2020-03-10 |Pulling in changes from subtree

.travis_build_linux.sh

@@ -10,5 +10,5 @@ if [ -n "$TRAVIS" ]; then
     echo "We are on travis"
     sudo dpkg -i ../*.deb
     sudo apt-get install -f 
-    python -c 'import moose; print(moose.__file__); print(moose.__version__)'
+    python -c 'import moose; print(moose.about())' || python3 -c 'import moose; print(moose.about())'
 fi

.travis_prepare_linux.sh

@@ -3,6 +3,7 @@ sudo apt-get update -qq
 sudo apt-get -y install libxml2-dev libbz2-dev wget
 sudo apt-get -y install libhdf5-serial-dev
 sudo apt-get -y install python-numpy python-setuptools python-networkx python-pip
+sudo apt-get -y install python3-numpy python3-setuptools python3-matplotlib
 sudo apt-get -y install cmake cdbs
 sudo apt-get -y install libgsl0-dev
 sudo apt-get -y install python-suds python-matplotlib 

CMakeLists.txt

@@ -2,22 +2,24 @@ cmake_minimum_required(VERSION 2.8)
 project(moose)
 set(CMAKE_BUILD_TYPE Release)
 
-# If from command line, version info is not passed, use the git to generate a
-# version file. If GIT fails, use the previous known version.
-find_program(GIT_EXEC "git")
-message( STATUS "Looking for git ${GIT_EXEC}" )
-if(VERSION_MOOSE)
-    message( STATUS "MOOSE version is set to ${VERSION_MOOSE} at build time" )
-elseif(GIT_EXEC)
-    message( STATUS "Getting version by reading git tags" )
-    execute_process( 
-        COMMAND ${GIT_EXEC} describe --tags --long
-        WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+set(Python_ADDITIONAL_VERSIONS 2.7)
+find_package(PythonInterp 3.5)
+if(NOT PYTHONINTERP_FOUND)
+  find_package(PythonInterp 2.7)
+endif()
+
+# NOTE: version should be changed in setup.py file.
+# If moose version is not given, use setup.py file to get the default version.
+if(NOT VERSION_MOOSE)
+    execute_process(COMMAND ${PYTHON_EXECUTABLE} setup.py --version
+        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/moose-core
         OUTPUT_VARIABLE VERSION_MOOSE
-        OUTPUT_STRIP_TRAILING_WHITESPACE
-    )
-endif( )
-message( STATUS "Building version ${VERSION_MOOSE}" )
+        OUTPUT_STRIP_TRAILING_WHITESPACE)
+endif()
+
+add_definitions(-DVERSION_MOOSE="${VERSION_MOOSE}")
+message(STATUS "MOOSE Version ${VERSION_MOOSE}")
+
 
 # Prefix
 message( STATUS "CMAKE_INSTALL_PREFIX= ${CMAKE_INSTALL_PREFIX}" )
@@ -79,7 +81,7 @@ add_custom_command( OUTPUT ${OUTPUT_MOOSEBIN}
     )
 add_custom_command( TARGET moose-core POST_BUILD 
     COMMAND ${CMAKE_COMMAND} -E chdir ${PYMOOSE_INSTALL_DIR} tar xvf
-    ${PYMOOSE_BUILD_DIR}/bdist/pymoose-${VERSION_MOOSE}.CMAKE.tar.gz
+    ${PYMOOSE_BUILD_DIR}/pymoose-${VERSION_MOOSE}.CMAKE.tar.gz
     COMMENT "Unarchiving pymoose bdist"
     VERBATIM
     )

cmake/build_moose-core.sh.in

@@ -22,4 +22,3 @@ cmake -DCMAKE_INSTALL_PREFIX=@PYMOOSE_INSTALL_DIR@ \
     @CMAKE_PYMOOSE_ARGS@ \
     @PYMOOSE_SOURCE_DIR@ 
 make $MAKEOPTS
-make bdist

debian/changelog

@@ -1,3 +1,9 @@
+moose (3.3.0.3ubuntu1) experimental; urgency=medium
+
+    * version bumped
+
+ -- Dilawar Singh <[email protected]>  Fri, 13 Mar 2020 11:21:25 +0530
+
 moose (3.2.0.3ubuntu1) experimental; urgency=medium
 
   * Version bumped.

debian/rules

@@ -1,14 +1,14 @@
 #!/usr/bin/make -f
 
-export MAKEOPTS=-j5
+export MAKEOPTS=-j$(shell nproc)
 
 export DH_VERBOSE=1
 
 %:
 	dh "$@" --buildsystem=cmake --with-python2
 
 override_dh_auto_configure:
-	dh_auto_configure -- -DVERSION_MOOSE=3.2.0-dev -DCMAKE_SKIP_RPATH=ON
+	dh_auto_configure -- -DCMAKE_SKIP_RPATH=ON
 
 override_dh_python2:
 	dh_numpy

moose-core/.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" ]

moose-core/.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

moose-core/.ci/coverage.sh

@@ -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 \
+    "$@"
+

moose-core/.ci/travis_build_linux.sh

@@ -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"

moose-core/.travis/travis_build_osx.sh → moose-core/.ci/travis_build_osx.sh

@@ -20,8 +20,9 @@
 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=$(nproc)
 (
     # Make sure not to pick up python from /opt.
     PATH=/usr/local/bin:/usr/bin:$PATH
@@ -33,22 +34,17 @@ set -e
     $PYTHON3 -m pip install python-libsbml --user
     $PYTHON3 -m pip install pyneuroml --user
 
-    mkdir -p _GSL_BUILD && cd _GSL_BUILD \
-        && cmake -DDEBUG=ON \
-        -DPYTHON_EXECUTABLE=$PYTHON3 \
+    mkdir -p $BUILDDIR && cd $BUILDDIR \
+        && cmake -DPYTHON_EXECUTABLE=$PYTHON3 \
         ..
-    make pylint -j3
-    make && ctest --output-on-failure 
+    make pylint -j$NPROC
+    make -j$NPROC && MOOSE_NUM_THREAD=$NPROC ctest --output-on-failure -j$NPROC
 
     cd .. # Now with boost.
-    mkdir -p _BOOST_BUILD && cd _BOOST_BUILD \
-        && cmake -DWITH_BOOST_ODE=ON -DDEBUG=ON \
+    mkdir -p $BUILDDIR && cd $BUILDDIR \
+        && cmake -DWITH_BOOST_ODE=ON \
         -DPYTHON_EXECUTABLE=`which python3` ..
 
-    make -j4 && ctest --output-on-failure 
-    cd ..
-    set +e
-
+    make -j$NPROC && MOOSE_NUM_THREAD=$NPROC ctest -j$NPROC --output-on-failure 
 )
 set +e
-

moose-core/.ci/travis_prepare_linux.sh

@@ -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

moose-core/.github/main.workflow

@@ -0,0 +1,15 @@
+workflow "build pymoose" {
+  resolves = "build"
+  on = "push"
+}
+
+action "build" {
+  uses = "./"
+  args = "install"
+  env = {
+    CMAKE_GIT_REPO = "https://github.com/dilawar/moose-core",
+    CMAKE_INSTALL_DEPS_SCRIPT = ".travis/travis_prepare_linux.sh",
+    CMAKE_FLAGS = "-DCMAKE_INSTALL_PREFIX:PATH=/tmp/foo",
+    CMAKE_BUILD_THREADS = "4"
+  }
+}