Merge pull request #113 from boutproject/ruff-lint

Switch to `ruff` for linting and formatting

.github/workflows/formatting.yml

@@ -12,26 +12,23 @@ jobs:
   format:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Setup Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.x
-    - name: Install black
+    - name: Install ruff
       run: |
         python -m pip install --upgrade pip
-        pip install black isort
+        pip install ruff
     - name: Version
       run: |
         python --version
-        black --version
-        isort --version
-    - name: Run isort
-      run: |
-        isort src
-    - name: Run black
-      run: |
-        black src
+        ruff --version
+    - name: Run ruff, sort imports
+      run: ruff check --select I . --fix
+    - name: Run ruff format
+      run: ruff format .
     - uses: stefanzweifel/git-auto-commit-action@v4
       with:
         commit_message: "[skip ci] Apply black/isort changes"

.github/workflows/test.yml

@@ -58,15 +58,15 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: "3.11"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8
-    - name: Lint with flake8
-      run: |
-        flake8 && echo "flake8 successful"
+        pip install ruff
+    # Update output format to enable automatic inline annotations.
+    - name: Run Ruff
+      run: ruff check --output-format=github .

pyproject.toml

@@ -47,6 +47,9 @@ tests = [
 docs = [
     "sphinx>=3.4,<5",
 ]
+lint = [
+    "ruff"
+]
 
 [project.scripts]
 bout-squashoutput = "boutdata.scripts.bout_squashoutput:main"
@@ -57,3 +60,38 @@ version = { attr = "setuptools_scm.get_version" }
 
 [tool.setuptools_scm]
 write_to = "src/boutdata/_version.py"
+
+[tool.ruff.lint]
+extend-select = [
+  # "B",           # flake8-bugbear
+  "I",           # isort
+  # "ARG",         # flake8-unused-arguments
+  # "C4",          # flake8-comprehensions
+  # "ICN",         # flake8-import-conventions
+  # "G",           # flake8-logging-format
+  # "PGH",         # pygrep-hooks
+  # "PIE",         # flake8-pie
+  # "PL",          # pylint
+  # "PT",          # flake8-pytest-style
+  # "PTH",         # flake8-use-pathlib
+  # "RET",         # flake8-return
+  # "RUF",         # Ruff-specific
+  # "SIM",         # flake8-simplify
+  # "UP",          # pyupgrade
+  # "YTT",         # flake8-2020
+  # "EXE",         # flake8-executable
+  # "NPY",         # NumPy specific rules
+  # "PD",          # pandas-vet
+  # "FURB",        # refurb
+]
+ignore = [
+  "PLR2004",     # magic-comparison
+#  "B9",          # flake8-bugbear opinionated warnings
+#  "PLC0414",     # useless-import-alias
+  "PLR0913",     # too-many-arguments
+  "PLR0917",     # too-many-positional
+  "PLR0914",     # too-many-locals
+  "PLR0915",     # too-many-statements
+  "PLR0912",     # too-many-branches
+  "PTH123",      # builtin-open
+]

src/boutdata/__init__.py

@@ -1,4 +1,4 @@
-""" Routines for exchanging data to/from BOUT++ """
+"""Routines for exchanging data to/from BOUT++"""
 
 from boutdata.collect import attributes, collect
 from boututils.boutarray import BoutArray
@@ -15,8 +15,6 @@
 __all__ = [
     "attributes",
     "collect",
-    "gen_surface",
-    "pol_slice",
     "BoutArray",
     "alwayswarn",
     "launch",

src/boutdata/collect.py

@@ -953,8 +953,9 @@ def _check_fieldperp_attributes(
         # and check they are unique
         if yindex_global is not None and yindex_global != temp_yindex:
             raise ValueError(
-                "Found FieldPerp {} at different global y-indices, {} "
-                "and {}".format(varname, temp_yindex, yindex_global)
+                "Found FieldPerp {} at different global y-indices, {} " "and {}".format(
+                    varname, temp_yindex, yindex_global
+                )
             )
         yindex_global = temp_yindex
         if fieldperp_yproc is not None and fieldperp_yproc != pe_yind:

src/boutdata/data.py

@@ -25,9 +25,23 @@
 from numpy import arctan as atan  # noqa: F401
 from numpy import arctan2 as atan2  # noqa: F401
 from numpy import arctanh as atanh  # noqa: F401
-from numpy import ceil, cos, cosh, exp, floor, log, log10, pi  # noqa: F401
+from numpy import (  # noqa: F401  # noqa: F401
+    ceil,
+    cos,
+    cosh,
+    exp,
+    floor,
+    log,
+    log10,
+    pi,
+    round,
+    sin,
+    sinh,
+    sqrt,
+    tan,
+    tanh,
+)
 from numpy import power as pow  # noqa: F401
-from numpy import round, sin, sinh, sqrt, tan, tanh  # noqa: F401
 
 from boutdata.collect import (
     _check_fieldperp_attributes,

src/boutdata/gen_surface.py

@@ -1,6 +1,4 @@
-"""Flux surface generator for tokamak grid files
-
-"""
+"""Flux surface generator for tokamak grid files"""
 
 from __future__ import print_function
 

src/boutdata/griddata.py

@@ -1,6 +1,4 @@
-"""Routines for manipulating grid files
-
-"""
+"""Routines for manipulating grid files"""
 
 import matplotlib.pyplot as plt
 import numpy as np

src/boutdata/input.py

@@ -1,6 +1,4 @@
-"""Fourier transform data for input to BOUT++
-
-"""
+"""Fourier transform data for input to BOUT++"""
 
 from numpy import ndarray
 from numpy.fft import rfft

src/boutdata/mms.py

@@ -1,5 +1,5 @@
-""" Functions for calculating sources for the
-    Method of Manufactured Solutions (MMS)
+"""Functions for calculating sources for the
+Method of Manufactured Solutions (MMS)
 
 """
 

src/boutdata/settings.py

@@ -1,6 +1,4 @@
-"""Parse BOUT.inp settings file
-
-"""
+"""Parse BOUT.inp settings file"""
 
 
 def get(filename, name, section=None):

src/boutdata/tests/test_collect.py

@@ -931,7 +931,7 @@ def test_core_min_files_append_time_split_raises(self, core_min, tmp_path):
         """
         Check output from a core-only case using the minimum number of processes
         """
-        data_path, expected, fieldperp_global_yind = core_min
+        data_path, _expected, _fieldperp_global_yind = core_min
         symlink_dump_files(data_path, tmp_path)
 
         collect_kwargs = {"xguards": True, "yguards": "include_upper"}

src/boututils/__init__.py

@@ -1,4 +1,4 @@
-""" Generic routines, useful for all data """
+"""Generic routines, useful for all data"""
 
 __all__ = []
 

src/boututils/ask.py

@@ -1,6 +1,4 @@
-"""Ask a yes/no question and return the answer.
-
-"""
+"""Ask a yes/no question and return the answer."""
 
 import sys
 

src/boututils/boutarray.py

@@ -1,6 +1,4 @@
-"""Wrapper for ndarray with extra attributes for BOUT++ fields.
-
-"""
+"""Wrapper for ndarray with extra attributes for BOUT++ fields."""
 
 import numpy
 

src/boututils/check_scaling.py

@@ -1,6 +1,4 @@
-"""Functions for checking the error scaling of MMS or MES results
-
-"""
+"""Functions for checking the error scaling of MMS or MES results"""
 
 from numpy import array, isclose, log, polyfit
 

src/boututils/surface_average.py

@@ -1,6 +1,4 @@
-"""Average over a surface
-
-"""
+"""Average over a surface"""
 
 import numpy as np
 import scipy

src/boututils/volume_integral.py

@@ -1,6 +1,4 @@
-"""Integrate over a volume
-
-"""
+"""Integrate over a volume"""
 
 import numpy as np
 from past.utils import old_div