Update pre-commits and pytest configuration

- pre-commit: use ruff and ruff formatting to replace black, isort, flake8
- pre-commit: remove hard-coded Python version
- tests: convert all warnings to errors

.pre-commit-config.yaml

@@ -1,37 +1,23 @@
-default_language_version:
-  python: python3.8
+exclude: 'dev'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
   - id: check-merge-conflict  # checks for files that contain merge conflict strings
   - id: check-toml  # checks toml files for parseable syntax
   - id: debug-statements  # checks for debugger imports and py37+ `breakpoint()` calls in python source
-#  - id: trailing-whitespace   # needs more checks
-#    args: [--markdown-linebreak-ext=md]
-#    exclude: 'ubermagtable/tests/test_sample/.*'
 
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.2
   hooks:
-  - id: isort
-
-- repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.7.0
-  hooks:
-  - id: nbqa-isort  # isort inside Jupyter notebooks
-
-- repo: https://github.com/PyCQA/flake8
-  rev: 6.1.0
-  hooks:
-  - id: flake8
-    additional_dependencies: [flake8-rst-docstrings]  #, flake8-docstrings]
-
-- repo: https://github.com/psf/black
-  rev: 23.9.1
-  hooks:
-  - id: black-jupyter
+    # Run the linter.
+    - id: ruff
+      types_or: [python, pyi, jupyter]
+      args: [--fix, --exit-non-zero-on-fix]
+    # Run the formatter.
+    - id: ruff-format
+      types_or: [python, pyi, jupyter]
 
 # - repo: https://github.com/codespell-project/codespell
 #   rev: v2.1.0

pyproject.toml

@@ -60,15 +60,51 @@ repository = "https://github.com/ubermag/ubermagtable"
 
 
 
-[tool.black]
-experimental-string-processing = true
 
 [tool.coverage.run]
 omit = ["ubermagtable/tests/*"]
 
-[tool.isort]
-profile = "black"
-skip_gitignore = true  # ignores files listed in .gitignore
+[tool.ruff]
+ignore-init-module-imports = true  # do not remove unused imports in __init__ and warn instead
+
+[tool.ruff.lint]
+select = [
+    "B",   # flake8-bugbear
+    "E",   # pycodestyle
+    "F",   # Pyflakes
+    "I",   # isort
+    "SIM", # flake8-simplify
+    "UP",  # pyupgrade
+]
+ignore = [
+    # conflict with other rules
+    "D203",  # one-blank-line-before-class (conflicts with D204)
+    "D212",  # multi-line-summary-first-line (conflicts with D213)
+    # conflict with formatter
+    "D206",  # indent-with-spaces
+    "D300",  # triple-single-quotes
+    "E111",  # indentation-with-invalid-multiple
+    "E114",  # indentation-with-invalid-multiple-comment
+    "E117",  # over-indented
+    # conflict with Python 3.6 compatibility
+    "UP022", # replace-stdout-stderr
+]
+
+[tool.ruff.lint.isort]
+known-local-folder = ["ubermagtable"]
+
+[tool.ruff.per-file-ignores]
+"*.ipynb" = [
+    "B018",  # "Found useless expression. Either assign it to a variable or remove it."; false positives when using implicit __repr__ in the notebook
+    "E501",  # line too long
+    "F811",  # 'redefined-while-unused'; many false positives in notebooks because ipywidgets decorated functions are not recognised
+]
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    "error",
+    "ignore:((.|\n)*)Sentinel is not a public part of the traitlets API((.|\n)*)",  # dependency of k3d
+]
 
 [tool.setuptools.packages.find]
 include = ["ubermagtable*"]

setup.cfg

@@ -1,30 +1,2 @@
-[flake8]
-exclude =
-  .git,
-  __pycache__,
-  build,
-  dev,
-  dist,
-  setup.py
-# black has a longer default line length
-max-line-length = 88
-# D107: missing docstring in __init__
-# E203: withespace before ':', required for black
-# RST210: Inline strong start-string without end-string.  # complains about "**kwargs" in docstrings
-extend-ignore = D107,RST210,E203
-per-file-ignores =
-  # imported but unused
-  __init__.py: F401
-  # ignore missing docstrings in tests
-  test_*.py: D100,D101,D102,D103
-docstring-convention: numpy
-# flake8-rst-docstrings:
-rst-roles =
-  py:class,
-  py:func,
-rst-directives =
-  seealso,
-  plot,
-
 [codespell]
 skip = .*,build/*,dev/*,dist/*