Adopt ruff for linting, formatting, and import sorting (#702)

.pre-commit-config.yaml

@@ -4,33 +4,27 @@ fail_fast: true
 
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
+      rev: v4.6.0
       hooks:
           - id: trailing-whitespace
           - id: end-of-file-fixer
           - id: check-yaml
 
-    - repo: https://github.com/psf/black
-      rev: 23.3.0
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.6.8
       hooks:
-          - id: black
-
-    - repo: https://github.com/timothycrosley/isort
-      rev: 5.12.0
-      hooks:
-          - id: isort
-
-    # Need to use flake8 GitHub mirror due to CentOS git issue with GitLab
-    # https://github.com/pre-commit/pre-commit/issues/1206
-    - repo: https://github.com/pycqa/flake8
-      rev: 6.0.0
-      hooks:
-          - id: flake8
-            args: ["--config=setup.cfg"]
-            additional_dependencies: [flake8-isort]
+          # Sort the imports
+          - id: ruff
+            name: ruff-sort-imports
+            args: [--select, I, --fix]
+          # Run the linter.
+          - id: ruff
+            args: [--fix]
+          # Run the formatter.
+          - id: ruff-format
 
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.4.0
+      rev: v1.11.2
       hooks:
           - id: mypy
             args: ["--config=pyproject.toml"]

.vscode/xcdat.code-workspace

@@ -20,17 +20,12 @@
         // ===================
         "[python]": {
             // editor.rulers: [comments, max line length, wrap line length],
-            // Black does not wrap comments.
             "editor.rulers": [80, 88, 120],
             "editor.wordWrap": "wordWrapColumn",
             "editor.wordWrapColumn": 120,
-            "editor.defaultFormatter": "ms-python.black-formatter"
+            "editor.defaultFormatter": "charliermarsh.ruff"
         },
-        "black-formatter.importStrategy": "fromEnvironment",
-        // Code Formatting and Linting
-        // ---------------------------
-        "flake8.args": ["--config=setup.cfg"],
-        "flake8.importStrategy": "fromEnvironment",
+        "ruff.importStrategy": "fromEnvironment",
         // Type checking
         // ---------------------------
         "mypy-type-checker.args": ["--config=pyproject.toml"],

CONTRIBUTING.rst

@@ -246,7 +246,7 @@ Here's a simple checklist for PRs:
   - Write new tests if needed.
   - Test the code using `Pytest`_. Running all tests (type ``make test`` or ``pytest`` in the root directory) takes a while, so feel free to only run the tests you think are needed based on your PR (example: ``pytest tests/test_dataset.py``). CI will catch any failing tests.
 
-- **Properly format your code** and verify that it passes the formatting guidelines set by `Black`_ and `Flake8`_.
+- **Properly format your code** and verify that it passes the formatting guidelines set by `Ruff`_.
   You can use `pre-commit`_ to run these automatically on each commit.
 
   - Run ``pre-commit run --all-files`` in the root directory. This may modify some files. Confirm and commit any formatting changes.
@@ -261,10 +261,8 @@ Code formatting
 
 xCDAT uses several tools to ensure a consistent code format throughout the project:
 
-- `Black`_ for standardized code formatting
-- `Flake8`_ for code linting
-- `isort`_ for standardized order of imports
-- `mypy`_ for static type checking on `type hints`_
+- `Ruff`_ for standardized code formatting, linting, and ordering of imports.
+- `MyPy`_ for static type checking on `type hints`_
 
 We highly recommend that you setup `pre-commit hooks`_ to automatically run all the
 above tools every time you make a git commit. Check out the :ref:`install pre-commit
@@ -277,10 +275,8 @@ hooks` section above for instructions.
 .. _pre-commit: https://pre-commit.com/
 .. _pre-commit hooks: https://pre-commit.com/
 .. _Pytest: http://doc.pytest.org/en/latest/
-.. _Black: https://black.readthedocs.io/en/stable/
-.. _Flake8: https://flake8.pycqa.org/en/latest/
-.. _isort: https://pycqa.github.io/isort/
-.. _mypy: http://mypy-lang.org/
+.. _Ruff: https://docs.astral.sh/ruff/
+.. _MyPy: http://MyPy-lang.org/
 .. _type hints: https://docs.python.org/3/library/typing.html
 
 Testing with continuous integration

Makefile

@@ -60,8 +60,12 @@ clean-test: ## remove test and coverage artifacts
 pre-commit:  # run pre-commit quality assurance checks
 	pre-commit run --all-files
 
-lint: ## check style with flake8
-	flake8 xcdat tests
+lint: ## check style ruff
+	ruff check --select I --fix
+	ruff check --fix
+
+format: ## format code using ruff
+	ruff format
 
 test: ## run tests quickly with the default Python and produces code coverage report
 	pytest

README.rst

@@ -21,7 +21,7 @@
    +--------------------+------------------------------------------------------+
    | DevOps             | |CI/CD Build Workflow| |codecov| |docs|              |
    +--------------------+------------------------------------------------------+
-   | Quality Assurance  | |pre-commit| |black| |flake8| |mypy|                 |
+   | Quality Assurance  | |pre-commit| |ruff| |mypy|                           |
    +--------------------+------------------------------------------------------+
 
    .. raw:: html
@@ -46,10 +46,8 @@
    :target: https://codecov.io/gh/xCDAT/xcdat
 .. |pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white
    :target: https://github.com/pre-commit/pre-commit
-.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
-   :target: https://github.com/psf/black
-.. |flake8| image:: https://img.shields.io/badge/flake8-enabled-green
-   :target: https://github.com/PyCQA/flake8
+.. |ruff| image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
+   :target: https://github.com/astral-sh/ruff
 .. |mypy| image:: http://www.mypy-lang.org/static/mypy_badge.svg
    :target: http://mypy-lang.org/
 

conda-env/dev.yml

@@ -36,12 +36,9 @@ dependencies:
     # ==================
     - types-python-dateutil
     # NOTE: If the tools below are updated, also update their 'rev' in `.pre-commit.config.yaml`
-    - black=23.3.0
-    - flake8=6.0.0
-    - flake8-isort=6.0.0
-    - isort=5.12.0
-    - mypy=1.4.0
     - pre-commit=3.2.0
+    - ruff=0.6.8
+    - mypy=1.11.2
     # Testing
     # ==================
     - pytest

pyproject.toml

@@ -1,34 +1,55 @@
-[tool.black]
-line-length = 88
-target-version = ['py36']
-include = '\.pyi?$'
-exclude = '''
-(
-  /(
-      \.eggs
-    | \.git
-    | \.hg
-    | \.mypy_cache
-    | \.tox
-    | \.idea
-    | venv
-    | _build
-    | buck-out
-    | build
-    | dist
-    | docs
-    | config
-  )/
-)
-'''
+[tool.ruff]
+# Exclude a variety of commonly ignored directories.
+exclude = [
+  ".bzr",
+  ".direnv",
+  ".eggs",
+  ".git",
+  ".git-rewrite",
+  ".hg",
+  ".ipynb_checkpoints",
+  ".mypy_cache",
+  ".nox",
+  ".pants.d",
+  ".pyenv",
+  ".pytest_cache",
+  ".pytype",
+  ".ruff_cache",
+  ".svn",
+  ".tox",
+  ".venv",
+  ".vscode",
+  "__pypackages__",
+  "_build",
+  "buck-out",
+  "build",
+  "dist",
+  "docs",
+  "node_modules",
+  "site-packages",
+  "venv",
+]
 
-[tool.isort]
-# Docs: https://pycqa.github.io/isort/docs/configuration/options.html#example-pyprojecttoml_4
-multi_line_output = 3
-include_trailing_comma = true
-force_grid_wrap = 0
-use_parentheses = true
-line_length = 88
+[tool.ruff.lint]
+# E4 - whitespace
+# E7 - multiple-statements
+# E9 - trailing-whitespace
+# F - Enable Pyflakes
+# B - Enable flake8-bugbear
+# W - Enable pycodestyle
+# C901 - complex-structure
+# D - Enable flake8-docstrings
+select = ["E4", "E7", "E9", "F", "B", "W", "C901"]
+
+# E501 - line-too-long
+ignore = ["E501"]
+
+[tool.ruff.lint.mccabe]
+# Flag errors (`C901`) whenever the complexity level exceeds 5.
+max-complexity = 10
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
 
 [tool.pytest.ini_options]
 # Docs: https://docs.pytest.org/en/7.2.x/reference/customize.html#configuration

tests/__init__.py

@@ -1,4 +1,5 @@
 """Unit test package for xcdat."""
+
 from xarray.core.options import set_options
 from xarray.tests import requires_dask  # noqa: F401
 

tests/fixtures.py

@@ -1,4 +1,5 @@
 """This module stores reusable test fixtures."""
+
 from typing import Literal
 
 import cftime

tests/test_bounds.py

@@ -847,7 +847,7 @@ def test_add_monthly_bounds_for_end_of_month_set_to_true(self):
         # Get time axis and create new axis with time set to first day of month.
         time = ds_with_bnds.time
         new_time = []
-        for i, t in enumerate(time.values):
+        for _, t in enumerate(time.values):
             y = t.year
             m = t.month
             nt = cftime.DatetimeGregorian(y, m, 1, 0)

tests/test_regrid.py

@@ -204,7 +204,12 @@ def test_methods(self):
         xgcm.XGCMRegridder(self.ds, self.output_grid, method="linear", target_data=None)
 
         with pytest.raises(ValueError, match="'dummy' is invalid, possible choices"):
-            xgcm.XGCMRegridder(self.ds, self.output_grid, method="dummy", target_data=None)  # type: ignore
+            xgcm.XGCMRegridder(
+                self.ds,
+                self.output_grid,
+                method="dummy",  # type: ignore
+                target_data=None,
+            )
 
     def test_missing_input_z_coord(self):
         ds = fixtures.generate_dataset(
@@ -663,7 +668,7 @@ def test_map_latitude_coarse_to_fine(self):
             np.testing.assert_allclose(x, y)
 
         for x2, y2 in zip(weights, expected_weigths):
-            np.testing.assert_allclose(x, y)
+            np.testing.assert_allclose(x2, y2)
 
     def test_map_latitude_fine_to_coarse(self):
         mapping, weights = regrid2._map_latitude(
@@ -1254,7 +1259,7 @@ def test_grid(self):
             ValueError,
             match=r".*lon\d?.*lon\d?.*",
         ):
-            ds_multi.regridder.grid
+            ds_multi.regridder.grid  # noqa: B018
 
     def test_grid_raises_error_when_dataset_has_multiple_dims_for_an_axis(self):
         ds_bounds = fixtures.generate_dataset(
@@ -1265,7 +1270,7 @@ def test_grid_raises_error_when_dataset_has_multiple_dims_for_an_axis(self):
         )
 
         with pytest.raises(ValueError):
-            ds_bounds.regridder.grid
+            ds_bounds.regridder.grid  # noqa: B018
 
     @mock.patch("xcdat.regridder.accessor._get_input_grid")
     def test_horizontal_tool_check(self, _get_input_grid):

xcdat/__init__.py

@@ -1,4 +1,5 @@
 """Top-level package for xcdat."""
+
 from xcdat.axis import (  # noqa: F401
     center_times,
     get_dim_coords,

xcdat/_logger.py

@@ -1,4 +1,5 @@
 """Logger module for setting up a logger."""
+
 import logging
 import logging.handlers
 

xcdat/bounds.py

@@ -1,8 +1,11 @@
 """Bounds module for functions related to coordinate bounds."""
+
+from __future__ import annotations
+
 import collections
 import datetime
 import warnings
-from typing import Dict, List, Literal, Optional, Union
+from typing import Dict, List, Literal, Optional, Tuple, Union
 
 import cf_xarray as cfxr  # noqa: F401
 import cftime
@@ -124,7 +127,7 @@ def keys(self) -> List[str]:
         )
 
     def add_missing_bounds(  # noqa: C901
-        self, axes: List[CFAxisKey] = ["X", "Y", "T"]
+        self, axes: List[CFAxisKey] | Tuple[CFAxisKey, ...] = ("X", "Y", "T")
     ) -> xr.Dataset:
         """Adds missing coordinate bounds for supported axes in the Dataset.
 
@@ -153,9 +156,9 @@ def add_missing_bounds(  # noqa: C901
 
         Parameters
         ----------
-        axes : List[str]
+        axes : List[CFAxesKey] | Tuple[CFAxisKey, ...]
             List of CF axes that function should operate on, by default
-            ["X", "Y", "T"]. Options include "X", "Y", "T", or "Z".
+            ("X", "Y", "T"). Options include "X", "Y", "T", or "Z".
 
         Returns
         -------
@@ -614,7 +617,11 @@ def _create_time_bounds(  # noqa: C901
                 hrs = diff.seconds / 3600
                 daily_subfreq = int(24 / hrs)  # type: ignore
 
-            time_bnds = self._create_daily_time_bounds(timesteps, obj_type, freq=daily_subfreq)  # type: ignore
+            time_bnds = self._create_daily_time_bounds(
+                timesteps,
+                obj_type,
+                freq=daily_subfreq,  # type: ignore
+            )
 
         # Create the bounds data array
         da_time_bnds = xr.DataArray(