def test_substitute_wo_including(self):
""" Test a simple substitution without include
"""
fname = os.path.join(self.dir_testdata, 'substitute_wo_including.yaml')
with open(fname, 'r') as f:
data = load(f)
self.assertEqual(data['mesh']['work_dir'], 'dir1')
def test_multiple_substitution_in_one_item(self):
""" Test multiple substitution in one item
"""
fname = os.path.join(self.dir_testdata,
'substitute_multiple_times_in_one_item.yaml')
with open(fname, 'r') as f:
data = load(f)
self.assertEqual(data['mesh']['work_dir'], 'dir1/file1')
def read(self, fpath, **kwargs):
with open(fpath, 'r') as f:
data = schism_yaml.load(f)['linestrings']
linestrings = []
for row in data:
linestrings.append(LineString(coordinates=row['coordinates'],
prop=dict([(k, row[k]) for k in row if k != 'coordinates'])))
return linestrings
def test_substitute_multiple_including(self):
""" Test substitution in multiple including
"""
fname = os.path.join(self.dir_testdata, 'substitute_w_including.yaml')
with open(fname, 'r') as f:
data = load(f)
self.assertEqual(data['mesh']['work_dir'], 'dir1')
fname = os.path.join(self.dir_testdata,
'substitute_w_including_typo.yaml')
with open(fname, 'r') as f:
self.assertRaises(ValueError, load, f)
def grid_opt_with_args(args):
""" Optimize grid with arguments parsed by argparse
"""
with open(args.optparam) as f:
opt_param = schism_yaml.load(f)
mesh = read_mesh(args.filename, nodestring_option='land')
with open(args.demfile, 'r') as f:
demfiles = schism_yaml.load(f)
# dir = os.path.dirname(args.demfile)
# demfiles_full = [os.path.join(dir, fname) for fname in demfiles]
logger = init_logger()
kwargs = {
'mesh': mesh,
'demfiles': demfiles, # demfiles_full,
'na_fill': args.na_fill,
'logger': logger
}
optimizer = GridOptimizer(**kwargs)
optimized = optimizer.optimize(opt_param)
fpath_output = args.optfile
write_mesh(mesh, fpath_output, node_attr=-optimized)
def prepare_schism(args, use_logging=True):
if use_logging is True:
setup_logger()
logger = logging.getLogger('SCHISM')
else:
logger = logging.getLogger('')
logger.info("Start pre-processing SCHISM inputs...")
in_fname = args.main_inputfile
if not os.path.exists(in_fname):
logger.error("The main input file, %s, is not found", in_fname)
raise ValueError("Main input file not found")
with open(in_fname, 'r') as f:
inputs = schism_yaml.load(f)
keys_top_level = ["mesh", "gr3",
"prop", "hydraulics",
"sources_sinks", "flow_outputs"] \
+ schism_yaml.include_keywords
logger.info("Processing the top level...")
check_and_suggest(list(inputs.keys()), keys_top_level, logger)
out_fname = os.path.splitext(in_fname)[0] \
+ '_echo' + os.path.splitext(in_fname)[1]
with open(out_fname, 'w') as f:
f.write(schism_yaml.safe_dump(inputs))
# Mesh section
if item_exist(inputs, 'mesh'):
logger.info("Processing mesh section...")
mesh_items = inputs['mesh']
keys_mesh_section = ["mesh_inputfile", "dem_list",
"open_boundaries",
"depth_optimization",
"gr3_outputfile", "ll_outputfile"] \
+ schism_yaml.include_keywords
check_and_suggest(list(mesh_items.keys()), keys_mesh_section)
if item_exist(inputs['mesh'], 'mesh_inputfile'):
# Read the grid file to be processed
mesh_input_fpath = \
os.path.expanduser(mesh_items['mesh_inputfile'])
s = create_schism_setup(mesh_input_fpath, logger)
update_spatial_inputs(s, inputs, logger)
else:
raise ValueError("No mesh input file in the mesh section.")
else:
raise ValueError("No mesh section in the main input.")
logger.info("Done.")