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chore: deprecated addNewAtom by stevenhua0320 · Pull Request #157 · diffpy/diffpy.structure · GitHub

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23 changes: 23 additions & 0 deletions news/deprecate-addNewItem.rst
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@@ -0,0 +1,23 @@
**Added:**

* No News Added: deprecate CamelCase function for addNewItem

**Changed:**

* <news item>

**Deprecated:**

* <news item>

**Removed:**

* <news item>

**Fixed:**

* <news item>

**Security:**

* <news item>
1 change: 1 addition & 0 deletions requirements/conda.txt
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Original file line number Diff line number Diff line change
@@ -1,2 +1,3 @@
numpy
pycifrw
diffpy.utils
1 change: 1 addition & 0 deletions requirements/pip.txt
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@@ -1,2 +1,3 @@
numpy
pycifrw
diffpy.utils
2 changes: 1 addition & 1 deletion src/diffpy/structure/parsers/p_cif.py
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Original file line number Diff line number Diff line change
Expand Up @@ -497,7 +497,7 @@ def _parse_atom_site_label(self, block):
if curlabel == "?":
continue
self.labelindex[curlabel] = len(self.stru)
self.stru.addNewAtom()
self.stru.add_new_atom()
a = self.stru.getLastAtom()
for fset, val in zip(prop_setters, values):
fset(a, val)
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2 changes: 1 addition & 1 deletion src/diffpy/structure/parsers/p_discus.py
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Original file line number Diff line number Diff line change
Expand Up @@ -264,7 +264,7 @@ def _parse_atom(self, words):
element = words[0][0:1].upper() + words[0][1:].lower()
xyz = [float(w) for w in words[1:4]]
Biso = float(words[4])
self.stru.addNewAtom(element, xyz)
self.stru.add_new_atom(element, xyz)
a = self.stru.getLastAtom()
a.Bisoequiv = Biso
return
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2 changes: 1 addition & 1 deletion src/diffpy/structure/parsers/p_pdb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -197,7 +197,7 @@ def parseLines(self, lines):
# get element from the first 2 characters of name
element = line[12:14].strip()
element = element[0].upper() + element[1:].lower()
stru.addNewAtom(element, occupancy=occupancy, label=name)
stru.add_new_atom(element, occupancy=occupancy, label=name)
last_atom = stru.getLastAtom()
last_atom.xyz_cartn = rc
last_atom.Uisoequiv = uiso
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2 changes: 1 addition & 1 deletion src/diffpy/structure/parsers/p_pdffit.py
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Expand Up @@ -132,7 +132,7 @@ def parseLines(self, lines):
element = wl1[0][0].upper() + wl1[0][1:].lower()
xyz = [float(w) for w in wl1[1:4]]
occ = float(wl1[4])
stru.addNewAtom(element, xyz=xyz, occupancy=occ)
stru.add_new_atom(element, xyz=xyz, occupancy=occ)
a = stru.getLastAtom()
p_nl += 1
wl2 = next(ilines).split()
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2 changes: 1 addition & 1 deletion src/diffpy/structure/parsers/p_rawxyz.py
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Expand Up @@ -103,7 +103,7 @@ def parseLines(self, lines):
xyz = [float(f) for f in fields[x_idx : x_idx + 3]]
if len(xyz) == 2:
xyz.append(0.0)
stru.addNewAtom(element, xyz=xyz)
stru.add_new_atom(element, xyz=xyz)
except ValueError:
emsg = "%d: invalid number" % p_nl
exc_type, exc_value, exc_traceback = sys.exc_info()
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2 changes: 1 addition & 1 deletion src/diffpy/structure/parsers/p_xcfg.py
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Original file line number Diff line number Diff line change
Expand Up @@ -269,7 +269,7 @@ def parseLines(self, lines):
elif len(words) == xcfg_entry_count and p_element is not None:
fields = [float(w) for w in words]
xyz = [xcfg_A * xi for xi in fields[:3]]
stru.addNewAtom(p_element, xyz=xyz)
stru.add_new_atom(p_element, xyz=xyz)
a = stru[-1]
_assign_auxiliaries(
a,
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2 changes: 1 addition & 1 deletion src/diffpy/structure/parsers/p_xyz.py
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Expand Up @@ -109,7 +109,7 @@ def parseLines(self, lines):
element = fields[0]
element = element[0].upper() + element[1:].lower()
xyz = [float(f) for f in fields[1:4]]
stru.addNewAtom(element, xyz=xyz)
stru.add_new_atom(element, xyz=xyz)
except ValueError:
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = "%d: invalid number format" % p_nl
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20 changes: 20 additions & 0 deletions src/diffpy/structure/structure.py
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Expand Up @@ -21,9 +21,19 @@
from diffpy.structure.atom import Atom
from diffpy.structure.lattice import Lattice
from diffpy.structure.utils import _linkAtomAttribute, atomBareSymbol, isiterable
from diffpy.utils._deprecator import build_deprecation_message, deprecated

# ----------------------------------------------------------------------------

base = "diffpy.structure.Structure"
removal_version = "4.0.0"
addNewAtom_deprecation_msg = build_deprecation_message(
base,
"addNewAtom",
"add_new_atom",
removal_version,
)


class Structure(list):
"""Define group of atoms in a specified lattice. Structure --> group
Expand Down Expand Up @@ -145,7 +155,17 @@ def __str__(self):
s_atoms = "\n".join([str(a) for a in self])
return s_lattice + "\n" + s_atoms

@deprecated(addNewAtom_deprecation_msg)
def addNewAtom(self, *args, **kwargs):
"""This function has been deprecated and will be removed in
version 4.0.0.

Please use diffpy.structure.Structure.add_new_atom instead.
"""
self.add_new_atom(*args, **kwargs)
return

def add_new_atom(self, *args, **kwargs):
"""Add new `Atom` instance to the end of this `Structure`.

Parameters
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25 changes: 25 additions & 0 deletions tests/test_structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -120,6 +120,31 @@ def test___copy__(self):
# """check Structure.getLastAtom()"""
# return

def test_add_new_atom(self):
s_lat = Lattice()
expected = Structure(lattice=s_lat)

length = len(expected)
expected.add_new_atom(atype="C", xyz=[0.1, 0.2, 0.3])

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Choose a reason Spam Abuse Off Topic Outdated Duplicate Resolved Low Quality

This test is done but the code is a bit lazily written. Please can we think more carefully to make it more readable? For example, isn't assert len(expected) == len(actual)? And "object", what object?

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Choose a reason Spam Abuse Off Topic Outdated Duplicate Resolved Low Quality

Since add_new_atom would return nothing in the original function, we must have a variable to check the length of the Structure object before and after the method. I also changed the object variable to a more precise name to atom_object. See the latest commit.

actual = length + 1
assert len(expected) == actual

object = expected[-1]
assert object.element == "C"
assert numpy.allclose(object.xyz, [0.1, 0.2, 0.3])

def test_addNewAtom(self):
s_lat = Lattice()
expected = Structure(lattice=s_lat)

length = len(expected)
expected.addNewAtom(atype="C", xyz=[0.1, 0.2, 0.3])
actual = length + 1
assert len(expected) == actual
object = expected[-1]
assert object.element == "C"
assert numpy.allclose(object.xyz, [0.1, 0.2, 0.3])

def test_assignUniqueLabels(self):
"""Check Structure.assignUniqueLabels()"""
self.assertEqual("", "".join([a.label for a in self.stru]))
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