Some more tweaks.

Author: Dilawar Singh

.docker/centos/Dockerfile

@@ -4,17 +4,18 @@ MAINTAINER Dilawar Singh <[email protected]>
 # Install dependencies.
 RUN yum -y update && yum -y install epel-release && yum -y update \
       && yum -y clean all --enablerepo='*'
-RUN yum install -y git cmake gcc gcc-c++ make \
+RUN yum install -y git cmake3 gcc gcc-c++ make \
       python3 python3-devel python3-setuptools python3-numpy \
       && yum -y clean all --enablerepo='*'
 RUN yum install -y gsl-devel  \
       && yum -y clean all --enablerepo='*'
 # These are required to run tests.
 RUN yum install -y python3-matplotlib python3-networkx graphviz python3-scipy  \
       && yum -y clean all --enablerepo='*'
+RUN ln -s /usr/bin/cmake3 /usr/bin/cmake 
 WORKDIR /home/root
 # RUN git clone  https://github.com/dilawar/moose-core -b devel
 # Run docker build from outside 
 COPY . moose-core
 RUN cd moose-core && python3 setup.py build && python3 setup.py install 
-RUN python3 -c 'import moose;moose.test()'
+CMD ["python3", "-c", "import moose;moose.test()'"]

pymoose/CMakeLists.txt

@@ -128,7 +128,9 @@ add_custom_command(TARGET _moose POST_BUILD
 add_custom_target(copy_python_tree ALL
   COMMAND ${CMAKE_COMMAND} -E copy_directory 
     ${CMAKE_SOURCE_DIR}/python ${CMAKE_BINARY_DIR}/python
-  DEPENDS _moose)
+    COMMENT "Copying python source tree: ${CMAKE_SOURCE_DIR} -> ${CMAKE_BINARY_DIR}"
+  DEPENDS _moose 
+  VERBATIM)
 
 
 install(CODE "execute_process(

python/InstallPyMoose.cmake

@@ -1,19 +1,18 @@
 # -*- coding: utf-8 -*-
 """
 Test MOOSE installation with moose-examples.
-
 """
 
 from __future__ import print_function, division
 
-__author__           = "Dilawar Singh"
-__copyright__        = "Copyright 2016, Dilawar Singh"
-__credits__          = ["NCBS Bangalore"]
-__license__          = "GNU GPL"
-__version__          = "1.0.0"
-__maintainer__       = "Dilawar Singh"
-__email__            = "[email protected]"
-__status__           = "Development"
+__author__ = "Dilawar Singh"
+__copyright__ = "Copyright 2016, Dilawar Singh"
+__credits__ = ["NCBS Bangalore"]
+__license__ = "GNU GPL"
+__version__ = "1.0.0"
+__maintainer__ = "Dilawar Singh"
+__email__ = "[email protected]"
+__status__ = "Development"
 
 import sys
 import os
@@ -26,24 +25,12 @@
 from collections import defaultdict
 import time
 
-logging.basicConfig(
-        level=logging.DEBUG,
-        format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s',
-        datefmt='%m-%d %H:%M'
-        )
-console = logging.StreamHandler()
-console.setLevel(logging.WARNING)
-formatter = logging.Formatter('%(name)-12s: %(levelname)-8s %(message)s')
-console.setFormatter(formatter)
-_logger = logging.getLogger('moose.test')
-_logger.addHandler(console)
-
 test_data_url_ = 'https://github.com/BhallaLab/moose-examples/archive/master.zip'
 test_repo_url_ = 'https://github.com/BhallaLab/moose-examples'
-test_dir_ = os.path.join( tempfile.gettempdir( ), 'moose-examples' )
+test_dir_ = os.path.join(tempfile.gettempdir(), 'moose-examples')
 
-ignored_dict_ = defaultdict( list )
-test_status_ = defaultdict( list )
+ignored_dict_ = defaultdict(list)
+test_status_ = defaultdict(list)
 total_ = 0
 
 matplotlibrc_ = '''
@@ -53,8 +40,8 @@
 
 # Handle CTRL+C
 def signal_handler(signal, frame):
-    print( 'You pressed Ctrl+C!' )
-    print_test_stat( )
+    print('You pressed Ctrl+C!')
+    print_test_stat()
     quit(-1)
 
 signal.signal(signal.SIGINT, signal_handler)
@@ -64,139 +51,144 @@ class Command(object):
     def __init__(self, cmd):
         self.cmd = cmd
         self.process = None
-        self.fnull = open( os.devnull, 'w' )
+        self.fnull = open(os.devnull, 'w')
 
-    def __repr__( self ):
-        return ' '.join( self.cmd )
+    def __repr__(self):
+        return ' '.join(self.cmd)
 
-    def run(self, timeout):
+    def run(self, timeout, **kwargs):
         def target():
-            _logger.info( "Running %s" % self )
-            self.process = subprocess.Popen(
-                    self.cmd, shell=False
-                    , stdout = self.fnull, stderr = subprocess.STDOUT
-                    )
+            logging.info("Running %s" % self)
+            self.process = subprocess.Popen(self.cmd,
+                                            shell=False,
+                                            stdout=self.fnull,
+                                            stderr=subprocess.STDOUT)
             self.process.communicate()
 
-        thread = threading.Thread( target = target )
+        thread = threading.Thread(target=target)
         thread.start()
         thread.join(timeout)
         if thread.is_alive():
             self.process.terminate()
             thread.join()
 
         if self.process.stderr is not None:
-            _logger.warn( '%s' % self.process.stderr.read() )
+            logging.warn('%s' % self.process.stderr.read())
 
         return self.process.returncode
 
-def init_test_dir( ):
+
+def init_test_dir():
     global test_dir_
     global test_url_
-    if( not os.path.exists( test_dir_ ) ):
-        os.makedirs( test_dir_ )
-        _logger.info( "Donwloading test repository" )
+    if (not os.path.exists(test_dir_)):
+        os.makedirs(test_dir_)
+        logging.info("Donwloading test repository")
         subprocess.call(
-                [ 'git', 'clone', '--depth=10', test_repo_url_, test_dir_ ]
-                )
-    os.chdir( test_dir_ )
+            ['git', 'clone', '--depth=10', test_repo_url_, test_dir_])
+    os.chdir(test_dir_)
+
 
-def suitable_for_testing( script ):
+def suitable_for_testing(script):
     with open(script, 'r', encoding='utf8') as f:
         txt = f.read()
-        if not re.search( r'main\(\s*\)', txt ):
-            _logger.debug( 'Script %s does not contain main( )' % script )
+        if not re.search(r'main\(\s*\)', txt):
+            logging.debug('Script %s does not contain main( )' % script)
             return False, 'main( ) not found'
-        if re.search( r'raw_input\(\s*\)', txt ):
-            _logger.debug( 'Script %s requires user input' % script )
+        if re.search(r'raw_input\(\s*\)', txt):
+            logging.debug('Script %s requires user input' % script)
             return False, 'waits for user input'
     return True, 'OK'
 
-def run_test( index, testfile, timeout,  **kwargs):
+
+def run_test(index, testfile, timeout, **kwargs):
     """Run a given test
     """
     global test_status_
     global total_
-    pyExec = os.environ.get( 'PYTHON_EXECUTABLE', sys.executable )
-    cmd = Command( [ pyExec, testfile ] )
+    pyExec = os.environ.get('PYTHON_EXECUTABLE', sys.executable)
+    cmd = Command([pyExec, testfile])
 
-    ti = time.time( )
-    name = os.path.basename( testfile )
+    ti = time.time()
+    name = os.path.basename(testfile)
     out = (name + '.' * 50)[:40]
-    print( '[TEST %3d/%d] %41s ' % (index, total_, out), end='' )
-    sys.stdout.flush( )
+    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( )
+    status = cmd.run(timeout=timeout, **kwargs)
+    t = time.time() - ti
+    print('% 7.2f s' % 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_ )
+    cwd = os.path.dirname(testfile)
+    os.chdir(cwd)
+    with open(os.path.join(cwd, 'matplotlibrc'), 'w') as f:
+        logging.debug('Writing matplotlibrc to %s' % cwd)
+        f.write(matplotlibrc_)
 
     if status != 0:
         if status == -15:
             msg = '% 4d TIMEOUT' % status
-            test_status_[ 'TIMED-OUT' ].append( testfile )
+            test_status_['TIMED-OUT'].append(testfile)
         else:
             msg = '% 4d FAILED' % status
-            test_status_[ 'FAILED' ].append( testfile )
-        print( msg )
+            test_status_['FAILED'].append(testfile)
+        print(msg)
     else:
-        print( '% 4d PASSED' % status )
-        test_status_[ 'PASSED' ].append( testfile )
+        print('% 4d PASSED' % status)
+        test_status_['PASSED'].append(testfile)
+
+    sys.stdout.flush()
 
-    sys.stdout.flush( )
 
-def print_test_stat( ):
+def print_test_stat():
     global test_status_
     for status in test_status_:
-        print( 'Total %d tests %s' % (len( test_status_[status] ), status ) )
+        print('Total %d tests %s' % (len(test_status_[status]), status))
 
-def test_all( timeout, **kwargs ):
+
+def test_all(timeout, **kwargs):
     global test_dir_
     global total_
-    scripts = [ ]
-    for d, ds, fs in os.walk( test_dir_ ):
+    scripts = []
+    for d, ds, fs in os.walk(test_dir_):
         for f in fs:
-            if not re.match( r'.+\.py$', f):
+            if not re.match(r'.+\.py$', f):
                 continue
-            filepath = os.path.join( d, f  )
-            isOK, msg = suitable_for_testing( filepath )
+            filepath = os.path.join(d, f)
+            isOK, msg = suitable_for_testing(filepath)
             if isOK:
-                scripts.append( filepath )
+                scripts.append(filepath)
             else:
-                ignored_dict_[ msg ].append( filepath )
+                ignored_dict_[msg].append(filepath)
 
     for k in ignored_dict_:
-        _logger.debug( '[INFO] Ignored due to %s' % k )
-        _logger.debug( '\n\t'.join( ignored_dict_[ k ] ) )
+        logging.debug('[INFO] Ignored due to %s' % k)
+        logging.debug('\n\t'.join(ignored_dict_[k]))
 
-    _logger.info( 'Total %d valid tests found' % len( scripts ) )
-    total_ = len( scripts )
-    for i, s in enumerate( scripts ):
-        _logger.info( 'Running test (timeout=%s) : %s' % (timeout,s))
-        run_test(i, s, timeout, **kwargs )
+    logging.info('Total %d valid tests found' % len(scripts))
+    total_ = len(scripts)
+    for i, s in enumerate(scripts):
+        logging.info('Running test (timeout=%s) : %s' % (timeout, s))
+        run_test(i, s, timeout, **kwargs)
 
 
-def test( timeout = 60, **kwargs ):
+def test(timeout=60, **kwargs):
     """Download and run tests.
 
     """
-    print( '[INFO] Running test with timeout %d sec' % timeout )
+    print('[INFO] Running test with timeout %d sec' % timeout)
     try:
-        init_test_dir( )
+        init_test_dir()
     except Exception as e:
-        print( '[INFO] Failed to clone moose-examples. Error was %s' % e )
-        quit( )
+        print('[INFO] Failed to clone moose-examples. Error was %s' % e)
+        quit()
+
+    test_all(timeout=timeout, **kwargs)
+    print_test_stat()
 
-    test_all( timeout = timeout, **kwargs  )
-    print_test_stat( )
 
 if __name__ == '__main__':
-    test( )
+    test()