Should Jupyter notebooks persist to /app/notebooks instead?

[charlesbmi]

Describe the bug

The recommended Docker command:
docker run -p 8888:8888 -v $(pwd)/notebooks:/ndk/notebooks -it ghcr.io/agencyenterprise/neurotechdevkit:latest
mounts notebooks to /ndk/notebooks, which makes it inaccessible from the Jupyter Lab server that runs at /app

A simple change is to run with -v $(pwd)/notebooks:/app/notebooks, but I wasn't sure if that should be necessary or if it is better fixed by ensuring that Jupyter opens in the /ndk working directory in a Docker config somewhere.

Steps to reproduce

docker run -p 8888:8888  -v $(pwd)/notebooks:/ndk/notebooks -it ghcr.io/agencyenterprise/neurotechdevkit:latest

Resulting logs:

(base) ➜  neurotechdevkit git:(main) ✗ docker run -p 8888:8888  -v $(pwd)/notebooks:/ndk/notebooks -it ghcr.io/agencyenterprise/neurotechdevkit:latest
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
[I 18:22:59.636 NotebookApp] Writing notebook server cookie secret to /root/.local/share/jupyter/runtime/notebook_cookie_secret

  _   _          _      _
 | | | |_ __  __| |__ _| |_ ___
 | |_| | '_ \/ _` / _` |  _/ -_)
  \___/| .__/\__,_\__,_|\__\___|
       |_|

Read the migration plan to Notebook 7 to learn about the new features and the actions to take if you are using extensions.

https://jupyter-notebook.readthedocs.io/en/latest/migrate_to_notebook7.html

Please note that updating to Notebook 7 might break some of your extensions.

[W 18:23:06.214 NotebookApp] Loading JupyterLab as a classic notebook (v6) extension.
[C 18:23:06.215 NotebookApp] You must use Jupyter Server v1 to load JupyterLab as notebook extension. You have v2.5.0 installed.
    You can fix this by executing:
        pip install -U "jupyter-server<2.0.0"
[I 18:23:06.236 NotebookApp] Serving notebooks from local directory: /app
[I 18:23:06.237 NotebookApp] Jupyter Notebook 6.5.4 is running at:
[I 18:23:06.237 NotebookApp] http://f7749ef3a33b:8888/?token=b87d2340dd376592df3c489eae78f46ea205ce4e72860312
[I 18:23:06.237 NotebookApp]  or http://127.0.0.1:8888/?token=b87d2340dd376592df3c489eae78f46ea205ce4e72860312
[I 18:23:06.237 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[W 18:23:06.256 NotebookApp] No web browser found: could not locate runnable browser.
[C 18:23:06.257 NotebookApp]

    To access the notebook, open this file in a browser:
        file:///root/.local/share/jupyter/runtime/nbserver-1-open.html
    Or copy and paste one of these URLs:
        http://f7749ef3a33b:8888/?token=b87d2340dd376592df3c489eae78f46ea205ce4e72860312
     or http://127.0.0.1:8888/?token=b87d2340dd376592df3c489eae78f46ea205ce4e72860312

Include a description of your setup including:

• Docker version: 4.18.0
• OS version and name: {'system': 'Darwin', 'node': 'Charles-MacBook.local', 'release': '22.5.0', 'version': 'Darwin Kernel Version 22.5.0: Thu Jun 8 22:22:20 PDT 2023; root:xnu-8796.121.3~7/RELEASE_ARM64_T6000', 'machine': 'arm64', 'processor': 'arm'}

Expected results

See notebooks folder in generated Jupyter Lab server

Actual results

From Jupyter notebook file explorer:

From Jupyter notebook shell:

# pwd
/app
# ls /
app  bin  boot  dev  etc  home  lib  lib64  media  mnt  ndk  opt  proc  root  run  sbin  srv  sys  tmp  usr  var  venv
# ls /ndk
notebooks
# ls
CONTRIBUTING.md  LICENSE   README.md    dist                docs        poetry.lock     src
Dockerfile       Makefile  SECURITY.md  docker-compose.yml  mkdocs.yml  pyproject.toml  tests