write test-created files to temporary directory (#3454)

pymatgen/analysis/cost.py

@@ -16,7 +16,6 @@
 
 import scipy.constants as const
 from monty.design_patterns import singleton
-from monty.string import unicode2str
 
 from pymatgen.analysis.phase_diagram import PDEntry, PhaseDiagram
 from pymatgen.core.composition import Composition
@@ -94,7 +93,7 @@ def __init__(self, filename):
         self._chemsys_entries = defaultdict(list)
         filename = os.path.join(os.path.dirname(__file__), filename)
         with open(filename) as f:
-            reader = csv.reader(f, quotechar=unicode2str("|"))
+            reader = csv.reader(f, quotechar="|")
             for row in reader:
                 comp = Composition(row[0])
                 cost_per_mol = float(row[1]) * comp.weight.to("kg") * const.N_A

pymatgen/core/xcfunc.py

@@ -6,7 +6,6 @@
 
 from monty.functools import lazy_property
 from monty.json import MSONable
-from monty.string import is_string
 
 from pymatgen.core.libxcfunc import LibxcFunc
 
@@ -122,7 +121,7 @@ def asxc(cls, obj):
         """Convert object into Xcfunc."""
         if isinstance(obj, cls):
             return obj
-        if is_string(obj):
+        if isinstance(obj, str):
             return cls.from_name(obj)
         raise TypeError(f"Don't know how to convert <{type(obj)}:{obj}> to Xcfunc")
 

pymatgen/entries/entry_tools.py

@@ -14,7 +14,6 @@
 from typing import TYPE_CHECKING, Literal
 
 from monty.json import MontyDecoder, MontyEncoder, MSONable
-from monty.string import unicode2str
 
 from pymatgen.analysis.phase_diagram import PDEntry
 from pymatgen.analysis.structure_matcher import SpeciesComparator, StructureMatcher
@@ -302,8 +301,8 @@ def to_csv(self, filename: str, latexify_names: bool = False) -> None:
         with open(filename, "w") as f:
             writer = csv.writer(
                 f,
-                delimiter=unicode2str(","),
-                quotechar=unicode2str('"'),
+                delimiter=",",
+                quotechar='"',
                 quoting=csv.QUOTE_MINIMAL,
             )
             writer.writerow(["Name"] + [el.symbol for el in elements] + ["Energy"])
@@ -326,8 +325,8 @@ def from_csv(cls, filename: str):
         with open(filename, encoding="utf-8") as f:
             reader = csv.reader(
                 f,
-                delimiter=unicode2str(","),
-                quotechar=unicode2str('"'),
+                delimiter=",",
+                quotechar='"',
                 quoting=csv.QUOTE_MINIMAL,
             )
             entries = []

pymatgen/io/abinit/abitimer.py

@@ -12,7 +12,6 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
-from monty.string import is_string, list_strings
 
 from pymatgen.io.core import ParseError
 from pymatgen.util.plotting import add_fig_kwargs, get_ax_fig
@@ -107,7 +106,8 @@ def parse(self, filenames):
 
         Return: list of successfully read files.
         """
-        filenames = list_strings(filenames)
+        if isinstance(filenames, str):
+            filenames = [filenames]
 
         read_ok = []
         for fname in filenames:
@@ -667,16 +667,16 @@ def get_section(self, section_name):
 
     def to_csv(self, fileobj=sys.stdout):
         """Write data on file fileobj using CSV format."""
-        openclose = is_string(fileobj)
+        is_str = isinstance(fileobj, str)
 
-        if openclose:
+        if is_str:
             fileobj = open(fileobj, "w")  # noqa: SIM115
 
         for idx, section in enumerate(self.sections):
             fileobj.write(section.to_csvline(with_header=(idx == 0)))
         fileobj.flush()
 
-        if openclose:
+        if is_str:
             fileobj.close()
 
     def to_table(self, sort_key="wall_time", stop=None):
@@ -718,7 +718,7 @@ def get_dataframe(self, sort_key="wall_time", **kwargs):
 
     def get_values(self, keys):
         """Return a list of values associated to a particular list of keys."""
-        if is_string(keys):
+        if isinstance(keys, str):
             return [s.__dict__[keys] for s in self.sections]
         values = []
         for k in keys:

pymatgen/io/abinit/inputs.py

@@ -18,7 +18,6 @@
 import numpy as np
 from monty.collections import AttrDict
 from monty.json import MSONable
-from monty.string import is_string, list_strings
 
 from pymatgen.core.structure import Structure
 from pymatgen.io.abinit import abiobjects as aobj
@@ -99,9 +98,7 @@
 
 
 # Default values used if user does not specify them
-_DEFAULTS = {
-    "kppa": 1000,
-}
+_DEFAULTS = {"kppa": 1000}
 
 
 def as_structure(obj):
@@ -115,7 +112,7 @@ def as_structure(obj):
     if isinstance(obj, Structure):
         return obj
 
-    if is_string(obj):
+    if isinstance(obj, str):
         return Structure.from_file(obj)
 
     if isinstance(obj, Mapping):
@@ -151,7 +148,7 @@ def from_object(cls, obj):
         """
         if isinstance(obj, cls):
             return obj
-        if is_string(obj):
+        if isinstance(obj, str):
             return cls(obj[0].upper())
         raise TypeError(f"The object provided is not handled: type {type(obj).__name__}")
 
@@ -676,8 +673,10 @@ def remove_vars(self, keys, strict=True):
             keys: string or list of strings with variable names.
             strict: If True, KeyError is raised if at least one variable is not present.
         """
+        if isinstance(keys, str):
+            keys = [keys]
         removed = {}
-        for key in list_strings(keys):
+        for key in keys:
             if strict and key not in self:
                 raise KeyError(f"{key=} not in self:\n {list(self)}")
             if key in self:
@@ -710,7 +709,7 @@ class BasicAbinitInput(AbstractInput, MSONable):
     def __init__(
         self,
         structure,
-        pseudos,
+        pseudos: str | list[str] | list[Pseudo] | PseudoTable,
         pseudo_dir=None,
         comment=None,
         abi_args=None,
@@ -745,11 +744,14 @@ def __init__(
         self._vars = dict(args)
         self.set_structure(structure)
 
+        if isinstance(pseudos, str):
+            pseudos = [pseudos]
+
         if pseudo_dir is not None:
             pseudo_dir = os.path.abspath(pseudo_dir)
             if not os.path.exists(pseudo_dir):
                 raise self.Error(f"Directory {pseudo_dir} does not exist")
-            pseudos = [os.path.join(pseudo_dir, p) for p in list_strings(pseudos)]
+            pseudos = [os.path.join(pseudo_dir, p) for p in pseudos]
 
         try:
             self._pseudos = PseudoTable.as_table(pseudos).get_pseudos_for_structure(self.structure)
@@ -1092,8 +1094,10 @@ def __init__(self, structure: Structure, pseudos, pseudo_dir="", ndtset=1):
 
         else:
             # String(s)
+            if isinstance(pseudos, str):
+                pseudos = [pseudos]
             pseudo_dir = os.path.abspath(pseudo_dir)
-            pseudo_paths = [os.path.join(pseudo_dir, p) for p in list_strings(pseudos)]
+            pseudo_paths = [os.path.join(pseudo_dir, p) for p in pseudos]
 
             missing = [p for p in pseudo_paths if not os.path.exists(p)]
             if missing:

pymatgen/io/abinit/pseudos.py

@@ -19,7 +19,6 @@
 from monty.itertools import iterator_from_slice
 from monty.json import MontyDecoder, MSONable
 from monty.os.path import find_exts
-from monty.string import is_string, list_strings
 from tabulate import tabulate
 
 from pymatgen.core.periodic_table import Element
@@ -612,7 +611,7 @@ def _dict_from_lines(lines, key_nums, sep=None):
     Raises:
         ValueError if parsing fails.
     """
-    if is_string(lines):
+    if isinstance(lines, str):
         lines = [lines]
 
     if not isinstance(key_nums, collections.abc.Iterable):
@@ -1611,8 +1610,8 @@ def __init__(self, pseudos: Sequence[Pseudo]) -> None:
         if not isinstance(pseudos, collections.abc.Iterable):
             pseudos = [pseudos]
 
-        if len(pseudos) and is_string(pseudos[0]):
-            pseudos = list_strings(pseudos)
+        if isinstance(pseudos, str):
+            pseudos = [pseudos]
 
         self._pseudos_with_z = defaultdict(list)
 
@@ -1772,7 +1771,9 @@ def select_symbols(self, symbols, ret_list=False):
                 Prepend the symbol string with "-", to exclude pseudos.
             ret_list: if True a list of pseudos is returned instead of a PseudoTable
         """
-        symbols = list_strings(symbols)
+        if isinstance(symbols, str):
+            symbols = [symbols]
+
         exclude = symbols[0].startswith("-")
 
         if exclude:

pymatgen/io/cif.py

@@ -18,7 +18,6 @@
 import numpy as np
 from monty.io import zopen
 from monty.serialization import loadfn
-from monty.string import remove_non_ascii
 
 from pymatgen.core.composition import Composition
 from pymatgen.core.lattice import Lattice
@@ -137,7 +136,7 @@ def _process_string(cls, string):
         # remove empty lines
         string = re.sub(r"^\s*\n", "", string, flags=re.MULTILINE)
         # remove non_ascii
-        string = remove_non_ascii(string)
+        string = string.encode("ascii", "ignore").decode("ascii")
         # since line breaks in .cif files are mostly meaningless,
         # break up into a stream of tokens to parse, rejoining multiline
         # strings (between semicolons)

pymatgen/io/vasp/sets.py

@@ -974,7 +974,7 @@ def __init__(
 
         updates: dict[str, float] = {}
         # select the KSPACING and smearing parameters based on the bandgap
-        if self.bandgap < 1e-4:
+        if self.bandgap < bandgap_tol:
             updates.update(KSPACING=0.22, SIGMA=0.2, ISMEAR=2)
         else:
             rmin = max(1.5, 25.22 - 2.87 * bandgap)  # Eq. 25

pymatgen/util/provenance.py

@@ -10,7 +10,6 @@
 from io import StringIO
 
 from monty.json import MontyDecoder, MontyEncoder
-from monty.string import remove_non_ascii
 
 try:
     from pybtex import errors
@@ -29,10 +28,10 @@
 __credits__ = "Dan Gunter"
 
 
-MAX_HNODE_SIZE = 64000  # maximum size (bytes) of SNL HistoryNode
-MAX_DATA_SIZE = 256000  # maximum size (bytes) of SNL data field
+MAX_HNODE_SIZE = 64_000  # maximum size (bytes) of SNL HistoryNode
+MAX_DATA_SIZE = 256_000  # maximum size (bytes) of SNL data field
 MAX_HNODES = 100  # maximum number of HistoryNodes in SNL file
-MAX_BIBTEX_CHARS = 20000  # maximum number of characters for BibTeX reference
+MAX_BIBTEX_CHARS = 20_000  # maximum number of characters for BibTeX reference
 
 
 def is_valid_bibtex(reference: str) -> bool:
@@ -46,7 +45,7 @@ def is_valid_bibtex(reference: str) -> bool:
     """
     # str is necessary since pybtex seems to have an issue with unicode. The
     # filter expression removes all non-ASCII characters.
-    sio = StringIO(remove_non_ascii(reference))
+    sio = StringIO(reference.encode("ascii", "ignore").decode("ascii"))
     parser = bibtex.Parser()
     errors.set_strict_mode(enable=False)
     bib_data = parser.parse_stream(sio)

tests/core/test_periodic_table.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import math
-import os
 import pickle
 import unittest
 from copy import deepcopy
@@ -405,13 +404,12 @@ def test_pickle(self):
         cs = Species("Cs1+")
         cl = Species("Cl1+")
 
-        with open("cscl.pickle", "wb") as file:
+        with open(f"{self.tmp_path}/cscl.pickle", "wb") as file:
             pickle.dump((cs, cl), file)
 
-        with open("cscl.pickle", "rb") as file:
+        with open(f"{self.tmp_path}/cscl.pickle", "rb") as file:
             tup = pickle.load(file)
             assert tup == (cs, cl)
-        os.remove("cscl.pickle")
 
     def test_get_crystal_field_spin(self):
         assert Species("Fe", 2).get_crystal_field_spin() == 4

tests/core/test_structure.py

@@ -2085,9 +2085,8 @@ def test_to_from_file_string(self):
             assert m == self.mol
             assert isinstance(m, Molecule)
 
-        self.mol.to(filename="CH4_testing.xyz")
-        assert os.path.isfile("CH4_testing.xyz")
-        os.remove("CH4_testing.xyz")
+        self.mol.to(filename=f"{self.tmp_path}/CH4_testing.xyz")
+        assert os.path.isfile(f"{self.tmp_path}/CH4_testing.xyz")
 
     def test_extract_cluster(self):
         species = self.mol.species * 2

tests/core/test_trajectory.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import copy
-import os
 
 import numpy as np
 from numpy.testing import assert_allclose
@@ -448,12 +447,11 @@ def test_variable_lattice(self):
         assert all(np.allclose(struct.lattice.matrix, structures[i].lattice.matrix) for i, struct in enumerate(traj))
 
         # Check if the file is written correctly when lattice is not constant.
-        traj.write_Xdatcar(filename="traj_test_XDATCAR")
+        traj.write_Xdatcar(filename=f"{self.tmp_path}/traj_test_XDATCAR")
 
-        # Load trajectory from written xdatcar and compare to original
-        written_traj = Trajectory.from_file("traj_test_XDATCAR", constant_lattice=False)
+        # Load trajectory from written XDATCAR and compare to original
+        written_traj = Trajectory.from_file(f"{self.tmp_path}/traj_test_XDATCAR", constant_lattice=False)
         self._check_traj_equality(traj, written_traj)
-        os.remove("traj_test_XDATCAR")
 
     def test_as_from_dict(self):
         d = self.traj.as_dict()
@@ -465,9 +463,8 @@ def test_as_from_dict(self):
         assert isinstance(traj, Trajectory)
 
     def test_xdatcar_write(self):
-        self.traj.write_Xdatcar(filename="traj_test_XDATCAR")
+        self.traj.write_Xdatcar(filename=f"{self.tmp_path}/traj_test_XDATCAR")
 
-        # Load trajectory from written xdatcar and compare to original
-        written_traj = Trajectory.from_file("traj_test_XDATCAR")
+        # Load trajectory from written XDATCAR and compare to original
+        written_traj = Trajectory.from_file(f"{self.tmp_path}/traj_test_XDATCAR")
         self._check_traj_equality(self.traj, written_traj)
-        os.remove("traj_test_XDATCAR")