Merge pull request #33 from pyscal/fix_delete

Fix delete

Author: srmnitc

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.1.8
+current_version = 3.1.9
 commit = True
 tag = True
 

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name='pyscal3',
-    version='3.1.8',
+    version='3.1.9',
     author='Sarath Menon',
     author_email='[email protected]',
     description='Python library written in C++ for calculation of local atomic structural environment',

src/pyscal3/atoms.py

@@ -302,13 +302,9 @@ def remove_selection(self, ids=None, indices=None, condition=None):
         self._apply_selection(masks)
 
     def delete(self, ids=None, indices=None, condition=None, selection=False):
-        #delete atoms
-        #reassign ids
-        #reassign indices
-        #reassign heads
         masks = self._generate_bool_list(ids=ids, indices=indices, condition=condition, selection=selection)
         delete_list = [masks[self["head"][x]] for x in range(self.ntotal)]
-        delete_ids = [x for x in range(self.ntotal) if masks[x]]
+        delete_ids = [x for x in range(self.ntotal) if delete_list[x]]
         self._delete_atoms(delete_ids)
 
     @property

tests/test_delete.py

@@ -0,0 +1,29 @@
+import pytest
+import os,sys,inspect
+import numpy as np
+import pyscal3.core as pc
+
+def test_delete():
+    sys = pc.System.create.element.Fe()
+    assert sys.natoms == 2
+
+    sys.delete(ids=[1])
+    assert sys.natoms == 1
+
+    sys = pc.System.create.element.Fe()
+    sys.delete(indices=[0])
+    assert sys.natoms == 1
+
+    def condition(atom):
+    	if atom.ids[0] == 1:
+    		return True
+
+    sys = pc.System.create.element.Fe()
+    sys.delete(condition=condition)
+    assert sys.natoms == 1
+
+    sys = pc.System.create.element.Fe()
+    sys.apply_selection(indices=[0])
+    sys.delete(selection=True)
+    assert sys.natoms == 1
+