[CI] Migrate from flake8, black, and isort to ruff (#164)

* [REF] Increase batch sizes, update results with more efficient matvecs

* [ADD] Update benchmark figures

* [CI] Migrate linter from `flake8` to `ruff`

* [DOC] Update changelog

* [FMT] Apply `black`

* [CI] Ignore PLR2004 and PLW2901

* [CI] Use `ruff format` instead of `black`

* [CI] Use ruff for import sorting

* [CI] Minor fixes

* [DOC] Update changelog

* [REF] Delete noqas of PLR2004

* [CI] Small fix

* [REF] Sort imports

.github/workflows/lint-darglint.yaml

@@ -1,13 +1,6 @@
 name: Lint-darglint
 
-on:
-  push:
-    branches:
-      - '*'
-  pull_request:
-    branches:
-      - '*'
-
+on: [push, pull_request]
 
 jobs:
   darglint:

.github/workflows/lint-flake8.yaml → .github/workflows/lint-format.yaml

@@ -1,15 +1,9 @@
-name: Lint-flake8
+name: Lint-format
 
-on:
-  push:
-    branches:
-      - '*'
-  pull_request:
-    branches:
-      - '*'
+on: [push, pull_request]
 
 jobs:
-  flake8:
+  ruff-format:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
@@ -22,6 +16,6 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         make install-lint
-    - name: Run flake8
+    - name: Run ruff format
       run: |
-        make flake8
+        make ruff-format-check

.github/workflows/lint-pydocstyle.yaml

@@ -1,12 +1,6 @@
 name: Lint-pydocstyle
 
-on:
-  push:
-    branches:
-      - '*'
-  pull_request:
-    branches:
-      - '*'
+on: [push, pull_request]
 
 jobs:
   pydocstyle:

.github/workflows/lint-black.yaml → .github/workflows/lint-ruff.yaml

@@ -1,16 +1,9 @@
-name: Lint-black
-
-on:
-  push:
-    branches:
-      - '*'
-  pull_request:
-    branches:
-      - '*'
+name: Lint-ruff
 
+on: [push, pull_request]
 
 jobs:
-  black:
+  ruff:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
@@ -23,6 +16,6 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         make install-lint
-    - name: Run black
+    - name: Run ruff
       run: |
-        make black-check
+        make ruff-check

.gitignore

@@ -5,3 +5,4 @@ src/
 .vscode/*
 .coverage
 .eggs
+**.DS_Store

changelog.md

@@ -53,6 +53,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Always run full tests
   ([PR](https://github.com/f-dangel/curvlinops/pull/161))
+- Migrate linting, formatting, and import sorting from `flake8`, `black`, and
+  `isort` to `ruff` ([PR](https://github.com/f-dangel/curvlinops/pull/164))
 
 - Modify logo
   ([PR](https://github.com/f-dangel/curvlinops/pull/169))

curvlinops/inverse.py

@@ -455,7 +455,8 @@ def _compute_inverse_factors(
                     warn(
                         f"Failed to compute Cholesky decomposition in {aaT.dtype} "
                         f"precision with error {error}. "
-                        "Retrying in double precision..."
+                        "Retrying in double precision...",
+                        stacklevel=2,
                     )
                     # Retry in double precision
                     original_type = aaT.dtype
@@ -476,7 +477,8 @@ def _compute_inverse_factors(
                     warn(
                         f"Failed to compute Cholesky decomposition in {ggT.dtype} "
                         f"precision with error {error}. "
-                        "Retrying in double precision..."
+                        "Retrying in double precision...",
+                        stacklevel=2,
                     )
                     # Retry in double precision
                     original_dtype = ggT.dtype

docs/examples/basic_usage/example_eigenvalues.py

@@ -169,11 +169,10 @@ def orthonormalize(v: numpy.ndarray, basis: List[numpy.ndarray]) -> numpy.ndarra
 
             if eigenvalue is None:
                 eigenvalue = tmp_eigenvalue
+            elif abs(eigenvalue - tmp_eigenvalue) / (abs(eigenvalue) + 1e-6) < tol:
+                break
             else:
-                if abs(eigenvalue - tmp_eigenvalue) / (abs(eigenvalue) + 1e-6) < tol:
-                    break
-                else:
-                    eigenvalue = tmp_eigenvalue
+                eigenvalue = tmp_eigenvalue
 
         eigenvalues.append(eigenvalue)
         eigenvectors.append(v)

docs/examples/basic_usage/memory_benchmark.py

@@ -21,7 +21,7 @@
 from curvlinops import KFACInverseLinearOperator, KFACLinearOperator
 
 
-def run_peakmem_benchmark(  # noqa: C901
+def run_peakmem_benchmark(  # noqa: C901, PLR0915
     linop_str: str, problem_str: str, device_str: str, op_str: str
 ):
     """Execute the memory benchmark for a given linear operator class and save results.

makefile

@@ -4,7 +4,7 @@ help:
 	@echo "install"
 	@echo "        Install curvlinops and dependencies"
 	@echo "uninstall"
-	@echo "        Unstall curvlinops"
+	@echo "        Uninstall curvlinops"
 	@echo "lint"
 	@echo "        Run all linting actions"
 	@echo "docs"
@@ -21,16 +21,14 @@ help:
 	@echo "        Run pytest on test and report coverage"
 	@echo "install-lint"
 	@echo "        Install curvlinops and the linter tools"
-	@echo "isort"
-	@echo "        Run isort (sort imports) on the project"
-	@echo "isort-check"
-	@echo "        Check if isort (sort imports) would change files"
-	@echo "black"
-	@echo "        Run black on the project"
-	@echo "black-check"
-	@echo "        Check if black would change files"
-	@echo "flake8"
-	@echo "        Run flake8 on the project"
+	@echo "ruff-format"
+	@echo "        Run ruff format on the project"
+	@echo "ruff-format-check"
+	@echo "        Check if ruff format would change files"
+	@echo "ruff"
+	@echo "        Run ruff on the project and fix errors"
+	@echo "ruff-check"
+	@echo "        Run ruff check on the project without fixing errors"
 	@echo "conda-env"
 	@echo "        Create conda environment 'curvlinops' with dev setup"
 	@echo "darglint-check"
@@ -81,26 +79,21 @@ test-light:
 install-lint:
 	@pip install -e .[lint]
 
-.PHONY: isort isort-check
+.PHONY: ruff-format ruff-format-check
 
-isort:
-	@isort .
+ruff-format:
+	@ruff format .
 
-isort-check:
-	@isort . --check --diff
+ruff-format-check:
+	@ruff format --check .
 
-.PHONY: black black-check
+.PHONY: ruff-check
 
-black:
-	@black . --config=black.toml
+ruff:
+	@ruff check . --fix
 
-black-check:
-	@black . --config=black.toml --check
-
-.PHONY: flake8
-
-flake8:
-	@flake8 .
+ruff-check:
+	@ruff check .
 
 .PHONY: darglint-check
 
@@ -120,8 +113,7 @@ conda-env:
 .PHONY: lint
 
 lint:
-	make black-check
-	make isort-check
-	make flake8
+	make ruff-format-check
+	make ruff-check
 	make darglint-check
 	make pydocstyle-check

pyproject.toml

@@ -64,18 +64,9 @@ test = [
 
 # Dependencies needed for linting.
 lint = [
-    "black",
-    "flake8",
-    "mccabe",
-    "pycodestyle",
-    "pyflakes",
-    "pep8-naming",
-    "flake8-bugbear",
-    "flake8-comprehensions",
-    "flake8-tidy-imports",
+    "ruff",
     "darglint",
     "pydocstyle",
-    "isort",
 ]
 
 # Dependencies needed to build/view the documentation.
@@ -95,14 +86,58 @@ docs = [
 ###############################################################################
 [tool.setuptools_scm]
 
-[tool.isort]
-profile = "black"
-multi_line_output = 3
-include_trailing_comma = true
-force_grid_wrap = 0
-use_parentheses = true
-
 [tool.pydocstyle]
 convention = "google"
 match = '.*\.py'
 match_dir = '^(?!(test|.git)).*'
+
+[tool.ruff]
+line-length = 88
+
+[tool.ruff.lint]
+# Enable all rules from flake8 (E, F), plus additional ones including isort (I)
+select = ["E", "F", "B", "C", "W", "B9", "PLE", "PLW", "PLR", "I"]
+ignore = [
+    # E501 max-line-length (replaced by B950 (max-line-length + 10%))
+    "E501",
+    # C408 use {} instead of dict() (ignored because pytorch uses dict)
+    "C408",
+    # E203 whitespace before :
+    "E203",
+    # E231 missing whitespace after ','
+    "E231",
+    # W291 trailing whitespace
+    "W291",
+    # E203 line break before binary operator (replaces W503)
+    "E203",
+    # Line break occurred after a binary operator (replaces W504)
+    "E226",
+    # B905 `zip()` without an explicit `strict=` parameter
+    "B905",
+    # Too many arguments in function definition (9 > 5)
+    "PLR0913",
+    # Magic value comparison
+    "PLR2004",
+    # Loop variable overwritten by assignment target
+    "PLW2901",
+]
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+skip-magic-trailing-comma = false
+line-ending = "auto"
+exclude = [
+    ".eggs",
+    ".git",
+    ".pytest_cache",
+    "docs/rtd",
+    "build",
+    "dist",
+]
+
+[tool.ruff.lint.per-file-ignores]
+# Add any per-file ignores here if needed
+
+[tool.ruff.lint.flake8-bugbear]
+extend-immutable-calls = ["pytest.raises", "pytest.warns", "pytest.mark.skip"]

setup.cfg

@@ -1,29 +1,6 @@
 # Note: These tools do not yet support `pyproject.toml`, but these options
 # should be moved there once support is added.
 
-[flake8]
-select = B,C,E,F,P,W,B9
-max-line-length = 88
-max-complexity = 10
-# E501 max-line-length (replaced by B950 (max-line-length + 10%))
-# C408 use {} instead of dict() (ignored because pytorch uses dict)
-# E203 whitespace before : (not Black-compatible)
-# E231 missing whitespace after ','
-# W291 trailing whitespace
-# W503 line break before binary operator
-# W504 line break after binary operator
-# B905 `zip()` without an explicit `strict=` parameter
-ignore =
-	E501,
-	C408,
-	E203,
-	E231,
-	W291,
-	W503,
-	W504,
-	B905,
-exclude = build, .git, docs/rtd, .eggs
-
 [darglint]
 docstring_style = google
 strictness = full