Improve compatibility with yaml

cosymlib/file_io/tools.py

@@ -36,7 +36,7 @@ def print_input_info(initial_geometries, output=sys.stdout):
 
 def add_extra_keywords(args, filename):
     with open(filename, 'r') as stream:
-        input_parameters = yaml.load(stream, Loader=yaml.FullLoader)
+        input_parameters = yaml.safe_load(stream)
     try:
         for key, value in input_parameters.items():
             if key.lower() in args:

cosymlib/shape/tools.py

@@ -28,7 +28,7 @@ def get_reference_structure(label, central_atom=0):
     if ideal_structures is None:
         file_path = os.path.dirname(os.path.abspath(__file__)) + '/ideal_structures_center.yaml'
         with open(file_path, 'r') as stream:
-            ideal_structures = yaml.load(stream, Loader=yaml.FullLoader)
+            ideal_structures = yaml.safe_load(stream)
 
     try:
         if central_atom == 0:

scripts/cchir

@@ -66,7 +66,7 @@ args = parser.parse_args()
 
 if args.yaml_input:
     with open(args.yaml_input, 'r') as stream:
-        input_parameters = yaml.load(stream, Loader=yaml.FullLoader)
+        input_parameters = yaml.safe_load(stream)
 
     for key, value in input_parameters.items():
         if key.lower() in args:

scripts/cosym

@@ -159,7 +159,7 @@ args = parser.parse_args(sys.argv[1:])
 
 if args.yaml_input:
     with open(args.yaml_input, 'r') as stream:
-        input_parameters = yaml.load(stream, Loader=yaml.FullLoader)
+        input_parameters = yaml.safe_load(stream)
 
     for key, value in input_parameters.items():
         if key.lower() in args:

scripts/esym

@@ -104,7 +104,7 @@ args = parser.parse_args()
 
 if args.yaml_input:
     with open(args.yaml_input, 'r') as stream:
-        input_parameters = yaml.load(stream, Loader=yaml.FullLoader)
+        input_parameters = yaml.safe_load(stream)
 
     for key, value in input_parameters.items():
         if key.lower() in args:

scripts/gsym

@@ -94,7 +94,7 @@ args = parser.parse_args()
 
 if args.yaml_input:
     with open(args.yaml_input, 'r') as stream:
-        input_parameters = yaml.load(stream, Loader=yaml.FullLoader)
+        input_parameters = yaml.safe_load(stream)
 
     for key, value in input_parameters.items():
         if key.lower() in args:

scripts/shape

@@ -101,7 +101,7 @@ args = parser.parse_args()
 
 if args.yaml_input:
     with open(args.yaml_input, 'r') as stream:
-        input_parameters = yaml.load(stream, Loader=yaml.FullLoader)
+        input_parameters = yaml.safe_load(stream)
 
     for key, value in input_parameters.items():
         if key.lower() in args:

scripts/shape_map

@@ -104,7 +104,7 @@ args = parser.parse_args()
 
 if args.yaml_input:
     with open(args.yaml_input, 'r') as stream:
-        input_parameters = yaml.load(stream, Loader=yaml.FullLoader)
+        input_parameters = yaml.safe_load(stream)
 
     for key, value in input_parameters.items():
         if key.lower() in args: