updated all cosymlib scripts.

Now they have common header and footer
All have a new argparse argument (-v or --version) which returns the actual cosymlib version
Fixed the yaml command input reading to return an error message when a key from the input is not an argument of the script

scripts/cosym

@@ -1,21 +1,24 @@
 #!/usr/bin/env python
-import argparse
-import numpy as np
-import yaml
-import sys
+from cosymlib import Cosymlib, __version__
 from cosymlib import file_io
-from cosymlib.molecule.geometry import Geometry
-from cosymlib import Cosymlib
+from cosymlib.file_io.tools import add_extra_keywords, print_header, print_footer, print_input_info
 from cosymlib.shape import tools
+from cosymlib.molecule.geometry import Geometry
+import argparse
+import sys
+import yaml
 import os
+import numpy as np
 
 
 parser = argparse.ArgumentParser(description='Cosym')
-parser.add_argument(type=str, dest='input_file', help='input file name(+extension)')
+parser.add_argument(type=str, dest='input_file', nargs='?', default=None, help='input file name(+extension)')
 parser.add_argument(type=str, dest="yaml_input", nargs='?', default=None,
                     help='Perform the calculations with the command file')
 parser.add_argument('-o', '--output_name', dest='output_name', default=None, help='save in file name')
-parser.add_argument('-info', action='store_true', default=False, help='return information about the input geometries')
+parser.add_argument('--info', action='store_true', default=False, help='return information about the input geometries')
+parser.add_argument('-v', '--version', dest='version', action='store_true', default=False,
+                    help='print information about the input structures')
 
 parser.add_argument('-c', '--central_atom', action='store', dest='central_atom',
                     type=int, default=0, help='position of the central atom if exist')
@@ -112,7 +115,7 @@ parser.add_argument('-mo_diagram', dest="mo_diagram", action='store_true', defau
 
 
 args = parser.parse_args(sys.argv[1:])
-print('Starting...')
+# print('Starting...')
 
 if args.yaml_input:
     with open(args.yaml_input, 'r') as stream:
@@ -124,7 +127,17 @@ if args.yaml_input:
         else:
             raise KeyError("Key %s is not valid" % key)
 
-if args.input_file is not None:
+if args.version:
+    print('Cosymlib version = {}'.format(__version__))
+    exit()
+
+common_output = open(args.output_name, 'w') if args.output_name is not None else sys.stdout
+print_header(common_output)
+
+if args.input_file is None:
+    print('No input file selected!'.format(args.input_file))
+    exit()
+else:
     structures = file_io.read_generic_structure_file(args.input_file, read_multiple=True)
     symobj = Cosymlib(structures)
 
@@ -155,7 +168,8 @@ if args.shp_references:
     # file_io.write_file_xyz(test_structure, output_name='ML{}_ref'.format(n_atoms))
 
 if args.info:
-    file_io.write_input_info(structures, output_name=args.output_name)
+    print_input_info(structures, output=common_output)
+    exit()
 
 # Shape's commands
 if args.shp_labels:
@@ -230,4 +244,5 @@ if args.pointgroup:
     for idm, pg in enumerate(symobj.get_point_group()):
         print('The point group of molecule{} is: {}'.format(idm, pg))
 
-print('\nEnd of cosym calculation')
+# print('\nEnd of cosym calculation')
+print_footer(common_output)

scripts/esym

@@ -1,17 +1,19 @@
 #!/usr/bin/env python
-from cosymlib.file_io.tools import add_extra_keywords, extract_geometries, print_header, print_footer, print_input_info
+from cosymlib import Cosymlib, __version__
+from cosymlib.file_io.tools import add_extra_keywords, print_header, print_footer, print_input_info
 from cosymlib.file_io import read_generic_structure_file
 from cosymlib.symmetry.tools import print_symmetry_labels
-from cosymlib import Cosymlib
 import argparse
 import sys
+import yaml
 
 
 parser = argparse.ArgumentParser(description='esym')
 
 # positional arguments
 parser.add_argument(type=str,
                     dest='input_file',
+                    nargs='?', default=None,
                     help='input file with structures')
 parser.add_argument(type=str,
                     dest="yaml_input",
@@ -23,17 +25,28 @@ parser.add_argument('-m', '--measure',
                     metavar='SG',
                     default=False,
                     help='compute the SG symmetry measure of the input structures')
-parser.add_argument('-l', '--labels',
-                    dest='labels',
-                    action='store_true',
-                    default=False,
-                    help='print the symmetry labels (SG) for the groups that can be used')
 parser.add_argument('-o', '--output',
                     dest='output_name',
                     metavar='filename',
                     default=None,
                     help='store output into a file')
 
+# Extra options
+parser.add_argument('-l', '--labels',
+                    dest='labels',
+                    action='store_true',
+                    default=False,
+                    help='print the symmetry labels (SG) for the groups that can be used')
+parser.add_argument('--info',
+                    action='store_true',
+                    default=False,
+                    help='print information about the input structures')
+parser.add_argument('-v', '--version',
+                    dest='version',
+                    action='store_true',
+                    default=False,
+                    help='print information about the input structures')
+
 # addtional print
 parser.add_argument('--trans_matrices',
                     dest='trans_matrices',
@@ -53,11 +66,6 @@ parser.add_argument('--irrep',
                     action='store_true',
                     help='print the irreducible representations')
 
-parser.add_argument('--info',
-                    action='store_true',
-                    default=False,
-                    help='print information about the input structures')
-
 # Modifiers
 parser.add_argument('--center',
                     dest='center',
@@ -84,11 +92,26 @@ parser.add_argument('--axis2',
 args = parser.parse_args()
 
 if args.yaml_input:
-    add_extra_keywords(args, args.yaml_input)
+    with open(args.yaml_input, 'r') as stream:
+        input_parameters = yaml.load(stream, Loader=yaml.FullLoader)
+
+    for key, value in input_parameters.items():
+        if key.lower() in args:
+            setattr(args, key.lower(), value)
+        else:
+            raise KeyError("Key %s is not valid" % key)
+
+if args.version:
+    print('Cosymlib version = {}'.format(__version__))
+    exit()
 
 common_output = open(args.output_name, 'w') if args.output_name is not None else sys.stdout
 print_header(common_output)
 
+if args.input_file is None:
+    print('No input file selected!'.format(args.input_file))
+    exit()
+
 structures = read_generic_structure_file(args.input_file, read_multiple=True)
 structure_set = Cosymlib(structures)
 

scripts/gsym

@@ -1,17 +1,19 @@
 #!/usr/bin/env python
-from cosymlib.file_io.tools import add_extra_keywords, extract_geometries, print_header, print_footer, print_input_info
+from cosymlib import Cosymlib, __version__
+from cosymlib.file_io.tools import add_extra_keywords, print_header, print_footer, print_input_info
 from cosymlib.file_io import read_generic_structure_file, get_connectivity_from_file
 from cosymlib.symmetry.tools import print_symmetry_labels
-from cosymlib import Cosymlib
 import argparse
 import sys
+import yaml
 
 
 parser = argparse.ArgumentParser(description='tsym')
 
 # positional arguments
 parser.add_argument(type=str,
                     dest='input_file',
+                    nargs='?', default=None,
                     help='input file with structures')
 parser.add_argument(type=str,
                     dest="yaml_input",
@@ -28,11 +30,6 @@ parser.add_argument('-s', '--structure',
                     action='store_true',
                     default=False,
                     help='returns the nearest SG-symmetric structure to the reference one')
-parser.add_argument('-l', '--labels',
-                    dest='labels',
-                    action='store_true',
-                    default=False,
-                    help='prints the symmetry labels (SG) for the groups that can be used')
 parser.add_argument('-o', '--output',
                     dest='output_name',
                     metavar='filename',
@@ -45,10 +42,22 @@ parser.add_argument('-c', '--central_atom',
                     type=int,
                     default=0,
                     help='central atom is in position N in the input structure')
+
+# Extra options
+parser.add_argument('-l', '--labels',
+                    dest='labels',
+                    action='store_true',
+                    default=False,
+                    help='prints the symmetry labels (SG) for the groups that can be used')
 parser.add_argument('--info',
                     action='store_true',
                     default=False,
                     help='print information about the input structures')
+parser.add_argument('-v', '--version',
+                    dest='version',
+                    action='store_true',
+                    default=False,
+                    help='print information about the input structures')
 
 # Modifiers
 parser.add_argument('--ignore_connectivity',
@@ -84,11 +93,26 @@ parser.add_argument('--center',
 args = parser.parse_args()
 
 if args.yaml_input:
-    add_extra_keywords(args, args.yaml_input)
+    with open(args.yaml_input, 'r') as stream:
+        input_parameters = yaml.load(stream, Loader=yaml.FullLoader)
+
+    for key, value in input_parameters.items():
+        if key.lower() in args:
+            setattr(args, key.lower(), value)
+        else:
+            raise KeyError("Key %s is not valid" % key)
+
+if args.version:
+    print('Cosymlib version = {}'.format(__version__))
+    exit()
 
 common_output = open(args.output_name, 'w') if args.output_name is not None else sys.stdout
 print_header(common_output)
 
+if args.input_file is None:
+    print('No input file selected!'.format(args.input_file))
+    exit()
+
 if args.connectivity_file:
     connectivity = get_connectivity_from_file(args.connectivity_file)
 else:

scripts/shape

@@ -1,17 +1,19 @@
 #!/usr/bin/env python
+from cosymlib import Cosymlib, __version__
 from cosymlib import file_io
-from cosymlib.shape import tools
 from cosymlib.file_io.tools import add_extra_keywords, print_header, print_footer, print_input_info
-from cosymlib.file_io import read_generic_structure_file
-from cosymlib import Cosymlib
+from cosymlib.shape import tools
 import argparse
 import sys
+import yaml
 
 
 # positional arguments
-parser = argparse.ArgumentParser(description='Shape')
+parser = argparse.ArgumentParser(description='Shape', allow_abbrev=False)
 parser.add_argument(type=str,
                     dest='input_file',
+                    nargs='?',
+                    default=None,
                     help='input file with structures')
 parser.add_argument(type=str,
                     dest="yaml_input",
@@ -61,6 +63,11 @@ parser.add_argument('--info',
                     action='store_true',
                     default=False,
                     help='print information about the input structures')
+parser.add_argument('-v', '--version',
+                    dest='version',
+                    action='store_true',
+                    default=False,
+                    help='print information about the input structures')
 
 # Modifiers
 parser.add_argument('--fix_permutation',
@@ -72,12 +79,27 @@ parser.add_argument('--fix_permutation',
 args = parser.parse_args()
 
 if args.yaml_input:
-    add_extra_keywords(args, args.yaml_input)
+    with open(args.yaml_input, 'r') as stream:
+        input_parameters = yaml.load(stream, Loader=yaml.FullLoader)
+
+    for key, value in input_parameters.items():
+        if key.lower() in args:
+            setattr(args, key.lower(), value)
+        else:
+            raise KeyError("Key %s is not valid" % key)
+
+if args.version:
+    print('Cosymlib version = {}'.format(__version__))
+    exit()
 
 common_output = open(args.output_name, 'w') if args.output_name is not None else sys.stdout
 print_header(common_output)
 
-structures = read_generic_structure_file(args.input_file, read_multiple=True)
+if args.input_file is None:
+    print('No input file selected!'.format(args.input_file))
+    exit()
+
+structures = file_io.read_generic_structure_file(args.input_file, read_multiple=True)
 structure_set = Cosymlib(structures)
 
 n_atoms = structure_set.get_n_atoms()