Unable to attach nvim to server on Windows

[sho-87]

I'm following the usage instructions and when I run :JupyniumStartAndAttachToServer in nvim, a window opens for a few seconds and closes - no browser or notebook appears

pip freeze shows that both jupynium and selenium packages are installed:

jupynium @ file:///C:/Users/Simon/AppData/Local/nvim-data/lazy/jupynium.nvim
selenium==4.8.0

Testing selenium from python also works OK:

from selenium import webdriver
driver = webdriver.Firefox()
driver.get("https://www.selenium.dev/selenium/web/web-form.html")

When I simply run jupynium from the terminal, firefox opens showing the notebook tree and the following info:

jupynium.cmds.jupynium:  439 - INFO - No nvim attached. Waiting for nvim to attach. Run jupynium --nvim_listen_addr /tmp/example (use `:echo v:servername` of nvim)

At this point, I go back to nvim and run :JupyniumAttachToServer but I get the following exception:

jupynium.cmds.jupynium:  225 - INFO - New nvim wants to attach: Namespace(attach_only=True, check_running=False, firefox_profile_name=None, firefox_profiles_ini_path=None, jupyter_command=['jupyter'], notebook_URL='http://localhost:8888/tree/', notebook_dir=None, nvim_listen_addr='\\\\\\\\.\\\\pipe\\\\nvim.24356.0', sleep_time_idle=0.05, version=False)
jupynium.pynvim_helpers:   11 - INFO - nvim addr: \\\\.\\pipe\\nvim.24356.0
jupynium.cmds.jupynium:  249 - ERROR - Exception occurred while attaching a new nvim. Ignoring.
Traceback (most recent call last):
  File "C:\Users\Simon\AppData\Roaming\Python\Python38\site-packages\jupynium\cmds\jupynium.py", line 230, in attach_new_neovim
    nvim = attach_and_init(new_args.nvim_listen_addr)
  File "C:\Users\Simon\AppData\Roaming\Python\Python38\site-packages\jupynium\pynvim_helpers.py", line 28, in attach_and_init
    raise TimeoutError("Timeout while waiting for nvim to start")
TimeoutError: Timeout while waiting for nvim to start

---

Not sure if this is related, but nvim doesn't seem to have access to any of the sync commands like JupyniumStartSync. it only sees these:

[kiyoon]

First of all, the commands will be initialised when you attach to the server, so that's normal.

I see that you're using Windows. Let me try on Windows and I'll get back to you soon.

[kiyoon]

What is your:echo &shell? Is it PowerShell?

[sho-87]

im launching nvim in powershell yes, but when I run :echo &shell it says cmd.exe, which is strange

I also use neovide...that says cmd.exe too

[kiyoon]

im launching nvim in powershell yes, but when I run :echo &shell it says cmd.exe, which is strange

I also use neovide...that says cmd.exe too

That is not strange. Unless you explicitly set it to powershell it will be cmd by default. It matters only when you execute shell commands inside vim.

I think many plugins assume cmd, so you may as well leave the setting as is. I'm still going to make this plugin compatible with powershell anyway though.

Can you test with branch fix/windows?

[kiyoon]

On my end the branch works, but I still have one last problem. I can't close neovim when I attach it to the server once.

[sho-87]

JupyniumStartAndAttachToServer works now - it starts notebook in firefox and asks me for password

2 problems at this stage:

1. the notebook start directory is always ~, even if I start nvim from a different directory (e.g. > cd Desktop > nvim), or if I change the cwd from within nvim
2. when I run JupyniumStartSync I get a kernel error:

Traceback (most recent call last):
  File "C:\Users\Simon\anaconda3\lib\site-packages\tornado\web.py", line 1704, in _execute
    result = await result
  File "C:\Users\Simon\anaconda3\lib\site-packages\tornado\gen.py", line 769, in run
    yielded = self.gen.throw(*exc_info)  # type: ignore
  File "C:\Users\Simon\anaconda3\lib\site-packages\notebook\services\sessions\handlers.py", line 69, in post
    model = yield maybe_future(
  File "C:\Users\Simon\anaconda3\lib\site-packages\tornado\gen.py", line 762, in run
    value = future.result()
  File "C:\Users\Simon\anaconda3\lib\site-packages\tornado\gen.py", line 769, in run
    yielded = self.gen.throw(*exc_info)  # type: ignore
  File "C:\Users\Simon\anaconda3\lib\site-packages\notebook\services\sessions\sessionmanager.py", line 98, in create_session
    kernel_id = yield self.start_kernel_for_session(session_id, path, name, type, kernel_name)
  File "C:\Users\Simon\anaconda3\lib\site-packages\tornado\gen.py", line 762, in run
    value = future.result()
  File "C:\Users\Simon\anaconda3\lib\site-packages\tornado\gen.py", line 769, in run
    yielded = self.gen.throw(*exc_info)  # type: ignore
  File "C:\Users\Simon\anaconda3\lib\site-packages\notebook\services\sessions\sessionmanager.py", line 110, in start_kernel_for_session
    kernel_id = yield maybe_future(
  File "C:\Users\Simon\anaconda3\lib\site-packages\tornado\gen.py", line 762, in run
    value = future.result()
  File "C:\Users\Simon\anaconda3\lib\site-packages\notebook\services\kernels\kernelmanager.py", line 176, in start_kernel
    kernel_id = await maybe_future(self.pinned_superclass.start_kernel(self, **kwargs))
  File "C:\Users\Simon\anaconda3\lib\site-packages\jupyter_client\multikernelmanager.py", line 186, in start_kernel
    km.start_kernel(**kwargs)
  File "C:\Users\Simon\anaconda3\lib\site-packages\jupyter_client\manager.py", line 341, in start_kernel
    self.kernel = self._launch_kernel(kernel_cmd, **kw)
  File "C:\Users\Simon\anaconda3\lib\site-packages\jupyter_client\manager.py", line 249, in _launch_kernel
    return launch_kernel(kernel_cmd, **kw)
  File "C:\Users\Simon\anaconda3\lib\site-packages\jupyter_client\launcher.py", line 132, in launch_kernel
    proc = Popen(cmd, **kwargs)
  File "C:\Users\Simon\anaconda3\lib\subprocess.py", line 858, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "C:\Users\Simon\anaconda3\lib\subprocess.py", line 1311, in _execute_child
    hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
OSError: [WinError 123] The filename, directory name, or volume label syntax is incorrect

[kiyoon]

For 1. did you start jupyter notebook by yourself, or are you letting Jupynium to start it for you?

If you started by yourself, it will just open localhost:8888 and there's no way it can know where the notebook root directory you set to, so it won't change the directory.

If it started the notebook, it should launch in your file's directory

EDIT: If it asked you for a password it means the notebook server is started from somewhere else. If you close the notebook server and try again, it won't ask you for a password and it will be in your file's directory

[kiyoon]

For 2. it works on my end. I think your Jupyter Notebook installation is corrupted.

Do you use Conda by any change? In that case I recommend setting the option jupyter_command

[sho-87]

I'll take a look at this in the morning, and maybe reinstall anaconda. Every time I run JupyniumStartAndAttachToServer to start things up it always takes me to a page that asks for a password

fyi this is using the base anaconda env, not in a separate env, if that makes a difference

[kiyoon]

I also use the base environment (so I can switch environments within notebook)

I noticed that the Notebook doesn't close automatically on Windows. I fixed this now btw, but
you should go to firefox/chrome and enter localhost:8888 to see if something's running already.

You can use

ps jupyter-notebook
Stop-Process <id>

to kill the running Notebook process.

Once you do it and update the plugin (still use branch fix/windows) then it will not ask password again.

[kiyoon]

I'm adding more commits to fix the issue, so when you test it again make sure you update the branch

[kiyoon]

Please set this and try again. I added support to be more consistent over platforms.

require("jupynium").setup({
  python_host = { "conda", "run", "--no-capture-output", "-n", "base", "python" },
  jupyter_command = { "conda", "run", "--no-capture-output", "-n", "base", "jupyter" },
})

[sho-87]

I did a completely fresh install of anaconda, and even wiped my nvim-data directory just for a fresh start. Using the latest on your windows branch and the new config you provided, I still run into the same problem as before. Here is my entire nvim config: https://github.com/sho-87/dotfiles/blob/jupynium/nvim/lua/plugins/modules/jupynium.lua

I'll try to be specific about my steps...

Problem 1 - trying to get basic syncing working

1. Start Terminal, cd Desktop -> nvim
2. :JupyniumStartAndAttachToServer ... firefox opens and notebook homepage loads
3. :JupyniumStartSync ... a new tab and notebook open (Untitled.ipynb), but it is syncing my nvim contents to the notebook (I expect this is the opposite of what is meant to happen). Nothing asked me which way I want to sync
4. The notebook started with a dead kernel and the same error as I posted above

Problem 2 - trying to get basic syncing working

1. Start Terminal, cd Desktop -> nvim
2. :JupyniumStartAndAttachToServer ... firefox opens and notebook homepage loads
3. In firefox, click on an existing notebook file. Renders fine in firefox, but with dead kernel as above
4. :JupyniumStartSync 2 to try to sync the new notebook tab to nvim ... I get a warning that my notebook contents will be removed. I expect it's wanting to replace the notebook with my nvim contents again:

Problem 3 - trying to load an existing notebook

1. Start Terminal, cd Desktop -> nvim
2. :JupyniumStartAndAttachToServer ... firefox opens and notebook homepage loads
3. In firefox, I open a notebook file that is on my desktop
4. :JupyniumLoadFromIpynbTabAndStartSync 2
5. nvim is frozen and command doesnt seem to get executed. Nothing happens in firefox and nvim remains unresponsive
6. Notebook page has the same dead kernel and error as above

---

The reason I tried (3) was because I remember I had syncing working at some point before the anaconda uninstall. I could scroll in nvim and I would see the change in firefox. I could even add cells and clear output; the problem was the dead kernel prevented me from running anything

So I guess my 2 overarching problems are 1) I don't know how to correctly "open" a notebook that already exists, and 2) how to get the kernel to run/restart so code can execute

Jupyter seems fine by itself. I can jupyter notebook and open files with a perfectly running kernel. This problem only comes up when I try do it through jupynium

[kiyoon]

1. By the way, this plugin only synchronises from neovim to notebook, not the other way around.
   You can load from notebook first, using :JupyniumLoadFromIpynbTabAndStartSync 2, but this will synchronise from neovim to notebook after.
   The whole point of this plugin is to edit within neovim, but still see the visualisation on the notebook.

2. I will fix the problem 3 soon.

3. About the dead kernel:
   Can you clarify if jupyter notebook is fine when you do it after conda activate? The program is merely running a code you configured which is conda run --no-capture-output -n base jupyter notebook ...
   Also, when you launch it from the command line which kernel do you get?

Is it Python 3 (ipykernel) or something like Conda ...

[kiyoon]

I cannot reproduce the problem 2 and 3.

I tried to also uninstall miniconda and install it again. The kernel and the command both works fine for me.. Maybe the dead kernel stuff is causing both problems

Can you try running conda run --no-capture-output -n base jupyter notebook and see if you also see dead kernel if the command is executed that way?

[kiyoon]

Btw, this is my entire init.lua

require("jupynium").setup({
	python_host = { "conda", "run", "--no-capture-output", "-n", "base", "python" },
	jupyter_command = { "conda", "run", "--no-capture-output", "-n", "base", "jupyter" },
})

And I just cloned this plugin at C:\Users\Kiyoon Kim\AppData\Local\nvim-data\site\pack\dev\start\jupynium.nvim (use fix/windows branch)

Maybe consider testing like this in a fresh environment. I doubt that the kernel error is related to the neovim configuration though. I think it's more related to how you installed jupyter notebook.

For me, after fresh installing miniconda3 I ran

conda activate
conda install python=3.10
pip install notebook
cd "C:\Users\Kiyoon Kim\AppData\Local\nvim-data\site\pack\dev\start\jupynium.nvim"
pip install -e .

[kiyoon]

You said running jupyter notebook manually doesn't have the kernel problem so another advice would be to open the jupyter notebook server by yourself and try Jupynium. It's less convenient but still usable like that, and maybe it will solve other problems you've had. I will keep trying to fix the kernel problem in the meantime.

[sho-87]

1. conda activate -> jupyter notebook works fine. I only get 1 kernel option, which is Python 3 (ipykernel):

2. conda run --no-capture-output -n base jupyter notebook also runs ok
3. using a barebones config leads to the same problem

(all of the above was with the latest commits you pushed)

One big difference here is that youre using miniconda, whereas im using the full anaconda stack: https://www.anaconda.com/products/distribution

Does anaconda install jupyter in some special way beyond simply a pip install?

[kiyoon]

Thank you. If you run notebook and then use Jupynium, do you still have the problem 3?

[sho-87]

what would be the correct commands in Jupynium if im starting the notebook myself first?

[kiyoon]

Same command. It will just not launch the notebook if you already have localhost:8888 running. It will only load it when it fails to load that page

[kiyoon]

I've never used anaconda but in my understanding they should be similar. I installed notebook with command pip install notebook but I don't know what will happen if you use conda install notebook.
In any case, the problem is that it does work normally and it doesn't when it's launched with Jupynium. Strange.. Maybe the parameters I passed are not supported with your notebook.

Hypothesis 1: Are you using Notebook 6.5? Maybe different version doesn't support some parameters.

Can you try running with this? This is the full command Jupynium should use to launch the server

conda run --no-capture-output -n base jupyter notebook --port 8888 --no-browser --NotebookApp.token abcdef --NotebookApp.notebook_dir C:\Users\username

Hypothesis 2: Maybe jupynium is just running the wrong command.

Check 1. Did you uninstall the previous conda environment completely?
Check 2. you should try running conda activate and jupynium --jupyter_command conda run " --no-capture-output" " -n" base jupyter. Then try jupynium again. You'll see the error logs there, it may be helpful.

[sho-87]

Running jupyter notebook manually and then :JupyniumStartAndAttachToServer works OK. JupyniumStartSync creates a new untitled notebook with a working kernel

:JupyniumLoadFromIpynbTab 2 and :JupyniumLoadFromIpynbTabAndStartSync 2 are both a bit temperamental as they sometimes freezes nvim, but that sounds like a different problem for now

---

looks like anaconda comes with notebook 6.4. will try an update to 6.5 soon

>>> importlib.metadata.version('notebook')
'6.4.12'

conda run --no-capture-output -n base jupyter notebook --port 8888 --no-browser --NotebookApp.token abcdef --NotebookApp.notebook_dir C:\Users\Simon\Desktop works ok and the kernel is fine

conda activate -> jupynium --jupyter_command conda run " --no-capture-output" " -n" base jupyter gives me an error as its not a program that I can run:

jupynium : The term 'jupynium' is not recognized as the name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was included, verify that the path is
correct and try again.

[kiyoon]

Okay, because of the last part, it sounds to me that you have two different conda installed. You didn't install jupynium in the new conda environment.

Hypothesis 2: Maybe jupynium is just running the wrong command. You shell's conda and neovim's conda can direct you to a different conda command.

Check 3. Run :call system("conda run --no-capture-output -n base jupyter notebook") within your neovim and see if it's still wrong. Check the conda version and install path etc. by calling :echo system("conda -V"), :echo system("conda list")

[kiyoon]

Or go to cmd.exe instead of powershell and see if your conda environment matches that of powershell.

[kiyoon]

You can also try setting the neovim's shell to powershell.exe and that may use the correct conda you're using as well.

[kiyoon]

About the freezing part I'll need to investigate later.

[sho-87]

1. :call system("conda run --no-capture-output -n base jupyter notebook") - kernel works ok
2. conda 23.1.0
3. echo system("conda list") # packages in environment at C:\Users\Simon\anaconda3
4. I dont see jupynium in the conda list, but when I do :echo system("pip freeze") I see jupynium: jupynium @ file:///C:/Users/Simon/AppData/Local/nvim-data/lazy/jupynium.nvim
5. using cmd.exe, the conda env is at the same location and gives all the same output as 3 and 4

[kiyoon]

Maybe that's not the case then..
Can you run jupynium like this?

conda activate
python -m jupynium --jupyter_command conda run " --no-capture-output" " -n" base jupyter

[sho-87]

ok i think this is a miniconda vs anaconda difference. I just completely uninstalled anaconda and installed a fresh miniconda, and went through these steps:

conda activate
conda install python=3.10
pip install notebook
cd "C:\Users\Simon\AppData\Local\nvim-data\lazy\jupynium.nvim"
pip install -e .

In nvim, JupyniumStartAndAttachToServer and then JupyniumStartSync leads to a working kernel

I'm not sure what the differences are in terms of how miniconda and anaconda install packages (pip vs conda, or something else), but off the bat there are differences in python (3.9 vs 3.10) and package versions (notebook 6.4 vs 6.5)

[kiyoon]

I see. Thanks for testing that setup and glad that it works! If you're happy I'll merge the PR later today.

In my experience sometimes the conda environment breaks. For example I noticed recently that the conda install doesn't install pytorch with GPU, even though I used the same command as before. Maybe they have some consistency and stability issues.

Also the hanging issue seems to be caused from invoking javascript to grab the content from the notebook. Not sure when it happens maybe I can add a timeout to the command so you wait only up to 10 seconds. If you find this keep happening feel free to open another issue.

[sho-87]

unfortunately I cant actually use miniconda permanently, as the stack at work uses the full anaconda setup - so ill have to try to see what the differences between the 2 actually are and figure out a solution

[kiyoon]

Fair enough. Maybe if you try matching the version it may work. The worst case you'll have to open the Notebook server by yourself but I think that's managable.

[kiyoon]

This got automatically closed by merging, but feel free to continue the discussion.