Merge branch 'master' into sphinx-7

Author: choldgraf

CHANGELOG.md

@@ -92,7 +92,7 @@ WARNING: 'jupyter_execute_notebooks' is deprecated for 'nb_execution_mode' [myst
 
 `nb_render_priority` has been removed and replaced by `nb_mime_priority_overrides`, which has a different format and is more flexible. See [Outputs MIME priority](docs/render/format_code_cells.md) for more information.
 
-As per the changes in [`myst_parser`](myst:develop/_changelog), the `dollarmath` syntax extension is no longer included by default.
+As per the changes in [`myst_parser`](inv:myst#develop/_changelog), the `dollarmath` syntax extension is no longer included by default.
 To re-add this extension, ensure that it is specified in your `conf.py`: `myst_enable_extensions = ["dollarmath"]`.
 
 For cell-level configuration the top-level key `render` has now been deprecated for `mystnb`.
@@ -168,7 +168,7 @@ See [Embedding outputs as variables](docs/render/glue.md) for more details.
   - `nbconvert`
 - Updated:
   - `Python`: `3.6+ -> 3.7+`
-  - `myst_parser`: [`0.15 -> 0.17`](myst:develop/_changelog)
+  - `myst_parser`: [`0.15 -> 0.17`](inv:myst#develop/_changelog)
   - `jupyter-cache`: [`0.4 -> 0.5`](https://github.com/executablebooks/jupyter-cache/blob/master/CHANGELOG.md)
   - `sphinx-togglebutton`: [`0.1 -> 0.3`](https://sphinx-togglebutton.readthedocs.io/en/latest/changelog.html)
 

docs/authoring/custom-formats.Rmd

@@ -21,7 +21,7 @@ nb_custom_formats = {
 ```
 
 - The string should be a Python function that will be loaded by `import mylibrary.converter_function`
-- The function should take a file's contents (as a `str`) and return an [nbformat.NotebookNode](nbformat:api)
+- The function should take a file's contents (as a `str`) and return an [nbformat.NotebookNode](inv:nbformat#api)
 
 If the function takes additional keyword arguments, then you can specify these as dictionary in a second argument.
 For example this is what the default conversion would look like:

docs/authoring/jupyter-notebooks.md

@@ -16,13 +16,13 @@ Sphinx using the MyST parser.[^download]
 
 :::{seealso}
 For more information about what you can write with MyST Markdown, see the
-[MyST Parser documentation](myst:intro/get-started).
+[MyST Parser documentation](inv:myst#intro/get-started).
 :::
 
 ### Configuration
 
-The MyST-NB parser derives from [the base MyST-Parser](myst:intro/get-started), and so all the same configuration options are available.
-See the [MyST configuration options](myst:sphinx/config-options) for the full set of options, and [MyST syntax guide](myst:syntax/core) for all the syntax options.
+The MyST-NB parser derives from [the base MyST-Parser](inv:myst#intro/get-started), and so all the same configuration options are available.
+See the [MyST configuration options](inv:myst#sphinx/config-options) for the full set of options, and [MyST syntax guide](inv:myst#syntax/core) for all the syntax options.
 
 To build documentation from this notebook, the following options are set:
 
@@ -38,7 +38,7 @@ myst_url_schemes = ("http", "https", "mailto")
 ```
 
 :::{note}
-Loading the `myst_nb` extension also activates the [`myst_parser`](myst:index) extension, for enabling the MyST flavour of Markdown.
+Loading the `myst_nb` extension also activates the [`myst_parser`](inv:myst#index) extension, for enabling the MyST flavour of Markdown.
 It is not required to add this explicitly in the list of `extensions`.
 :::
 
@@ -53,7 +53,7 @@ For example, here's the MyST-NB logo:
 
 ![myst-nb logo](../_static/logo-wide.svg)
 
-By adding `"html_image"` to the `myst_enable_extensions` list in the sphinx configuration ([see here](myst:syntax/images)), you can even add HTML `img` tags with attributes:
+By adding `"html_image"` to the `myst_enable_extensions` list in the sphinx configuration ([see here](inv:myst#syntax/images)), you can even add HTML `img` tags with attributes:
 
 ```html
 <img src="../_static/logo-wide.svg" alt="logo" width="200px" class="shadow mb-2">
@@ -66,7 +66,7 @@ For example, here's a note admonition block:
 
 :::::{note}
 **Wow**, a note!
-It was generated with this code ([as explained here](myst:syntax/admonitions)):
+It was generated with this code ([as explained here](inv:myst:std:label#syntax/admonitions)):
 
 ````md
 :::{note}
@@ -77,7 +77,7 @@ It was generated with this code ([as explained here](myst:syntax/admonitions)):
 :::::
 
 If you wish to use "bare" LaTeX equations, then you should add `"amsmath"` to the `myst_enable_extensions` list in the sphinx configuration.
-This is [explained here](myst:syntax/amsmath), and works as such:
+This is [explained here](inv:myst:std:label#syntax/amsmath), and works as such:
 
 ```latex
 \begin{equation}
@@ -110,7 +110,7 @@ $$e^{i\pi} + 1 = 0$$ (euler)
 Euler's identity, equation {math:numref}`euler`, was elected one of the
 most beautiful mathematical formulas.
 
-You can see the syntax used for this example [here in the MyST documentation](myst:syntax/math).
+You can see the syntax used for this example [here in the MyST documentation](inv:myst:std:label#syntax/math).
 
 ## Code cells and outputs
 

docs/index.md

@@ -86,7 +86,7 @@ Build single or collections of documents into multiple formats (HTML, PDF, ...).
 
 MyST-NB is a module within the [Executable Books Project](https://executablebooks.org),
 an international collaboration to build open source tools that facilitate publishing computational narratives using the Jupyter ecosystem.
-It is also a core component of [Jupyter Book](jb:intro).
+It is also a core component of [Jupyter Book](inv:jb#intro).
 
 Check out the [Gallery of Jupyter Books](https://executablebooks.org/en/latest/gallery),
 for inspiration from across the community.

myst_nb/core/config.py

@@ -195,6 +195,14 @@ def __post_init__(self):
             "sections": (Section.global_lvl, Section.execute),
         },
     )
+    eval_name_regex: str = dc.field(
+        default=r"^[a-zA-Z_][a-zA-Z0-9_]*$",
+        metadata={
+            "validator": instance_of(str),
+            "help": "Regex that matches permitted values of eval expressions",
+            "sections": (Section.global_lvl, Section.file_lvl, Section.execute),
+        },
+    )
     execution_mode: Literal["off", "force", "auto", "cache", "inline"] = dc.field(
         default="auto",
         metadata={

myst_nb/core/execute/base.py

@@ -2,7 +2,6 @@
 from __future__ import annotations
 
 from pathlib import Path
-import re
 from typing import Any
 
 from nbformat import NotebookNode
@@ -39,9 +38,6 @@ class EvalNameError(Exception):
     """An exception for if an evaluation variable name is invalid."""
 
 
-EVAL_NAME_REGEX = re.compile(r"^[a-zA-Z_][a-zA-Z0-9_]*$")
-
-
 class NotebookClientBase:
     """A base client for interacting with Jupyter notebooks.
 

myst_nb/core/execute/inline.py

@@ -3,6 +3,7 @@
 
 import asyncio
 from datetime import datetime
+import re
 import shutil
 from tempfile import mkdtemp
 import time
@@ -22,7 +23,7 @@
 
 from myst_nb.ext.glue import extract_glue_data_cell
 
-from .base import EVAL_NAME_REGEX, EvalNameError, ExecutionError, NotebookClientBase
+from .base import EvalNameError, ExecutionError, NotebookClientBase
 
 
 class NotebookClientInline(NotebookClientBase):
@@ -148,7 +149,7 @@ def code_cell_outputs(
         return cell.get("execution_count", None), cell.get("outputs", [])
 
     def eval_variable(self, name: str) -> list[NotebookNode]:
-        if not EVAL_NAME_REGEX.match(name):
+        if not re.match(self.nb_config.eval_name_regex, name):
             raise EvalNameError(name)
         return self._client.eval_expression(name)
 

myst_nb/ext/eval/__init__.py

@@ -43,11 +43,13 @@ def retrieve_eval_data(document: nodes.document, key: str) -> list[VariableOutpu
     except NotImplementedError:
         raise RetrievalError("This document does not have a running kernel")
     except EvalNameError:
-        raise RetrievalError(f"The variable {key!r} is not a valid name")
+        raise RetrievalError(
+            f"The expression {key!r} is not valid according to the configured pattern"
+        )
     except Exception as exc:
         raise RetrievalError(f"variable evaluation error: {exc}")
     if not outputs:
-        raise RetrievalError(f"variable {key!r} does not return any outputs")
+        raise RetrievalError(f"expression {key!r} does not return any outputs")
 
     # the returned outputs could be one of the following:
     # https://nbformat.readthedocs.io/en/latest/format_description.html#code-cell-outputs

pyproject.toml

@@ -38,7 +38,7 @@ dependencies = [
     "ipython",
     "jupyter-cache>=0.5,<0.7",
     "nbclient",  # nbclient version pinned by jupyter-client
-    "myst-parser>=0.18.0",
+    "myst-parser~=1.0.0",
     "nbformat~=5.0",
     "pyyaml",
     "sphinx>=4",
@@ -79,7 +79,7 @@ rtd = [
     "numpy",
     "pandas",
     "plotly",
-    "sphinx-book-theme>=0.3",
+    "sphinx-book-theme~=1.0.0",
     "sphinx-copybutton",
     "sphinx-design~=0.4.0",
     "sphinxcontrib-bibtex",