Move PymatgenTest.TEST_FILES_DIR attribute into module scope (#3227)

* fix IonEntry doc str + type hints

* move TEST_FILES_DIR attr from PymatgenTest into module scope

* PymatgenTest.TEST_FILES_DIR -> TEST_FILES_DIR

* delete TEST_FILES_DIR conftest fixture

* fix AttributeError: type object 'TestChgcar' has no attribute 'TEST_FILES_DIR'

tests/io/vasp/test_outputs.py:1444

* os.path.join(TEST_FILES_DIR, "...") -> f"{TEST_FILES_DIR}/..."

pymatgen/analysis/pourbaix_diagram.py

@@ -277,7 +277,7 @@ def __init__(self, entry_list, weights=None):
             entry_list ([PourbaixEntry]): List of component PourbaixEntries
             weights ([float]): Weights associated with each entry. Default is None
         """
-        self.weights = [1.0] * len(entry_list) if weights is None else weights
+        self.weights = weights or [1.0] * len(entry_list)
         self.entry_list = entry_list
 
     def __getattr__(self, attr):
@@ -320,16 +320,16 @@ def as_dict(self):
         }
 
     @classmethod
-    def from_dict(cls, d):
+    def from_dict(cls, dct):
         """
         Args:
-            d (): Dict representation.
+            d (dict): Dict representation.
 
         Returns:
             MultiEntry
         """
-        entry_list = [PourbaixEntry.from_dict(e) for e in d.get("entry_list")]
-        return cls(entry_list, d.get("weights"))
+        entry_list = [PourbaixEntry.from_dict(entry) for entry in dct.get("entry_list")]
+        return cls(entry_list, dct.get("weights"))
 
 
 # TODO: this class isn't particularly useful in its current form, could be
@@ -346,13 +346,14 @@ class IonEntry(PDEntry):
         set to some other string for display purposes.
     """
 
-    def __init__(self, ion, energy, name=None, attribute=None):
+    def __init__(self, ion: Ion, energy: float, name: str | None = None, attribute=None):
         """
         Args:
             ion: Ion object
             energy: Energy for composition.
             name: Optional parameter to name the entry. Defaults to the
                 chemical formula.
+            attribute: Optional attribute of the entry, e.g., band gap.
         """
         self.ion = ion
         # Auto-assign name

pymatgen/io/abinit/inputs.py

@@ -85,16 +85,6 @@
     "ird1wf",
 }
 
-# Name of the (default) tolerance used by the runlevels.
-_runl2tolname = {
-    "scf": "tolvrs",
-    "nscf": "tolwfr",
-    "dfpt": "toldfe",  # ?
-    "screening": "toldfe",  # dummy
-    "sigma": "toldfe",  # dummy
-    "bse": "toldfe",  # ?
-    "relax": "tolrff",
-}
 
 # Tolerances for the different levels of accuracy.
 
@@ -155,7 +145,7 @@ class ShiftMode(Enum):
     def from_object(cls, obj):
         """
         Returns an instance of ShiftMode based on the type of object passed. Converts strings to ShiftMode depending
-        on the iniital letter of the string. G for GammaCenterd, M for MonkhorstPack,
+        on the initial letter of the string. G for GammaCentered, M for MonkhorstPack,
         S for Symmetric, O for OneSymmetric.
         Case insensitive.
         """
@@ -166,14 +156,25 @@ def from_object(cls, obj):
         raise TypeError(f"The object provided is not handled: type {type(obj).__name__}")
 
 
-def _stopping_criterion(runlevel, accuracy):
-    """Return the stopping criterion for this runlevel with the given accuracy."""
-    tolname = _runl2tolname[runlevel]
-    return {tolname: getattr(_tolerances[tolname], accuracy)}
+def _stopping_criterion(run_level, accuracy):
+    """Return the stopping criterion for this run_level with the given accuracy."""
+
+    # Name of the (default) tolerance used by the run levels.
+    _run_level_tolname_map = {
+        "scf": "tolvrs",
+        "nscf": "tolwfr",
+        "dfpt": "toldfe",  # ?
+        "screening": "toldfe",  # dummy
+        "sigma": "toldfe",  # dummy
+        "bse": "toldfe",  # ?
+        "relax": "tolrff",
+    }
+    tol_name = _run_level_tolname_map[run_level]
+    return {tol_name: getattr(_tolerances[tol_name], accuracy)}
 
 
 def _find_ecut_pawecutdg(ecut, pawecutdg, pseudos, accuracy):
-    """Return a |AttrDict| with the value of ``ecut`` and ``pawecutdg``."""
+    """Return a |AttrDict| with the value of ecut and pawecutdg."""
     # Get ecut and pawecutdg from the pseudo hints.
     if ecut is None or (pawecutdg is None and any(p.ispaw for p in pseudos)):
         has_hints = all(p.has_hints for p in pseudos)
@@ -194,18 +195,18 @@ def _find_ecut_pawecutdg(ecut, pawecutdg, pseudos, accuracy):
 
 
 def _find_scf_nband(structure, pseudos, electrons, spinat=None):
-    """Find the value of ``nband``."""
+    """Find the value of nband."""
     if electrons.nband is not None:
         return electrons.nband
 
     nsppol, smearing = electrons.nsppol, electrons.smearing
 
     # Number of valence electrons including possible extra charge
-    nval = num_valence_electrons(structure, pseudos)
-    nval -= electrons.charge
+    n_val_elec = num_valence_electrons(structure, pseudos)
+    n_val_elec -= electrons.charge
 
     # First guess (semiconductors)
-    nband = nval // 2
+    nband = n_val_elec // 2
 
     # TODO: Find better algorithm
     # If nband is too small we may kill the job, increase nband and restart
@@ -234,7 +235,7 @@ def _get_shifts(shift_mode, structure):
         centered otherwise.
 
     Note: for some cases (e.g. body centered tetragonal), both the Symmetric and OneSymmetric may fail to satisfy the
-        ``chksymbreak`` condition (Abinit input variable).
+        chksymbreak condition (Abinit input variable).
     """
     if shift_mode == ShiftMode.GammaCentered:
         return ((0, 0, 0),)
@@ -475,7 +476,7 @@ def ion_ioncell_relax_input(
 
 def calc_shiftk(structure, symprec: float = 0.01, angle_tolerance=5):
     """
-    Find the values of ``shiftk`` and ``nshiftk`` appropriated for the sampling of the Brillouin zone.
+    Find the values of shiftk and nshiftk appropriated for the sampling of the Brillouin zone.
 
     When the primitive vectors of the lattice do NOT form a FCC or a BCC lattice,
     the usual (shifted) Monkhorst-Pack grids are formed by using nshiftk=1 and shiftk 0.5 0.5 0.5 .
@@ -611,7 +612,7 @@ def __str__(self):
         return self.to_str()
 
     def write(self, filepath="run.abi"):
-        """Write the input file to file to ``filepath``."""
+        """Write the input file to file to filepath."""
         dirname = os.path.dirname(os.path.abspath(filepath))
         if not os.path.exists(dirname):
             os.makedirs(dirname)
@@ -699,7 +700,7 @@ def to_str(self):
 
 
 class BasicAbinitInputError(Exception):
-    """Base error class for exceptions raised by ``BasicAbinitInput``."""
+    """Base error class for exceptions raised by BasicAbinitInput."""
 
 
 class BasicAbinitInput(AbstractInput, MSONable):
@@ -790,7 +791,7 @@ def from_dict(cls, d):
 
     def add_abiobjects(self, *abi_objects):
         """
-        This function receive a list of ``AbiVarable`` objects and add
+        This function receive a list of AbiVarable objects and add
         the corresponding variables to the input.
         """
         dct = {}
@@ -1010,7 +1011,7 @@ class BasicMultiDataset:
     that provides an easy-to-use interface to apply global changes to the
     the inputs stored in the objects.
 
-    Let's assume for example that multi contains two ``BasicAbinitInput`` objects and we
+    Let's assume for example that multi contains two BasicAbinitInput objects and we
     want to set `ecut` to 1 in both dictionaries. The direct approach would be:
 
         for inp in multi:
@@ -1204,7 +1205,7 @@ def extend(self, abinit_inputs):
         self._inputs.extend(abinit_inputs)
 
     def addnew_from(self, dtindex):
-        """Add a new entry in the multidataset by copying the input with index ``dtindex``."""
+        """Add a new entry in the multidataset by copying the input with index dtindex."""
         self.append(self[dtindex].deepcopy())
 
     def split_datasets(self):
@@ -1301,7 +1302,7 @@ def has_same_variable(kref, vref, other_inp):
 
     def write(self, filepath="run.abi"):
         """
-        Write ``ndset`` input files to disk. The name of the file
+        Write ndset input files to disk. The name of the file
         is constructed from the dataset index e.g. run0.abi.
         """
         root, ext = os.path.splitext(filepath)

pymatgen/io/vasp/inputs.py

@@ -1084,7 +1084,7 @@ def __init__(
         The default behavior of the constructor is for a Gamma centered,
         1x1x1 KPOINTS with no shift.
         """
-        if num_kpts > 0 and (not labels) and (not kpts_weights):
+        if num_kpts > 0 and not labels and not kpts_weights:
             raise ValueError("For explicit or line-mode kpoints, either the labels or kpts_weights must be specified.")
 
         self.comment = comment
@@ -1100,10 +1100,9 @@ def __init__(
         self.tet_connections = tet_connections
 
     @property
-    def style(self):
+    def style(self) -> KpointsSupportedModes:
         """
-        :return: Style for kpoint generation. One of Kpoints_supported_modes
-            enum.
+        Style for kpoint generation. One of Kpoints_supported_modes enum.
         """
         return self._style
 
@@ -1119,11 +1118,7 @@ def style(self, style):
 
         if (
             style
-            in (
-                Kpoints.supported_modes.Automatic,
-                Kpoints.supported_modes.Gamma,
-                Kpoints.supported_modes.Monkhorst,
-            )
+            in (Kpoints.supported_modes.Automatic, Kpoints.supported_modes.Gamma, Kpoints.supported_modes.Monkhorst)
             and len(self.kpts) > 1
         ):
             raise ValueError(
@@ -1150,10 +1145,7 @@ def automatic(subdivisions):
             Kpoints object
         """
         return Kpoints(
-            "Fully automatic kpoint scheme",
-            0,
-            style=Kpoints.supported_modes.Automatic,
-            kpts=[[subdivisions]],
+            "Fully automatic kpoint scheme", 0, style=Kpoints.supported_modes.Automatic, kpts=[[subdivisions]]
         )
 
     @staticmethod
@@ -1170,13 +1162,7 @@ def gamma_automatic(kpts: tuple[int, int, int] = (1, 1, 1), shift: Vector3D = (0
         Returns:
             Kpoints object
         """
-        return Kpoints(
-            "Automatic kpoint scheme",
-            0,
-            Kpoints.supported_modes.Gamma,
-            kpts=[kpts],
-            kpts_shift=shift,
-        )
+        return Kpoints("Automatic kpoint scheme", 0, Kpoints.supported_modes.Gamma, kpts=[kpts], kpts_shift=shift)
 
     @staticmethod
     def monkhorst_automatic(kpts: tuple[int, int, int] = (2, 2, 2), shift: Vector3D = (0, 0, 0)):
@@ -1192,13 +1178,7 @@ def monkhorst_automatic(kpts: tuple[int, int, int] = (2, 2, 2), shift: Vector3D
         Returns:
             Kpoints object
         """
-        return Kpoints(
-            "Automatic kpoint scheme",
-            0,
-            Kpoints.supported_modes.Monkhorst,
-            kpts=[kpts],
-            kpts_shift=shift,
-        )
+        return Kpoints("Automatic kpoint scheme", 0, Kpoints.supported_modes.Monkhorst, kpts=[kpts], kpts_shift=shift)
 
     @staticmethod
     def automatic_density(structure: Structure, kppa: float, force_gamma: bool = False):
@@ -1864,11 +1844,13 @@ def electron_configuration(self):
 
     def write_file(self, filename: str) -> None:
         """
-        Writes PotcarSingle to a file.
-        :param filename: Filename.
+        Write PotcarSingle to a file.
+
+        Args:
+            filename (str): Filename to write to.
         """
-        with zopen(filename, "wt") as f:
-            f.write(str(self))
+        with zopen(filename, "wt") as file:
+            file.write(str(self))
 
     @staticmethod
     def from_file(filename: str) -> PotcarSingle:

pymatgen/util/testing.py

@@ -22,14 +22,16 @@
 
 from pymatgen.core import SETTINGS, Structure
 
+MODULE_DIR = Path(__file__).absolute().parent
+
+TEST_FILES_DIR = Path(SETTINGS.get("PMG_TEST_FILES_DIR", MODULE_DIR / ".." / ".." / "tests" / "files"))
+
 
 class PymatgenTest(unittest.TestCase):
     """Extends unittest.TestCase with several assert methods for array and str comparison."""
 
     _multiprocess_shared_ = True
-    MODULE_DIR = Path(__file__).absolute().parent
     STRUCTURES_DIR = MODULE_DIR / "structures"
-    TEST_FILES_DIR = Path(SETTINGS.get("PMG_TEST_FILES_DIR", MODULE_DIR / ".." / ".." / "tests" / "files"))
 
     TEST_STRUCTURES: ClassVar[dict[str, Structure]] = {}  # Dict for test structures to aid testing.
 

pyproject.toml

@@ -98,24 +98,24 @@ omit = [
   "pymatgen/cli/pmg_plot.py",
   "pymatgen/cli/pmg_potcar.py",
   "pymatgen/cli/pmg_query.py",
-  "pymatgen/dao.py"
+  "pymatgen/dao.py",
 ]
 
 [tool.coverage.report]
 exclude_also = [
   "@deprecated",
+  "@np.deprecate",
   "def __repr__",
   "if 0:",
+  "if TYPE_CHECKING:",
   "if __name__ == .__main__.:",
   "if self.debug:",
   "if settings.DEBUG",
+  "if typing.TYPE_CHECKING:",
   "pragma: no cover",
   "raise AssertionError",
   "raise NotImplementedError",
   "show_plot",
-  "if TYPE_CHECKING:",
-  "if typing.TYPE_CHECKING:",
-  "@np.deprecate"
 ]
 
 [tool.mypy]

tests/alchemy/test_filters.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import json
-import os
 import unittest
 
 from monty.json import MontyDecoder
@@ -17,7 +16,7 @@
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.periodic_table import Species
 from pymatgen.core.structure import Structure
-from pymatgen.util.testing import PymatgenTest
+from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 
 
 class TestContainsSpecieFilter(PymatgenTest):
@@ -75,7 +74,7 @@ def test_to_from_dict(self):
 
 class TestRemoveDuplicatesFilter(unittest.TestCase):
     def setUp(self):
-        with open(os.path.join(PymatgenTest.TEST_FILES_DIR, "TiO2_entries.json")) as file:
+        with open(f"{TEST_FILES_DIR}/TiO2_entries.json") as file:
             entries = json.load(file, cls=MontyDecoder)
         self._struct_list = [e.structure for e in entries]
         self._sm = StructureMatcher()
@@ -94,7 +93,7 @@ def test_to_from_dict(self):
 
 class TestRemoveExistingFilter(unittest.TestCase):
     def setUp(self):
-        with open(os.path.join(PymatgenTest.TEST_FILES_DIR, "TiO2_entries.json")) as fp:
+        with open(f"{TEST_FILES_DIR}/TiO2_entries.json") as fp:
             entries = json.load(fp, cls=MontyDecoder)
         self._struct_list = [e.structure for e in entries]
         self._sm = StructureMatcher()