update pre-commit config (#8)

Update pre-commit configuration to use ruff as the default linter. Increased line width of ruff to 120. Kind of works in most scenarios.

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: jkanche

.coveragerc

@@ -1,7 +1,7 @@
 # .coveragerc to control coverage.py
 [run]
 branch = True
-source = delayedarray 
+source = delayedarray
 # omit = bad_file.py
 
 [paths]

.github/workflows/pypi-publish.yml

@@ -48,4 +48,4 @@ jobs:
       uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
       with:
         user: __token__
-        password: ${{ secrets.PYPI_PASSWORD }}
+        password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/pypi-test.yml

@@ -32,4 +32,4 @@ jobs:
     #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with tox
       run: |
-        tox
+        tox

.pre-commit-config.yaml

@@ -17,49 +17,34 @@ repos:
   - id: mixed-line-ending
     args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
 
-## If you want to automatically "modernize" your Python code:
-# - repo: https://github.com/asottile/pyupgrade
-#   rev: v3.7.0
-#   hooks:
-#   - id: pyupgrade
-#     args: ['--py37-plus']
-
-## If you want to avoid flake8 errors due to unused vars or imports:
-# - repo: https://github.com/PyCQA/autoflake
-#   rev: v2.1.1
-#   hooks:
-#   - id: autoflake
-#     args: [
-#       --in-place,
-#       --remove-all-unused-imports,
-#       --remove-unused-variables,
-#     ]
-
-- repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
+- repo: https://github.com/PyCQA/docformatter
+  rev: v1.7.5
   hooks:
-  - id: isort
+    - id: docformatter
+      additional_dependencies: [tomli]
+      args: [-r, --black, -in-place]
+      # --config, ./pyproject.toml
 
 - repo: https://github.com/psf/black
   rev: 23.7.0
   hooks:
   - id: black
     language_version: python3
 
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.0.285
+  hooks:
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]
+
 ## If like to embrace black styles even in the docs:
 # - repo: https://github.com/asottile/blacken-docs
 #   rev: v1.13.0
 #   hooks:
 #   - id: blacken-docs
 #     additional_dependencies: [black]
 
-- repo: https://github.com/PyCQA/flake8
-  rev: 6.1.0
-  hooks:
-  - id: flake8
-  ## You can add flake8 plugins via `additional_dependencies`:
-  #  additional_dependencies: [flake8-bugbear]
-
 ## Check for misspells in documentation files:
 # - repo: https://github.com/codespell-project/codespell
 #   rev: v2.2.5

CHANGELOG.md

@@ -6,4 +6,4 @@
 
 ## Version 0.0.3
 
-- separate dense and sparse matrix classes
+- separate dense and sparse matrix classes

docs/requirements.txt

@@ -1,7 +1,7 @@
+furo
 # Requirements file for ReadTheDocs, check .readthedocs.yml.
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!
 # sphinx_rtd_theme
 myst-parser[linkify]
 sphinx>=3.2.1
-furo

pyproject.toml

@@ -9,8 +9,9 @@ build-backend = "setuptools.build_meta"
 version_scheme = "no-guess-dev"
 
 [tool.ruff]
-line-length = 100
+line-length = 120
 src = ["src"]
+exclude = ["tests"]
 
 [tool.ruff.pydocstyle]
 convention = "google"

setup.py

@@ -1,10 +1,8 @@
-"""
-    Setup file for DelayedArray.
-    Use setup.cfg to configure your project.
+"""Setup file for DelayedArray. Use setup.cfg to configure your project.
 
-    This file was generated with PyScaffold 4.5.
-    PyScaffold helps you to put up the scaffold of your new Python project.
-    Learn more under: https://pyscaffold.org/
+This file was generated with PyScaffold 4.5.
+PyScaffold helps you to put up the scaffold of your new Python project.
+Learn more under: https://pyscaffold.org/
 """
 from setuptools import setup
 

src/delayedarray/SparseNdarray.py

@@ -119,10 +119,10 @@ def dtype(self) -> numpy.dtype:
 
     @property
     def contents(self):
-        """Contents of the array.
-        This is intended to be read-only; in general, ``contents`` should only be modified by developers of
-        :py:meth:`~delayedarray.interface.extract_sparse_array` methods or creators of new
-        :py:class:`~delayedarray.DelayedArray.DelayedArray` instances.
+        """Contents of the array. This is intended to be read-only; in general,
+        ``contents`` should only be modified by developers of
+        :py:meth:`~delayedarray.interface.extract_sparse_array` methods or creators of
+        new :py:class:`~delayedarray.DelayedArray.DelayedArray` instances.
 
         Returns:
             A nested list, for a n-dimensional array where n > 1.

src/delayedarray/Subset.py

@@ -96,10 +96,10 @@ def is_subset_noop(idx, full):
 
 
 class Subset:
-    """Delayed subset operation.
-    This will slice the array along one or more dimensions, equivalent to the outer product of
-    subset indices. The subset can also be used to reduce the dimensionality of the array by
-    extracting only one element from one or more dimensions.
+    """Delayed subset operation. This will slice the array along one or more dimensions,
+    equivalent to the outer product of subset indices. The subset can also be used to
+    reduce the dimensionality of the array by extracting only one element from one or
+    more dimensions.
 
     Attributes:
         seed:
@@ -227,8 +227,8 @@ def _extract_dense_array_Subset(x: Subset, idx: Tuple[Sequence, ...]) -> ndarray
     if len(not_lost) < len(mappings):
         if len(not_lost):
             final_shape = []
-            for l in not_lost:
-                final_shape.append(len(mappings[l]))
+            for nl in not_lost:
+                final_shape.append(len(mappings[nl]))
             expanded = expanded.reshape(*final_shape)
         else:
             idx = [0] * len(mappings)

src/delayedarray/UnaryIsometricOpSimple.py

@@ -44,7 +44,8 @@ def _choose_operator(op: OP):
 
 
 class UnaryIsometricOpSimple:
-    """Unary isometric operation involving an n-dimensional seed array with no additional arguments.
+    """Unary isometric operation involving an n-dimensional seed array with no
+    additional arguments.
 
     Attributes:
         seed: An array-like object.

src/delayedarray/UnaryIsometricOpWithArgs.py

@@ -57,14 +57,14 @@ def _choose_operator(op: OP, inplace: bool = False):
 
 
 class UnaryIsometricOpWithArgs:
-    """Unary isometric operation involving an n-dimensional seed array with a scalar or 
+    """Unary isometric operation involving an n-dimensional seed array with a scalar or
     1-dimensional vector.
-    
+
     This is based on Bioconductor's ``DelayedArray::DelayedUnaryIsoOpWithArgs`` class.
     Only one n-dimensional array is involved here, hence the "unary" in the name.
 
-    The data type of the result is determined by NumPy casting given the ``seed`` and ``value`` 
-    data types. We suggest supplying a floating-point ``value`` to avoid unexpected results from 
+    The data type of the result is determined by NumPy casting given the ``seed`` and ``value``
+    data types. We suggest supplying a floating-point ``value`` to avoid unexpected results from
     integer truncation or overflow.
 
     Attributes:
@@ -84,8 +84,8 @@ class UnaryIsometricOpWithArgs:
             Ignored for commutative operations in ``op``.
 
         along (int, optional):
-            Dimension along which the ``value`` is to be added, if ``value`` is a 
-            -dimensional array. This assumes that ``value`` is of length equal to the dimension's 
+            Dimension along which the ``value`` is to be added, if ``value`` is a
+            -dimensional array. This assumes that ``value`` is of length equal to the dimension's
             extent. Ignored if ``value`` is a scalar.
     """
 

tests/conftest.py

@@ -1,10 +1,9 @@
-"""
-    Dummy conftest.py for delayedarray.
+"""Dummy conftest.py for delayedarray.
 
-    If you don't know what this is for, just leave it empty.
-    Read more about conftest.py under:
-    - https://docs.pytest.org/en/stable/fixture.html
-    - https://docs.pytest.org/en/stable/writing_plugins.html
+If you don't know what this is for, just leave it empty.
+Read more about conftest.py under:
+- https://docs.pytest.org/en/stable/fixture.html
+- https://docs.pytest.org/en/stable/writing_plugins.html
 """
 
 # import pytest

tests/test_DelayedArray.py

@@ -1,11 +1,9 @@
 import warnings
-import copy
 
 import delayedarray
-import pytest
 from utils import *
 import numpy
-import math
+
 
 def test_DelayedArray_dense():
     raw = (numpy.random.rand(40, 30) * 5 - 10).astype(numpy.int32)
@@ -146,7 +144,7 @@ def test_DelayedArray_isometric_multiply():
 
 def test_DelayedArray_isometric_divide():
     test_shape = (35, 25)
-    contents = mock_SparseNdarray_contents(test_shape, lower = 1, upper = 10)
+    contents = mock_SparseNdarray_contents(test_shape, lower=1, upper=10)
     y = delayedarray.SparseNdarray(test_shape, contents)
     x = delayedarray.DelayedArray(y)
     expanded = numpy.array(x)
@@ -179,7 +177,7 @@ def test_DelayedArray_isometric_divide():
 
 def test_DelayedArray_isometric_modulo():
     test_shape = (22, 44)
-    contents = mock_SparseNdarray_contents(test_shape, lower = 1, upper = 10)
+    contents = mock_SparseNdarray_contents(test_shape, lower=1, upper=10)
     y = delayedarray.SparseNdarray(test_shape, contents)
     x = delayedarray.DelayedArray(y)
     expanded = numpy.array(x)
@@ -250,30 +248,30 @@ def test_DelayedArray_isometric_floordivide():
     x = delayedarray.DelayedArray(y)
     expanded = numpy.array(x)
 
-    z = x ** 2
+    z = x**2
     assert isinstance(z, delayedarray.DelayedArray)
     assert delayedarray.is_sparse(z)
     assert z.shape == x.shape
-    assert (numpy.array(z) == expanded ** 2).all()
+    assert (numpy.array(z) == expanded**2).all()
 
-    z = 5 ** x
+    z = 5**x
     assert isinstance(z, delayedarray.DelayedArray)
     assert not delayedarray.is_sparse(z)
     assert z.shape == x.shape
-    assert (numpy.array(z) == 5 ** expanded).all()
+    assert (numpy.array(z) == 5**expanded).all()
 
     v = numpy.random.rand(55)
-    z = v ** x
+    z = v**x
     assert isinstance(z, delayedarray.DelayedArray)
     assert not delayedarray.is_sparse(z)
     assert z.shape == x.shape
-    assert (numpy.array(z) == v ** expanded).all()
+    assert (numpy.array(z) == v**expanded).all()
 
-    z = x ** v
+    z = x**v
     assert isinstance(z, delayedarray.DelayedArray)
     assert delayedarray.is_sparse(z)
     assert z.shape == x.shape
-    assert (numpy.array(z) == expanded ** v).all()
+    assert (numpy.array(z) == expanded**v).all()
 
 
 def test_DelayedArray_isometric_simple():
@@ -296,15 +294,30 @@ def test_DelayedArray_isometric_simple():
     assert (numpy.array(z) == abs(expanded)).all()
 
     for op in [
-        "log", "log1p", "log2", "log10", 
-        "exp", "expm1", 
-        "sqrt", "abs", 
-        "sin", "cos", "tan", 
-        "sinh", "cosh", "tanh", 
-        "arcsin", "arccos", "arctan", 
-        "arcsinh", "arccosh", "arctanh",
-        "ceil", "floor", "trunc", 
-        "sign"
+        "log",
+        "log1p",
+        "log2",
+        "log10",
+        "exp",
+        "expm1",
+        "sqrt",
+        "abs",
+        "sin",
+        "cos",
+        "tan",
+        "sinh",
+        "cosh",
+        "tanh",
+        "arcsin",
+        "arccos",
+        "arctan",
+        "arcsinh",
+        "arccosh",
+        "arctanh",
+        "ceil",
+        "floor",
+        "trunc",
+        "sign",
     ]:
         with warnings.catch_warnings():
             warnings.simplefilter("ignore")
@@ -331,13 +344,15 @@ def test_DelayedArray_subset():
     y = delayedarray.SparseNdarray(test_shape, contents)
     x = delayedarray.DelayedArray(y)
 
-    sub = x[2,[20,30,40],[10,11,12,13]]
-    assert sub.shape == (3,4)
+    sub = x[2, [20, 30, 40], [10, 11, 12, 13]]
+    assert sub.shape == (3, 4)
     assert isinstance(sub._seed, delayedarray.Subset)
-    assert (numpy.array(sub) == numpy.array(x)[2,:,:][numpy.ix_([20,30,40], [10,11,12,13])]).all()
+    assert (
+        numpy.array(sub)
+        == numpy.array(x)[2, :, :][numpy.ix_([20, 30, 40], [10, 11, 12, 13])]
+    ).all()
 
-    sub = x[:,:,range(0, 20, 2)]
-    assert sub.shape == (30,55,10)
+    sub = x[:, :, range(0, 20, 2)]
+    assert sub.shape == (30, 55, 10)
     assert isinstance(sub._seed, delayedarray.Subset)
-    assert (numpy.array(sub) == numpy.array(x)[:,:,range(0, 20, 2)]).all()
-
+    assert (numpy.array(sub) == numpy.array(x)[:, :, range(0, 20, 2)]).all()