Merge branch 'master' into LSODE

Author: dilawar

.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"
+  }
+}

.github/workflows/build.yml

@@ -0,0 +1,21 @@
+name: C/C++ CI
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install dependencies
+      run: |
+        sudo apt update
+        sudo apt install libgsl-dev g++ cmake python3-dev python3-numpy
+    - name: configure
+      run: mkdir -p build && cd build && cmake ..
+    - name: make
+      run: cd build && make
+    - name: ctest --output-on-failure
+      run: cd build && make check

.travis.yml

@@ -1,12 +1,13 @@
 language: cpp
 sudo: required
-addons:
-  apt:
-    update: true
 
-os:
-- linux
-- osx
+matrix:
+    include:
+    - os: linux
+      dist: xenial
+    - os: osx
+      osx_image: xcode10.2
+
 notifications:
   email:
     recipients:
@@ -21,22 +22,11 @@ addons:
       update: true
 
 before_script:
-- echo "OSX related"
 - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then nvm get head || true; fi
 - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_prepare_osx.sh; fi
 - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo ./.travis/travis_prepare_linux.sh; fi
 
-
-before_script:
-- echo "OSX related"
-- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then nvm get head || true; fi
-- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_prepare_osx.sh; fi
-- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo ./.travis/travis_prepare_linux.sh;
-  fi
 script:
-
-- python2 -m compileall -q . || echo "Python2 not found"
-- if type python3 > /dev/null; then python3 -m compileall -q . ; fi
 - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_build_osx.sh; fi
 - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./.travis/travis_build_linux.sh; fi
 

.travis/run_pylint.sh

@@ -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

.travis/travis_build_linux.sh

@@ -40,42 +40,38 @@ unset PYTHONPATH
 $PYTHON2 -m compileall -q .
 if type $PYTHON3 > /dev/null; then $PYTHON3 -m compileall -q . ; fi
 
+# Python2 and GSL.
 echo "Currently in `pwd`"
 (
     MOOSE_INSTALL_PREFIX=/tmp/moose/usr
     rm -rf $MOOSE_INSTALL_PREFIX && mkdir -p $MOOSE_INSTALL_PREFIX/{bin,lib}
     mkdir -p _GSL_BUILD && cd _GSL_BUILD
     cmake -DDEBUG=ON -DPYTHON_EXECUTABLE="$PYTHON2" ..
-    $MAKE && ctest --output-on-failure 
+    $MAKE && ctest --output-on-failure -E ".*socket_streamer.*"
     sudo make install && cd  /tmp
     $PYTHON2 -c 'import moose;print(moose.__file__);print(moose.version())'
 )
 
-(
-    # Now with boost.
-    mkdir -p _BOOST_BUILD && cd _BOOST_BUILD && \
-        cmake -DWITH_BOOST_ODE=ON -DDEBUG=ON -DPYTHON_EXECUTABLE="$PYTHON2" ..
-    $MAKE && ctest --output-on-failure 
-)
-
-# This is only applicable on linux build.
+# Python3 with GSL and BOOST. This should be the only build after we drop
+# python2 support.
 echo "Python3: Removed python2-networkx and install python3"
 if type $PYTHON3 > /dev/null; then
-    if type apt-get --help > /dev/null; then
-        sudo apt-get remove -qq python-networkx
-        sudo apt-get install -qq python3-networkx
-    fi
+    sudo apt-get remove -qq python-networkx || echo "Error with apt"
+    sudo apt-get install -qq python3-networkx || echo "Error with apt"
+    # GSL.
     (
-        mkdir -p _GSL_BUILD2 && cd _GSL_BUILD2 && \
-            cmake -DPYTHON_EXECUTABLE="$PYTHON3" ..
-        $MAKE && ctest --output-on-failure 
+        mkdir -p _GSL_BUILD_PY3 && cd _GSL_BUILD_PY3 && \
+            cmake -DWITH_NSDF=ON -DPYTHON_EXECUTABLE="$PYTHON3" -DDEBUG=ON ..
+        $MAKE && ctest --output-on-failure -E ".*socket_streamer.*"
     )
+
+    # BOOST
     (
-        mkdir -p _BOOST_BUILD2 && cd _BOOST_BUILD2 && \
-            cmake -DWITH_BOOST_ODE=ON -DPYTHON_EXECUTABLE="$PYTHON3" ..
-        $MAKE && ctest --output-on-failure 
+        mkdir -p _BOOST_BUILD_PY3 && cd _BOOST_BUILD_PY3 && \
+            cmake -DWITH_NSDF=ON -DWITH_BOOST_ODE=ON -DPYTHON_EXECUTABLE="$PYTHON3" ..
+        $MAKE && ctest --output-on-failure -E ".*socket_streamer.*"
     )
     echo "All done"
 else
     echo "Python3 is not found. Build disabled"
-fi
+fi

.travis/travis_build_osx.sh

@@ -23,20 +23,29 @@ set -e
 # NOTE: On travis, don't enable -j`nproc` option. It may not compile properly.
 
 (
-
     # Make sure not to pick up python from /opt.
-    PATH=/usr/bin:/usr/local/bin:$PATH
+    PATH=/usr/local/bin:/usr/bin:$PATH
+
+    PYTHON3=$(which python3)
+
+    # Get pylint
+    $PYTHON3 -m pip install pylint --user
+    $PYTHON3 -m pip install python-libsbml --user
+    $PYTHON3 -m pip install pyneuroml --user
+
     mkdir -p _GSL_BUILD && cd _GSL_BUILD \
         && cmake -DDEBUG=ON \
-        -DPYTHON_EXECUTABLE=`which python` ..
-    make && ctest --output-on-failure
+        -DPYTHON_EXECUTABLE=$PYTHON3 \
+        ..
+    make pylint -j3
+    make && ctest --output-on-failure 
 
     cd .. # Now with boost.
     mkdir -p _BOOST_BUILD && cd _BOOST_BUILD \
         && cmake -DWITH_BOOST_ODE=ON -DDEBUG=ON \
-        -DPYTHON_EXECUTABLE=`which python` ..
+        -DPYTHON_EXECUTABLE=`which python3` ..
 
-    make && ctest --output-on-failure
+    make -j4 && ctest --output-on-failure 
     cd ..
     set +e
 

.travis/travis_prepare_linux.sh

@@ -10,7 +10,7 @@
 #       OPTIONS: ---
 #  REQUIREMENTS: ---
 #          BUGS: ---
-#         NOTES: ---
+#         NOTES: Always run with sudo permission.
 #        AUTHOR: Dilawar Singh (), [email protected]
 #  ORGANIZATION: NCBS Bangalore
 #       CREATED: 01/02/2017 10:10:02 AM
@@ -21,15 +21,28 @@ set -o nounset                              # Treat unset variables as an error
 set +e  # Let installation fail in some command
 
 apt-get install -qq libxml2-dev libbz2-dev
-apt-get install -qq libhdf5-serial-dev
 apt-get install -qq make cmake
 apt-get install -qq python-numpy python-matplotlib python-networkx python-pip
+apt-get install -qq python3-lxml python-lxml
 apt-get install -qq python3-numpy python3-matplotlib python3-dev
-apt-get install -qq libboost-all-dev
-apt-get install -qq libgsl0-dev
 apt-get install -qq python-pip python3-pip
-apt-get install -qq libgraphviz-dev
+apt-get install -qq python-tk python3-tk
+apt-get install -qq libgraphviz-dev 
+
+# Gsl
+apt-get install -qq libgsl0-dev || apt-get install -qq libgsl-dev
+
+# hdf5
+apt-get install -qq libhdf5-serial-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
-#pip install pyNeuroML libNeuroML
+apt-get install -qq python-lxml python3-lxml
+apt-get install -qq python-setuptools python3-setuptools
+apt-get install -qq python-tornado python3-tornado
+/usr/bin/python2 -m pip install pyNeuroML libNeuroML
+/usr/bin/python3 -m pip install pyNeuroML libNeuroML

.travis/travis_prepare_osx.sh

@@ -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