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Dilawar Singh
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Merge branch 'master' into LSODE
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‎.ci/Dockerfile‎

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# Run this script from top directory
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# docker build . --file .ci/Dockerfile --tag bhallalab/build-wheels:$(date +%s)
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FROM bhallalab/python-wheels:latest
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MAINTAINER Dilawar Singh <[email protected]>
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WORKDIR /root
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COPY . /root/moose-core/
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# RUN ./build_wheels.sh
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CMD [ "./build_wheels.sh" ]

‎.ci/build_wheels_osx.sh‎

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#!/bin/bash
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set -e
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set -x
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BRANCH=$(cat ./BRANCH)
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VERSION=3.2.dev$(date +%Y%m%d)
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# Just to be sure on homebrew.
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export PATH=/usr/local/bin:$PATH
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brew update || echo "Failed to update brew"
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brew install gsl || brew upgrade gsl
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brew upgrade python3 || echo "Failed to upgrade python3"
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brew upgrade python2 || echo "Failed to upgrade python2"
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brew upgrade python || echo "Failed to upgrade python"
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# Following are to remove numpy; It is breaking the build on Xcode9.4.
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brew uninstall gdal postgis || echo "Failed to uninstall gdal/postgis"
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brew uninstall numpy || echo "Failed to uninstall numpy"
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SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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MOOSE_SOURCE_DIR=`pwd`/moose-core
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if [ ! -d $MOOSE_SOURCE_DIR ]; then
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git clone https://github.com/BhallaLab/moose-core -b $BRANCH --depth 10
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fi
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cd moose-core && git pull
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WHEELHOUSE=$HOME/wheelhouse
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mkdir -p $WHEELHOUSE
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# Current version 0.7.4 seems to be broken with python3.7 .
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# See https://travis-ci.org/BhallaLab/deploy/jobs/435219820
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sudo /usr/local/bin/python -m pip install delocate virtualenv
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sudo /usr/local/bin/python3 -m pip install delocate virtualenv
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DELOCATE_WHEEL=/usr/local/bin/delocate-wheel
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# Always prefer brew version.
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for _py in 3 2; do
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PYTHON=/usr/local/bin/python$_py
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if [ ! -f $PYTHON ]; then
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echo "Not found $PYTHON"
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continue
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fi
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$PYTHON -m pip install setuptools --upgrade --user
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$PYTHON -m pip install wheel --upgrade --user
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$PYTHON -m pip install numpy --upgrade --user
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$PYTHON -m pip install twine --upgrade --user
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PLATFORM=$($PYTHON -c "import distutils.util; print(distutils.util.get_platform())")
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(
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cd $MOOSE_SOURCE_DIR
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BUILDDIR=_build_$_py
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mkdir -p $BUILDDIR && cd $BUILDDIR
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echo " -- Building wheel for $PLATFORM"
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cmake -DVERSION_MOOSE=$VERSION -DPYTHON_EXECUTABLE=$PYTHON ..
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make -j4
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(
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cd python
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ls *.py
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sed "s/from distutils.*setup/from setuptools import setup/g" \
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setup.cmake.py > setup.wheel.py
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$PYTHON setup.wheel.py bdist_wheel -p $PLATFORM
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# Now fix the wheel using delocate.
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$DELOCATE_WHEEL -w $WHEELHOUSE -v dist/*.whl
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)
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ls $WHEELHOUSE/pymoose*-py${_py}-*.whl
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# create a virtualenv and test this.
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rm -rf $HOME/Py${_py}
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(
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python3 -m virtualenv -p $PYTHON $HOME/Py${_py}
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source $HOME/Py${_py}/bin/activate
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set +x
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python -m pip install $WHEELHOUSE/pymoose*-py${_py}-*.whl
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echo "Testing wheel in virtualenv"
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which python
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python --version
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python -c 'import moose; print( moose.__version__ )'
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deactivate
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set -x
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)
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)
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if [ ! -z "$PYPI_PASSWORD" ]; then
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echo "Did you test the wheels? I am uploading anyway ..."
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$PYTHON -m twine upload -u bhallalab -p $PYPI_PASSWORD \
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$HOME/wheelhouse/pymoose*.whl || echo "Failed to upload to PyPi"
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fi
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done

‎.travis/deploy_pypi.sh‎ renamed to ‎.ci/deploy_pypi.sh‎

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‎.travis/download_and_run_doqcs.sh‎ renamed to ‎.ci/download_and_run_doqcs.sh‎

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‎.ci/run_pylint.sh‎

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#!/usr/bin/env bash
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set -e
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python3 -m pip install pylint --user
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PYLINT="python3 -m pylint -E \
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--disable=no-member --disable=no-name-in-module \
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--disable=invalid-unary-operand-type \
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--disable=import-error \
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"
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function do_pylint() {
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echo "Checking $1"
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DIR=$(dirname $1)
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SNAME=$(basename $1)
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(
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cd $DIR
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$PYLINT $@ $SNAME
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)
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}
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FILES=$(find . -type f -name "*.py" | shuf)
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N=4
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i=0
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for f in $FILES; do
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#i=$((i+1))
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#if [ $i -eq $N ]; then
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# i=0
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# wait;
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#fi
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# do_pylint "$f"
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echo "Checking $f"
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DIR=$(dirname $f)
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SNAME=$(basename $f)
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(
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cd $DIR
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$PYLINT $@ $SNAME
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)
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done

‎.ci/travis_build_linux.sh‎

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#!/usr/bin/env bash
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#
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# DESCRIPTION: Build on linux environment.
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#
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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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set -e
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set -x
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BUILDDIR=_build_travis
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mkdir -p $BUILDDIR
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PYTHON2="/usr/bin/python2"
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PYTHON3="/usr/bin/python3"
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$PYTHON2 -m pip install pip --upgrade --user
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$PYTHON2 -m pip install libNeuroML pyNeuroML python-libsbml --upgrade --user
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$PYTHON3 -m pip install pip --upgrade --user
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$PYTHON3 -m pip install libNeuroML pyNeuroML python-libsbml --upgrade --user
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# sympy is only needed for pretty-priting for one test.
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$PYTHON3 -m pip install sympy --upgrade --user
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NPROC=$(nproc)
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MAKE="make -j$NPROC"
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unset PYTHONPATH
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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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$PYTHON2 -m compileall -q .
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$PYTHON3 -m compileall -q .
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# Python3 with GSL in debug more.
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(
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mkdir -p $BUILDDIR && cd $BUILDDIR && \
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cmake -DPYTHON_EXECUTABLE=$PYTHON3 \
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-DCMAKE_INSTALL_PREFIX=/usr -DDEBUG=ON ..
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$MAKE
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# Run with valgrind to log any memory leak.
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valgrind --leak-check=full ./moose.bin -q -u
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# Run all tests in debug mode.
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MOOSE_NUM_THREADS=$NPROC ctest -j$NPROC --output-on-failure
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make install || sudo make install
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cd /tmp
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$PYTHON3 -c 'import moose;print(moose.__file__);print(moose.version())'
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)
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# GSL and python2, failure is allowed
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set +e
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(
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mkdir -p $BUILDDIR && cd $BUILDDIR && \
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cmake -DPYTHON_EXECUTABLE=$PYTHON2 -DCMAKE_INSTALL_PREFIX=/usr ..
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$MAKE && MOOSE_NUM_THREADS=$NPROC ctest -j$NPROC --output-on-failure
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)
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set -e
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# BOOST and python3
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(
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mkdir -p $BUILDDIR && cd $BUILDDIR && \
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cmake -DWITH_BOOST_ODE=ON -DPYTHON_EXECUTABLE="$PYTHON3" \
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-DCMAKE_INSTALL_PREFIX=/usr ..
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$MAKE && MOOSE_NUM_THREADS=$NPROC ctest -j$NPROC --output-on-failure
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)
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echo "All done"

‎.travis/travis_build_osx.sh‎ renamed to ‎.ci/travis_build_osx.sh‎

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set -o nounset # Treat unset variables as an error
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set -e
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# NOTE: On travis, don't enable -j`nproc` option. It may not compile properly.
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BUILDDIR=_build_travis
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NPROC=$(nproc)
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(
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# Make sure not to pick up python from /opt.
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PATH=/usr/bin:/usr/local/bin:$PATH
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mkdir -p _GSL_BUILD && cd _GSL_BUILD \
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&& cmake -DDEBUG=ON \
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-DPYTHON_EXECUTABLE=`which python` ..
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make && ctest --output-on-failure
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PATH=/usr/local/bin:/usr/bin:$PATH
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cd .. # Now with boost.
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mkdir -p _BOOST_BUILD && cd _BOOST_BUILD \
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&& cmake -DWITH_BOOST_ODE=ON -DDEBUG=ON \
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-DPYTHON_EXECUTABLE=`which python` ..
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PYTHON3=$(which python3)
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# Get pylint
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$PYTHON3 -m pip install pylint --user
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$PYTHON3 -m pip install python-libsbml --user
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$PYTHON3 -m pip install pyneuroml --user
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make && ctest --output-on-failure
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cd ..
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set +e
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mkdir -p $BUILDDIR && cd $BUILDDIR \
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&& cmake -DPYTHON_EXECUTABLE=$PYTHON3 \
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..
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make pylint -j$NPROC
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make -j$NPROC && MOOSE_NUM_THREAD=$NPROC ctest --output-on-failure -j$NPROC
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cd .. # Now with boost.
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mkdir -p $BUILDDIR && cd $BUILDDIR \
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&& cmake -DWITH_BOOST_ODE=ON \
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-DPYTHON_EXECUTABLE=`which python3` ..
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make -j$NPROC && MOOSE_NUM_THREAD=$NPROC ctest -j$NPROC --output-on-failure
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)
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set +e
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‎.ci/travis_prepare_linux.sh‎

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#!/bin/bash -
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#
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# DESCRIPTION: Prepare linux build environment on travis.
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# NOTES: Always run with sudo permission.
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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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set -e -x
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apt update
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apt-get install -qq libxml2-dev libbz2-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 python-pip
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apt-get install -qq python3-numpy python3-matplotlib python3-networkx python3-pip
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apt-get install -qq python-tk python3-tk
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apt-get install -qq valgrind
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# Gsl
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apt-get install -qq libgsl0-dev || apt-get install -qq libgsl-dev
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# Boost related.
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apt-get install -qq liblapack-dev
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apt-get install -qq libboost-all-dev
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# Dependencies for NML2
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apt-get install -qq python-scipy python3-scipy
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apt-get install -qq python-lxml python3-lxml
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apt-get install -qq python-setuptools python3-setuptools
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# Install twine
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python3 -m pip install twine

‎.travis/travis_prepare_osx.sh‎ renamed to ‎.ci/travis_prepare_osx.sh‎

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set -o nounset # Treat unset variables as an error
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set +e
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#rvm get head
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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 update || echo "failed to update"
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brew outdated cmake || brew install cmake
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brew install gsl || brew upgrade gsl
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brew install hdf5
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brew install python
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brew install numpy
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brew install boost
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PYTHON3=$(which python3)
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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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#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")' >> $HOME/Library/Python/2.7/lib/python/site-packages/homebrew.pth
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# To make sure that we do not pick python from /opt etc.
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PATH=/usr/local/bin:/usr/bin:$PATH
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# ensurepip
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python -m ensurepip
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python -m pip install matplotlib --user --upgrade
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python -m pip install pyNeuroML libNeuroML --user
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python -m pip install scipy --user
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$PYTHON3 -m ensurepip
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$PYTHON3 -m pip install matplotlib --user --upgrade
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$PYTHON3 -m pip install pyNeuroML libNeuroML --user
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$PYTHON3 -m pip install scipy --user
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$PYTHON3 -m pip install pylint --user

‎.github/main.workflow‎

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workflow "build pymoose" {
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resolves = "build"
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on = "push"
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}
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action "build" {
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uses = "./"
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args = "install"
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env = {
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CMAKE_GIT_REPO = "https://github.com/dilawar/moose-core",
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CMAKE_INSTALL_DEPS_SCRIPT = ".travis/travis_prepare_linux.sh",
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CMAKE_FLAGS = "-DCMAKE_INSTALL_PREFIX:PATH=/tmp/foo",
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CMAKE_BUILD_THREADS = "4"
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}
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}

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