chore: add pre-commit configuration file, run ruff-isort (#634)

Continuing from #633, this PR adds support for the `pre-commit` via its
configuration file, which works with https://pre-commit.ci.
- I have suppressed all failing rules to get `pre-commit` passing in
68e3dda, so that we can fix them all
later.
- At most, the style changes in this PR are the imports that have been
tidied up and sorted using the `ruff check . --select I --fix && ruff
format .` command.
- The pre-commit config configuration file was added

Additionally, to automatically enable `pre-commit` as a Git hook
locally, type:

```bash
pip install pre-commit
pre-commit install
```

and subsequently, it would not allow creating commits that fail the
style rules we have set in `pyproject.toml` or those in
`.pre-commit-config.yaml`.

.pre-commit-config.yaml

@@ -0,0 +1,33 @@
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-yaml
+        exclude: conda_recipe/conda.yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.6.2"
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: python-check-blanket-type-ignore
+        exclude: ^src/vector/backends/_numba_object.py$
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal

autograd/__init__.py

@@ -1,23 +1,24 @@
+from autograd.core import primitive_with_deprecation_warnings as primitive
+
+from .builtins import dict, isinstance, list, tuple, type
 from .differential_operators import (
-    make_vjp,
-    grad,
-    multigrad_dict,
+    checkpoint,
+    deriv,
     elementwise_grad,
-    value_and_grad,
+    grad,
     grad_and_aux,
+    grad_named,
+    hessian,
     hessian_tensor_product,
     hessian_vector_product,
-    hessian,
+    holomorphic_grad,
     jacobian,
-    tensor_jacobian_product,
-    vector_jacobian_product,
-    grad_named,
-    checkpoint,
+    make_ggnvp,
     make_hvp,
     make_jvp,
-    make_ggnvp,
-    deriv,
-    holomorphic_grad,
+    make_vjp,
+    multigrad_dict,
+    tensor_jacobian_product,
+    value_and_grad,
+    vector_jacobian_product,
 )
-from .builtins import isinstance, type, tuple, list, dict
-from autograd.core import primitive_with_deprecation_warnings as primitive

autograd/builtins.py

@@ -1,16 +1,16 @@
-from .util import subvals
 from .extend import (
     Box,
-    primitive,
-    notrace_primitive,
-    VSpace,
-    vspace,
     SparseObject,
-    defvjp,
-    defvjp_argnum,
+    VSpace,
     defjvp,
     defjvp_argnum,
+    defvjp,
+    defvjp_argnum,
+    notrace_primitive,
+    primitive,
+    vspace,
 )
+from .util import subvals
 
 isinstance_ = isinstance
 isinstance = notrace_primitive(isinstance)

autograd/core.py

@@ -1,6 +1,7 @@
-from itertools import count
 from functools import reduce
-from .tracer import trace, primitive, toposort, Node, Box, isbox, getval
+from itertools import count
+
+from .tracer import Box, Node, getval, isbox, primitive, toposort, trace
 from .util import func, subval
 
 # -------------------- reverse mode --------------------
@@ -40,9 +41,7 @@ def __init__(self, value, fun, args, kwargs, parent_argnums, parents):
             vjpmaker = primitive_vjps[fun]
         except KeyError:
             fun_name = getattr(fun, "__name__", fun)
-            raise NotImplementedError(
-                f"VJP of {fun_name} wrt argnums {parent_argnums} not defined"
-            )
+            raise NotImplementedError(f"VJP of {fun_name} wrt argnums {parent_argnums} not defined")
         self.vjp = vjpmaker(parent_argnums, value, args, kwargs)
 
     def initialize_root(self):

autograd/differential_operators.py

@@ -1,6 +1,5 @@
 """Convenience functions built on top of `make_vjp`."""
 
-from functools import partial
 from collections import OrderedDict
 
 try:
@@ -9,13 +8,14 @@
     from inspect import getargspec as _getargspec  # Python 2
 import warnings
 
-from .wrap_util import unary_to_nary
-from .builtins import tuple as atuple
-from .core import make_vjp as _make_vjp, make_jvp as _make_jvp
-from .extend import primitive, defvjp_argnum, vspace
-
 import autograd.numpy as np
 
+from .builtins import tuple as atuple
+from .core import make_jvp as _make_jvp
+from .core import make_vjp as _make_vjp
+from .extend import defvjp_argnum, primitive, vspace
+from .wrap_util import unary_to_nary
+
 make_vjp = unary_to_nary(_make_vjp)
 make_jvp = unary_to_nary(_make_jvp)
 

autograd/extend.py

@@ -1,16 +1,16 @@
 # Exposes API for extending autograd
-from .tracer import Box, primitive, register_notrace, notrace_primitive
 from .core import (
+    JVPNode,
     SparseObject,
-    VSpace,
-    vspace,
     VJPNode,
-    JVPNode,
-    defvjp_argnums,
-    defvjp_argnum,
-    defvjp,
-    defjvp_argnums,
-    defjvp_argnum,
-    defjvp,
+    VSpace,
     def_linear,
+    defjvp,
+    defjvp_argnum,
+    defjvp_argnums,
+    defvjp,
+    defvjp_argnum,
+    defvjp_argnums,
+    vspace,
 )
+from .tracer import Box, notrace_primitive, primitive, register_notrace

autograd/misc/__init__.py

@@ -1,2 +1,2 @@
-from .tracers import const_graph
 from .flatten import flatten
+from .tracers import const_graph

autograd/misc/fixed_points.py

@@ -1,6 +1,6 @@
-from autograd.extend import primitive, defvjp, vspace
-from autograd.builtins import tuple
 from autograd import make_vjp
+from autograd.builtins import tuple
+from autograd.extend import defvjp, primitive, vspace
 
 
 @primitive

autograd/misc/flatten.py

@@ -3,9 +3,9 @@
 arrays. The main purpose is to make examples and optimizers simpler.
 """
 
+import autograd.numpy as np
 from autograd import make_vjp
 from autograd.builtins import type
-import autograd.numpy as np
 
 
 def flatten(value):

autograd/misc/optimizers.py

@@ -7,7 +7,6 @@
 These routines can optimize functions whose inputs are structured
 objects, such as dicts of numpy arrays."""
 
-
 import autograd.numpy as np
 from autograd.misc import flatten
 from autograd.wrap_util import wraps

autograd/misc/tracers.py

@@ -1,8 +1,9 @@
+from functools import partial
 from itertools import repeat
-from autograd.wrap_util import wraps
+
+from autograd.tracer import Node, trace
 from autograd.util import subvals, toposort
-from autograd.tracer import trace, Node
-from functools import partial
+from autograd.wrap_util import wraps
 
 
 class ConstGraphNode(Node):

autograd/numpy/__init__.py

@@ -1,8 +1,2 @@
+from . import fft, linalg, numpy_boxes, numpy_jvps, numpy_vjps, numpy_vspaces, random
 from .numpy_wrapper import *
-from . import numpy_boxes
-from . import numpy_vspaces
-from . import numpy_vjps
-from . import numpy_jvps
-from . import linalg
-from . import fft
-from . import random

autograd/numpy/fft.py

@@ -1,8 +1,10 @@
 import numpy.fft as ffto
-from .numpy_wrapper import wrap_namespace
-from .numpy_vjps import match_complex
+
+from autograd.extend import defvjp, primitive, vspace
+
 from . import numpy_wrapper as anp
-from autograd.extend import primitive, defvjp, vspace
+from .numpy_vjps import match_complex
+from .numpy_wrapper import wrap_namespace
 
 wrap_namespace(ffto.__dict__, globals())
 

autograd/numpy/linalg.py

@@ -1,8 +1,11 @@
 from functools import partial
+
 import numpy.linalg as npla
-from .numpy_wrapper import wrap_namespace
+
+from autograd.extend import defjvp, defvjp
+
 from . import numpy_wrapper as anp
-from autograd.extend import defvjp, defjvp
+from .numpy_wrapper import wrap_namespace
 
 wrap_namespace(npla.__dict__, globals())
 

autograd/numpy/numpy_boxes.py

@@ -1,6 +1,8 @@
 import numpy as np
-from autograd.extend import Box, primitive
+
 from autograd.builtins import SequenceBox
+from autograd.extend import Box, primitive
+
 from . import numpy_wrapper as anp
 
 Box.__array_priority__ = 90.0

autograd/numpy/numpy_jvps.py

@@ -1,19 +1,21 @@
 import numpy as onp
+
+from autograd.extend import JVPNode, def_linear, defjvp, defjvp_argnum, register_notrace, vspace
+
+from ..util import func
 from . import numpy_wrapper as anp
+from .numpy_boxes import ArrayBox
 from .numpy_vjps import (
-    untake,
     balanced_eq,
-    match_complex,
-    replace_zero,
     dot_adjoint_0,
     dot_adjoint_1,
+    match_complex,
+    nograd_functions,
+    replace_zero,
     tensordot_adjoint_0,
     tensordot_adjoint_1,
-    nograd_functions,
+    untake,
 )
-from autograd.extend import defjvp, defjvp_argnum, def_linear, vspace, JVPNode, register_notrace
-from ..util import func
-from .numpy_boxes import ArrayBox
 
 for fun in nograd_functions:
     register_notrace(JVPNode, fun)

autograd/numpy/numpy_vjps.py

@@ -1,9 +1,12 @@
 from functools import partial
+
 import numpy as onp
+
+from autograd.extend import SparseObject, VJPNode, defvjp, defvjp_argnum, primitive, register_notrace, vspace
+
 from ..util import func
 from . import numpy_wrapper as anp
 from .numpy_boxes import ArrayBox
-from autograd.extend import primitive, vspace, defvjp, defvjp_argnum, SparseObject, VJPNode, register_notrace
 
 # ----- Non-differentiable functions -----
 

autograd/numpy/numpy_vspaces.py

@@ -1,6 +1,7 @@
 import numpy as np
-from autograd.extend import VSpace
+
 from autograd.builtins import NamedTupleVSpace
+from autograd.extend import VSpace
 
 
 class ArrayVSpace(VSpace):

autograd/numpy/numpy_wrapper.py

@@ -1,8 +1,9 @@
-import types
 import warnings
-from autograd.extend import primitive, notrace_primitive
+
 import numpy as _np
+
 import autograd.builtins as builtins
+from autograd.extend import notrace_primitive, primitive
 
 if _np.lib.NumpyVersion(_np.__version__) >= "2.0.0":
     from numpy._core.einsumfunc import _parse_einsum_input
@@ -75,9 +76,7 @@ def array(A, *args, **kwargs):
 def wrap_if_boxes_inside(raw_array, slow_op_name=None):
     if raw_array.dtype is _np.dtype("O"):
         if slow_op_name:
-            warnings.warn(
-                "{} is slow for array inputs. " "np.concatenate() is faster.".format(slow_op_name)
-            )
+            warnings.warn("{} is slow for array inputs. " "np.concatenate() is faster.".format(slow_op_name))
         return array_from_args((), {}, *raw_array.ravel()).reshape(raw_array.shape)
     else:
         return raw_array

autograd/numpy/random.py

@@ -1,4 +1,5 @@
 import numpy.random as npr
+
 from .numpy_wrapper import wrap_namespace
 
 wrap_namespace(npr.__dict__, globals())

autograd/scipy/__init__.py

@@ -1,7 +1,4 @@
-from . import integrate
-from . import signal
-from . import special
-from . import stats
+from . import integrate, signal, special, stats
 
 try:
     from . import misc

autograd/scipy/integrate.py

@@ -1,10 +1,10 @@
 import scipy.integrate
 
 import autograd.numpy as np
-from autograd.extend import primitive, defvjp_argnums
 from autograd import make_vjp
-from autograd.misc import flatten
 from autograd.builtins import tuple
+from autograd.extend import defvjp_argnums, primitive
+from autograd.misc import flatten
 
 odeint = primitive(scipy.integrate.odeint)
 

autograd/scipy/linalg.py

@@ -1,9 +1,10 @@
 from functools import partial
+
 import scipy.linalg
 
 import autograd.numpy as anp
+from autograd.extend import defjvp, defjvp_argnums, defvjp, defvjp_argnums
 from autograd.numpy.numpy_wrapper import wrap_namespace
-from autograd.extend import defvjp, defvjp_argnums, defjvp, defjvp_argnums
 
 wrap_namespace(scipy.linalg.__dict__, globals())  # populates module namespace
 

autograd/scipy/misc.py

@@ -1,4 +1,5 @@
 import scipy.misc as osp_misc
+
 from ..scipy import special
 
 if hasattr(osp_misc, "logsumexp"):