Ruff fixes (#3564)

* fix ruff SIM300 Yoda asserts

ruff ignore ANN101 COM812 NPY002 PTH PLC1901 PLW1514
ruff ignore ANN201 S101 for tests/
rename f->file

* fix ruff F841 local var assigned but never used

* fix ruff SIM113 use enumerate() for index variable

* fix ruff RUF021 parenthesize `a and b` when chaining `and` and `or` together

* fix likely unintentional operator precedence in LobsterEnv._find_relevant_atoms_additional_condition()

(val1 < 0.0 < val2) or (val2 < 0.0 < val1) was not evaluated together

* fix ruff E226 missing whitespace around arithmetic op

* fix super.__init__() call missing parens

* fix ZeroDivisionError in >               self.logger.debug(f"Average time per combi = {(now - start_time) / idx} seconds")

Author: janosh

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.13
+    rev: v0.1.14
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -269,8 +269,8 @@ def get_weights(self, weights_options):
         "+-------------------------------------------------------------+\n"
     )
 
-    with open("ce_pairs.json") as f:
-        ce_pairs = json.load(f)
+    with open("ce_pairs.json") as file:
+        ce_pairs = json.load(file)
     self_weight_max_csms: dict[str, list[float]] = {}
     self_weight_max_csms_per_cn: dict[str, list[float]] = {}
     all_self_max_csms = []

pymatgen/alchemy/filters.py

@@ -265,9 +265,11 @@ def get_sg(s):
 
         for s in self.existing_structures:
             if (
-                self.structure_matcher._comparator.get_hash(structure.composition)
-                == self.structure_matcher._comparator.get_hash(s.composition)
-                and self.symprec is None
+                (
+                    self.structure_matcher._comparator.get_hash(structure.composition)
+                    == self.structure_matcher._comparator.get_hash(s.composition)
+                    and self.symprec is None
+                )
                 or get_sg(s) == get_sg(structure)
             ) and self.structure_matcher.fit(s, structure):
                 return False

pymatgen/analysis/adsorption.py

@@ -582,7 +582,7 @@ def substitute(site, i):
 
         for idx, site in enumerate(sym_slab):
             if dist - range_tol < site.frac_coords[2] < dist + range_tol and (
-                target_species and site.species_string in target_species or not target_species
+                (target_species and site.species_string in target_species) or not target_species
             ):
                 substituted_slabs.append(substitute(site, idx))
 

pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py

@@ -1062,7 +1062,7 @@ def __init__(
         :param max_csm:
         :param symmetry_measure_type:
         """
-        super.__init__(
+        super().__init__(
             self,
             structure_environments,
             additional_condition=additional_condition,

pymatgen/analysis/chemenv/coordination_environments/structure_environments.py

@@ -1763,10 +1763,8 @@ def get_site_info_for_specie_allces(self, specie, min_fraction=0):
         oxi_state = specie.oxi_state
         for isite, site in enumerate(self.structure):
             if (
-                element in [sp.symbol for sp in site.species]
-                and self.valences == "undefined"
-                or oxi_state == self.valences[isite]
-            ):
+                element in [sp.symbol for sp in site.species] and self.valences == "undefined"
+            ) or oxi_state == self.valences[isite]:
                 if self.coordination_environments[isite] is None:
                     continue
                 for ce_dict in self.coordination_environments[isite]:

pymatgen/analysis/diffraction/tem.py

@@ -20,9 +20,6 @@
 if TYPE_CHECKING:
     from pymatgen.core import Structure
 
-with open(os.path.join(os.path.dirname(__file__), "atomic_scattering_params.json")) as f:
-    ATOMIC_SCATTERING_PARAMS = json.load(f)
-
 __author__ = "Frank Wan, Jason Liang"
 __copyright__ = "Copyright 2020, The Materials Project"
 __version__ = "0.22"
@@ -31,13 +28,18 @@
 __date__ = "03/31/2020"
 
 
+module_dir = os.path.dirname(__file__)
+with open(f"{module_dir}/atomic_scattering_params.json") as file:
+    ATOMIC_SCATTERING_PARAMS = json.load(file)
+
+
 class TEMCalculator(AbstractDiffractionPatternCalculator):
     """
     Computes the TEM pattern of a crystal structure for multiple Laue zones.
     Code partially inspired from XRD calculation implementation. X-ray factor to electron factor
         conversion based on the International Table of Crystallography.
     #TODO: Could add "number of iterations", "magnification", "critical value of beam",
-            "twin direction" for certain materials, "sample thickness", and "excitation error s".
+        "twin direction" for certain materials, "sample thickness", and "excitation error s".
     """
 
     def __init__(

pymatgen/analysis/local_env.py

@@ -1211,9 +1211,9 @@ def __init__(
 
         # Load elemental radii table
         bonds_file = f"{module_dir}/bonds_jmol_ob.yaml"
-        with open(bonds_file) as f:
+        with open(bonds_file) as file:
             yaml = YAML()
-            self.el_radius = yaml.load(f)
+            self.el_radius = yaml.load(file)
 
         # Update any user preference elemental radii
         if el_radius_updates:

pymatgen/analysis/magnetism/heisenberg.py

@@ -146,11 +146,9 @@ def _get_unique_sites(structure):
         unique_site_ids = {}
         wyckoff_ids = {}
 
-        i = 0
-        for indices, symbol in zip(equivalent_indices, wyckoff_symbols):
-            unique_site_ids[tuple(indices)] = i
-            wyckoff_ids[i] = symbol
-            i += 1
+        for idx, (indices, symbol) in enumerate(zip(equivalent_indices, wyckoff_symbols)):
+            unique_site_ids[tuple(indices)] = idx
+            wyckoff_ids[idx] = symbol
             for index in indices:
                 wyckoff[index] = symbol
 

pymatgen/apps/borg/hive.py

@@ -224,7 +224,7 @@ def assimilate(self, path):
             else:
                 for filename in filenames:
                     files = sorted(glob(os.path.join(path, filename + "*")))
-                    if len(files) == 1 or filename in ("INCAR", "POTCAR") or len(files) == 1 and filename == "DYNMAT":
+                    if len(files) == 1 or filename in ("INCAR", "POTCAR") or (len(files) == 1 and filename == "DYNMAT"):
                         files_to_parse[filename] = files[0]
                     elif len(files) > 1:
                         # Since multiple files are ambiguous, we will always

pymatgen/apps/borg/queen.py

@@ -74,13 +74,11 @@ def serial_assimilate(self, rootpath):
         for parent, subdirs, files in os.walk(rootpath):
             valid_paths.extend(self._drone.get_valid_paths((parent, subdirs, files)))
         data = []
-        count = 0
         total = len(valid_paths)
-        for path in valid_paths:
+        for idx, path in enumerate(valid_paths, 1):
             new_data = self._drone.assimilate(path)
             self._data.append(new_data)
-            count += 1
-            logger.info(f"{count}/{total} ({count / total:.2%}) done")
+            logger.info(f"{idx}/{total} ({idx / total:.2%}) done")
         for json_str in data:
             self._data.append(json.loads(json_str, cls=MontyDecoder))
 

pymatgen/cli/pmg_potcar.py

@@ -10,18 +10,18 @@
 from pymatgen.io.vasp import Potcar
 
 
-def proc_dir(dirname, procfilefunction):
+def proc_dir(dirname, proc_file_function):
     """Process a directory.
 
     Args:
         dirname (str): Directory name.
-        procfilefunction (callable): Callable to execute on directory.
+        proc_file_function (callable): Callable to execute on directory.
     """
     for f in os.listdir(dirname):
         if os.path.isdir(os.path.join(dirname, f)):
-            proc_dir(os.path.join(dirname, f), procfilefunction)
+            proc_dir(os.path.join(dirname, f), proc_file_function)
         else:
-            procfilefunction(dirname, f)
+            proc_file_function(dirname, f)
 
 
 def gen_potcar(dirname, filename):

pymatgen/command_line/critic2_caller.py

@@ -93,8 +93,8 @@ def __init__(self, input_script):
         # not otherwise used
         self._input_script = input_script
 
-        with open("input_script.cri", mode="w") as f:
-            f.write(input_script)
+        with open("input_script.cri", mode="w") as file:
+            file.write(input_script)
 
         args = ["critic2", "input_script.cri"]
         with subprocess.Popen(args, stdout=subprocess.PIPE, stdin=subprocess.PIPE, close_fds=True) as rs:

pymatgen/command_line/gulp_caller.py

@@ -526,7 +526,9 @@ def get_energy(gout: str):
         """
         energy = None
         for line in gout.split("\n"):
-            if "Total lattice energy" in line and "eV" in line or "Non-primitive unit cell" in line and "eV" in line:
+            if ("Total lattice energy" in line and "eV" in line) or (
+                "Non-primitive unit cell" in line and "eV" in line
+            ):
                 energy = line.split()
         if energy:
             return float(energy[4])
@@ -863,9 +865,9 @@ class TersoffPotential:
 
     def __init__(self):
         """Init TersoffPotential."""
-        with open(f"{module_dir}/OxideTersoffPotentials") as f:
+        with open(f"{module_dir}/OxideTersoffPotentials") as file:
             data = {}
-            for row in f:
+            for row in file:
                 metaloxi = row.split()[0]
                 line = row.split(")")
                 data[metaloxi] = line[1]

pymatgen/command_line/vampire_caller.py

@@ -225,8 +225,8 @@ def _create_mat(self):
 
         self.mat_id_dict = mat_id_dict
 
-        with open(mat_file_name, mode="w") as f:
-            f.write(mat_file)
+        with open(mat_file_name, mode="w") as file:
+            file.write(mat_file)
 
     def _create_input(self):
         structure = self.structure
@@ -330,12 +330,12 @@ def _create_ucf(self):
 
         # J_ij exchange interaction matrix
         sgraph = self.sgraph
-        ninter = 0
+        n_inter = 0
         for idx in range(len(sgraph.graph.nodes)):
-            ninter += sgraph.get_coordination_of_site(idx)
+            n_inter += sgraph.get_coordination_of_site(idx)
 
         ucf += ["# Interactions"]
-        ucf += [f"{ninter} isotropic"]
+        ucf += [f"{n_inter} isotropic"]
 
         iid = 0  # counts number of interaction
         for idx in range(len(sgraph.graph.nodes)):
@@ -363,8 +363,8 @@ def _create_ucf(self):
         ucf = "\n".join(ucf)
         ucf_file_name = mat_name + ".ucf"
 
-        with open(ucf_file_name, mode="w") as f:
-            f.write(ucf)
+        with open(ucf_file_name, mode="w") as file:
+            file.write(ucf)
 
     @staticmethod
     def parse_stdout(vamp_stdout, n_mats: int) -> tuple:

pymatgen/core/bonds.py

@@ -19,9 +19,9 @@
 
 def _load_bond_length_data():
     """Loads bond length data from json file."""
-    with open(os.path.join(os.path.dirname(__file__), "bond_lengths.json")) as f:
+    with open(os.path.join(os.path.dirname(__file__), "bond_lengths.json")) as file:
         data = collections.defaultdict(dict)
-        for row in json.load(f):
+        for row in json.load(file):
             els = sorted(row["elements"])
             data[tuple(els)][row["bond_order"]] = row["length"]
         return data

pymatgen/core/structure.py

@@ -3621,8 +3621,8 @@ def from_file(cls, filename):
         filename = str(filename)
         from pymatgen.io.gaussian import GaussianOutput
 
-        with zopen(filename) as f:
-            contents = f.read()
+        with zopen(filename) as file:
+            contents = file.read()
         fname = filename.lower()
         if fnmatch(fname, "*.xyz*"):
             return cls.from_str(contents, fmt="xyz")

pymatgen/core/trajectory.py

@@ -239,7 +239,8 @@ def extend(self, trajectory: Trajectory) -> None:
         if (
             self.lattice is None  # is molecules
             and trajectory.lattice is not None  # is structures
-            or self.lattice is not None  # is structures
+        ) or (
+            self.lattice is not None  # is structures
             and trajectory.lattice is None  # is molecules
         ):
             raise ValueError("Cannot combine `Molecule`- and `Structure`-based `Trajectory`. objects.")
@@ -442,8 +443,8 @@ def write_Xdatcar(
 
         xdatcar_string = "\n".join(lines) + "\n"
 
-        with zopen(filename, mode="wt") as f:
-            f.write(xdatcar_string)
+        with zopen(filename, mode="wt") as file:
+            file.write(xdatcar_string)
 
     def as_dict(self) -> dict:
         """Return the trajectory as a MSONable dict."""

pymatgen/electronic_structure/boltztrap.py

@@ -2139,29 +2139,26 @@ def read_cube_file(filename):
     """
     with open(filename) as file:
         natoms = 0
-        count_line = 0
-        for line in file:
+        for idx, line in enumerate(file):
             line = line.rstrip("\n")
-            if count_line == 0 and "CUBE" not in line:
+            if idx == 0 and "CUBE" not in line:
                 raise ValueError("CUBE file format not recognized")
 
-            if count_line == 2:
+            if idx == 2:
                 tokens = line.split()
                 natoms = int(tokens[0])
-            if count_line == 3:
+            if idx == 3:
                 tokens = line.split()
                 n1 = int(tokens[0])
-            elif count_line == 4:
+            elif idx == 4:
                 tokens = line.split()
                 n2 = int(tokens[0])
-            elif count_line == 5:
+            elif idx == 5:
                 tokens = line.split()
                 n3 = int(tokens[0])
-            elif count_line > 5:
+            elif idx > 5:
                 break
 
-            count_line += 1
-
     if "fort.30" in filename:
         energy_data = np.genfromtxt(filename, skip_header=natoms + 6, skip_footer=1)
         nlines_data = len(energy_data)

pymatgen/io/abinit/abiobjects.py

@@ -112,7 +112,7 @@ def structure_from_abivars(cls=None, *args, **kwargs) -> Structure:
             znucl=13,
         )
 
-    `xred` can be replaced with `xcart` or `xangst`.
+    xred can be replaced with xcart or xangst.
     """
     kwargs.update(dict(*args))
     cls = cls or Structure
@@ -307,8 +307,7 @@ def contract(string):
 
 class AbivarAble(metaclass=abc.ABCMeta):
     """
-    An `AbivarAble` object provides a method `to_abivars`
-    that returns a dictionary with the abinit variables.
+    An AbivarAble object provides a method to_abivars that returns a dictionary with the abinit variables.
     """
 
     @abc.abstractmethod
@@ -369,17 +368,13 @@ def as_spinmode(cls, obj):
 
         # Assume a string with mode
         try:
-            return _mode2spinvars[obj]
+            return _mode_to_spin_vars[obj]
         except KeyError:
             raise KeyError(f"Wrong value for spin_mode: {obj}")
 
     def to_abivars(self):
         """Dictionary with Abinit input variables."""
-        return {
-            "nsppol": self.nsppol,
-            "nspinor": self.nspinor,
-            "nspden": self.nspden,
-        }
+        return {"nsppol": self.nsppol, "nspinor": self.nspinor, "nspden": self.nspden}
 
     def as_dict(self):
         """Convert object to dict."""
@@ -394,7 +389,7 @@ def from_dict(cls, d):
 
 
 # An handy Multiton
-_mode2spinvars = {
+_mode_to_spin_vars = {
     "unpolarized": SpinMode("unpolarized", 1, 1, 1),
     "polarized": SpinMode("polarized", 2, 1, 2),
     "afm": SpinMode("afm", 1, 1, 2),