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Adjust pp_file as an unnessary parameter in save to abacus/stru #752

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merged 5 commits into from
Nov 8, 2024
Merged

Adjust pp_file as an unnessary parameter in save to abacus/stru #752

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e623b91
Adjust pp_file as an unnessary parameter in save to abacus/stru
Nov 8, 2024
50c138e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 8, 2024
d5f23ce
add test
Nov 8, 2024
da7b908
Merge branch 'abacus-pp' of https://github.com/pxlxingliang/dpdata in…
Nov 8, 2024
aaa12e6
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 8, 2024
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25 changes: 17 additions & 8 deletions dpdata/abacus/scf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -635,7 +635,7 @@ def get_frame_from_stru(fname):
def make_unlabeled_stru(
data,
frame_idx,
pp_file,
pp_file=None,
numerical_orbital=None,
numerical_descriptor=None,
mass=None,
Expand Down Expand Up @@ -759,7 +759,15 @@ def process_file_input(file_input, atom_names, input_name):

# ATOMIC_SPECIES block
out = "ATOMIC_SPECIES\n"
ppfiles = process_file_input(ndarray2list(pp_file), data["atom_names"], "pp_file")
if pp_file is not None:
ppfiles = process_file_input(
ndarray2list(pp_file), data["atom_names"], "pp_file"
)
else:
warnings.warn(
"pp_file is not provided, will use empty string for pseudo potential file."
)
ppfiles = [""] * len(data["atom_names"])
Comment on lines +762 to +770
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🛠️ Refactor suggestion

Enhance warning implementation and add test coverage.

  1. Add stacklevel to the warning to help trace its origin
  2. Add test coverage for the None case
-        warnings.warn(
-            "pp_file is not provided, will use empty string for pseudo potential file."
-        )
+        warnings.warn(
+            "pp_file is not provided, will use empty string for pseudo potential file.",
+            stacklevel=2
+        )

Would you like me to help create test cases for the scenario where pp_file is None?

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
if pp_file is not None:
ppfiles = process_file_input(
ndarray2list(pp_file), data["atom_names"], "pp_file"
)
else:
warnings.warn(
"pp_file is not provided, will use empty string for pseudo potential file."
)
ppfiles = [""] * len(data["atom_names"])
if pp_file is not None:
ppfiles = process_file_input(
ndarray2list(pp_file), data["atom_names"], "pp_file"
)
else:
warnings.warn(
"pp_file is not provided, will use empty string for pseudo potential file.",
stacklevel=2
)
ppfiles = [""] * len(data["atom_names"])
🧰 Tools
🪛 GitHub Check: codecov/patch

[warning] 767-767: dpdata/abacus/scf.py#L767
Added line #L767 was not covered by tests

[warning] 770-770: dpdata/abacus/scf.py#L770
Added line #L770 was not covered by tests

🪛 Ruff

767-767: No explicit stacklevel keyword argument found

(B028)


for iele in range(len(data["atom_names"])):
if data["atom_numbs"][iele] == 0:
Expand All @@ -771,12 +779,13 @@ def process_file_input(file_input, atom_names, input_name):
out += "1 "

ipp_file = ppfiles[iele]
if not link_file:
out += ipp_file
else:
out += os.path.basename(ipp_file.rstrip("/"))
if dest_dir is not None:
_link_file(dest_dir, ipp_file)
if ipp_file != "":
if not link_file:
out += ipp_file
else:
out += os.path.basename(ipp_file.rstrip("/"))
if dest_dir is not None:
_link_file(dest_dir, ipp_file)
out += "\n"
out += "\n"

Expand Down
4 changes: 4 additions & 0 deletions tests/test_abacus_stru_dump.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,10 @@ def test_dump_stru(self):
)
myfilecmp(self, "abacus.scf/stru_test", "STRU_tmp")

def test_dump_stru_without_pporb(self):
self.system_ch4.to("stru", "STRU_tmp", mass=[12, 1])
self.assertTrue(os.path.isfile("STRU_tmp"))

def test_dumpStruLinkFile(self):
os.makedirs("abacus.scf/tmp", exist_ok=True)
self.system_ch4.to(
Expand Down