From 8fd181bbf312f4a0bfccebbf27b0f954d118947c Mon Sep 17 00:00:00 2001
From: Aaron Kaplan <33381112+esoteric-ephemera@users.noreply.github.com>
Date: Thu, 29 Feb 2024 11:49:22 -0800
Subject: [PATCH] Remove BadPoscarWarning when POSCAR elements set by POTCAR
 (#3662)

* remove BadPoscarWarning when elements set by POTCAR

* ruffin' it (get it?)
---
 .pre-commit-config.yaml                               |  2 +-
 dev_scripts/potcar_scrambler.py                       |  1 -
 pymatgen/analysis/chemenv/utils/scripts_utils.py      |  1 -
 pymatgen/analysis/ferroelectricity/polarization.py    |  1 -
 pymatgen/analysis/functional_groups.py                |  1 -
 pymatgen/analysis/thermochemistry.py                  |  1 -
 pymatgen/apps/battery/plotter.py                      |  1 -
 pymatgen/cli/pmg_potcar.py                            |  1 -
 pymatgen/io/aims/outputs.py                           |  1 +
 pymatgen/io/aims/parsers.py                           |  1 +
 pymatgen/io/aims/sets/base.py                         |  1 +
 pymatgen/io/aims/sets/bs.py                           |  1 +
 pymatgen/io/aims/sets/core.py                         |  1 +
 pymatgen/io/cif.py                                    |  6 +++---
 pymatgen/io/feff/outputs.py                           |  1 -
 pymatgen/io/lammps/utils.py                           |  7 ++++---
 pymatgen/io/lmto.py                                   |  1 -
 pymatgen/io/pwmat/__init__.py                         |  1 +
 pymatgen/io/vasp/inputs.py                            | 11 +++++------
 pymatgen/symmetry/groups.py                           |  6 ++----
 pymatgen/util/io_utils.py                             |  1 -
 tests/analysis/diffraction/__init__.py                |  1 -
 tests/apps/borg/test_queen.py                         |  1 -
 tests/command_line/test_bader_caller.py               |  7 +++++--
 tests/io/aims/test_sets/test_bs_generator.py          |  1 +
 tests/io/aims/test_sets/test_gw_generator.py          |  1 +
 .../test_static_restart_from_relax_generator.py       |  1 +
 27 files changed, 29 insertions(+), 31 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 74778b0437d..1ae91e88764 100644
--- a/.pre-commit-config.yaml
+++ b/.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]
diff --git a/dev_scripts/potcar_scrambler.py b/dev_scripts/potcar_scrambler.py
index ea9e3777d56..5fe40c3852d 100644
--- a/dev_scripts/potcar_scrambler.py
+++ b/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
diff --git a/pymatgen/analysis/chemenv/utils/scripts_utils.py b/pymatgen/analysis/chemenv/utils/scripts_utils.py
index 389cd261d2d..c538946d8a8 100644
--- a/pymatgen/analysis/chemenv/utils/scripts_utils.py
+++ b/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
diff --git a/pymatgen/analysis/ferroelectricity/polarization.py b/pymatgen/analysis/ferroelectricity/polarization.py
index 49fd7ef478d..349fc133827 100644
--- a/pymatgen/analysis/ferroelectricity/polarization.py
+++ b/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
diff --git a/pymatgen/analysis/functional_groups.py b/pymatgen/analysis/functional_groups.py
index a92b4c2f5aa..7242d13aa78 100644
--- a/pymatgen/analysis/functional_groups.py
+++ b/pymatgen/analysis/functional_groups.py
@@ -1,6 +1,5 @@
 """Determine functional groups present in a Molecule."""
 
-
 from __future__ import annotations
 
 import copy
diff --git a/pymatgen/analysis/thermochemistry.py b/pymatgen/analysis/thermochemistry.py
index b467aea3351..0dd3eb8a6a9 100644
--- a/pymatgen/analysis/thermochemistry.py
+++ b/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
diff --git a/pymatgen/apps/battery/plotter.py b/pymatgen/apps/battery/plotter.py
index 30330697a87..8d77aeac0d2 100644
--- a/pymatgen/apps/battery/plotter.py
+++ b/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
diff --git a/pymatgen/cli/pmg_potcar.py b/pymatgen/cli/pmg_potcar.py
index b49e4d2da6a..66398ed62b1 100755
--- a/pymatgen/cli/pmg_potcar.py
+++ b/pymatgen/cli/pmg_potcar.py
@@ -2,7 +2,6 @@
 
 """Implementation for `pmg potcar` CLI."""
 
-
 from __future__ import annotations
 
 import os
diff --git a/pymatgen/io/aims/outputs.py b/pymatgen/io/aims/outputs.py
index e9e7f040fcd..b6a189dece7 100644
--- a/pymatgen/io/aims/outputs.py
+++ b/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
diff --git a/pymatgen/io/aims/parsers.py b/pymatgen/io/aims/parsers.py
index 9884c7c1c00..789f68fd531 100644
--- a/pymatgen/io/aims/parsers.py
+++ b/pymatgen/io/aims/parsers.py
@@ -1,4 +1,5 @@
 """AIMS output parser, taken from ASE with modifications."""
+
 from __future__ import annotations
 
 import gzip
diff --git a/pymatgen/io/aims/sets/base.py b/pymatgen/io/aims/sets/base.py
index 9b205823d70..df8a8597159 100644
--- a/pymatgen/io/aims/sets/base.py
+++ b/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
diff --git a/pymatgen/io/aims/sets/bs.py b/pymatgen/io/aims/sets/bs.py
index ac0ef112bfb..89cab4f0ada 100644
--- a/pymatgen/io/aims/sets/bs.py
+++ b/pymatgen/io/aims/sets/bs.py
@@ -1,4 +1,5 @@
 """Input sets for band structure calculations."""
+
 from __future__ import annotations
 
 from dataclasses import dataclass
diff --git a/pymatgen/io/aims/sets/core.py b/pymatgen/io/aims/sets/core.py
index 4c74c235439..e1b4880367a 100644
--- a/pymatgen/io/aims/sets/core.py
+++ b/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
diff --git a/pymatgen/io/cif.py b/pymatgen/io/cif.py
index d332a10ef48..0ff60e099d2 100644
--- a/pymatgen/io/cif.py
+++ b/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])
diff --git a/pymatgen/io/feff/outputs.py b/pymatgen/io/feff/outputs.py
index bc736a1cba0..7895f6c51fd 100644
--- a/pymatgen/io/feff/outputs.py
+++ b/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
diff --git a/pymatgen/io/lammps/utils.py b/pymatgen/io/lammps/utils.py
index 53a07c10ba3..808f6cd68d2 100644
--- a/pymatgen/io/lammps/utils.py
+++ b/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):
diff --git a/pymatgen/io/lmto.py b/pymatgen/io/lmto.py
index 3c95376f936..89740618824 100644
--- a/pymatgen/io/lmto.py
+++ b/pymatgen/io/lmto.py
@@ -4,7 +4,6 @@
 Structure object in the pymatgen.electronic_structure.cohp.py module.
 """
 
-
 from __future__ import annotations
 
 import re
diff --git a/pymatgen/io/pwmat/__init__.py b/pymatgen/io/pwmat/__init__.py
index 344ed9f9875..01fd80cfadc 100644
--- a/pymatgen/io/pwmat/__init__.py
+++ b/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
diff --git a/pymatgen/io/vasp/inputs.py b/pymatgen/io/vasp/inputs.py
index f8969a79827..f7d2dbe5a05 100644
--- a/pymatgen/io/vasp/inputs.py
+++ b/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)
diff --git a/pymatgen/symmetry/groups.py b/pymatgen/symmetry/groups.py
index 4867193c062..8b6b40401b4 100644
--- a/pymatgen/symmetry/groups.py
+++ b/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]
diff --git a/pymatgen/util/io_utils.py b/pymatgen/util/io_utils.py
index f3c839a1cf4..b59e2520727 100644
--- a/pymatgen/util/io_utils.py
+++ b/pymatgen/util/io_utils.py
@@ -1,6 +1,5 @@
 """This module provides utility classes for io operations."""
 
-
 from __future__ import annotations
 
 import os
diff --git a/tests/analysis/diffraction/__init__.py b/tests/analysis/diffraction/__init__.py
index 6706a39d634..8303844e475 100644
--- a/tests/analysis/diffraction/__init__.py
+++ b/tests/analysis/diffraction/__init__.py
@@ -1,6 +1,5 @@
 """TODO: Modify module doc."""
 
-
 from __future__ import annotations
 
 __author__ = "Shyue Ping Ong"
diff --git a/tests/apps/borg/test_queen.py b/tests/apps/borg/test_queen.py
index c6be59aa7be..1b33c8759b6 100644
--- a/tests/apps/borg/test_queen.py
+++ b/tests/apps/borg/test_queen.py
@@ -1,6 +1,5 @@
 """Created on Mar 18, 2012."""
 
-
 from __future__ import annotations
 
 import unittest
diff --git a/tests/command_line/test_bader_caller.py b/tests/command_line/test_bader_caller.py
index 00ca00b3675..1abab791cd4 100644
--- a/tests/command_line/test_bader_caller.py
+++ b/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="")
diff --git a/tests/io/aims/test_sets/test_bs_generator.py b/tests/io/aims/test_sets/test_bs_generator.py
index 3a957e0b566..2dfe1e36b53 100644
--- a/tests/io/aims/test_sets/test_bs_generator.py
+++ b/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
diff --git a/tests/io/aims/test_sets/test_gw_generator.py b/tests/io/aims/test_sets/test_gw_generator.py
index 56a215dc039..a1f5fef8cac 100644
--- a/tests/io/aims/test_sets/test_gw_generator.py
+++ b/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
diff --git a/tests/io/aims/test_sets/test_static_restart_from_relax_generator.py b/tests/io/aims/test_sets/test_static_restart_from_relax_generator.py
index bfa9623be8e..07d1e0ca295 100644
--- a/tests/io/aims/test_sets/test_static_restart_from_relax_generator.py
+++ b/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