Merge pull request #862 from jarrodmillman/precommit-2-26

jarrodmillman · web-flow · commit 13121a592b51 · 2026-02-03T07:30:04.000-08:00
Update pre-commit repos
diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -10,3 +10,4 @@ d8966d848af75751823e825eb76c5bbff58f5c07
 1fd0ce6759be32be38bbfab32e83d157a82dfe25
 406488494019fb199474fea7f1694e9f0d0347bc
 968df447681ba7d33c9088d4446b8a92ec0a1389
+ed709e41bd10763dcb376a982dd1eb72b742ccc9
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: cef0300fd0fc4d2a87a85fa2093c6b283ea36f4b # frozen: v5.0.0
+    rev: 3e8a8703264a2f4a69428a0aa4dcb512790b2c8c # frozen: v6.0.0
     hooks:
       - id: check-added-large-files
       - id: check-ast
@@ -19,27 +19,27 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/rbubley/mirrors-prettier
-    rev: 787fb9f542b140ba0b2aced38e6a3e68021647a3 # frozen: v3.5.3
+    rev: c2bc67fe8f8f549cc489e00ba8b45aa18ee713b1 # frozen: v3.8.1
     hooks:
       - id: prettier
         files: \.(md|rst|yml|yaml)
         args: [--prose-wrap=preserve]
 
   - repo: https://github.com/MarcoGorelli/cython-lint
-    rev: 1ac5158c1b0f405350517c218f03d3a21bbb381c # frozen: v0.16.6
+    rev: 7c6152f6c8f9087684ff2e09a9227941e233bafb # frozen: v0.19.0
     hooks:
       - id: cython-lint
         args: [--no-pycodestyle, --max-line-length=88]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: e84319e627902e1b348574ecf3238dc511933dc7 # frozen: v0.11.7
+    rev: 45ef068da5f21267bb2a7ec4a623092959f09ce5 # frozen: v0.14.14
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes", "--exit-non-zero-on-fix"]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "f40886d54c729f533f864ed6ce584e920feb0af7" # frozen: v1.15.0
+    rev: "a66e98df7b4aeeb3724184b332785976d062b92e" # frozen: v1.19.1
     hooks:
       - id: mypy
         additional_dependencies:
diff --git a/advanced/advanced_numpy/index.md b/advanced/advanced_numpy/index.md
@@ -330,7 +330,6 @@ etc. for loading sound data...
 ##### Casting
 
 - Casting in arithmetic, in nutshell:
-
   - only type (not value!) of operands matters
   - largest "safe" type able to represent both is picked
   - scalars can "lose" to arrays in some situations
@@ -1007,7 +1006,6 @@ x.strides, y.strides
 
 - CPU pulls data from main memory to its cache in blocks
 - If many array items consecutively operated on fit in a single block (small stride):
-
   - $\Rightarrow$ fewer transfers needed
   - $\Rightarrow$ faster
 
@@ -1671,13 +1669,11 @@ Get this tutorial: <https://www.euroscipy.org/talk/882>
 ### Reporting bugs
 
 - Bug tracker (prefer **this**)
-
   - <https://github.com/numpy/numpy/issues>
   - <https://github.com/scipy/scipy/issues>
   - Click the "Sign up" link to get an account
 
 - Mailing lists (<https://numpy.org/community/>)
-
   - If you're unsure
   - No replies in a week or so? Just file a bug ticket.
 
@@ -1712,7 +1708,6 @@ I'm using NumPy 1.4.1, built from the official tarball, on Windows
 
 0. What are you trying to do?
 1. **Small code snippet reproducing the bug** (if possible)
-
    - What actually happens
    - What you'd expect
 
@@ -1736,17 +1731,14 @@ If unsure, try to remove existing NumPy installations, and reinstall...
 ### Contributing to documentation
 
 1. Documentation editor
-
    - <https://numpy.org/doc/stable/>
 
    - Registration
-
      - Register an account
 
      - Subscribe to `scipy-dev` mailing list (subscribers-only)
 
      - Problem with mailing lists: you get mail
-
        - But: **you can turn mail delivery off**
 
        - "change your subscription options", at the bottom of
@@ -1767,7 +1759,6 @@ If unsure, try to remove existing NumPy installations, and reinstall...
        ```
 
    - Check the style guide:
-
      - <https://numpy.org/doc/stable/>
      - Don't be intimidated; to fix a small thing, just fix it
 
@@ -1784,21 +1775,16 @@ The contribution of features is documented on <https://numpy.org/doc/stable/dev/
 ### How to help, in general
 
 - Bug fixes always welcome!
-
   - What irks you most
   - Browse the tracker
 
 - Documentation work
-
   - API docs: improvements to docstrings
-
     - Know some SciPy module well?
 
   - _User guide_
-
     - <https://numpy.org/doc/stable/user/>
 
 - Ask on communication channels:
-
   - `numpy-discussion` list
   - `scipy-dev` list
diff --git a/advanced/advanced_python/index.md b/advanced/advanced_python/index.md
@@ -1028,7 +1028,6 @@ the source of a program.
 - <https://pypi.org/project/decorator>
 
 - Bruce Eckel
-
   - [Decorators I]: Introduction to Python Decorators
   - [Python Decorators II]: Decorator Arguments
   - [Python Decorators III]: A Decorator-Based Build System
@@ -1118,15 +1117,13 @@ used and it is most convenient to have the support built in. With each
 release, Python provides support in more places:
 
 - all file-like objects:
-
   - `file` ➔ automatically closed
   - `fileinput`, `tempfile`
   - `bz2.BZ2File`, `gzip.GzipFile`,
     `tarfile.TarFile`, `zipfile.ZipFile`
   - `ftplib`, `nntplib` ➔ close connection
 
 - locks
-
   - `multiprocessing.RLock` ➔ lock and unlock
   - `multiprocessing.Semaphore`
   - `memoryview` ➔ automatically release
@@ -1140,7 +1137,6 @@ release, Python provides support in more places:
 - `contextlib.closing` ➔ the same as the example above, call `close`
 
 - parallel programming
-
   - `concurrent.futures.ThreadPoolExecutor` ➔ invoke in parallel then kill thread pool
   - `concurrent.futures.ProcessPoolExecutor` ➔ invoke in parallel then kill process pool
   - `nogil` ➔ solve the GIL problem temporarily (cython only :( )
diff --git a/advanced/debugging/index.md b/advanced/debugging/index.md
@@ -47,11 +47,9 @@ when you write it, how will you ever debug it?”_
 - Write your code with testing and debugging in mind.
 
 - Keep It Simple, Stupid (KISS).
-
   - What is the simplest thing that could possibly work?
 
 - Don't Repeat Yourself (DRY).
-
   - Every piece of knowledge must have a single, unambiguous,
     authoritative representation within a system.
   - Constants, algorithms, etc...
@@ -88,7 +86,6 @@ You can bind a key to run pyflakes in the current buffer.
 
 - **In kate**
   Menu: 'settings -> configure kate
-
   - In plugins enable 'external tools'
   - In external Tools', add `pyflakes`:
 
@@ -143,9 +140,7 @@ You can bind a key to run pyflakes in the current buffer.
 #### A type-as-go spell-checker like integration
 
 - **In vim**
-
   - Use the pyflakes.vim plugin:
-
     1. download the zip file from
        <https://www.vim.org/scripts/script.php?script_id=2441>
     2. extract the files in `~/.vim/ftplugin/python`
@@ -185,7 +180,6 @@ code, with short modify-run-fail cycles.**
 
 2. Divide and Conquer. Once you have a failing test case, isolate the
    failing code.
-
    - Which module.
    - Which function.
    - Which line of code.
diff --git a/advanced/interfacing_with_c/interfacing_with_c.md b/advanced/interfacing_with_c/interfacing_with_c.md
@@ -854,7 +854,6 @@ interesting. If you have good ideas for exercises, please let us know!
    fragile and respond badly to input errors. Look for ways to crash the
    examples, figure what the problem is and devise a potential solution.
    Here are some ideas:
-
    1. Numerical overflow.
    2. Input and output arrays that have different lengths.
    3. Multidimensional array.
diff --git a/advanced/mathematical_optimization/helper/compare_optimizers.py b/advanced/mathematical_optimization/helper/compare_optimizers.py
@@ -65,7 +65,7 @@ def bencher(cost_name, ndim, method_name, x0):
 
 # Bench with gradients
 def bencher_gradient(cost_name, ndim, method_name, x0):
-    cost_function, cost_function_prime, hessian = mk_costs(ndim)[0][cost_name]
+    cost_function, cost_function_prime, _hessian = mk_costs(ndim)[0][cost_name]
     method = methods[method_name]
     f_prime = CountingFunction(cost_function_prime)
     f = LoggingFunction(cost_function, counter=f_prime.counter)
diff --git a/advanced/mathematical_optimization/index.md b/advanced/mathematical_optimization/index.md
@@ -98,7 +98,6 @@ on which the search is performed.
     :doc: optimization_examples.md
     :::
 - - **A convex function**:
-
     - $f$ is above all its tangents.
     - Equivalently, for two points $A, B$, $f(C)$ lies below the segment
       $[f(A), f(B])]$, if $A < C < B$.
diff --git a/advanced/optimizing/demo.py b/advanced/optimizing/demo.py
@@ -10,7 +10,7 @@
 def test():
     rng = np.random.default_rng()
     data = rng.random((5000, 100))
-    u, s, v = sp.linalg.svd(data)
+    u, _s, _v = sp.linalg.svd(data)
     pca = u[:, :10].T @ data
     results = fastica(pca.T, whiten=False)
 
diff --git a/advanced/optimizing/demo_opt.py b/advanced/optimizing/demo_opt.py
@@ -9,7 +9,7 @@
 def test():
     rng = np.random.default_rng()
     data = rng.random((5000, 100))
-    u, s, v = sp.linalg.svd(data, full_matrices=False)
+    u, _s, _v = sp.linalg.svd(data, full_matrices=False)
     pca = u[:, :10].T @ data
     results = fastica(pca.T, whiten=False)
 
diff --git a/advanced/optimizing/ica.py b/advanced/optimizing/ica.py
@@ -72,7 +72,7 @@ def _ica_par(X, tol, g, gprime, fun_args, maxit, w_init):
     Used internally by FastICA.
 
     """
-    n, p = X.shape
+    _n, p = X.shape
 
     W = _sym_decorrelation(w_init)
 
diff --git a/advanced/scipy_sparse/bsr_array.md b/advanced/scipy_sparse/bsr_array.md
@@ -23,10 +23,8 @@ import scipy as sp
 
 - basically a CSR with dense sub-matrices of fixed shape instead of scalar
   items
-
   - block size `(R, C)` must evenly divide the shape of the matrix `(M, N)`
   - three NumPy arrays: `indices`, `indptr`, `data`
-
     - `indices` is array of column indices for each block
 
     - `data` is array of corresponding nonzero values of shape `(nnz, R, C)`
diff --git a/advanced/scipy_sparse/coo_array.md b/advanced/scipy_sparse/coo_array.md
@@ -40,7 +40,6 @@ import scipy as sp
   - manipulate data array directly (fast NumPy machinery)
 - no slicing, no arithmetic (directly, converts to CSR)
 - use:
-
   - facilitates fast conversion among sparse formats
 
   - when converting to other format (usually CSR or CSC), duplicate
diff --git a/advanced/scipy_sparse/introduction.md b/advanced/scipy_sparse/introduction.md
@@ -53,16 +53,13 @@ plt.ylabel('memory [MB]')
 ## Typical Applications
 
 - solution of partial differential equations (PDEs)
-
   - the _finite element method_
   - mechanical engineering, electrotechnics, physics, ...
 
 - graph theory
-
   - nonzero at `(i, j)` means that node `i` is connected to node `j`
 
 - natural language processing
-
   - nonzero at `(i, j)` means that the document `i` contains the word `j`
 
 - ...
diff --git a/advanced/scipy_sparse/solvers.md b/advanced/scipy_sparse/solvers.md
@@ -131,12 +131,10 @@ print("Error: %s" % (mtx2 * x - rhs))
 ### Common Parameters
 
 - mandatory:
-
   - `A` : The N-by-N matrix of the linear system.
   - `b`: Right hand side of the linear system. Has shape (N,) or (N,1).
 
 - optional:
-
   - `x0`: Starting guess for the solution.
   - `tol` : Relative tolerance to achieve before terminating.
   - `maxiter` : Maximum number of iterations. Iteration will stop after maxiter
@@ -195,7 +193,6 @@ A * np.ones(2)
 - `lobpcg`: (Locally Optimal Block Preconditioned Conjugate
   Gradient Method); \* works very well in combination with
   [PyAMG](https://github.com/pyamg/pyamg)
-
   - example by Nathan Bell:
 
     {download}`examples/pyamg_with_lobpcg.py`
diff --git a/advanced/scipy_sparse/storage_schemes.md b/advanced/scipy_sparse/storage_schemes.md
@@ -16,7 +16,6 @@ kernelspec:
 ## Sparse Array Classes
 
 - There are seven sparse array types in scipy.sparse:
-
   1. [csr_array](csr_array): Compressed Sparse Row format
   2. [csc_array](csc_array): Compressed Sparse Column format
   3. [bsr_array](csc_array): Block Sparse Row format
diff --git a/intro/language/basic_types.md b/intro/language/basic_types.md
@@ -573,7 +573,6 @@ id(a)
 ```
 
 - the key concept here is **mutable vs. immutable**
-
   - mutable objects can be changed in place
   - immutable objects cannot be modified once created
 
diff --git a/intro/language/io.md b/intro/language/io.md
@@ -65,13 +65,11 @@ f.close()
 - Read-only: `r`
 
 - Write-only: `w`
-
   - Note: Create a new file or _overwrite_ existing file.
 
 - Append a file: `a`
 
 - Read and Write: `r+`
 
 - Binary mode: `b`
-
   - Note: Use for binary files, especially on Windows.
diff --git a/intro/matplotlib/index.md b/intro/matplotlib/index.md
@@ -1462,20 +1462,17 @@ community of users and developers. Here are some links of interest:
 ### Tutorials
 
 - [Pyplot tutorial](https://matplotlib.org/users/pyplot_tutorial.html)
-
   - Introduction
   - Controlling line properties
   - Working with multiple figures and axes
   - Working with text
 
 - [Image tutorial](https://matplotlib.org/users/image_tutorial.html)
-
   - Startup commands
   - Importing image data into NumPy arrays
   - Plotting NumPy arrays as images
 
 - [Text tutorial](https://matplotlib.org/users/index_text.html)
-
   - Text introduction
   - Basic text commands
   - Text properties and layout
@@ -1484,7 +1481,6 @@ community of users and developers. Here are some links of interest:
   - Annotating text
 
 - [Artist tutorial](https://matplotlib.org/users/artists.html)
-
   - Introduction
   - Customizing your objects
   - Object containers
@@ -1494,13 +1490,11 @@ community of users and developers. Here are some links of interest:
   - Tick containers
 
 - [Path tutorial](https://matplotlib.org/users/path_tutorial.html)
-
   - Introduction
   - Bézier example
   - Compound paths
 
 - [Transforms tutorial](https://matplotlib.org/users/transforms_tutorial.html)
-
   - Introduction
   - Data coordinates
   - Axes coordinates
@@ -1515,7 +1509,6 @@ community of users and developers. Here are some links of interest:
 - [User guide](https://matplotlib.org/users/index.html)
 
 - [FAQ](https://matplotlib.org/faq/index.html)
-
   - Installation
   - Usage
   - How-To
diff --git a/intro/numpy/array_object.md b/intro/numpy/array_object.md
@@ -792,7 +792,6 @@ for j in range(2, N_max + 1):
 Skim through `help(np.nonzero)`, and print the prime numbers
 
 - Follow-up:
-
   - Move the above code into a script file named `prime_sieve.py`
   - Run it to check it works
   - Use the optimization suggested in [the sieve of Eratosthenes](https://en.wikipedia.org/wiki/Sieve_of_Eratosthenes):
diff --git a/intro/numpy/operations.md b/intro/numpy/operations.md
diff --git a/packages/scikit-learn/index.md b/packages/scikit-learn/index.md
