Move towards using Ruff as a linter and formatter

.pre-commit-config.yaml

@@ -1,24 +1,11 @@
 repos:
-  - repo: https://github.com/timothycrosley/isort
-    rev: "5.12.0"
-    hooks:
-      - id: isort
-        additional_dependencies: [toml]
-        args: ["--profile", "black", "--filter-files","--line-length=80"]
-  - repo: https://github.com/psf/black
-    rev: "23.1.0"
-    hooks:
-      - id: black-jupyter
-        args: [--line-length=80]
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
-    hooks:
-      - id: pyupgrade
-        args: [--py38-plus]
-  - repo: https://github.com/nbQA-dev/nbQA
-    rev: "1.6.1"
-    hooks:
-      - id: nbqa-pyupgrade
-        additional_dependencies: [pyupgrade==3.3.1]
-        args: [--py38-plus]
-
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.1
+    hooks:
+      # Run the linting tool
+      - id: ruff
+        types_or: [ python, pyi ]
+        args: [--fix]
+        # Run the formatter
+      - id: ruff-format
+        types_or: [ python, pyi ]

pyproject.toml

@@ -7,5 +7,85 @@ build-backend = "setuptools.build_meta"
 version_variable = "setup.py:__version__"
 version_source = "tag"
 
-[tool.black]
-line-length = 79
+[tool.ruff]
+target-version = "py39"
+line-length = 120
+force-exclude = true
+
+[tool.ruff.lint]
+select = ["ALL"]
+ignore = [
+        # Rule families
+    "ANN",  # flake8-annotations (not ready, require types for ALL args)
+    "ARG",  # Check for unused function arguments
+    "BLE",  # General catch of Exception
+    "C90",  # Check for functions with a high McCabe complexity
+    "COM",  # flake8-commas (conflict with line wrapper)
+    "CPY",  # Missing copyright notice at top of file (need preview mode)
+    "EM",   # Format nice error messages
+    "ERA",  # Check for commented-out code
+    "FIX",  # Check for FIXME, TODO and other developer notes
+    "FURB", # refurb (need preview mode, too many preview errors)
+    "G",    # Validate logging format strings
+    "INP",  # Ban PEP-420 implicit namespace packages
+    "N",    # PEP8-naming (many var/arg names are intended)
+    "PTH",  # Prefer pathlib over os.path
+    "SLF",  # Access "private" class members
+    "T20",  # Check for print/pprint
+    "TD",   # TODO tags related
+
+    # Single rules
+    "B023",    # Function definition does not bind loop variable
+    "B028",    # No explicit stacklevel keyword argument found
+    "B904",    # Within an except clause, raise exceptions with ...
+    "C408",    # unnecessary-collection-call
+    "D105",    # Missing docstring in magic method
+    "D205",    # One blank line required between summary line and description
+    "D212",    # Multi-line docstring summary should start at the first line
+    "E501",    # Line too long
+    "E722",    # Do not use bare `except` TODO fix this
+    "FBT001",  # Boolean-typed positional argument in function definition
+    "FBT002",  # Boolean default positional argument in function
+    "ISC001", 
+    "NPY201",  # TODO: enable after migration to NumPy 2.0
+    "PD901",   # pandas-df-variable-name
+    "PERF203", # Use of try-except in for/while loop
+    "PERF401", # Replace "for" loops with list comprehension
+    "PLR0911", # Too many return statements
+    "PLR0912", # Too many branches
+    "PLR0913", # Too many arguments
+    "PLR0915", # Too many statements
+    "PLR2004", # Magic-value-comparison TODO fix these
+    "PLW2901", # Outer for loop variable overwritten by inner assignment target
+    "PLW0603", # Using the global statement to update `_el_ox_states_wiki` is discouraged TODO fix these
+    "PT009",   # Use a regular `assert` instead of unittest-style `assertAlmostEqual`
+    "PT011",   # `pytest.raises(ValueError)` is too broad, set the `match` parameter or use a more specific exception TODO fix these
+    "PT013",   # Incorrect import of pytest
+    "RET505",  # Unnecessary `else` after `return` statement
+    "S101",    # Use of "assert"
+    "S110",    # Log for try-except-pass
+    "S112",    # Log for try-except-continue
+    "S301",    # `pickle` and modules that wrap it can be unsafe when used to deserialize untrusted data, possible security issue
+    "S311",    # Use random module for cryptographic purposes
+    "S314",    # Replace xml with defusedxml to avoid XML attacks
+    "S603",    # Check source for use of "subprocess" call
+    "S607",    # Start process with relative path
+    "S608",    # Possible SQL injection vector through string-based query construction
+    "SIM105",  # Use contextlib.suppress() instead of try-except-pass
+    "TRY002",  # Create your own exception TODO fix these
+    "TRY003",  # Avoid specifying long messages outside the exception class
+    "TRY300",  # Check for return statements in try blocks
+    "TRY301",  # Check for raise statements within try blocks
+    "E741",    # Ambigous variable
+]
+exclude = ["docs/conf.py","smact/utils/*", "docs/*"]
+pydocstyle.convention = "google"
+isort.required-imports = ["from __future__ import annotations"]
+
+[tool.ruff.format]
+docstring-code-format = true
+
+
+[tool.ruff.lint.per-file-ignores]
+"smact/utils/*" = ["D"]
+"smact/tests/*" = ["D"]

setup.py

@@ -1,28 +1,29 @@
-#!/usr/bin/env python
+"""Installation for SMACT."""
+
+from __future__ import annotations
 
 __author__ = "Daniel W. Davies"
 __author_email__ = "[email protected]"
-__copyright__ = (
-    "Copyright Daniel W. Davies, Adam J. Jackson, Keith T. Butler (2019)"
-)
+__copyright__ = "Copyright Daniel W. Davies, Adam J. Jackson, Keith T. Butler (2019)"
 __version__ = "2.6"
 __maintainer__ = "Anthony O. Onwuli"
 __maintaier_email__ = "[email protected]"
 __date__ = "July 10 2024"
 
 import os
-import unittest
 
-from setuptools import Extension, setup
+from setuptools import setup
 
 module_dir = os.path.dirname(os.path.abspath(__file__))
+with open(os.path.join(module_dir, "README.md")) as f:
+    long_description = f.read()
 
 if __name__ == "__main__":
     setup(
         name="SMACT",
         version=__version__,
         description="Semiconducting Materials by Analogy and Chemical Theory",
-        long_description=open(os.path.join(module_dir, "README.md")).read(),
+        long_description=long_description,
         long_description_content_type="text/markdown",
         url="https://github.com/WMD-group/SMACT",
         author=__author__,