Update pre-commit hooks

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/psf/black
-  rev: 23.12.0
+  rev: 24.10.0
   hooks:
   - id: black
     name: black
@@ -23,7 +23,7 @@ repos:
     additional_dependencies: [".[jupyter]"]
 
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.7.1
+  rev: 1.9.1
   hooks:
     - id: nbqa-pyupgrade
       args: ["--py310-plus"]
@@ -32,14 +32,14 @@ repos:
       args: ["--extend-ignore=E402"]
 
 - repo: https://github.com/kynan/nbstripout
-  rev: 0.6.1
+  rev: 0.8.1
   hooks:
     - id: nbstripout
       description: Strip output from jupyter notebooks
       args: [--drop-empty-cells]
 
 - repo: https://github.com/pycqa/flake8
-  rev: 6.1.0
+  rev: 7.1.1
   hooks:
     - id: flake8
       additional_dependencies:
@@ -48,19 +48,21 @@ repos:
         - flake8-simplify
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.15.0
+  rev: v3.19.1
   hooks:
   -   id: pyupgrade
-      args: [--py38-plus]
+      args: [--py310-plus]
 
-- repo: https://github.com/asottile/reorder-python-imports
-  rev: v3.12.0
+- repo: https://github.com/PyCQA/isort
+  rev: 5.13.2
   hooks:
-  - id: reorder-python-imports
-    args: [--py310-plus, --add-import, "from __future__ import annotations"]
+  - id: isort
+    name: isort (python)
+    args: [--add-import, "from __future__ import annotations"]
+    types: [python]
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v5.0.0
   hooks:
     - id: check-builtin-literals
     - id: check-added-large-files
@@ -81,14 +83,14 @@ repos:
     - id: name-tests-test
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.1.8
+  rev: v0.9.2
   hooks:
     - id: ruff
       files: sequence/.*\.py$
       args: [--fix]
 
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.7.1
+  rev: v1.14.1
   hooks:
   - id: mypy
     language_version: python3.12

docs/tutorials/notebooks/example.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "2815939c",
+   "id": "0",
    "metadata": {},
    "source": [
     "![Sequence Logo](https://raw.githubusercontent.com/sequence-dev/sequence/develop/docs/_static/sequence-logo-text-lowercase.png)\n",
@@ -14,7 +14,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "722b40f1",
+   "id": "1",
    "metadata": {},
    "source": [
     "# Create the *sequence* model grid\n",
@@ -25,7 +25,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c90feada",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -38,7 +38,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1f44bed6",
+   "id": "3",
    "metadata": {},
    "source": [
     "The following code create a new grid with 100 vertical stacks that are each 1000 m in width. We then set the initial topoography (and bathymetry) for the model as well as setting sea level."
@@ -47,7 +47,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "43bc9d89",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -58,7 +58,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "753b28ce",
+   "id": "5",
    "metadata": {},
    "source": [
     "# Create the process components\n",
@@ -73,7 +73,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "96d9cc6f",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -110,7 +110,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9f2dce0a",
+   "id": "7",
    "metadata": {},
    "source": [
     "# Create a new *Sequence* model\n",
@@ -121,7 +121,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1ba92be6",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -141,7 +141,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "282f70e1",
+   "id": "9",
    "metadata": {},
    "source": [
     "Run the model for 3000 time steps."
@@ -150,7 +150,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "55057e5e",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -161,7 +161,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "82ce0bad",
+   "id": "11",
    "metadata": {},
    "source": [
     "# Dynamically change parameters\n",
@@ -174,7 +174,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "97b28fe7",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -184,7 +184,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "64d17bdf",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -195,7 +195,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "bd7345df",
+   "id": "14",
    "metadata": {},
    "source": [
     "## Create a vertical fault\n",
@@ -206,7 +206,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "740e6641",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -217,7 +217,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b21a4edd",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -227,7 +227,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "796b0042",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [

news/87.misc

@@ -0,0 +1,2 @@
+
+Updated the *pre-commit* hooks and fixed some newly-found lint.

pyproject.toml

@@ -82,11 +82,9 @@ sequence = [
 ]
 
 [tool.isort]
-multi_line_output = 3
-include_trailing_comma = true
-force_grid_wrap = 0
-combine_as_imports = true
-line_length = 88
+known_first_party = "sequence"
+profile = "black"
+force_single_line = true
 
 [tool.mypy]
 check_untyped_defs = true

sequence/__init__.py

@@ -1,4 +1,5 @@
 """A sequence-stratigraphic model of a 1D profile written with *Landlab*."""
+
 from __future__ import annotations
 
 from sequence._version import __version__

sequence/bathymetry.py

@@ -3,6 +3,7 @@
 This module contains *Landlab* components to read bathymetry into a
 `SequenceModelGrid`.
 """
+
 from __future__ import annotations
 
 from os import PathLike

sequence/cli.py

@@ -1,4 +1,5 @@
 """The command line interface for *Sequence*."""
+
 from __future__ import annotations
 
 import inspect

sequence/errors.py

@@ -1,4 +1,5 @@
 """Errors used by *sequence*."""
+
 from __future__ import annotations
 
 from collections.abc import Iterable

sequence/fluvial.py

@@ -3,6 +3,7 @@
 This module contains *Landlab* components that add a sand fraction to a
 `SequenceModelGrid`.
 """
+
 from __future__ import annotations
 
 import numpy as np

sequence/grid.py

@@ -1,4 +1,5 @@
 """Define the grid used for creating *Sequence* models."""
+
 from __future__ import annotations
 
 import os

sequence/input_reader.py

@@ -2,6 +2,7 @@
 
 This module contains utilities for reading *Sequence* input data.
 """
+
 from __future__ import annotations
 
 import inspect

sequence/logging.py

@@ -1,4 +1,5 @@
 """Logger used for printing Sequence log messages."""
+
 from __future__ import annotations
 
 import contextlib
@@ -47,7 +48,7 @@ def emit(self, record: logging.LogRecord) -> None:
 
 
 @contextlib.contextmanager
-def logging_handler() -> Generator[None, None, None]:
+def logging_handler() -> Generator[None]:
     """Change, temporarily, the current logger."""
     handler = LoggingHandler()
     logger.addHandler(handler)

sequence/netcdf.py

@@ -1,4 +1,5 @@
 """Write a `SequenceModelGrid` to a NetCDF file."""
+
 from __future__ import annotations
 
 import contextlib

sequence/output_writer.py

@@ -1,4 +1,5 @@
 """Write a `SequenceModelGrid` to a file."""
+
 from __future__ import annotations
 
 import errno

sequence/plot.py

@@ -1,4 +1,5 @@
 """Plot the layers of a `SequenceModelGrid`."""
+
 from __future__ import annotations
 
 from functools import partial

sequence/processes.py

@@ -1,4 +1,5 @@
 """All available processes to include in a *Sequence* model."""
+
 from __future__ import annotations
 
 from compaction.landlab import Compact

sequence/sea_level.py

@@ -3,6 +3,7 @@
 This module contains *Landlab* components used for adjusting
 a grid's sea level.
 """
+
 from __future__ import annotations
 
 from collections.abc import Callable