def main():
"""
Entry point for the main script ``mpas_analysis``
"""
parser = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('-v',
'--version',
action='version',
version='mpas_analysis {}'.format(
mpas_analysis.__version__),
help="Show version number and exit")
parser.add_argument("--setup_only",
dest="setup_only",
action='store_true',
help="If only the setup phase, not the run or HTML "
"generation phases, should be executed.")
parser.add_argument("--html_only",
dest="html_only",
action='store_true',
help="If only the setup and HTML generation phases, "
"not the run phase, should be executed.")
parser.add_argument("-g",
"--generate",
dest="generate",
help="A list of analysis modules to generate "
"(nearly identical generate option in config file).",
metavar="ANALYSIS1[,ANALYSIS2,ANALYSIS3,...]")
parser.add_argument("-l",
"--list",
dest="list",
action='store_true',
help="List the available analysis tasks")
parser.add_argument("-p",
"--purge",
dest="purge",
action='store_true',
help="Purge the analysis by deleting the output"
"directory before running")
parser.add_argument('configFiles',
metavar='CONFIG',
type=str,
nargs='*',
help='config file')
parser.add_argument("--plot_colormaps",
dest="plot_colormaps",
action='store_true',
help="Make a plot displaying all available colormaps")
parser.add_argument("--verbose",
dest="verbose",
action='store_true',
help="Verbose error reporting during setup-and-check "
"phase")
args = parser.parse_args()
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
for configFile in args.configFiles:
if not os.path.exists(configFile):
raise OSError('Config file {} not found.'.format(configFile))
# add config.default to cover default not included in the config files
# provided on the command line
if pkg_resources.resource_exists('mpas_analysis', 'config.default'):
defaultConfig = pkg_resources.resource_filename(
'mpas_analysis', 'config.default')
configFiles = [defaultConfig] + args.configFiles
else:
print('WARNING: Did not find config.default. Assuming other config '
'file(s) contain a\n'
'full set of configuration options.')
defaultConfig = None
configFiles = args.configFiles
config = MpasAnalysisConfigParser()
config.read(configFiles)
if args.list:
analyses = build_analysis_list(config, controlConfig=None)
for analysisTask in analyses:
print('task: {}'.format(analysisTask.taskName))
print(' component: {}'.format(analysisTask.componentName)),
print(' tags: {}'.format(', '.join(analysisTask.tags)))
sys.exit(0)
if args.plot_colormaps:
_register_custom_colormaps()
_plot_color_gradients()
sys.exit(0)
if config.has_option('runs', 'controlRunConfigFile'):
controlConfigFile = config.get('runs', 'controlRunConfigFile')
if not os.path.exists(controlConfigFile):
raise OSError('A control config file {} was specified but the '
'file does not exist'.format(controlConfigFile))
controlConfigFiles = [controlConfigFile]
if defaultConfig is not None:
controlConfigFiles = [defaultConfig] + controlConfigFiles
controlConfig = MpasAnalysisConfigParser()
controlConfig.read(controlConfigFiles)
# replace the log directory so log files get written to this run's
# log directory, not the control run's
logsDirectory = build_config_full_path(config, 'output',
'logsSubdirectory')
controlConfig.set('output', 'logsSubdirectory', logsDirectory)
print('Comparing to control run {} rather than observations. \n'
'Make sure that MPAS-Analysis has been run previously with the '
'control config file.'.format(
controlConfig.get('runs', 'mainRunName')))
else:
controlConfig = None
if args.purge:
purge_output(config)
if config.has_option('runs', 'mainRunConfigFile'):
symlink_main_run(config, defaultConfig)
if args.generate:
update_generate(config, args.generate)
if controlConfig is not None:
# we want to use the "generate" option from the current run, not
# the control config file
controlConfig.set('output', 'generate',
config.get('output', 'generate'))
logsDirectory = build_config_full_path(config, 'output',
'logsSubdirectory')
make_directories(logsDirectory)
update_time_bounds_in_config(config)
file_cache_maxsize = config.getint('input', 'file_cache_maxsize')
try:
xarray.set_options(file_cache_maxsize=file_cache_maxsize)
except ValueError:
# xarray version doesn't support file_cache_maxsize yet...
pass
startTime = time.time()
analyses = build_analysis_list(config, controlConfig)
analyses = determine_analyses_to_generate(analyses, args.verbose)
setupDuration = time.time() - startTime
if not args.setup_only and not args.html_only:
run_analysis(config, analyses)
runDuration = time.time() - startTime
m, s = divmod(setupDuration, 60)
h, m = divmod(int(m), 60)
print('Total setup time: {}:{:02d}:{:05.2f}'.format(h, m, s))
m, s = divmod(runDuration, 60)
h, m = divmod(int(m), 60)
print('Total run time: {}:{:02d}:{:05.2f}'.format(h, m, s))
if not args.setup_only:
generate_html(config, analyses, controlConfig)
class TestMPASAnalysisConfigParser(TestCase):
def setup_config(self):
configPath = self.datadir.join('config.analysis')
self.config = MpasAnalysisConfigParser()
self.config.read(str(configPath))
def check_container(self, container, container_type, item_type):
assert isinstance(container, container_type)
for item in container:
assert isinstance(item, item_type)
def test_read_config(self):
self.setup_config()
colorMapName = self.config.get('sst_modelvsobs', 'cmapDiff')
self.assertEqual(colorMapName, 'coolwarm')
self.assertEqual(self.config.getint('Test', 'testInt'), 15)
self.assertEqual(self.config.getExpression('Test', 'testInt'), 15)
self.assertEqual(self.config.getfloat('Test', 'testFloat'), 18.0)
self.assertEqual(self.config.getExpression('Test', 'testFloat'), 18.0)
self.assertEqual(self.config.getfloat('Test', 'testFloat2'), 3.)
self.assertEqual(self.config.getExpression('Test', 'testFloat2'), 3.)
self.assertEqual(self.config.getboolean('Test', 'testBool'), True)
self.assertEqual(self.config.getExpression('Test', 'testBool'), True)
testList = self.config.getExpression('sst_modelvsobs',
'cmapIndicesModelObs')
self.check_container(testList, list, int)
self.assertEqual(testList, [0, 40, 80, 110, 140, 170, 200, 230, 255])
testList = self.config.getExpression('sst_modelvsobs',
'cmapIndicesModelObs',
elementType=float)
self.check_container(testList, list, float)
self.assertEqual(testList,
[0., 40., 80., 110., 140., 170., 200., 230., 255.])
testList = self.config.getExpression('sst_modelvsobs',
'comparisonTimes')
self.check_container(testList, list, str)
self.assertEqual(testList, ['JFM', 'JAS', 'ANN'])
testList = self.config.getExpression('Test', 'testList')
self.check_container(testList, list, float)
self.assertEqual(testList, [0.5, 0.1, 0.5])
testTuple = self.config.getExpression('Test', 'testTuple')
assert isinstance(testTuple, tuple)
self.assertEqual(testTuple, (5, 0.1, 'string'))
testDict = self.config.getExpression('Test', 'testDict')
assert isinstance(testDict, dict)
self.assertEqual(testDict, {
'key1': 'string',
'key2': -12,
'key3': False
})
with six.assertRaisesRegex(
self, configparser.NoOptionError,
"No option 'doesntexist' in section: 'Test'"):
self.config.getExpression(str('Test'), str('doesntexist'))
@requires_numpy
def test_read_config_numpy(self):
self.setup_config()
# tests numpy evaluation capability
import numpy as np
for testname in ['testNumpyarange' + str(ii) for ii in np.arange(3)]:
self.assertArrayEqual(
self.config.getExpression('TestNumpy',
testname,
usenumpyfunc=True),
np.arange(0, 1, 10))
for testname in ['testNumpylinspace' + str(ii) for ii in np.arange(3)]:
self.assertArrayEqual(
self.config.getExpression('TestNumpy',
testname,
usenumpyfunc=True),
np.linspace(0, 1, 10))
for testNumpy in ['testNumpypi' + str(ii) for ii in np.arange(3)] + \
['testNumpyPi']:
self.assertEqual(
self.config.getExpression('TestNumpy',
testNumpy,
usenumpyfunc=True), np.pi)
with six.assertRaisesRegex(
self, AssertionError,
"'__' is not allowed in .* for `usenumpyfunc=True`"):
self.config.getExpression('TestNumpy',
'testBadStr',
usenumpyfunc=True),
def test_get_with_default(self):
self.setup_config()
def check_get_with_default(name, value, dtype):
# test an options that doesn't exist using getWithDefault
var = self.config.getWithDefault('sst_modelvsobs', name, value)
assert isinstance(var, dtype)
self.assertEqual(var, value)
# test several types with getWithDefault
check_get_with_default(name='aBool', value=True, dtype=bool)
check_get_with_default(name='anInt', value=1, dtype=six.integer_types)
check_get_with_default(name='aFloat', value=1.0, dtype=float)
check_get_with_default(name='aList', value=[1, 2, 3], dtype=list)
check_get_with_default(name='aTuple', value=(1, 2, 3), dtype=tuple)
check_get_with_default(name='aDict', value={'blah': 1}, dtype=dict)
check_get_with_default(name='aStr',
value='blah',
dtype=six.string_types)
