Remove BadPoscarWarning when POSCAR elements set by POTCAR (#3662)

* remove BadPoscarWarning when elements set by POTCAR

* ruffin' it (get it?)

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.1
+    rev: v0.3.0
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]

dev_scripts/potcar_scrambler.py

@@ -15,7 +15,6 @@
 
 
 class PotcarScrambler:
-
     """
     Takes a POTCAR and replaces its values with completely random values
     Does type matching and attempts precision matching on floats to ensure

pymatgen/analysis/chemenv/utils/scripts_utils.py

@@ -1,6 +1,5 @@
 """This module contains some script utils that are used in the chemenv package."""
 
-
 from __future__ import annotations
 
 import re

pymatgen/analysis/ferroelectricity/polarization.py

@@ -43,7 +43,6 @@
 determine the spontaneous polarization because it serves as a reference point.
 """
 
-
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

pymatgen/analysis/functional_groups.py

@@ -1,6 +1,5 @@
 """Determine functional groups present in a Molecule."""
 
-
 from __future__ import annotations
 
 import copy

pymatgen/analysis/thermochemistry.py

@@ -1,6 +1,5 @@
 """A module to perform experimental thermochemical data analysis."""
 
-
 from __future__ import annotations
 
 from pymatgen.core.composition import Composition

pymatgen/apps/battery/plotter.py

@@ -1,6 +1,5 @@
 """This module provides plotting capabilities for battery related applications."""
 
-
 from __future__ import annotations
 
 import matplotlib.pyplot as plt

pymatgen/cli/pmg_potcar.py

@@ -2,7 +2,6 @@
 
 """Implementation for `pmg potcar` CLI."""
 
-
 from __future__ import annotations
 
 import os

pymatgen/io/aims/outputs.py

@@ -1,4 +1,5 @@
 """A representation of FHI-aims output (based on ASE output parser)."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING, Any

pymatgen/io/aims/parsers.py

@@ -1,4 +1,5 @@
 """AIMS output parser, taken from ASE with modifications."""
+
 from __future__ import annotations
 
 import gzip

pymatgen/io/aims/sets/base.py

@@ -1,4 +1,5 @@
 """Module defining base FHI-aims input set and generator."""
+
 from __future__ import annotations
 
 import copy

pymatgen/io/aims/sets/bs.py

@@ -1,4 +1,5 @@
 """Input sets for band structure calculations."""
+
 from __future__ import annotations
 
 from dataclasses import dataclass

pymatgen/io/aims/sets/core.py

@@ -1,4 +1,5 @@
 """Module defining core FHI-aims input set generators."""
+
 from __future__ import annotations
 
 from dataclasses import dataclass

pymatgen/io/cif.py

@@ -445,9 +445,9 @@ def _sanitize_data(self, data):
                         # Extract element name and its occupancy from the
                         # string, and store it as a
                         # key-value pair in "els_occ".
-                        els_occu[
-                            str(re.findall(r"\D+", symbol_str_lst[elocc_idx].strip())[1]).replace("<sup>", "")
-                        ] = float("0" + re.findall(r"\.?\d+", symbol_str_lst[elocc_idx].strip())[1])
+                        els_occu[str(re.findall(r"\D+", symbol_str_lst[elocc_idx].strip())[1]).replace("<sup>", "")] = (
+                            float("0" + re.findall(r"\.?\d+", symbol_str_lst[elocc_idx].strip())[1])
+                        )
 
                     x = str2float(data["_atom_site_fract_x"][idx])
                     y = str2float(data["_atom_site_fract_y"][idx])

pymatgen/io/feff/outputs.py

@@ -4,7 +4,6 @@
 Currently supports the xmu.dat, ldos.dat output files are for non-spin case.
 """
 
-
 from __future__ import annotations
 
 import re

pymatgen/io/lammps/utils.py

@@ -309,9 +309,10 @@ def run(self, site_property: str | None = None) -> Molecule:
         """
         with tempfile.TemporaryDirectory() as scratch_dir:
             self._write_input(input_dir=scratch_dir)
-            with open(os.path.join(scratch_dir, self.input_file)) as packmol_input, Popen(
-                self.packmol_bin, stdin=packmol_input, stdout=PIPE, stderr=PIPE
-            ) as proc:
+            with (
+                open(os.path.join(scratch_dir, self.input_file)) as packmol_input,
+                Popen(self.packmol_bin, stdin=packmol_input, stdout=PIPE, stderr=PIPE) as proc,
+            ):
                 stdout, stderr = proc.communicate()
             output_file = self.control_params["output"]
             if os.path.isfile(output_file):

pymatgen/io/lmto.py

@@ -4,7 +4,6 @@
 Structure object in the pymatgen.electronic_structure.cohp.py module.
 """
 
-
 from __future__ import annotations
 
 import re

pymatgen/io/pwmat/__init__.py

@@ -1,4 +1,5 @@
 """This package implements modules for input and output to and from PWmat."""
+
 from __future__ import annotations
 
 from .inputs import AtomConfig

pymatgen/io/vasp/inputs.py

@@ -263,9 +263,6 @@ def from_file(cls, filename, check_for_potcar=True, read_velocities=True, **kwar
                     potcar = Potcar.from_file(sorted(potcars)[0])
                     names = [sym.split("_")[0] for sym in potcar.symbols]
                     [get_el_sp(n) for n in names]  # ensure valid names
-                    warnings.warn(
-                        "Cannot determine elements in POSCAR. Falling back to manual assignment.", BadPoscarWarning
-                    )
                 except Exception:
                     names = None
         with zopen(filename, mode="rt") as file:
@@ -2714,7 +2711,9 @@ def run_vasp(
         if not vasp_cmd:
             raise RuntimeError("You need to supply vasp_cmd or set the PMG_VASP_EXE in .pmgrc.yaml to run VASP.")
 
-        with cd(run_dir), open(output_file, mode="w", encoding="utf-8") as stdout_file, open(
-            err_file, mode="w", encoding="utf-8", buffering=1
-        ) as stderr_file:
+        with (
+            cd(run_dir),
+            open(output_file, mode="w", encoding="utf-8") as stdout_file,
+            open(err_file, mode="w", encoding="utf-8", buffering=1) as stderr_file,
+        ):
             subprocess.check_call(vasp_cmd, stdout=stdout_file, stderr=stderr_file)

pymatgen/symmetry/groups.py

@@ -53,12 +53,10 @@ def __hash__(self) -> int:
         return len(self)
 
     @overload
-    def __getitem__(self, item: int) -> SymmOp:
-        ...
+    def __getitem__(self, item: int) -> SymmOp: ...
 
     @overload
-    def __getitem__(self, item: slice) -> Sequence[SymmOp]:
-        ...
+    def __getitem__(self, item: slice) -> Sequence[SymmOp]: ...
 
     def __getitem__(self, item: int | slice) -> SymmOp | Sequence[SymmOp]:
         return list(self.symmetry_ops)[item]

pymatgen/util/io_utils.py

@@ -1,6 +1,5 @@
 """This module provides utility classes for io operations."""
 
-
 from __future__ import annotations
 
 import os

tests/analysis/diffraction/__init__.py

@@ -1,6 +1,5 @@
 """TODO: Modify module doc."""
 
-
 from __future__ import annotations
 
 __author__ = "Shyue Ping Ong"

tests/apps/borg/test_queen.py

@@ -1,6 +1,5 @@
 """Created on Mar 18, 2012."""
 
-
 from __future__ import annotations
 
 import unittest

tests/command_line/test_bader_caller.py

@@ -133,7 +133,10 @@ def test_atom_parsing(self):
     def test_missing_file_bader_exe_path(self):
         pytest.skip("doesn't reliably raise RuntimeError")
         # mock which("bader") to return None so we always fall back to use bader_exe_path
-        with patch("shutil.which", return_value=None), pytest.raises(
-            RuntimeError, match="BaderAnalysis requires the executable bader be in the PATH or the full path "
+        with (
+            patch("shutil.which", return_value=None),
+            pytest.raises(
+                RuntimeError, match="BaderAnalysis requires the executable bader be in the PATH or the full path "
+            ),
         ):
             BaderAnalysis(chgcar_filename=f"{TEST_FILES_DIR}/CHGCAR.Fe3O4", bader_exe_path="")

tests/io/aims/test_sets/test_bs_generator.py

@@ -1,4 +1,5 @@
 """Tests the band structure input set generator"""
+
 from __future__ import annotations
 
 from pathlib import Path

tests/io/aims/test_sets/test_gw_generator.py

@@ -1,4 +1,5 @@
 """Tests the GW input set generator"""
+
 from __future__ import annotations
 
 from pathlib import Path

tests/io/aims/test_sets/test_static_restart_from_relax_generator.py

@@ -1,4 +1,5 @@
 """The test of input sets generating from restart information"""
+
 from __future__ import annotations
 
 from pathlib import Path