Introduce pre-commit. (pydata#617)

* Introduce pre-commit.

* Enable auto-fixes.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Fix imports to get tests passing.

* Resolve linting issues.

* Add back missing version information.

* Add back missing top-level members.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Fix fall-through return.

* Replace all string interpolation with f-strings.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

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

.codecov.yml

@@ -8,13 +8,13 @@ coverage:
           # Total project must not drop by more than 3%
           target: auto
           threshold: "3%"
-    
+
     patch:
       default:
           # Patch coverage must be 92%
           target: auto
           threshold: "92%"
-  
+
   precision: 2
   round: down
   range: 70...98

.github/CODE_OF_CONDUCT.md

@@ -1,3 +1,3 @@
 # Code of Conduct
 
-Please see [`docs/conduct.md`](../docs/conduct.rst)
+Please see [`docs/conduct.md`](docs/conduct.rst)

.github/workflows/ci.yml

@@ -1,6 +1,6 @@
 jobs:
   test:
-    defaults:  
+    defaults:
       run:
         shell: bash -el {0}
     strategy:
@@ -57,7 +57,7 @@ jobs:
         with:
           files: "**/test-*.xml"
   docs:
-    defaults:  
+    defaults:
       run:
         shell: bash -el {0}
     runs-on: ubuntu-latest

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+    - id: check-yaml
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+    - id: fix-byte-order-marker
+    - id: destroyed-symlinks
+    - id: fix-encoding-pragma
+      args: ["--remove"]
+    - id: mixed-line-ending
+    - id: name-tests-test
+      args: ["--pytest-test-first"]
+    - id: no-commit-to-branch
+    - id: pretty-format-json
+      args: ["--autofix", "--no-ensure-ascii"]
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.1.9
+  hooks:
+    - id: ruff
+      args: ["--fix"]
+      types_or: [ python, pyi, jupyter ]
+    - id: ruff-format
+      types_or: [ python, pyi, jupyter ]

.readthedocs.yml

@@ -13,4 +13,4 @@ python:
   - method: pip
     path: .
     extra_requirements:
-      - docs
+      - docs

asv.conf.json

@@ -1,11 +1,11 @@
 {
-    "version": 1,
-    "project": "sparse",
-    "project_url": "https://sparse.pydata.org/",
-    "repo": ".",
-    "dvcs": "git",
-    "environment_type": "conda",
-    "env_dir": ".asv/env",
-    "results_dir": ".asv/results",
-    "html_dir": ".asv/html"
+  "dvcs": "git",
+  "env_dir": ".asv/env",
+  "environment_type": "conda",
+  "html_dir": ".asv/html",
+  "project": "sparse",
+  "project_url": "https://sparse.pydata.org/",
+  "repo": ".",
+  "results_dir": ".asv/results",
+  "version": 1
 }

benchmarks/benchmark_coo.py

@@ -1,7 +1,7 @@
-import numpy as np
-
 import sparse
 
+import numpy as np
+
 
 class MatrixMultiplySuite:
     def setup(self):

benchmarks/benchmark_gcxs.py

@@ -1,7 +1,7 @@
-import numpy as np
-
 import sparse
 
+import numpy as np
+
 
 class MatrixMultiplySuite:
     def setup(self):

benchmarks/benchmark_matmul.py

@@ -1,6 +1,7 @@
-import numpy as np
 import sparse
 
+import numpy as np
+
 
 class Matmul_Sparse:
     params = (["coo", "gcxs"], [0, 1, None])

benchmarks/benchmark_tensordot.py

@@ -1,6 +1,7 @@
-import numpy as np
 import sparse
 
+import numpy as np
+
 
 class TensordotSuiteDenseSparse:
     """
@@ -32,9 +33,7 @@ def setup(self):
         self.s2 = sparse.random((100, 100, 100, 100), density=0.01)
 
     def time_dense(self):
-        sparse.tensordot(
-            self.s1, self.s2, axes=([0, 1], [0, 2]), return_type=np.ndarray
-        )
+        sparse.tensordot(self.s1, self.s2, axes=([0, 1], [0, 2]), return_type=np.ndarray)
 
     def time_sparse(self):
         sparse.tensordot(self.s1, self.s2, axes=([0, 1], [0, 2]))

docs/conf.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 #
 # sparse documentation build configuration file, created by
 # sphinx-quickstart on Fri Dec 29 20:58:03 2017.
@@ -21,7 +20,7 @@
 import sys
 
 sys.path.insert(0, os.path.abspath(".."))
-from sparse import __version__  # flake8: noqa E402
+from sparse import __version__  # noqa: E402
 
 # -- General configuration ------------------------------------------------
 
@@ -49,9 +48,7 @@
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
-mathjax_path = (
-    "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
-)
+mathjax_path = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
@@ -154,9 +151,7 @@
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
-latex_documents = [
-    (master_doc, "sparse.tex", "sparse Documentation", "Sparse Developers", "manual")
-]
+latex_documents = [(master_doc, "sparse.tex", "sparse Documentation", "Sparse Developers", "manual")]
 
 # -- Options for manual page output ---------------------------------------
 

docs/construct.rst

@@ -142,7 +142,7 @@ DOK arrays also support fancy indexing assignment if and only if all dimensions
 
 Alongside indexing assignment and retrieval, :obj:`DOK` arrays support any arbitrary broadcasting function
 to any number of arguments where the arguments can be :obj:`SparseArray` objects, :obj:`scipy.sparse.spmatrix`
-objects, or :obj:`numpy.ndarrays`. 
+objects, or :obj:`numpy.ndarrays`.
 
 .. code-block:: python
 
@@ -161,7 +161,7 @@ and return a new boolean :obj:`DOK` array.
    y = np.random.random((10, 10))
    x == y
 
-:obj:`DOK` arrays are returned from elemwise functions and standard ufuncs if and only if all 
+:obj:`DOK` arrays are returned from elemwise functions and standard ufuncs if and only if all
 :obj:`SparseArray` objects are obj:`DOK` arrays. Otherwise, a :obj:`COO` array or dense array are returned.
 
 At the end, you can convert the :obj:`DOK` array to a :obj:`COO` arrays.

docs/contributing.rst

@@ -36,7 +36,7 @@ Contributing Code
 
 This project has a number of requirements for all code contributed.
 
-* We use ``flake8`` to automatically lint the code and maintain code style.
+* We use ``pre-commit`` to automatically lint the code and maintain code style.
 * We use Numpy-style docstrings.
 * It's ideal if user-facing API changes or new features have documentation added.
 * 100% code coverage is recommended for all new code in any submitted PR. Doctests

docs/gen_logo.py

@@ -1,4 +1,5 @@
 import xml.etree.ElementTree as et
+
 import numpy as np
 
 
@@ -62,9 +63,7 @@ def fill(rs):
         root,
         "rect",
         style=f"{colors['orange']};{fill(rs)};",
-        transform=transform(
-            1, b, 0, 1, (i + 5) * s + offset_x, (i * b + j) * s + offset_y
-        ),
+        transform=transform(1, b, 0, 1, (i + 5) * s + offset_x, (i * b + j) * s + offset_y),
         **kwargs,
     )
 
@@ -104,9 +103,7 @@ def fill(rs):
             root,
             "rect",
             style=f"{colors['blue']};{fill(rs)};",
-            transform=transform(
-                1, b, 0, 1, i * s + offset_x, (i * b + j + y2) * s + offset_y
-            ),
+            transform=transform(1, b, 0, 1, i * s + offset_x, (i * b + j + y2) * s + offset_y),
             **kwargs,
         )
 
@@ -122,9 +119,7 @@ def fill(rs):
         root,
         "rect",
         style=f"{colors['grey']};{fill(rs)};",
-        transform=transform(
-            1, -b, 0, 1, (i + 5) * s + offset_x, ((10 - i) * b + j + 5) * s + offset_y
-        ),
+        transform=transform(1, -b, 0, 1, (i + 5) * s + offset_x, ((10 - i) * b + j + 5) * s + offset_y),
         **kwargs,
     )
 

docs/generated/sparse.COO.T.rst

@@ -3,4 +3,4 @@ COO\.T
 
 .. currentmodule:: sparse
 
-.. autoattribute:: COO.T
+.. autoattribute:: COO.T

docs/generated/sparse.COO.all.rst

@@ -3,4 +3,4 @@ COO.all
 
 .. currentmodule:: sparse
 
-.. automethod:: COO.all
+.. automethod:: COO.all

docs/generated/sparse.COO.any.rst

@@ -3,4 +3,4 @@ COO.any
 
 .. currentmodule:: sparse
 
-.. automethod:: COO.any
+.. automethod:: COO.any

docs/generated/sparse.COO.asformat.rst

@@ -3,4 +3,4 @@ COO.asformat
 
 .. currentmodule:: sparse
 
-.. automethod:: COO.asformat
+.. automethod:: COO.asformat

docs/generated/sparse.COO.astype.rst

@@ -3,4 +3,4 @@ COO\.astype
 
 .. currentmodule:: sparse
 
-.. automethod:: COO.astype
+.. automethod:: COO.astype

docs/generated/sparse.COO.broadcast_to.rst

@@ -3,4 +3,4 @@ COO\.broadcast\_to
 
 .. currentmodule:: sparse
 
-.. automethod:: COO.broadcast_to
+.. automethod:: COO.broadcast_to

docs/generated/sparse.COO.dot.rst

@@ -3,4 +3,4 @@ COO\.dot
 
 .. currentmodule:: sparse
 
-.. automethod:: COO.dot
+.. automethod:: COO.dot

docs/generated/sparse.COO.dtype.rst

@@ -3,4 +3,4 @@ COO\.dtype
 
 .. currentmodule:: sparse
 
-.. autoattribute:: COO.dtype
+.. autoattribute:: COO.dtype

docs/generated/sparse.COO.enable_caching.rst

@@ -3,4 +3,4 @@ COO\.enable\_caching
 
 .. currentmodule:: sparse
 
-.. automethod:: COO.enable_caching
+.. automethod:: COO.enable_caching

docs/generated/sparse.COO.flatten.rst

@@ -3,4 +3,4 @@ COO.flatten
 
 .. currentmodule:: sparse
 
-.. automethod:: COO.flatten
+.. automethod:: COO.flatten

docs/generated/sparse.COO.from_iter.rst

@@ -3,4 +3,4 @@ COO.from\_iter
 
 .. currentmodule:: sparse
 
-.. automethod:: COO.from_iter
+.. automethod:: COO.from_iter

docs/generated/sparse.COO.from_numpy.rst

@@ -3,4 +3,4 @@ COO\.from\_numpy
 
 .. currentmodule:: sparse
 
-.. automethod:: COO.from_numpy
+.. automethod:: COO.from_numpy

docs/generated/sparse.COO.from_scipy_sparse.rst

@@ -3,4 +3,4 @@ COO\.from\_scipy\_sparse
 
 .. currentmodule:: sparse
 
-.. automethod:: COO.from_scipy_sparse
+.. automethod:: COO.from_scipy_sparse

docs/generated/sparse.COO.linear_loc.rst

@@ -3,4 +3,4 @@ COO\.linear\_loc
 
 .. currentmodule:: sparse
 
-.. automethod:: COO.linear_loc
+.. automethod:: COO.linear_loc

docs/generated/sparse.COO.max.rst

@@ -3,4 +3,4 @@ COO\.max
 
 .. currentmodule:: sparse
 
-.. automethod:: COO.max
+.. automethod:: COO.max

docs/generated/sparse.COO.maybe_densify.rst

@@ -3,4 +3,4 @@ COO\.maybe\_densify
 
 .. currentmodule:: sparse
 
-.. automethod:: COO.maybe_densify
+.. automethod:: COO.maybe_densify

docs/generated/sparse.COO.min.rst

@@ -3,4 +3,4 @@ COO\.min
 
 .. currentmodule:: sparse
 
-.. automethod:: COO.min
+.. automethod:: COO.min

docs/generated/sparse.COO.nbytes.rst

@@ -3,4 +3,4 @@ COO\.nbytes
 
 .. currentmodule:: sparse
 
-.. autoattribute:: COO.nbytes
+.. autoattribute:: COO.nbytes

docs/generated/sparse.COO.ndim.rst

@@ -3,4 +3,4 @@ COO\.ndim
 
 .. currentmodule:: sparse
 
-.. autoattribute:: COO.ndim
+.. autoattribute:: COO.ndim

docs/generated/sparse.COO.nnz.rst

@@ -3,4 +3,4 @@ COO\.nnz
 
 .. currentmodule:: sparse
 
-.. autoattribute:: COO.nnz
+.. autoattribute:: COO.nnz

docs/generated/sparse.COO.nonzero.rst

@@ -3,4 +3,4 @@ COO.nonzero
 
 .. currentmodule:: sparse
 
-.. automethod:: COO.nonzero
+.. automethod:: COO.nonzero

docs/generated/sparse.COO.prod.rst

@@ -3,4 +3,4 @@ COO\.prod
 
 .. currentmodule:: sparse
 
-.. automethod:: COO.prod
+.. automethod:: COO.prod