Set up lint workflow

Author: peytondmurray

.github/workflows/lint.yml

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+name: pre-commit
+
+on:
+  pull_request:
+  push:
+     branches: [master]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+    - uses: pre-commit/action@v3.0.1

.pre-commit-config.yaml

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+# pre-commit is a tool to perform a predefined set of tasks manually and/or
+# automatically before git commits are made.
+#
+# Config reference: https://pre-commit.com/#pre-commit-configyaml---top-level
+#
+# Common tasks
+#
+# - Register git hooks: pre-commit install --install-hooks
+# - Run on all files:   pre-commit run --all-files
+#
+# These pre-commit hooks are run as CI.
+#
+# NOTE: if it can be avoided, add configs/args in pyproject.toml or below instead of creating a new `.config.file`.
+# https://pre-commit.ci/#configuration
+ci:
+  autoupdate_schedule: monthly
+  autofix_commit_msg: |
+    [pre-commit.ci] Apply automatic pre-commit fixes
+
+repos:
+  # general
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: end-of-file-fixer
+        exclude: '\.svg$'
+      - id: trailing-whitespace
+        exclude: '\.svg$'
+      - id: check-json
+      - id: check-yaml
+        args: [--allow-multiple-documents, --unsafe]
+      - id: check-toml
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.6
+    hooks:
+      - id: ruff
+        args: ["--fix"]

pyproject.toml

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+[build-system]
+requires = [
+  "setuptools",
+  "wheel",
+]
+
+[tool.ruff]
+line-length = 88
+
+[tool.ruff.lint]
+select = [
+    # pycodestyle
+    "E",
+    "W",
+    # Pyflakes
+    "F",
+    # pyupgrade
+    "UP",
+    # flake8-bugbear
+    "B",
+    # flake8-simplify
+    "SIM",
+    # isort
+    "I",
+    # pep8 naming
+    "N",
+    # pydocstyle
+    "D",
+    # annotations
+    "ANN",
+    # debugger
+    "T10",
+    # flake8-pytest
+    "PT",
+    # flake8-return
+    "RET",
+    # flake8-unused-arguments
+    "ARG",
+    # flake8-fixme
+    "FIX",
+    # flake8-eradicate
+    "ERA",
+    # pandas-vet
+    "PD",
+    # numpy-specific rules
+    "NPY",
+]
+ignore = [
+    "ANN002", # Missing type annotation for `*args`
+    "ANN003", # Missing type annotation for `**kwargs`
+    "ANN101", # Missing type annotation for `self`
+    "ANN102", # Missing type annotation for `cls` in classmethod
+    "ANN201", # Missing return type annotation for public function (makes no sense for NoneType return types...)
+    "ANN204", # Missing return type annotation for special method
+    "D100", # Missing docstring in public module
+    "D104", # Missing docstring in public package
+    "D105", # Missing docstring in magic method
+    "D107", # Missing docstring in `__init__`
+    "D203", # 1 blank line before after class docstring
+    "D204", # 1 blank line required after class docstring
+    "D206", # Advised to disable by ruff-format
+    "D211", # No blank line before class
+    "D213", # Multiline summary second line
+    "D413", # 1 blank line after parameters
+    "E501", # Advised to disable by ruff-format
+    "N802", # Function name should be lowercase; unittest uses mixed case
+    "PD901", # Avoid using 'df' for pandas dataframes. Perfectly fine in functions with limited scope
+    "SIM108", # Simplify if/else to one line; not always clearer
+    "W191", # Advised to disable by ruff-format
+
+    # These are issues which remain to be fixed
+    "ANN001", # Missing type annotation for function argument
+    "ANN202", # Missing return type for private function
+    "ANN206", # Missing return type annotation for classmethod
+    "ANN401", # Dynamically typed expressions (typing.Any) are disallowed
+    "ARG002", # Unused method argument
+    "B007", # Loop control variable not used within loop body
+    "B008", # Do not perform function call in argument defaults
+    "B018", # Found useless expression
+    "B024", # <class> is an abstract base class,  but it has no abstract methods
+    "D101", # Missing docstring in public class
+    "D102", # Missing docstring in public method
+    "D103", # Missing docstring in public function
+    "D200", # One-line docstring should fit on one line
+    "D401", # First line of docstring should be in imperative mood
+    "D404", # First word of the docstring should not be "This"
+    "E721", # Use `is` and `is not` for type comparisons, or `isinstance()` for isinstance checks
+    "ERA001", # Dead code
+    "FIX002", # Line contains TODO, consider resolving the issue
+    "PD011", # Use `.to_numpy()` instead of `.values`
+    "PD013", # `.melt` is preferred to `.stack`
+    "RET504", # Unncessary assignment before `return`
+    "RET505", # Unncessary `else` after `return` statement
+    "SIM101", # Multiple `isinstance` calls, merge into a single call
+    "SIM102", # Use a single `if` statement instead of nested `if` statements
+    "SIM105", # Replace with `contextlib.suppress(FileNotFoundError)`
+    "SIM110", # Use `return all(...)` instead of `for` loop
+    "SIM117", # Use a single `with` statement with multiple contexts instead of nested `with` statements
+    "SIM118", # Use `key in dict` instead of `key in dict.keys()`
+    "UP008", # Use `super()` instead of `super(__class__, self)`
+    "UP031", # Use format specifiers instead of percent format
+]
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = [
+    "F401", # Unused import
+]
+"*_test.py" = [
+    "ANN001", # Type annotations aren't needed for tests; these are fixtures or parametrizations
+    "PT009", # Use a regular `assert` instead of a unittest-style `assertEqual`
+    "PT027", # Use `pytest.raises` instead of unittest-style `assertRaisesRegex`
+
+    # Missing docstrings; probably want to fill these out for tests. For now, we just disable
+    "D101", # Missing docstring in public class
+    "D102", # Missing docstring in public method
+
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
+[tool.isort]
+profile = "black"