[Help] Setup for Neovim Flatpak?

[OrelEagle]

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I migrated my laptop from Manjaro (based on Arch) to Tuxedo OS (based on Ubuntu) and installed nvim Flatpak version, as the version in the repos is too old. I installed zk as recommended in the README. The install on Manjaro worked without issues and I copied the config during the migration.

When I open a file with zk, I get the following error message and the zk language server is not started:

Spawning language server with cmd: `zk` failed. The language server is either not installed, missing from PATH, or not executable.
Error detected while processing BufReadPost Autocommands for "*":
Error executing lua callback: /app/share/nvim/runtime/filetype.lua:21: Error executing lua: /app/share/nvim/runtime/filetype.lua:22: BufReadPost Autocommands for "*"..FileType Autocommands for "markdown": Vim(lua):E5108: Error executing lua /app/share/nvim/runtime/lua/vim/lsp.lua:1630: client_id: expected number, got nil
stack traceback:
        [C]: in function 'error'
        vim/shared.lua: in function 'validate'
        /app/share/nvim/runtime/lua/vim/lsp.lua:1630: in function 'buf_attach_client'
        ...im/data/nvim/site/pack/paqs/start/zk-nvim/lua/zk/lsp.lua:44: in function 'buf_add'
        ...m.nvim/data/nvim/site/pack/paqs/start/zk-nvim/lua/zk.lua:33: in function '_lsp_buf_auto_add'
        [string ":lua"]:1: in main chunk
        [C]: in function 'nvim_cmd'
        /app/share/nvim/runtime/filetype.lua:22: in function </app/share/nvim/runtime/filetype.lua:21>
        [C]: in function 'nvim_buf_call'
        /app/share/nvim/runtime/filetype.lua:21: in function </app/share/nvim/runtime/filetype.lua:10>
stack traceback:
        [C]: in function 'nvim_cmd'
        /app/share/nvim/runtime/filetype.lua:22: in function </app/share/nvim/runtime/filetype.lua:21>
        [C]: in function 'nvim_buf_call'
        /app/share/nvim/runtime/filetype.lua:21: in function </app/share/nvim/runtime/filetype.lua:10>
stack traceback:
        [C]: in function 'nvim_buf_call'
        /app/share/nvim/runtime/filetype.lua:21: in function </app/share/nvim/runtime/filetype.lua:10>
Press ENTER or type command to continue

Here is my nvim init config ~/.config/nvim/init.lua:

require "paq" {
  "savq/paq-nvim";                  -- Let Paq manage itself
  "neovim/nvim-lspconfig";          -- Mind the semi-colons
  "mickael-menu/zk-nvim";
  "hrsh7th/nvim-cmp";
  "hrsh7th/cmp-vsnip";
  "hrsh7th/vim-vsnip";
  'hrsh7th/cmp-nvim-lsp';
  'hrsh7th/cmp-buffer';
  'hrsh7th/cmp-path';
  'hrsh7th/cmp-cmdline';
  'hrsh7th/nvim-cmp';
  'junegunn/fzf';
  'windwp/nvim-autopairs'; -- for brackets autocomplete
  'nvim-tree/nvim-web-devicons'; -- Recommended (for coloured icons)
  {'akinsho/bufferline.nvim', tag = "v3.*", requires = 'nvim-tree/nvim-web-devicons'};
  {
    "kylechui/nvim-surround",
    tag = "*", -- Use for stability; omit to use `main` branch for the latest features
    config = function()
        require("nvim-surround").setup({
            -- Configuration here, or leave empty to use defaults
        })
    end
};
  "ixru/nvim-markdown";
  'projekt0n/github-nvim-theme'; -- great theme
  {'nvim-treesitter/nvim-treesitter', run = ':TSUpdate'}; -- for better syntax highlighting
  'nvim-tree/nvim-web-devicons'; -- For file icons
  'ibhagwan/fzf-lua'; -- File search

{
   "iamcco/markdown-preview.nvim",
   run = function() vim.fn["mkdp#util#install"]() end
};
}

require("keybindings")

-- useful options
require("setup")

-- zk and cmp must be before lsp
require('plugs.zk')
require('plugs.cmp')
require('lsp')

-- plugins
require("plugs.bufferline")
require('plugs.vim_autopairs')
require("plugs.treesitter")

-- surround plugin
require("nvim-surround").setup{}

The nvim-zk config ~/.config/nvim/lua/plugs/zk.lua

require("zk").setup({
  -- can be "telescope", "fzf" or "select" (`vim.ui.select`)
  -- it's recommended to use "telescope" or "fzf"
  -- picker = "select",
  picker = "select",

  lsp = {
    -- `config` is passed to `vim.lsp.start_client(config)`
    config = {
      cmd = { "zk", "lsp" },
      name = "zk",
      -- on_attach = ...
      -- etc, see `:h vim.lsp.start_client()`
    },

    -- automatically attach buffers in a zk notebook that match the given filetypes
    auto_attach = {
      enabled = true,
      filetypes = { "markdown" },
    },
  },
})

And the LSP config ~/.config/nvim/lua/lsp.lua

-- LSP mapping 2023-02-05
-- Mappings.
-- See `:help vim.diagnostic.*` for documentation on any of the below functions
local opts = { noremap=true, silent=true }
vim.keymap.set('n', '<space>e', vim.diagnostic.open_float, opts)
vim.keymap.set('n', '[d', vim.diagnostic.goto_prev, opts)
vim.keymap.set('n', ']d', vim.diagnostic.goto_next, opts)
vim.keymap.set('n', '<space>q', vim.diagnostic.setloclist, opts)

-- Use an on_attach function to only map the following keys
-- after the language server attaches to the current buffer
local on_attach = function(client, bufnr)
  -- Enable completion triggered by <c-x><c-o>
  vim.api.nvim_buf_set_option(bufnr, 'omnifunc', 'v:lua.vim.lsp.omnifunc')

  -- Mappings.
  -- See `:help vim.lsp.*` for documentation on any of the below functions
  local bufopts = { noremap=true, silent=true, buffer=bufnr }
  vim.keymap.set('n', 'gD', vim.lsp.buf.declaration, bufopts)
  vim.keymap.set('n', 'gd', vim.lsp.buf.definition, bufopts)
  vim.keymap.set('n', 'K', vim.lsp.buf.hover, bufopts)
  vim.keymap.set('n', 'gi', vim.lsp.buf.implementation, bufopts)
  vim.keymap.set('n', '<C-k>', vim.lsp.buf.signature_help, bufopts)
  vim.keymap.set('n', '<space>wa', vim.lsp.buf.add_workspace_folder, bufopts)
  vim.keymap.set('n', '<space>wr', vim.lsp.buf.remove_workspace_folder, bufopts)
  vim.keymap.set('n', '<space>wl', function()
    print(vim.inspect(vim.lsp.buf.list_workspace_folders()))
  end, bufopts)
  vim.keymap.set('n', '<space>D', vim.lsp.buf.type_definition, bufopts)
  vim.keymap.set('n', '<space>rn', vim.lsp.buf.rename, bufopts)
  vim.keymap.set('n', '<space>ca', vim.lsp.buf.code_action, bufopts)
  vim.keymap.set('n', 'gr', vim.lsp.buf.references, bufopts)
  vim.keymap.set('n', '<space>f', function() vim.lsp.buf.format { async = true } end, bufopts)
end

local lsp_flags = {
  -- This is the default in Nvim 0.7+
  debounce_text_changes = 150,
}
require('lspconfig')['pyright'].setup{
    on_attach = on_attach,
    flags = lsp_flags,
}
require('lspconfig')['tsserver'].setup{
    on_attach = on_attach,
    flags = lsp_flags,
}
require('lspconfig')['rust_analyzer'].setup{
    on_attach = on_attach,
    flags = lsp_flags,
    -- Server-specific settings...
    settings = {
      ["rust-analyzer"] = {}
    }
}


  -- Set up lspconfig.
  local capabilities = require('cmp_nvim_lsp').default_capabilities()
  -- Replace <YOUR_LSP_SERVER> with each lsp server you've enabled.
  require('lspconfig')['zk'].setup {
    capabilities = capabilities,
    -- to use the mapping defined below
    on_attach = on_attach,
  }

During the nvim setup, I created symbolic links from ~/.var/app/io.neovim.nvim/config to ~/.config/nvim and from ~/.var/app/io.neovim.nvim/data to ~/.local/share/nvim.

I have also tried to give the Neovim Flatpak app acces to /usr/bin and to all user files, without success.

Am I missing something?

[mcDevnagh]

So the issue here is that the flatpak needs access to the zk executable, and it does not. I'm not sure of the rules for FlatPak sandboxing, but I'd imagine running arbitrary executables from the host machine is not allowed.

Have you tried installing zk via mason?

You could run into issues having multiple installs of zk: i.e. different versions of zk. However, if you only use zk through neovim, it should be fine.