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Dilawar Singh
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Changes from master branch.
Test on macosx as well as linux.
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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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dist: trusty
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sudo: required
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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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notifications:
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email:
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recipients:
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- [email protected]
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- [email protected]
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- [email protected]
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- [email protected]
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on_success: change
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on_failure: always
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@@ -21,47 +19,17 @@ env:
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cache: apt
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matrix:
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allow_failures:
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compiler:
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- clang
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before_script:
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- sudo apt-get install -qq libxml2-dev libbz2-dev
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- sudo apt-get install -qq libhdf5-serial-dev
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- sudo apt-get install -qq make cmake
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- sudo apt-get install -qq python-numpy python-matplotlib python-networkx
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- sudo apt-get install -qq python3-numpy python3-matplotlib python3-dev
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- sudo apt-get install -qq libboost-all-dev
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- sudo apt-get install -qq libgsl0-dev
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- sudo apt-get install -qq python-pip python3-pip
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- sudo apt-get install -qq libgraphviz-dev
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#- sudo pip install python-libsbml
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#- sudo pip3 install python-libsbml
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#- sudo pip3 install pygraphviz
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install:
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- echo "nothing to do here"
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allow_failure:
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os: osx
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before_script :
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- echo "OSX related"
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- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_prepare_osx.sh; fi
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- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo ./.travis/travis_prepare_linux.sh; fi
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script:
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- # checking if any python3 incompatible file is in the source tree.
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- python2 -m compileall -q .
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- python3 -m compileall -q .
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- # Then run the old make scripts
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- make
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- ## CMAKE based flow
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- mkdir -p _GSL_BUILD && cd _GSL_BUILD && cmake -DDEBUG=ON -DPYTHON_EXECUTABLE=/usr/bin/python ..
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- make && ctest --output-on-failure
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- cd .. # Now with boost.
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- mkdir -p _BOOST_BUILD && cd _BOOST_BUILD && cmake -DWITH_BOOST=ON -DDEBUG=ON -DPYTHON_EXECUTABLE=/usr/bin/python ..
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- make && ctest --output-on-failure
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- cd ..
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- echo "Python3 support. Removed python2-networkx and install python3"
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- sudo apt-get remove -qq python-networkx
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- sudo apt-get install -qq python3-networkx
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- mkdir -p _GSL_BUILD2 && cd _GSL_BUILD2 && cmake -DDEBUG=ON -DPYTHON_EXECUTABLE=/usr/bin/python3 ..
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- make && ctest --output-on-failure
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- cd .. # Now with BOOST and python3
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- mkdir -p _BOOST_BUILD2 && cd _BOOST_BUILD2 && cmake -DWITH_BOOST=ON -DDEBUG=ON -DPYTHON_EXECUTABLE=/usr/bin/python3 ..
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- make && ctest --output-on-failure
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- cd ..
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- echo "All done. Phew"
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- if type python3 -c 'import sys' > /dev/null; then python3 -m compileall -q . ; fi
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- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_build_osx.sh; fi
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- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./.travis/travis_build_linux.sh; fi

‎.travis/travis_build_linux.sh‎

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#!/bin/bash -
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#===============================================================================
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#
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# FILE: travis_build_linux.sh
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#
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# USAGE: ./travis_build_linux.sh
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#
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# DESCRIPTION: Build on linux environment.
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#
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# OPTIONS: ---
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# REQUIREMENTS: ---
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# BUGS: ---
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# NOTES: ---
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# AUTHOR: Dilawar Singh (), [email protected]
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# ORGANIZATION: NCBS Bangalore
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# CREATED: 01/02/2017 10:11:46 AM
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# REVISION: ---
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#===============================================================================
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set -o nounset # Treat unset variables as an error
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set -e
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PYTHON2="/usr/bin/python2"
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PYTHON3="/usr/bin/python3"
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#MAKEFLAGS="-j 4"
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# Bug: `which python` returns /opt/bin/python* etc on travis. For which numpy
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# many not be available. Therefore, it is neccessary to use fixed path for
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# python executable.
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(
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# Old makefile based flow.
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python2 -m compileall -q .
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if type python3 -c 'import sys' > /dev/null; then python3 -m compileall -q . ; fi
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# Traditional make.
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make
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## CMAKE based flow
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mkdir -p _GSL_BUILD && cd _GSL_BUILD && \
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cmake -DDEBUG=ON -DPYTHON_EXECUTABLE="$PYTHON2" ..
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make && ctest --output-on-failure
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cd .. # Now with boost.
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mkdir -p _BOOST_BUILD && cd _BOOST_BUILD && \
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cmake -DWITH_BOOST=ON -DDEBUG=ON -DPYTHON_EXECUTABLE="$PYTHON2" ..
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make && ctest --output-on-failure
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cd ..
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# This is only applicable on linux build.
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echo "Python3 support. Removed python2-networkx and install python3"
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if type $PYTHON3 -c 'import os' > /dev/null; then
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sudo apt-get remove -qq python-networkx
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sudo apt-get install -qq python3-networkx
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mkdir -p _GSL_BUILD2 && cd _GSL_BUILD2 && \
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cmake -DDEBUG=ON -DPYTHON_EXECUTABLE="$PYTHON3" ..
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make && ctest --output-on-failure
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cd .. # Now with BOOST and python3
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mkdir -p _BOOST_BUILD2 && cd _BOOST_BUILD2 && \
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cmake -DWITH_BOOST=ON -DDEBUG=ON -DPYTHON_EXECUTABLE="$PYTHON3" ..
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make && ctest --output-on-failure
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cd .. && echo "All done"
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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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)

‎.travis/travis_build_osx.sh‎

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#!/bin/bash -
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#===============================================================================
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#
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# FILE: travis_build_linux.sh
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#
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# USAGE: ./travis_build_linux.sh
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#
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# DESCRIPTION: Build on linux environment.
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#
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# OPTIONS: ---
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# REQUIREMENTS: ---
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# BUGS: ---
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# NOTES: ---
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# AUTHOR: Dilawar Singh (), [email protected]
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# ORGANIZATION: NCBS Bangalore
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# CREATED: 01/02/2017 10:11:46 AM
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# REVISION: ---
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#===============================================================================
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set -o nounset # Treat unset variables as an error
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set -e
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(
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mkdir -p _GSL_BUILD && cd _GSL_BUILD && cmake -DDEBUG=ON -DPYTHON_EXECUTABLE=`which python` ..
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make && ctest --output-on-failure
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cd .. # Now with boost.
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mkdir -p _BOOST_BUILD && cd _BOOST_BUILD && cmake -DWITH_BOOST=ON -DDEBUG=ON -DPYTHON_EXECUTABLE=`which python` ..
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make && ctest --output-on-failure
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cd ..
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)

‎.travis/travis_prepare_linux.sh‎

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#!/bin/bash -
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#===============================================================================
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#
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# FILE: travis_prepare_linux.sh
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#
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# USAGE: ./travis_prepare_linux.sh
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#
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# DESCRIPTION: Prepare linux build environment on travis.
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#
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# OPTIONS: ---
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# REQUIREMENTS: ---
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# BUGS: ---
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# NOTES: ---
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# AUTHOR: Dilawar Singh (), [email protected]
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# ORGANIZATION: NCBS Bangalore
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# CREATED: 01/02/2017 10:10:02 AM
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# REVISION: ---
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#===============================================================================
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set -o nounset # Treat unset variables as an error
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set +e # Let installation fail in some command
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apt-get install -qq libxml2-dev libbz2-dev
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apt-get install -qq libhdf5-serial-dev
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apt-get install -qq make cmake
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apt-get install -qq python-numpy python-matplotlib python-networkx
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apt-get install -qq python3-numpy python3-matplotlib python3-dev
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apt-get install -qq libboost-all-dev
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apt-get install -qq libgsl0-dev
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apt-get install -qq python-pip python3-pip
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apt-get install -qq libgraphviz-dev

‎.travis/travis_prepare_osx.sh‎

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#!/bin/bash -
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#===============================================================================
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#
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# FILE: travis_prepare_osx.sh
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#
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# USAGE: ./travis_prepare_osx.sh
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#
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# DESCRIPTION: Script to prepare OSX build on Travis CI.
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#
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# OPTIONS: ---
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# REQUIREMENTS: ---
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# BUGS: ---
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# NOTES: ---
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# AUTHOR: Dilawar Singh (), [email protected]
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# ORGANIZATION: NCBS Bangalore
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# CREATED: 01/02/2017 10:09:00 AM
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# REVISION: ---
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#===============================================================================
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set -o nounset # Treat unset variables as an error
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set +e
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brew update
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#brew outdated cmake || brew install cmake
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brew install gsl
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brew outdated hdf5 || brew install homebrew/science/hdf5
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brew outdated libsbml || brew install homebrew/science/libsbml
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#brew outdated python || brew install python
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#brew outdated numpy || brew install homebrew/python/numpy
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#brew unlink numpy && brew link numpy || echo "Failed to link numpy"
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# Numpy caveats
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mkdir -p $HOME/Library/Python/2.7/lib/python/site-packages
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echo 'import sys; sys.path.insert(1, "/usr/local/lib/python2.7/site-packages")' >> $HOME/Library/Python/2.7/lib/python/site-packages/homebrew.pth
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pip install matplotlib
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