Pre-commit fixes

CONTRIBUTING.md

@@ -4,7 +4,7 @@ This is a quick guide on how to follow best practice and contribute smoothly to
 
 ## Workflow
 
-We follow the [GitHub flow](<https://docs.github.com/en/get-started/using-github/github-flow>), using
+We follow the [GitHub flow](https://docs.github.com/en/get-started/using-github/github-flow), using
 branches for new work and pull requests for verifying the work.
 
 The steps for a new piece of work can be summarised as follows:

docs/smact.utils.rst

@@ -1,7 +1,7 @@
 SMACT Utilities module
 ===========================
 
-The utilities module provides some utilty functions to support the core functionalities of SMACT
+The utilities module provides some utility functions to support the core functionalities of SMACT
 
 Submodules
 ----------

pyproject.toml

@@ -269,5 +269,6 @@ ignore-words-list = [
             "Cm",
             "Bk",
             "eles",
-            "assertIn"
+            "assertIn",
+            "Mater",
         ]

setup.py

@@ -7,7 +7,7 @@
 __author__ = "The SMACT Developers"
 __author_email__ = "a.walsh@imperial.ac.uk"
 __copyright__ = "Copyright Daniel W. Davies, Adam J. Jackson, Keith T. Butler (2019)"
-__version__ = "2.6"
+__version__ = "2.7"
 __maintainer__ = "Anthony O. Onwuli"
 __maintainer_email__ = "anthony.onwuli16@imperial.ac.uk"
 __date__ = "August 30 2024"
@@ -33,7 +33,6 @@
         author_email=__author_email__,
         maintainer=__maintainer__,
         maintainer_email=__maintainer_email__,
-        maintainer_email=__maintainer_email__,
         license="MIT",
         packages=[
             "smact",

smact/__init__.py

@@ -160,9 +160,7 @@ def __init__(self, symbol: str, oxi_states_custom_filepath: str | None = None):
             num_valence = None
 
         valence_data = data_loader.lookup_element_valence_data(symbol)
-        num_valence_modified = (
-            valence_data["NValence"] if valence_data else None
-        )
+        num_valence_modified = valence_data["NValence"] if valence_data else None
 
         for attribute, value in (
             ("coord_envs", coord_envs),

smact/data_loader.py

@@ -825,7 +825,6 @@ def lookup_element_magpie_data(symbol: str, copy: bool = True):
 
 
     """
-
     global _element_magpie_data
 
     if _element_magpie_data is None:
@@ -865,10 +864,7 @@ def lookup_element_magpie_data(symbol: str, copy: bool = True):
         return _element_magpie_data[symbol]
     else:
         if _print_warnings:
-            print(
-                "WARNING: Magpie data for element {} not "
-                "found.".format(symbol)
-            )
+            print(f"WARNING: Magpie data for element {symbol} not " "found.")
 
         return None
 
@@ -897,15 +893,12 @@ def lookup_element_valence_data(symbol: str, copy: bool = True):
         Returns None if the element was not found among the external
         data.
     """
-
     global _element_valence_data
 
     if _element_valence_data is None:
         _element_valence_data = {}
 
-        df = pd.read_csv(
-            os.path.join(data_directory, "element_valence_modified.csv")
-        )
+        df = pd.read_csv(os.path.join(data_directory, "element_valence_modified.csv"))
         for _index, row in df.iterrows():
             key = row.iloc[0]
 
@@ -916,9 +909,6 @@ def lookup_element_valence_data(symbol: str, copy: bool = True):
         return _element_valence_data[symbol]
     else:
         if _print_warnings:
-            print(
-                "WARNING: Valence data for element {} not "
-                "found.".format(symbol)
-            )
+            print(f"WARNING: Valence data for element {symbol} not " "found.")
 
         return None

smact/properties.py

@@ -184,9 +184,7 @@ def get_element_valence(element: str) -> int:
         try:
             return smact.Element(element).num_valence_modified
         except NameError:
-            raise ValueError(
-                f"Valence data not found for element: {element}"
-            ) from None
+            raise ValueError(f"Valence data not found for element: {element}") from None
 
     element_stoich = parse_formula(compound)
 
@@ -203,5 +201,4 @@ def get_element_valence(element: str) -> int:
     if total_stoich == 0:
         return 0.0
 
-    vec = total_valence / total_stoich
-    return vec
+    return total_valence / total_stoich

smact/screening.py

@@ -337,13 +337,13 @@ def smact_filter(
     species_unique: bool = True,
     oxidation_states_set: str = "smact14",
     comp_tuple: bool = False,
-) -> Union[List[Tuple[str, int, int]], List[Tuple[str, int]]]:
+) -> list[tuple[str, int, int]] | list[tuple[str, int]]:
     """Function that applies the charge neutrality and electronegativity
     tests in one go for simple application in external scripts that
     wish to apply the general 'smact test'.
 
      .. warning::
-        For backwards compatability in SMACT >=2.7, expllicitly set oxidation_states_set to 'smact14' if you wish to use the 2014 SMACT default oxidation states.
+        For backwards compatibility in SMACT >=2.7, expllicitly set oxidation_states_set to 'smact14' if you wish to use the 2014 SMACT default oxidation states.
         In SMACT 3.0, the smact_filter function will be set to use a new default oxidation states set.
 
     Args:
@@ -354,6 +354,7 @@ def smact_filter(
         species_unique (bool): Whether or not to consider elements in different oxidation states as unique in the results.
         oxidation_states_set (string): A string to choose which set of oxidation states should be chosen. Options are 'smact14', 'icsd', 'pymatgen' and 'wiki' for the  2014 SMACT default, 2016 ICSD, pymatgen structure predictor and Wikipedia (https://en.wikipedia.org/wiki/Template:List_of_oxidation_states_of_the_elements) oxidation states respectively. A filepath to an oxidation states text file can also be supplied as well.
         comp_tuple (bool): Whether or not to return the results as a named tuple of elements and stoichiometries (True) or as a normal tuple of elements and stoichiometries (False).
+
     Returns:
     -------
         allowed_comps (list): Allowed compositions for that chemical system
@@ -436,15 +437,15 @@ def smact_validity(
     composition: pymatgen.core.Composition | str,
     use_pauling_test: bool = True,
     include_alloys: bool = True,
-    oxidation_states_set: Union[str, bytes, os.PathLike] = "smact14",
+    oxidation_states_set: str | bytes | os.PathLike = "smact14",
 ) -> bool:
     """
     Check if a composition is valid according to the SMACT rules.
 
     Composition is considered valid if it passes the charge neutrality test and the Pauling electronegativity test.
 
      .. warning::
-        For backwards compatability in SMACT >=2.7, expllicitly set oxidation_states_set to 'smact14' if you wish to use the 2014 SMACT default oxidation states.
+        For backwards compatibility in SMACT >=2.7, expllicitly set oxidation_states_set to 'smact14' if you wish to use the 2014 SMACT default oxidation states.
         In SMACT 3.0, the smact_filter function will be set to use a new default oxidation states set.
 
     Args:

smact/tests/test_core.py

@@ -4,6 +4,7 @@
 import os
 import unittest
 
+import pytest
 from pymatgen.core import Structure
 from pymatgen.core.periodic_table import Specie
 
@@ -96,10 +97,10 @@ def test_valence_electron_count(self):
         self.assertEqual(valence_electron_count(""), 0.0)
 
         # Test invalid elements and formats
-        with self.assertRaises(ValueError):
+        with pytest.raises(ValueError):
             valence_electron_count("Xx2O3")  # Xx is not a real element
 
-        with self.assertRaises(ValueError):
+        with pytest.raises(ValueError):
             valence_electron_count("LrO")
 
     # ---------------- BUILDER ----------------

smact/tests/test_utils.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import unittest
 
 from pymatgen.core import Composition
@@ -59,9 +61,7 @@ def test_comp_maker(self):
         self.assertEqual(Composition("FeO"), comp2)
         self.assertEqual(Composition({"Fe2+": 1, "O2-": 1}), comp1)
         self.assertEqual(Composition({"Fe2+": 1, "Fe3+": 2, "O2-": 4}), comp3)
-        self.assertEqual(
-            Composition({"Li+": 10, "Ge4+": 1, "P5+": 2, "S2-": 12}), comp4
-        )
+        self.assertEqual(Composition({"Li+": 10, "Ge4+": 1, "P5+": 2, "S2-": 12}), comp4)
 
     def test_formula_maker(self):
         """Test the formula_maker function"""

smact/utils/composition.py

@@ -1,4 +1,5 @@
 """Utility functioms for handling elements, species, formulas and composition"""
+
 from __future__ import annotations
 
 import re
@@ -27,9 +28,7 @@ def parse_formula(formula: str) -> dict[str, float]:
         if m.group(2) != "":
             factor = float(m.group(2))
         unit_sym_dict = _get_sym_dict(m.group(1), factor)
-        expanded_sym = "".join(
-            [f"{el}{amt}" for el, amt in unit_sym_dict.items()]
-        )
+        expanded_sym = "".join([f"{el}{amt}" for el, amt in unit_sym_dict.items()])
         expanded_formula = formula.replace(m.group(), expanded_sym)
         return parse_formula(expanded_formula)
     return _get_sym_dict(formula, 1)
@@ -53,9 +52,7 @@ def _get_sym_dict(formula: str, factor: float) -> dict[str, float]:
     return sym_dict
 
 
-def comp_maker(
-    smact_filter_output: tuple[str, int, int] | tuple[str, int]
-) -> Composition:
+def comp_maker(smact_filter_output: tuple[str, int, int] | tuple[str, int]) -> Composition:
     """Convert an item in the output of smact.screening.smact_filer into a Pymatgen Composition.
 
     Args:
@@ -82,9 +79,7 @@ def comp_maker(
     return Composition(form)
 
 
-def formula_maker(
-    smact_filter_output: tuple[str, int, int] | tuple[str, int]
-) -> str:
+def formula_maker(smact_filter_output: tuple[str, int, int] | tuple[str, int]) -> str:
     """Convert an item in the output of smact.screening.smact_filter into a chemical formula.
 
     Args: