTHON_EXECUTABLE} -c "import moose"
+ )
-# # This test always fails when -X is not working which is usually the case on
-# # Travis and OBS.
-# if(WITH_GUI)
-# add_test( NAME test_gui_sanity
-# COMMAND ${PYTHON_EXECUTABLE} ${MOOSE_GUI_INSTALL_DIR}/mgui.py
-# WORKING_DIRECTORY ${MOOSE_GUI_INSTALL_DIR}
-# )
-# endif()
+ if(WITH_GUI)
+ add_test( NAME test_gui_sanity
+ COMMAND ${PYTHON_EXECUTABLE} ${MOOSE_GUI_INSTALL_DIR}/mgui.py
+ WORKING_DIRECTORY ${MOOSE_GUI_INSTALL_DIR}
+ )
+ endif()
+ set_tests_properties( test_pymoose_sanity
+ PROPERTIES ENVIRONMENT "PYTHONPATH=${PYMOOSE_BUILD_DIR}/python"
+ )
+endif()
diff --git a/debian/changelog b/debian/changelog
index c0c7780432af2bfb26002bb751fff79cceaec304..bd52b2950921cc03ea6ee5dc7099e67dad7765d0 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,15 +1,18 @@
-moose (3.2.git) UNRELEASED; urgency=medium
+moose (3.1.3ubuntu1) experimental; urgency=medium
- * Nightly build.
+ * Version bumped.
- -- Dilawar Singh <dilawars@ncbs.res.in> Sat, 16 Dec 2017 10:17:08 +0530
+ -- Dilawar Singh <dilawars@ncbs.res.in> Thu, 01 Feb 2018 12:26:15 +0530
-moose (3.0.2) unstable; urgency=low
+moose (3.1.2) unstable; urgency=medium
- * Initial release
- * Feature-freeze release.
- * trunk series. Experimental branch.
- * 3.0.2 relase.
- * Just packed with SBML and GSL-1.6 support.
+ * Chamcham release (3.1.x) series.
- -- Dilawar Singh <dilawars@ncbs.res.in> Sun, 05 Jul 2015 13:41:58 +0530
+ -- Dilawar Singh <dilawars@ncbs.res.in> Mon, 08 May 2017 13:43:42 +0530
+
+moose (3.1.2) unstable; urgency=low
+
+ * Bugfixes over 3.1.1
+ * Enhanced rdesigneur interface.
+
+ -- Dilawar <dilawars@ncbs.res.in> Sat, 22 Apr 2017 13:41:58 +0530
diff --git a/debian/control b/debian/control
index a0a1af49bb3ceb8e0ac7ff82d34190d01d130380..aa3360cbab2afdf31f6ff181e201e9ec663624f1 100644
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,7 @@ Homepage: http://moose.ncbs.res.in
Package: moose
Architecture: any
-Depends: ${shlibs:Depends},python-numpy-abi9, libhdf5-7 | libhdf5-serial-1.8.4, python-lxml, python-numpy, python-matplotlib, python-networkx, python-qt4, libgsl0ldbl
+Depends: ${misc:Depends}, ${shlibs:Depends}, ${python:Depends}
Description: the Multiscale Object-Oriented Simulation Environment
It is the base and numerical core for large, detailed simulations including Computational Neuroscience and Systems Biology.
.
diff --git a/debian/install b/debian/install
index f3eed99f2351a925e2a381f52d1dff583b5b1979..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 100644
--- a/debian/install
+++ b/debian/install
@@ -1,3 +0,0 @@
-usr/lib/moose
-usr/lib/python*
-usr/bin/moosegui
diff --git a/debian/rules b/debian/rules
index b9f79dc0cd7a928b5f2ac09e7e1742a20df7bc4d..da3f99b809eefdb95c515e37da81515d7b052e55 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,31 +1,13 @@
#!/usr/bin/make -f
-# export DH_VERBOSE=1
-
-## Here goes the debian make.
+export DH_VERBOSE=1
%:
- dh "$@"
-
-# Override clean target.
-override_dh_auto_clean:
- rm -rf $(BUILD_DIR_MOOSE)
+ dh "$@" --buildsystem=cmake --with-python2
-# consider using -DUSE_VERSIONED_DIR=ON if backporting
override_dh_auto_configure:
- cmake -DCMAKE_INSTALL_PREFIX=debian/tmp/usr -DCMAKE_VERSION=3.2.git
-
-override_dh_auto_build:
- make VERBOSE=0 -j`nproc`
-
-override_dh_auto_install:
- make install
-
-override_dh_auto_test:
- echo "Nothing to do here"
-
-override_dh_shlibdeps:
- dh_shlibdeps --dpkg-shlibdeps-params=--ignore-missing-info
+ dh_auto_configure -- -DVERSION_MOOSE=3.1.3 -DCMAKE_SKIP_RPATH=ON
override_dh_python2:
- dh_python2 --no-guessing-versions
+ dh_numpy
+ dh_python2