diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index b999e43e..8cf61b07 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -23,6 +23,7 @@ jobs:
tests:
strategy:
+ fail-fast: false
matrix:
os: [ubuntu-latest]
python-version: [3.6, 3.7, 3.8]
diff --git a/docs/conf.py b/docs/conf.py
index f88e8702..890f6652 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -61,6 +61,7 @@
"repository_branch": "master",
"use_edit_page_button": True,
"path_to_docs": "docs/",
+ "show_navbar_depth": 2,
}
intersphinx_mapping = {
@@ -96,10 +97,13 @@
execution_show_tb = "READTHEDOCS" in os.environ
execution_timeout = 60 # Note: 30 was timing out on RTD
-myst_admonition_enable = True
-myst_amsmath_enable = True
-myst_html_img_enable = True
-myst_deflist_enable = True
+myst_enable_extensions = [
+ "amsmath",
+ "colon_fence",
+ "deflist",
+ "dollarmath",
+ "html_image",
+]
myst_url_schemes = ("http", "https", "mailto")
panels_add_bootstrap_css = False
diff --git a/docs/examples/basic.md b/docs/examples/basic.md
index 9e331bef..f7b9de56 100644
--- a/docs/examples/basic.md
+++ b/docs/examples/basic.md
@@ -30,9 +30,13 @@ See the [MyST configuration options](myst:intro/config-options) for the full set
To build documentation from this notebook, the following options are set:
```python
-myst_admonition_enable = True
-myst_amsmath_enable = True
-myst_html_img_enable = True
+myst_enable_extensions = [
+ "amsmath",
+ "colon_fence",
+ "deflist",
+ "dollarmath",
+ "html_image",
+]
myst_url_schemes = ("http", "https", "mailto")
```
@@ -47,7 +51,7 @@ For example, here's the MyST-NB logo:
-With the `myst_html_img_enable=True` ([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](myst:syntax/images)), you can even add HTML `img` tags with attributes:
```html
@@ -70,7 +74,7 @@ It was generated with this code ([as explained here](myst:syntax/admonitions)):
:::::
-If you wish to use "bare" LaTeX equations, then you should set `myst_amsmath_enable = True` in the sphinx configuration.
+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:
```latex
diff --git a/docs/examples/custom-formats.Rmd b/docs/examples/custom-formats.Rmd
index a43afe7f..3d37c215 100644
--- a/docs/examples/custom-formats.Rmd
+++ b/docs/examples/custom-formats.Rmd
@@ -71,7 +71,7 @@ nb_custom_formats = {
```
:::{important}
-For full compatibility with `myst-nb`, `jupytext>=1.6.0` should be used.
+For full compatibility with `myst-nb`, `jupytext>=1.8.0` should be used.
:::
For example:
diff --git a/myst_nb/__init__.py b/myst_nb/__init__.py
index c3763926..c0e2178f 100644
--- a/myst_nb/__init__.py
+++ b/myst_nb/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "0.10.1"
+__version__ = "0.11.0"
from collections.abc import Sequence
import os
diff --git a/setup.py b/setup.py
index 44301b49..d717cebc 100644
--- a/setup.py
+++ b/setup.py
@@ -49,7 +49,7 @@
python_requires=">=3.6",
package_data={"myst_nb": ["_static/*"]},
install_requires=[
- "myst-parser~=0.12.9",
+ "myst-parser~=0.13.1",
"docutils>=0.15",
"sphinx>=2,<4",
# TODO 0.3.2 requires some changes to the pytests
@@ -74,10 +74,10 @@
"numpy",
"sympy",
"pandas",
- "jupytext>=1.6.0",
+ "jupytext~=1.8.0",
],
"rtd": [
- "jupytext>=1.6.0",
+ "jupytext~=1.8.0",
"coconut~=1.4.3",
"sphinxcontrib-bibtex",
"ipywidgets",
diff --git a/tests/notebooks/complex_outputs_unrun_timeout.ipynb b/tests/notebooks/complex_outputs_unrun_timeout.ipynb
deleted file mode 100644
index 572fc144..00000000
--- a/tests/notebooks/complex_outputs_unrun_timeout.ipynb
+++ /dev/null
@@ -1,463 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "init_cell": true,
- "slideshow": {
- "slide_type": "skip"
- }
- },
- "outputs": [],
- "source": [
- "import matplotlib.pyplot as plt\n",
- "import pandas as pd\n",
- "pd.set_option('display.latex.repr', True)\n",
- "import sympy as sym\n",
- "sym.init_printing(use_latex=True)\n",
- "import numpy as np\n",
- "from IPython.display import Image, Latex"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "ipub": {
- "slide": true
- }
- },
- "source": [
- "# Markdown"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "ipub": {
- "slide": true
- }
- },
- "source": [
- "## General"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "ipub": {
- "slide": true
- }
- },
- "source": [
- "Some markdown text.\n",
- "\n",
- "A list:\n",
- "\n",
- "- something\n",
- "- something else\n",
- "\n",
- "A numbered list\n",
- "\n",
- "1. something\n",
- "2. something else\n",
- "\n",
- "non-ascii characters TODO"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "ipub": {}
- },
- "source": [
- "This is a long section of text, which we only want in a document (not a presentation)\n",
- "some text\n",
- "some more text\n",
- "some more text\n",
- "some more text\n",
- "some more text\n",
- "some more text\n",
- "some more text\n",
- "some more text\n",
- "some more text\n"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "ipub": {
- "slide": true,
- "slideonly": true
- }
- },
- "source": [
- "This is an abbreviated section of the document text, which we only want in a presentation\n",
- "\n",
- "- summary of document text"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "ipub": {
- "slide": true
- }
- },
- "source": [
- "## References and Citations"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "ipub": {
- "slide": true
- }
- },
- "source": [
- "References to \\cref{fig:example}, \\cref{tbl:example}, =@eqn:example_sympy and \\cref{code:example_mpl}.\n",
- "\n",
- "A latex citation.\\cite{zelenyak_molecular_2016}\n",
- "\n",
- "A html citation.(Kirkeminde, 2012) "
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "ipub": {
- "slide": true
- }
- },
- "source": [
- "## Todo notes"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "ipub": {
- "slide": true
- }
- },
- "source": [
- "\\todo[inline]{an inline todo}\n",
- "\n",
- "Some text.\\todo{a todo in the margins}"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "# Text Output"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "ipub": {
- "text": {
- "format": {
- "backgroundcolor": "\\color{blue!10}"
- }
- }
- }
- },
- "outputs": [],
- "source": [
- "print(\"\"\"\n",
- "This is some printed text,\n",
- "with a nicely formatted output.\n",
- "\"\"\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "# Images and Figures"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Displaying a plot with its code"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "ipub": {
- "caption": "fig:example_mpl"
- }
- },
- "source": [
- "A matplotlib figure, with the caption set in the markdowncell above the figure."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "ipub": {
- "caption": "code:example_mpl"
- }
- },
- "source": [
- "The plotting code for a matplotlib figure (\\cref{fig:example_mpl})."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "slideshow": {
- "slide_type": "slide"
- }
- },
- "source": [
- "# Tables (with pandas)"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "ipub": {
- "caption": "code:example_pd"
- }
- },
- "source": [
- "The plotting code for a pandas Dataframe table (\\cref{tbl:example})."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "ipub": {
- "code": {
- "asfloat": true,
- "caption": "",
- "label": "code:example_pd",
- "placement": "H",
- "widefigure": false
- },
- "table": {
- "alternate": "gray!20",
- "caption": "An example of a table created with pandas dataframe.",
- "label": "tbl:example",
- "placement": "H"
- }
- }
- },
- "outputs": [],
- "source": [
- "np.random.seed(0) \n",
- "df = pd.DataFrame(np.random.rand(3,4),columns=['a','b','c','d'])\n",
- "df.a = ['$\\delta$','x','y']\n",
- "df.b = ['l','m','n']\n",
- "df.set_index(['a','b'])\n",
- "df.round(3)"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "# Equations (with ipython or sympy)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "ipub": {
- "equation": {
- "label": "eqn:example_ipy"
- }
- }
- },
- "outputs": [],
- "source": [
- "Latex('$$ a = b+c $$')"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "ipub": {
- "caption": "code:example_sym"
- }
- },
- "source": [
- "The plotting code for a sympy equation (=@eqn:example_sympy)."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "ipub": {
- "code": {
- "asfloat": true,
- "caption": "",
- "label": "code:example_sym",
- "placement": "H",
- "widefigure": false
- },
- "equation": {
- "environment": "equation",
- "label": "eqn:example_sympy"
- }
- }
- },
- "outputs": [],
- "source": [
- "y = sym.Function('y')\n",
- "n = sym.symbols(r'\\alpha')\n",
- "f = y(n)-2*y(n-1/sym.pi)-5*y(n-2)\n",
- "sym.rsolve(f,y(n),[1,4])"
- ]
- }
- ],
- "metadata": {
- "celltoolbar": "Edit Metadata",
- "hide_input": false,
- "execution": {
- "timeout": 1
- },
- "ipub": {
- "bibliography": "example.bib",
- "biboptions": [
- "super",
- "sort"
- ],
- "bibstyle": "unsrtnat",
- "language": "portuges",
- "listcode": true,
- "listfigures": true,
- "listtables": true,
- "pandoc": {
- "at_notation": true,
- "use_numref": true
- },
- "sphinx": {
- "bib_title": "My Bibliography"
- },
- "titlepage": {
- "author": "Authors Name",
- "email": "authors@email.com",
- "institution": [
- "Institution1",
- "Institution2"
- ],
- "logo": "logo_example.png",
- "subtitle": "Sub-Title",
- "supervisors": [
- "First Supervisor",
- "Second Supervisor"
- ],
- "tagline": "A tagline for the report.",
- "title": "Main-Title"
- },
- "toc": {
- "depth": 2
- }
- },
- "jupytext": {
- "notebook_metadata_filter": "ipub"
- },
- "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": "3.6.10"
- },
- "latex_envs": {
- "LaTeX_envs_menu_present": true,
- "autocomplete": true,
- "bibliofile": "example.bib",
- "cite_by": "apalike",
- "current_citInitial": 1,
- "eqLabelWithNumbers": true,
- "eqNumInitial": 1,
- "hotkeys": {
- "equation": "Ctrl-E",
- "itemize": "Ctrl-I"
- },
- "labels_anchors": false,
- "latex_user_defs": false,
- "report_style_numbering": false,
- "user_envs_cfg": true
- },
- "nav_menu": {},
- "toc": {
- "colors": {
- "hover_highlight": "#DAA520",
- "navigate_num": "#000000",
- "navigate_text": "#333333",
- "running_highlight": "#FF0000",
- "selected_highlight": "#FFD700",
- "sidebar_border": "#EEEEEE",
- "wrapper_background": "#FFFFFF"
- },
- "moveMenuLeft": true,
- "nav_menu": {
- "height": "161px",
- "width": "252px"
- },
- "navigate_menu": true,
- "number_sections": true,
- "sideBar": true,
- "threshold": 4,
- "toc_cell": false,
- "toc_section_display": "block",
- "toc_window_display": true,
- "widenNotebook": false
- },
- "varInspector": {
- "cols": {
- "lenName": 16,
- "lenType": 16,
- "lenVar": 40
- },
- "kernels_config": {
- "python": {
- "delete_cmd_postfix": "",
- "delete_cmd_prefix": "del ",
- "library": "var_list.py",
- "varRefreshCmd": "print(var_dic_list())"
- },
- "r": {
- "delete_cmd_postfix": ") ",
- "delete_cmd_prefix": "rm(",
- "library": "var_list.r",
- "varRefreshCmd": "cat(var_dic_list()) "
- }
- },
- "types_to_exclude": [
- "module",
- "function",
- "builtin_function_or_method",
- "instance",
- "_Feature"
- ],
- "window_display": false
- }
- },
- "nbformat": 4,
- "nbformat_minor": 2
-}
diff --git a/tests/notebooks/sleep_10.ipynb b/tests/notebooks/sleep_10.ipynb
new file mode 100644
index 00000000..7473264a
--- /dev/null
+++ b/tests/notebooks/sleep_10.ipynb
@@ -0,0 +1,41 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "init_cell": true
+ },
+ "outputs": [],
+ "source": [
+ "import time\n",
+ "time.sleep(10)"
+ ]
+ }
+ ],
+ "metadata": {
+ "celltoolbar": "Edit Metadata",
+ "hide_input": false,
+ "execution": {},
+ "jupytext": {},
+ "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": "3.6.10"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/tests/notebooks/sleep_10_metadata_timeout.ipynb b/tests/notebooks/sleep_10_metadata_timeout.ipynb
new file mode 100644
index 00000000..946cb38a
--- /dev/null
+++ b/tests/notebooks/sleep_10_metadata_timeout.ipynb
@@ -0,0 +1,43 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "init_cell": true
+ },
+ "outputs": [],
+ "source": [
+ "import time\n",
+ "time.sleep(10)"
+ ]
+ }
+ ],
+ "metadata": {
+ "celltoolbar": "Edit Metadata",
+ "hide_input": false,
+ "execution": {
+ "timeout": 1
+ },
+ "jupytext": {},
+ "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": "3.6.10"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/tests/test_execute.py b/tests/test_execute.py
index b6ddb2ba..42216438 100644
--- a/tests/test_execute.py
+++ b/tests/test_execute.py
@@ -228,7 +228,7 @@ def test_relative_path_force(sphinx_run, file_regression, check_nbs):
# Execution timeout configuration
@pytest.mark.sphinx_params(
- "complex_outputs_unrun.ipynb",
+ "sleep_10.ipynb",
conf={"jupyter_execute_notebooks": "cache", "execution_timeout": 1},
)
def test_execution_timeout(sphinx_run, file_regression, check_nbs):
@@ -239,7 +239,7 @@ def test_execution_timeout(sphinx_run, file_regression, check_nbs):
@pytest.mark.sphinx_params(
- "complex_outputs_unrun_timeout.ipynb",
+ "sleep_10_metadata_timeout.ipynb",
conf={"jupyter_execute_notebooks": "cache", "execution_timeout": 60},
)
def test_execution_metadata_timeout(sphinx_run, file_regression, check_nbs):
diff --git a/tox.ini b/tox.ini
index 63a4450d..29f61ffc 100644
--- a/tox.ini
+++ b/tox.ini
@@ -28,7 +28,10 @@ commands = pytest {posargs}
extras = rtd
deps =
ipython<=7.11.0 # required by coconut
-whitelist_externals = rm
+whitelist_externals =
+ echo
+ rm
commands =
clean: rm -rf docs/_build
sphinx-build -nW --keep-going -b {posargs:html} docs/ docs/_build/{posargs:html}
+commands_post = echo "open file://{toxinidir}/docs/_build/{posargs:html}/index.html"