Add pip support to build system | pip install pymoose will work on all platforms

.ci/Dockerfile

@@ -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" ]

.ci/build_wheels_osx.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

.ci/travis_build_linux.sh

@@ -0,0 +1,65 @@
+#!/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
+
+PYTHON2="/usr/bin/python2"
+PYTHON3="/usr/bin/python3"
+
+$PYTHON2 -m pip install pip --upgrade --user
+$PYTHON2 -m pip install libNeuroML pyNeuroML --upgrade --user
+
+$PYTHON3 -m pip install pip --upgrade --user
+$PYTHON3 -m pip install libNeuroML pyNeuroML --upgrade --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. 
+echo "Python3: Removed python2-networkx and install python3"
+
+# GSL.
+(
+    mkdir -p _GSL_BUILD_PY3 && cd _GSL_BUILD_PY3 && \
+        cmake -DPYTHON_EXECUTABLE=$PYTHON3 \
+        -DCMAKE_INSTALL_PREFIX=/usr -DDEBUG=ON ..
+    $MAKE && ctest -j$NPROC --output-on-failure -E ".*socket_streamer.*"
+    make install || sudo make install 
+    cd /tmp
+    $PYTHON3 -c 'import moose;print(moose.__file__);print(moose.version())'
+)
+
+# BOOST and python3
+(
+    mkdir -p _BOOST_BUILD_PY3 && cd _BOOST_BUILD_PY3 && \
+        cmake -DWITH_BOOST_ODE=ON -DPYTHON_EXECUTABLE="$PYTHON3" \
+        -DCMAKE_INSTALL_PREFIX=/usr ..
+    $MAKE && ctest -j$NPROC --output-on-failure -E ".*socket_streamer.*"
+)
+
+# GSL and python2, failure is allowed
+set +e
+(
+    BUILDDIR=_GSL_PY2
+    mkdir -p $BUILDDIR && cd $BUILDDIR && \
+        cmake -DPYTHON_EXECUTABLE=$PYTHON2 -DCMAKE_INSTALL_PREFIX=/usr ..
+    $MAKE && ctest -j$NPROC --output-on-failure -E ".*socket_streamer.*"
+)
+set -e
+
+echo "All done"

.travis/travis_build_osx.sh → .ci/travis_build_osx.sh

@@ -21,7 +21,7 @@ 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.
-
+NPROC=$(nproc)
 (
     # Make sure not to pick up python from /opt.
     PATH=/usr/local/bin:/usr/bin:$PATH
@@ -37,18 +37,14 @@ set -e
         && cmake -DDEBUG=ON \
         -DPYTHON_EXECUTABLE=$PYTHON3 \
         ..
-    make pylint -j3
-    make && ctest --output-on-failure 
+    make pylint -j$NPROC
+    make -j$NPROC && ctest --output-on-failure -$NPROC
 
     cd .. # Now with boost.
     mkdir -p _BOOST_BUILD && cd _BOOST_BUILD \
         && cmake -DWITH_BOOST_ODE=ON -DDEBUG=ON \
         -DPYTHON_EXECUTABLE=`which python3` ..
 
-    make -j4 && ctest --output-on-failure 
-    cd ..
-    set +e
-
+    make -j$NPROC && ctest -j$NPROC --output-on-failure 
 )
 set +e
-

.ci/travis_prepare_linux.sh

@@ -0,0 +1,30 @@
+#!/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
+
+# 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

.docker/centos/Dockerfile

@@ -0,0 +1,25 @@
+FROM centos:7
+MAINTAINER Dilawar Singh <[email protected]>
+
+# Install dependencies.
+RUN yum -y update && yum -y install epel-release && yum -y update \
+      && yum -y clean all --enablerepo='*'
+RUN yum install -y git cmake3 gcc gcc-c++ make \
+      python3 python3-devel python3-setuptools python3-numpy \
+      && yum -y clean all --enablerepo='*'
+RUN yum install -y gsl-devel  \
+      && yum -y clean all --enablerepo='*'
+# These are required to run tests.
+RUN yum install -y python3-matplotlib python3-networkx graphviz python3-scipy  \
+      && yum -y clean all --enablerepo='*'
+RUN yum install -y python-matplotlib python-networkx python-scipy python-numpy \
+      && yum -y clean all --enablerepo='*'
+RUN ln -s /usr/bin/cmake3 /usr/bin/cmake 
+RUN ln -s /usr/bin/ctest3 /usr/bin/ctest 
+WORKDIR /home/root
+# RUN git clone  https://github.com/dilawar/moose-core -b devel
+# Run docker build from outside 
+COPY . moose-core
+RUN cd moose-core && python3 setup.py build test install
+RUN cd moose-core && python2 setup.py build test install
+CMD ["/usr/bin/python3", "-c", "'import moose;moose.test()'"]

.docker/centos/Makefile

@@ -0,0 +1,18 @@
+NAME:=dilawars/centos-moose
+VERSION:=$(shell date +%Y.%m.%d)
+
+PROJECT_ROOT_DIR:=(PWD)/../..
+
+all : build
+
+build : Dockerfile
+	cd ../../ && docker build -t $(NAME):$(VERSION) -f $(PWD)/Dockerfile .
+	cd ../../ && docker build -t $(NAME):latest -f $(PWD)/Dockerfile .
+
+upload :
+	docker push $(NAME):$(VERSION)
+	docker push $(NAME):latest
+
+run :
+	docker run -ti $(NAME):$(VERSION) bash
+

.docker/opensuse/Dockerfile

@@ -0,0 +1,18 @@
+FROM opensuse/leap
+MAINTAINER Dilawar Singh <[email protected]>
+
+# Install dependencies.
+RUN zypper install -y git cmake gcc gcc-c++ make \
+      python3 python3-devel python3-setuptools python3-numpy-devel \
+      && rm -rf /var/cache/zypp/packages/*
+RUN zypper install -y gsl-devel  \
+      && rm -rf /var/cache/zypp/packages/*
+# These are required to run tests.
+RUN zypper install -y python3-matplotlib python3-networkx graphviz python3-scipy  \
+      && rm -rf /var/cache/zypp/packages/*
+WORKDIR /home/root
+# RUN git clone  https://github.com/dilawar/moose-core -b devel
+# Run docker build from outside 
+COPY . moose-core
+RUN cd moose-core && python3 setup.py build test install 
+CMD ["/usr/bin/python3", "-c", "'import moose;moose.test()'"]

.docker/opensuse/Makefile

@@ -0,0 +1,18 @@
+NAME:=dilawars/centos-moose
+VERSION:=$(shell date +%Y.%m.%d)
+
+PROJECT_ROOT_DIR:=(PWD)/../..
+
+all : build
+
+build : Dockerfile
+	cd ../../ && docker build -t $(NAME):$(VERSION) -f $(PWD)/Dockerfile .
+	cd ../../ && docker build -t $(NAME):latest -f $(PWD)/Dockerfile .
+
+upload :
+	docker push $(NAME):$(VERSION)
+	docker push $(NAME):latest
+
+run :
+	docker run $(NAME):$(VERSION) /bin/bash -c "python3 -c 'import moose; moose.test()'"
+

.docker/travis/Dockerfile

@@ -0,0 +1,11 @@
+FROM ubuntu:xenial
+MAINTAINER Dilawar Singh <[email protected]>
+
+# Install dependencies.
+RUN apt update && apt install -y git cmake gcc g++ make vim-athena \
+      && rm -rf /var/lib/apt/lists/*
+
+RUN git config --global user.name "Dilawar Singh" \
+  && git config --global user.email "[email protected]"
+RUN git clone https://github.com/dilawar/vim ~/.vim -b minimal --depth 1
+WORKDIR /root

.docker/travis/Makefile

@@ -0,0 +1,18 @@
+NAME:=dilawars/moose-travis
+VERSION:=$(shell date +"%Y%m%d")
+
+PROJECT_ROOT_DIR:=(PWD)/../..
+
+all : build
+
+build : Dockerfile
+	docker build -t $(NAME):$(VERSION) .
+	docker build -t $(NAME):latest .
+
+upload :
+	docker push $(NAME):$(VERSION)
+	docker push $(NAME):latest
+
+run :
+	docker run -it $(NAME):latest bash
+

.docker/wheel/Dockerfile

@@ -0,0 +1,23 @@
+FROM quay.io/pypa/manylinux2010_x86_64
+
+ARG PYPI_PASSWORD
+
+MAINTAINER Dilawar Singh <[email protected]>
+ENV PATH=/usr/local/bin:$PATH
+RUN yum update -y
+RUN yum install -y cmake3 wget curl && yum clean all
+RUN ln -s /usr/bin/cmake3 /usr/local/bin/cmake
+RUN ln -s /usr/bin/ctest3 /usr/local/bin/ctest
+RUN curl -O https://ftp.gnu.org/gnu/gsl/gsl-2.4.tar.gz \
+    && tar xvf gsl-2.4.tar.gz  \
+    && cd gsl-2.4  \
+    && CFLAGS=-fPIC ./configure --enable-static && make $MAKEOPTS \
+    && make install  \
+    && cd ..
+RUN yum install -y git vim  && yum clean all
+RUN git config --global user.name 'Dilawar Singh' \
+    &&  git config --global user.email '[email protected]' \
+    && git clone https://github.com/dilawar/vim ~/.vim -b minimal
+WORKDIR /root
+COPY ./build_wheels.sh /root
+COPY ./test_and_upload.sh /root

.docker/wheel/Makefile

@@ -0,0 +1,16 @@
+VERSION := 3.2.dev$(shell date +"%Y%m%d")
+
+all : wheels
+
+DOCKERFILE:="bhallalab/python-wheels"
+
+wheels : ./Dockerfile 
+	docker build  -t $(DOCKERFILE):$(VERSION) .
+	docker build  -t $(DOCKERFILE):latest .
+
+upload:
+	docker push $(DOCKERFILE):$(VERSION)
+	docker push $(DOCKERFILE):latest
+
+run: 
+	docker run -it $(DOCKERFILE):latest bash

.docker/wheel/README.md

@@ -0,0 +1,3 @@
+This docker image can be used to build pymoose wheels. 
+
+This image is based on manylinux_2010 https://www.python.org/dev/peps/pep-0571/.