Merge pull request #56 from ubermag/precommit_updates

Update pre-commits and pytest configuration

.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: v0.4.4
   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 +60,50 @@ 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.lint]
+ignore-init-module-imports = true  # do not remove unused imports in __init__ and warn instead
+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.lint.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
+    "ignore:((.|\n)*)`ipykernel.pylab.backend_inline` is deprecated((.|\n)*)",  # dependency of ipywidgets
+]
 
 [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/*

tasks.py

@@ -1,4 +1,5 @@
 """Tasks to release the package."""
+
 import os
 import shutil
 

ubermagtable/__init__.py

@@ -1,12 +1,13 @@
 """Manipulation of tabular data."""
+
 import importlib.metadata
 import os
 
 import matplotlib.pyplot as plt
 import pytest
 
-from .interact import interact
-from .table import Table
+from .interact import interact as interact
+from .table import Table as Table
 
 # Enable default plotting style.
 dirname = os.path.abspath(os.path.dirname(__file__))

ubermagtable/table.py

@@ -698,10 +698,7 @@ def slider(self, x=None, multiplier=None, description=None, **kwargs):
         labels = np.around(values / multiplier, decimals=2)
         options = list(zip(labels, values))
 
-        if x == "t":
-            units = f" ({ubermagutil.units.rsi_prefixes[multiplier]}s)"
-        else:
-            units = ""
+        units = f" ({ubermagutil.units.rsi_prefixes[multiplier]}s)" if x == "t" else ""
         if description is None:
             description = f"{x}{units}:"
 

ubermagtable/tests/test_table.py

@@ -69,7 +69,7 @@ def test_init(self):
 
     def test_fromfile(self):
         for odtfile in self.odtfiles:
-            for rename in [True, False]:
+            for _rename in [True, False]:
                 table = ut.Table.fromfile(odtfile)
                 check_table(table)
 

ubermagtable/tests/test_util.py

@@ -41,7 +41,7 @@ def test_units():
             units = uu.units(odtfile, rename=rename)
 
             assert isinstance(units, dict)
-            assert all(isinstance(unit, str) for unit in units.keys())
+            assert all(isinstance(unit, str) for unit in units)
             assert all(isinstance(unit, str) for unit in units.values())
             assert "J" in units.values()  # Energy is always in
             assert "" in units.values()  # Columns with no units are always in

ubermagtable/util/__init__.py

@@ -1,2 +1,5 @@
 """Utility tools"""
-from .util import columns, data, units
+
+from .util import columns as columns
+from .util import data as data
+from .util import units as units

ubermagtable/util/util.py

@@ -135,10 +135,10 @@
 
 
 def rename_column(name, cols_dict):
-    if name in cols_dict.keys():
+    if name in cols_dict:
         return cols_dict[name]
 
-    for key in cols_dict.keys():
+    for key in cols_dict:
         if len(key.split("::")) == 2:
             start, end = key.split("::")
             name_split = name.split(":")