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dilawardilawar
authoredSep 17, 2018
Merged all components on Sep 11. (#240)
* Build using Travis. * Scripts to test OSX and Linux packages. * Pull from branch chhennapoda. * No clang. * Made scripts executable. * New version. * Squashed 'moose-core/' changes from d229eba..406fee2 406fee2 Temp commit to test on OSX. cc3c604 Merge branch 'master' into chhennapoda 3420928 Update moose_test.py (#301) 61f4f66 show timeout in moose.test() . abf822c with python2, just test with GSL. Build python3 first. 088c616 Made changes to build system so that pymoose directory can be built in isolation. Build system is bit more module. Ideally I should make sure that each subdirectory can built in isolation. 3c0ff27 Few changes to build with python3.6. 5d688f6 Use option --relative in setup.py and tell cmake not to look into usr prefix anymore. 1f3fe9f Merge branch 'chhennapoda' of github.com:BhallaLab/moose-core into chhennapoda 3e19983 removed unneeded library which is never used. c2fbab8 cmake related changes to build on centos5 (manylinux docker image). git-subtree-dir: moose-core git-subtree-split: 406fee2a068f43af14be9918825e6fa88cc7377e * Squashed 'moose-examples/' changes from 2d98492..1502a55 1502a55 removed old script. git-subtree-dir: moose-examples git-subtree-split: 1502a550706e049ee726f8adb4694a77feb63bbd * Squashed 'moose-gui/' changes from d226931..8dae832 8dae832 kkitViewcontrol both the groups size are updated if moved from-to is different 44b53bc default: addSolver->mooseAddChemSolver, kkitViewcontrol: while rubberbandselection if entire group is selected then delete if partly selected then delete all the items under the selection 80b599f mgui: is popup exist then close, objectedit: objectwindowTitle is updated with name when changed, kkit: in positionChange all the neutral is updated with size, kkitViewcontrol:when moose object is moved from Compt/group to group/compartment then mooseobject path is set and for qgraphicalItem and qlineitem objects the parentItem is set which will be grpItem or comptItem git-subtree-dir: moose-gui git-subtree-split: 8dae832c3513bac92b3fba9601e9a77b4ec36653 * Install gsl-dev on travis. * Build chhennapoda branch. * Run tests as well. * Squashed 'moose-core/' changes from 406fee2..b608810 b608810 Fixes for linux. git-subtree-dir: moose-core git-subtree-split: b6088109bf8ba75cb072d97dd306bec9ab2b0e9a * Squashed 'moose-core/' changes from d229eba..3420928 3420928 Update moose_test.py (#301) git-subtree-dir: moose-core git-subtree-split: 342092829ca21e457c785a5ce791429d403b79e7 * Squashed 'moose-examples/' changes from 2d98492..1502a55 1502a55 removed old script. git-subtree-dir: moose-examples git-subtree-split: 1502a550706e049ee726f8adb4694a77feb63bbd * Squashed 'moose-gui/' changes from d226931..8dae832 8dae832 kkitViewcontrol both the groups size are updated if moved from-to is different 44b53bc default: addSolver->mooseAddChemSolver, kkitViewcontrol: while rubberbandselection if entire group is selected then delete if partly selected then delete all the items under the selection 80b599f mgui: is popup exist then close, objectedit: objectwindowTitle is updated with name when changed, kkit: in positionChange all the neutral is updated with size, kkitViewcontrol:when moose object is moved from Compt/group to group/compartment then mooseobject path is set and for qgraphicalItem and qlineitem objects the parentItem is set which will be grpItem or comptItem git-subtree-dir: moose-gui git-subtree-split: 8dae832c3513bac92b3fba9601e9a77b4ec36653 * Build nightly version.
1 parent 2253b11 commit 2d914db

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‎.travis.yml

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sudo: required
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dist: trusty
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language: cpp
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compiler:
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- gcc
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- clang
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os:
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- linux
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- osx
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branches:
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only:
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- master
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- chamcham
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- chennapoda
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- chhennapoda
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notifications:
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email:
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recipients:
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- dilawar.s.rajput@gmail.com
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- bhalla@ncbs.res.in
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- hrani@ncbs.res.in
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on_success: change
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on_failure: always
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env:
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- CTEST_MODEL=Nightly
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cache: apt
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before_script:
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- sudo apt-get update -qq
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- sudo apt-get install libxml2-dev libbz2-dev wget
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- sudo apt-get install libhdf5-serial-dev
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- sudo apt-get install python-numpy python-setuptools python-networkx python-pip
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- sudo apt-get install cmake cdbs
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- sudo apt-get install python-suds python-matplotlib python-nose
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- sudo apt-get install python-qt4-dev python-qt4-gl python-sip-dev libqt4-dev libopenscenegraph-dev
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- sudo apt-get install doxygen python-sphinx python-lxml
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- sudo apt-get install git-buildpackage
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install:
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- wget http://ftp.debian.org/debian/pool/main/g/gsl/libgsl0ldbl_1.16+dfsg-2_amd64.deb -O gsl_1.16.deb
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- sudo dpkg -i gsl_1.16.deb
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- wget http://ftp.debian.org/debian/pool/main/g/gsl/libgsl0-dev_1.16+dfsg-2_amd64.deb -O gsl_1.16-dev.deb
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- sudo dpkg -i gsl_1.16-dev.deb
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- sudo apt-get install -f
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- sudo ldconfig /usr/lib64
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- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./.travis_prepare_linux.sh; fi
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script:
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- ./.travis_build.sh
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- sudo dpkg -i ../moose*.deb
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- /usr/bin/python -c 'import moose;print(moose.version());print(moose.__file__)'
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- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./.travis_build_linux.sh; fi
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- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis_build_osx.sh; fi

‎.travis_build.sh

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This file was deleted.

‎.travis_build_linux.sh

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#!/usr/bin/env bash
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set -o nounset # Treat unset variables as an error
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set -e -x
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PATH=/usr/bin:/usr/local/bin:$PATH
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gbp buildpackage --git-ignore-branch --git-ignore-new -uc -us -d | tee _gbp.log
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pwd

‎.travis_build_osx.sh

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#!/usr/bin/env bash
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brew tap BhallaLab/moose
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brew install --HEAD moose-nightly
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python -m pip install networkx python-libsbml pyNeuroML matplotlib
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python -c 'import moose; print( moose.__version__ )'
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python -c 'import moose; print( moose.test() )'

‎.travis_prepare_linux.sh

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#!/usr/bin/env bash
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sudo apt-get update -qq
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sudo apt-get -y install libxml2-dev libbz2-dev wget
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sudo apt-get -y install libhdf5-serial-dev
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sudo apt-get -y install python-numpy python-setuptools python-networkx python-pip
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sudo apt-get -y install cmake cdbs
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sudo apt-get -y install libgsl0-dev
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sudo apt-get -y install python-suds python-matplotlib
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sudo apt-get -y install python-qt4-dev python-qt4-gl python-sip-dev libqt4-dev libopenscenegraph-dev
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sudo apt-get -y install doxygen python-sphinx python-lxml
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sudo apt-get -y install git-buildpackage
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sudo apt-get -y install -f
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sudo ldconfig /usr/lib64

‎debian/changelog

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moose (3.2.0.3ubuntu1) experimental; urgency=medium
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* Version bumped.
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-- Dilawar Singh <dilawars@ncbs.res.in> Tue, 11 Sep 2018 12:26:15 +0530
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moose (3.1.3ubuntu1) experimental; urgency=medium
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* Version bumped.

‎debian/rules

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dh "$@" --buildsystem=cmake --with-python2
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override_dh_auto_configure:
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dh_auto_configure -- -DVERSION_MOOSE=3.1.3 -DCMAKE_SKIP_RPATH=ON
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dh_auto_configure -- -DVERSION_MOOSE=3.2.0-dev -DCMAKE_SKIP_RPATH=ON
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override_dh_python2:
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dh_numpy

‎moose-core/.travis/travis_build_linux.sh

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@@ -40,32 +40,20 @@ unset PYTHONPATH
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$PYTHON2 -m compileall -q .
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if type $PYTHON3 > /dev/null; then $PYTHON3 -m compileall -q . ; fi
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echo "Currently in `pwd`"
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(
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mkdir -p _GSL_BUILD && cd _GSL_BUILD
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cmake -DDEBUG=ON -DPYTHON_EXECUTABLE="$PYTHON2" ..
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$MAKE && ctest --output-on-failure
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sudo make install && cd /tmp
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$PYTHON2 -c 'import moose;print(moose.__file__);print(moose.version())'
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)
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(
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# Now with boost.
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mkdir -p _BOOST_BUILD && cd _BOOST_BUILD && \
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cmake -DWITH_BOOST_ODE=ON -DDEBUG=ON -DPYTHON_EXECUTABLE="$PYTHON2" ..
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$MAKE && ctest --output-on-failure
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)
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# This is only applicable on linux build.
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echo "Python3: Removed python2-networkx and install python3"
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if type $PYTHON3 > /dev/null; then
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sudo apt-get remove -qq python-networkx || echo "Error with apt"
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sudo apt-get install -qq python3-networkx || echo "Error with apt"
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# GSL.
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(
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mkdir -p _GSL_BUILD2 && cd _GSL_BUILD2 && \
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cmake -DPYTHON_EXECUTABLE="$PYTHON3" ..
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cmake -DPYTHON_EXECUTABLE="$PYTHON3" -DDEBUG=ON ..
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$MAKE && ctest --output-on-failure
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)
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# BOOST
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(
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mkdir -p _BOOST_BUILD2 && cd _BOOST_BUILD2 && \
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cmake -DWITH_BOOST_ODE=ON -DPYTHON_EXECUTABLE="$PYTHON3" ..
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else
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echo "Python3 is not found. Build disabled"
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fi
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# PYTHON2. Soon to be deprecated.
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echo "Currently in `pwd`"
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(
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mkdir -p _GSL_BUILD && cd _GSL_BUILD
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cmake -DDEBUG=OFF -DPYTHON_EXECUTABLE="$PYTHON2" ..
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$MAKE && ctest --output-on-failure
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sudo make install && cd /tmp
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$PYTHON2 -c 'import moose;print(moose.__file__);print(moose.version())'
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)

‎moose-core/CMakeLists.txt

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endif(NOT HDF5_HL_LIBRARIES)
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list(APPEND HDF5_LIBRARIES ${HDF5_HL_LIBRARIES})
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message(STATUS "MOOSE will use following HDF5 ${HDF5_LIBRARIES}" )
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# message(STATUS "MOOSE will use following HDF5 ${HDF5_LIBRARIES}" )
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foreach(HDF5_LIB ${HDF5_LIBRARIES})
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if(HDF5_LIB)
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get_filename_component( HDF5_LIB_EXT ${HDF5_LIB} EXT )
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message( STATUS "Using static libraries ${GSL_STATIC_LIBRARIES}" )
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list(APPEND STATIC_LIBRARIES ${GSL_STATIC_LIBRARIES})
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else( )
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message(STATUS "Using gsl libraries: ${GSL_LIBRARIES}")
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# message(DEBUG "Using gsl libraries: ${GSL_LIBRARIES}")
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foreach(GSL_LIB ${GSL_LIBRARIES} )
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if(GSL_LIB)
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get_filename_component( GSL_LIB_EXT ${GSL_LIB} EXT )
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endif( )
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# MAC linker does not understand many of gnu-ld options.
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message( STATUS "Shared libs: ${SYSTEM_SHARED_LIBS}")
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# message( DEBUG "Shared libs: ${SYSTEM_SHARED_LIBS}")
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if(MACOSX)
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target_link_libraries(libmoose
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"-Wl,-all_load"
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message(STATUS "binary distribution file ${PYMOOSE_BDIST_FILE}")
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add_custom_target(bdist ALL DEPENDS ${PYMOOSE_BDIST_FILE} )
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# Any command using setup.cmake.py must run in the same directory.
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# Any command using setup.cmake.py must run in the same directory. Use option
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# `--relative` to prefix is aways fixed.
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add_custom_command( OUTPUT ${PYMOOSE_BDIST_FILE}
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COMMAND ${PYTHON_EXECUTABLE} setup.cmake.py bdist_dumb -p ${_platform}
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-d ${PYMOOSE_BDIST_DIR}
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-d ${PYMOOSE_BDIST_DIR} --relative
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/python
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COMMENT "bdist is saved to ${PYMOOSE_BDIST_DIR}"
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VERBATIM
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install(TARGETS moose.bin DESTINATION bin CONFIGURATIONS Debug)
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install(TARGETS libmoose DESTINATION lib CONFIGURATIONS Debug)
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# install pymoose bdist. The bdist comes with predefined /usr; remove it.
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install(DIRECTORY ${PYMOOSE_BDIST_INSTALL_DIR}/usr/
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# install pymoose bdist.
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install(DIRECTORY ${PYMOOSE_BDIST_INSTALL_DIR}/
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DESTINATION ${CMAKE_INSTALL_PREFIX}
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CONFIGURATIONS Release Debug
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)

‎moose-core/basecode/CMakeLists.txt

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cmake_minimum_required(VERSION 2.6)
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include_directories(../msg)
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cmake_minimum_required(VERSION 2.8)
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include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake )
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add_library(basecode
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consts.cpp
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Element.cpp

‎moose-core/basecode/Conv.h

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#ifndef _CONV_H
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#define _CONV_H
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#include <string>
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#include <cstring>
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/**
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* This set of templates defines converters. The conversions are from

‎moose-core/basecode/header.h

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#include <iostream>
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#include <sstream>
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#include <typeinfo> // used in Conv.h to extract compiler independent typeid
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#include <climits> // Required for g++ 4.3.2
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#include <cstring> // Required for g++ 4.3.2
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#include <cstdlib> // Required for g++ 4.3.2
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// Used for INT_MAX and UINT_MAX, but may be done within the compiler
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// #include <limits.h>
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//
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#include <cassert>
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using namespace std;
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#ifndef MOOSE_VERSION
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#define MOOSE_VERSION "3.0.2"
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#endif
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/**
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* Looks up and uniquely identifies functions, on a per-Cinfo basis.

‎moose-core/cmake_modules/FindNumPy.cmake

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# Finding NumPy involves calling the Python interpreter
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message( STATUS "Using python ${PYTHON_EXECUTABLE} to locate numpy" )
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message( STATUS "Using ${PYTHON_EXECUTABLE} to locate numpy" )
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execute_process(COMMAND ${PYTHON_EXECUTABLE} -c
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"import numpy as n; print(n.__version__); print(n.get_include());"
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RESULT_VARIABLE _NUMPY_SEARCH_SUCCESS

‎moose-core/external/tinyxml/CMakeLists.txt

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