Open tpike3 opened 3 weeks ago
Thanks @tpike3 for reporting :+1:
It may be related to jupyterlite-xeus
. There were a few issues recently, maybe @martinRenou or @DerThorsten may no more about this.
In the meantime, you could try to use a different kernel (for example https://github.com/jupyterlite/pyodide-kernel), to see if the build passes.
Thanks @jtpio will do.
It may also be the directory the build is in. The way I can replicate that error on my local machine if the output directory (jupyterlite_dir) doesn't match.
Your logs don't contain much, it looks like the actual error message is being hidden (we don't know why the jupyterlite build command failed)
Your logs don't contain much, it looks like the actual error message is being hidden (we don't know why the jupyterlite build command failed) Thanks @martinRenou for the help and interest!
Here is the traceback from the readthedocs build ....
writing additional pages... search done
dumping search index in English (code: en)... done
dumping object inventory... done
Updating searchtools for Read the Docs search...
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo-test/conda/latest/lib/python3.10/site-packages/sphinx/events.py", line 97, in emit
results.append(listener.handler(self.app, *args))
File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo-test/conda/latest/lib/python3.10/site-packages/jupyterlite_sphinx/jupyterlite_sphinx.py", line 707, in jupyterlite_build
completed_process: CompletedProcess[bytes] = subprocess.run(
File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo-test/conda/latest/lib/python3.10/subprocess.py", line 524, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['jupyter', 'lite', 'build', '--debug', '--contents', 'tutorials/intro_tutorial.ipynb', '--contents', '/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo-test/checkouts/latest/docs/source/_contents', '--output-dir', '/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo-test/checkouts/latest/_readthedocs/html/lite', '--apps', 'notebooks', '--apps', 'edit', '--apps', 'lab', '--apps', 'repl', '--apps', 'tree', '--apps', 'consoles', '--lite-dir', '/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo-test/checkouts/latest/docs/source']' returned non-zero exit status 3.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo-test/conda/latest/lib/python3.10/site-packages/sphinx/cmd/build.py", line 337, in build_main
app.build(args.force_all, args.filenames)
File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo-test/conda/latest/lib/python3.10/site-packages/sphinx/application.py", line 353, in build
self.events.emit('build-finished', None)
File "/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo-test/conda/latest/lib/python3.10/site-packages/sphinx/events.py", line 108, in emit
raise ExtensionError(
sphinx.errors.ExtensionError: Handler <function jupyterlite_build at 0x7effb8c75360> for event 'build-finished' threw an exception (exception: Command '['jupyter', 'lite', 'build', '--debug', '--contents', 'tutorials/intro_tutorial.ipynb', '--contents', '/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo-test/checkouts/latest/docs/source/_contents', '--output-dir', '/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo-test/checkouts/latest/_readthedocs/html/lite', '--apps', 'notebooks', '--apps', 'edit', '--apps', 'lab', '--apps', 'repl', '--apps', 'tree', '--apps', 'consoles', '--lite-dir', '/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo-test/checkouts/latest/docs/source']' returned non-zero exit status 3.)
Extension error (jupyterlite_sphinx.jupyterlite_sphinx):
Handler <function jupyterlite_build at 0x7effb8c75360> for event 'build-finished' threw an exception (exception: Command '['jupyter', 'lite', 'build', '--debug', '--contents', 'tutorials/intro_tutorial.ipynb', '--contents', '/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo-test/checkouts/latest/docs/source/_contents', '--output-dir', '/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo-test/checkouts/latest/_readthedocs/html/lite', '--apps', 'notebooks', '--apps', 'edit', '--apps', 'lab', '--apps', 'repl', '--apps', 'tree', '--apps', 'consoles', '--lite-dir', '/home/docs/checkouts/readthedocs.org/user_builds/mesa-geo-test/checkouts/latest/docs/source']' returned non-zero exit status 3.)
[jupyterlite-sphinx] Running JupyterLite build
Right now I am thinking it is one of 2 things (but could be way off)
That it the way my directories are set up as I am using a source directory and a build directory, but even when I change structure to match jupyterlite sphinx its doesnt work and my .jupyterlite.doit.db
never ends up where it should be and so never gets cleaned as it should here https://github.com/jupyterlite/jupyterlite-sphinx/blob/d50e2465d5bf67cb03897f68abc9a827658fae69/jupyterlite_sphinx/jupyterlite_sphinx.py#L731
Or that need to build an environment in my pyproject.toml like jupyterlite-sphinx does here https://github.com/jupyterlite/jupyterlite-sphinx/blob/d50e2465d5bf67cb03897f68abc9a827658fae69/pyproject.toml#L43C1-L47C60
Well I should pay closer attention to the documentation I set jupyterlite_silence = False
and I am getting good traceback information.
However, it is not immediately obvious to me what the issue is.
Thanks @tpike3.
These two lines at the top of the logs seem to indicate an issue with jupyterlite-xeus
:
ValidationError(ValueError("'emscripten' is not a valid Platform"))
ValidationError(ValueError("'emscripten' is not a valid Platform"))
Which should likely be fixed by https://github.com/conda/conda/pull/13962?
In the meantime, I think the workaround might be to use the latest pre-release of jupyterlite-xeus
, and add micromamba
to the build environment, similar to https://github.com/voila-dashboards/voici/pull/120 which had the same issue.
@tpike3 looks like this is indeed an issue with jupyterlite-xeus
: https://github.com/jupyterlite/jupyterlite-sphinx/pull/179
@martinRenou @DerThorsten maybe we should document the fix somewhere (for example in the jupyterlite-xeus
repo) until it is fixed in conda?
Thanks @jtpio!!! I am getting closer but now I am getting this error--- error libmamba ZSTD decompression error: Unknown frame descriptor
Thanks @tpike3 for reporting 👍
It may be related to
jupyterlite-xeus
. There were a few issues recently, maybe @martinRenou or @DerThorsten may no more about this.In the meantime, you could try to use a different kernel (for example https://github.com/jupyterlite/pyodide-kernel), to see if the build passes.
@jtpio Apologies should have done this earlier, I did switch to a pyodide-kernel
and the build works. Working to see how to pre-install packages now.
@tpike3 you could also continue using jupyterlite-xeus
but update to the latest pre-release (as in https://github.com/jupyterlite/jupyterlite-sphinx/pull/179), which should fix the issue.
@tpike3 you could also continue using
jupyterlite-xeus
but update to the latest pre-release (as in #179), which should fix the issue.
@jtpio I still cannot get the xeus-python
to build into RTD.
[LiteBuildApp] creating folder /home/docs/checkouts/readthedocs.org/user_builds/mesa-geo-test/checkouts/latest/_readthedocs/html/lite/static
139 | error libmamba ZSTD decompression error: Unknown frame descriptor
Of course I realized pyodide
won't work with piplite
as Mesa
doesn't have a pure python wheel
Normally this issue should not be related to Pyodide since you are using xeus-python
, and also because this is happening a build time (when the JupyterLite site is built) and not at runtime (when opening JupyterLite in a web browser).
Looks like this could be due to a malformed package on emscripten forge or conda forge?
error libmamba ZSTD decompression error: Unknown frame descriptor
I believe this should not cause the build to fail. You probably have another error somewhere.
Description
I am integrating jupyterlite-sphinx into mesa-geo readthedocs but my build keeps failing with the following error on in read the docs (no issues if doing jupyter lite build on my local machine)
Reproduce
You can see the build at ----
https://app.readthedocs.org/projects/mesa-geo-test/builds/24708569/
Expected behavior
Mesa-Geo docs render with xeus-python kernel
Context
Thank you for your time. Attached are my conf.txt readthedocs.txt and environment.txt
I feel like this is going to be something very simple but just cant figure out the right combination