Merge pull request #50 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: 'ubermagutil/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: 1.6.3
-  hooks:
-  - id: nbqa-isort  # isort inside Jupyter notebooks
-
-- repo: https://github.com/PyCQA/flake8
-  rev: 6.0.0
-  hooks:
-  - id: flake8
-    additional_dependencies: [flake8-rst-docstrings]  #, flake8-docstrings]
-
-- repo: https://github.com/psf/black
-  rev: 23.1.0
-  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

@@ -57,15 +57,49 @@ repository = "https://github.com/ubermag/ubermagutil"
 
 
 
-[tool.black]
-experimental-string-processing = true
 
 [tool.coverage.run]
 omit = ["ubermagutil/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 = ["ubermagutil"]
+
+[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
+]
 
 [tool.setuptools.packages.find]
 include = ["ubermagutil*"]

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
 

ubermagutil/__init__.py

@@ -1,12 +1,14 @@
 """Utilities used across Ubermag."""
+
 import importlib.metadata
 
 import pytest
 
-from . import progress
-from .basic_logging import setup_logging
-from .inherit_docs import inherit_docs
-from .tools import changedir, hysteresis_values
+from . import progress as progress
+from .basic_logging import setup_logging as setup_logging
+from .inherit_docs import inherit_docs as inherit_docs
+from .tools import changedir as changedir
+from .tools import hysteresis_values as hysteresis_values
 
 __version__ = importlib.metadata.version(__package__)
 

ubermagutil/basic_logging.py

@@ -1,4 +1,5 @@
 """Setup basic logging for all ubermag packages."""
+
 import logging
 
 

ubermagutil/progress.py

@@ -88,7 +88,7 @@ def summary(package_name, runner_name):
         yield
     finally:
         toc = time.time()
-        seconds = "({:0.1f} s)".format(toc - tic)
+        seconds = f"({toc - tic:0.1f} s)"
         print(seconds)  # append seconds to the previous print.
 
 

ubermagutil/tests/test_tools.py

@@ -33,9 +33,8 @@ def test_hysteresis_values():
 
 
 def test_changedir(tmp_path):
-    with uu.changedir(tmp_path):
-        with open("test.txt", "wt", encoding="utf-8") as f:
-            f.write("")
+    with uu.changedir(tmp_path), open("test.txt", "w", encoding="utf-8") as f:
+        f.write("")
 
     assert (tmp_path / "test.txt").exists()
     assert not (pathlib.Path() / "test.txt").exists()

ubermagutil/tools.py

@@ -1,4 +1,5 @@
 """Additional tools."""
+
 import contextlib
 import os
 

ubermagutil/typesystem/__init__.py

@@ -1,12 +1,11 @@
 """Typesystem utility."""
-from .descriptors import (
-    Descriptor,
-    Dictionary,
-    Name,
-    Parameter,
-    Scalar,
-    Subset,
-    Typed,
-    Vector,
-)
-from .typesystem import typesystem
+
+from .descriptors import Descriptor as Descriptor
+from .descriptors import Dictionary as Dictionary
+from .descriptors import Name as Name
+from .descriptors import Parameter as Parameter
+from .descriptors import Scalar as Scalar
+from .descriptors import Subset as Subset
+from .descriptors import Typed as Typed
+from .descriptors import Vector as Vector
+from .typesystem import typesystem as typesystem

ubermagutil/typesystem/descriptors.py

@@ -196,10 +196,9 @@ class Typed(Descriptor):
     """
 
     def __set__(self, instance, value):
-        if hasattr(self, "allow_none"):
-            if self.allow_none and value is None:
-                super().__set__(instance, value)
-                return None
+        if hasattr(self, "allow_none") and self.allow_none and value is None:
+            super().__set__(instance, value)
+            return None
         if not isinstance(value, self.expected_type):
             msg = f"Cannot set {self.name} with {type(value)}."
             raise TypeError(msg)
@@ -280,25 +279,21 @@ class Scalar(Descriptor):
     """
 
     def __set__(self, instance, value):
-        if hasattr(self, "otherwise"):
-            if isinstance(value, self.otherwise):
-                super().__set__(instance, value)
-                return None
+        if hasattr(self, "otherwise") and isinstance(value, self.otherwise):
+            super().__set__(instance, value)
+            return None
         if not isinstance(value, numbers.Real):
             msg = f"Cannot set {self.name} with {type(value)}."
             raise TypeError(msg)
-        if hasattr(self, "expected_type"):
-            if not isinstance(value, self.expected_type):
-                msg = f"Cannot set {self.name} with {type(value)}."
-                raise TypeError(msg)
-        if hasattr(self, "unsigned"):
-            if self.unsigned and value < 0:
-                msg = f"Cannot set {self.name} with value = {value} < 0."
-                raise ValueError(msg)
-        if hasattr(self, "positive"):
-            if self.positive and value <= 0:
-                msg = f"Cannot set {self.name} with value = {value} <= 0."
-                raise ValueError(msg)
+        if hasattr(self, "expected_type") and not isinstance(value, self.expected_type):
+            msg = f"Cannot set {self.name} with {type(value)}."
+            raise TypeError(msg)
+        if hasattr(self, "unsigned") and self.unsigned and value < 0:
+            msg = f"Cannot set {self.name} with value = {value} < 0."
+            raise ValueError(msg)
+        if hasattr(self, "positive") and self.positive and value <= 0:
+            msg = f"Cannot set {self.name} with value = {value} <= 0."
+            raise ValueError(msg)
         super().__set__(instance, value)
 
 
@@ -390,30 +385,27 @@ class Vector(Descriptor):
     """
 
     def __set__(self, instance, value):
-        if hasattr(self, "otherwise"):
-            if isinstance(value, self.otherwise):
-                super().__set__(instance, value)
-                return None
+        if hasattr(self, "otherwise") and isinstance(value, self.otherwise):
+            super().__set__(instance, value)
+            return None
         if not isinstance(value, (tuple, list, np.ndarray)):
             msg = f"Cannot set {self.name} with {type(value)}."
             raise TypeError(msg)
         if not all(isinstance(i, numbers.Real) for i in value):
             msg = "Allowed only type(value[i]) == numbers.Real."
             raise TypeError(msg)
-        if hasattr(self, "size"):
-            if len(value) != self.size:
-                msg = f"Cannot set {self.name} with length {len(value)} value."
-                raise ValueError(msg)
-        if hasattr(self, "component_type"):
-            if not all(isinstance(i, self.component_type) for i in value):
-                msg = f"Allowed only type(value[i]) == {self.component_type}."
-                raise TypeError(msg)
-        if hasattr(self, "unsigned"):
-            if self.unsigned and not all(i >= 0 for i in value):
-                raise ValueError("Allowed only value[i] >= 0.")
-        if hasattr(self, "positive"):
-            if self.positive and not all(i > 0 for i in value):
-                raise ValueError("Allowed only value[i] > 0.")
+        if hasattr(self, "size") and len(value) != self.size:
+            msg = f"Cannot set {self.name} with length {len(value)} value."
+            raise ValueError(msg)
+        if hasattr(self, "component_type") and any(
+            not isinstance(i, self.component_type) for i in value
+        ):
+            msg = f"Allowed only type(value[i]) == {self.component_type}."
+            raise TypeError(msg)
+        if hasattr(self, "unsigned") and self.unsigned and any(i < 0 for i in value):
+            raise ValueError("Allowed only value[i] >= 0.")
+        if hasattr(self, "positive") and self.positive and any(i <= 0 for i in value):
+            raise ValueError("Allowed only value[i] > 0.")
         super().__set__(instance, value)
 
 
@@ -572,10 +564,9 @@ class Dictionary(Descriptor):
     """
 
     def __set__(self, instance, value):
-        if hasattr(self, "otherwise"):
-            if isinstance(value, self.otherwise):
-                super().__set__(instance, value)
-                return None
+        if hasattr(self, "otherwise") and isinstance(value, self.otherwise):
+            super().__set__(instance, value)
+            return None
         if not isinstance(value, dict):
             msg = f"Cannot set {self.name} with {type(value)}."
             raise TypeError(msg)
@@ -652,10 +643,9 @@ class Parameter(Descriptor):
     """
 
     def __set__(self, instance, value):
-        if hasattr(self, "otherwise"):
-            if isinstance(value, self.otherwise):
-                super().__set__(instance, value)
-                return None
+        if hasattr(self, "otherwise") and isinstance(value, self.otherwise):
+            super().__set__(instance, value)
+            return None
         if isinstance(value, dict):
             dictdescriptor = Dictionary(
                 key_descriptor=Name(allowed_char=":"), value_descriptor=self.descriptor
@@ -714,10 +704,9 @@ class Subset(Descriptor):
     """
 
     def __set__(self, instance, value):
-        if hasattr(self, "otherwise"):
-            if isinstance(value, self.otherwise):
-                super().__set__(instance, value)
-                return None
+        if hasattr(self, "otherwise") and isinstance(value, self.otherwise):
+            super().__set__(instance, value)
+            return None
         if self.unpack:
             val = set(value)
             if not val.issubset(self.sample_set):

ubermagutil/typesystem/typesystem.py

@@ -42,7 +42,7 @@ def typesystem(**kwargs):  # noqa: D401
     def decorate(cls):
         for key, value in kwargs.items():
             if isinstance(value, Descriptor):
-                setattr(value, "name", key)
+                value.name = key
                 setattr(cls, key, value)
         return cls
 

ubermagutil/units/__init__.py

@@ -1,2 +1,6 @@
 """SI multiplier utility."""
-from .units import rsi_prefixes, si_max_multiplier, si_multiplier, si_prefixes
+
+from .units import rsi_prefixes as rsi_prefixes
+from .units import si_max_multiplier as si_max_multiplier
+from .units import si_multiplier as si_multiplier
+from .units import si_prefixes as si_prefixes

ubermagutil/units/units.py

@@ -1,4 +1,5 @@
 """SI multiplier utility."""
+
 import collections
 
 si_prefixes = collections.OrderedDict(
@@ -64,7 +65,7 @@ def si_multiplier(value):
     if value == 0:
         return 1
     else:
-        for prefix, multiplier in reversed(si_prefixes.items()):
+        for _prefix, multiplier in reversed(si_prefixes.items()):
             if 1 <= abs(value) / multiplier < 1e3:
                 return multiplier
         else: