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Use shutil.copyfile instead of os.system("cp") in packing (Windows portability) #1343

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Use shutil.copyfile instead of os.system("cp") in packing (Windows portability) #1343

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4 changes: 2 additions & 2 deletions mbuild/packing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1211,7 +1211,7 @@ def _run_packmol(input_text, filled_xyz, temp_file, packmol_file):
"Packmol finished with imperfect packing. Using the .xyz_FORCED "
"file instead. This may not be a sufficient packing result."
)
os.system(f"cp {filled_xyz.name}_FORCED {filled_xyz.name}")
shutil.copyfile(f"{filled_xyz.name}_FORCED", filled_xyz.name)

if "ERROR" in out or proc.returncode != 0:
_packmol_error(out, err)
Expand All @@ -1220,7 +1220,7 @@ def _run_packmol(input_text, filled_xyz, temp_file, packmol_file):
os.remove(packmol_inp.name)

if temp_file is not None:
os.system("cp {0} {1}".format(filled_xyz.name, os.path.join(temp_file)))
shutil.copyfile(filled_xyz.name, temp_file)


def _check_packmol(PACKMOL): # pragma: no cover
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