Replace formatters with Ruff (#183)

* Replace formatters with Ruff

* Reintroduce pydocstyle

* Update the GitHub action

* Include the format-and-lint merge of format and lint in the documentation

* Update the workflows again...

.github/workflows/ci.yaml

@@ -24,9 +24,9 @@ jobs:
       - name: Install dependencies
         run: |
           pip install --upgrade pip
-          pip install .[cpu,lint]
+          pip install .[cpu,format-and-lint]
       - name: Apply linter
-        run: make lint
+        run: make format-and-lint
   test:
     name: Test with ${{ matrix.python-version }} on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}

.pre-commit-config.yaml

@@ -3,32 +3,30 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
       - id: check-merge-conflict
-  - repo: https://github.com/psf/black
-    rev: 23.9.1
-    hooks:
-      - id: black
-        language_version: python3
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        name: isort
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.292
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.4.5
     hooks:
+      # Run the linter.
       - id: ruff
+        args: [--fix]
+      # Run the formatter.
+      - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.10.0
     hooks:
       - id: mypy
-        args: [--ignore-missing-imports]
+        args:
+          - --no-strict-optional
+          - --ignore-missing-imports
+          - --explicit-package-bases
   - repo: https://github.com/lyz-code/yamlfix/
-    rev: 1.13.0
+    rev: 1.16.0
     hooks:
       - id: yamlfix

Makefile

@@ -1,13 +1,9 @@
-format:
-	isort .  --quiet
-	black .  --quiet
-	blackdoc *.md  --line-length 82
-
-lint:
+format-and-lint:
 	pre-commit run --all-files
+	blackdoc *.md  --line-length 82
 
 test:
-	pytest -x -v
+	pytest
 	python -m doctest README.md
 	python -m doctest matfree/*.py
 

README.md

@@ -115,24 +115,14 @@ make test
 
 Install all formatting-related dependencies via
 ```commandline
-pip install .[format]
+pip install .[format-and-lint]
+pre-commit install
 ```
 and format the code via
 ```commandline
-make format
+make format-and-lint
 ```
 
-To lint the code, install the pre-commit hook
-
-```commandline
-pip install .[lint]
-pre-commit install
-
-```
-and run the linters via
-```commandline
-make lint
-```
 
 Install the documentation-related dependencies as
 
@@ -169,7 +159,7 @@ To make a pull request, proceed as follows:
 - Fork the repository.
 - Install all dependencies with `pip install .[full]` or `pip install -e .[full]`.
 - Make your changes.
-- From the root of the project, run the tests via `make test`, and check out `make format` and `make lint` as well. Use the pre-commit hook if you like.
+- From the root of the project, run the tests via `make test`, and check out `make format-and-lint` as well. Use the pre-commit hook if you like.
 
 
 When making a pull request, keep in mind the following (rough) guidelines:

matfree/backend/containers.py

@@ -1,4 +1,3 @@
 """Container types."""
 
-
 from typing import NamedTuple  # noqa: F401

matfree/backend/prng.py

@@ -1,6 +1,5 @@
 """Pseudo-random-number utilities."""
 
-
 import jax.random
 
 

matfree/backend/typing.py

@@ -1,4 +1,5 @@
 """Types."""
+
 # fmt: off
 from collections.abc import Callable  # noqa: F401
 from typing import Any, Generic, Iterable, Sequence, Tuple, TypeVar  # noqa: F401, UP035

matfree/bounds.py

@@ -4,7 +4,7 @@
 
 
 def baigolub96_logdet_spd(bound_spectrum, /, nrows, trace, norm_frobenius_squared):
-    """Bound the log-determinant of a symmatric, positive definite matrix.
+    """Bound the log-determinant of a symmetric, positive definite matrix.
 
     This function implements Theorem 2 in the paper by Bai and Golub (1996).
 

matfree/lanczos.py

@@ -365,10 +365,7 @@ def _validate_unit_2_norm(v, /):
     # but we can make it obvious that the result is unusable.
     is_not_normalized = np.abs(linalg.vector_norm(v) - 1.0) > 10 * np.finfo_eps(v.dtype)
     return control_flow.cond(
-        is_not_normalized,
-        lambda s: np.nan() * np.ones_like(s),
-        lambda s: s,
-        v,
+        is_not_normalized, lambda s: np.nan() * np.ones_like(s), lambda s: s, v
     )
 
 

pyproject.toml

@@ -33,13 +33,10 @@ test =[
     "pytest",
     "pytest-cases",
 ]
-lint =[
+format-and-lint =[
     "matfree[test]",
     "pre-commit",
-]
-format =[
-    "isort",
-    "black",
+    "blackdoc",
 ]
 doc = [
     "mkdocs",
@@ -54,8 +51,7 @@ doc = [
 full = [
     "matfree[cpu]",
     "matfree[test]",
-    "matfree[lint]",
-    "matfree[format]",
+    "matfree[format-and-lint]",
     "matfree[doc]",
 ]
 
@@ -74,17 +70,18 @@ version_file = "matfree/_version.py"
 "Issue tracker" = "https://github.com/pnkraemer/matfree/issues"
 
 
+
 [tool.ruff]
-include = ["*.py", "**/pyproject.toml", "*.ipynb"]
+include = ["**.py", "**/pyproject.toml", "**.ipynb"]
+
+[tool.ruff.lint]
 # See: https://beta.ruff.rs/docs/rules/
 select = [
     # pycodestyle (warning, error)
     "W",
     "E",
     # Pyflakes:
     "F",
-    # pydocstyle:
-    "D",
     # pyupgrade:
     "UP",
     # flake8-bugbear:
@@ -119,24 +116,25 @@ ignore = [
     "D213",
     # zip(..., strict=True/False) is not supported on Python < 3.10
     "B905",
-    # Magic methods don't need a docstring:
-    "D105",
 ]
 
-[tool.ruff.per-file-ignores]
-# We don't write docstrings for the backend
-"matfree/backend/*.py" = ["D103"]
+[tool.ruff.format]
+# Use `\n` line endings for all files
+line-ending = "lf"
+# Prefer single quotes over double quotes.
+quote-style = "double"
+skip-magic-trailing-comma = true
+
+[tool.ruff.lint.isort]
+split-on-trailing-comma = false
+
 
 [tool.ruff.pydocstyle]
 convention = "numpy"
 
 
-[tool.isort]
-multi_line_output = "3"
-include_trailing_comma = "true"
-force_grid_wrap = "0"
-use_parentheses = "true"
-line_length = "88"
-
-[tool.black]
-line-length = "88"
+[tool.pytest.ini_options]
+addopts = "-v"
+testpaths = [
+    "tests"
+]

scripts/generate_api_docs.py

@@ -1,4 +1,5 @@
 """Generate API docs from the source."""
+
 import pathlib
 
 

scripts/tutorials_to_py_light.py

@@ -1,4 +1,5 @@
 """Transform py:light scripts into Jupyter notebooks."""
+
 import contextlib
 import os
 from re import sub

tests/test_hutchinson/test_frobeniusnorm_squared.py

@@ -1,4 +1,5 @@
 """Test the estimation of squared Frobenius-norms."""
+
 from matfree import hutchinson
 from matfree.backend import func, linalg, np, prng, tree_util
 

tests/test_hutchinson/test_trace.py

@@ -1,4 +1,5 @@
 """Test trace estimation."""
+
 from matfree import hutchinson
 from matfree.backend import func, linalg, np, prng, tree_util
 

tests/test_hutchinson/test_trace_and_diagonal.py

@@ -1,4 +1,5 @@
 """Test joint trace and diagonal estimation."""
+
 from matfree import hutchinson
 from matfree.backend import func, np, prng, tree_util
 

tests/test_lanczos/test_funm_vector_product.py

@@ -1,4 +1,5 @@
 """Test matrix-function-vector products via Lanczos' algorithm."""
+
 from matfree import lanczos, test_util
 from matfree.backend import linalg, np, prng
 

tests/test_lanczos/test_svd_approx.py

@@ -1,6 +1,5 @@
 """Tests for SVD functionality."""
 
-
 from matfree import lanczos, test_util
 from matfree.backend import linalg, np, testing
 

tests/test_pinv/test_pseudo_inverse_correct.py

@@ -1,4 +1,5 @@
 """Tests for pseudo-inverse functionality."""
+
 from matfree import pinv
 from matfree.backend import func, linalg, np, prng, testing
 

tests/test_polynomial/test_funm_vector_product_chebyshev.py

@@ -1,4 +1,5 @@
 """Test matrix-polynomial-vector algorithms via Chebyshev's recursion."""
+
 from matfree import polynomial, test_util
 from matfree.backend import linalg, np, prng