Run pyupgrade and flake8-simplify through ruff (#2851)

* sort [tool.ruff] select array

* add rule class "SIM" to ruff select

* ruff check . --fix

* ignore flake8-simplify rules in pre-commit.ci

* fix Undefined name `densities` in pymatgen/electronic_structure/dos.py:871:76: F821

and pymatgen/electronic_structure/dos.py:1062:76: F821 Undefined name `densities`
pymatgen/electronic_structure/dos.py:1118:76: F821 Undefined name `densities`

* fix some mypy errors

* ignore remaining 5 mypy errors

.github/workflows/lint.yml

@@ -31,7 +31,7 @@ jobs:
       - name: ruff
         run: |
           ruff --version
-          ruff check . --ignore D
+          ruff check . --ignore 'D,SIM'
 
       - name: black
         run: |

.pre-commit-config.yaml

@@ -9,18 +9,7 @@ repos:
     rev: v0.0.247
     hooks:
       - id: ruff
-        args: [--fix, --ignore, D]
-
-  - repo: https://github.com/PyCQA/autoflake
-    rev: v2.0.1
-    hooks:
-      - id: autoflake
-
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
-    hooks:
-      - id: pyupgrade
-        args: [--py38-plus]
+        args: [--fix, --ignore, 'D,SIM']
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
@@ -30,12 +19,6 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        args: [--profile, black]
-
   - repo: https://github.com/psf/black
     rev: 23.1.0
     hooks:

dev_scripts/chemenv/test_algos_all_geoms.py

@@ -46,10 +46,7 @@
         symbol_name_mapping = allcg.get_symbol_name_mapping(coordination=coordination)
 
         if perms_def == "standard":
-            if coordination > 6:
-                test = "500"
-            else:
-                test = "all"
+            test = "500" if coordination > 6 else "all"
         elif perms_def == "ndefined":
             test = nperms  # type: ignore[assignment]
         else:

dev_scripts/update_pt_data.py

@@ -182,10 +182,7 @@ def parse_shannon_radii():
             if cn not in radii[el][charge]:
                 radii[el][charge][cn] = {}
 
-        if sheet[f"D{i}"].value is not None:
-            spin = sheet[f"D{i}"].value
-        else:
-            spin = ""
+        spin = sheet[f"D{i}"].value if sheet[f"D{i}"].value is not None else ""
 
         radii[el][charge][cn][spin] = {
             "crystal_radius": float(sheet[f"E{i}"].value),
@@ -300,10 +297,7 @@ def add_ionization_energies():
         if row:
             Z = int(row[0])
             val = re.sub(r"\s", "", row[8].strip("()[]"))
-            if val == "":
-                val = None
-            else:
-                val = float(val)
+            val = None if val == "" else float(val)
             data[Z].append(val)
     print(data)
     print(data[51])

pymatgen/alchemy/filters.py

@@ -161,9 +161,8 @@ def test(self, structure):
                 nn = structure.get_neighbors(site, max_r)
                 for sp in sp_to_test:
                     for nn_site, dist, *_ in nn:
-                        if sp in nn_site.species:
-                            if dist < self.specie_and_min_dist[sp]:
-                                return False
+                        if sp in nn_site.species and dist < self.specie_and_min_dist[sp]:
+                            return False
         return True
 
     def as_dict(self):

pymatgen/alchemy/materials.py

@@ -247,7 +247,7 @@ def was_modified(self) -> bool:
         is in the case of performing a substitution transformation on the
         structure when the specie to replace isn't in the structure.
         """
-        return not self.final_structure == self.structures[-2]
+        return self.final_structure != self.structures[-2]
 
     @property
     def structures(self) -> list[Structure]:

pymatgen/alchemy/tests/test_materials.py

@@ -34,7 +34,7 @@ def setUp(self):
     def test_append_transformation(self):
         t = SubstitutionTransformation({"Fe": "Mn"})
         self.trans.append_transformation(t)
-        assert "NaMnPO4" == self.trans.final_structure.composition.reduced_formula
+        assert self.trans.final_structure.composition.reduced_formula == "NaMnPO4"
         assert len(self.trans.structures) == 3
         coords = []
         coords.append([0, 0, 0])
@@ -59,19 +59,19 @@ def test_append_filter(self):
     def test_get_vasp_input(self):
         SETTINGS["PMG_VASP_PSP_DIR"] = PymatgenTest.TEST_FILES_DIR
         potcar = self.trans.get_vasp_input(MPRelaxSet)["POTCAR"]
-        assert "Na_pv\nFe_pv\nP\nO" == "\n".join(p.symbol for p in potcar)
+        assert "\n".join(p.symbol for p in potcar) == "Na_pv\nFe_pv\nP\nO"
         assert len(self.trans.structures) == 2
 
     def test_final_structure(self):
-        assert "NaFePO4" == self.trans.final_structure.composition.reduced_formula
+        assert self.trans.final_structure.composition.reduced_formula == "NaFePO4"
 
     def test_from_dict(self):
         d = json.load(open(os.path.join(PymatgenTest.TEST_FILES_DIR, "transformations.json")))
         d["other_parameters"] = {"tags": ["test"]}
         ts = TransformedStructure.from_dict(d)
         ts.other_parameters["author"] = "Will"
         ts.append_transformation(SubstitutionTransformation({"Fe": "Mn"}))
-        assert "MnPO4" == ts.final_structure.composition.reduced_formula
+        assert ts.final_structure.composition.reduced_formula == "MnPO4"
         assert ts.other_parameters == {"author": "Will", "tags": ["test"]}
 
     def test_undo_and_redo_last_change(self):
@@ -80,17 +80,17 @@ def test_undo_and_redo_last_change(self):
             SubstitutionTransformation({"Fe": "Mn"}),
         ]
         ts = TransformedStructure(self.structure, trans)
-        assert "NaMnPO4" == ts.final_structure.composition.reduced_formula
+        assert ts.final_structure.composition.reduced_formula == "NaMnPO4"
         ts.undo_last_change()
-        assert "NaFePO4" == ts.final_structure.composition.reduced_formula
+        assert ts.final_structure.composition.reduced_formula == "NaFePO4"
         ts.undo_last_change()
-        assert "LiFePO4" == ts.final_structure.composition.reduced_formula
+        assert ts.final_structure.composition.reduced_formula == "LiFePO4"
         with pytest.raises(IndexError):
             ts.undo_last_change()
         ts.redo_next_change()
-        assert "NaFePO4" == ts.final_structure.composition.reduced_formula
+        assert ts.final_structure.composition.reduced_formula == "NaFePO4"
         ts.redo_next_change()
-        assert "NaMnPO4" == ts.final_structure.composition.reduced_formula
+        assert ts.final_structure.composition.reduced_formula == "NaMnPO4"
         with pytest.raises(IndexError):
             ts.redo_next_change()
         # Make sure that this works with filters.

pymatgen/analysis/bond_dissociation.py

@@ -207,10 +207,9 @@ def fragment_and_process(self, bonds):
                     if frag_pair[1].isomorphic_to(frags[1]):
                         frags_done = True
                         break
-                elif frag_pair[1].isomorphic_to(frags[0]):
-                    if frag_pair[0].isomorphic_to(frags[1]):
-                        frags_done = True
-                        break
+                elif frag_pair[1].isomorphic_to(frags[0]) and frag_pair[0].isomorphic_to(frags[1]):
+                    frags_done = True
+                    break
             if not frags_done:
                 # If we haven't, we save this pair and search for the relevant fragment entries:
                 self.done_frag_pairs += [frags]
@@ -343,20 +342,19 @@ def filter_fragment_entries(self, fragment_entries):
             found_similar_entry = False
             # Check for uniqueness
             for ii, filtered_entry in enumerate(self.filtered_entries):
-                if filtered_entry["formula_pretty"] == entry["formula_pretty"]:
-                    if (
-                        filtered_entry["initial_molgraph"].isomorphic_to(entry["initial_molgraph"])
-                        and filtered_entry["final_molgraph"].isomorphic_to(entry["final_molgraph"])
-                        and filtered_entry["initial_molecule"]["charge"] == entry["initial_molecule"]["charge"]
-                    ):
-                        found_similar_entry = True
-                        # If two entries are found that pass the above similarity check, take the one with the lower
-                        # energy:
-                        if entry["final_energy"] < filtered_entry["final_energy"]:
-                            self.filtered_entries[ii] = entry
-                        # Note that this will essentially choose between singlet and triplet entries assuming both have
-                        # the same structural details
-                        break
+                if filtered_entry["formula_pretty"] == entry["formula_pretty"] and (
+                    filtered_entry["initial_molgraph"].isomorphic_to(entry["initial_molgraph"])
+                    and filtered_entry["final_molgraph"].isomorphic_to(entry["final_molgraph"])
+                    and filtered_entry["initial_molecule"]["charge"] == entry["initial_molecule"]["charge"]
+                ):
+                    found_similar_entry = True
+                    # If two entries are found that pass the above similarity check, take the one with the lower
+                    # energy:
+                    if entry["final_energy"] < filtered_entry["final_energy"]:
+                        self.filtered_entries[ii] = entry
+                    # Note that this will essentially choose between singlet and triplet entries assuming both have
+                    # the same structural details
+                    break
             if not found_similar_entry:
                 self.filtered_entries += [entry]
 

pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -240,10 +240,7 @@ def __init__(
             for edge in links:
                 env_node1 = edge[0]
                 env_node2 = edge[1]
-                if len(edge) == 2:
-                    key = None
-                else:
-                    key = edge[2]
+                key = None if len(edge) == 2 else edge[2]
                 if (not self._connected_subgraph.has_node(env_node1)) or (
                     not self._connected_subgraph.has_node(env_node2)
                 ):
@@ -550,10 +547,7 @@ def show_graph(self, graph=None, save_file=None, drawing_type="internal", pltsho
         """
         import matplotlib.pyplot as plt
 
-        if graph is None:
-            shown_graph = self._connected_subgraph
-        else:
-            shown_graph = graph
+        shown_graph = self._connected_subgraph if graph is None else graph
 
         plt.figure()
         # pos = nx.spring_layout(shown_graph)

pymatgen/analysis/chemenv/connectivity/connectivity_finder.py

@@ -8,9 +8,7 @@
 
 import numpy as np
 
-from pymatgen.analysis.chemenv.connectivity.structure_connectivity import (
-    StructureConnectivity,
-)
+from pymatgen.analysis.chemenv.connectivity.structure_connectivity import StructureConnectivity
 
 __author__ = "David Waroquiers"
 __copyright__ = "Copyright 2012, The Materials Project"
@@ -73,9 +71,6 @@ def setup_parameters(self, multiple_environments_choice):
         """
         Setup of the parameters for the connectivity finder.
         """
-        if multiple_environments_choice is not None:
-            if multiple_environments_choice not in ["TAKE_HIGHEST_FRACTION"]:
-                raise ValueError(
-                    f"Option {multiple_environments_choice!r} for multiple_environments_choice is not allowed"
-                )
+        if multiple_environments_choice is not None and multiple_environments_choice not in ["TAKE_HIGHEST_FRACTION"]:
+            raise ValueError(f"Option {multiple_environments_choice!r} for multiple_environments_choice is not allowed")
         self.multiple_environments_choice = multiple_environments_choice

pymatgen/analysis/chemenv/connectivity/structure_connectivity.py

@@ -123,12 +123,11 @@ def add_bonds(self, isite, site_neighbors_set):
             else:
                 if isite == nb_index_unitcell:
                     for isite1, ineighb1, data1 in existing_edges:
-                        if isite1 == ineighb1:
-                            if np.allclose(data1["delta"], nb_image_cell) or np.allclose(
-                                data1["delta"], -nb_image_cell
-                            ):
-                                exists = True
-                                break
+                        if isite1 == ineighb1 and (
+                            np.allclose(data1["delta"], nb_image_cell) or np.allclose(data1["delta"], -nb_image_cell)
+                        ):
+                            exists = True
+                            break
                 else:
                     for _, ineighb1, data1 in existing_edges:
                         if nb_index_unitcell == ineighb1:

pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py

@@ -2725,10 +2725,7 @@ def get_site_coordination_environments_fractions(
                             dict_fractions["Fraction"] = nb_set_fraction * fraction
                             ce_dict_fractions.append(dict_fractions)
                             ce_maps.append(cn_map)
-        if ordered:
-            indices = np.argsort(ce_fractions)[::-1]
-        else:
-            indices = list(range(len(ce_fractions)))
+        indices = np.argsort(ce_fractions)[::-1] if ordered else list(range(len(ce_fractions)))
 
         fractions_info_list = [
             {

pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py

@@ -858,10 +858,7 @@ def faces(self, sites, permutation=None):
         Returns the list of faces of this coordination geometry. Each face is given as a
         list of its vertices coordinates.
         """
-        if permutation is None:
-            coords = [site.coords for site in sites]
-        else:
-            coords = [sites[ii].coords for ii in permutation]
+        coords = [site.coords for site in sites] if permutation is None else [sites[ii].coords for ii in permutation]
         return [[coords[ii] for ii in f] for f in self._faces]
 
     def edges(self, sites, permutation=None, input="sites"):
@@ -896,10 +893,7 @@ def get_pmeshes(self, sites, permutation=None):
         """
         pmeshes = []
         # _vertices = [site.coords for site in sites]
-        if permutation is None:
-            _vertices = [site.coords for site in sites]
-        else:
-            _vertices = [sites[ii].coords for ii in permutation]
+        _vertices = [site.coords for site in sites] if permutation is None else [sites[ii].coords for ii in permutation]
         _face_centers = []
         number_of_faces = 0
         for face in self._faces:
@@ -1234,36 +1228,30 @@ def is_a_valid_coordination_geometry(
         if mp_symbol is not None:
             try:
                 cg = self.get_geometry_from_mp_symbol(mp_symbol)
-                if IUPAC_symbol is not None:
-                    if IUPAC_symbol != cg.IUPAC_symbol:
-                        return False
-                if IUCr_symbol is not None:
-                    if IUCr_symbol != cg.IUCr_symbol:
-                        return False
-                if cn is not None:
-                    if int(cn) != int(cg.coordination_number):
-                        return False
+                if IUPAC_symbol is not None and IUPAC_symbol != cg.IUPAC_symbol:
+                    return False
+                if IUCr_symbol is not None and IUCr_symbol != cg.IUCr_symbol:
+                    return False
+                if cn is not None and int(cn) != int(cg.coordination_number):
+                    return False
                 return True
             except LookupError:
                 return False
         elif IUPAC_symbol is not None:
             try:
                 cg = self.get_geometry_from_IUPAC_symbol(IUPAC_symbol)
-                if IUCr_symbol is not None:
-                    if IUCr_symbol != cg.IUCr_symbol:
-                        return False
-                if cn is not None:
-                    if cn != cg.coordination_number:
-                        return False
+                if IUCr_symbol is not None and IUCr_symbol != cg.IUCr_symbol:
+                    return False
+                if cn is not None and cn != cg.coordination_number:
+                    return False
                 return True
             except LookupError:
                 return False
         elif IUCr_symbol is not None:
             try:
                 cg = self.get_geometry_from_IUCr_symbol(IUCr_symbol)
-                if cn is not None:
-                    if cn != cg.coordination_number:
-                        return False
+                if cn is not None and cn != cg.coordination_number:
+                    return False
                 return True
             except LookupError:
                 return True
@@ -1319,10 +1307,7 @@ def pretty_print(self, type="implemented_geometries", maxcn=8, additional_info=N
                     for cg in self.get_implemented_geometries(coordination=cn):
                         if additional_info is not None:
                             if "nb_hints" in additional_info:
-                                if cg.neighbors_sets_hints is not None:
-                                    addinfo = " *"
-                                else:
-                                    addinfo = ""
+                                addinfo = " *" if cg.neighbors_sets_hints is not None else ""
                             else:
                                 addinfo = ""
                         else: