jupynium 0.1.1

Neovim plugin that automates Jupyter Notebook editing/browsing using Selenium.

Jupynium: Control Jupyter Notebook on Neovim with ZERO Compromise

It's just like a markdown live preview, but it's Jupyter Notebook live preview!

Jupynium uses Selenium to automate Jupyter Notebook, synchronising everything you type on Neovim.
Never leave Neovim. Switch tabs on the browser as you switch files on Neovim.

Note that it doesn't sync from Notebook to Neovim so only modify from Neovim.

How does it work?

The Jupynium server will receive events from Neovim, keep the copy of the buffer and apply that to the Jupyter Notebook by using Selenium browser automation. It interacts only through the front end so it doesn't require installing extensions on the kernel etc., which makes it possible to

• Develop locally, run remotely (or vice versa)
• Use university-hosted Jupyter Notebook
• Use any other languages / kernels such as R

🛠️ Installation

Requirements

• 💻 Linux, macOS and Windows (CMD, PowerShell, WSL2)
• 🦊 Firefox (Other browsers are not supported due to their limitation with Selenium)
• ✌️ Neovim >= v0.8
• 🐍 Python >= 3.7
• 📔 Jupyter Notebook >= 6.2 (Doesn't support Jupyter Lab)

Don't have system python 3.7? You can use Conda.

conda create -n jupynium python=3
conda activate jupynium

Upgrade pip. This solves many problems.

pip3 install --upgrade pip

Install with vim-plug:

Plug 'kiyoon/jupynium.nvim', { 'do': 'pip3 install --user .' }
" Plug 'kiyoon/jupynium.nvim', { 'do': '~/miniconda3/envs/jupynium/bin/pip install .' }
Plug 'rcarriga/nvim-notify'  " optional

Install with packer.nvim:

use { "kiyoon/jupynium.nvim", run = "pip3 install --user ." }
-- use { "kiyoon/jupynium.nvim", run = "~/miniconda3/envs/jupynium/bin/pip install ." }
use { "rcarriga/nvim-notify" }  -- optional

Install with 💤lazy.nvim

  {
    "kiyoon/jupynium.nvim",
    build = "pip3 install --user .",
    -- build = "~/miniconda3/envs/jupynium/bin/pip install .",
    -- enabled = vim.fn.isdirectory(vim.fn.expand "~/miniconda3/envs/jupynium"),
  },
  "rcarriga/nvim-notify",  -- optional

Setup is optional for system python users and here are the defaults. Conda users need to change the python_host.

Mac troubleshooting: Homebrew Python 3.10 and above are broken in the latest pip release. See https://github.com/pypa/pip/issues/11539.
Use build = "/usr/bin/pip3 install --user ." and change python_host = "/usr/bin/python3" in the settings below, to use the system python.

Click to see setup defaults

require("jupynium").setup({
  -- Conda users:
  -- python_host = "~/miniconda3/envs/jupynium/bin/python",
  python_host = vim.g.python3_host_prog or "python3",

  default_notebook_URL = "localhost:8888",

  -- Write jupyter command but without "notebook"
  -- When you call :JupyniumStartAndAttachToServer and no notebook is open,
  -- then Jupynium will open the server for you using this command. (only when notebook_URL is localhost)
  jupyter_command = "jupyter",
  -- jupyter_command = "~/miniconda3/bin/jupyter",

  -- Used when notebook is launched by using jupyter_command.
  -- If nil or "", it will open at the git directory of the current buffer,
  -- but still navigate to the directory of the current buffer. (e.g. localhost:8888/tree/path/to/buffer)
  notebook_dir = nil,

  -- Used to remember the last session (password etc.).
  -- You may need to change the path.
  firefox_profiles_ini_path = vim.fn.isdirectory(vim.fn.expand "~/snap/firefox/common/.mozilla/firefox")
      and "~/snap/firefox/common/.mozilla/firefox/profiles.ini"
    or "~/.mozilla/firefox/profiles.ini",
  firefox_profile_name = nil, -- nil means the default profile

  -- Open the Jupynium server if it is not already running
  -- which means that it will open the Selenium browser when you open this file.
  -- Related command :JupyniumStartAndAttachToServer
  auto_start_server = {
    enable = false,
    file_pattern = { "*.ju.*" },
  },

  -- Attach current nvim to the Jupynium server
  -- Without this step, you can't use :JupyniumStartSync
  -- Related command :JupyniumAttachToServer
  auto_attach_to_server = {
    enable = true,
    file_pattern = { "*.ju.*", "*.md" },
  },

  -- Automatically open an Untitled.ipynb file on Notebook
  -- when you open a .ju.py file on nvim.
  -- Related command :JupyniumStartSync
  auto_start_sync = {
    enable = false,
    file_pattern = { "*.ju.*", "*.md" },
  },

  -- Automatically keep filename.ipynb copy of filename.ju.py
  -- by downloading from the Jupyter Notebook server.
  -- WARNING: this will overwrite the file without asking
  -- Related command :JupyniumDownloadIpynb
  auto_download_ipynb = true,

  -- Always scroll to the current cell.
  -- Related command :JupyniumScrollToCell
  autoscroll = {
    enable = true,
    mode = "always", -- "always" or "invisible"
    cell = {
      top_margin_percent = 20,
    },
  },

  scroll = {
    page = { step = 0.5 },
    cell = {
      top_margin_percent = 20,
    },
  },

  use_default_keybindings = true,
  textobjects = {
    use_default_keybindings = true,
  },

  -- Dim all cells except the current one
  -- Related command :JupyniumShortsightedToggle
  shortsighted = false,
})

🚦 Usage

First, I recommend setting password on your notebook (rather than using tokens)

$ jupyter notebook password
Enter password: 🔒

$ jupyter notebook 			# leave notebook opened

Jupynium server stays alive as long as the browser is alive.
So you can see them as the same thing in this doc.
For example:

• Starting Jupynium server = opening a Selenium browser
• Manually closing the browser = closing the Jupynium server

Open and attach to a Jupynium server

This is for local neovim only. For remote neovim, see Command-Line Usage.

Running :JupyniumStartAndAttachToServer will open the notebook.
Type password and once you need to be on the main page (file browser) for the next steps.

New in 0.1.1:
Jupynium will open Jupyter Notebook server for you if not found.
It will also open the ipynb file in the current directory and ask you if you want to sync from vim or from ipynb.

Sync current buffer to the Jupynium server

You attached your nvim instance to the server, but it won't automatically start syncing.
Run :JupyniumStartSync to create a new ipynb file and start syncing from vim to notebook.

You can also:

1. :JupyniumStartSync filename to give name (filename.ipynb) instead of Untitled.ipynb.

• This will not open a file if it exists. Instead filename will be ignored.

2. Manually open the file from the browser, and :JupyniumStartSync 2 to sync using the 2nd tab (count from 1).

Use multiple buffers

Run :JupyniumStartSync again with a new buffer you want to sync.

Use multiple neovim

You can run :JupyniumStartSync on a new neovim instance.
If you have auto_attach_to_server = false during setup, you need to run :JupyniumAttachToServer and :JupyniumStartSync.

📝 .ju.py (or .ju.*) file format

The file format is designed to be LSP friendly even with markdown code injected in it. The markdown cells will be part of python string """%% ... %%""".

Code cell separators:
i.e. Any code below this line (and before the next separator) will be a code cell.

• # %%: recommended
• %%""": use when you want to close markdown cell
• %%'''

Markdown cell separators:

• """%%: recommended
• '''%%
• # %%%
• # %% [md]
• # %% [markdown]

Explicitly specify the first cell separator to use it like a notebook.

• If there is one or more cells, it works as a notebook mode.
  • Contents before the first cell are ignored, so use it as a heading (shebang etc.)
• If there is no cell, it works as a markdown preview mode.
  • It will still open ipynb file but will one have one markdown cell.

⌨️ Keybindings

• <space>x: Execute selected cells
• <space>c: Clear selected cells
• <space>S: Scroll to cell (if autoscroll is disabled)
• <PageUp>, <PageDown>: Scroll notebook

If you want custom keymaps, add use_default_keybindings = false and follow M.default_keybindings() in lua/jupynium/init.lua.

Textobjects

• [j, ]j: go to previous / next cell separator
  • Repeat with ; and , if you have nvim-treesitter-textobjects. Follow their instructions for keybindings for this.
• <space>j: go to current cell separator
• vaj,vij, vaJ, viJ: select current cell
  • a: include separator, i: exclude separator
  • j: exclude next separator, J: include next separator

If you want custom keymaps, add textobjects = { use_default_keybindings = false } and follow M.default_keybindings() in lua/jupynium/textobj.lua.

📡 Available Vim Commands

" Server (only used when neovim is local. See Command-Line Usage for remote neovim)
:JupyniumStartAndAttachToServer [notebook_URL]
:JupyniumAttachToServer [notebook_URL]

" Sync
:JupyniumStartSync [filename / tab_index]
:JupyniumStopSync
:JupyniumLoadFromIpynbTab tab_index
:JupyniumLoadFromIpynbTabAndStartSync tab_index

" Notebook (while syncing)
:JupyniumSaveIpynb
:JupyniumDownloadIpynb [filename]
:JupyniumAutoDownloadIpynbToggle

:JupyniumScrollToCell
:JupyniumScrollUp
:JupyniumScrollDown
:JupyniumAutoscrollToggle

:JupyniumExecuteSelectedCells
:JupyniumClearSelectedCellsOutputs
:JupyniumToggleSelectedCellsOutputsScroll

" Highlight
:JupyniumShortsightedToggle

👨‍💻️ Command-Line Usage (Attach to Remote NeoVim)

You don't need to install the vim plugin to use Jupynium.
The plugin is responsible of adding :JupyniumStartAndAttachToServer etc. that just calls the command line program,
plus it has textobjects and shortsighted support.

Install Jupynium if you haven't.

$ pip3 install jupynium

Open a python/markdown file with nvim and see :echo v:servername.
Run Jupynium like:

$ jupynium --nvim_listen_addr /tmp/your_socket_path

Or, you can run Neovim like

$ nvim --listen localhost:18898 notebook.ju.py

Then start Jupynium as well as attaching the neovim to it.

$ jupynium --nvim_listen_addr localhost:18898

Note that you can attach to remote neovim by changing localhost to servername.com or using SSH port forwarding.

This will open Firefox with Selenium, defaulting to http://localhost:8888.

Additionally,

• You can run jupynium command multiple times to attach more than one Neovim instance.
• jupynium --notebook_URL localhost:18888 to view different notebook.
• You can just run jupynium without arguments to just let the server / browser running and wait for nvim to attach.

Converting ipynb to Jupynium file

ipynb2jupy [-h] [--stdout] file.ipynb [file.ju.py]

⚠️ Caution

The program is in an alpha stage. If it crashes it's likely that the whole browser turns off without saving!

Rules:

1. Always leave the home page accessible. Jupynium interacts with it to open files. Do not close, or move to another website.

• It's okay to move between directories.

2. It's OK to close the notebook pages. If you do so, it will stop syncing that buffer.
3. Changing tab ordering or making it to a separate window is OK.

🌽 Using different languages / kernels

Instead of *.ju.py if you make files named *.ju.* (e.g. *.ju.r) you will see all the keybindings and commands.
All the procedure should be the same, except that you would need to manually change the kernel from the browser.

📰 Fun Facts

• I spent my whole Christmas and New Year holidays (and more) just making this plugin.