[pre-commit.ci] pre-commit autoupdate

.bumpversion.cfg

@@ -3,7 +3,7 @@ current_version = 0.0.10-dev
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?(?:\+(?P<build>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?
-serialize = 
+serialize =
 	{major}.{minor}.{patch}-{release}+{build}
 	{major}.{minor}.{patch}+{build}
 	{major}.{minor}.{patch}-{release}
@@ -12,7 +12,7 @@ serialize =
 [bumpversion:part:release]
 optional_value = production
 first_value = dev
-values = 
+values =
 	dev
 	production
 

.gitignore

@@ -389,4 +389,4 @@ $RECYCLE.BIN/
 
 # End of https://www.toptal.com/developers/gitignore/api/linux,macos,python,pycharm,windows,vim,visualstudiocode,jupyternotebooks
 scratch/
-dev/
+dev/

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ default_language_version:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v5.0.0
     hooks:
       - id: check-executables-have-shebangs
       - id: fix-encoding-pragma
@@ -19,39 +19,39 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/jorisroovers/gitlint
-    rev: v0.15.1
+    rev: v0.19.1
     hooks:
       - id: gitlint
 
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 6.0.0
     hooks:
       - id: isort
 
-  - repo: https://github.com/ambv/black
-    rev: 21.9b0
+  - repo: https://github.com/psf/black
+    rev: 25.1.0
     hooks:
       - id: black
 
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.9.2
+  - repo: https://github.com/PyCQA/flake8
+    rev: 7.1.1
     hooks:
       - id: flake8
 
   - repo: https://github.com/pycqa/bandit
-    rev: 1.7.0
+    rev: 1.8.2
     hooks:
       - id: bandit
         # Bandit does not need to run on test code
         exclude: tests/*
 
   - repo: https://github.com/pycqa/pydocstyle
-    rev: 6.1.1
+    rev: 6.3.0
     hooks:
       - id: pydocstyle
 
   - repo: https://github.com/btford/write-good
-    rev: v1.0.4
+    rev: v1.0.8
     hooks:
       - id: write-good
         files: "\\.(rst|md|markdown|mdown|mkdn)$"

README.md

@@ -13,7 +13,7 @@
         <img alt="Tests" src="https://github.com/kjappelbaum/structuregraph-helpers/workflows/Tests/badge.svg" />
     </a>
     <a href="https://github.com/cthoyt/cookiecutter-python-package">
-        <img alt="Cookiecutter template from @cthoyt" src="https://img.shields.io/badge/Cookiecutter-python--package-yellow" /> 
+        <img alt="Cookiecutter template from @cthoyt" src="https://img.shields.io/badge/Cookiecutter-python--package-yellow" />
     </a>
     <a href="https://pypi.org/project/structuregraph_helpers">
         <img alt="PyPI" src="https://img.shields.io/pypi/v/structuregraph_helpers" />
@@ -116,7 +116,7 @@ This package was created with [@audreyfeldroy](https://github.com/audreyfeldroy)
 <details>
   <summary>See developer instrutions</summary>
 
-  
+
 The final section of the README is for if you want to get involved by making a code contribution.
 
 ### ❓ Testing

binder/postBuild

@@ -1 +1 @@
-python -m pip install --upgrade .
+python -m pip install --upgrade .

binder/runtime.txt

@@ -1 +1 @@
-python-3.8
+python-3.8

docs/Makefile

@@ -16,4 +16,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/source/api.rst

@@ -33,10 +33,10 @@ Hash
 
 
 
-Logging 
+Logging
 ---------
 
-structuregraph_helpers uses the `loguru <https://loguru.readthedocs.io/en/stable/index.html>`_  for logging. 
+structuregraph_helpers uses the `loguru <https://loguru.readthedocs.io/en/stable/index.html>`_  for logging.
 By default, logging from structuregraph_helpers is disabled to not interfere with your logs.
 
 However, you can easily customize the logging:
@@ -46,17 +46,17 @@ However, you can easily customize the logging:
     import sys
     from loguru import logger
 
-    # enable structuregraph_helpers logging 
+    # enable structuregraph_helpers logging
     logger.enable("structuregraph_helpers")
-    
+
     # define the logging level
     LEVEL = "INFO || DEBUG || WARNING || etc."
 
     # set the handler
     # for logging to stdout
-    logger.add(sys.stdout, level=LEVEL) 
+    logger.add(sys.stdout, level=LEVEL)
     # or for logging to a file
-    logger.add("my_log_file.log", level=LEVEL, enqueue=True) 
+    logger.add("my_log_file.log", level=LEVEL, enqueue=True)
 
 
 In many cases, however, you might find it convenient to simply call :py:meth:`~structuregraph_helpers.utils.enable_logging`
@@ -67,4 +67,4 @@ In many cases, however, you might find it convenient to simply call :py:meth:`~s
 
     enable_logging()
 
-which will enable logging with sane defaults (i.e. logging to ``stderr`` for ``INFO`` and ``WARNING`` levels).
+which will enable logging with sane defaults (i.e. logging to ``stderr`` for ``INFO`` and ``WARNING`` levels).

docs/source/index.rst

@@ -2,7 +2,7 @@ structuregraph_helpers |release| Documentation
 ==============================================
 
 :code:`structuregraph_helpers` is a collection of helper functions
-that can be useful when working with :code:`pymatgen`'s :code:`StructureGraph`. 
+that can be useful when working with :code:`pymatgen`'s :code:`StructureGraph`.
 
 .. toctree::
    :maxdepth: 2

setup.cfg

@@ -70,9 +70,9 @@ package_dir =
 where = src
 
 [options.extras_require]
-plotting = 
+plotting =
     plotly
-lint = 
+lint =
     isort
     black
     flake8
@@ -168,4 +168,4 @@ application-import-names =
     structuregraph_helpers
     tests
 per-file-ignores =
-    tests/*.py:DAR101, D205, D100, DAR101, DAR201, D209, D103
+    tests/*.py:DAR101, D205, D100, DAR101, DAR201, D209, D103

src/structuregraph_helpers/_hasher.py

@@ -1,7 +1,8 @@
+# -*- coding: utf-8 -*-
 """
-Code below is taken from networkx. 
+Code below is taken from networkx.
 
-License: 
+License:
 
 NetworkX is distributed with the 3-clause BSD license.
 

src/structuregraph_helpers/analysis.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """Helpers for analysing structure graphs."""
 from typing import List
 

src/structuregraph_helpers/cli.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """Command-line interface for StructureGraphHelpers."""
 import concurrent.futures
 import os

src/structuregraph_helpers/create.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """Helpers for creating graphs."""
 import os
 from typing import Iterable, Tuple

src/structuregraph_helpers/delete.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """Helpers for deleting parts of graphs."""
 from collections import defaultdict
 from copy import deepcopy

src/structuregraph_helpers/hash.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """Create hash strings for structure graphs.
 
 Note that two LQGs of the same net (crystallographic net)

src/structuregraph_helpers/plotting.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """Plotting helpers."""
 import plotly.graph_objs as go
 

src/structuregraph_helpers/subgraph.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """Extract subgraphs from structure graphs."""
 import warnings
 from collections import defaultdict

src/structuregraph_helpers/utils.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import json
 import sys
 from typing import List

tests/conftest.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import os
 
 import pytest

tests/test_analysis.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from pymatgen.analysis.graphs import StructureGraph
 
 from structuregraph_helpers.analysis import get_cn, get_dimensionality_larsen, get_leaf_nodes

tests/test_cli.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import os
 
 from click.testing import CliRunner

tests/test_create.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import networkx as nx
 from pymatgen.analysis.graphs import StructureGraph
 

tests/test_delete.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import networkx as nx
 from pymatgen.analysis.graphs import StructureGraph
 

tests/test_hash.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from pymatgen.analysis.graphs import StructureGraph
 from pymatgen.transformations.standard_transformations import RotationTransformation
 

tests/test_subgraph.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import numpy as np
 from pymatgen.analysis.graphs import MoleculeGraph
 from pymatgen.core import Molecule