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chore: deprecated addNewAtom #157

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Merged
sbillinge merged 11 commits into from
Feb 20, 2026
Merged

chore: deprecated addNewAtom #157

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9ed7fc6
build: deprecate addNewItem
stevenhua0320 Feb 19, 2026
6e99082
build: change body of deprecated function
stevenhua0320 Feb 19, 2026
95138f7
build: add test cases for addNewAtom to test it & show deprecation me…
stevenhua0320 Feb 19, 2026
3f285b6
fix: refine test code to avoid if logic
stevenhua0320 Feb 19, 2026
1fc8a34
test: add docstring and comments to the test.
stevenhua0320 Feb 19, 2026
cb7aec0
fix: add more test cases and refine behavior of add_new_atom
stevenhua0320 Feb 20, 2026
114f3d6
fix: add docstring for hyperparamter for add_new_atom
stevenhua0320 Feb 20, 2026
40e8773
fix: fix comment with syntax error
stevenhua0320 Feb 20, 2026
8f8253c
fix: change behavior to warning and use pytest parametrize to test it.
stevenhua0320 Feb 20, 2026
15ccba1
[pre-commit.ci] auto fixes from pre-commit hooks
pre-commit-ci[bot] Feb 20, 2026
52c99e6
fix: fix comment for UserWarning.
stevenhua0320 Feb 20, 2026
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fix: refine test code to avoid if logic
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@stevenhua0320
stevenhua0320 committed Feb 19, 2026
commit 3f285b6ef555f504ae487972a54361e67bdcfe96
15 changes: 4 additions & 11 deletions tests/test_structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -122,7 +122,6 @@ def test___copy__(self):

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

length = len(expected)
Expand All @@ -131,26 +130,20 @@ def test_add_new_atom(self):
assert len(expected) == actual

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

def test_addNewAtom(self):
s_lat = Lattice()
other_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]
if hasattr(object, "element"):
assert object.element == "C"
if hasattr(object, "xyz"):
assert numpy.allclose(object.xyz, [0.1, 0.2, 0.3])
assert object.element == "C"
assert numpy.allclose(object.xyz, [0.1, 0.2, 0.3])

def test_assignUniqueLabels(self):
"""Check Structure.assignUniqueLabels()"""
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