From 9ffae0aeee24bae06ef96c1252275c9585cd5f30 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 6 Jun 2022 19:57:58 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/asottile/pyupgrade: v2.31.0 → v2.32.1](https://github.com/asottile/pyupgrade/compare/v2.31.0...v2.32.1)
- [github.com/pre-commit/pre-commit-hooks: v4.1.0 → v4.2.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.1.0...v4.2.0)
- [github.com/psf/black: 22.1.0 → 22.3.0](https://github.com/psf/black/compare/22.1.0...22.3.0)
- [github.com/pre-commit/mirrors-mypy: v0.930 → v0.960](https://github.com/pre-commit/mirrors-mypy/compare/v0.930...v0.960)
---
 .pre-commit-config.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4a2cd7a6..d885ae77 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -21,13 +21,13 @@ repos:
           - --ignore-init-module-imports
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.31.0
+    rev: v2.32.1
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v4.2.0
     hooks:
       - id: check-yaml
         exclude: pymatgen/analysis/vesta_cutoffs.yaml
@@ -41,7 +41,7 @@ repos:
         args: ["--profile", "black"]
 
   - repo: https://github.com/psf/black
-    rev: 22.1.0
+    rev: 22.3.0
     hooks:
       - id: black
 
@@ -51,6 +51,6 @@ repos:
       - id: flake8
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.930
+    rev: v0.960
     hooks:
       - id: mypy

From 5f38b8ee45119b4a1ee158831b36a4b5667542b4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 6 Jun 2022 19:58:56 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pymatgen/analysis/diffusion/aimd/rdf.py                  | 5 ++---
 pymatgen/analysis/diffusion/aimd/tests/test_pathway.py   | 5 ++++-
 pymatgen/analysis/diffusion/aimd/tests/test_rdf.py       | 1 -
 pymatgen/analysis/diffusion/aimd/tests/test_van_hove.py  | 7 +++++--
 pymatgen/analysis/diffusion/aimd/van_hove.py             | 4 ++--
 pymatgen/analysis/diffusion/analyzer.py                  | 5 ++++-
 pymatgen/analysis/diffusion/neb/full_path_mapper.py      | 5 ++++-
 pymatgen/analysis/diffusion/neb/pathfinder.py            | 5 ++++-
 pymatgen/analysis/diffusion/neb/tests/test_pathfinder.py | 6 +++++-
 pymatgen/analysis/diffusion/tests/test_analyzer.py       | 6 +++++-
 pymatgen/analysis/diffusion/utils/edge_data_from_sc.py   | 9 +++++++--
 pymatgen/analysis/diffusion/utils/supercells.py          | 4 +++-
 .../diffusion/utils/tests/test_edge_data_from_sc.py      | 6 +++++-
 requirements-ci.txt                                      | 2 +-
 requirements.txt                                         | 2 +-
 setup.py                                                 | 4 ++--
 tasks.py                                                 | 6 +++---
 17 files changed, 57 insertions(+), 25 deletions(-)

diff --git a/pymatgen/analysis/diffusion/aimd/rdf.py b/pymatgen/analysis/diffusion/aimd/rdf.py
index d1fd63e7..52791a5b 100644
--- a/pymatgen/analysis/diffusion/aimd/rdf.py
+++ b/pymatgen/analysis/diffusion/aimd/rdf.py
@@ -12,13 +12,12 @@
 
 import numpy as np
 from joblib import Parallel, delayed
+from pymatgen.core import Structure
+from pymatgen.util.plotting import pretty_plot
 from scipy.ndimage import gaussian_filter1d
 from scipy.signal import find_peaks
 from scipy.stats import norm
 
-from pymatgen.core import Structure
-from pymatgen.util.plotting import pretty_plot
-
 
 class RadialDistributionFunction:
     """
diff --git a/pymatgen/analysis/diffusion/aimd/tests/test_pathway.py b/pymatgen/analysis/diffusion/aimd/tests/test_pathway.py
index 48d4794c..5b2767ad 100644
--- a/pymatgen/analysis/diffusion/aimd/tests/test_pathway.py
+++ b/pymatgen/analysis/diffusion/aimd/tests/test_pathway.py
@@ -12,7 +12,10 @@
 from pymatgen.core import Structure
 from pymatgen.io.vasp import Chgcar
 
-from pymatgen.analysis.diffusion.aimd.pathway import ProbabilityDensityAnalysis, SiteOccupancyAnalyzer
+from pymatgen.analysis.diffusion.aimd.pathway import (
+    ProbabilityDensityAnalysis,
+    SiteOccupancyAnalyzer,
+)
 from pymatgen.analysis.diffusion.analyzer import DiffusionAnalyzer
 
 tests_dir = os.path.dirname(os.path.abspath(__file__))
diff --git a/pymatgen/analysis/diffusion/aimd/tests/test_rdf.py b/pymatgen/analysis/diffusion/aimd/tests/test_rdf.py
index 86b561ed..30203534 100644
--- a/pymatgen/analysis/diffusion/aimd/tests/test_rdf.py
+++ b/pymatgen/analysis/diffusion/aimd/tests/test_rdf.py
@@ -20,7 +20,6 @@ def test_rdf(self):
             structure_list.append(s)
             if i == 9:
                 break
-        species = ["Na", "P", "S"]
 
         # Test from_species
         obj = RadialDistributionFunctionFast(structures=structure_list, ngrid=101, rmax=10.0, sigma=0.1)
diff --git a/pymatgen/analysis/diffusion/aimd/tests/test_van_hove.py b/pymatgen/analysis/diffusion/aimd/tests/test_van_hove.py
index 1e336275..1e0bf1d8 100644
--- a/pymatgen/analysis/diffusion/aimd/tests/test_van_hove.py
+++ b/pymatgen/analysis/diffusion/aimd/tests/test_van_hove.py
@@ -14,8 +14,11 @@
 import numpy as np
 from monty.serialization import loadfn
 
-from pymatgen.analysis.diffusion.aimd.van_hove import EvolutionAnalyzer, RadialDistributionFunction, VanHoveAnalysis
-from pymatgen.analysis.diffusion.analyzer import DiffusionAnalyzer
+from pymatgen.analysis.diffusion.aimd.van_hove import (
+    EvolutionAnalyzer,
+    RadialDistributionFunction,
+    VanHoveAnalysis,
+)
 
 matplotlib.use("pdf")
 tests_dir = os.path.dirname(os.path.abspath(__file__))
diff --git a/pymatgen/analysis/diffusion/aimd/van_hove.py b/pymatgen/analysis/diffusion/aimd/van_hove.py
index 7a6071af..61f99de4 100644
--- a/pymatgen/analysis/diffusion/aimd/van_hove.py
+++ b/pymatgen/analysis/diffusion/aimd/van_hove.py
@@ -12,11 +12,11 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pds
-from scipy.stats import norm
-
 from pymatgen.core import Structure
 from pymatgen.util.plotting import pretty_plot
 from pymatgen.util.typing import ArrayLike
+from scipy.stats import norm
+
 from pymatgen.analysis.diffusion.analyzer import DiffusionAnalyzer
 
 from .rdf import RadialDistributionFunction
diff --git a/pymatgen/analysis/diffusion/analyzer.py b/pymatgen/analysis/diffusion/analyzer.py
index 74ec7562..16956b47 100644
--- a/pymatgen/analysis/diffusion/analyzer.py
+++ b/pymatgen/analysis/diffusion/analyzer.py
@@ -24,7 +24,10 @@
 import numpy as np
 import scipy.constants as const
 from monty.json import MSONable
-from pymatgen.analysis.structure_matcher import OrderDisorderElementComparator, StructureMatcher
+from pymatgen.analysis.structure_matcher import (
+    OrderDisorderElementComparator,
+    StructureMatcher,
+)
 from pymatgen.core.periodic_table import get_el_sp
 from pymatgen.core.structure import Structure
 from pymatgen.io.vasp.outputs import Vasprun
diff --git a/pymatgen/analysis/diffusion/neb/full_path_mapper.py b/pymatgen/analysis/diffusion/neb/full_path_mapper.py
index 1d3fbc6d..e1bfa13f 100644
--- a/pymatgen/analysis/diffusion/neb/full_path_mapper.py
+++ b/pymatgen/analysis/diffusion/neb/full_path_mapper.py
@@ -29,7 +29,10 @@
 from pymatgen.symmetry.structure import SymmetrizedStructure
 
 from pymatgen.analysis.diffusion.neb.pathfinder import MigrationHop
-from pymatgen.analysis.diffusion.neb.periodic_dijkstra import get_optimal_pathway_rev, periodic_dijkstra
+from pymatgen.analysis.diffusion.neb.periodic_dijkstra import (
+    get_optimal_pathway_rev,
+    periodic_dijkstra,
+)
 from pymatgen.analysis.diffusion.utils.parse_entries import process_entries
 
 logger = logging.getLogger(__name__)
diff --git a/pymatgen/analysis/diffusion/neb/pathfinder.py b/pymatgen/analysis/diffusion/neb/pathfinder.py
index 787921b7..e1975d91 100644
--- a/pymatgen/analysis/diffusion/neb/pathfinder.py
+++ b/pymatgen/analysis/diffusion/neb/pathfinder.py
@@ -24,7 +24,10 @@
 # TODO: (1) ipython notebook example files, unittests
 from pymatgen.symmetry.structure import SymmetrizedStructure
 
-from pymatgen.analysis.diffusion.utils.supercells import get_sc_fromstruct, get_start_end_structures
+from pymatgen.analysis.diffusion.utils.supercells import (
+    get_sc_fromstruct,
+    get_start_end_structures,
+)
 
 logger = logging.getLogger(__name__)
 
diff --git a/pymatgen/analysis/diffusion/neb/tests/test_pathfinder.py b/pymatgen/analysis/diffusion/neb/tests/test_pathfinder.py
index 8d73b438..9de23910 100644
--- a/pymatgen/analysis/diffusion/neb/tests/test_pathfinder.py
+++ b/pymatgen/analysis/diffusion/neb/tests/test_pathfinder.py
@@ -10,7 +10,11 @@
 from pymatgen.util.testing import PymatgenTest
 
 from pymatgen.analysis.diffusion.neb.full_path_mapper import MigrationGraph
-from pymatgen.analysis.diffusion.neb.pathfinder import DistinctPathFinder, IDPPSolver, MigrationHop
+from pymatgen.analysis.diffusion.neb.pathfinder import (
+    DistinctPathFinder,
+    IDPPSolver,
+    MigrationHop,
+)
 from pymatgen.analysis.diffusion.utils.supercells import get_start_end_structures
 
 __author__ = "Iek-Heng Chu"
diff --git a/pymatgen/analysis/diffusion/tests/test_analyzer.py b/pymatgen/analysis/diffusion/tests/test_analyzer.py
index 18e95c60..841ddfae 100644
--- a/pymatgen/analysis/diffusion/tests/test_analyzer.py
+++ b/pymatgen/analysis/diffusion/tests/test_analyzer.py
@@ -14,7 +14,11 @@
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import PymatgenTest
 
-from pymatgen.analysis.diffusion.analyzer import DiffusionAnalyzer, fit_arrhenius, get_conversion_factor
+from pymatgen.analysis.diffusion.analyzer import (
+    DiffusionAnalyzer,
+    fit_arrhenius,
+    get_conversion_factor,
+)
 
 module_dir = os.path.dirname(os.path.abspath(__file__))
 
diff --git a/pymatgen/analysis/diffusion/utils/edge_data_from_sc.py b/pymatgen/analysis/diffusion/utils/edge_data_from_sc.py
index 7f63244f..35dd321b 100644
--- a/pymatgen/analysis/diffusion/utils/edge_data_from_sc.py
+++ b/pymatgen/analysis/diffusion/utils/edge_data_from_sc.py
@@ -19,8 +19,13 @@
 from pymatgen.core.structure import PeriodicSite, Structure
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
-from pymatgen.analysis.diffusion.neb.full_path_mapper import MigrationGraph, MigrationHop
-from pymatgen.analysis.diffusion.utils.parse_entries import get_matched_structure_mapping
+from pymatgen.analysis.diffusion.neb.full_path_mapper import (
+    MigrationGraph,
+    MigrationHop,
+)
+from pymatgen.analysis.diffusion.utils.parse_entries import (
+    get_matched_structure_mapping,
+)
 
 logger = logging.getLogger(__name__)
 
diff --git a/pymatgen/analysis/diffusion/utils/supercells.py b/pymatgen/analysis/diffusion/utils/supercells.py
index 3b9c2d0b..63bf9bc7 100644
--- a/pymatgen/analysis/diffusion/utils/supercells.py
+++ b/pymatgen/analysis/diffusion/utils/supercells.py
@@ -11,7 +11,9 @@
 # from ase.build import find_optimal_cell_shape, get_deviation_from_optimal_cell_shape
 # from pymatgen.io.ase import AseAtomsAdaptor
 from pymatgen.core import PeriodicSite, Structure
-from pymatgen.transformations.advanced_transformations import CubicSupercellTransformation
+from pymatgen.transformations.advanced_transformations import (
+    CubicSupercellTransformation,
+)
 
 __author__ = "Jimmy Shen"
 __copyright__ = "Copyright 2019, The Materials Project"
diff --git a/pymatgen/analysis/diffusion/utils/tests/test_edge_data_from_sc.py b/pymatgen/analysis/diffusion/utils/tests/test_edge_data_from_sc.py
index c8573aa5..0da1d3dd 100644
--- a/pymatgen/analysis/diffusion/utils/tests/test_edge_data_from_sc.py
+++ b/pymatgen/analysis/diffusion/utils/tests/test_edge_data_from_sc.py
@@ -9,7 +9,11 @@
 from pymatgen.core.structure import PeriodicSite, Structure
 
 from pymatgen.analysis.diffusion.neb.full_path_mapper import MigrationGraph
-from pymatgen.analysis.diffusion.utils.edge_data_from_sc import add_edge_data_from_sc, get_uc_pos, get_unique_hop
+from pymatgen.analysis.diffusion.utils.edge_data_from_sc import (
+    add_edge_data_from_sc,
+    get_uc_pos,
+    get_unique_hop,
+)
 
 test_dir = os.path.dirname(os.path.realpath(__file__))
 
diff --git a/requirements-ci.txt b/requirements-ci.txt
index 7167c7d2..a1459e5f 100644
--- a/requirements-ci.txt
+++ b/requirements-ci.txt
@@ -7,4 +7,4 @@ flake8
 pylint
 black
 treon==0.1.3
-maggma==0.39.1
\ No newline at end of file
+maggma==0.39.1
diff --git a/requirements.txt b/requirements.txt
index 172e9c1e..4ac18b73 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,3 @@
 pymatgen==2022.5.19
 joblib==1.1.0
-ase==3.22.1
\ No newline at end of file
+ase==3.22.1
diff --git a/setup.py b/setup.py
index 59401356..d2edac25 100644
--- a/setup.py
+++ b/setup.py
@@ -1,10 +1,10 @@
 # Copyright (c) Materials Virtual Lab
 # Distributed under the terms of the Modified BSD License.
 
-from setuptools import setup, find_namespace_packages
-
 import os
 
+from setuptools import find_namespace_packages, setup
+
 SETUP_PTH = os.path.dirname(os.path.abspath(__file__))
 
 with open(os.path.join(SETUP_PTH, "README.rst")) as f:
diff --git a/tasks.py b/tasks.py
index 11137e56..ddfba815 100644
--- a/tasks.py
+++ b/tasks.py
@@ -5,13 +5,13 @@
 """
 
 
-import glob
 import datetime
-import re
+import glob
 import json
-import requests
 import os
+import re
 
+import requests
 from invoke import task
 from monty.os import cd