Merge branch 'master' of github.com:bjmorgan/vasppy

requirements.txt

@@ -1,4 +1,4 @@
-numpy
+numpy>=1.16.2
 monty
 pandas
 pymatgen

tests/test_summary.py

@@ -68,6 +68,7 @@ def setUp( self, mock_parse_vaspun, MockVASPMeta ):
         self.summary = Summary()
         self.summary.vasprun = Mock( spec=Vasprun )
         self.summary.meta = Mock( spec=VASPMeta )
+        self.summary.meta.notes = None
 
     def test_functional_not_PBE( self ):
         self.summary.potcars_are_pbe = Mock( return_value=False )
@@ -169,6 +170,17 @@ def test_print_title( self, mock_stdout ):
         self.summary.print_title()
         self.assertEqual( mock_stdout.getvalue(), 'title: TITLE\n' )
 
+    @patch('sys.stdout', new_callable=StringIO)
+    def test_print_notes( self, mock_stdout ):
+        self.summary.meta.notes = 'NOTES'
+        self.summary.print_notes()
+        self.assertEqual( mock_stdout.getvalue(), 'notes: NOTES\n' )
+
+    @patch('sys.stdout', new_callable=StringIO)
+    def test_print_notes_handles_empty_notes_attribute( self, mock_stdout ):
+        self.summary.print_notes()
+        self.assertEqual( mock_stdout.getvalue(), 'notes: ~\n' )
+
 class SummaryHelperFunctionsTestCase( unittest.TestCase ):
 
     def test_md5sum( self ):
@@ -209,5 +221,6 @@ def test_load_vasp_summary( self ):
         vasp_summary = load_vasp_summary( vasp_summary_test_filename )
         self.assertEqual( vasp_summary, expected_dict )     
 
+
 if __name__ == '__main__':
     unittest.main()

vasppy/__init__.py

@@ -1 +1 @@
-__version__ = '0.4.0.9'
+__version__ = '0.4.0.11'

vasppy/calculation.py

@@ -137,7 +137,7 @@ def import_calculations_from_file( filename ):
     """
     calcs = {}
     with open( filename, 'r' ) as stream:
-        docs = yaml.load_all( stream )
+        docs = yaml.load_all( stream, Loader=yaml.SafeLoader )
         for d in docs:
             stoichiometry = Counter()
             for s in d['stoichiometry']:

vasppy/data/potcar_data.py

@@ -10,8 +10,8 @@
 
 for potcar_set in potcar_sets:
     with open( '{}_md5.yaml'.format( os.path.join( my_path, potcar_set ) ), 'r' ) as stream:
-        potcar_md5sum_data[ potcar_set ] = yaml.load( stream )
+        potcar_md5sum_data[ potcar_set ] = yaml.load( stream, Loader=yaml.SafeLoader  )
 
 for potcar_set in potcar_sets:
     with open( '{}_nelect.yaml'.format( os.path.join( my_path, potcar_set ) ), 'r' ) as stream:
-        potcar_nelect[ potcar_set ] = yaml.load( stream )
+        potcar_nelect[ potcar_set ] = yaml.load( stream, Loader=yaml.SafeLoader  )

vasppy/scripts/vasp_summary.py

@@ -39,7 +39,7 @@ def main():
         sys.exit()
     if args.file:
         with open( args.file, 'r' ) as stream:
-            settings = yaml.load( stream ) 
+            settings = yaml.load( stream, Loader=yaml.SafeLoader ) 
         if 'to_print' in settings:
             to_print = settings['to_print']
         if 'titles' in settings:

vasppy/summary.py

@@ -46,7 +46,7 @@ def load_vasp_summary( filename ):
 
     """
     with open( filename, 'r' ) as stream:
-        docs = yaml.load_all( stream )
+        docs = yaml.load_all( stream, Loader=yaml.SafeLoader )
         data = { d['title']: d for d in docs }
     return data
 
@@ -256,7 +256,10 @@ def print_description( self ):
         print( "description: {}".format( self.meta.description.strip() ) )
 
     def print_notes( self ):
-        print( "notes: {}".format( self.meta.notes.strip() ) )
+        if self.meta.notes:
+            print( "notes: {}".format( self.meta.notes.strip() ) )
+        else:
+            print( "notes: ~" )
 
     def print_status( self ):
         print( "status: {}".format( self.meta.status ) )

vasppy/vaspmeta.py

@@ -55,7 +55,7 @@ def from_file( cls, filename ):
             (vasppy.VASPMeta): the VASPMeta object
         """
         with open( filename, 'r' ) as stream:
-            data = yaml.load( stream )
+            data = yaml.load( stream, Loader=yaml.SafeLoader )
             notes = data.get( 'notes' )
             v_type = data.get( 'type' )
             track = data.get( 'track' )