[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -29,14 +29,14 @@ repos:
     - id: trailing-whitespace
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.20
+    rev: v0.16.6
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]
     - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v2.1.0
+    rev: v2.3.1
     hooks:
     - id: mypy
       args: [--config-file=pyproject.toml]
@@ -52,7 +52,7 @@ repos:
         )$
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.2
+    rev: v2.4.3
     hooks:
     - id: codespell
       args: ["-S", "*.ipynb"]

docs/authoring/basics.md

@@ -18,9 +18,9 @@ the [source_suffix](https://www.sphinx-doc.org/en/master/usage/configuration.htm
 ```python
 extensions = ["myst_nb"]
 source_suffix = {
-    '.rst': 'restructuredtext',
-    '.ipynb': 'myst-nb',
-    '.myst': 'myst-nb',
+    ".rst": "restructuredtext",
+    ".ipynb": "myst-nb",
+    ".myst": "myst-nb",
 }
 ```
 

docs/computation/execute.md

@@ -71,7 +71,7 @@ nb_execution_mode = "off"
 To exclude certain file patterns from execution, use the following configuration:
 
 ```python
-nb_execution_excludepatterns = ['list', 'of', '*patterns']
+nb_execution_excludepatterns = ["list", "of", "*patterns"]
 ```
 
 Any file that matches one of the items in `nb_execution_excludepatterns` will not be executed.

docs/quickstart.md

@@ -17,10 +17,7 @@ mystnb-quickstart my_project/docs/
 or simply add `myst_nb` to your existing Sphinx configuration:
 
 ```python
-extensions = [
-    ...,
-    "myst_nb"
-]
+extensions = [..., "myst_nb"]
 ```
 
 By default, MyST-NB will now parse both markdown (`.md`) and notebooks (`.ipynb`).

docs/render/format_code_cells.md

@@ -124,9 +124,9 @@ For example, the following configuration applies in order:
 
 ```python
 nb_mime_priority_overrides = [
-  ('html', 'text/plain', 0),
-  ('latex', 'image/jpeg', None),
-  ('*', 'customtype', 20)
+    ("html", "text/plain", 0),
+    ("latex", "image/jpeg", None),
+    ("*", "customtype", 20),
 ]
 ```
 

docs/render/interactive.md

@@ -61,7 +61,9 @@ fig
 You may need to supply the `require.js` for plotly to display; in your `conf.py`:
 
 ```python
-html_js_files = ["https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"]
+html_js_files = [
+    "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"
+]
 ```
 
 :::

docs/render/orphaned_nb.ipynb

@@ -89,8 +89,8 @@
     }
    ],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
     "data = np.random.rand(3, 100) * 100\n",
     "\n",

myst_nb/core/config.py

@@ -1,8 +1,9 @@
 """Configuration for myst-nb."""
 
+from collections.abc import Callable, Iterable, Sequence
 import dataclasses as dc
 from enum import Enum
-from typing import Any, Callable, Dict, Iterable, Literal, Optional, Sequence, Tuple
+from typing import Any, Literal
 
 from myst_parser.config.dc_validators import (
     ValidatorType,
@@ -17,11 +18,11 @@
 from myst_nb.warnings_ import MystNBWarnings
 
 
-def custom_formats_converter(value: dict) -> Dict[str, Tuple[str, dict, bool]]:
+def custom_formats_converter(value: dict) -> dict[str, tuple[str, dict, bool]]:
     """Convert the custom format dict."""
     if not isinstance(value, dict):
         raise TypeError(f"`nb_custom_formats` must be a dict: {value}")
-    output: Dict[str, Tuple[str, dict, bool]] = {}
+    output: dict[str, tuple[str, dict, bool]] = {}
     for suffix, reader in value.items():
         if not isinstance(suffix, str):
             raise TypeError(f"`nb_custom_formats` keys must be a string: {suffix}")
@@ -56,7 +57,7 @@ def custom_formats_converter(value: dict) -> Dict[str, Tuple[str, dict, bool]]:
     return output
 
 
-def ipywidgets_js_factory() -> Dict[str, Dict[str, str]]:
+def ipywidgets_js_factory() -> dict[str, dict[str, str]]:
     """Create a default ipywidgets js dict."""
     # see: https://ipywidgets.readthedocs.io/en/7.6.5/embedding.html
     return {
@@ -128,7 +129,7 @@ def __post_init__(self):
 
     # file read options
 
-    custom_formats: Dict[str, Tuple[str, dict, bool]] = dc.field(
+    custom_formats: dict[str, tuple[str, dict, bool]] = dc.field(
         default_factory=dict,
         metadata={
             "help": "Custom formats for reading notebook; suffix -> reader",
@@ -180,7 +181,7 @@ def __post_init__(self):
 
     # notebook execution options
 
-    kernel_rgx_aliases: Dict[str, str] = dc.field(
+    kernel_rgx_aliases: dict[str, str] = dc.field(
         default_factory=dict,
         metadata={
             "validator": deep_mapping(instance_of(str), instance_of(str)),
@@ -400,7 +401,7 @@ def __post_init__(self):
         },
         repr=False,
     )
-    mime_priority_overrides: Sequence[Tuple[str, str, Optional[int]]] = dc.field(
+    mime_priority_overrides: Sequence[tuple[str, str, int | None]] = dc.field(
         default=(),
         metadata={
             "validator": deep_iterable(
@@ -472,7 +473,7 @@ def __post_init__(self):
             ),
         },
     )
-    render_image_options: Dict[str, str] = dc.field(
+    render_image_options: dict[str, str] = dc.field(
         default_factory=dict,
         # see https://docutils.sourceforge.io/docs/ref/rst/directives.html#image
         metadata={
@@ -489,7 +490,7 @@ def __post_init__(self):
             ),
         },
     )
-    render_figure_options: Dict[str, str] = dc.field(
+    render_figure_options: dict[str, str] = dc.field(
         default_factory=dict,
         # see https://docutils.sourceforge.io/docs/ref/rst/directives.html#figure
         metadata={
@@ -522,7 +523,7 @@ def __post_init__(self):
     # TODO jupyter_sphinx_require_url and jupyter_sphinx_embed_url (undocumented),
     # are no longer used by this package, replaced by ipywidgets_js
     # do we add any deprecation warnings?
-    ipywidgets_js: Dict[str, Dict[str, str]] = dc.field(
+    ipywidgets_js: dict[str, dict[str, str]] = dc.field(
         default_factory=ipywidgets_js_factory,
         metadata={
             "validator": deep_mapping(
@@ -562,13 +563,13 @@ def __post_init__(self):
     )
 
     @classmethod
-    def get_fields(cls) -> Tuple[dc.Field, ...]:
+    def get_fields(cls) -> tuple[dc.Field, ...]:
         return dc.fields(cls)
 
     def as_dict(self, dict_factory=dict) -> dict:
         return dc.asdict(self, dict_factory=dict_factory)
 
-    def as_triple(self) -> Iterable[Tuple[str, Any, dc.Field]]:
+    def as_triple(self) -> Iterable[tuple[str, Any, dc.Field]]:
         """Yield triples of (name, value, field)."""
         fields = {f.name: f for f in dc.fields(self.__class__)}
         for name, value in dc.asdict(self).items():

myst_nb/core/execute/__init__.py

@@ -9,8 +9,8 @@
 from .inline import NotebookClientInline
 
 if TYPE_CHECKING:
-    from nbformat import NotebookNode
     from jupyter_client import KernelManager
+    from nbformat import NotebookNode
 
     from myst_nb.core.config import NbParserConfig
     from myst_nb.core.loggers import LoggerType

myst_nb/core/execute/base.py

@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 from pathlib import Path
-from typing import Any, TYPE_CHECKING
+from typing import TYPE_CHECKING, Any
 
 from nbformat import NotebookNode
 from typing_extensions import TypedDict, final

myst_nb/core/read.py

@@ -2,11 +2,11 @@
 
 from __future__ import annotations
 
+from collections.abc import Callable, Iterator
 import dataclasses as dc
 from functools import partial
 import json
 from pathlib import Path
-from typing import Callable, Iterator
 
 from docutils.parsers.rst import Directive
 from markdown_it.renderer import RendererHTML
@@ -326,9 +326,7 @@ def _read_fenced_cell(token, cell_index, cell_type):
     )
     if result.warnings:
         raise MystMetadataParsingError(
-            "{} cell {} at line {} could not be read: {}".format(
-                cell_type, cell_index, token.map[0] + 1, result.warnings[0]
-            )
+            f"{cell_type} cell {cell_index} at line {token.map[0] + 1} could not be read: {result.warnings[0]}"
         )
 
     return result.options, result.body
@@ -341,15 +339,11 @@ def _read_cell_metadata(token, cell_index):
             metadata = json.loads(token.content.strip())
         except Exception as err:
             raise MystMetadataParsingError(
-                "Markdown cell {} at line {} could not be read: {}".format(
-                    cell_index, token.map[0] + 1, err
-                )
+                f"Markdown cell {cell_index} at line {token.map[0] + 1} could not be read: {err}"
             )
         if not isinstance(metadata, dict):
             raise MystMetadataParsingError(
-                "Markdown cell {} at line {} is not a dict".format(
-                    cell_index, token.map[0] + 1
-                )
+                f"Markdown cell {cell_index} at line {token.map[0] + 1} is not a dict"
             )
 
     return metadata

myst_nb/core/render.py

@@ -7,6 +7,7 @@
 from __future__ import annotations
 
 from binascii import a2b_base64
+from collections.abc import Iterator, Sequence
 from contextlib import contextmanager
 import dataclasses as dc
 from functools import lru_cache
@@ -16,7 +17,7 @@
 import os
 from pathlib import Path
 import re
-from typing import TYPE_CHECKING, Any, ClassVar, Iterator, Sequence, Union
+from typing import TYPE_CHECKING, Any, ClassVar, Union
 
 from docutils import nodes
 from docutils.parsers.rst import directives as options_spec
@@ -935,7 +936,7 @@ def strip_latex_delimiters(source):
     https://github.com/jupyter/jupyter-sphinx/issues/90 for discussion.
     """
     source = source.strip()
-    delimiter_pairs = (pair.split() for pair in r"\( \),\[ \],$$ $$,$ $".split(","))
+    delimiter_pairs = (pair.split() for pair in [r"\( \)", r"\[ \]", r"$$ $$", r"$ $"])
     for start, end in delimiter_pairs:
         if source.startswith(start) and source.endswith(end):
             return source[len(start) : -len(end)]

myst_nb/docutils_.py

@@ -6,7 +6,7 @@
 from functools import lru_cache, partial
 from importlib import resources as import_resources
 import os
-from typing import Any, TYPE_CHECKING
+from typing import TYPE_CHECKING, Any
 
 from docutils import nodes
 from docutils.core import default_description, publish_cmdline
@@ -153,7 +153,7 @@ def _parse(self, inputstring: str, document: nodes.document) -> None:
         notebook = nb_reader.read(inputstring)
 
         # update the global markdown config with the file-level config
-        warning = lambda wtype, msg: create_warning(  # noqa: E731
+        warning = lambda wtype, msg: create_warning(
             document, msg, line=1, append_to=document, subtype=wtype
         )
         nb_reader.md_config = merge_file_level(

myst_nb/ext/execution_tables.py

@@ -7,9 +7,11 @@
 
 from __future__ import annotations
 
+from collections import defaultdict
+from collections.abc import Callable
 from datetime import datetime
 import posixpath
-from typing import Any, Callable, DefaultDict
+from typing import Any
 
 from docutils import nodes
 from sphinx.addnodes import pending_xref
@@ -104,7 +106,7 @@ def run(self, **kwargs) -> None:
 
 
 def make_stat_table(
-    parent_docname: str, metadata: DefaultDict[str, dict]
+    parent_docname: str, metadata: defaultdict[str, dict]
 ) -> nodes.table:
     """Create a table of statistics on executed notebooks."""
 
@@ -158,7 +160,7 @@ def make_stat_table(
         row.append(nodes.entry("", paragraph))
 
         # other rows
-        for name in _key2header.keys():
+        for name in _key2header:
             paragraph = nodes.paragraph()
             if name == "succeeded" and data[name] is False:
                 paragraph += nodes.abbreviation(

myst_nb/ext/glue/crossref.py

@@ -7,13 +7,14 @@
 from __future__ import annotations
 
 from binascii import a2b_base64
+from collections.abc import Sequence
 from functools import lru_cache
 import hashlib
 import json
 from mimetypes import guess_extension
-from pathlib import Path
-from typing import Any, Sequence
 import os
+from pathlib import Path
+from typing import Any
 
 from docutils import nodes
 from sphinx.builders import Builder