BhallaLab
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diff --git a/‎.ci/build_wheels_osx.sh‎
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diff --git a/‎.travis/deploy_pypi.sh‎ renamed to ‎.ci/deploy_pypi.sh‎ b/‎.travis/deploy_pypi.sh‎ renamed to ‎.ci/deploy_pypi.sh‎
diff --git a/‎.travis/download_and_run_doqcs.sh‎ renamed to ‎.ci/download_and_run_doqcs.sh‎ b/‎.travis/download_and_run_doqcs.sh‎ renamed to ‎.ci/download_and_run_doqcs.sh‎
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diff --git a/‎.ci/travis_build_linux.sh‎
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diff --git a/‎.travis/travis_build_osx.sh‎ renamed to ‎.ci/travis_build_osx.sh‎
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@@ -0,0 +1,8 @@
+# Run this script from top directory
+# docker build . --file .ci/Dockerfile --tag bhallalab/build-wheels:$(date +%s)
+FROM bhallalab/python-wheels:latest
+MAINTAINER Dilawar Singh <[email protected]>
+WORKDIR /root
+COPY . /root/moose-core/
+# RUN ./build_wheels.sh
+CMD [ "./build_wheels.sh" ]
@@ -0,0 +1,94 @@
+#!/bin/bash
+set -e 
+set -x
+
+BRANCH=$(cat ./BRANCH)
+VERSION=3.2.dev$(date +%Y%m%d)
+
+# Just to be sure on homebrew.
+export PATH=/usr/local/bin:$PATH
+
+brew update || echo "Failed to update brew"
+brew install gsl  || brew upgrade gsl 
+brew upgrade python3 || echo "Failed to upgrade python3"
+brew upgrade python2 || echo "Failed to upgrade python2"
+brew upgrade python || echo "Failed to upgrade python"
+
+# Following are to remove numpy; It is breaking the build on Xcode9.4.
+brew uninstall gdal postgis || echo "Failed to uninstall gdal/postgis"
+brew uninstall numpy || echo "Failed to uninstall numpy"
+
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+MOOSE_SOURCE_DIR=`pwd`/moose-core
+
+if [ ! -d $MOOSE_SOURCE_DIR ]; then
+    git clone https://github.com/BhallaLab/moose-core -b $BRANCH --depth 10
+fi
+cd moose-core && git pull
+WHEELHOUSE=$HOME/wheelhouse
+mkdir -p $WHEELHOUSE
+# Current version 0.7.4 seems to be broken with python3.7 .
+# See https://travis-ci.org/BhallaLab/deploy/jobs/435219820
+sudo /usr/local/bin/python -m pip install delocate virtualenv
+sudo /usr/local/bin/python3 -m pip install delocate virtualenv
+DELOCATE_WHEEL=/usr/local/bin/delocate-wheel
+
+# Always prefer brew version.
+for _py in 3 2; do
+    PYTHON=/usr/local/bin/python$_py
+
+    if [ ! -f $PYTHON ]; then
+        echo "Not found $PYTHON"
+        continue
+    fi
+
+    $PYTHON -m pip install setuptools --upgrade --user
+    $PYTHON -m pip install wheel --upgrade --user
+    $PYTHON -m pip install numpy --upgrade --user
+    $PYTHON -m pip install twine  --upgrade  --user
+
+    PLATFORM=$($PYTHON -c "import distutils.util; print(distutils.util.get_platform())")
+
+    ( 
+        cd $MOOSE_SOURCE_DIR
+	BUILDDIR=_build_$_py
+        mkdir -p $BUILDDIR && cd $BUILDDIR
+        echo " -- Building wheel for $PLATFORM"
+        cmake -DVERSION_MOOSE=$VERSION -DPYTHON_EXECUTABLE=$PYTHON ..
+
+        make -j4
+        ( 
+            cd python 
+            ls *.py
+            sed "s/from distutils.*setup/from setuptools import setup/g" \
+                setup.cmake.py > setup.wheel.py
+            $PYTHON setup.wheel.py bdist_wheel -p $PLATFORM 
+            # Now fix the wheel using delocate.
+            $DELOCATE_WHEEL -w $WHEELHOUSE -v dist/*.whl
+        )
+
+        ls $WHEELHOUSE/pymoose*-py${_py}-*.whl
+
+        # create a virtualenv and test this.
+        rm -rf $HOME/Py${_py}
+        (
+            python3 -m virtualenv -p $PYTHON $HOME/Py${_py}
+            source $HOME/Py${_py}/bin/activate
+            set +x 
+            python -m pip install $WHEELHOUSE/pymoose*-py${_py}-*.whl
+            echo "Testing wheel in virtualenv"
+            which python
+            python --version
+            python -c 'import moose; print( moose.__version__ )'
+            deactivate
+            set -x
+        )
+    )
+
+    if [ ! -z "$PYPI_PASSWORD" ]; then
+        echo "Did you test the wheels? I am uploading anyway ..."
+        $PYTHON -m twine upload -u bhallalab -p $PYPI_PASSWORD \
+            $HOME/wheelhouse/pymoose*.whl || echo "Failed to upload to PyPi"
+    fi
+done
@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+python3 -m trace --count \
+    --ignore-dir=/usr/lib64 \
+    --ignore-module=libsbml \
+    --ignore-module=numpy \
+    --ignore-module=neuroml \
+    "$@"
+
@@ -0,0 +1,36 @@
+#!/usr/bin/env bash 
+set -e
+python3 -m pip install pylint --user 
+PYLINT="python3 -m pylint -E \
+    --disable=no-member --disable=no-name-in-module \
+    --disable=invalid-unary-operand-type \
+    --disable=import-error \
+    "
+function do_pylint() {
+    echo "Checking $1"
+    DIR=$(dirname $1)
+    SNAME=$(basename $1)
+    ( 
+        cd $DIR
+        $PYLINT $@ $SNAME
+    )
+}
+
+FILES=$(find . -type f -name "*.py" | shuf)
+N=4
+i=0
+for f in $FILES; do 
+    #i=$((i+1))
+    #if [ $i -eq $N ]; then
+    #    i=0
+    #    wait;
+    #fi
+    # do_pylint "$f"
+    echo "Checking $f"
+    DIR=$(dirname $f)
+    SNAME=$(basename $f)
+    ( 
+        cd $DIR
+        $PYLINT $@ $SNAME
+    )
+done
@@ -0,0 +1,80 @@
+#!/usr/bin/env bash
+#
+#   DESCRIPTION:  Build  on linux environment.
+#
+#        AUTHOR: Dilawar Singh (), [email protected]
+#  ORGANIZATION: NCBS Bangalore
+#       CREATED: 01/02/2017 10:11:46 AM
+
+set -e
+set -x
+
+BUILDDIR=_build_travis
+mkdir -p $BUILDDIR
+
+PYTHON2="/usr/bin/python2"
+PYTHON3="/usr/bin/python3"
+
+$PYTHON2 -m pip install pip --upgrade --user
+$PYTHON2 -m pip install libNeuroML numpy==1.14 scipy==1.2 \
+    pyNeuroML python-libsbml --upgrade --user
+
+$PYTHON3 -m pip install pip --upgrade --user
+$PYTHON3 -m pip install libNeuroML pyNeuroML python-libsbml --upgrade --user
+
+# sympy is only needed for pretty-priting for one test.
+$PYTHON3 -m pip install numpy sympy scipy --upgrade --user   
+
+# pytest requirements.
+$PYTHON3 -m pip install -r ./tests/requirements.txt --user
+ 
+NPROC=$(nproc)
+MAKE="make -j$NPROC"
+
+unset PYTHONPATH
+
+# Bug: `which python` returns /opt/bin/python* etc on travis. For which numpy
+# many not be available. Therefore, it is neccessary to use fixed path for
+# python executable.
+
+$PYTHON2 -m compileall -q .
+$PYTHON3 -m compileall -q . 
+
+# Python3 with GSL in debug more.
+(
+    mkdir -p $BUILDDIR && cd $BUILDDIR && \
+        cmake -DPYTHON_EXECUTABLE=$PYTHON3 \
+        -DCMAKE_INSTALL_PREFIX=/usr -DDEBUG=ON ..
+    $MAKE
+    # Run with valgrind to log any memory leak.
+    valgrind --leak-check=full ./moose.bin -q -u 
+
+    # Run all tests in debug mode.
+    MOOSE_NUM_THREADS=$NPROC ctest -j$NPROC --output-on-failure 
+
+
+    make install || sudo make install 
+    cd /tmp
+    $PYTHON3 -c 'import moose;print(moose.__file__);print(moose.version())'
+)
+
+# BOOST and python3
+(
+    mkdir -p $BUILDDIR && cd $BUILDDIR && \
+        cmake -DWITH_BOOST_ODE=ON -DPYTHON_EXECUTABLE="$PYTHON3" \
+        -DCMAKE_INSTALL_PREFIX=/usr ..
+    # Run coverage 
+    export MOOSE_NUM_THREADS=3
+    make coverage 
+)
+
+# GSL and python2, failure is allowed
+set +e
+(
+    mkdir -p $BUILDDIR && cd $BUILDDIR && \
+        cmake -DPYTHON_EXECUTABLE=$PYTHON2 -DCMAKE_INSTALL_PREFIX=/usr ..
+    $MAKE && MOOSE_NUM_THREADS=$NPROC ctest -j$NPROC --output-on-failure
+)
+set -e
+
+echo "All done"
@@ -20,26 +20,31 @@
 set -o nounset                              # Treat unset variables as an error
 set -e
 
-# NOTE: On travis, don't enable -j`nproc` option. It may not compile properly.
+BUILDDIR=_build_travis
 
+NPROC=$(nproc)
 (
-
     # Make sure not to pick up python from /opt.
-    PATH=/usr/bin:/usr/local/bin:$PATH
-    mkdir -p _GSL_BUILD && cd _GSL_BUILD \
-        && cmake -DDEBUG=ON \
-        -DPYTHON_EXECUTABLE=`which python` ..
-    make && ctest --output-on-failure
+    PATH=/usr/local/bin:/usr/bin:$PATH
 
-    cd .. # Now with boost.
-    mkdir -p _BOOST_BUILD && cd _BOOST_BUILD \
-        && cmake -DWITH_BOOST_ODE=ON -DDEBUG=ON \
-        -DPYTHON_EXECUTABLE=`which python` ..
+    PYTHON3=$(which python3)
+
+    # Get pylint
+    $PYTHON3 -m pip install pylint --user
+    $PYTHON3 -m pip install python-libsbml --user
+    $PYTHON3 -m pip install pyneuroml --user
 
-    make && ctest --output-on-failure
-    cd ..
-    set +e
+    mkdir -p $BUILDDIR && cd $BUILDDIR \
+        && cmake -DPYTHON_EXECUTABLE=$PYTHON3 \
+        ..
+    make pylint -j$NPROC
+    make -j$NPROC && MOOSE_NUM_THREAD=$NPROC ctest --output-on-failure -j$NPROC
 
+    cd .. # Now with boost.
+    mkdir -p $BUILDDIR && cd $BUILDDIR \
+        && cmake -DWITH_BOOST_ODE=ON \
+        -DPYTHON_EXECUTABLE=`which python3` ..
+
+    make -j$NPROC && MOOSE_NUM_THREAD=$NPROC ctest -j$NPROC --output-on-failure 
 )
 set +e
-
 
@@ -0,0 +1,31 @@
+#!/bin/bash -
+#
+#   DESCRIPTION:  Prepare linux build environment on travis.
+#         NOTES: Always run with sudo permission.
+#        AUTHOR: Dilawar Singh (), [email protected]
+#  ORGANIZATION: NCBS Bangalore
+#       CREATED: 01/02/2017 10:10:02 AM
+
+set -e -x
+apt update
+apt-get install -qq libxml2-dev libbz2-dev
+apt-get install -qq make cmake
+apt-get install -qq python-numpy python-matplotlib python-networkx python-pip
+apt-get install -qq python3-numpy python3-matplotlib python3-networkx python3-pip
+apt-get install -qq python-tk python3-tk
+apt-get install -qq valgrind
+
+# Gsl
+apt-get install -qq libgsl0-dev || apt-get install -qq libgsl-dev
+
+# Boost related.
+apt-get install -qq liblapack-dev
+apt-get install -qq libboost-all-dev
+
+# Dependencies for NML2
+apt-get install -qq python-scipy python3-scipy
+apt-get install -qq python-lxml python3-lxml
+apt-get install -qq python-setuptools python3-setuptools
+
+# Install twine
+python3 -m pip install twine
@@ -20,25 +20,28 @@
 set -o nounset                              # Treat unset variables as an error
 set +e
 #rvm get head
-#brew update
-#brew outdated cmake || brew install cmake
-brew install gsl
+brew update || echo "failed to update"
+brew outdated cmake || brew install cmake
+brew install gsl || brew upgrade gsl
 brew install hdf5
 brew install python
 brew install numpy
 brew install boost
 
+PYTHON3=$(which python3)
+
 #brew outdated python || brew install python
 #brew outdated numpy || brew install homebrew/python/numpy
 brew unlink numpy && brew link numpy || echo "Failed to link numpy"
 # Numpy caveats
-mkdir -p $HOME/Library/Python/2.7/lib/python/site-packages
-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
+#mkdir -p $HOME/Library/Python/2.7/lib/python/site-packages
+#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
 
 # To make sure that we do not pick python from /opt etc.
 PATH=/usr/local/bin:/usr/bin:$PATH
 # ensurepip
-python -m ensurepip
-python -m pip install matplotlib --user --upgrade
-python -m pip install pyNeuroML libNeuroML --user
-python -m pip install scipy --user
+$PYTHON3 -m ensurepip
+$PYTHON3 -m pip install matplotlib --user --upgrade
+$PYTHON3 -m pip install pyNeuroML libNeuroML --user
+$PYTHON3 -m pip install scipy --user
+$PYTHON3 -m pip install pylint --user