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Lab 3.5.0 hides cells with a markdown horizontal line (---) #13342

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fperez opened this issue Oct 31, 2022 · 25 comments
Closed

Lab 3.5.0 hides cells with a markdown horizontal line (---) #13342

fperez opened this issue Oct 31, 2022 · 25 comments
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@fperez
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fperez commented Oct 31, 2022

Description

In Lab 3.5.0, any markdown cell that begins with a horizontal ruler marker is rendered invisible, as illustrated here:

image

Reproduce

All it takes is making a markdown cell with

---
Any content

and once rendered, it gets displayed as a blank space as shown above.

As best I can tell, this is a new bug, and I'd say pretty critical - horizontal lines are extremely common in content people use, and many are going to be mighty confused when they can't find their seemingly gone cells.

I searched other bugs and the closest I found was #12652. Not the same thing, but I wonder if an attempt at addressing that caused this issue...

@fperez fperez added bug status:Needs Triage Applied to new issues that need triage labels Oct 31, 2022
@fperez
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fperez commented Oct 31, 2022

I should add that the cells with a line also get removed from the navigation outline (left bar). That makes the bug doubly nasty, as those cells become extremely hard to find - they appear to be gone from the notebook.

@JasonWeill JasonWeill removed the status:Needs Triage Applied to new issues that need triage label Oct 31, 2022
@fperez
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fperez commented Oct 31, 2022

Interestingly, on another machine I'm not being able to reproduce this. So while it's happening somewhere, it may not be so widespread as to be critical.

I'll do more testing to see if I can identify what the causing issue is.

@afshin
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afshin commented Oct 31, 2022

I was unable to reproduce this issue on 3.5.0 with Firefox 106.0.1 on macOS. Has anyone else reproduced it?

@jasongrout
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jasongrout commented Oct 31, 2022

I am not seeing this on JLab 3.5.0 or JLab 3.4.8 with Firefox 106.0.3 on macOS.

@andrii-i
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I can't reproduce this on jupyterlab 3.5.0 with Google Chrome 07.0.5304.62 on macos Monterey 12.6.1

@andrii-i
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@fperez could you please advise on the browser / environment you are using when seeing this bug?

@fperez
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fperez commented Oct 31, 2022

Mmh, the plot thickens... I've been able to reproduce the problem again on my M1 MacBook Pro 14", running Monterey (MacOS 12.6), with all three major browsers:

image

On my Intel Mac Mini it's not happening, but it's happening on all three here. System has been rebooted, and while I keep several ad blockers and similar on FFox, I have less on Chrome and none on Safari.

This is really weird. Glad to see others aren't hitting it, but it would still be good to unerstand what's going on...

@fperez
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fperez commented Oct 31, 2022

One more data point - if I add a blank line before the --- marker, the cell renders fine.

As for @afshin's question this morning - I looked at the JS consoles and there's nothing reported other than this message, which I don't think is related:

BackgroundUpdate: _reasonsToNotScheduleUpdates: Failed to check for Maintenance Service Registry Key: [Exception... "Component returned failure code: 0x80004001 (NS_ERROR_NOT_IMPLEMENTED) [nsIUpdateProcessor.getServiceRegKeyExists]"  nsresult: "0x80004001 (NS_ERROR_NOT_IMPLEMENTED)"  location: "JS frame :: resource://gre/modules/BackgroundUpdate.jsm :: _reasonsToNotScheduleUpdates :: line 250"  data: no]

In any case, odd bug... I hope it's not hitting anyone else, though I somehow doubt it...

@jasongrout
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As a next debugging step: can you open up the DOM inspector and see what the DOM looks like? Does the DOM contain the contents of the markdown cell, and the rendering is not tall enough to display it, or is the contents of the rendered markdown cell missing?

@ellisonbg
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ellisonbg commented Oct 31, 2022

@andrii-i should have time to tackle this on Wednesday of this week.

@fperez
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fperez commented Nov 1, 2022

@jasongrout I'm not an expert at DOM debugging, but from what I can see, it looks like the contents of the rendered markdown is indeed missing. I see an enclosing div, but nothing inside, while for a correctly rendered cell, the DOM tree has further nodes and I can read the text inside in the DOM browser...

I only checked this in FFox, but I'm guessing it's the same in all three.

@krassowski
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  1. Approximately, how many cells were in the notebook? Can you share the example notebook?
  2. Did you use table of contents?
  3. Could you share the list of extensions? I seejupyterlab-favourites.

@fperez
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fperez commented Nov 2, 2022

@krassowski any new notebook with any cell like this:

---
Any content

shows the problem. But only on this one laptop so far!! Really odd...

@fperez
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fperez commented Nov 2, 2022

As for 3 - I don't have my laptop handy right now but will update when I do...

@andrii-i
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andrii-i commented Nov 2, 2022

Hi @fperez. I surfaced this bug during todays jupyterlab call and asked participants to attempt to reproduce it and we had 0 hits. Getting more info about your environment would be helpful. Following up and expanding on what @krassowski asked above, could you please (in the environment in which you're getting the bug):

  1. Run jupyter --version in terminal and share output
  2. Run jupyter serverextension list in terminal and share output
  3. Run jupyter labextension list in terminal and share output
  4. Run jupyter troubleshoot in terminal and share output
  5. Reproduce the bug in a notebook and share / upload the notebook so we could try opening it locally and seeing if the bug persists
  6. Record a video reproducing the bug in fresh (conda) environment, in new notebook, in new cell (just in case, mac has a built-in recording capabilities)

@jasongrout
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Also, you can try reproducing with JupyterLite: https://jupyter.org/try-jupyter/lab/

Also, what notebook settings do you have set on that computer? In particular, any settings around virtualized cells?

@andrii-i
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andrii-i commented Nov 2, 2022

Replicating this bug using https://jupyter.org/try-jupyter/lab/ or binder would help us verify if problem has to do with jupyterlab or with local environment

@ellisonbg
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ellisonbg commented Nov 2, 2022 via email

@fperez
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fperez commented Nov 3, 2022

Hi folks, thanks for the help! Today I updated my laptop to macOS 13 (ventura). Bug still there.

Summary of info requests

`jupyter --version`
(base) alpamayo[~]> jupyter --version
Selected Jupyter core packages...
IPython          : 8.5.0
ipykernel        : 6.15.2
ipywidgets       : 7.7.2
jupyter_client   : 7.3.5
jupyter_core     : 4.11.1
jupyter_server   : 1.15.6
jupyterlab       : 3.5.0
nbclient         : 0.5.13
nbconvert        : 5.6.1
nbformat         : 5.4.0
notebook         : 6.4.12
qtconsole        : not installed
traitlets        : 5.3.0
`jupyter serverextension list`
(base) alpamayo[~]> jupyter serverextension list
config dir: /Users/fperez/.jupyter
    jupyterlab  enabled
    - Validating...
      jupyterlab 3.5.0 OK
    hide_code  enabled
    - Validating...
Error loading server extension hide_code
      X is hide_code importable?
config dir: /Users/fperez/.local/etc/jupyter
    nbdime  enabled
    - Validating...
      nbdime 3.1.1 OK
config dir: /Users/fperez/local/conda/etc/jupyter
    dask_labextension  enabled
    - Validating...
      dask_labextension 6.0.0 OK
    ipyparallel  enabled
    - Validating...
      ipyparallel 8.4.1 OK
    jupyter_lsp  enabled
    - Validating...
      jupyter_lsp 1.5.1 OK
    jupyter_server_proxy  enabled
    - Validating...
      jupyter_server_proxy  OK
    jupyter_resource_usage  enabled
    - Validating...
      jupyter_resource_usage 0.6.3 OK
    jupyterlab  enabled
    - Validating...
      jupyterlab 3.5.0 OK
    jupyterlab_git  enabled
    - Validating...
      jupyterlab_git 0.39.3 OK
    jupytext  enabled
    - Validating...
      jupytext 1.14.0 OK
    nbdime  enabled
    - Validating...
      nbdime 3.1.1 OK
`jupyter labextension list`
(base) alpamayo[~]> jupyter labextension list
JupyterLab v3.5.0
/Users/fperez/.local/share/jupyter/labextensions
        nbdime-jupyterlab v2.1.1 enabled OK
        @jupyter-widgets/jupyterlab-manager v3.1.1 enabled OK (python, jupyterlab_widgets)

/Users/fperez/local/conda/share/jupyter/labextensions
jupyterlab-jupytext v1.3.8+dev enabled OK (python, jupytext)
jupyterlab-favorites v3.0.0 enabled OK (python, jupyterlab-favorites)
jupyterlab-myst v0.1.6 enabled OK (python, jupyterlab-myst)
jupyterlab-drawio v0.9.0 enabled OK (python, jupyterlab-drawio)
ipydatagrid v1.1.13 enabled OK
dask-labextension v6.0.0 enabled OK (python, dask_labextension)
jupyterlab_pygments v0.2.2 enabled OK (python, jupyterlab_pygments)
bqplot v0.5.37 enabled OK (python, bqplot)
ipycanvas v0.13.1 enabled OK
jupyterlab-topbar-extension v0.6.1 enabled OK (python, jupyterlab-topbar)
jupyter-matplotlib v0.11.2 enabled OK
ipyparallel-labextension v8.4.1 enabled OK
jupyterlab-blockly-extension v0.2.0 enabled OK (python, jupyterlab_blockly)
jupyter-leaflet v0.17.2 enabled OK
ipysheet v0.6.0 enabled OK (python, ipysheet)
jupyterlab-plotly v5.11.0 enabled OK
@jupyter-server/resource-usage v0.6.3 enabled OK (python, jupyter-resource-usage)
@lckr/jupyterlab_variableinspector v3.0.9 enabled OK (python, lckr_jupyterlab_variableinspector)
@krassowski/jupyterlab-lsp v3.10.2 enabled OK (python, jupyterlab-lsp)
@agoose77/jupyterlab-markup v1.0.1 enabled OK (python, jupyterlab_markup)
@jupyterlab/server-proxy v3.2.2 enabled OK
@jupyterlab/geojson-extension v3.2.0 enabled OK (python, jupyterlab-geojson)
@jupyterlab/git v0.39.3 enabled OK (python, jupyterlab-git)

Other labextensions (built into JupyterLab)
app dir: /Users/fperez/local/conda/share/jupyter/lab

</details>

<details>
<summary>`jupyter troubleshoot` </summary>

(base) alpamayo[~]> jupyter troubleshoot
$PATH:
/Users/fperez/local/conda/bin
/Users/fperez/local/conda/condabin
.
/Users/fperez/tmp/junk/bin
/Users/fperez/usr/bin
/Users/fperez/usr/local/bin
/Users/fperez/.local/bin
/opt/homebrew/bin
/opt/homebrew/sbin
/usr/local/bin
/usr/local/sbin
/usr/local/bin
/System/Cryptexes/App/usr/bin
/usr/bin
/bin
/usr/sbin
/sbin
/Library/TeX/texbin

sys.path:
/Users/fperez/local/conda/bin
/Users/fperez/local/conda/lib/python39.zip
/Users/fperez/local/conda/lib/python3.9
/Users/fperez/local/conda/lib/python3.9/lib-dynload
/Users/fperez/.local/lib/python3.9/site-packages
/Users/fperez/local/conda/lib/python3.9/site-packages

sys.executable:
/Users/fperez/local/conda/bin/python

sys.version:
3.9.13 | packaged by conda-forge | (main, May 27 2022, 17:00:33)
[Clang 13.0.1 ]

platform.platform():
macOS-13.0-arm64-arm-64bit

which -a jupyter:
/Users/fperez/local/conda/bin/jupyter
/Users/fperez/.local/bin/jupyter

pip list:
Package Version
----------------------------- -----------
alabaster 0.7.12
anyio 3.6.1
appnope 0.1.3
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
asttokens 2.0.8
attrs 20.3.0
Babel 2.10.3
backcall 0.2.0
beautifulsoup4 4.11.1
bleach 5.0.1
build 0.8.0
certifi 2022.6.15.1
cffi 1.15.1
charset-normalizer 2.1.1
click 8.1.3
colorama 0.4.5
cycler 0.11.0
datascience 0.17.5
debugpy 1.6.3
decorator 5.1.1
defusedxml 0.7.1
docutils 0.16
entrypoints 0.4
executing 1.0.0
fastjsonschema 2.16.1
fonttools 4.37.1
gitdb 4.0.9
GitPython 3.1.27
idna 3.3
imageio 2.21.2
imagesize 1.4.1
importlib-metadata 4.12.0
ipykernel 6.15.2
ipython 8.5.0
ipython-genutils 0.2.0
ipywidgets 7.7.2
jedi 0.18.1
joblib 1.1.0
jsonschema 4.16.0
jupyter-book 0.9.1
jupyter-cache 0.4.3
jupyter_client 7.3.5
jupyter-core 4.11.1
jupyter-server 1.15.6
jupyter-server-mathjax 0.2.6
jupyter-sphinx 0.3.1
jupyterlab-widgets 1.1.1
kiwisolver 1.4.4
latexcodec 2.0.1
markdown-it-py 0.5.8
MarkupSafe 2.1.1
matplotlib 3.5.3
matplotlib-inline 0.1.6
mistune 0.8.4
myst-nb 0.10.2
myst-parser 0.12.10
nbclient 0.5.13
nbconvert 5.6.1
nbdime 3.1.1
nbformat 5.4.0
nest-asyncio 1.5.5
nested-lookup 0.2.25
networkx 2.8.6
notebook 6.4.12
numpy 1.23.3
oset 0.1.3
packaging 21.3
pandas 1.4.4
pandocfilters 1.5.0
parso 0.8.3
pep517 0.13.0
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.2.0
prometheus-client 0.14.1
prompt-toolkit 3.0.31
psutil 5.9.2
ptyprocess 0.7.0
pure-eval 0.2.2
pybtex 0.24.0
pybtex-docutils 1.0.2
pycparser 2.21
pydata-sphinx-theme 0.8.1
Pygments 2.13.0
pyparsing 3.0.9
pyrsistent 0.18.1
python-dateutil 2.8.2
pytz 2022.2.1
PyWavelets 1.3.0
PyYAML 6.0
pyzmq 23.2.1
requests 2.28.1
scikit-image 0.19.3
scikit-learn 1.1.2
scipy 1.9.1
Send2Trash 1.8.0
six 1.16.0
smmap 5.0.0
sniffio 1.3.0
snowballstemmer 2.2.0
soupsieve 2.3.2.post1
Sphinx 3.5.4
sphinx-book-theme 0.3.3
sphinx-comments 0.0.3
sphinx-copybutton 0.5.0
sphinx-panels 0.5.2
sphinx-thebe 0.1.2
sphinx-togglebutton 0.2.3
sphinxcontrib-applehelp 1.0.2
sphinxcontrib-bibtex 1.0.0
sphinxcontrib-devhelp 1.0.2
sphinxcontrib-htmlhelp 2.0.0
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.3
sphinxcontrib-serializinghtml 1.1.5
SQLAlchemy 1.4.41
stack-data 0.5.0
terminado 0.15.0
testpath 0.6.0
threadpoolctl 3.1.0
tifffile 2022.8.12
tornado 6.2
traitlets 5.3.0
urllib3 1.26.12
wcwidth 0.2.5
webencodings 0.5.1
websocket-client 1.4.1
widgetsnbextension 3.6.1
zipp 3.8.1

conda list:
# packages in environment at /Users/fperez/local/conda:
#
# Name Version Build Channel
abseil-cpp 20220623.0 he4e09e4_5 conda-forge
affine 2.3.1 pyhd8ed1ab_0 conda-forge
aiohttp 3.8.3 py39h02fc5c5_1 conda-forge
aiosignal 1.2.0 pyhd8ed1ab_0 conda-forge
alabaster 0.7.12 py_0 conda-forge
altair 4.2.0 pyhd8ed1ab_1 conda-forge
anyio 3.6.2 pyhd8ed1ab_0 conda-forge
aom 3.5.0 h7ea286d_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
appnope 0.1.3 pyhd8ed1ab_0 conda-forge
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py39h02fc5c5_3 conda-forge
arrow-cpp 9.0.0 py39h7ad6bcf_10_cpu conda-forge
asciitree 0.3.3 py_2 conda-forge
asn1crypto 1.5.1 pyhd8ed1ab_0 conda-forge
astroid 2.12.12 py39h2804cbe_1 conda-forge
asttokens 2.1.0 pyhd8ed1ab_0 conda-forge
async-timeout 4.0.2 pyhd8ed1ab_0 conda-forge
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
autopep8 1.6.0 pyhd8ed1ab_1 conda-forge
aws-c-cal 0.5.11 h4530763_0 conda-forge
aws-c-common 0.6.2 h3422bc3_0 conda-forge
aws-c-event-stream 0.2.7 h9972306_13 conda-forge
aws-c-io 0.10.5 hea86ef8_0 conda-forge
aws-checksums 0.1.11 h487e1a8_7 conda-forge
aws-sdk-cpp 1.8.186 h392f50b_4 conda-forge
babel 2.10.3 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
backports.zoneinfo 0.2.1 py39h2804cbe_7 conda-forge
bcrypt 3.2.2 py39h02fc5c5_1 conda-forge
beautifulsoup4 4.11.1 pyha770c72_0 conda-forge
black 22.10.0 py39h2804cbe_2 conda-forge
bleach 5.0.1 pyhd8ed1ab_0 conda-forge
blosc 1.21.1 hd414afc_3 conda-forge
bokeh 2.4.3 pyhd8ed1ab_3 conda-forge
boost-cpp 1.78.0 h1cb353e_1 conda-forge
bqplot 0.12.36 pyhd8ed1ab_0 conda-forge
branca 0.5.0 pyhd8ed1ab_0 conda-forge
brotli 1.0.9 h1a8c8d9_8 conda-forge
brotli-bin 1.0.9 h1a8c8d9_8 conda-forge
brotlipy 0.7.0 py39h02fc5c5_1005 conda-forge
brunsli 0.1 h9f76cd9_0 conda-forge
bzip2 1.0.8 h3422bc3_4 conda-forge
c-ares 1.18.1 h3422bc3_0 conda-forge
c-blosc2 2.4.3 h303ed30_0 conda-forge
ca-certificates 2022.9.24 h4653dfc_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.16.0 h73a0509_1014 conda-forge
cartopy 0.21.0 py39h5c53a9d_1 conda-forge
certifi 2022.9.24 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py39h7e6b969_1 conda-forge
cfitsio 4.1.0 hd4f5c17_0 conda-forge
cftime 1.6.2 py39h4d8bf0d_1 conda-forge
chardet 5.0.0 py39h2804cbe_1 conda-forge
charls 2.3.4 hbdafb3b_0 conda-forge
charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge
click 8.1.3 unix_pyhd8ed1ab_2 conda-forge
click-completion 0.5.0 py_1 conda-forge
click-log 0.4.0 pyhd8ed1ab_0 conda-forge
click-plugins 1.1.1 py_0 conda-forge
cligj 0.7.2 pyhd8ed1ab_1 conda-forge
cloudpickle 2.2.0 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
conda 22.9.0 py39h2804cbe_1 conda-forge
conda-package-handling 1.9.0 py39h02fc5c5_1 conda-forge
contourpy 1.0.6 py39haaf3ac1_0 conda-forge
coverage 6.5.0 py39h02fc5c5_1 conda-forge
cryptography 38.0.3 py39haa0b8cc_0 conda-forge
curl 7.86.0 hd538317_1 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 0.29.32 py39h23fbdae_1 conda-forge
cytoolz 0.12.0 py39h02fc5c5_1 conda-forge
dask 2022.10.2 pyhd8ed1ab_0 conda-forge
dask-core 2022.10.2 pyhd8ed1ab_0 conda-forge
dask-labextension 6.0.0 pyhd8ed1ab_0 conda-forge
dataclasses 0.8 pyhc8e2a94_3 conda-forge
dav1d 1.0.0 he4db4b2_1 conda-forge
debugpy 1.6.3 py39h23fbdae_1 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
dill 0.3.6 pyhd8ed1ab_1 conda-forge
distributed 2022.10.2 pyhd8ed1ab_0 conda-forge
distro 1.6.0 pyhd8ed1ab_0 conda-forge
docker-py 6.0.0 pyhd8ed1ab_0 conda-forge
docker-pycreds 0.4.0 py_0 conda-forge
docopt 0.6.2 py_1 conda-forge
docutils 0.17.1 py39h2804cbe_3 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
escapism 1.0.1 pyh9f0ad1d_0 conda-forge
exceptiongroup 1.0.0 pyhd8ed1ab_0 conda-forge
executing 1.2.0 pyhd8ed1ab_0 conda-forge
expat 2.5.0 hb7217d7_0 conda-forge
fasteners 0.17.3 pyhd8ed1ab_0 conda-forge
fastprogress 1.0.3 pyhd8ed1ab_0 conda-forge
fiona 1.8.22 py39hb828934_1 conda-forge
flake8 4.0.1 pyhd8ed1ab_2 conda-forge
flit-core 3.7.1 pyhd8ed1ab_0 conda-forge
fmt 9.1.0 hffc8910_0 conda-forge
folium 0.13.0 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.1 h82840c6_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.38.0 py39h02fc5c5_1 conda-forge
fortran-magic 0.7 py_1001 conda-forge
freetype 2.12.1 hd633e50_0 conda-forge
freexl 1.0.6 h1a8c8d9_1 conda-forge
frozenlist 1.3.1 py39h02fc5c5_1 conda-forge
fsspec 2022.10.0 pyhd8ed1ab_0 conda-forge
gast 0.4.0 pyh9f0ad1d_0 conda-forge
gdal 3.5.3 py39h07a3771_1 conda-forge
geopandas 0.12.1 pyhd8ed1ab_0 conda-forge
geopandas-base 0.12.1 pyha770c72_0 conda-forge
geos 3.11.0 h9a09cb3_0 conda-forge
geotiff 1.7.1 h90559a4_4 conda-forge
gettext 0.21.1 h0186832_0 conda-forge
gflags 2.2.2 hc88da5d_1004 conda-forge
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gitdb 4.0.9 pyhd8ed1ab_0 conda-forge
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xorg-libxau 1.0.9 h27ca646_0 conda-forge
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xyzservices 2022.9.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h57fd34a_0 conda-forge
yaml 0.2.5 h3422bc3_2 conda-forge
yaml-cpp 0.7.0 hb7217d7_2 conda-forge
yapf 0.32.0 pyhd8ed1ab_0 conda-forge
yarl 1.8.1 py39h02fc5c5_0 conda-forge
zarr 2.13.3 pyhd8ed1ab_0 conda-forge
zeromq 4.3.4 hbdafb3b_1 conda-forge
zfp 1.0.0 hb6e4faa_3 conda-forge
zict 2.2.0 pyhd8ed1ab_0 conda-forge
zipp 3.10.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h03a7124_4 conda-forge
zlib-ng 2.0.6 he4db4b2_0 conda-forge
zstd 1.5.2 h68b4297_4 conda-forge

conda env:
name: base
channels:
- conda-forge
- defaults
dependencies:
- abseil-cpp=20220623.0=he4e09e4_5
- affine=2.3.1=pyhd8ed1ab_0
- aiohttp=3.8.3=py39h02fc5c5_1
- aiosignal=1.2.0=pyhd8ed1ab_0
- alabaster=0.7.12=py_0
- altair=4.2.0=pyhd8ed1ab_1
- anyio=3.6.2=pyhd8ed1ab_0
- aom=3.5.0=h7ea286d_0
- appdirs=1.4.4=pyh9f0ad1d_0
- appnope=0.1.3=pyhd8ed1ab_0
- argon2-cffi=21.3.0=pyhd8ed1ab_0
- argon2-cffi-bindings=21.2.0=py39h02fc5c5_3
- arrow-cpp=9.0.0=py39h7ad6bcf_10_cpu
- asciitree=0.3.3=py_2
- asn1crypto=1.5.1=pyhd8ed1ab_0
- astroid=2.12.12=py39h2804cbe_1
- asttokens=2.1.0=pyhd8ed1ab_0
- async-timeout=4.0.2=pyhd8ed1ab_0
- attrs=21.4.0=pyhd8ed1ab_0
- autopep8=1.6.0=pyhd8ed1ab_1
- aws-c-cal=0.5.11=h4530763_0
- aws-c-common=0.6.2=h3422bc3_0
- aws-c-event-stream=0.2.7=h9972306_13
- aws-c-io=0.10.5=hea86ef8_0
- aws-checksums=0.1.11=h487e1a8_7
- aws-sdk-cpp=1.8.186=h392f50b_4
- babel=2.10.3=pyhd8ed1ab_0
- backcall=0.2.0=pyh9f0ad1d_0
- backports=1.0=py_2
- backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
- backports.zoneinfo=0.2.1=py39h2804cbe_7
- bcrypt=3.2.2=py39h02fc5c5_1
- beautifulsoup4=4.11.1=pyha770c72_0
- black=22.10.0=py39h2804cbe_2
- bleach=5.0.1=pyhd8ed1ab_0
- blosc=1.21.1=hd414afc_3
- bokeh=2.4.3=pyhd8ed1ab_3
- boost-cpp=1.78.0=h1cb353e_1
- bqplot=0.12.36=pyhd8ed1ab_0
- branca=0.5.0=pyhd8ed1ab_0
- brotli=1.0.9=h1a8c8d9_8
- brotli-bin=1.0.9=h1a8c8d9_8
- brotlipy=0.7.0=py39h02fc5c5_1005
- brunsli=0.1=h9f76cd9_0
- bzip2=1.0.8=h3422bc3_4
- c-ares=1.18.1=h3422bc3_0
- c-blosc2=2.4.3=h303ed30_0
- ca-certificates=2022.9.24=h4653dfc_0
- cached-property=1.5.2=hd8ed1ab_1
- cached_property=1.5.2=pyha770c72_1
- cairo=1.16.0=h73a0509_1014
- cartopy=0.21.0=py39h5c53a9d_1
- certifi=2022.9.24=pyhd8ed1ab_0
- cffi=1.15.1=py39h7e6b969_1
- cfitsio=4.1.0=hd4f5c17_0
- cftime=1.6.2=py39h4d8bf0d_1
- chardet=5.0.0=py39h2804cbe_1
- charls=2.3.4=hbdafb3b_0
- charset-normalizer=2.1.1=pyhd8ed1ab_0
- click=8.1.3=unix_pyhd8ed1ab_2
- click-completion=0.5.0=py_1
- click-log=0.4.0=pyhd8ed1ab_0
- click-plugins=1.1.1=py_0
- cligj=0.7.2=pyhd8ed1ab_1
- cloudpickle=2.2.0=pyhd8ed1ab_0
- colorama=0.4.6=pyhd8ed1ab_0
- conda=22.9.0=py39h2804cbe_1
- conda-package-handling=1.9.0=py39h02fc5c5_1
- contourpy=1.0.6=py39haaf3ac1_0
- coverage=6.5.0=py39h02fc5c5_1
- cryptography=38.0.3=py39haa0b8cc_0
- curl=7.86.0=hd538317_1
- cycler=0.11.0=pyhd8ed1ab_0
- cython=0.29.32=py39h23fbdae_1
- cytoolz=0.12.0=py39h02fc5c5_1
- dask=2022.10.2=pyhd8ed1ab_0
- dask-core=2022.10.2=pyhd8ed1ab_0
- dask-labextension=6.0.0=pyhd8ed1ab_0
- dataclasses=0.8=pyhc8e2a94_3
- dav1d=1.0.0=he4db4b2_1
- debugpy=1.6.3=py39h23fbdae_1
- decorator=5.1.1=pyhd8ed1ab_0
- defusedxml=0.7.1=pyhd8ed1ab_0
- dill=0.3.6=pyhd8ed1ab_1
- distributed=2022.10.2=pyhd8ed1ab_0
- distro=1.6.0=pyhd8ed1ab_0
- docker-py=6.0.0=pyhd8ed1ab_0
- docker-pycreds=0.4.0=py_0
- docopt=0.6.2=py_1
- docutils=0.17.1=py39h2804cbe_3
- entrypoints=0.4=pyhd8ed1ab_0
- escapism=1.0.1=pyh9f0ad1d_0
- exceptiongroup=1.0.0=pyhd8ed1ab_0
- executing=1.2.0=pyhd8ed1ab_0
- expat=2.5.0=hb7217d7_0
- fasteners=0.17.3=pyhd8ed1ab_0
- fastprogress=1.0.3=pyhd8ed1ab_0
- fiona=1.8.22=py39hb828934_1
- flake8=4.0.1=pyhd8ed1ab_2
- flit-core=3.7.1=pyhd8ed1ab_0
- fmt=9.1.0=hffc8910_0
- folium=0.13.0=pyhd8ed1ab_0
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- font-ttf-inconsolata=3.000=h77eed37_0
- font-ttf-source-code-pro=2.038=h77eed37_0
- font-ttf-ubuntu=0.83=hab24e00_0
- fontconfig=2.14.1=h82840c6_0
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- fonttools=4.38.0=py39h02fc5c5_1
- fortran-magic=0.7=py_1001
- freetype=2.12.1=hd633e50_0
- freexl=1.0.6=h1a8c8d9_1
- frozenlist=1.3.1=py39h02fc5c5_1
- fsspec=2022.10.0=pyhd8ed1ab_0
- gast=0.4.0=pyh9f0ad1d_0
- gdal=3.5.3=py39h07a3771_1
- geopandas=0.12.1=pyhd8ed1ab_0
- geopandas-base=0.12.1=pyha770c72_0
- geos=3.11.0=h9a09cb3_0
- geotiff=1.7.1=h90559a4_4
- gettext=0.21.1=h0186832_0
- gflags=2.2.2=hc88da5d_1004
- giflib=5.2.1=h27ca646_2
- gitdb=4.0.9=pyhd8ed1ab_0
- gitpython=3.1.29=pyhd8ed1ab_0
- glog=0.6.0=h6da1cb0_0
- gmp=6.2.1=h9f76cd9_0
- gmpy2=2.1.2=py39h0b4f9c6_1
- greenlet=2.0.0=py39h23fbdae_0
- grpc-cpp=1.49.1=h7747421_1
- h5netcdf=1.0.2=pyhd8ed1ab_0
- h5py=3.7.0=nompi_py39hc9149d8_102
- hdf4=4.2.15=h1a38d6a_5
- hdf5=1.12.2=nompi_h8968d4b_100
- heapdict=1.0.1=py_0
- hypothesis=6.56.4=pyha770c72_0
- icu=70.1=h6b3803e_0
- idna=3.4=pyhd8ed1ab_0
- imagecodecs=2022.9.26=py39hefd8678_3
- imageio=2.22.0=pyhfa7a67d_0
- imagesize=1.4.1=pyhd8ed1ab_0
- importlib-metadata=5.0.0=pyha770c72_1
- importlib_metadata=5.0.0=hd8ed1ab_1
- importlib_resources=5.10.0=pyhd8ed1ab_0
- iniconfig=1.1.1=pyh9f0ad1d_0
- intake=0.6.6=pyhd8ed1ab_0
- intake-esm=2022.9.18=pyhd8ed1ab_0
- intake-geopandas=0.4.0=pyhd8ed1ab_0
- intake-stac=0.4.0=pyhd8ed1ab_0
- intake-xarray=0.6.1=pyhd8ed1ab_0
- ipycanvas=0.13.1=pyhd8ed1ab_0
- ipydatagrid=1.1.13=pyhd8ed1ab_0
- ipykernel=6.17.0=pyh736e0ef_0
- ipyleaflet=0.17.2=pyhd8ed1ab_0
- ipympl=0.9.2=pyhd8ed1ab_0
- ipyparallel=8.4.1=pyhd8ed1ab_0
- ipysheet=0.6.0=pyhd8ed1ab_0
- ipython=8.6.0=pyhd1c38e8_1
- ipython-sql=0.3.9=pyhd8ed1ab_1004
- ipython_genutils=0.2.0=py_1
- ipywidgets=7.6.5=pyhd8ed1ab_0
- iso8601=1.1.0=pyhd8ed1ab_0
- isort=5.10.1=pyhd8ed1ab_0
- jedi=0.18.1=pyhd8ed1ab_2
- jinja2=3.0.3=pyhd8ed1ab_0
- joblib=1.2.0=pyhd8ed1ab_0
- jpeg=9e=he4db4b2_2
- json-c=0.16=hc449e50_0
- json5=0.9.5=pyh9f0ad1d_0
- jsonschema=3.2.0=pyhd8ed1ab_3
- jupyter=1.0.0=py39h2804cbe_7
- jupyter-book=0.13.1=pyhd8ed1ab_0
- jupyter-cache=0.4.3=pyhd8ed1ab_0
- jupyter-lsp=1.5.1=pyhd8ed1ab_0
- jupyter-repo2docker=2022.10.0=pyhd8ed1ab_0
- jupyter-resource-usage=0.6.3=pyhd8ed1ab_0
- jupyter-server-mathjax=0.2.6=pyhc268e32_0
- jupyter-server-proxy=3.2.2=pyhd8ed1ab_0
- jupyter-sphinx=0.3.2=pyhd8ed1ab_1
- jupyter_client=7.3.4=pyhd8ed1ab_0
- jupyter_console=6.4.4=pyhd8ed1ab_0
- jupyter_core=4.11.2=py39h2804cbe_0
- jupyter_server=1.21.0=pyhd8ed1ab_0
- jupyterlab=3.5.0=pyhd8ed1ab_0
- jupyterlab-blockly=0.2.1=pyhd8ed1ab_0
- jupyterlab-drawio=0.9.0=pyhd8ed1ab_0
- jupyterlab-favorites=3.0.0=pyhd8ed1ab_0
- jupyterlab-geojson=3.2.0=pyhd8ed1ab_0
- jupyterlab-git=0.39.3=pyhd8ed1ab_0
- jupyterlab-lsp=3.10.2=pyhd8ed1ab_0
- jupyterlab-markup=1.0.1=pyhd8ed1ab_0
- jupyterlab-myst=0.1.6=pyhd8ed1ab_0
- jupyterlab-topbar=0.6.1=pyhd8ed1ab_2
- jupyterlab-variableinspector=3.0.9=pyhd8ed1ab_0
- jupyterlab_pygments=0.2.2=pyhd8ed1ab_0
- jupyterlab_server=2.16.2=pyhd8ed1ab_0
- jupyterlab_widgets=3.0.3=pyhd8ed1ab_0
- jupytext=1.14.0=pyheef035f_0
- jxrlib=1.1=h27ca646_2
- kealib=1.4.15=h02ce806_1
- kiwisolver=1.4.4=py39haaf3ac1_1
- krb5=1.19.3=hf9b2bbe_0
- latexcodec=2.0.1=pyh9f0ad1d_0
- lazy-object-proxy=1.8.0=py39h02fc5c5_0
- lcms2=2.14=h8193b64_0
- lerc=4.0.0=h9a09cb3_0
- libabseil=20220623.0=cxx17_h28b99d4_5
- libaec=1.0.6=hbdafb3b_0
- libarchive=3.5.2=h69ec738_3
- libavif=0.11.1=h3d80962_0
- libblas=3.9.0=16_osxarm64_openblas
- libbrotlicommon=1.0.9=h1a8c8d9_8
- libbrotlidec=1.0.9=h1a8c8d9_8
- libbrotlienc=1.0.9=h1a8c8d9_8
- libcblas=3.9.0=16_osxarm64_openblas
- libcrc32c=1.1.2=hbdafb3b_0
- libcurl=7.86.0=hd538317_1
- libcxx=14.0.6=h04bba0f_0
- libdap4=3.20.6=h8510809_2
- libdeflate=1.14=h1a8c8d9_0
- libedit=3.1.20191231=hc8eb9b7_2
- libev=4.33=h642e427_1
- libevent=2.1.10=hbae9a57_4
- libffi=3.4.2=h3422bc3_5
- libgdal=3.5.3=h86acc50_1
- libgfortran=5.0.0=11_3_0_hd922786_25
- libgfortran5=11.3.0=hdaf2cc0_25
- libglib=2.74.1=h14ed1c1_0
- libgoogle-cloud=2.3.0=hb5048ff_1
- libgrpc=1.49.1=h503f348_1
- libiconv=1.17=he4db4b2_0
- libkml=1.3.0=h41464e4_1015
- liblapack=3.9.0=16_osxarm64_openblas
- libllvm10=10.0.1=h4468dd5_2
- libllvm11=11.1.0=hfa12f05_5
- libmamba=1.0.0=h85d17d7_1
- libmambapy=1.0.0=py39hf173a79_1
- libnetcdf=4.8.1=nompi_h2510be2_106
- libnghttp2=1.47.0=h232270b_1
- libopenblas=0.3.21=openmp_hc731615_3
- libpng=1.6.38=h76d750c_0
- libpq=14.5=h3f71257_1
- libprotobuf=3.21.9=hb5ab8b9_0
- librttopo=1.1.0=h275bb25_11
- libsodium=1.0.18=h27ca646_1
- libsolv=0.7.22=h1280f1d_0
- libspatialindex=1.9.3=hbdafb3b_4
- libspatialite=5.0.1=hca80f78_21
- libsqlite=3.39.4=h76d750c_0
- libssh2=1.10.0=hb80f160_3
- libthrift=0.16.0=h1a74c4f_2
- libtiff=4.4.0=hfa0b094_4
- libutf8proc=2.8.0=h1a8c8d9_0
- libuv=1.44.2=he4db4b2_0
- libwebp=1.2.4=h328b37c_0
- libwebp-base=1.2.4=h57fd34a_0
- libxcb=1.13=h9b22ae9_1004
- libxml2=2.10.3=h87b0503_0
- libxslt=1.1.37=h1bd8bc4_0
- libzip=1.9.2=h96606af_1
- libzlib=1.2.13=h03a7124_4
- libzopfli=1.0.3=h9f76cd9_0
- linkify-it-py=1.0.3=pyhd8ed1ab_0
- llvm-openmp=14.0.4=hd125106_0
- llvmlite=0.39.1=py39h8ca5d33_1
- locket=1.0.0=pyhd8ed1ab_0
- lxml=4.9.1=py39h0520ce3_1
- lz4=4.0.2=py39hb35ce34_0
- lz4-c=1.9.3=hbdafb3b_1
- lzo=2.10=h642e427_1000
- mamba=1.0.0=py39hde45b87_1
- mapclassify=2.4.3=pyhd8ed1ab_0
- markdown-it-py=1.1.0=pyhd8ed1ab_0
- markupsafe=2.1.1=py39h02fc5c5_2
- matplotlib=3.6.1=py39hdf13c20_1
- matplotlib-base=3.6.1=py39h35e9e80_1
- mccabe=0.6.1=py_1
- mdit-py-plugins=0.2.8=pyhd8ed1ab_0
- mistune=0.8.4=py39h5161555_1005
- mock=4.0.3=pyhd8ed1ab_4
- mpc=1.2.1=h309154c_0
- mpfr=4.1.0=h6d7a090_1
- mpmath=1.2.1=pyhd8ed1ab_0
- msgpack-python=1.0.4=py39haaf3ac1_1
- multidict=6.0.2=py39h02fc5c5_2
- munch=2.5.0=py_0
- munkres=1.1.4=pyh9f0ad1d_0
- mypy_extensions=0.4.3=py39h2804cbe_6
- myst-nb=0.13.2=pyhd8ed1ab_0
- myst-parser=0.15.2=pyhd8ed1ab_0
- nbclassic=0.4.7=pyhd8ed1ab_0
- nbclient=0.5.13=pyhd8ed1ab_0
- nbconvert=6.5.3=pyhd8ed1ab_0
- nbconvert-core=6.5.3=pyhd8ed1ab_0
- nbconvert-pandoc=6.5.3=pyhd8ed1ab_0
- nbdime=3.1.1=pyhd8ed1ab_0
- nbformat=5.7.0=pyhd8ed1ab_0
- ncurses=6.3=h07bb92c_1
- nest-asyncio=1.5.6=pyhd8ed1ab_0
- netcdf4=1.6.1=nompi_py39h8ded8ba_101
- networkx=2.8.8=pyhd8ed1ab_0
- nodejs=18.11.0=haa6f3e8_0
- notebook=6.5.2=pyha770c72_0
- notebook-shim=0.2.0=pyhd8ed1ab_0
- nspr=4.32=hbdafb3b_1
- nss=3.78=h1483a63_0
- numba=0.56.3=py39h251cc7c_0
- numcodecs=0.10.2=py39h3c22d25_0
- numpy=1.23.4=py39hefdcf20_1
- numpydoc=1.5.0=pyhd8ed1ab_0
- openjpeg=2.5.0=h5d4e404_1
- openssl=1.1.1s=h03a7124_0
- orc=1.8.0=hef0d403_0
- packaging=21.3=pyhd8ed1ab_0
- pandas=1.5.1=py39hde7b980_1
- pandoc=2.19.2=hce30654_1
- pandocfilters=1.5.0=pyhd8ed1ab_0
- paramiko=2.11.0=pyhd8ed1ab_0
- parquet-cpp=1.5.1=2
- parso=0.8.3=pyhd8ed1ab_0
- partd=1.3.0=pyhd8ed1ab_0
- pathspec=0.10.1=pyhd8ed1ab_0
- patsy=0.5.3=pyhd8ed1ab_0
- pcre=8.45=hbdafb3b_0
- pcre2=10.37=hcf5f1cc_1
- pep8=1.7.1=py_0
- pexpect=4.8.0=pyh9f0ad1d_2
- pickleshare=0.7.5=py_1003
- pillow=9.2.0=py39h139752e_3
- pip=22.3=pyhd8ed1ab_0
- pixman=0.40.0=h27ca646_0
- platformdirs=2.5.2=pyhd8ed1ab_1
- plotly=5.11.0=pyhd8ed1ab_0
- pluggy=1.0.0=pyhd8ed1ab_5
- pooch=1.6.0=pyhd8ed1ab_0
- poppler=22.11.0=hae7f5f0_0
- poppler-data=0.4.11=hd8ed1ab_0
- postgresql=14.5=hf80b784_1
- prettytable=3.4.1=pyhd8ed1ab_0
- proj=9.1.0=h3bdf472_0
- prometheus_client=0.15.0=pyhd8ed1ab_0
- prompt-toolkit=3.0.31=pyha770c72_0
- prompt_toolkit=3.0.31=hd8ed1ab_0
- pscript=0.7.7=pyhd8ed1ab_0
- psutil=5.9.3=py39h02fc5c5_1
- pthread-stubs=0.4=h27ca646_1001
- ptyprocess=0.7.0=pyhd3deb0d_0
- pure_eval=0.2.2=pyhd8ed1ab_0
- py=1.11.0=pyh6c4a22f_0
- py2vega=0.6.1=pyhd8ed1ab_0
- pyarrow=9.0.0=py39h6e2a28c_10_cpu
- pybind11-abi=4=hd8ed1ab_3
- pybtex=0.24.0=pyhd8ed1ab_2
- pybtex-docutils=1.0.2=py39h2804cbe_2
- pycodestyle=2.8.0=pyhd8ed1ab_0
- pycosat=0.6.4=py39h02fc5c5_1
- pycparser=2.21=pyhd8ed1ab_0
- pydantic=1.10.2=py39h02fc5c5_1
- pydap=3.3.0=pyhd8ed1ab_0
- pydata-sphinx-theme=0.8.1=pyhd8ed1ab_0
- pydocstyle=6.1.1=pyhd8ed1ab_0
- pyflakes=2.4.0=pyhd8ed1ab_0
- pygments=2.13.0=pyhd8ed1ab_0
- pylint=2.15.5=pyhd8ed1ab_0
- pynacl=1.5.0=py39h02fc5c5_2
- pyopenssl=22.1.0=pyhd8ed1ab_0
- pyparsing=3.0.9=pyhd8ed1ab_0
- pyproj=3.4.0=py39h8a4ac70_2
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- pip:
- matplotlib-inline==0.1.4
prefix: /Users/fperez/local/conda

@fperez
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fperez commented Nov 3, 2022

Other info

  • JupyterLite: problem doesn't happen.
  • Notebook to reproduce: it happens with any notebook with a cell that starts with a ---, pre-existing or freshly made...

Recording of the problem

hruler-jlab-bug

@fperez
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fperez commented Nov 3, 2022

And I think @ellisonbg is onto something here ;)

@fperez
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fperez commented Nov 3, 2022

BTW, here's another recording showing how the cell disappears from the TOC sidebar - it happens at render time. Something is entirely removing it:

hruler-jlab-bug2

@jangenoe
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@fperez Does the problem persists after

pip uninstall jupyterlab-myst ?

I guess it is related to the notebook-level metadata implementation.

@fperez
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fperez commented Nov 16, 2022

Bingo @jangenoe!!! That was it indeed. Great eye, thank you!

The myst parser needs to distinguish between a full YAML metadata block and a simple md ruler.

Excellent, will close this and open over there, much appreciated!

I wasn't crazy folks - I know you all think I am, but I swear, these bugs do happen ;)

@ellisonbg
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ellisonbg commented Nov 16, 2022 via email

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