From 3d5562e827543f73c61f48292e205358cbd21f00 Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Tue, 21 Jan 2025 13:22:03 -0700
Subject: [PATCH 01/10] use new form for Generator type hint

---
 sequence/logging.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sequence/logging.py b/sequence/logging.py
index 5991a8c..ba5ca92 100644
--- a/sequence/logging.py
+++ b/sequence/logging.py
@@ -47,7 +47,7 @@ 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)

From 2838b509de6c7169da149e56dce6f4e103bb07a7 Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Tue, 21 Jan 2025 13:22:29 -0700
Subject: [PATCH 02/10] use isostasy_time property

---
 sequence/sediment_flexure.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/sequence/sediment_flexure.py b/sequence/sediment_flexure.py
index aee8d16..28ae7f9 100644
--- a/sequence/sediment_flexure.py
+++ b/sequence/sediment_flexure.py
@@ -162,9 +162,9 @@ def __init__(
             "Flexure parameters\n"
             + toml.dumps(
                 {
-                    "isostasy_time": 0.0
-                    if self._isostasy_time is None
-                    else self._isostasy_time,
+                    "isostasy_time": (
+                        0.0 if self._isostasy_time is None else self._isostasy_time
+                    ),
                     "alpha": self.alpha,
                     "rigidity": self.rigidity,
                     "gamma_mantle": self.gamma_mantle,
@@ -350,9 +350,9 @@ def __init__(
                     "sand_density": self._sand_density,
                     "mud_density": self._mud_density,
                     "water_density": self._water_density,
-                    "isostasy_time": 0.0
-                    if self.isostasy_time is None
-                    else self.isostasy_time,
+                    "isostasy_time": (
+                        0.0 if self.isostasy_time is None else self.isostasy_time
+                    ),
                     "alpha": self.alpha,
                     "rigidity": self.rigidity,
                     "gamma_mantle": self.gamma_mantle,

From d6ffffe64a66dfedc3134ba2272f28e81398438f Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Tue, 21 Jan 2025 13:22:46 -0700
Subject: [PATCH 03/10] bump version of pre-commit hooks

---
 .pre-commit-config.yaml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 5b615c1..46753de 100644
--- a/.pre-commit-config.yaml
+++ b/.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 +48,19 @@ repos:
         - flake8-simplify
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.15.0
+  rev: v3.19.1
   hooks:
   -   id: pyupgrade
       args: [--py38-plus]
 
 - repo: https://github.com/asottile/reorder-python-imports
-  rev: v3.12.0
+  rev: v3.14.0
   hooks:
   - id: reorder-python-imports
     args: [--py310-plus, --add-import, "from __future__ import annotations"]
 
 - 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 +81,14 @@ 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

From 4276884e602bb781848e7add6665f3dcf022fcc0 Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Tue, 21 Jan 2025 13:36:47 -0700
Subject: [PATCH 04/10] use isort instead of reorder-python-imports

---
 .pre-commit-config.yaml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 46753de..b2032fd 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -53,11 +53,13 @@ repos:
   -   id: pyupgrade
       args: [--py38-plus]
 
-- repo: https://github.com/asottile/reorder-python-imports
-  rev: v3.14.0
+- 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: v5.0.0

From 8d5f12d21873cbf85fff2363b69e8ce239fb5756 Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Tue, 21 Jan 2025 13:37:29 -0700
Subject: [PATCH 05/10] update isort configuration

---
 pyproject.toml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index b719199..4cad335 100644
--- a/pyproject.toml
+++ b/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

From 2d723c7a3421eadeee64ec2193b6f7015e0e410a Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Tue, 21 Jan 2025 13:37:51 -0700
Subject: [PATCH 06/10] add blank line above imports for new version of black

---
 sequence/__init__.py         | 1 +
 sequence/bathymetry.py       | 1 +
 sequence/cli.py              | 1 +
 sequence/errors.py           | 1 +
 sequence/fluvial.py          | 1 +
 sequence/grid.py             | 1 +
 sequence/input_reader.py     | 1 +
 sequence/logging.py          | 1 +
 sequence/netcdf.py           | 1 +
 sequence/output_writer.py    | 1 +
 sequence/plot.py             | 1 +
 sequence/processes.py        | 1 +
 sequence/sea_level.py        | 1 +
 sequence/sediment_flexure.py | 1 +
 sequence/sequence.py         | 1 +
 sequence/sequence_model.py   | 3 ++-
 sequence/shoreline.py        | 1 +
 sequence/submarine.py        | 1 +
 sequence/subsidence.py       | 1 +
 tests/shoreline_test.py      | 1 +
 20 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/sequence/__init__.py b/sequence/__init__.py
index 351b252..4123e30 100644
--- a/sequence/__init__.py
+++ b/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__
diff --git a/sequence/bathymetry.py b/sequence/bathymetry.py
index 3f84cdb..1a55bc9 100644
--- a/sequence/bathymetry.py
+++ b/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
diff --git a/sequence/cli.py b/sequence/cli.py
index 6ab3aa5..5516594 100644
--- a/sequence/cli.py
+++ b/sequence/cli.py
@@ -1,4 +1,5 @@
 """The command line interface for *Sequence*."""
+
 from __future__ import annotations
 
 import inspect
diff --git a/sequence/errors.py b/sequence/errors.py
index 349d205..cdbd70b 100644
--- a/sequence/errors.py
+++ b/sequence/errors.py
@@ -1,4 +1,5 @@
 """Errors used by *sequence*."""
+
 from __future__ import annotations
 
 from collections.abc import Iterable
diff --git a/sequence/fluvial.py b/sequence/fluvial.py
index 8430ff3..4630604 100644
--- a/sequence/fluvial.py
+++ b/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
diff --git a/sequence/grid.py b/sequence/grid.py
index b9f7e8d..8f6d47a 100644
--- a/sequence/grid.py
+++ b/sequence/grid.py
@@ -1,4 +1,5 @@
 """Define the grid used for creating *Sequence* models."""
+
 from __future__ import annotations
 
 import os
diff --git a/sequence/input_reader.py b/sequence/input_reader.py
index 7109d30..11d7218 100644
--- a/sequence/input_reader.py
+++ b/sequence/input_reader.py
@@ -2,6 +2,7 @@
 
 This module contains utilities for reading *Sequence* input data.
 """
+
 from __future__ import annotations
 
 import inspect
diff --git a/sequence/logging.py b/sequence/logging.py
index ba5ca92..c2d704d 100644
--- a/sequence/logging.py
+++ b/sequence/logging.py
@@ -1,4 +1,5 @@
 """Logger used for printing Sequence log messages."""
+
 from __future__ import annotations
 
 import contextlib
diff --git a/sequence/netcdf.py b/sequence/netcdf.py
index dcf61a9..2c24431 100644
--- a/sequence/netcdf.py
+++ b/sequence/netcdf.py
@@ -1,4 +1,5 @@
 """Write a `SequenceModelGrid` to a NetCDF file."""
+
 from __future__ import annotations
 
 import contextlib
diff --git a/sequence/output_writer.py b/sequence/output_writer.py
index 14bf3d2..c2f3d6e 100644
--- a/sequence/output_writer.py
+++ b/sequence/output_writer.py
@@ -1,4 +1,5 @@
 """Write a `SequenceModelGrid` to a file."""
+
 from __future__ import annotations
 
 import errno
diff --git a/sequence/plot.py b/sequence/plot.py
index 265f22f..ad7125c 100644
--- a/sequence/plot.py
+++ b/sequence/plot.py
@@ -1,4 +1,5 @@
 """Plot the layers of a `SequenceModelGrid`."""
+
 from __future__ import annotations
 
 from functools import partial
diff --git a/sequence/processes.py b/sequence/processes.py
index ac9700b..78a75f0 100644
--- a/sequence/processes.py
+++ b/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
diff --git a/sequence/sea_level.py b/sequence/sea_level.py
index 27a4d9b..5ef9758 100644
--- a/sequence/sea_level.py
+++ b/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
diff --git a/sequence/sediment_flexure.py b/sequence/sediment_flexure.py
index 28ae7f9..ad36939 100644
--- a/sequence/sediment_flexure.py
+++ b/sequence/sediment_flexure.py
@@ -1,4 +1,5 @@
 """Subside a `SequenceModelGrid` using flexure."""
+
 from __future__ import annotations
 
 import logging
diff --git a/sequence/sequence.py b/sequence/sequence.py
index 87edccf..b96b98b 100644
--- a/sequence/sequence.py
+++ b/sequence/sequence.py
@@ -1,4 +1,5 @@
 """*Sequence*'s main API for constructing sequence-stratigraphic models."""
+
 from __future__ import annotations
 
 from collections.abc import Iterable
diff --git a/sequence/sequence_model.py b/sequence/sequence_model.py
index d3542e0..504d5a1 100644
--- a/sequence/sequence_model.py
+++ b/sequence/sequence_model.py
@@ -1,11 +1,12 @@
 """Build a `SequenceModelGrid` model from collection of components."""
+
 from __future__ import annotations
 
 import logging
 import os
 import time
-from collections import defaultdict
 from collections import OrderedDict
+from collections import defaultdict
 from collections.abc import Iterable
 from contextlib import suppress
 from typing import Any
diff --git a/sequence/shoreline.py b/sequence/shoreline.py
index d562a9e..b2b796a 100644
--- a/sequence/shoreline.py
+++ b/sequence/shoreline.py
@@ -3,6 +3,7 @@
 This module contains methods for calculating a grid's shoreline and
 shelf edge.
 """
+
 from __future__ import annotations
 
 import bisect
diff --git a/sequence/submarine.py b/sequence/submarine.py
index c66a58f..9ca9637 100644
--- a/sequence/submarine.py
+++ b/sequence/submarine.py
@@ -1,4 +1,5 @@
 """Diffuse sediment along a profile."""
+
 from __future__ import annotations
 
 from typing import Any
diff --git a/sequence/subsidence.py b/sequence/subsidence.py
index d72f0d9..4877bfa 100644
--- a/sequence/subsidence.py
+++ b/sequence/subsidence.py
@@ -1,4 +1,5 @@
 """Subside a `SequenceModelGrid`."""
+
 from __future__ import annotations
 
 import os
diff --git a/tests/shoreline_test.py b/tests/shoreline_test.py
index 8788471..091457e 100644
--- a/tests/shoreline_test.py
+++ b/tests/shoreline_test.py
@@ -1,4 +1,5 @@
 """Test the shoreline.find_shoreline function."""
+
 from __future__ import annotations
 
 import numpy as np

From 330461db2459ed043d5fd752d7389d65811a8f2c Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Tue, 21 Jan 2025 13:46:32 -0700
Subject: [PATCH 07/10] remove the lint workflow, use pre-commit.ci instead

---
 .github/workflows/lint.yml | 27 ---------------------------
 1 file changed, 27 deletions(-)
 delete mode 100644 .github/workflows/lint.yml

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
deleted file mode 100644
index 92ddc7c..0000000
--- a/.github/workflows/lint.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-name: Lint
-
-on: [push, pull_request]
-
-jobs:
-
-  lint:
-    name: Check for lint
-    # We want to run on external PRs, but not on our own internal PRs as they'll be run
-    # by the push to the branch. Without this if check, checks are duplicated since
-    # internal PRs match both the push and pull_request events.
-    if:
-      github.event_name == 'push' || github.event.pull_request.head.repo.full_name !=
-      github.repository
-
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python 3.12
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.12
-
-      - name: Lint
-        run: |
-          pip install nox
-          nox -s lint

From ffeedd833cc1874e4e6f655875731d76f9952f44 Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Tue, 21 Jan 2025 13:52:54 -0700
Subject: [PATCH 08/10] set python 3.10+ for pyupgrade

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b2032fd..df7d607 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -51,7 +51,7 @@ repos:
   rev: v3.19.1
   hooks:
   -   id: pyupgrade
-      args: [--py38-plus]
+      args: [--py310-plus]
 
 - repo: https://github.com/PyCQA/isort
   rev: 5.13.2

From fde9bd130eff2a8762f175258c2a74ab0e3a7bca Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Tue, 21 Jan 2025 13:57:12 -0700
Subject: [PATCH 09/10] add news fragment

---
 news/87.misc | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 news/87.misc

diff --git a/news/87.misc b/news/87.misc
new file mode 100644
index 0000000..7120b4a
--- /dev/null
+++ b/news/87.misc
@@ -0,0 +1,2 @@
+
+Updated the *pre-commit* hooks and fixed some newly-found lint.

From 3eecb4481439034b0b46b8b635522b8fe884fa2f Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Tue, 21 Jan 2025 13:57:33 -0700
Subject: [PATCH 10/10] remove notebook output

---
 docs/tutorials/notebooks/example.ipynb | 36 +++++++++++++-------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/docs/tutorials/notebooks/example.ipynb b/docs/tutorials/notebooks/example.ipynb
index 2cdd2ce..c66d7c9 100644
--- a/docs/tutorials/notebooks/example.ipynb
+++ b/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": [