bug fix

examples/__main__.py

@@ -19,6 +19,28 @@
 #from pathlib import Path
 
 
+def run(module):
+	def __main__(args):
+		if hasattr(module, 'data_file'):
+			if hasattr(module, 'data_dir'):
+				data_dir = module.data_dir
+			else:
+				data_dir = ''
+			local = os.path.join(module.data_dir, module.data_file)
+			if not os.path.exists(local) and hasattr(module, 'data_server'):
+				print('downloading {}... '.format(module.data_file), end='')
+				try:
+					request.urlretrieve(os.path.join(module.data_server, \
+							module.data_file), local)
+					print('[done]')
+				except:
+					print('[failed]')
+		args = args.__dict__
+		del args['func']
+		module.main(**args)
+	return __main__
+
+
 def main():
 	demo_dir = os.path.dirname(__file__)
 	demo_path = __package__
@@ -65,37 +87,22 @@ def main():
 			short_help = None
 		demo_parser = hub.add_parser(demo, help=short_help)
 		if hasattr(module, 'arguments'):
-			for arg, opt in module.arguments:
+			for args, kwargs in module.arguments:
+				if not isinstance(args, (tuple, list)):
+					args = (args,)
 				try:
-					demo_parser.add_argument(arg, **opt)
+					demo_parser.add_argument(*args, **kwargs)
 				except:
-					print('failed to add argument: {}'.format(arg))
-		demo_parser.set_defaults(func=demo)
+					print('failed to add argument: {}'.format(args))
+		demo_parser.set_defaults(func=run(module))
 
 	# parse
 	args = parser.parse_args()
 	#module = demos[args.demo]
 	if not hasattr(args, 'func'):
 		parser.print_help()
 		parser.exit(0)
-	module = demos[args.func]
-	if hasattr(module, 'data_file'):
-		if hasattr(module, 'data_dir'):
-			data_dir = module.data_dir
-		else:
-			data_dir = ''
-		local = os.path.join(module.data_dir, module.data_file)
-		if not os.path.exists(local) and hasattr(module, 'data_server'):
-			print('downloading {}... '.format(module.data_file), end='')
-			try:
-				request.urlretrieve(os.path.join(module.data_server, \
-						module.data_file), local)
-				print('[done]')
-			except:
-				print('[failed]')
-	args = args.__dict__
-	del args['func']
-	module.main(**args)
+	args.func(args)
 
 
 if __name__ == '__main__':

examples/glycine_receptor.py

@@ -13,8 +13,8 @@
 
 methods = ['grid', 'kdtree', 'kmeans', 'gwr']
 default_localization_error = 0.001
-default_priorD = 0.01
-default_priorV = 0.1
+default_prior_diffusivity = 0.01
+default_prior_potential = 0.1
 
 
 arguments = [
@@ -37,7 +37,7 @@
 
 def main(**kwargs):
 
-	warnings.simplefilter('error')
+	#warnings.simplefilter('error')
 
 	local = os.path.join(data_dir, data_file)
 	if not os.path.isfile(local):

tramway/__main__.py

@@ -92,8 +92,8 @@ def main():
 	global_arguments = [
 		('-v', '--verbose', dict(action='store_true', help='increase verbosity')),
 		('-i', '--input', dict(action='append', default=[],
-			help='path to input file or directory')),
-		('-o', '--output', dict(help='path to output file'))]
+			metavar='FILE', help='path to input file or directory')),
+		('-o', '--output', dict(metavar='FILE', help='path to output file'))]
 	for arg1, arg2, kwargs in global_arguments:
 		parser.add_argument(arg1, arg2, dest=arg1[1]+'pre', **kwargs)
 	sub = parser.add_subparsers(title='commands', \

tramway/helper/inference.py

@@ -22,6 +22,7 @@
 import os
 from time import time
 import collections
+import traceback
 
 
 sub_extensions = dict([(ext.upper(), ext) for ext in ['d', 'df', 'dd', 'dv', 'dx']])
@@ -120,6 +121,7 @@ def infer(cells, mode='D', output_file=None, imt_selectors={}, verbose=False, \
 		if verbose:
 			print('writing file: {}'.format(output_file))
 		try:
+			# Python 3.6 raises tables.exceptions.PerformanceWarning
 			store = HDF5Store(output_file, 'w')
 			if callable(mode):
 				store.poke('mode', '(callable)')
@@ -131,9 +133,9 @@ def infer(cells, mode='D', output_file=None, imt_selectors={}, verbose=False, \
 			if localization_error is not None:
 				store.poke('localization_error', localization_error)
 			if priorD is not None:
-				store.poke('priorD', priorD)
+				store.poke('prior_diffusivity', priorD)
 			if priorV is not None:
-				store.poke('priorV', priorV)
+				store.poke('prior_potential', priorV)
 			if jeffreys_prior is not None:
 				store.poke('jeffreys_prior', jeffreys_prior)
 			if kwargs:
@@ -144,10 +146,11 @@ def infer(cells, mode='D', output_file=None, imt_selectors={}, verbose=False, \
 				store.poke('rwa_file', input_file)
 			else:
 				store.poke('tesselation_param', cells.param)
-			store.poke('version', 1.0)
+			store.poke('version', 1.1)
 			store.poke('runtime', runtime)
 			store.close()
 		except:
+			print(traceback.format_exc())
 			warn('HDF5 libraries may not be installed', ImportWarning)
 
 	if input_file: