Comments (15)
alisterburt
commented on July 28, 2024
1
yep! very strange. This only happens for me when building docs on CI, not when building locally so I haven't got it figured out
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alisterburt
commented on July 28, 2024
1
sure!
- MacOS 11.5.2
- python 3.9.6 (conda-forge)
conda list:
# packages in environment at /opt/homebrew/Caskroom/miniforge/base/envs/napari-workshop:
#
# Name Version Build Channel
alabaster 0.7.12 pypi_0 pypi
anyio 3.3.0 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
appnope 0.1.2 py39hecd8cb5_1001
argon2-cffi 20.1.0 py39h9ed2024_1
async_generator 1.10 pyhd3eb1b0_0
attrs 20.3.0 pypi_0 pypi
babel 2.9.1 pypi_0 pypi
backcall 0.2.0 pyhd3eb1b0_0
beautifulsoup4 4.9.3 pypi_0 pypi
bleach 4.0.0 pyhd3eb1b0_0
ca-certificates 2021.7.5 hecd8cb5_1
cachey 0.2.1 pypi_0 pypi
cellpose 0.6.5 pypi_0 pypi
cellpose-napari 0.1.3 pypi_0 pypi
certifi 2021.5.30 py39hecd8cb5_0
cffi 1.14.6 py39h2125817_0
charset-normalizer 2.0.4 pypi_0 pypi
click 7.1.2 pypi_0 pypi
cloudpickle 1.6.0 pypi_0 pypi
colorama 0.4.4 pypi_0 pypi
cycler 0.10.0 pypi_0 pypi
dask 2021.8.0 pypi_0 pypi
debugpy 1.4.1 pypi_0 pypi
decorator 5.0.9 pyhd3eb1b0_0
defusedxml 0.7.1 pyhd3eb1b0_0
docstring-parser 0.10 pypi_0 pypi
docutils 0.16 pypi_0 pypi
entrypoints 0.3 pypi_0 pypi
freetype-py 2.2.0 pypi_0 pypi
fsspec 2021.7.0 pypi_0 pypi
gitdb 4.0.7 pypi_0 pypi
gitpython 3.1.18 pypi_0 pypi
greenlet 1.1.1 pypi_0 pypi
heapdict 1.0.1 pypi_0 pypi
hsluv 5.0.2 pypi_0 pypi
icu 58.2 h0a44026_3
idna 3.2 pypi_0 pypi
imagecodecs 2021.8.26 pypi_0 pypi
imageio 2.9.0 pypi_0 pypi
imagesize 1.2.0 pypi_0 pypi
importlib-metadata 4.6.4 pypi_0 pypi
importlib_metadata 3.10.0 hd3eb1b0_0
ipykernel 6.2.0 pypi_0 pypi
ipython 7.26.0 py39h01d92e1_0
ipython_genutils 0.2.0 pyhd3eb1b0_1
ipywidgets 7.6.3 pyhd3eb1b0_1
jedi 0.18.0 py39hecd8cb5_1
jinja2 3.0.1 pyhd3eb1b0_0
jpeg 9b he5867d9_2
jsonschema 3.2.0 py_2
jupyter 1.0.0 py39hecd8cb5_7
jupyter-book 0.11.2 pypi_0 pypi
jupyter-cache 0.4.3 pypi_0 pypi
jupyter-client 7.0.1 pypi_0 pypi
jupyter-server 1.10.2 pypi_0 pypi
jupyter-server-mathjax 0.2.3 pypi_0 pypi
jupyter-sphinx 0.3.2 pypi_0 pypi
jupyter_client 6.1.12 pyhd3eb1b0_0
jupyter_console 6.4.0 pyhd3eb1b0_0
jupyter_core 4.7.1 py39hecd8cb5_0
jupyterlab_pygments 0.1.2 py_0
jupyterlab_widgets 1.0.0 pyhd3eb1b0_1
jupytext 1.10.3 pypi_0 pypi
kiwisolver 1.3.1 pypi_0 pypi
latexcodec 2.0.1 pypi_0 pypi
libcxx 10.0.0 1
libffi 3.3 hb1e8313_2
libpng 1.6.37 ha441bb4_0
libsodium 1.0.18 h1de35cc_0
linkify-it-py 1.0.1 pypi_0 pypi
llvmlite 0.37.0 pypi_0 pypi
locket 0.2.1 pypi_0 pypi
magicgui 0.2.10 pypi_0 pypi
markdown-it-py 0.6.2 pypi_0 pypi
markupsafe 2.0.1 py39h9ed2024_0
matplotlib 3.4.3 pypi_0 pypi
matplotlib-inline 0.1.2 pyhd3eb1b0_2
mdit-py-plugins 0.2.6 pypi_0 pypi
mistune 0.8.4 py39h9ed2024_1000
myst-nb 0.12.3 pypi_0 pypi
myst-parser 0.13.7 pypi_0 pypi
napari 0.4.11rc2 pypi_0 pypi
napari-console 0.0.3 pypi_0 pypi
napari-plugin-engine 0.1.9 pypi_0 pypi
napari-svg 0.1.5 pypi_0 pypi
natsort 7.1.1 pypi_0 pypi
nbclient 0.5.4 pypi_0 pypi
nbconvert 5.6.1 pypi_0 pypi
nbdime 3.1.0 pypi_0 pypi
nbformat 5.1.3 pyhd3eb1b0_0
ncurses 6.2 h0a44026_1
nest-asyncio 1.5.1 pyhd3eb1b0_0
networkx 2.6.2 pypi_0 pypi
notebook 6.4.3 py39hecd8cb5_0
numba 0.54.0 pypi_0 pypi
numpy 1.20.3 pypi_0 pypi
numpydoc 1.1.0 pypi_0 pypi
opencv-python-headless 4.5.3.56 pypi_0 pypi
openssl 1.1.1k h9ed2024_0
packaging 21.0 pyhd3eb1b0_0
pandocfilters 1.4.3 py39hecd8cb5_1
parso 0.8.2 pyhd3eb1b0_0
partd 1.2.0 pypi_0 pypi
pexpect 4.8.0 pyhd3eb1b0_3
pickleshare 0.7.5 pyhd3eb1b0_1003
pillow 8.3.1 pypi_0 pypi
pint 0.17 pypi_0 pypi
pip 21.2.4 py37hecd8cb5_0
pooch 1.4.0 pypi_0 pypi
prometheus_client 0.11.0 pyhd3eb1b0_0
prompt-toolkit 3.0.19 pypi_0 pypi
prompt_toolkit 3.0.17 hd3eb1b0_0
psutil 5.8.0 pypi_0 pypi
ptyprocess 0.7.0 pyhd3eb1b0_2
pybtex 0.24.0 pypi_0 pypi
pybtex-docutils 1.0.1 pypi_0 pypi
pycparser 2.20 py_2
pydantic 1.8.2 pypi_0 pypi
pydata-sphinx-theme 0.6.3 pypi_0 pypi
pygments 2.10.0 pyhd3eb1b0_0
pyopengl 3.1.5 pypi_0 pypi
pyparsing 2.4.7 pyhd3eb1b0_0
pyqt 5.9.2 py39h23ab428_6
pyqt5 5.15.4 pypi_0 pypi
pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.9.0 pypi_0 pypi
pyrsistent 0.18.0 py39h9ed2024_0
python 3.9.6 h88f2d9e_1
python-dateutil 2.8.2 pyhd3eb1b0_0
pytz 2021.1 pypi_0 pypi
pywavelets 1.1.1 pypi_0 pypi
pyyaml 5.4.1 pypi_0 pypi
pyzmq 22.2.1 py39h23ab428_1
qt 5.9.7 h468cd18_1
qtconsole 5.1.0 pyhd3eb1b0_0
qtpy 1.9.0 py_0
readline 8.1 h9ed2024_0
requests 2.26.0 pypi_0 pypi
requests-unixsocket 0.2.0 pypi_0 pypi
scikit-image 0.18.2 pypi_0 pypi
scipy 1.7.1 pypi_0 pypi
send2trash 1.8.0 pypi_0 pypi
setuptools 52.0.0 py39hecd8cb5_0
sip 4.19.13 py39h23ab428_0
six 1.16.0 pyhd3eb1b0_0
smmap 4.0.0 pypi_0 pypi
sniffio 1.2.0 pypi_0 pypi
snowballstemmer 2.1.0 pypi_0 pypi
soupsieve 2.2.1 pypi_0 pypi
sphinx 3.5.4 pypi_0 pypi
sphinx-book-theme 0.1.2 pypi_0 pypi
sphinx-comments 0.0.3 pypi_0 pypi
sphinx-copybutton 0.4.0 pypi_0 pypi
sphinx-external-toc 0.2.3 pypi_0 pypi
sphinx-jupyterbook-latex 0.4.2 pypi_0 pypi
sphinx-multitoc-numbering 0.1.3 pypi_0 pypi
sphinx-panels 0.5.2 pypi_0 pypi
sphinx-thebe 0.0.8 pypi_0 pypi
sphinx-togglebutton 0.2.3 pypi_0 pypi
sphinxcontrib-applehelp 1.0.2 pypi_0 pypi
sphinxcontrib-bibtex 2.2.1 pypi_0 pypi
sphinxcontrib-devhelp 1.0.2 pypi_0 pypi
sphinxcontrib-htmlhelp 2.0.0 pypi_0 pypi
sphinxcontrib-jsmath 1.0.1 pypi_0 pypi
sphinxcontrib-qthelp 1.0.3 pypi_0 pypi
sphinxcontrib-serializinghtml 1.1.5 pypi_0 pypi
sqlalchemy 1.4.23 pypi_0 pypi
sqlite 3.36.0 hce871da_0
superqt 0.2.3 pypi_0 pypi
terminado 0.11.1 pypi_0 pypi
testpath 0.5.0 pyhd3eb1b0_0
tifffile 2021.8.8 pypi_0 pypi
tk 8.6.10 hb0a8c7a_0
toml 0.10.2 pypi_0 pypi
toolz 0.11.1 pypi_0 pypi
torch 1.9.0 pypi_0 pypi
tornado 6.1 py39h9ed2024_0
tqdm 4.62.1 pypi_0 pypi
traitlets 5.0.5 pyhd3eb1b0_0
typing-extensions 3.10.0.0 pypi_0 pypi
tzdata 2021a h5d7bf9c_0
uc-micro-py 1.0.1 pypi_0 pypi
urllib3 1.26.6 pypi_0 pypi
vispy 0.8.0 pypi_0 pypi
wcwidth 0.2.5 py_0
webencodings 0.5.1 pypi_0 pypi
websocket-client 1.2.1 pypi_0 pypi
wheel 0.37.0 pyhd3eb1b0_0
widgetsnbextension 3.5.1 py39hecd8cb5_0
wrapt 1.12.1 pypi_0 pypi
xz 5.2.5 h1de35cc_0
zeromq 4.3.4 h23ab428_0
zipp 3.5.0 pyhd3eb1b0_0
zlib 1.2.11 h1de35cc_3
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codemonkey800
commented on July 28, 2024
1
I ran the napari.org deploy workflow using the macos-11 (Big Sur) runner and it's still having the same problems with images not rendering in CI 😢
The link to the staging site above should have 9 screenshots (6 rendered, 3 static), but it only has the 3 static screenshots.
I'm also seeing Tornado errors (#161) in the CI, but I'm not sure if they're related
ERROR:tornado.general:Uncaught exception in ZMQStream callback
Traceback (most recent call last):
File "/Users/runner/hostedtoolcache/Python/3.8.12/x64/lib/python3.8/site-packages/zmq/eventloop/zmqstream.py", line 431, in _run_callback
callback(*args, **kwargs)
File "/Users/runner/hostedtoolcache/Python/3.8.12/x64/lib/python3.8/site-packages/jupyter_client/threaded.py", line 121, in _handle_recv
msg_list = self.ioloop._asyncio_event_loop.run_until_complete(get_msg(future_msg))
File "/Users/runner/hostedtoolcache/Python/3.8.12/x64/lib/python3.8/asyncio/base_events.py", line 592, in run_until_complete
self._check_running()
File "/Users/runner/hostedtoolcache/Python/3.8.12/x64/lib/python3.8/asyncio/base_events.py", line 554, in _check_running
raise RuntimeError(
RuntimeError: Cannot run the event loop while another loop is running
ERROR:tornado.general:Uncaught exception in zmqstream callback
I wonder if there's something special about my Conda Forge environment 🤔
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alisterburt
commented on July 28, 2024
I’m not sure what’s going on with the site (lots of activity on the repo!) but if it’s still jupyter-book I noticed this same issue if there were cells tagged with ‘remove-cell’ in the source
… On 22 Sep 2021, at 22:17, Jeremy Asuncion ***@***.***> wrote:
I noticed that some of the screenshots from the code examples are no longer rendering during deployment. Here's an example from https://napari.org/tutorials/fundamentals/viewer.html:
And here's the same page when built locally:
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alisterburt
commented on July 28, 2024
Again, this was only in CI not when built locally
… On 22 Sep 2021, at 22:39, Alister Burt ***@***.***> wrote:
I’m not sure what’s going on with the site (lots of activity on the repo!) but if it’s still jupyter-book I noticed this same issue if there were cells tagged with ‘remove-cell’ in the source
>> On 22 Sep 2021, at 22:17, Jeremy Asuncion ***@***.***> wrote:
>>
>
> I noticed that some of the screenshots from the code examples are no longer rendering during deployment. Here's an example from https://napari.org/tutorials/fundamentals/viewer.html:
>
>
>
> And here's the same page when built locally:
>
>
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub, or unsubscribe.
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GenevieveBuckley
commented on July 28, 2024
Do we think it's related to #161?
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GenevieveBuckley
commented on July 28, 2024
@alisterburt the nbscreenshot commands are all marked [hide-input]. The only [remove-cell] tags I see are for closing all the opened viewers, and once for changing the theme back to dark mode.
Jupytext source code: https://github.com/napari/napari.github.io/blob/main/tutorials/fundamentals/viewer.md
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alisterburt
commented on July 28, 2024
@GenevieveBuckley this matches the behaviour that I was seeing - the presence of [remove-cell] anywhere stopped images from being correctly rendered elsewhere in the document. e.g. this napari workshop
I haven't found a solution yet besides building locally but it's almost certainly some easy fix
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GenevieveBuckley
commented on July 28, 2024
@GenevieveBuckley this matches the behaviour that I was seeing - the presence of [remove-cell] anywhere stopped images from being correctly rendered elsewhere in the document. e.g. this napari workshop
I haven't found a solution yet besides building locally but it's almost certainly some easy fix
Wait, really? [remove-cell] being anywhere in the notebook has caused problems for unrelated cells in the notebook? That seems like a problem...
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GenevieveBuckley
commented on July 28, 2024
@alisterburt would you also be kind enough to give us the details of your local environment?
- Operating system
- Python version
- conda list / pip list
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GenevieveBuckley
commented on July 28, 2024
At the meeting today it was suggested that we see this error on Linux (but not for people on Macs, etc.)
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alisterburt
commented on July 28, 2024
hmm, slightly more problematic - is running the deploy workflow on macos too hacky a solution? seems like it shouldn't be necessary but might solve the problem quickly...
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GenevieveBuckley
commented on July 28, 2024
I would guess that yes, those tornado errors are related. Hmm...
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melissawm
commented on July 28, 2024
I believe this has been solved, anyone else experiencing this or can we close?
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melissawm
commented on July 28, 2024
I am closing this as it seems to be resolved, please reopen otherwise!
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