Update the pre-commit hook (and fix deprecations) to modernise probdi…

…ffeq's CI (#742)

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: end-of-file-fixer
       - id: check-merge-conflict
@@ -13,15 +13,15 @@ repos:
       - id: yamlfix
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.1.9
+    rev: v0.4.8
     hooks:
       # Run the linter.
       - id: ruff
         args: [--fix]
       # Run the formatter.
       - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.8.0
+    rev: v1.10.0
     hooks:
       - id: mypy
         args: [--ignore-missing-imports]

docs/benchmarks/hires/run_hires.py

@@ -2,6 +2,7 @@
 
 See makefile for instructions.
 """
+
 import argparse
 import functools
 import os

docs/benchmarks/lotkavolterra/run_lotkavolterra.py

@@ -2,6 +2,7 @@
 
 See makefile for instructions.
 """
+
 import argparse
 import functools
 import os

docs/benchmarks/pleiades/run_pleiades.py

@@ -2,6 +2,7 @@
 
 See makefile for instructions.
 """
+
 import argparse
 import functools
 import os

docs/benchmarks/taylor_fitzhughnagumo/run_taylor_fitzhughnagumo.py

@@ -2,6 +2,7 @@
 
 See makefile for instructions.
 """
+
 import argparse
 import functools
 import os

docs/benchmarks/taylor_node/run_taylor_node.py

@@ -2,6 +2,7 @@
 
 See makefile for instructions.
 """
+
 import argparse
 import functools
 import os

docs/benchmarks/taylor_pleiades/run_taylor_pleiades.py

@@ -2,6 +2,7 @@
 
 See makefile for instructions.
 """
+
 import argparse
 import functools
 import os

docs/benchmarks/vanderpol/run_vanderpol.py

@@ -2,6 +2,7 @@
 
 See makefile for instructions.
 """
+
 import argparse
 import functools
 import os

docs/examples_parameter_estimation/neural_ode.py

@@ -19,6 +19,7 @@
 
 # +
 """Train a neural ODE with ProbDiffEq and Optax."""
+
 import jax
 import jax.numpy as jnp
 import matplotlib.pyplot as plt

docs/examples_solver_config/conditioning-on-zero-residual.py

@@ -20,6 +20,7 @@
 
 # +
 """Demonstrate how probabilistic solvers work via conditioning on constraints."""
+
 import jax
 import jax.numpy as jnp
 import matplotlib.pyplot as plt

probdiffeq/__init__.py

@@ -1,2 +1,3 @@
 """Probabilistic solvers for differential equations."""
+
 from probdiffeq._version import version as __version__  # noqa: F401

probdiffeq/adaptive.py

@@ -1,4 +1,5 @@
 """Adaptive solvers for initial value problems (IVPs)."""
+
 from probdiffeq import controls
 from probdiffeq.backend import containers, control_flow, functools, linalg, tree_util
 from probdiffeq.backend import numpy as np

probdiffeq/backend/abc.py

@@ -1,6 +1,5 @@
 """Abstract base classes."""
 
-
 import abc
 
 

probdiffeq/backend/functools.py

@@ -1,4 +1,5 @@
 """Function transformation tools."""
+
 import functools
 
 import jax

probdiffeq/backend/ode.py

@@ -1,4 +1,5 @@
 """ODE stuff."""
+
 import diffeqzoo.ivps
 import diffrax
 import jax

probdiffeq/backend/testing.py

@@ -8,6 +8,7 @@
 have been very inconsistent.
 This is not good for extendability of the test suite.
 """
+
 import jax.numpy as jnp
 import jax.tree_util
 import pytest

probdiffeq/backend/warnings.py

@@ -1,4 +1,5 @@
 """Warnings."""
+
 import warnings
 
 

probdiffeq/impl/__init__.py

@@ -1,4 +1,5 @@
 """State-space model implementations."""
+
 from probdiffeq.impl import _impl
 
 impl = _impl.Impl()

probdiffeq/impl/_conditional.py

@@ -1,4 +1,5 @@
 """Conditionals."""
+
 from probdiffeq.backend import abc
 
 

probdiffeq/impl/_impl.py

@@ -1,4 +1,5 @@
 """State-space model impl."""
+
 import warnings
 
 from probdiffeq.backend import abc

probdiffeq/impl/blockdiag/_conditional.py

@@ -1,4 +1,5 @@
 """Conditional implementation."""
+
 from probdiffeq.backend import functools
 from probdiffeq.backend import numpy as np
 from probdiffeq.impl import _conditional

probdiffeq/impl/blockdiag/_linearise.py

@@ -1,4 +1,5 @@
 """Linearisation."""
+
 from probdiffeq.impl import _linearise
 from probdiffeq.util import linop_util
 

probdiffeq/impl/blockdiag/_ssm_util.py

@@ -1,4 +1,5 @@
 """State-space model utilities."""
+
 from probdiffeq.backend import functools
 from probdiffeq.backend import numpy as np
 from probdiffeq.impl import _ssm_util

probdiffeq/impl/blockdiag/_transform.py

@@ -1,4 +1,5 @@
 """Random-variable transformation."""
+
 from probdiffeq.backend import functools
 from probdiffeq.backend import numpy as np
 from probdiffeq.impl import _transform

probdiffeq/impl/blockdiag/factorised_impl.py

@@ -1,4 +1,5 @@
 """Factorisations."""
+
 from probdiffeq.impl import _impl
 from probdiffeq.impl.blockdiag import (
     _conditional,

probdiffeq/impl/dense/_conditional.py

@@ -1,4 +1,5 @@
 """Conditional implementation."""
+
 from probdiffeq.impl import _conditional
 from probdiffeq.impl.dense import _normal
 from probdiffeq.util import cholesky_util, cond_util

probdiffeq/impl/dense/_linearise.py

@@ -1,6 +1,5 @@
 """Linearisation."""
 
-
 from probdiffeq.backend import functools
 from probdiffeq.backend import numpy as np
 from probdiffeq.impl import _linearise

probdiffeq/impl/dense/_transform.py

@@ -1,4 +1,5 @@
 """Random variable transformations."""
+
 from probdiffeq.backend import containers
 from probdiffeq.backend.typing import Array, Callable
 from probdiffeq.impl import _transform

probdiffeq/impl/dense/factorised_impl.py

@@ -1,4 +1,5 @@
 """API for dense factorisations."""
+
 from probdiffeq.impl import _impl
 from probdiffeq.impl.dense import (
     _conditional,

probdiffeq/impl/isotropic/_linearise.py

@@ -1,4 +1,5 @@
 """Linearisation."""
+
 from probdiffeq.impl import _linearise
 from probdiffeq.util import linop_util
 

probdiffeq/impl/isotropic/_ssm_util.py

@@ -1,4 +1,5 @@
 """State-space model utilities."""
+
 from probdiffeq.backend import numpy as np
 from probdiffeq.impl import _ssm_util
 from probdiffeq.impl.isotropic import _normal

probdiffeq/impl/isotropic/factorised_impl.py

@@ -1,4 +1,5 @@
 """Isotropic factorisation."""
+
 from probdiffeq.impl import _impl
 from probdiffeq.impl.isotropic import (
     _conditional,

probdiffeq/impl/scalar/_conditional.py

@@ -1,4 +1,5 @@
 """Conditionals."""
+
 from probdiffeq.backend import linalg
 from probdiffeq.backend import numpy as np
 from probdiffeq.impl import _conditional

probdiffeq/impl/scalar/_hidden_model.py

@@ -1,4 +1,5 @@
 """Hidden state-space model implementation."""
+
 from probdiffeq.backend import functools
 from probdiffeq.backend import numpy as np
 from probdiffeq.impl import _hidden_model

probdiffeq/impl/scalar/_linearise.py

@@ -1,4 +1,5 @@
 """Linearisation."""
+
 from probdiffeq.impl import _linearise
 
 

probdiffeq/impl/scalar/_ssm_util.py

@@ -1,4 +1,5 @@
 """SSM utilities."""
+
 from probdiffeq.backend import numpy as np
 from probdiffeq.impl import _ssm_util
 from probdiffeq.impl.scalar import _normal

probdiffeq/impl/scalar/_stats.py

@@ -1,4 +1,5 @@
 """Random variable implementation."""
+
 from probdiffeq.backend import functools, linalg
 from probdiffeq.backend import numpy as np
 from probdiffeq.impl import _stats

probdiffeq/impl/scalar/_transform.py

@@ -1,4 +1,5 @@
 """Random variable transformations."""
+
 from probdiffeq.backend import numpy as np
 from probdiffeq.impl import _transform
 from probdiffeq.impl.scalar import _normal

probdiffeq/impl/scalar/factorised_impl.py

@@ -1,4 +1,5 @@
 """Scalar factorisation."""
+
 from probdiffeq.impl import _impl
 from probdiffeq.impl.scalar import (
     _conditional,

probdiffeq/solvers/_solver.py

@@ -1,6 +1,5 @@
 """IVP-solver API."""
 
-
 from probdiffeq import _interp
 from probdiffeq.backend import abc
 from probdiffeq.backend import numpy as np

probdiffeq/solvers/calibrated.py

@@ -1,4 +1,5 @@
 """Calibrated IVP solvers."""
+
 from probdiffeq import _interp
 from probdiffeq.backend import abc, tree_util
 from probdiffeq.impl import impl

probdiffeq/solvers/strategies/components/cubature.py

@@ -1,6 +1,5 @@
 """Cubature rules."""
 
-
 from probdiffeq.backend import containers, special, tree_util
 from probdiffeq.backend import numpy as np
 from probdiffeq.backend.typing import Array

probdiffeq/solvers/strategies/components/priors.py

@@ -1,6 +1,5 @@
 """Prior models."""
 
-
 from probdiffeq.backend import functools
 from probdiffeq.backend import numpy as np
 from probdiffeq.impl import impl

probdiffeq/taylor/autodiff.py

@@ -1,6 +1,5 @@
 r"""Taylor-expand the solution of an initial value problem (IVP)."""
 
-
 from probdiffeq.backend import control_flow, functools, itertools, tree_util
 from probdiffeq.backend import numpy as np
 from probdiffeq.backend.typing import Array, Callable

probdiffeq/taylor/estim.py

@@ -1,6 +1,5 @@
 r"""Taylor-expand the solution of an initial value problem (IVP)."""
 
-
 from probdiffeq.backend import functools, ode
 from probdiffeq.backend import numpy as np
 from probdiffeq.impl import impl

probdiffeq/timestep.py

@@ -1,6 +1,5 @@
 """Time-stepping utilities."""
 
-
 from probdiffeq.backend import linalg
 from probdiffeq.backend import numpy as np
 

probdiffeq/util/cond_util.py

@@ -1,4 +1,5 @@
 """Conditional-utilities."""
+
 from probdiffeq.backend import containers
 from probdiffeq.backend.typing import Any, Array
 

pyproject.toml

@@ -105,7 +105,12 @@ exclude_also = [
 
 [tool.ruff]
 include = ["**.py", "**/pyproject.toml", "**.ipynb"]
+# Same as Black.
+line-length = 88
+indent-width = 4
+
 # See: https://beta.ruff.rs/docs/rules/
+[tool.ruff.lint]
 select = [
     # pycodestyle (warning, error)
     "W",
@@ -151,26 +156,24 @@ ignore = [
     # Magic methods don't need a docstring:
     "D105",
 ]
-# Same as Black.
-line-length = 88
-indent-width = 4
-
-[tool.ruff.format]
-# Use `\n` line endings for all files
-line-ending = "lf"
-# Prefer single quotes over double quotes.
-quote-style = "double"
-skip-magic-trailing-comma = true
 
-[tool.ruff.isort]
+[tool.ruff.lint.isort]
 split-on-trailing-comma = false
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 # Auxiliary functions and tests don't need docstring-enforcement:
 "probdiffeq/util/*" = ["D102", "D103"]
 "probdiffeq/impl/*" = ["D102"]
 "probdiffeq/backend/*" = ["D103"]
 "tests/*" = ["D103"]
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "numpy"
+
+
+[tool.ruff.format]
+# Use `\n` line endings for all files
+line-ending = "lf"
+# Prefer single quotes over double quotes.
+quote-style = "double"
+skip-magic-trailing-comma = true

tests/__init__.py

@@ -1,4 +1,5 @@
 """Tests."""
+
 import os
 
 from tests.setup import setup

tests/setup.py

@@ -1,6 +1,5 @@
 """Test-setup."""
 
-
 from probdiffeq.backend import config, ode, warnings
 from probdiffeq.backend import numpy as np
 from probdiffeq.impl import impl