[BUG] Missing package molten after `enable=true`

xvrdm commented 6 months ago

Field	Description
Plugin	`molten`
Nixpkgs	`23.11`

[X] I have read the FAQ and my bug is not listed there.

Description

I am trying to use the molten package. Even though I enabled the package (found in the doc), I don't get any :Molten* command in nvim. Do I need to require it manually?

I started from nix flake init --template github:nix-community/nixvim and only changed config/default.nix. The other changes (colorschemes, lualine, lsp) were correctly pulled/activated.

Thanks for the awesome project!

Minimal, Reproducible Example (MRE)

in config/default.nix

{self, pkgs, ...}: {
# Import all your configuration modules here
    imports = [
        ./bufferline.nix
    ];
    colorschemes.gruvbox.enable = true;

    plugins = {
        lualine.enable = true;
    };

    plugins.lsp = {
        enable = true;
        servers = {
            tsserver.enable = true;
            lua-ls.enable = true;
            nixd.enable = true;
                        pyright.enable = true;
        };
    };

    plugins.molten = {
      enable = true;
    };
}

GaetanLepage commented 6 months ago

No, there is no require for this plugin. However, you need to properly set up the dependencies. :UpdateRemoteDependencies should be recognized as a command. However, it fails on my side, saying that it misses the jupyter_client module.

xvrdm commented 6 months ago

Thanks a lot for looking at it so swiftly. jupyter is indeed a dependency of molten. However, even when do create a temp shell that has jupyter, :UpdateRemoteDependencies continues to fail.

# in my `nix flake init --template github:nix-community/nixvim` dir
nix-shell -p "python3.withPackages(ps: with ps; [ numpy pandas jupyter ])"
nix run .#

Obviously, feel free to tell me if this is outside the scope of nixnvim support. I just wasn't sure if :UpdateRemoteDependencies was even supported or if it breaks nix paradigms.

traxys commented 6 months ago

I think we need to add it to the extraPythonPackages of nixvim

xvrdm commented 6 months ago

That's exactly what I was looking at. Here is the molten example for nixos: https://github.com/benlubas/molten-nvim/blob/main/docs/NixOS.md

Using home-manager, they have this part:

...
      extraPython3Packages = ps: with ps; [
        # ... other python packages
        pynvim
        jupyter-client
        cairosvg # for image rendering
        pnglatex # for image rendering
        plotly # for image rendering
        pyperclip
      ];
...

Is there a similar user-defined argument in nixvim?

traxys commented 6 months ago

We have this option: https://nix-community.github.io/nixvim/NeovimOptions/index.html?highlight=python#extrapython3packages

xvrdm commented 6 months ago

This helped a lot to go forward.

Now I have:

a tiny shell.nix for the environment (to be replaced by a flake)

{ pkgs ? import <nixpkgs> {} }:
pkgs.mkShell {
  nativeBuildInputs = with pkgs; [
    python311
    quarto
  ];

  LD_LIBRARY_PATH = "${pkgs.stdenv.cc.cc.lib}/lib";
}

Some molten python package dependency for nvim declared in the nixvim config/default.nix

{ self
, pkgs
, ...
}: {
  # Import all your configuration modules here
  imports = [
    ./bufferline.nix
  ];

  extraPython3Packages = p: with p; [ jupyter-client pynvim cairosvg pnglatex plotly pyperclip ];

  extraPlugins = [
    { plugin = pkgs.vimPlugins.quarto-nvim; }
    { plugin = pkgs.vimPlugins.otter-nvim; }
    {
      plugin = pkgs.vimUtils.buildVimPlugin {
        name = "jupytext-nvim";
        src = pkgs.fetchFromGitHub {
          owner = "GCBallesteros";
          repo = "jupytext.nvim";
          rev = "68fddf28119dbaddfaea6b71f3d6aa1e081afb93";
          sha256 = "x5emW+qfUTUDR72B9QdDgVdrb8wGH9D7AdtRrQm80sI=";
        };
      };
    }
  ];

  extraConfigLua = ''
        require("jupytext").setup({
                style = "markdown",
                output_extension = "md",
                force_ft = "markdown",
                })
  '';

  plugins.lsp = {
    enable = true;
    servers = {
      tsserver.enable = true;
      lua-ls.enable = true;
      rnix-lsp.enable = true;
      pyright.enable = true;
    };
  };

  plugins.molten = {
    enable = true;
  };

}

The jupiter kernel and jupytext cli installed in a venv

With these three parts, I can :MoltenInit and run code in notebook cells 🥳

The current blocker is that I could only make this works with the line:

  LD_LIBRARY_PATH = "${pkgs.stdenv.cc.cc.lib}/lib";

in shell.nix, which helps pass :UpdateRemotePlugins but also seem to break the pyright lsp. Without it I have normal LSP support, with it the LSP fails to attach to the buffer with the :LspLog error message:

/lib/libstdc++.so.6: version `GLIBXX_3.4.32' not found

Charging1948 commented 6 months ago

I also had the same problem, where molten would never load by just enabling it. I fixed it by fetching the plugin manually from github and passing the required dependencies through to it.

  plugins.molten = {
    enable = true;
    package = pkgs.vimUtils.buildVimPlugin {
      pname = "molten-nvim";
      version = "2024-02-23";
      src = pkgs.fetchFromGitHub {
        owner = "benlubas";
        repo = "molten-nvim";
        rev = "8346bba69e0de96278dad2038e9be74605908b7d";
        # sha256 = lib.fakeSha256;
        sha256 = "08f3zxzka43f87fks56594476h57yq01x7a1zdsn4acc278xg1nb";
      };
      passthru.python3Dependencies = ps:
        with ps; [
          pynvim
          jupyter-client
          cairosvg
          ipython
          nbformat
        ];
      meta.homepage = "https://github.com/benlubas/molten-nvim/";
    };
  };

Maybe the original package in nixpkgs can also be overwritten with overrideAttrs but the above code worked for me, so i did not experiment further.

xvrdm commented 6 months ago

Thank you for sharing @Charging1948 I tried it but for me it did not change the situation.

With LD_LIBRARY_PATH = "${pkgs.stdenv.cc.cc.lib}/lib"; in shell.nix (which breaks pyright LSP): molten is responsive and I get results below cells.

Without LD_LIBRARY_PATH = "${pkgs.stdenv.cc.cc.lib}/lib"; in shell.nix (which fixes pyright LSP): the entire nvim becomes extremely sluggish after :MoltenInit and I get "on hold" below cells.

Charging1948 commented 6 months ago

@xvrdm Very Interesting. I do not override the LD_LIBRARY_PATH and it just works.

My config is a mess, but maybe it helps: https://github.com/Charging1948/neovim

xvrdm commented 6 months ago

@Charging1948 I actually tried your config after your first config, very impressive, but a bit overwhelming for my level of understanding. Definitely an inspiration.

I put my tiny attempt here: https://github.com/xvrdm/nixvim_sandbox

Charging1948 commented 6 months ago

@xvrdm I tried to replicate the behavior you are experiencing, but i was able to use molten without problems:

The only thing i have added was the ipykernel, because it was missing.

At this point i dont know what the problem could be, sorry.

xvrdm commented 6 months ago

Thanks a lot for trying. So you manage to have both molten working and LSP support in normal python files 🤔 ? I wonder if it could be because I am trying on an arm vm. I will try it on another architecture.

GaetanLepage commented 6 months ago

In the end, I am not sure about what we could/should do at the nixvim level. Should we add the few recommended packages to extraPython3Packages ? What do you think @traxys ?

xvrdm commented 6 months ago

@GaetanLepage, do you mean that they could have been automatically when a user enable molten?

From a user perspective, I think it makes sense that I have to add these python packages via the extrapython3packages argument @traxys pointed me to. Except if for other packages you tend to do it for the user (but I guess it would be quite challenging to keep track of).

traxys commented 6 months ago

I think we should add the required package to the extraPython3Packages

nix-community / nixvim

[BUG] Missing package molten after `enable=true` #1206

Description

Minimal, Reproducible Example (MRE)