Update formatting and linting

Former-commit-id: d6aea62

.github/workflows/lint.yml

@@ -31,19 +31,20 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install setuptools setuptools_scm wheel
-          pip install pydocstyle black flake8 isort
+          pip install pydocstyle black flake8 ruff
           pip install -e .[tests]
 
-      - name: sort imports
+      - name: ruff
         run:  |
-          isort . --atomic --profile black
+          ruff --version
+          ruff --fix shakenbreak
 
       - name: check docstrings
         run:  |
           pydocstyle --version
           pydocstyle -e --count --convention=google --add-ignore=D400,D415,D212,D205,D417,D107 shakenbreak
 
-      - name: black
+      - name: black  # max line length 107 specified in pyproject.toml
         run:  |
           black --version
           black --color shakenbreak

.pre-commit-config.yaml

@@ -2,7 +2,12 @@
 # See https://pre-commit.com/hooks.html for more hooks
 exclude: ^(docs|tests|SnB_input_files|.github|shakenbreak/scripts|CITATION*|MANIFEST*)
 repos:
-
+  # Lint and format, isort, docstrings...
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.3.7
+    hooks:
+      - id: ruff
+        args: [--fix]
 
  # Remove trailing whitespace, leave empty line at end of file
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -12,18 +17,6 @@ repos:
     -   id: end-of-file-fixer
     -   id: check-yaml
 
-#  - repo: https://github.com/pre-commit/mirrors-mypy
-#    rev: v0.971
-#    hooks:
-#      - id: mypy
-
-# Sort/format imports
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        args: [--profile, black]
-
 # Check docstrings
   - repo: https://github.com/pycqa/pydocstyle
     rev: 4.0.0  # pick a git hash / tag to point to
@@ -32,8 +25,8 @@ repos:
         args: [-e, --count, "--convention=google", "--add-ignore=D107,D202,D400,D415,D212,D205,D417,D413"]
 
 # Code formatting
-  - repo: https://github.com/psf/black
-    rev: 22.6.0
+  - repo: https://github.com/psf/black  # max line length 107 specified in pyproject.toml
+    rev: 24.2.0
     hooks:
       - id: black
         args: [--color]

docs/Contributing.rst

@@ -27,12 +27,12 @@ workflow to do so and follow the `PEP8 <https://peps.python.org/pep-0008/>`_ sty
 
     .. NOTE::
         Alternatively, if you prefer not to use ``pre-commit hooks``, you can manually run the following in the **correct sequence**
-        on your local machine. From the ``shakenbreak`` top directory, run `isort <https://pycqa.github.io/isort/>`_ to sort and format your imports, followed by
+        on your local machine. From the ``shakenbreak`` top directory, run `ruff --fix <https://docs.astral.sh/ruff/>`_ to lint and format, followed by
         `black <https://black.readthedocs.io/en/stable/index.html>`_, which will automatically reformat the code to ``PEP8`` conventions:
 
         .. code:: bash
 
-            $ isort . --profile black
+            $ ruff --fix
             $ black  --diff --color shakenbreak
 
         Then run `pycodestyle <https://pycodestyle.pycqa.org/en/latest/>`_ to check the docstrings,

pyproject.toml

@@ -4,3 +4,53 @@ requires = [
     "wheel"
 ]
 build-backend = "setuptools.build_meta"
+
+[tool.black]
+line-length = 107
+
+[tool.ruff]
+line-length = 107
+lint.pydocstyle.convention = "google"
+lint.isort.split-on-trailing-comma = false
+lint.select = [  # from pymatgen
+  "B",   # flake8-bugbear
+  "C4",  # flake8-comprehensions
+  "D",   # pydocstyle
+  "E",   # pycodestyle error
+  "EXE", # flake8-executable
+  "F",   # pyflakes
+  "FLY", # flynt
+  "I",   # isort
+  "ICN", # flake8-import-conventions
+  "ISC", # flake8-implicit-str-concat
+  "PD",  # pandas-vet
+  "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
+  "TCH", # flake8-type-checking
+  "TID", # tidy imports
+  "TID", # flake8-tidy-imports
+  "UP",  # pyupgrade
+  "W",   # pycodestyle warning
+  "YTT", # flake8-2020
+]
+lint.ignore = [
+  "B028",    # No explicit stacklevel keyword argument found
+  "D101",    # Missing docstring in public class (docstring in init instead)
+  "D200",    # One-line docstring should fit on one line with quotes
+  "D205",    # 1 blank line required between summary line and description
+  "D212",    # Multi-line docstring summary should start at the first line
+  "PLR2004", # Magic number
+  "PLR",     # pylint refactor
+  "W605",    # Invalid escape sequence
+  "PT011",   # too broad pytest.raises()
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/*" = ["D102"]

setup.py

@@ -1,4 +1,4 @@
-"""This is a setup.py script to install ShakeNBreak"""
+"""This is a setup.py script to install ShakeNBreak."""
 
 import os
 import warnings
@@ -32,9 +32,7 @@ def _install_custom_font():
 
         # Copy the font file to matplotlib's True Type font directory
         fonts_dir = f"{path_to_file}/shakenbreak/"
-        ttf_fonts = [
-            file_name for file_name in os.listdir(fonts_dir) if ".ttf" in file_name
-        ]
+        ttf_fonts = [file_name for file_name in os.listdir(fonts_dir) if ".ttf" in file_name]
         try:
             for font in ttf_fonts:  # must be in ttf format for matplotlib
                 old_path = os.path.join(fonts_dir, font)
@@ -104,7 +102,7 @@ def run(self):
 
 
 class CustomEggInfoCommand(egg_info):
-    """Post-installation"""
+    """Post-installation."""
 
     def run(self):
         """
@@ -120,14 +118,14 @@ def run(self):
 def package_files(directory):
     """Include package data."""
     paths = []
-    for path, directories, filenames in os.walk(directory):
+    for path, _dir, filenames in os.walk(directory):
         paths.extend(os.path.join("..", path, filename) for filename in filenames)
     return paths
 
 
 input_files = package_files("SnB_input_files/")
 
-with open("README.md", "r", encoding="utf-8") as file:
+with open("README.md", encoding="utf-8") as file:
     long_description = file.read()
 
 
@@ -194,7 +192,7 @@ def package_files(directory):
     },
     # Specify any non-python files to be distributed with the package
     package_data={
-        "shakenbreak": ["shakenbreak/*"] + input_files,
+        "shakenbreak": ["shakenbreak/*", *input_files],
     },
     include_package_data=True,
     # Specify the custom installation class