⬆️ UPGRADE: myst-parser v0.12.9

Minor upgrade with bug fixes

Author: chrisjsewell

docs/examples/custom-formats.Rmd

@@ -71,7 +71,7 @@ nb_custom_formats = {
 ```
 
 :::{important}
-It is necessary to use `jupytext<=1.4.0,>=1.5.0`, due to an incompatibility with the `myst-parser` version in `jupytext=1.4`.
+For full compatibility with `myst-nb`, `jupytext>=1.6.0` should be used.
 :::
 
 For example:

docs/examples/interactive.md

@@ -67,6 +67,16 @@ fig = px.scatter(df, x="sepal_width", y="sepal_length", color="species", size="s
 fig
 ```
 
+:::{important}
+
+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"]
+```
+
+:::
+
 ## Bokeh
 
 Bokeh provides several options for interactive visualizations, and is part of the PyViz ecosystem. See

docs/use/markdown.md

@@ -263,7 +263,7 @@ For more information, see [the MyST-NB Sphinx extension documentation](index.md)
 ## MyST Notebooks in Jupyter Book
 
 In addition to using MyST Notebooks with Sphinx, you may also use them with the
-Jupyter Book project. See {doc}`jb:content-types/myst-notebooks`.
+Jupyter Book project. See {doc}`jb:file-types/myst-notebooks`.
 
 
 (myst-nb/jupyter-interfaces)=

myst_nb/execution.py

@@ -20,7 +20,7 @@
 from sphinx.application import Sphinx
 from sphinx.builders import Builder
 from sphinx.environment import BuildEnvironment
-from sphinx.util import logging
+from sphinx.util import logging, progress_message
 
 from jupyter_cache import get_cache
 from jupyter_cache.executors import load_executor
@@ -273,14 +273,15 @@ def _stage_and_execute(
 
     # can leverage parallel execution implemented in jupyter-cache here
     try:
-        execute_staged_nb(
-            cache_base,
-            pk_list or None,
-            timeout=timeout,
-            exec_in_temp=exec_in_temp,
-            allow_errors=allow_errors,
-            env=env,
-        )
+        with progress_message("executing outdated notebooks"):
+            execute_staged_nb(
+                cache_base,
+                pk_list or None,
+                timeout=timeout,
+                exec_in_temp=exec_in_temp,
+                allow_errors=allow_errors,
+                env=env,
+            )
     except OSError as err:
         # This is a 'fix' for obscure cases, such as if you
         # remove name.ipynb and add name.md (i.e. same name, different extension)

myst_nb/nb_glue/domain.py

@@ -30,9 +30,13 @@ def key(self):
         return self.attributes["key"]
 
     def copy(self):
-        return self.__class__(
+        obj = self.__class__(
             self.key, **{k: v for k, v in self.attributes.items() if k != "key"}
         )
+        obj.document = self.document
+        obj.source = self.source
+        obj.line = self.line
+        return obj
 
     def create_node(self, output: dict, document, env):
         """Create the output node, give the cell output."""

myst_nb/nodes.py

@@ -52,9 +52,13 @@ def renderer(self) -> str:
         return self._renderer
 
     def copy(self):
-        return self.__class__(
+        obj = self.__class__(
             outputs=self._outputs,
             renderer=self._renderer,
             metadata=self._metadata,
             **self.attributes,
         )
+        obj.document = self.document
+        obj.source = self.source
+        obj.line = self.line
+        return obj

myst_nb/render_outputs.py

@@ -2,6 +2,7 @@
 from abc import ABC, abstractmethod
 import os
 from typing import List, Optional
+from unittest import mock
 
 from importlib_metadata import entry_points
 from docutils import nodes
@@ -19,6 +20,7 @@
 from jupyter_sphinx.utils import sphinx_abs_dir
 
 from myst_parser.main import default_parser, MdParserConfig
+from myst_parser.docutils_renderer import make_document
 
 from .nodes import CellOutputBundleNode
 
@@ -118,7 +120,15 @@ def run(self):
             if "candidates" in node:
                 continue
             col = ImageCollector()
-            col.process_doc(self.app, node)
+
+            # use the node docname, where possible, to deal with single document builds
+            docname = (
+                self.app.env.path2doc(node.source)
+                if node.source
+                else self.app.env.docname
+            )
+            with mock.patch.dict(self.app.env.temp_data, {"docname": docname}):
+                col.process_doc(self.app, node)
 
 
 class CellOutputRendererBase(ABC):
@@ -227,9 +237,25 @@ def parse_markdown(
     ) -> List[nodes.Node]:
         """Parse text as CommonMark, in a new document."""
         parser = default_parser(MdParserConfig(commonmark_only=True))
-        parent = parent or nodes.container()
+
+        # setup parent node
+        if parent is None:
+            parent = nodes.container()
+            self.add_source_and_line(parent)
         parser.options["current_node"] = parent
-        parser.render(text)
+
+        # setup containing document
+        new_doc = make_document(self.node.source)
+        new_doc.settings = self.document.settings
+        new_doc.reporter = self.document.reporter
+        parser.options["document"] = new_doc
+
+        # use the node docname, where possible, to deal with single document builds
+        with mock.patch.dict(
+            self.env.temp_data, {"docname": self.env.path2doc(self.node.source)}
+        ):
+            parser.render(text)
+
         # TODO is there any transforms we should retroactively carry out?
         return parent.children
 

setup.py

@@ -49,7 +49,7 @@
     python_requires=">=3.6",
     package_data={"myst_nb": ["_static/*"]},
     install_requires=[
-        "myst-parser~=0.12.5",
+        "myst-parser~=0.12.9",
         "docutils>=0.15",
         "sphinx>=2,<4",
         "jupyter_sphinx~=0.3.1",
@@ -73,11 +73,10 @@
             "numpy",
             "sympy",
             "pandas",
-            # greater versions currently have a version conflict with myst-parser
-            "jupytext<=1.4.0",
+            "jupytext>=1.6.0",
         ],
         "rtd": [
-            "jupytext<=1.4.0",
+            "jupytext>=1.6.0",
             "coconut~=1.4.3",
             "sphinxcontrib-bibtex",
             "ipywidgets",

tests/nb_fixtures/basic.txt

@@ -135,11 +135,11 @@ cells:
 <document source="notset">
     <docinfo>
     <paragraph>
-        <pending_xref refdomain="True" refexplicit="True" reftarget="before" reftype="myst" refwarn="True">
+        <pending_xref refdoc="mock_docname" refdomain="True" refexplicit="True" reftarget="before" reftype="myst" refwarn="True">
             <inline classes="xref myst">
                 a
 
-        <pending_xref refdomain="True" refexplicit="True" reftarget="after" reftype="myst" refwarn="True">
+        <pending_xref refdoc="mock_docname" refdomain="True" refexplicit="True" reftarget="after" reftype="myst" refwarn="True">
             <inline classes="xref myst">
                 b
 .

tox.ini

@@ -11,7 +11,7 @@
 # then then deleting compiled files has been found to fix it: `find . -name \*.pyc -delete`
 
 [tox]
-envlist = py{36,37,38}-sphinx{2,3}
+envlist = py37-sphinx3
 
 [testenv]
 # only recreate the environment when we use `tox -r`
@@ -31,4 +31,4 @@ deps =
 whitelist_externals = rm
 commands =
     clean: rm -rf docs/_build
-    sphinx-build {posargs} -nW --keep-going -b html docs/ docs/_build/html
+    sphinx-build -nW --keep-going -b {posargs:html} docs/ docs/_build/{posargs:html}