Merge fda9c18 into 6315470

pymatgen/analysis/diffusion/aimd/tests/test_pathway.py

@@ -11,7 +11,8 @@
 import numpy as np
 from pymatgen.core import Structure
 
-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__))

pymatgen/analysis/diffusion/aimd/tests/test_van_hove.py

@@ -14,7 +14,8 @@
 import numpy as np
 from monty.serialization import loadfn
 
-from pymatgen.analysis.diffusion.aimd.van_hove import EvolutionAnalyzer, RadialDistributionFunction, VanHoveAnalysis
+from pymatgen.analysis.diffusion.aimd.van_hove import (
+    EvolutionAnalyzer, RadialDistributionFunction, VanHoveAnalysis)
 from pymatgen.analysis.diffusion.analyzer import DiffusionAnalyzer
 
 matplotlib.use("pdf")

pymatgen/analysis/diffusion/analyzer.py

@@ -24,7 +24,8 @@
 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

pymatgen/analysis/diffusion/neb/full_path_mapper.py

@@ -23,13 +23,15 @@
 from pymatgen.analysis.local_env import MinimumDistanceNN, NearNeighbors
 from pymatgen.analysis.path_finder import ChgcarPotential, NEBPathfinder
 from pymatgen.core import Composition, PeriodicSite, Structure
-from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
+from pymatgen.entries.computed_entries import (ComputedEntry,
+                                               ComputedStructureEntry)
 from pymatgen.io.vasp import VolumetricData
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 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__)

pymatgen/analysis/diffusion/neb/pathfinder.py

@@ -24,7 +24,8 @@
 # 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__)
 

pymatgen/analysis/diffusion/neb/tests/test_full_path_mapper.py

@@ -9,13 +9,10 @@
 from pymatgen.io.vasp import Chgcar
 
 from pymatgen.analysis.diffusion.neb.full_path_mapper import (
-    ChargeBarrierGraph,
-    MigrationGraph,
-    MigrationHop,
-    get_hop_site_sequence,
-    order_path,
-)
-from pymatgen.analysis.diffusion.neb.periodic_dijkstra import _get_adjacency_with_images
+    ChargeBarrierGraph, MigrationGraph, MigrationHop, get_hop_site_sequence,
+    order_path)
+from pymatgen.analysis.diffusion.neb.periodic_dijkstra import \
+    _get_adjacency_with_images
 
 dir_path = os.path.dirname(os.path.realpath(__file__))
 

pymatgen/analysis/diffusion/neb/tests/test_io.py

@@ -3,12 +3,9 @@
 
 from pymatgen.core import Structure
 
-from pymatgen.analysis.diffusion.neb.io import (
-    MVLCINEBEndPointSet,
-    MVLCINEBSet,
-    get_endpoint_dist,
-    get_endpoints_from_index,
-)
+from pymatgen.analysis.diffusion.neb.io import (MVLCINEBEndPointSet,
+                                                MVLCINEBSet, get_endpoint_dist,
+                                                get_endpoints_from_index)
 
 __author__ = "hat003"
 

pymatgen/analysis/diffusion/neb/tests/test_pathfinder.py

@@ -10,8 +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.utils.supercells import get_start_end_structures
+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"
 __version__ = "1.0"

pymatgen/analysis/diffusion/tests/test_analyzer.py

@@ -14,7 +14,9 @@
 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__))
 

pymatgen/analysis/diffusion/utils/edge_data_from_sc.py

@@ -19,8 +19,10 @@
 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__)
 

pymatgen/analysis/diffusion/utils/parse_entries.py

@@ -8,9 +8,11 @@
 from typing import Dict, List, Optional, Union
 
 import numpy as np
-from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher
+from pymatgen.analysis.structure_matcher import (ElementComparator,
+                                                 StructureMatcher)
 from pymatgen.core import Composition, Lattice, Structure
-from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
+from pymatgen.entries.computed_entries import (ComputedEntry,
+                                               ComputedStructureEntry)
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
 __author__ = "Jimmy Shen"

pymatgen/analysis/diffusion/utils/supercells.py

@@ -7,11 +7,11 @@
 from typing import List, Optional, Tuple, Union
 
 import numpy as np
-
 # 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"

pymatgen/analysis/diffusion/utils/tests/test_edge_data_from_sc.py

@@ -9,7 +9,8 @@
 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__))
 

pymatgen/analysis/diffusion/utils/tests/test_parse_entries.py

@@ -10,12 +10,8 @@
 from pymatgen.entries.computed_entries import ComputedStructureEntry
 
 from pymatgen.analysis.diffusion.utils.parse_entries import (
-    _filter_and_merge,
-    get_inserted_on_base,
-    get_insertion_energy,
-    get_sym_migration_ion_sites,
-    process_entries,
-)
+    _filter_and_merge, get_inserted_on_base, get_insertion_energy,
+    get_sym_migration_ion_sites, process_entries)
 
 dir_path = os.path.dirname(os.path.realpath(__file__)) + "/test_files"
 

requirements-ci.txt

@@ -7,4 +7,4 @@ flake8==4.0.1
 pylint==2.12.2
 black==22.1.0
 treon==0.1.3
-maggma==0.39.1
+maggma==0.40.0

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:

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