[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ ci:
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v5.0.0
   hooks:
   - id: check-yaml
   - id: fix-encoding-pragma
@@ -18,33 +18,33 @@ repos:
     args: ['--maxkb=3000']
 
 - repo: https://github.com/psf/black
-  rev: 23.9.1
+  rev: 24.10.0
   hooks:
   - id: black
 
 - repo: https://github.com/asottile/blacken-docs
-  rev: 1.16.0
+  rev: 1.19.1
   hooks:
   - id: blacken-docs
     additional_dependencies: [black==23.1.0]
     exclude: README.md
 
 - repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+  rev: 5.13.2
   hooks:
   - id: isort
     name: isort (python)
     args:
     - --profile=black
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.13.0
+  rev: v3.19.1
   hooks:
     - id: pyupgrade
       args: [--py38-plus]
 
 - repo: https://github.com/PyCQA/autoflake
-  rev: v2.2.1
+  rev: v2.3.1
   hooks:
     - id: autoflake
       args:
@@ -56,7 +56,7 @@ repos:
 
 # Temporarily downgrade flake8 because it gives 'str' is not callable error.
 - repo: https://github.com/PyCQA/flake8
-  rev: 5.0.4
+  rev: 7.1.1
   hooks:
   - id: flake8
     files: ^WFacer/
@@ -80,9 +80,9 @@ repos:
   - id: rst-inline-touching-normal
 
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.6
+  rev: v2.3.0
   hooks:
     - id: codespell
-      stages: [commit, commit-msg]
+      stages: [pre-commit, commit-msg]
       exclude_types: [html]
       args: [--ignore-words-list, 'nd, tread, mater, titel, atomate, Atomate', --skip, "*.ipynb"]

WFacer/convergence.py

@@ -1,4 +1,5 @@
 """Convergence checks."""
+
 import numpy as np
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from smol.cofe import ClusterExpansion

WFacer/fit.py

@@ -1,4 +1,5 @@
 """Fit ECIs from Wrangler."""
+
 from warnings import warn
 
 import numpy as np

WFacer/jobs.py

@@ -1,4 +1,5 @@
 """Unitary jobs used by an atomate2 workflow."""
+
 import importlib
 import logging
 from copy import deepcopy

WFacer/maker.py

@@ -1,4 +1,5 @@
 """Automatic cluster expansion workflow maker."""
+
 from dataclasses import dataclass, field
 from warnings import warn
 

WFacer/sample_generators/mc_generators.py

@@ -1,4 +1,5 @@
 """Monte-carlo to estimate ground states and sample structures."""
+
 import itertools
 from abc import ABCMeta, abstractmethod
 from warnings import warn

WFacer/schema.py

@@ -1,4 +1,5 @@
 """Defines the standard output schema for automated cluster expansion workflows."""
+
 from typing import Any, Dict, List, Union
 
 from pydantic import BaseModel, Field

WFacer/specie_decorators/__init__.py

@@ -11,7 +11,7 @@
     PmgGuessChargeDecorator,
 )
 
-allowed_decorators = defaultdict(lambda: [])
+allowed_decorators = defaultdict(list)
 for subclass in get_subclasses(BaseDecorator).values():
     prop = subclass.decorated_prop_name
     if subclass.required_prop_names is not None:

WFacer/specie_decorators/base.py

@@ -116,7 +116,7 @@ def group_site_by_species(entries):
             defaultdict:
                (Entry index, site index) belonging to each species.
         """
-        groups_by_species = defaultdict(lambda: [])
+        groups_by_species = defaultdict(list)
 
         # These entries should not contain Vacancy.
         for e_id, entry in enumerate(entries):
@@ -249,7 +249,7 @@ def _process(self, entries, decorate_rules):
                     species_decor.append(sp)
 
             # Preserve all information.
-            site_properties = defaultdict(lambda: [])
+            site_properties = defaultdict(list)
             for site in s_undecor:
                 for p in site.properties:
                     site_properties[p].append(site.properties[p])

WFacer/utils/convex_hull.py

@@ -1,4 +1,5 @@
 """Utilities to obtain minimum energies per composition and the convex hull."""
+
 from collections import defaultdict
 
 import numpy as np

WFacer/utils/duplicacy.py

@@ -1,4 +1,5 @@
 """Check duplicacy between structures."""
+
 import numpy as np
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from pymatgen.core import DummySpecies, Element, Species, Structure

WFacer/utils/occu.py

@@ -1,4 +1,5 @@
 """Random occupancy generation."""
+
 import numpy as np
 
 

WFacer/utils/query.py

@@ -1,4 +1,5 @@
 """Rules to query nested task documents and dictionaries."""
+
 import random
 from warnings import warn
 

WFacer/utils/selection.py

@@ -1,4 +1,5 @@
 """Structure selection methods from feature matrices."""
+
 from warnings import warn
 
 import numpy as np

WFacer/utils/sparselm_estimators.py

@@ -1,4 +1,5 @@
 """Utility functions to prepare sparse-lm estimators."""
+
 from warnings import warn
 
 import numpy as np

docs/src/example_scripts/semi_automation_BCC_AlLi/fit_model.py

@@ -1,4 +1,5 @@
 """Parse and fit cluster expansion."""
+
 import json
 
 from emmet.core.tasks import TaskDoc  # emmet-core >= 0.60.0

docs/src/example_scripts/semi_automation_BCC_AlLi/generate.py

@@ -1,4 +1,5 @@
 """Generate structures for a next iteration."""
+
 from warnings import warn
 
 from fireworks import LaunchPad

docs/src/example_scripts/semi_automation_BCC_AlLi/initialize.py

@@ -1,4 +1,5 @@
 """An example to semi-automate with fireworks. Generate initial document."""
+
 import json
 
 from monty.json import jsanitize

tests/test_convergence.py

@@ -1,4 +1,5 @@
 """Test convergence functions."""
+
 import numpy as np
 from pymatgen.entries.computed_entries import ComputedStructureEntry
 from smol.cofe import ClusterExpansion

tests/test_enumeration.py

@@ -1,4 +1,5 @@
 """Test enumerating functions."""
+
 from collections import defaultdict
 from itertools import chain
 from warnings import warn
@@ -170,7 +171,7 @@ def test_enumerate_structures(single_expansion):
         for occu, mid in zip(occus, mids)
     ]
     # When keeping the ground states, each composition must have at least 1 state.
-    count_occurences = defaultdict(lambda: 0)
+    count_occurences = defaultdict(int)
     for n in ns:
         count_occurences[n] += 1
 

tests/test_fit.py

@@ -1,4 +1,5 @@
 """Test the fitting functions."""
+
 import os
 
 import cvxpy as cp

tests/test_jobs.py

@@ -1,4 +1,5 @@
 """Test running jobs."""
+
 from copy import deepcopy
 from itertools import chain
 

tests/test_maker.py

@@ -1,4 +1,5 @@
 """Test the trigger job and the flow maker."""
+
 import numpy as np
 import pytest
 from jobflow import Flow, Job, Response

tests/test_mc_generators.py

@@ -1,4 +1,5 @@
 """Test sample generators."""
+
 import random
 from itertools import chain
 

tests/test_preprocessing.py

@@ -1,4 +1,5 @@
 """Test preprocessing functions."""
+
 import os
 
 import numpy as np

tests/test_schema.py

@@ -1,4 +1,5 @@
 """Test initialization of the CeOutputsDocument schema."""
+
 import numpy as np
 import pytest
 

tests/test_utils/test_occu.py

@@ -1,4 +1,5 @@
 """Test occupancy generation."""
+
 import numpy as np
 import numpy.testing as npt
 from smol.moca.occu_utils import get_dim_ids_table, occu_to_counts

tests/test_utils/test_query.py

@@ -1,4 +1,5 @@
 """Test query rules."""
+
 import numpy as np
 import numpy.testing as npt
 import pytest

tests/test_utils/test_sparselm_estimators.py

@@ -1,4 +1,5 @@
 """Test sparselm estimator utilities."""
+
 from itertools import chain
 
 import numpy as np

tests/test_utils/test_task_document.py

@@ -1,4 +1,5 @@
 """Test single_taskdocument utilities."""
+
 import numpy as np
 import pytest
 from emmet.core.tasks import TaskDoc