Incompatible with Jupytext plugin (notebook corruption)

goerz commented 11 months ago

Description

The jupyter-collaboration plugin appears to be incompatible with the jupytext plugin. It is unclear which plugin's "fault" this is.

See https://github.com/mwouts/jupytext/issues/1124

Reproduce

As described in https://github.com/mwouts/jupytext/issues/1124#issuecomment-1723280296:

Create a test notebook with the content print('test')
Pair this with jupytext to a corresponding script file (e.g., light, OP used percent)
Close and shutdown the kernel.
Open the .py file in Jupyter Lab and execute the first cell.
Close and shutdown the kernel.
Open the original .ipynb in Jupyter Lab.

Context

Operating System and version: Linux Ubuntu 20.04
Browser and version: Safari/Chrome/Arq (not browser dependent)
Jupyter was installed via Miniforge 23.1-1: conda install jupyterlab notebook jupyterlab_execute_time nbdime jupytext ipywidgets ipyparallel jupyter-collaboration
JupyterLab version: 4.0.8
Jupytext version: 1.15.2
Jupyter-collaboration version: 1.2.0

Troubleshoot Output

$PATH:
        /home/goerz/.pyenv/versions/miniforge3-23.3.1-1/bin
        /home/goerz/.pyenv/libexec
        /home/goerz/.pyenv/plugins/python-build/bin
        /home/goerz/.pyenv/plugins/pyenv-virtualenv/bin
        /home/goerz/bin
        /home/goerz/.pyenv/shims
        /home/goerz/.julia/juliaup//bin
        /home/goerz/.pyenv/bin
        /home/goerz/.local/bin
        /home/goerz/bin
        /home/goerz/.julia/juliaup//bin
        /home/goerz/.pyenv/bin
        /home/goerz/.local/bin
        /usr/local/sbin
        /usr/local/bin
        /usr/sbin
        /usr/bin
        /sbin
        /bin
        /usr/games
        /usr/local/games
        /snap/bin

sys.path:
        /home/goerz/.pyenv/versions/miniforge3-23.3.1-1/bin
        /home/goerz/.pyenv/versions/miniforge3-23.3.1-1/lib/python310.zip
        /home/goerz/.pyenv/versions/miniforge3-23.3.1-1/lib/python3.10
        /home/goerz/.pyenv/versions/miniforge3-23.3.1-1/lib/python3.10/lib-dynload
        /home/goerz/.pyenv/versions/miniforge3-23.3.1-1/lib/python3.10/site-packages

sys.executable:
        /home/goerz/.pyenv/versions/miniforge3-23.3.1-1/bin/python

sys.version:
        3.10.12 | packaged by conda-forge | (main, Jun 23 2023, 22:40:32) [GCC 12.3.0]

platform.platform():
        Linux-5.13.0-37-generic-x86_64-with-glibc2.31

which -a jupyter:
        /home/goerz/.pyenv/versions/miniforge3-23.3.1-1/bin/jupyter
        /home/goerz/.pyenv/shims/jupyter

welcome[bot] commented 11 months ago

Thank you for opening your first issue in this project! Engagement like this is essential for open source projects! :hugs:
If you haven't done so already, check out Jupyter's Code of Conduct. Also, please try to follow the issue template as it helps other other community members to contribute more effectively. welcome You can meet the other Jovyans by joining our Discourse forum. There is also an intro thread there where you can stop by and say Hi! :wave:
Welcome to the Jupyter community! :tada:

jtpio commented 10 months ago

Thanks @goerz for the report.

Would you be able to try with the new 2.0.0 release, to see if it might fix the issue? https://github.com/jupyterlab/jupyter-collaboration/releases/tag/v2.0.0

goerz commented 10 months ago

~~I don't seem to be able to install the new release:~~

Edit: never mind, got it working on Linux (will try to test for the bug next)

:> conda install jupyter-collaboration==2.0.0
Channels:
 - conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides pycrdt >=0.7.0,<0.8.0 needed by pycrdt-websocket-0.12.5-pyhd8ed1ab_0
  - cannot install both pin-1-1 and pin-1-1

Could not solve for environment specs
The following packages are incompatible
├─ jupyter-collaboration 2.0.0  is not installable because it requires
│  └─ pycrdt-websocket >=0.12.5,<0.13.0 , which requires
│     └─ pycrdt >=0.7.0,<0.8.0 , which does not exist (perhaps a missing channel);
└─ pin-1 is installable with the potential options
   ├─ pin-1 1, which can be installed;
   └─ pin-1 1 conflicts with any installable versions previously reported.

Pins seem to be involved in the conflict. Currently pinned specs:
 - python 3.10.* (labeled as 'pin-1')

jtpio commented 10 months ago

I don't seem to be able to install the new release:

cc @davidbrochart as this seems related to the recent pycrdt change

goerz commented 10 months ago

Unfortunately, the issue persists in version 2.0, with the same steps to reproduce.

I've tested this on Linux in a fresh conda environment:

environment.yml

name: jupytest
channels:
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - aiosqlite=0.19.0=pyhd8ed1ab_0
  - alsa-lib=1.2.10=hd590300_0
  - anyio=4.1.0=pyhd8ed1ab_0
  - archspec=0.2.2=pyhd8ed1ab_0
  - argon2-cffi=23.1.0=pyhd8ed1ab_0
  - argon2-cffi-bindings=21.2.0=py310h2372a71_4
  - arrow=1.3.0=pyhd8ed1ab_0
  - asttokens=2.4.1=pyhd8ed1ab_0
  - async-lru=2.0.4=pyhd8ed1ab_0
  - attr=2.5.1=h166bdaf_1
  - attrs=23.1.0=pyh71513ae_1
  - babel=2.14.0=pyhd8ed1ab_0
  - beautifulsoup4=4.12.2=pyha770c72_0
  - black=23.11.0=py310hff52083_0
  - bleach=6.1.0=pyhd8ed1ab_0
  - boltons=23.0.0=pyhd8ed1ab_0
  - brotli=1.1.0=hd590300_1
  - brotli-bin=1.1.0=hd590300_1
  - brotli-python=1.1.0=py310hc6cd4ac_1
  - bzip2=1.0.8=hd590300_5
  - c-ares=1.23.0=hd590300_0
  - ca-certificates=2023.11.17=hbcca054_0
  - cached-property=1.5.2=hd8ed1ab_1
  - cached_property=1.5.2=pyha770c72_1
  - cairo=1.18.0=h3faef2a_0
  - certifi=2023.11.17=pyhd8ed1ab_0
  - cffi=1.16.0=py310h2fee648_0
  - charset-normalizer=3.3.2=pyhd8ed1ab_0
  - click=8.1.7=unix_pyh707e725_0
  - colorama=0.4.6=pyhd8ed1ab_0
  - comm=0.1.4=pyhd8ed1ab_0
  - conda=23.10.0=py310hff52083_1
  - conda-libmamba-solver=23.12.0=pyhd8ed1ab_0
  - conda-package-handling=2.2.0=pyh38be061_0
  - conda-package-streaming=0.9.0=pyhd8ed1ab_0
  - contourpy=1.2.0=py310hd41b1e2_0
  - cycler=0.12.1=pyhd8ed1ab_0
  - dbus=1.13.6=h5008d03_3
  - debugpy=1.8.0=py310hc6cd4ac_1
  - decorator=5.1.1=pyhd8ed1ab_0
  - defusedxml=0.7.1=pyhd8ed1ab_0
  - entrypoints=0.4=pyhd8ed1ab_0
  - exceptiongroup=1.2.0=pyhd8ed1ab_0
  - executing=2.0.1=pyhd8ed1ab_0
  - expat=2.5.0=hcb278e6_1
  - fmt=10.1.1=h00ab1b0_1
  - 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=h77eed37_1
  - fontconfig=2.14.2=h14ed4e7_0
  - fonts-conda-ecosystem=1=0
  - fonts-conda-forge=1=0
  - fonttools=4.46.0=py310h2372a71_0
  - fqdn=1.5.1=pyhd8ed1ab_0
  - freetype=2.12.1=h267a509_2
  - gettext=0.21.1=h27087fc_0
  - gitdb=4.0.11=pyhd8ed1ab_0
  - gitpython=3.1.40=pyhd8ed1ab_0
  - glib=2.78.3=hfc55251_0
  - glib-tools=2.78.3=hfc55251_0
  - gmp=6.3.0=h59595ed_0
  - gmpy2=2.1.2=py310h3ec546c_1
  - graphite2=1.3.13=h58526e2_1001
  - gst-plugins-base=1.22.7=h8e1006c_1
  - gstreamer=1.22.7=h98fc4e7_1
  - harfbuzz=8.3.0=h3d44ed6_0
  - icu=73.2=h59595ed_0
  - idna=3.6=pyhd8ed1ab_0
  - importlib-metadata=7.0.0=pyha770c72_0
  - importlib_metadata=7.0.0=hd8ed1ab_0
  - importlib_resources=6.1.1=pyhd8ed1ab_0
  - ipykernel=6.26.0=pyhf8b6a83_0
  - ipyparallel=8.6.1=pyhd8ed1ab_0
  - ipython=8.18.1=pyh707e725_3
  - ipywidgets=8.1.1=pyhd8ed1ab_0
  - isoduration=20.11.0=pyhd8ed1ab_0
  - isort=5.13.2=pyhd8ed1ab_0
  - jedi=0.19.1=pyhd8ed1ab_0
  - jinja2=3.1.2=pyhd8ed1ab_1
  - json5=0.9.14=pyhd8ed1ab_0
  - jsonpatch=1.33=pyhd8ed1ab_0
  - jsonpointer=2.4=py310hff52083_3
  - jsonschema=4.20.0=pyhd8ed1ab_0
  - jsonschema-specifications=2023.11.2=pyhd8ed1ab_0
  - jsonschema-with-format-nongpl=4.20.0=pyhd8ed1ab_0
  - jupyter-collaboration=2.0.0=pyhd8ed1ab_0
  - jupyter-lsp=2.2.1=pyhd8ed1ab_0
  - jupyter-server-mathjax=0.2.6=pyh5bfe37b_1
  - jupyter_client=8.6.0=pyhd8ed1ab_0
  - jupyter_core=5.5.0=py310hff52083_0
  - jupyter_events=0.9.0=pyhd8ed1ab_0
  - jupyter_server=2.12.1=pyhd8ed1ab_0
  - jupyter_server_fileid=0.9.0=pyhd8ed1ab_0
  - jupyter_server_terminals=0.5.0=pyhd8ed1ab_0
  - jupyter_ydoc=2.0.0=pyhd8ed1ab_0
  - jupyterlab=4.0.9=pyhd8ed1ab_0
  - jupyterlab_execute_time=3.1.0=pyhd8ed1ab_0
  - jupyterlab_pygments=0.3.0=pyhd8ed1ab_0
  - jupyterlab_server=2.25.2=pyhd8ed1ab_0
  - jupyterlab_widgets=3.0.9=pyhd8ed1ab_0
  - jupytext=1.16.0=pyhd8ed1ab_0
  - keyutils=1.6.1=h166bdaf_0
  - kiwisolver=1.4.5=py310hd41b1e2_1
  - krb5=1.21.2=h659d440_0
  - lame=3.100=h166bdaf_1003
  - lcms2=2.16=hb7c19ff_0
  - ld_impl_linux-64=2.40=h41732ed_0
  - lerc=4.0.0=h27087fc_0
  - libarchive=3.7.2=h2aa1ff5_1
  - libblas=3.9.0=20_linux64_openblas
  - libbrotlicommon=1.1.0=hd590300_1
  - libbrotlidec=1.1.0=hd590300_1
  - libbrotlienc=1.1.0=hd590300_1
  - libcap=2.69=h0f662aa_0
  - libcblas=3.9.0=20_linux64_openblas
  - libclang=15.0.7=default_hb11cfb5_4
  - libclang13=15.0.7=default_ha2b6cf4_4
  - libcups=2.3.3=h4637d8d_4
  - libcurl=8.5.0=hca28451_0
  - libdeflate=1.19=hd590300_0
  - libedit=3.1.20191231=he28a2e2_2
  - libev=4.33=hd590300_2
  - libevent=2.1.12=hf998b51_1
  - libexpat=2.5.0=hcb278e6_1
  - libffi=3.4.2=h7f98852_5
  - libflac=1.4.3=h59595ed_0
  - libgcc-ng=13.2.0=h807b86a_3
  - libgcrypt=1.10.3=hd590300_0
  - libgfortran-ng=13.2.0=h69a702a_3
  - libgfortran5=13.2.0=ha4646dd_3
  - libglib=2.78.3=h783c2da_0
  - libgomp=13.2.0=h807b86a_3
  - libgpg-error=1.47=h71f35ed_0
  - libiconv=1.17=hd590300_1
  - libjpeg-turbo=3.0.0=hd590300_1
  - liblapack=3.9.0=20_linux64_openblas
  - libllvm15=15.0.7=hb3ce162_4
  - libmamba=1.5.3=had39da4_2
  - libmambapy=1.5.3=py310h39ff949_2
  - libnghttp2=1.58.0=h47da74e_1
  - libnsl=2.0.1=hd590300_0
  - libogg=1.3.4=h7f98852_1
  - libopenblas=0.3.25=pthreads_h413a1c8_0
  - libopus=1.3.1=h7f98852_1
  - libpng=1.6.39=h753d276_0
  - libpq=16.1=h33b98f1_7
  - libsndfile=1.2.2=hc60ed4a_1
  - libsodium=1.0.18=h36c2ea0_1
  - libsolv=0.7.27=hfc55251_0
  - libsqlite=3.44.2=h2797004_0
  - libssh2=1.11.0=h0841786_0
  - libstdcxx-ng=13.2.0=h7e041cc_3
  - libsystemd0=255=h3516f8a_0
  - libtiff=4.6.0=ha9c0a0a_2
  - libuuid=2.38.1=h0b41bf4_0
  - libuv=1.46.0=hd590300_0
  - libvorbis=1.3.7=h9c3ff4c_0
  - libwebp-base=1.3.2=hd590300_0
  - libxcb=1.15=h0b41bf4_0
  - libxkbcommon=1.6.0=hd429924_1
  - libxml2=2.12.3=h232c23b_0
  - libzlib=1.2.13=hd590300_5
  - lz4-c=1.9.4=hcb278e6_0
  - lzo=2.10=h516909a_1000
  - mamba=1.5.3=py310h51d5547_2
  - markdown=3.5.1=pyhd8ed1ab_0
  - markdown-it-py=3.0.0=pyhd8ed1ab_0
  - markdown-kernel=0.2.1=py_0
  - markupsafe=2.1.3=py310h2372a71_1
  - matplotlib=3.8.2=py310hff52083_0
  - matplotlib-base=3.8.2=py310h62c0568_0
  - matplotlib-inline=0.1.6=pyhd8ed1ab_0
  - mdit-py-plugins=0.4.0=pyhd8ed1ab_0
  - mdurl=0.1.0=pyhd8ed1ab_0
  - mistune=3.0.2=pyhd8ed1ab_0
  - mpc=1.3.1=hfe3b2da_0
  - mpfr=4.2.1=h9458935_0
  - mpg123=1.32.3=h59595ed_0
  - mpmath=1.3.0=pyhd8ed1ab_0
  - munkres=1.1.4=pyh9f0ad1d_0
  - mypy_extensions=1.0.0=pyha770c72_0
  - mysql-common=8.0.33=hf1915f5_6
  - mysql-libs=8.0.33=hca2cd23_6
  - nbclient=0.8.0=pyhd8ed1ab_0
  - nbconvert-core=7.12.0=pyhd8ed1ab_0
  - nbdime=4.0.1=pyhd8ed1ab_0
  - nbformat=5.9.2=pyhd8ed1ab_0
  - ncurses=6.4=h59595ed_2
  - nest-asyncio=1.5.8=pyhd8ed1ab_0
  - nodejs=20.9.0=hb753e55_0
  - notebook=7.0.6=pyhd8ed1ab_0
  - notebook-shim=0.2.3=pyhd8ed1ab_0
  - nspr=4.35=h27087fc_0
  - nss=3.95=h1d7d5a4_0
  - numpy=1.26.2=py310hb13e2d6_0
  - openjpeg=2.5.0=h488ebb8_3
  - openssl=3.2.0=hd590300_1
  - overrides=7.4.0=pyhd8ed1ab_0
  - packaging=23.2=pyhd8ed1ab_0
  - pandoc=3.1.3=h32600fe_0
  - pandocfilters=1.5.0=pyhd8ed1ab_0
  - parso=0.8.3=pyhd8ed1ab_0
  - pathspec=0.12.1=pyhd8ed1ab_0
  - pcre2=10.42=hcad00b1_0
  - pexpect=4.8.0=pyh1a96a4e_2
  - pickleshare=0.7.5=py_1003
  - pillow=10.1.0=py310h01dd4db_0
  - pip=23.3.1=pyhd8ed1ab_0
  - pixman=0.42.2=h59595ed_0
  - pkgutil-resolve-name=1.3.10=pyhd8ed1ab_1
  - platformdirs=4.1.0=pyhd8ed1ab_0
  - pluggy=1.3.0=pyhd8ed1ab_0
  - ply=3.11=py_1
  - prometheus_client=0.19.0=pyhd8ed1ab_0
  - prompt-toolkit=3.0.42=pyha770c72_0
  - psutil=5.9.5=py310h2372a71_1
  - pthread-stubs=0.4=h36c2ea0_1001
  - ptyprocess=0.7.0=pyhd3deb0d_0
  - pulseaudio-client=16.1=hb77b528_5
  - pure_eval=0.2.2=pyhd8ed1ab_0
  - pybind11-abi=4=hd8ed1ab_3
  - pycosat=0.6.6=py310h2372a71_0
  - pycparser=2.21=pyhd8ed1ab_0
  - pycrdt=0.7.2=py310hcb5633a_0
  - pycrdt-websocket=0.12.5=pyhd8ed1ab_0
  - pygments=2.17.2=pyhd8ed1ab_0
  - pyparsing=3.1.1=pyhd8ed1ab_0
  - pyqt=5.15.9=py310h04931ad_5
  - pyqt5-sip=12.12.2=py310hc6cd4ac_5
  - pysocks=1.7.1=pyha2e5f31_6
  - python=3.10.13=hd12c33a_0_cpython
  - python-dateutil=2.8.2=pyhd8ed1ab_0
  - python-fastjsonschema=2.19.0=pyhd8ed1ab_0
  - python-json-logger=2.0.7=pyhd8ed1ab_0
  - python_abi=3.10=4_cp310
  - pytz=2023.3.post1=pyhd8ed1ab_0
  - pyyaml=6.0.1=py310h2372a71_1
  - pyzmq=25.1.2=py310h795f18f_0
  - qt-main=5.15.8=h450f30e_18
  - qutip=4.7.3=py310hcb52e73_1
  - readline=8.2=h8228510_1
  - referencing=0.32.0=pyhd8ed1ab_0
  - reproc=14.2.4.post0=hd590300_1
  - reproc-cpp=14.2.4.post0=h59595ed_1
  - requests=2.31.0=pyhd8ed1ab_0
  - rfc3339-validator=0.1.4=pyhd8ed1ab_0
  - rfc3986-validator=0.1.1=pyh9f0ad1d_0
  - rpds-py=0.13.2=py310hcb5633a_0
  - ruamel.yaml=0.18.5=py310h2372a71_0
  - ruamel.yaml.clib=0.2.7=py310h2372a71_2
  - scipy=1.11.4=py310hb13e2d6_0
  - send2trash=1.8.2=pyh41d4057_0
  - setuptools=68.2.2=pyhd8ed1ab_0
  - sip=6.7.12=py310hc6cd4ac_0
  - six=1.16.0=pyh6c4a22f_0
  - smmap=5.0.0=pyhd8ed1ab_0
  - sniffio=1.3.0=pyhd8ed1ab_0
  - soupsieve=2.5=pyhd8ed1ab_1
  - stack_data=0.6.2=pyhd8ed1ab_0
  - sympy=1.12=pypyh9d50eac_103
  - terminado=0.18.0=pyh0d859eb_0
  - tinycss2=1.2.1=pyhd8ed1ab_0
  - tk=8.6.13=noxft_h4845f30_101
  - toml=0.10.2=pyhd8ed1ab_0
  - tomli=2.0.1=pyhd8ed1ab_0
  - tornado=6.3.3=py310h2372a71_1
  - tqdm=4.66.1=pyhd8ed1ab_0
  - traitlets=5.14.0=pyhd8ed1ab_0
  - truststore=0.8.0=pyhd8ed1ab_0
  - types-python-dateutil=2.8.19.14=pyhd8ed1ab_0
  - typing-extensions=4.9.0=hd8ed1ab_0
  - typing_extensions=4.9.0=pyha770c72_0
  - typing_utils=0.1.0=pyhd8ed1ab_0
  - tzdata=2023c=h71feb2d_0
  - unicodedata2=15.1.0=py310h2372a71_0
  - uri-template=1.3.0=pyhd8ed1ab_0
  - urllib3=2.1.0=pyhd8ed1ab_0
  - wcwidth=0.2.12=pyhd8ed1ab_0
  - webcolors=1.13=pyhd8ed1ab_0
  - webencodings=0.5.1=pyhd8ed1ab_2
  - websocket-client=1.7.0=pyhd8ed1ab_0
  - wheel=0.42.0=pyhd8ed1ab_0
  - widgetsnbextension=4.0.9=pyhd8ed1ab_0
  - xcb-util=0.4.0=hd590300_1
  - xcb-util-image=0.4.0=h8ee46fc_1
  - xcb-util-keysyms=0.4.0=h8ee46fc_1
  - xcb-util-renderutil=0.3.9=hd590300_1
  - xcb-util-wm=0.4.1=h8ee46fc_1
  - xkeyboard-config=2.40=hd590300_0
  - xorg-kbproto=1.0.7=h7f98852_1002
  - xorg-libice=1.1.1=hd590300_0
  - xorg-libsm=1.2.4=h7391055_0
  - xorg-libx11=1.8.7=h8ee46fc_0
  - xorg-libxau=1.0.11=hd590300_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xorg-libxext=1.3.4=h0b41bf4_2
  - xorg-libxrender=0.9.11=hd590300_0
  - xorg-renderproto=0.11.1=h7f98852_1002
  - xorg-xextproto=7.3.0=h0b41bf4_1003
  - xorg-xf86vidmodeproto=2.3.1=h7f98852_1002
  - xorg-xproto=7.0.31=h7f98852_1007
  - xz=5.2.6=h166bdaf_0
  - yaml=0.2.5=h7f98852_2
  - yaml-cpp=0.8.0=h59595ed_0
  - zeromq=4.3.5=h59595ed_0
  - zipp=3.17.0=pyhd8ed1ab_0
  - zlib=1.2.13=hd590300_5
  - zstandard=0.22.0=py310h1275a96_0
  - zstd=1.5.5=hfc55251_0
prefix: /home/goerz/.pyenv/versions/miniforge3-23.3.1-1/envs/jupytest

EduardDurech commented 7 months ago

I'm having this issue with jupyter-collaboration==2.0.3 https://github.com/jupyterlab/jupyter-collaboration/issues/162#issuecomment-2003657168

mwouts commented 6 months ago

I have had a quick look at this, and I confirm that I can reproduce the issue.

I created a notebook jupyter_collaboration.ipynb

[I 2024-03-24 18:54:33.716 ServerApp] Saving the content from room json:notebook:8eba183d-2923-4c6a-838e-e8cdcaf223cd
[I 2024-03-24 18:54:33.719 YDocExtension] Saving file: jupyter_collaboration.ipynb
[I 2024-03-24 18:54:33.724 ServerApp] Saving jupyter_collaboration.ipynb

Then I paired it to the py:percent format (File->Jupytext->Pair with percent format, then save)

[I 2024-03-24 18:55:12.392 ServerApp] Saving the content from room json:notebook:8eba183d-2923-4c6a-838e-e8cdcaf223cd
[I 2024-03-24 18:55:12.395 YDocExtension] Saving file: jupyter_collaboration.ipynb
[I 2024-03-24 18:55:12.413 ServerApp] Saving jupyter_collaboration.ipynb
[I 2024-03-24 18:55:12.447 ServerApp] Saving jupyter_collaboration.py in format py:percent

I closed and then re-opened the .ipynb document:

[I 2024-03-24 18:55:53.324 ServerApp] Starting buffering for 98ea9cbe-7609-4865-9f6e-733de9af1621:6e18dfb5-3b2a-494b-9006-f64f6d6e8602
[I 2024-03-24 18:55:53.327 ServerApp] Cleaning room: json:notebook:8eba183d-2923-4c6a-838e-e8cdcaf223cd
[I 2024-03-24 18:55:54.842 ServerApp] Request for Y document 'jupyter_collaboration.ipynb' with room ID: 8eba183d-2923-4c6a-838e-e8cdcaf223cd
[I 2024-03-24 18:56:00.408 YDocExtension] Processed 16 Y patches in one minute
[I 2024-03-24 18:56:00.409 YDocExtension] Connected Y users: 1
[I 2024-03-24 18:56:53.329 ServerApp] Deleting Y document from memory: json:notebook:8eba183d-2923-4c6a-838e-e8cdcaf223cd
[I 2024-03-24 18:56:53.329 ServerApp] Room json:notebook:8eba183d-2923-4c6a-838e-e8cdcaf223cd deleted
[I 2024-03-24 18:56:53.330 ServerApp] Deleting file jupyter_collaboration.ipynb
[I 2024-03-24 18:56:53.333 YDocExtension] Creating FileLoader for: jupyter_collaboration.ipynb
[I 2024-03-24 18:56:53.334 YDocExtension] Watching file: jupyter_collaboration.ipynb
[I 2024-03-24 18:56:53.336 ServerApp] Initializing room json:notebook:8eba183d-2923-4c6a-838e-e8cdcaf223cd
[I 2024-03-24 18:56:53.374 ServerApp] Reading SOURCE from jupyter_collaboration.py
[I 2024-03-24 18:56:53.417 ServerApp] Content in room json:notebook:8eba183d-2923-4c6a-838e-e8cdcaf223cd loaded from the ystore SQLiteYStore
[I 2024-03-24 18:56:53.418 ServerApp] Content in file jupyter_collaboration.ipynb is out-of-sync with the ystore SQLiteYStore
[I 2024-03-24 18:56:53.418 ServerApp] Content in room json:notebook:8eba183d-2923-4c6a-838e-e8cdcaf223cd loaded from file jupyter_collaboration.ipynb
[I 2024-03-24 18:56:53.493 ServerApp] Connecting to kernel 98ea9cbe-7609-4865-9f6e-733de9af1621.
[I 2024-03-24 18:57:00.410 YDocExtension] Processed 8 Y patches in one minute

Then my notebook has a single code cell with this content:

IyAtLS0KIyBqdXB5dGVyOgojICAganVweXRleHQ6CiMgICAgIGZvcm1hdHM6IGlweW5iLHB5OnBl
cmNlbnQKIyAgICAgdGV4dF9yZXByZXNlbnRhdGlvbjoKIyAgICAgICBleHRlbnNpb246IC5weQoj
ICAgICAgIGZvcm1hdF9uYW1lOiBwZXJjZW50CiMgICAgICAgZm9ybWF0X3ZlcnNpb246ICcxLjMn
CiMgICAgICAganVweXRleHRfdmVyc2lvbjogMS4xNi4xCiMgICBrZXJuZWxzcGVjOgojICAgICBk
aXNwbGF5X25hbWU6IFB5dGhvbiAzIChpcHlrZXJuZWwpCiMgICAgIGxhbmd1YWdlOiBweXRob24K
IyAgICAgbmFtZTogcHl0aG9uMwojIC0tLQoKIyAlJQoxICsgMQoKIyAlJSBbbWFya2Rvd25dCiMg
bWFya2Rvd24KCiMgJSUK

I confirm that text in the first cell of the notebook is a b64 encoding of the text notebook:

text = """IyAtLS0K(...)"""
print(base64.b64decode("".join(text.splitlines())).decode('utf8'))

# ---
# jupyter:
#   jupytext:
#     formats: ipynb,py:percent
#     text_representation:
#       extension: .py
#       format_name: percent
#       format_version: '1.3'
#       jupytext_version: 1.16.1
#   kernelspec:
#     display_name: Python 3 (ipykernel)
#     language: python
#     name: python3
# ---

# %%
1 + 1

# %% [markdown]
# markdown

# %%

Interestingly, this base64 encoded content is what is returned by the parent contents manager (here, a LargeFileContentsManager as Jupytext does not support async CM yet).

I think it's a bit odd that the parent CM would return a base64 encoded value, so that's maybe what I would suggest to fix. @fcollonval do you think this could be related to using the non-async CM? (I mean, possibly Jupyter-collaboration has been tested focusing on the async contents manager?)

jupyterlab / jupyter-collaboration