More tests and some rearrangements (#363)

* Rearranged tests. Any tests which is in alpha has been moved to
tests/alpha directory. To run these tests, use configuration Devel with
ctest.

* Added this script in regression tests. Seems to be passing #239
Reopen it if this is not a fix.

* Issue #47 is WONTFIX.

* Refactoring script related to #93 .

* Fixed return statement outside function error. So silly!

* bumped xcode version to 10.2

* On OSX, use python3 only.

* Fix #364 .

* Fixed boost include paths.

* Reverting xcode to default on travis.

* Also test with xcode image 10.2 but allow failure.
Removed insource odeint library since centos7 has the required version
of boost. CentOS6 is EOL.

* moose.test() is python3 compatible.

10.2 seems to be buggy on travis. making failure non-strict on it. Must
build with xcode9.4

Added xcode10.2 image.

Author: dilawar

.travis.yml

@@ -6,7 +6,11 @@ matrix:
         - os : linux
           dist: xenial
         - os : osx
-          osx_image: xcode10.1
+            - osx_image: xcode9.4
+            - osx_image: xcode10.2
+    allow_failures:
+        - os: osx
+          - osx_image: xcode10.2
 
 notifications:
   email:

.travis/travis_build_osx.sh

@@ -26,23 +26,26 @@ set -e
     # Make sure not to pick up python from /opt.
     PATH=/usr/local/bin:/usr/bin:$PATH
 
+    PYTHON3=$(which python3)
+
     # Get pylint
-    python -m pip install pylint --user
-    python -m pip install python-libsbml --user
-    python -m pip install pyneuroml --user
+    $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` ..
+        -DPYTHON_EXECUTABLE=$PYTHON3 \
+        ..
     make pylint -j3
-    make && ctest --output-on-failure -E ".*socket_streamer.*"
+    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 -E ".*socket_streamer.*"
+    make -j4 && ctest --output-on-failure 
     cd ..
     set +e
 

.travis/travis_prepare_osx.sh

@@ -28,17 +28,20 @@ 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 #brew outdated python || brew install python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

CMakeLists.txt

@@ -143,11 +143,10 @@ set(STATIC_LIBRARIES "" )
 set(SYSTEM_SHARED_LIBS ${LibXML2_LIBRARIES})
 
 # BOOST ode library performs better than GSL and ideally should be made default.
-# Making boost default means that we get rid of gsl. Boost does not have a very
-# good matrix library; it has ublas which is not well maintained and emit a lot
+# Unfortunately Boost does not have a very good matrix library; it has ublas
+# which is not well maintained and emit a lot
 # of warning during compilation. Nonetheless, WITH_BOOST_ODE works fine and
-# produce results quicker than GSL. Both boost ode and ublas are in moose source
-# tree ./external/odeint-v2 and ./external/boost-numeric-bindings
+# produce results quicker than GSL. 
 if(WITH_GSL)
     find_package(GSL 1.16 REQUIRED)
     if(NOT GSL_FOUND)
@@ -172,13 +171,14 @@ if(WITH_GSL)
     # top level.
     include_directories( ${GSL_INCLUDE_DIRS} )
 elseif(WITH_BOOST_ODE)
-    find_package(Boost 1.44 REQUIRED)
-    find_package( LAPACK REQUIRED )
+    find_package(Boost 1.53 REQUIRED)
+    find_package(LAPACK REQUIRED)
 endif()
 
 # if boost ode is being used, don't use GSL.
 if(WITH_BOOST_ODE)
     add_definitions(-DUSE_BOOST_ODE -UUSE_GSL)
+    include_directories(${Boost_INCLUDE_DIRS})
 endif()
 
 # Openmpi
@@ -441,6 +441,7 @@ set(PYMOOSE_TEST_DIRECTORY ${CMAKE_SOURCE_DIR}/tests/python)
 # Collect all python script in tests folder and run them.
 file(GLOB PY_TEST_SCRIPTS "${PYMOOSE_TEST_DIRECTORY}/test_*.py" )
 
+
 # Run python tests.
 foreach( _test_script ${PY_TEST_SCRIPTS} )
     get_filename_component( _test_name ${_test_script} NAME_WE)
@@ -453,6 +454,36 @@ foreach( _test_script ${PY_TEST_SCRIPTS} )
         )
 endforeach( )
 
+# Alpha tests. These should not run by default.
+set(MOOSE_ALPHA_TEST_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests/alpha)
+file(GLOB PY_ALPHA_TEST_SCRIPTS "${PYMOOSE_ALPHA_TEST_DIRECTORY}/*.py" )
+foreach( _test_script ${PY_ALPHA_TEST_SCRIPTS} )
+    get_filename_component( _test_name ${_test_script} NAME_WE)
+    add_test( NAME ${_test_name}
+        COMMAND ${PYTHON_EXECUTABLE} ${_test_script}
+	CONFIGURATIONS Devel
+	WORKING_DIRECTORY ${PYMOOSE_ALPHA_TEST_DIRECTORY}
+        )
+     set_tests_properties( ${_test_name}
+         PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}/python"
+        )
+endforeach( )
+
+# Regression and github issues. These should not run by default.
+set(PYMOOSE_ISSUES_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests/issues)
+file(GLOB PY_ISSUES_SCRIPTS "${PYMOOSE_ISSUES_DIRECTORY}/*.py" )
+foreach( _test_script ${PY_ISSUES_SCRIPTS} )
+    get_filename_component( _test_name ${_test_script} NAME_WE)
+    add_test( NAME ${_test_name}
+        COMMAND ${PYTHON_EXECUTABLE} ${_test_script}
+	CONFIGURATIONS Devel
+	WORKING_DIRECTORY ${PYMOOSE_ISSUES_DIRECTORY}
+        )
+     set_tests_properties( ${_test_name}
+         PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}/python"
+        )
+endforeach( )
+
 # add pylint target.
 set(PYSCRIPTS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/python )
 file(GLOB_RECURSE PY_SCRIPTS  "python/*.py")
@@ -476,4 +507,5 @@ foreach( _py_script ${PY_SCRIPTS} )
 endforeach( )
 
 ############################ CPACK ######################################
+# This is not maintained anymore since packaging is done using OpenBuildService 
 include(${CMAKE_CURRENT_SOURCE_DIR}/cmake_moose_cpack.cmake)

diffusion/CMakeLists.txt

@@ -1,6 +1,10 @@
 cmake_minimum_required(VERSION 2.8)
 include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)
-include_directories(${GSL_INCLUDE_DIRS})
+
+if(WITH_GSL)
+   include_directories(${GSL_INCLUDE_DIRS})
+endif(WITH_GSL)
+
 add_library(diffusion
 	FastMatrixElim.cpp
 	DiffPoolVec.cpp