# Issues Using Jupyterlab Extensions with Flox

**URL:** <https://discourse.flox.dev/t/issues-using-jupyterlab-extensions-with-flox/958>\
**Category:** Bug Reports\
**Created:** [September 2, 2024, 8:18pm UTC](https://discourse.flox.dev/t/issues-using-jupyterlab-extensions-with-flox/958 "2024-09-02T20:18:15Z")\
**Posts on this page:** 14\
**Page:** 1

<div class="post-metadata">

**Author:** ![max](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.flox.dev/max/32/680_2.png) [@max](https://discourse.flox.dev/u/max)\
**Post date:** [September 2, 2024, 8:18pm UTC](https://discourse.flox.dev/t/issues-using-jupyterlab-extensions-with-flox/958/1 "2024-09-02T20:18:15Z")

</div>

I’m having some trouble getting widgets (specifically jupyterlab-widgets) to work in my flox environment. I’m able to install them (along with node), but they aren’t recognized by my jupyter environment.

My `manifest.toml` includes the following specifics.

```auto
...
[install]
psycopg.pkg-path = "python312Packages.psycopg"
tqdm.pkg-path = "python312Packages.tqdm"
datasets.pkg-path = "python312Packages.datasets"
ipywidgets.pkg-path = "python312Packages.ipywidgets"
huggingface-hub.pkg-path = "python312Packages.huggingface-hub"
jupyterlab-widgets.pkg-path = "python312Packages.jupyterlab-widgets"
nodejs.pkg-path = "nodejs"
widgetsnbextension.pkg-path = "python312Packages.widgetsnbextension"
pip.pkg-path = "python312Packages.pip"
jupyter.pkg-path = "jupyter"
btop.pkg-path = "btop"
postgresql_15.pkg-path = "postgresql_15"
tmux.pkg-path = "tmux"
ripgrep.pkg-path = "ripgrep"
[hook]
on-activate = '''
   export JUPYTER_PATH=${FLOX_ENV}
   export JUPYTER_CONFIG_PATH=${FLOX_ENV}
'''
...

```

If I check my paths, I see the following.

```auto
ubuntu@ip-172-31-29-88:~/embedding-testing$ jupyter --paths
config:
    /home/ubuntu/.jupyter
    /nix/store/l014xp1qxdl6gim3zc0jv3mpxhbp346s-python3-3.12.4/etc/jupyter
    /usr/local/etc/jupyter
    /etc/jupyter
data:
    /nix/store/2gydn23nxsry8dka3v9wwv0cdn7k3814-jupyter-kernels
    /home/ubuntu/.local/share/jupyter
    /nix/store/l014xp1qxdl6gim3zc0jv3mpxhbp346s-python3-3.12.4/share/jupyter
    /usr/local/share/jupyter
    /usr/share/jupyter
runtime:
    /home/ubuntu/.local/share/jupyter/runtime

```

but it appears that my extensions are not recognized. Below is the result of running the command `jupyter labextension list` in a terminal in the notebook.

```auto
`sys_prefix` level settings are read-only, using `user` level for migration to `lockedExtensions`
JupyterLab v4.2.4

```

But when I run that same command directly in my flox shell, I get a different result:

```auto
`sys_prefix` level settings are read-only, using `user` level for migration to `lockedExtensions`
JupyterLab v4.2.4
/nix/store/0q0gkxd4gfn8w9cqym8a0xrdpclz37b5-python3-3.12.4-env/share/jupyter/labextensions
        jupyterlab_pygments v0.3.0 enabled OK (python, jupyterlab_pygments)
        @jupyter-notebook/lab-extension v7.2.1 enabled OK

```

The last thing I was trying was directly specifying the jupter lab config dir to a directory that isn’t read only. That did not seem to make a difference though.

---

<div class="post-metadata">

**Author:** ![ghudgins](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.flox.dev/ghudgins/32/588_2.png) [@ghudgins](https://discourse.flox.dev/u/ghudgins)\
**Post date:** [September 3, 2024, 4:42pm UTC](https://discourse.flox.dev/t/issues-using-jupyterlab-extensions-with-flox/958/2 "2024-09-03T16:42:28Z")

</div>

taking a look! initial guess is the init of the kernels may be the issue. some of us have seen issues with telling jupyter to start **this** python interpreter with **this** env var when you spin up kernels.

---

<div class="post-metadata">

**Author:** ![ghudgins](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.flox.dev/ghudgins/32/588_2.png) [@ghudgins](https://discourse.flox.dev/u/ghudgins)\
**Post date:** [September 6, 2024, 12:07am UTC](https://discourse.flox.dev/t/issues-using-jupyterlab-extensions-with-flox/958/3 "2024-09-06T00:07:00Z")

</div>

i’m not so sure there’s a solution with this particular extension (happy if someone can prove me wrong). this issue [Enable labextension for user only · Issue #15574 · jupyterlab/jupyterlab · GitHub](https://github.com/jupyterlab/jupyterlab/issues/15574) makes me think it’s not available yet for read only deployments like Flox and Nix have (and there’s a whole string of issues about it). i’m going to ask a few others to take a look to see if they have any other ideas…

what you can do to work around this in Flox: install the dependency with pip using a venv and don’t rely on Flox for this specific extension. Check out this environment’s hook on FloxHub: [FloxHub](https://hub.flox.dev/flox/nb)

(pasting here if you haven’t signed up yet–it’s free!)

```auto
  if [[-d $PYTHON_ENV]]; then
    echo; echo -n "⚡️ Activating existing venv in $PYTHON_ENV..."
    . $PYTHON_ENV/bin/activate
    echo "done."
  fi

  # If we see a requirements.txt file, install its contents
  # into a virtual environment

  if [[-f requirements.txt]]; then
    echo -n "🐍 Processing requirements.txt..."
    [! -d $PYTHON_ENV] && python -m venv $PYTHON_ENV
    . $PYTHON_ENV/bin/activate
    pip3 -qq install -r requirements.txt
    echo "done."
  fi

```

---

<div class="post-metadata">

**Author:** ![zmitchell](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.flox.dev/zmitchell/32/639_2.png) [@zmitchell](https://discourse.flox.dev/u/zmitchell)\
**Post date:** [September 6, 2024, 12:17am UTC](https://discourse.flox.dev/t/issues-using-jupyterlab-extensions-with-flox/958/4 "2024-09-06T00:17:35Z")

</div>

Just to be super clear, Max when you ran `jupyter labextension list` in the terminal it didn’t show any paths (the second to last terminal output in your original post)? I’m not a Jupyter user myself but that’s a bit unexpected if Flox is listing more paths but also not finding the plugins.

---

<div class="post-metadata">

**Author:** ![zmitchell](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.flox.dev/zmitchell/32/639_2.png) [@zmitchell](https://discourse.flox.dev/u/zmitchell)\
**Post date:** [September 6, 2024, 12:50am UTC](https://discourse.flox.dev/t/issues-using-jupyterlab-extensions-with-flox/958/5 "2024-09-06T00:50:09Z")

</div>

So I’ve taken the `manifest.toml` that was provided in the original post and built an environment around it for testing.

When I poke around inside of it, it looks like the widgets are installed (`jupyter-widgets` specifically):

```auto
✦ ❯ ls $FLOX_ENV/share/jupyter/labextensions
@jupyter-notebook @jupyter-widgets jupyterlab_pygments

```

But when you ask `jupyter` which extensions are installed, it only lists two of them:

```auto
✦ ❯ jupyter labextension list
`sys_prefix` level settings are read-only, using `user` level for migration to `lockedExtensions`
JupyterLab v4.2.4
/nix/store/ni927g0pp68wmkbmanw5x5z92d91zgna-python3-3.12.5-env/share/jupyter/labextensions
        jupyterlab_pygments v0.3.0 enabled OK (python, jupyterlab_pygments)
        @jupyter-notebook/lab-extension v7.2.1 enabled OK

```

_The plot thickens_

---

<div class="post-metadata">

**Author:** ![zmitchell](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.flox.dev/zmitchell/32/639_2.png) [@zmitchell](https://discourse.flox.dev/u/zmitchell)\
**Post date:** [September 6, 2024, 1:12am UTC](https://discourse.flox.dev/t/issues-using-jupyterlab-extensions-with-flox/958/6 "2024-09-06T01:12:20Z")

</div>

Alright, so here’s the difference:

```auto
✦ ❯ readlink "$FLOX_ENV/share/jupyter/labextensions/@jupyter-notebook"
/nix/store/ni927g0pp68wmkbmanw5x5z92d91zgna-python3-3.12.5-env/share/jupyter/labextensions/@jupyter-notebook
✦ ❯ readlink "$FLOX_ENV/share/jupyter/labextensions/jupyterlab_pygments"
/nix/store/ni927g0pp68wmkbmanw5x5z92d91zgna-python3-3.12.5-env/share/jupyter/labextensions/jupyterlab_pygments
✦ ❯ readlink "$FLOX_ENV/share/jupyter/labextensions/@jupyter-widgets"
/nix/store/lcgcbxvdzdvm3dgh4h9j6bgcl7v70imp-python3.12-jupyterlab-widgets-3.0.11/share/jupyter/labextensions/@jupyter-widgets

```

Those first two packages are coming from the same store path. I’m betting that one of the programs involved has a wrapper script that sets a `*PATH` variable to that first store path only.

---

<div class="post-metadata">

**Author:** ![max](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.flox.dev/max/32/680_2.png) [@max](https://discourse.flox.dev/u/max)\
**Post date:** [September 6, 2024, 1:25am UTC](https://discourse.flox.dev/t/issues-using-jupyterlab-extensions-with-flox/958/7 "2024-09-06T01:25:11Z")

</div>

Ah to be more precise–the following output was the result of launching jupyterlab from my flox environment, opening a terminal within that jupyterlab environment, and then running `jupyter labextension list`

```auto
`sys_prefix` level settings are read-only, using `user` level for migration to `lockedExtensions`
JupyterLab v4.2.4

```

---

<div class="post-metadata">

**Author:** ![zmitchell](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.flox.dev/zmitchell/32/639_2.png) [@zmitchell](https://discourse.flox.dev/u/zmitchell)\
**Post date:** [September 6, 2024, 4:24pm UTC](https://discourse.flox.dev/t/issues-using-jupyterlab-extensions-with-flox/958/8 "2024-09-06T16:24:19Z")

</div>

I’ve created a tracking issue where I’m going to put my debugging breadcrumbs instead of blowing up this thread: [Some Jupyter notebook extensions aren't found · Issue #2067 · flox/flox · GitHub](https://github.com/flox/flox/issues/2067). Feel free to leave comments in there if you have other details to add (namely, is it just the `jupyterlab-widgets` extension that isn’t found, or are there others).

---

<div class="post-metadata">

**Author:** ![zmitchell](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.flox.dev/zmitchell/32/639_2.png) [@zmitchell](https://discourse.flox.dev/u/zmitchell)\
**Post date:** [September 6, 2024, 5:04pm UTC](https://discourse.flox.dev/t/issues-using-jupyterlab-extensions-with-flox/958/9 "2024-09-06T17:04:30Z")

</div>

Alright, I think I’ve found a solution.

```auto
❯ JUPYTER_DATA_DIR="$FLOX_ENV/share/jupyter" jupyter labextension list
`sys_prefix` level settings are read-only, using `user` level for migration to `lockedExtensions`
JupyterLab v4.2.4
/nix/store/ni927g0pp68wmkbmanw5x5z92d91zgna-python3-3.12.5-env/share/jupyter/labextensions
        jupyterlab_pygments v0.3.0 enabled OK (python, jupyterlab_pygments)
        @jupyter-notebook/lab-extension v7.2.1 enabled OK

/Users/zmitchell/src/jupyter-flox/.flox/run/aarch64-darwin.jupyter-flox/share/jupyter/labextensions
        @jupyter-widgets/jupyterlab-manager v5.0.11 enabled OK (python, jupyterlab_widgets)

```

So, get rid of the other `JUPYTER_*` variables in your `on-activate` hook (just in case those mess anything else up), and try

```auto
export JUPYTER_DATA_DIR="$FLOX_ENV/share/jupyter"

```

---

<div class="post-metadata">

**Author:** ![ghudgins](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.flox.dev/ghudgins/32/588_2.png) [@ghudgins](https://discourse.flox.dev/u/ghudgins)\
**Post date:** [September 6, 2024, 6:29pm UTC](https://discourse.flox.dev/t/issues-using-jupyterlab-extensions-with-flox/958/10 "2024-09-06T18:29:43Z")

</div>

it worked for me! As discussed off line I logged an enhancement to do this variable setting automatically when we detect the right packages installed: [Add python activation logic for jupyter labextensions · Issue #2068 · flox/flox · GitHub](https://github.com/flox/flox/issues/2068)

---

<div class="post-metadata">

**Author:** ![max](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.flox.dev/max/32/680_2.png) [@max](https://discourse.flox.dev/u/max)\
**Post date:** [September 8, 2024, 3:33am UTC](https://discourse.flox.dev/t/issues-using-jupyterlab-extensions-with-flox/958/11 "2024-09-08T03:33:28Z")

</div>

> [@zmitchell](#):
>
> `JUPYTER_DATA_DIR="$FLOX_ENV/share/jupyter"`

This did allow me to see the installed widgets via `jupyter labextension list`, but permission issues then prevent the jupyter environment from launching:

```auto
JUPYTER_DATA_DIR="$FLOX_ENV/share/jupyter" jupyter lab --ip=0.0.0.0
[I 2024-09-08 03:27:21.738 ServerApp] jupyter_lsp | extension was successfully linked.
[I 2024-09-08 03:27:21.741 ServerApp] jupyter_server_terminals | extension was successfully linked.
[I 2024-09-08 03:27:21.744 ServerApp] jupyterlab | extension was successfully linked.
[I 2024-09-08 03:27:21.747 ServerApp] notebook | extension was successfully linked.
[W 2024-09-08 03:27:21.747 ServerApp] notebook_shim | error linking extension: [Errno 13] Permission denied: '/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/share/jupyter/runtime'
    Traceback (most recent call last):
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/traitlets/traitlets.py", line 632, in get
        value = obj._trait_values[self.name]
                ~~~~~~~~~~~~~~~~~ ^^^^^^^^^^^
    KeyError: 'browser_open_file'

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/traitlets/traitlets.py", line 632, in get
        value = obj._trait_values[self.name]
                ~~~~~~~~~~~~~~~~~ ^^^^^^^^^^^
    KeyError: 'runtime_dir'

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/jupyter_server/extension/manager.py", line 346, in link_extension
        extension.link_all_points(self.serverapp)
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/jupyter_server/extension/manager.py", line 228, in link_all_points
        self.link_point(point_name, serverapp)
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/jupyter_server/extension/manager.py", line 218, in link_point
        point.link(serverapp)
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/jupyter_server/extension/manager.py", line 140, in link
        linker(serverapp)
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/notebook_shim/nbserver.py", line 109, in _link_jupyter_server_extension
        members = diff_members(serverapp, nbapp)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/notebook_shim/nbserver.py", line 62, in diff_members
        m1 = public_members(obj1)
             ^^^^^^^^^^^^^^^^^^^^
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/notebook_shim/nbserver.py", line 56, in public_members
        members = inspect.getmembers(obj)
                  ^^^^^^^^^^^^^^^^^^^^^^^
      File "/nix/store/pgb120fb7srbh418v4i2a70aq1w9dawd-python3-3.12.5/lib/python3.12/inspect.py", line 614, in getmembers
        return _getmembers(object, predicate, getattr)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/nix/store/pgb120fb7srbh418v4i2a70aq1w9dawd-python3-3.12.5/lib/python3.12/inspect.py", line 592, in _getmembers
        value = getter(object, key)
                ^^^^^^^^^^^^^^^^^^^
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/traitlets/traitlets.py", line 687, in __get__
        return t.cast(G, self.get(obj, cls)) # the G should encode the Optional
                         ^^^^^^^^^^^^^^^^^^
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/traitlets/traitlets.py", line 635, in get
        default = obj.trait_defaults(self.name)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/traitlets/traitlets.py", line 1897, in trait_defaults
        return t.cast(Sentinel, self._get_trait_default_generator(names[0])(self))
                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/traitlets/traitlets.py", line 1241, in __call__
        return self.func(*args, **kwargs)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/jupyter_server/serverapp.py", line 1756, in _default_browser_open_file
        return os.path.join(self.runtime_dir, basename)
                            ^^^^^^^^^^^^^^^^
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/traitlets/traitlets.py", line 687, in __get__
        return t.cast(G, self.get(obj, cls)) # the G should encode the Optional
                         ^^^^^^^^^^^^^^^^^^
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/traitlets/traitlets.py", line 635, in get
        default = obj.trait_defaults(self.name)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/traitlets/traitlets.py", line 1897, in trait_defaults
        return t.cast(Sentinel, self._get_trait_default_generator(names[0])(self))
                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/jupyter_core/application.py", line 111, in _runtime_dir_default
        ensure_dir_exists(rd, mode=0o700)
      File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/jupyter_core/utils/ __init__.py", line 26, in ensure_dir_exists
        Path(path).mkdir(parents=True, mode=mode)
      File "/nix/store/pgb120fb7srbh418v4i2a70aq1w9dawd-python3-3.12.5/lib/python3.12/pathlib.py", line 1311, in mkdir
        os.mkdir(self, mode)
    PermissionError: [Errno 13] Permission denied: '/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/share/jupyter/runtime'
Traceback (most recent call last):
  File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/traitlets/traitlets.py", line 632, in get
    value = obj._trait_values[self.name]
            ~~~~~~~~~~~~~~~~~ ^^^^^^^^^^^
KeyError: 'runtime_dir'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/nix/store/jdaydbij5skwjlijmi350yc8vzlw0zhd-python3.12-jupyterlab-4.2.4/bin/.jupyter-lab-wrapped", line 9, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/jupyter_server/extension/application.py", line 616, in launch_instance
    serverapp = cls.initialize_server(argv=args)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/jupyter_server/extension/application.py", line 586, in initialize_server
    serverapp.initialize(
  File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/traitlets/config/application.py", line 118, in inner
    return method(app, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/jupyter_server/serverapp.py", line 2755, in initialize
    self.init_configurables()
  File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/jupyter_server/serverapp.py", line 2065, in init_configurables
    "connection_dir": self.runtime_dir,
                      ^^^^^^^^^^^^^^^^
  File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/traitlets/traitlets.py", line 687, in __get__
    return t.cast(G, self.get(obj, cls)) # the G should encode the Optional
                     ^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/traitlets/traitlets.py", line 635, in get
    default = obj.trait_defaults(self.name)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/traitlets/traitlets.py", line 1897, in trait_defaults
    return t.cast(Sentinel, self._get_trait_default_generator(names[0])(self))
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/jupyter_core/application.py", line 111, in _runtime_dir_default
    ensure_dir_exists(rd, mode=0o700)
  File "/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/lib/python3.12/site-packages/jupyter_core/utils/ __init__.py", line 26, in ensure_dir_exists
    Path(path).mkdir(parents=True, mode=mode)
  File "/nix/store/pgb120fb7srbh418v4i2a70aq1w9dawd-python3-3.12.5/lib/python3.12/pathlib.py", line 1311, in mkdir
    os.mkdir(self, mode)
PermissionError: [Errno 13] Permission denied: '/home/ubuntu/embedding-testing/embedding-testing-2/.flox/run/x86_64-linux.embedding-testing-2/share/jupyter/runtime'

```

---

<div class="post-metadata">

**Author:** ![mkenigs](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.flox.dev/mkenigs/32/520_2.png) [@mkenigs](https://discourse.flox.dev/u/mkenigs)\
**Post date:** [September 30, 2024, 5:35pm UTC](https://discourse.flox.dev/t/issues-using-jupyterlab-extensions-with-flox/958/12 "2024-09-30T17:35:59Z")

</div>

We had to fix an issue in nixpkgs where `JUPYTER_PATH` wasn’t being respected. If you run `flox upgrade` does it work now? Looking back at your original post, I think you may have to `export JUPYTER_PATH="${FLOX_ENV}/share/jupyter"` as well (adding the `share/jupyter`)

---

<div class="post-metadata">

**Author:** ![max](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.flox.dev/max/32/680_2.png) [@max](https://discourse.flox.dev/u/max)\
**Post date:** [October 2, 2024, 8:43pm UTC](https://discourse.flox.dev/t/issues-using-jupyterlab-extensions-with-flox/958/13 "2024-10-02T20:43:46Z")

</div>

This seems to be working! I’m going to continue testing this, but here is my manifest.

```auto
version = 1
[install]
psycopg.pkg-path = "python312Packages.psycopg"
tqdm.pkg-path = "python312Packages.tqdm"
datasets.pkg-path = "python312Packages.datasets"
ipywidgets.pkg-path = "python312Packages.ipywidgets"
huggingface-hub.pkg-path = "python312Packages.huggingface-hub"
jupyterlab-widgets.pkg-path = "python312Packages.jupyterlab-widgets"
nodejs.pkg-path = "nodejs"
widgetsnbextension.pkg-path = "python312Packages.widgetsnbextension"
pip.pkg-path = "python312Packages.pip"
jupyter.pkg-path = "jupyter"
btop.pkg-path = "btop"
postgresql_15.pkg-path = "postgresql_15"
tmux.pkg-path = "tmux"
ripgrep.pkg-path = "ripgrep"
pymongo.pkg-path = "python312Packages.pymongo"
[vars]
virtualEnv='./nb-venv/'
[hook]
on-activate = '''
        export PATH=/home/ubuntu/.local/bin:$PATH
        export JUPYTER_PATH="${FLOX_ENV}/share/jupyter"
'''
[profile]
common = """
  alias nb="jupyter lab --ip 0.0.0.0"
  echo; echo "Jupyter environment ready - start notebook with 'nb'."
"""
[options]
systems = ["aarch64-darwin", "aarch64-linux", "x86_64-darwin", "x86_64-linux"]

```

---

<div class="post-metadata">

**Author:** ![mkenigs](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.flox.dev/mkenigs/32/520_2.png) [@mkenigs](https://discourse.flox.dev/u/mkenigs)\
**Post date:** [October 2, 2024, 8:57pm UTC](https://discourse.flox.dev/t/issues-using-jupyterlab-extensions-with-flox/958/14 "2024-10-02T20:57:18Z")

</div>

Amazing! We may add logic to `flox activate` so that it does the `export JUPYTER_PATH="${FLOX_ENV}/share/jupyter"` automatically. We’re tracking that in [Some Jupyter notebook extensions aren't found · Issue #2067 · flox/flox · GitHub](https://github.com/flox/flox/issues/2067)