enable ruff PLR0402 PLR1714 PLR5501 in pyproject.toml and auto-fix

pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -241,17 +241,16 @@ def __init__(
                 if links_data is None:
                     edge_data = None
 
+                elif (env_node1, env_node2, key) in links_data:
+                    edge_data = links_data[(env_node1, env_node2, key)]
+                elif (env_node2, env_node1, key) in links_data:
+                    edge_data = links_data[(env_node2, env_node1, key)]
+                elif (env_node1, env_node2) in links_data:
+                    edge_data = links_data[(env_node1, env_node2)]
+                elif (env_node2, env_node1) in links_data:
+                    edge_data = links_data[(env_node2, env_node1)]
                 else:
-                    if (env_node1, env_node2, key) in links_data:
-                        edge_data = links_data[(env_node1, env_node2, key)]
-                    elif (env_node2, env_node1, key) in links_data:
-                        edge_data = links_data[(env_node2, env_node1, key)]
-                    elif (env_node1, env_node2) in links_data:
-                        edge_data = links_data[(env_node1, env_node2)]
-                    elif (env_node2, env_node1) in links_data:
-                        edge_data = links_data[(env_node2, env_node1)]
-                    else:
-                        edge_data = None
+                    edge_data = None
 
                 if edge_data:
                     self._connected_subgraph.add_edge(env_node1, env_node2, key, **edge_data)

pymatgen/electronic_structure/cohp.py

@@ -772,57 +772,52 @@ def from_file(
                     # LMTO COHPs have 5 significant figures
                     avg_data[i].update({spin: np.array([round_to_sigfigs(a, 5) for a in avg], dtype=float)})
             avg_cohp = Cohp(efermi, energies, avg_data["COHP"], icohp=avg_data["ICOHP"])
+        elif not are_multi_center_cobis:
+            avg_cohp = Cohp(
+                efermi,
+                energies,
+                cohp_data["average"]["COHP"],
+                icohp=cohp_data["average"]["ICOHP"],
+                are_coops=are_coops,
+                are_cobis=are_cobis,
+                are_multi_center_cobis=are_multi_center_cobis,
+            )
+            del cohp_data["average"]
         else:
-            if not are_multi_center_cobis:
-                avg_cohp = Cohp(
-                    efermi,
-                    energies,
-                    cohp_data["average"]["COHP"],
-                    icohp=cohp_data["average"]["ICOHP"],
-                    are_coops=are_coops,
-                    are_cobis=are_cobis,
-                    are_multi_center_cobis=are_multi_center_cobis,
-                )
-                del cohp_data["average"]
-            else:
-                # only include two-center cobis in average
-                # do this for both spin channels
-                cohp = {}
-                cohp[Spin.up] = np.array(
-                    [np.array(c["COHP"][Spin.up]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
+            # only include two-center cobis in average
+            # do this for both spin channels
+            cohp = {}
+            cohp[Spin.up] = np.array(
+                [np.array(c["COHP"][Spin.up]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
+            ).mean(axis=0)
+            try:
+                cohp[Spin.down] = np.array(
+                    [np.array(c["COHP"][Spin.down]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
+                ).mean(axis=0)
+            except KeyError:
+                pass
+            try:
+                icohp = {}
+                icohp[Spin.up] = np.array(
+                    [np.array(c["ICOHP"][Spin.up]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
                 ).mean(axis=0)
                 try:
-                    cohp[Spin.down] = np.array(
-                        [np.array(c["COHP"][Spin.down]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
+                    icohp[Spin.down] = np.array(
+                        [np.array(c["ICOHP"][Spin.down]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
                     ).mean(axis=0)
                 except KeyError:
                     pass
-                try:
-                    icohp = {}
-                    icohp[Spin.up] = np.array(
-                        [np.array(c["ICOHP"][Spin.up]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
-                    ).mean(axis=0)
-                    try:
-                        icohp[Spin.down] = np.array(
-                            [
-                                np.array(c["ICOHP"][Spin.down])
-                                for c in cohp_file.cohp_data.values()
-                                if len(c["sites"]) <= 2
-                            ]
-                        ).mean(axis=0)
-                    except KeyError:
-                        pass
-                except KeyError:
-                    icohp = None
-                avg_cohp = Cohp(
-                    efermi,
-                    energies,
-                    cohp,
-                    icohp=icohp,
-                    are_coops=are_coops,
-                    are_cobis=are_cobis,
-                    are_multi_center_cobis=are_multi_center_cobis,
-                )
+            except KeyError:
+                icohp = None
+            avg_cohp = Cohp(
+                efermi,
+                energies,
+                cohp,
+                icohp=icohp,
+                are_coops=are_coops,
+                are_cobis=are_cobis,
+                are_multi_center_cobis=are_multi_center_cobis,
+            )
 
         cohp_dict = {
             key: Cohp(

pymatgen/io/aims/sets/bs.py

@@ -45,9 +45,8 @@ def prepare_band_input(structure: Structure, density: float = 20):
                 current_segment["length"] += 1
                 lines_and_labels.append(current_segment)
                 current_segment = None
-        else:
-            if current_segment is not None:
-                current_segment["length"] += 1
+        elif current_segment is not None:
+            current_segment["length"] += 1
 
     bands = []
     for segment in lines_and_labels:

pymatgen/io/vasp/outputs.py

@@ -355,7 +355,7 @@ def _parse(self, stream, parse_dos, parse_eigen, parse_projected_eigen):
                     # The start event tells us when we have entered blocks
                     if tag == "calculation":
                         parsed_header = True
-                    elif tag == "eigenvalues_kpoints_opt" or tag == "projected_kpoints_opt":
+                    elif tag in ("eigenvalues_kpoints_opt", "projected_kpoints_opt"):
                         in_kpoints_opt = True
                 else:  # event == "end":
                     # The end event happens when we have read a block, so have
@@ -411,7 +411,7 @@ def _parse(self, stream, parse_dos, parse_eigen, parse_projected_eigen):
                         self.eigenvalues = self._parse_eigen(elem)
                     elif parse_projected_eigen and tag == "projected" and not in_kpoints_opt:
                         self.projected_eigenvalues, self.projected_magnetisation = self._parse_projected_eigen(elem)
-                    elif tag == "eigenvalues_kpoints_opt" or tag == "projected_kpoints_opt":
+                    elif tag in ("eigenvalues_kpoints_opt", "projected_kpoints_opt"):
                         in_kpoints_opt = False
                         if self.kpoints_opt_props is None:
                             self.kpoints_opt_props = KpointOptProps()
@@ -1615,54 +1615,53 @@ def __init__(
                         or (tag == "dos" and elem.attrib.get("comment") == "kpoints_opt")
                     ):
                         in_kpoints_opt = True
-                else:  # if event == "end":
-                    if not parsed_header:
-                        if tag == "generator":
-                            self.generator = self._parse_params(elem)
-                        elif tag == "incar":
-                            self.incar = self._parse_params(elem)
-                        elif tag == "kpoints":
-                            self.kpoints, self.actual_kpoints, self.actual_kpoints_weights = self._parse_kpoints(elem)
-                        elif tag == "parameters":
-                            self.parameters = self._parse_params(elem)
-                        elif tag == "atominfo":
-                            self.atomic_symbols, self.potcar_symbols = self._parse_atominfo(elem)
-                            self.potcar_spec = [
-                                {"titel": p, "hash": None, "summary_stats": {}} for p in self.potcar_symbols
-                            ]
-                            parsed_header = True
-                    elif tag == "i" and elem.attrib.get("name") == "efermi":
-                        if in_kpoints_opt:
-                            if self.kpoints_opt_props is None:
-                                self.kpoints_opt_props = KpointOptProps()
-                            self.kpoints_opt_props.efermi = float(elem.text)
-                            in_kpoints_opt = False
-                        else:
-                            self.efermi = float(elem.text)
-                    elif tag == "eigenvalues" and not in_kpoints_opt:
-                        self.eigenvalues = self._parse_eigen(elem)
-                    elif parse_projected_eigen and tag == "projected" and not in_kpoints_opt:
-                        self.projected_eigenvalues, self.projected_magnetisation = self._parse_projected_eigen(elem)
-                    elif tag == "eigenvalues_kpoints_opt" or tag == "projected_kpoints_opt":
+                elif not parsed_header:
+                    if tag == "generator":
+                        self.generator = self._parse_params(elem)
+                    elif tag == "incar":
+                        self.incar = self._parse_params(elem)
+                    elif tag == "kpoints":
+                        self.kpoints, self.actual_kpoints, self.actual_kpoints_weights = self._parse_kpoints(elem)
+                    elif tag == "parameters":
+                        self.parameters = self._parse_params(elem)
+                    elif tag == "atominfo":
+                        self.atomic_symbols, self.potcar_symbols = self._parse_atominfo(elem)
+                        self.potcar_spec = [
+                            {"titel": p, "hash": None, "summary_stats": {}} for p in self.potcar_symbols
+                        ]
+                        parsed_header = True
+                elif tag == "i" and elem.attrib.get("name") == "efermi":
+                    if in_kpoints_opt:
                         if self.kpoints_opt_props is None:
                             self.kpoints_opt_props = KpointOptProps()
+                        self.kpoints_opt_props.efermi = float(elem.text)
                         in_kpoints_opt = False
-                        # projected_kpoints_opt includes occupation information whereas
-                        # eigenvalues_kpoints_opt doesn't.
-                        self.kpoints_opt_props.eigenvalues = self._parse_eigen(elem.find("eigenvalues"))
-                        if tag == "eigenvalues_kpoints_opt":
-                            (
-                                self.kpoints_opt_props.kpoints,
-                                self.kpoints_opt_props.actual_kpoints,
-                                self.kpoints_opt_props.actual_kpoints_weights,
-                            ) = self._parse_kpoints(elem.find("kpoints"))
-                        elif parse_projected_eigen:  # and tag == "projected_kpoints_opt": (implied)
-                            (
-                                self.kpoints_opt_props.projected_eigenvalues,
-                                self.kpoints_opt_props.projected_magnetisation,
-                            ) = self._parse_projected_eigen(elem)
-                    elif tag == "structure" and elem.attrib.get("name") == "finalpos":
-                        self.final_structure = self._parse_structure(elem)
+                    else:
+                        self.efermi = float(elem.text)
+                elif tag == "eigenvalues" and not in_kpoints_opt:
+                    self.eigenvalues = self._parse_eigen(elem)
+                elif parse_projected_eigen and tag == "projected" and not in_kpoints_opt:
+                    self.projected_eigenvalues, self.projected_magnetisation = self._parse_projected_eigen(elem)
+                elif tag in ("eigenvalues_kpoints_opt", "projected_kpoints_opt"):
+                    if self.kpoints_opt_props is None:
+                        self.kpoints_opt_props = KpointOptProps()
+                    in_kpoints_opt = False
+                    # projected_kpoints_opt includes occupation information whereas
+                    # eigenvalues_kpoints_opt doesn't.
+                    self.kpoints_opt_props.eigenvalues = self._parse_eigen(elem.find("eigenvalues"))
+                    if tag == "eigenvalues_kpoints_opt":
+                        (
+                            self.kpoints_opt_props.kpoints,
+                            self.kpoints_opt_props.actual_kpoints,
+                            self.kpoints_opt_props.actual_kpoints_weights,
+                        ) = self._parse_kpoints(elem.find("kpoints"))
+                    elif parse_projected_eigen:  # and tag == "projected_kpoints_opt": (implied)
+                        (
+                            self.kpoints_opt_props.projected_eigenvalues,
+                            self.kpoints_opt_props.projected_magnetisation,
+                        ) = self._parse_projected_eigen(elem)
+                elif tag == "structure" and elem.attrib.get("name") == "finalpos":
+                    self.final_structure = self._parse_structure(elem)
         self.vasp_version = self.generator["version"]
         if parse_potcar_file:
             self.update_potcar_spec(parse_potcar_file)

pymatgen/io/vasp/sets.py

@@ -1114,11 +1114,10 @@ def calculate_ng(
 
         if custom_encut is not None:
             encut = custom_encut
+        elif self.incar.get("ENCUT", 0) > 0:
+            encut = self.incar["ENCUT"]  # get the ENCUT val
         else:
-            if self.incar.get("ENCUT", 0) > 0:
-                encut = self.incar["ENCUT"]  # get the ENCUT val
-            else:
-                encut = max(i_species.enmax for i_species in self.get_vasp_input()["POTCAR"])
+            encut = max(i_species.enmax for i_species in self.get_vasp_input()["POTCAR"])
 
         # PREC=Normal is VASP default
         PREC = self.incar.get("PREC", "Normal") if custom_prec is None else custom_prec

pymatgen/phonon/plotter.py

@@ -205,15 +205,14 @@ def get_plot(
             ax.set_xlim(xlim)
         if ylim:
             ax.set_ylim(ylim)
+        elif invert_axes:
+            _ylim = ax.get_ylim()
+            relevant_x = [p[1] for p in all_pts if _ylim[0] < p[0] < _ylim[1]] or ax.get_xlim()
+            ax.set_xlim((min(relevant_x), max(relevant_x)))
         else:
-            if invert_axes:
-                _ylim = ax.get_ylim()
-                relevant_x = [p[1] for p in all_pts if _ylim[0] < p[0] < _ylim[1]] or ax.get_xlim()
-                ax.set_xlim((min(relevant_x), max(relevant_x)))
-            else:
-                _xlim = ax.get_xlim()
-                relevant_y = [p[1] for p in all_pts if _xlim[0] < p[0] < _xlim[1]] or ax.get_ylim()
-                ax.set_ylim((min(relevant_y), max(relevant_y)))
+            _xlim = ax.get_xlim()
+            relevant_y = [p[1] for p in all_pts if _xlim[0] < p[0] < _xlim[1]] or ax.get_ylim()
+            ax.set_ylim((min(relevant_y), max(relevant_y)))
 
         if invert_axes:
             ax.axhline(0, linewidth=2, color="black", linestyle="--")

pymatgen/vis/structure_vtk.py

@@ -988,7 +988,7 @@ def apply_tags(self):
         tags = {}
         for tag in self.tags:
             istruct = tag.get("istruct", "all")
-            if istruct != "all" and istruct != self.istruct:
+            if istruct not in ("all", self.istruct):
                 continue
             site_index = tag["site_index"]
             color = tag.get("color", [0.5, 0.5, 0.5])

pyproject.toml

@@ -23,35 +23,38 @@ repair-wheel-command = "delocate-wheel --require-archs {delocate_archs} -w {dest
 target-version = "py39"
 line-length = 120
 lint.select = [
-  "B",      # flake8-bugbear
-  "C4",     # flake8-comprehensions
-  "D",      # pydocstyle
-  "E",      # pycodestyle error
-  "EXE",    # flake8-executable
-  "F",      # pyflakes
-  "FA",     # flake8-future-annotations
-  "FBT003", # boolean-positional-value-in-call
-  "FLY",    # flynt
-  "I",      # isort
-  "ICN",    # flake8-import-conventions
-  "ISC",    # flake8-implicit-str-concat
-  "PD",     # pandas-vet
-  "PERF",   # perflint
-  "PIE",    # flake8-pie
-  "PL",     # pylint
-  "PT",     # flake8-pytest-style
-  "PYI",    # flakes8-pyi
-  "Q",      # flake8-quotes
-  "RET",    # flake8-return
-  "RSE",    # flake8-raise
-  "RUF",    # Ruff-specific rules
-  "SIM",    # flake8-simplify
-  "SLOT",   # flake8-slots
-  "TCH",    # flake8-type-checking
-  "TID",    # flake8-tidy-imports
-  "UP",     # pyupgrade
-  "W",      # pycodestyle warning
-  "YTT",    # flake8-2020
+  "B",       # flake8-bugbear
+  "C4",      # flake8-comprehensions
+  "D",       # pydocstyle
+  "E",       # pycodestyle error
+  "EXE",     # flake8-executable
+  "F",       # pyflakes
+  "FA",      # flake8-future-annotations
+  "FBT003",  # boolean-positional-value-in-call
+  "FLY",     # flynt
+  "I",       # isort
+  "ICN",     # flake8-import-conventions
+  "ISC",     # flake8-implicit-str-concat
+  "PD",      # pandas-vet
+  "PERF",    # perflint
+  "PIE",     # flake8-pie
+  "PL",      # pylint
+  "PLR0402",
+  "PLR1714",
+  "PLR5501",
+  "PT",      # flake8-pytest-style
+  "PYI",     # flakes8-pyi
+  "Q",       # flake8-quotes
+  "RET",     # flake8-return
+  "RSE",     # flake8-raise
+  "RUF",     # Ruff-specific rules
+  "SIM",     # flake8-simplify
+  "SLOT",    # flake8-slots
+  "TCH",     # flake8-type-checking
+  "TID",     # flake8-tidy-imports
+  "UP",      # pyupgrade
+  "W",       # pycodestyle warning
+  "YTT",     # flake8-2020
 ]
 lint.ignore = [
   "B023",    # Function definition does not bind loop variable

tests/io/vasp/test_outputs.py

@@ -4,10 +4,10 @@
 import json
 import os
 import sys
-import xml.etree.ElementTree as ElementTree
 from io import StringIO
 from pathlib import Path
 from shutil import copyfile, copyfileobj
+from xml.etree import ElementTree
 
 import numpy as np
 import pytest

tests/phonon/test_init.py

@@ -2,9 +2,8 @@
 
 import pymatgen.phonon as ph
 import pymatgen.phonon.bandstructure as bs
-import pymatgen.phonon.dos as dos
 import pymatgen.phonon.gruneisen as gru
-import pymatgen.phonon.plotter as plotter
+from pymatgen.phonon import dos, plotter
 
 
 def test_convenience_imports():