diff --git a/moose-core/.travis/travis_build_linux.sh b/moose-core/.travis/travis_build_linux.sh
index ff3cdf0987389f4c7ac73b263219cc4c16b99550..49b7aa6ae5014ed1a53ad62c2edee002ba1a331c 100755
--- a/moose-core/.travis/travis_build_linux.sh
+++ b/moose-core/.travis/travis_build_linux.sh
@@ -1,4 +1,4 @@
-#!/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" ..
diff --git a/moose-core/CMakeLists.txt b/moose-core/CMakeLists.txt
index aa1c243d0ffd727d1926ec67bd07d9d31a38a087..128743396ace18dd14648f837608d71b97991035 100644
--- a/moose-core/CMakeLists.txt
+++ b/moose-core/CMakeLists.txt
@@ -1,5 +1,6 @@
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
diff --git a/moose-core/python/moose/genesis/writeKkit.py b/moose-core/python/moose/genesis/writeKkit.py
index ba71603148d5e5096a41e14499027a7a11b442c2..4f2ea99a5b674235f2b7bf715c339e8b7e186435 100644
--- a/moose-core/python/moose/genesis/writeKkit.py
+++ b/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")
diff --git a/moose-core/python/moose/moose.py b/moose-core/python/moose/moose.py
index 99babb8ac0dc7612be6166e5119a19bdc87d232d..9257a5cde162273a945af677b9c9f2eef88ab6c9 100644
--- a/moose-core/python/moose/moose.py
+++ b/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)
diff --git a/moose-core/python/moose/moose_test.py b/moose-core/python/moose/moose_test.py
index c6ff029f2c29643f2a24db529c283ebcab42db8d..e5f908bcfd8e05191510946f056bfc53dbda11ee 100644
--- a/moose-core/python/moose/moose_test.py
+++ b/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__':