[Bug] Neovim remote plugin clear PYTHONPATH environment

[Tias-dev]

• OS: NixOS
• NeoVim Version: 0.11.6
• Python Version: 3.13
• Python is installed with: home-manager

`:checkhealth molten`

molten-nvim ~

• ✅ OK NeoVim >=0.9
• ✅ OK Python >=3.10
• ✅ OK Python module pynvim found
• ✅ OK Python module jupyter-client found
• ✅ OK Python module cairosvg found
• ✅ OK Python module pnglatex found
• ✅ OK Python module plotly found
• ⚠️ WARNING Optional python module kaleido not found
  • ADVICE:
    • pip install kaleido
• ✅ OK Python module pyperclip found
• ✅ OK Python module nbformat found
• ✅ OK Python module pillow found

Description

When i call MoltenInit and choose kernel. Neovim became very laggy without any errors and clues. After dig inside plugin code i found that stucks happens in file rplugin/python3/molten/runtime.py line 217

            self.kernel_client.wait_for_ready(timeout=0)

There always RuntimeError is thrown, so after adding debug notification with this error

            except RuntimeError:
                return False
# become to
            except RuntimeError as e:
                notify_error(self.nvim, str(e))
                return False

i found following error message

03:14:56 PM notify.error [Molten] Kernel died before replying to kernel_info

To figure out why this happen i dig even deeper and connect stdout and stderr outputs from running ipykernel_launch by adding this (line 57):

            self.kernel_manager.start_kernel()
# change to this
            stdout=open("/tmp/kernelStdout.log", "wb")
            stderr=open("/tmp/kernelStderr.log", "wb")
            self.kernel_manager.start_kernel(stdout=stdout, stderr=stderr)

and in file /tmp/kernelStderr.log i found

/nix/store/44rn0p64x92bnnh7cwn6x6ybvflybmvz-python3-3.13.12/bin/python: No module named ipykernel_launcher

but in my nix-shell(neovim also started from nix-shell) i can run

/nix/store/44rn0p64x92bnnh7cwn6x6ybvflybmvz-python3-3.13.12/bin/python -m ipykernel_launcher

and it is found

So after some investigations i found that by some reason molten (launched as remote plugin) have no PYTHONPATH environment variable is set(nix-shell have this env) and after manually adding this environment

all works

I don't really know why environment variable PYTHONPATH is cleared in remote plugin runtime but it is was really hard to figure out

Reproduction Steps

I use lazyvim config
with following molten config:

local filetypes = { "quarto", "markdown", "jupyter", "json" }
return {
  {
    "benlubas/molten-nvim",
    version = "*", -- use version <2.0.0 to avoid breaking changes
    dependencies = { "3rd/image.nvim" },
    build = ":UpdateRemotePlugins",
    init = function()
      -- these are examples, not defaults. Please see the readme
      vim.g.molten_image_provider = "image.nvim"
      vim.g.molten_output_win_max_height = 20
			vim.g.molten_tick_rate = 1000
			vim.g.molten_auto_image_popup = true
			vim.g.molten_auto_open_output = true
    end,
    ft = filetypes,
  },
  {
    "3rd/image.nvim",
    build = false, -- so that it doesn't build the rock https://github.com/3rd/image.nvim/issues/91#issuecomment-2453430239
    version = "1.1.0",
    opts = {
      processor = "magick_cli",
      backend = "kitty", -- Kitty will provide the best experience, but you need a compatible terminal
      integrations = {}, -- do whatever you want with image.nvim's integrations
      max_width = 100, -- tweak to preference
      max_height = 12, -- ^
      max_height_window_percentage = math.huge, -- this is necessary for a good experience
      max_width_window_percentage = math.huge,
      window_overlap_clear_enabled = true,
      window_overlap_clear_ft_ignore = { "cmp_menu", "cmp_docs", "" },
    },
    ft = filetypes,
  },
  {
    "quarto-dev/quarto-nvim",
    opts = {
      ft = filetypes,
      lspFeatures = {
        -- NOTE: put whatever languages you want here:
        languages = { "python" },
        chunks = "all",
        diagnostics = {
          enabled = true,
          triggers = { "BufWritePost" },
        },
        completion = {
          enabled = true,
        },
      },
      keymap = {
        -- NOTE: setup your own keymaps:
        hover = "K",
        definition = "gd",
        rename = "<leader>rn",
        references = "gr",
        format = "<leader>gf",
      },
      codeRunner = {
        enabled = true,
        default_method = "molten",
      },
    },
  },
  {
    "GCBallesteros/jupytext.nvim",
    dependencies = {
      "jmbuhr/otter.nvim",
      "nvim-treesitter/nvim-treesitter",
    },
    ft = filetypes,
		lazy=false,
    opts = {
      style = "markdown",
      output_extension = "md",
      force_ft = "markdown",
    },
  },
}

And following home-manager based neovim setup:

{ pkgs, ... }:
{
  programs.neovim = {
    enable = true;
    defaultEditor = true;
    # whatever other neovim configuration you have
    extraPackages = with pkgs; [
      tree-sitter

      # formatters
      alejandra
      tex-fmt

      # lsp
      stylua
      nil
      lua-language-server
      texlab
      clang-tools
      omnisharp-roslyn

      imagemagick # for image rendering
    ];
    extraLuaPackages =
      ps: with ps; [
        # ... other lua packages
        magick # for image rendering
      ];
    extraPython3Packages =
      ps: with ps; [
        pynvim
        nbformat
        jupyter-client
        ipykernel
        cairosvg # for image rendering
        pnglatex # for image rendering
        plotly # for image rendering
        pyperclip
      ];
  };
}

and following shell.nix file

{
  pkgs ? import <nixpkgs> { },
}:
pkgs.mkShell {
  buildInputs = [
    pkgs.python3
    (pkgs.python313.withPackages (
      ps: with ps; [
        notebook
        pynvim
				ipykernel
        jupyter-client
        jupyter-console
      ]
    ))
  ];
  shellHook = ''
    export LD_LIBRARY_PATH="${pkgs.stdenv.cc.cc.lib}/lib:$LD_LIBRARY_PATH"
    export JUPYTER_ALLOW_INSECURE_WRITES=1
  '';
  packages = [
    pkgs.python3
    (pkgs.python313.withPackages (
      ps: with ps; [
        notebook
        pynvim
				ipykernel
        jupyter-client
        jupyter-console
      ]
    ))
  ];
}

In this repo:

https://github.com/Timur-ux/AILabs-CV/tree/molten-issue

Maybe there exist simple nix config option to handle this or it is really bug in nix based configurations?