Merge commit '99b934e9'

moose-core/.travis/travis_build_linux.sh

-#!/bin/bash - 
+#!/usr/bin/env bash
 #===============================================================================
 #
 #          FILE: travis_build_linux.sh
@@ -22,7 +22,7 @@ set -e
 
 PYTHON2="/usr/bin/python2"
 PYTHON3="/usr/bin/python3"
-#MAKEFLAGS="-j 4"
+#MAKEFLAGS="-j4"
 
 # 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
@@ -32,6 +32,7 @@ PYTHON3="/usr/bin/python3"
     # Old makefile based flow.
     $PYTHON2 -m compileall -q .
     if type $PYTHON3 > /dev/null; then $PYTHON3 -m compileall -q . ; fi
+
     ## CMAKE based flow
     mkdir -p _GSL_BUILD && cd _GSL_BUILD && \
         cmake -DDEBUG=ON -DPYTHON_EXECUTABLE="$PYTHON2" ..

moose-core/CMakeLists.txt

 set(CMAKE_LEGACY_CYGWIN_WIN32 0)
-cmake_minimum_required(VERSION 2.6.0 FATAL_ERROR)
+cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
+project(MOOSE)
 
 if(COMMAND cmake_policy)
     cmake_policy(SET CMP0003 NEW)
@@ -9,7 +10,6 @@ if(COMMAND cmake_policy)
     endif(POLICY CMP0050)
 endif(COMMAND cmake_policy)
 
-project(MOOSE)
 
 include(CheckCXXCompiler.cmake)
 include(CheckIncludeFileCXX)
@@ -48,8 +48,6 @@ message( STATUS "MOOSE Version ${MOOSE_VERSION}" )
 # sure that we don't have any stray generated files lying around in the tree
 # (which would end up getting picked up by header search, instead of the correct
 # versions).
-
-message(STATUS "CMAKE_INSTALL_PREFIX : ${CMAKE_INSTALL_PREFIX}")
 if( CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_BINARY_DIR AND NOT MSVC_IDE )
     message(FATAL_ERROR 
         "======================================================================\n"
@@ -415,17 +413,26 @@ install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/scripts/moose
     DESTINATION bin
     )
 
-# This target is built by pymoose/CMakeLists.txt file.
+# INSTALL python module.
+# This target is built by pymoose/CMakeLists.txt file. Using the --prefix option
+# always override debian default installation directory. It will be installed in
+# site-packages instead of dist-packages. 
+# See https://bugs.launchpad.net/ubuntu/+source/python2.6/+bug/362570
+# HACK: Some trickery is involved. Don't pass --prefix if CMAKE_INSTALL_PREFIX is 
+# just /usr. This fixes debian builds.
 if(WITH_PYTHON)
+    if( "${CMAKE_INSTALL_PREFIX}" STREQUAL "/usr" )
+        set(EXTRA_ARGS "" )
+    else()
+        set(EXTRA_ARGS "--prefix ${CMAKE_INSTALL_PREFIX}")
+    endif( )
+
     install(CODE 
-        "
-        execute_process(
-            COMMAND ${PYTHON_EXECUTABLE} setup.py install --prefix=${CMAKE_INSTALL_PREFIX}
+        "execute_process( 
+            COMMAND ${PYTHON_EXECUTABLE} setup.py install ${EXTRA_ARGS} 
             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/python
+            )" 
             )
-        "
-        )
-
 endif(WITH_PYTHON)
 
 # Print message to start build process

moose-core/python/moose/genesis/writeKkit.py

@@ -14,6 +14,7 @@ import random
 import re
 import matplotlib
 import moose
+
 from moose.chemUtil.chemConnectUtil import *
 from moose.chemUtil.graphUtils import *
 
@@ -624,6 +625,6 @@ if __name__ == "__main__":
     output = modelpath+"_.g"
     written = write('/'+modelpath,output)
     if written:
-            print((" file written to ",output))
+            print(" file written to ",output)
     else:
             print(" could be written to kkit format")

moose-core/python/moose/moose.py

@@ -12,9 +12,15 @@ from io import StringIO
 
 import moose.SBML.readSBML as _readSBML
 import moose.SBML.writeSBML as _writeSBML
-import moose.genesis.writeKkit as _writeKkit
 import moose.chemUtil as _chemUtil
 
+kkitImport_, kkitImport_error_ = True, ''
+try:
+    import moose.genesis.writeKkit as _writeKkit
+except ImportError as e:
+    kkitImport_ = False
+    kkitImport_err_ = '%s' % e 
+
 # Import function from C++ module into moose namespace.
 from moose._moose import *
 
@@ -88,6 +94,11 @@ def mooseWriteKkit(modelpath, filepath,sceneitems={}):
     modelpath -- model path in moose \n
     filepath -- Path of output file.
     """
+    global kkitImport_, kkitImport_err_
+    if not kkitImport_:
+        print( '[WARN] Could not import module to enable this function' )
+        print( '\tError was %s' % kkitImport_error_ )
+        return False
     return _writeKkit.mooseWriteKkit(modelpath, filepath,sceneitems)
 
 

moose-core/python/moose/moose_test.py

@@ -110,37 +110,45 @@ def suitable_for_testing( script ):
             return False, 'waits for user input'
     return True, 'OK'
 
-def run_test( index, testfile ):
+def run_test( index, testfile, timeout,  **kwargs):
     """Run a given test
     """
     global test_status_
     global total_
     pyExec = os.environ.get( 'PYTHON_EXECUTABLE', '/usr/bin/python' )
     cmd = Command( [ pyExec, testfile ] )
+
     ti = time.time( )
-    status = cmd.run( timeout = 60 )
     name = os.path.basename( testfile )
+    out = (name + '.' * 50)[:40]
+    print( '[TEST %3d/%d] %41s ' % (index, total_, out), end='' )
+    sys.stdout.flush( )
+
+    # Run the test.
+    status = cmd.run( timeout = timeout )
     t = time.time( ) - ti
+    print( '% 7.2f ' % t, end='' )
+    sys.stdout.flush( )
+
+    # Change to directory and copy before running then test.
     cwd = os.path.dirname( testfile )
     os.chdir( cwd )
     with open( os.path.join( cwd, 'matplotlibrc' ), 'w' ) as f:
         _logger.debug( 'Writing matplotlibrc to %s' % cwd )
         f.write( matplotlibrc_ )
 
-    out = (name + '.' * 50)[:50]
-    print( '[TEST %3d/%d] %50s %.2f sec ' % (index, total_, out, t), end='' )
-    sys.stdout.flush( )
     if status != 0:
         if status == -15:
-            msg = '%2d TIMEOUT' % status
+            msg = '% 4d TIMEOUT' % status
             test_status_[ 'TIMED-OUT' ].append( testfile )
         else:
-            msg = '%2d FAILED' % status
+            msg = '% 4d FAILED' % status
             test_status_[ 'FAILED' ].append( testfile )
         print( msg )
     else:
-        print( '%2d PASSED' % status )
+        print( '% 4d PASSED' % status )
         test_status_[ 'PASSED' ].append( testfile )
+
     sys.stdout.flush( )
 
 def print_test_stat( ):
@@ -148,7 +156,7 @@ def print_test_stat( ):
     for status in test_status_:
         print( 'Total %d tests %s' % (len( test_status_[status] ), status ) )
 
-def test_all( ):
+def test_all( timeout, **kwargs ):
     global test_dir_ 
     global total_
     scripts = [ ]
@@ -171,20 +179,21 @@ def test_all( ):
     total_ = len( scripts )
     for i, s in enumerate( scripts ):
         _logger.info( 'Running test : %s' % s )
-        run_test(i, s )
+        run_test(i, s, timeout, **kwargs )
 
 
-def test( ):
+def test( timeout = 60, **kwargs ):
     """Download and run tests.
 
     """
+    print( '[INFO] Running test with timeout %d sec' % timeout )
     try:
         init_test_dir( )
     except Exception as e:
         print( '[INFO] Failed to clone moose-examples. Error was %s' % e )
         quit( )
 
-    test_all( )
+    test_all( timeout = timeout, **kwargs  )
     print_test_stat( )
 
 if __name__ == '__main__':