[pre-commit.ci] pre-commit autoupdate (#646)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v5.0.0](pre-commit/pre-commit-hooks@v4.5.0...v5.0.0)
- [github.com/astral-sh/ruff-pre-commit: v0.1.4 → v0.11.4](astral-sh/ruff-pre-commit@v0.1.4...v0.11.4)
- [github.com/pre-commit/mirrors-mypy: v1.6.1 → v1.15.0](pre-commit/mirrors-mypy@v1.6.1...v1.15.0)
- [github.com/codespell-project/codespell: v2.2.6 → v2.4.1](codespell-project/codespell@v2.2.6...v2.4.1)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* TST: update expected outputs

* MAINT: adding ruff ignores for the test notebooks

* MAINT: fix myst lint error

* Do not auto-format include generated notebooks

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Brigitta Sipőcz <[email protected]>

Author: pre-commit-ci[bot]

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ ci:
 repos:
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
     - id: check-json
     - id: check-yaml
@@ -28,14 +28,14 @@ repos:
     - id: trailing-whitespace
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.4
+    rev: v0.11.4
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]
     - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.6.1
+    rev: v1.15.0
     hooks:
     - id: mypy
       args: [--config-file=pyproject.toml]
@@ -51,7 +51,7 @@ repos:
         )$
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.4.1
     hooks:
     - id: codespell
       args: ["-S", "*.ipynb"]

docs/render/orphaned_nb.ipynb

@@ -33,8 +33,9 @@
    ],
    "source": [
     "from myst_nb import glue\n",
+    "\n",
     "glue(\"var_text\", \"My orphaned variable!\")\n",
-    "glue(\"var_float\", 1.0/3.0)"
+    "glue(\"var_float\", 1.0 / 3.0)"
    ]
   }
  ],

myst_nb/__init__.py

@@ -1,4 +1,5 @@
 """A docutils/sphinx parser for Jupyter Notebooks."""
+
 __version__ = "1.2.0"
 
 

myst_nb/cli.py

@@ -1,4 +1,5 @@
 """A basic CLI for quickstart of a myst_nb project."""
+
 from __future__ import annotations
 
 import argparse
@@ -81,7 +82,7 @@ def generate_conf_py() -> str:
         if field.metadata.get("sphinx_exclude"):
             continue
         if field.metadata.get("help"):
-            settings += f'{field.metadata.get("help")}\n'
+            settings += f"{field.metadata.get('help')}\n"
         settings += f"nb_{name} = {value!r}\n\n"
     content += "\n" + indent(settings, "# ").rstrip() + "\n"
 

myst_nb/core/config.py

@@ -1,4 +1,5 @@
 """Configuration for myst-nb."""
+
 import dataclasses as dc
 from enum import Enum
 from typing import Any, Callable, Dict, Iterable, Literal, Optional, Sequence, Tuple

myst_nb/core/execute/base.py

@@ -1,4 +1,5 @@
 """Module for executing notebooks."""
+
 from __future__ import annotations
 
 from pathlib import Path

myst_nb/core/execute/cache.py

@@ -1,4 +1,5 @@
 """Execute a notebook from the cache."""
+
 from __future__ import annotations
 
 from contextlib import nullcontext, suppress
@@ -58,7 +59,7 @@ def start_client(self):
         # TODO do in try/except, in case of db write errors
         NbProjectRecord.remove_tracebacks([stage_record.pk], cache.db)
         cwd_context: ContextManager[str] = (
-            TemporaryDirectory()  # type: ignore
+            TemporaryDirectory()
             if self.nb_config.execution_in_temp
             else nullcontext(str(self.path.parent))
         )

myst_nb/core/execute/direct.py

@@ -1,4 +1,5 @@
 """Execute a notebook directly."""
+
 from __future__ import annotations
 
 from contextlib import nullcontext

myst_nb/core/execute/inline.py

@@ -1,4 +1,5 @@
 """Execute a notebook inline."""
+
 from __future__ import annotations
 
 import asyncio

myst_nb/core/lexers.py

@@ -1,4 +1,5 @@
 """Pygments lexers"""
+
 from __future__ import annotations
 
 import re

myst_nb/core/loggers.py

@@ -9,6 +9,7 @@
 ``logger.warning("message", line=1, subtype="foo")``
 
 """
+
 import logging
 from typing import Union
 

myst_nb/core/nb_to_tokens.py

@@ -1,4 +1,5 @@
 """Module for parsing notebooks to Markdown-it tokens."""
+
 from __future__ import annotations
 
 from typing import Any

myst_nb/core/read.py

@@ -1,4 +1,5 @@
 """Module for reading notebook formats from a string input."""
+
 from __future__ import annotations
 
 import dataclasses as dc

myst_nb/core/render.py

@@ -3,6 +3,7 @@
 Note, this module purposely does not import any Sphinx modules at the top-level,
 in order for docutils-only use.
 """
+
 from __future__ import annotations
 
 from binascii import a2b_base64

myst_nb/core/utils.py

@@ -1,4 +1,5 @@
 """Shared utilities."""
+
 from __future__ import annotations
 
 import re

myst_nb/core/variables.py

@@ -1,4 +1,5 @@
 """Utilities for rendering code output variables."""
+
 from __future__ import annotations
 
 from ast import literal_eval

myst_nb/docutils_.py

@@ -1,4 +1,5 @@
 """The docutils parser implementation for myst-nb."""
+
 from __future__ import annotations
 
 from dataclasses import dataclass, field

myst_nb/ext/eval/__init__.py

@@ -1,4 +1,5 @@
 """Roles/directives for evaluating variables in the notebook."""
+
 from __future__ import annotations
 
 from functools import partial
@@ -161,9 +162,9 @@ def run(self):
         render: dict[str, Any] = {}
         for key in ("alt", "height", "width", "scale", "class"):
             if key in self.options:
-                render.setdefault("image", {})[
-                    key.replace("classes", "class")
-                ] = self.options[key]
+                render.setdefault("image", {})[key.replace("classes", "class")] = (
+                    self.options[key]
+                )
 
         mime_nodes = render_variable_outputs(
             data, self.document, self.line, self.source, render=render

myst_nb/ext/execution_tables.py

@@ -4,6 +4,7 @@
 which is then replaced by a table of statistics in a post-transformation
 (once all the documents have been executed and these statistics are available).
 """
+
 from __future__ import annotations
 
 from datetime import datetime

myst_nb/ext/glue/__init__.py

@@ -1,6 +1,7 @@
 """Functionality for storing special data in notebook code cells,
 which can then be inserted into the document body.
 """
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING, Any

myst_nb/ext/glue/crossref.py

@@ -3,6 +3,7 @@
 Note, we restrict this to a only a subset of mime-types and data -> nodes transforms,
 since adding these nodes in a post-transform will not apply any transforms to them.
 """
+
 from __future__ import annotations
 
 from functools import lru_cache

myst_nb/ext/glue/directives.py

@@ -3,6 +3,7 @@
 We intentionally do no import sphinx in this module,
 in order to allow docutils-only use without sphinx installed.
 """
+
 from typing import TYPE_CHECKING, Any, Dict, List
 
 from docutils import nodes
@@ -151,9 +152,9 @@ def run(self):
         render: Dict[str, Any] = {}
         for key in ("alt", "height", "width", "scale", "class"):
             if key in self.options:
-                render.setdefault("image", {})[
-                    key.replace("classes", "class")
-                ] = self.options[key]
+                render.setdefault("image", {})[key.replace("classes", "class")] = (
+                    self.options[key]
+                )
         paste_nodes = render_variable_outputs(
             [data], self.document, self.line, self.source, render=render
         )

myst_nb/ext/glue/domain.py

@@ -2,6 +2,7 @@
 
 This is required for any directive/role names using `:`.
 """
+
 from sphinx.domains import Domain
 
 from .directives import (

myst_nb/ext/glue/roles.py

@@ -3,6 +3,7 @@
 We intentionally do no import sphinx in this module,
 in order to allow docutils-only use without sphinx installed.
 """
+
 from __future__ import annotations
 
 from docutils import nodes

myst_nb/ext/glue/utils.py

@@ -3,6 +3,7 @@
 We intentionally do no import sphinx in this module,
 in order to allow docutils-only use without sphinx installed.
 """
+
 from __future__ import annotations
 
 from functools import partial

myst_nb/ext/utils.py

@@ -3,6 +3,7 @@
 We intentionally do no import sphinx in this module,
 in order to allow docutils-only use without sphinx installed.
 """
+
 from __future__ import annotations
 
 from typing import Any

myst_nb/sphinx_.py

@@ -1,4 +1,5 @@
 """The sphinx parser implementation for myst-nb."""
+
 from __future__ import annotations
 
 from collections import defaultdict

myst_nb/sphinx_ext.py

@@ -1,4 +1,5 @@
 """Setup for the myst-nb sphinx extension."""
+
 from __future__ import annotations
 
 import contextlib

myst_nb/warnings_.py

@@ -1,4 +1,5 @@
 """Central handling of warnings for the myst-nb extension."""
+
 from __future__ import annotations
 
 from enum import Enum

pyproject.toml

@@ -148,9 +148,16 @@ ignore = [
     "E203",    # Whitespace before punctuation
 ]
 
+[tool.ruff.lint.extend-per-file-ignores]
+"tests/*/*ipynb" = ["E402"]   # module-import-not-at-top-of-file
+
 [tool.ruff.lint.isort]
 force-sort-within-sections = true
 
+[tool.ruff.format]
+# These are reference outputs and reformatting them makes a mess
+exclude = ["tests/test_codecell_file/*ipynb"]
+
 [tool.pytest.ini_options]
 filterwarnings = [
     'error',

tests/notebooks/basic_failing.ipynb

@@ -1,44 +1,44 @@
 {
-  "cells": [
-    {
-      "cell_type": "markdown",
-      "metadata": {},
-      "source": [
-        "# a title\n",
-        "\n",
-        "some text\n"
-      ]
-    },
-    {
-      "cell_type": "code",
-      "execution_count": null,
-      "metadata": {},
-      "source": [
-        "raise Exception('oopsie!')"
-      ],
-      "outputs": []
-    }
-  ],
-  "metadata": {
-    "test_name": "notebook1",
-    "kernelspec": {
-      "display_name": "Python 3",
-      "language": "python",
-      "name": "python3"
-    },
-    "language_info": {
-      "codemirror_mode": {
-        "name": "ipython",
-        "version": 3
-      },
-      "file_extension": ".py",
-      "mimetype": "text/x-python",
-      "name": "python",
-      "nbconvert_exporter": "python",
-      "pygments_lexer": "ipython3",
-      "version": "3.6.1"
-    }
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# a title\n",
+    "\n",
+    "some text\n"
+   ]
   },
-  "nbformat": 4,
-  "nbformat_minor": 2
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "raise Exception(\"oopsie!\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.1"
+  },
+  "test_name": "notebook1"
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
 }