first commit

apps/neovim/autopairs.lua

@@ -0,0 +1 @@
+require("nvim-autopairs").setup {}

apps/neovim/catppuccin.lua

@@ -0,0 +1,76 @@
+require("catppuccin").setup({
+    flavour = "auto", -- latte, frappe, macchiato, mocha
+    background = { -- :h background
+        light = "latte",
+        dark = "mocha",
+    },
+    transparent_background = false, -- disables setting the background color.
+    float = {
+        transparent = false, -- enable transparent floating windows
+        solid = false, -- use solid styling for floating windows, see |winborder|
+    },
+    show_end_of_buffer = false, -- shows the '~' characters after the end of buffers
+    term_colors = false, -- sets terminal colors (e.g. `g:terminal_color_0`)
+    dim_inactive = {
+        enabled = false, -- dims the background color of inactive window
+        shade = "dark",
+        percentage = 0.15, -- percentage of the shade to apply to the inactive window
+    },
+    no_italic = false, -- Force no italic
+    no_bold = false, -- Force no bold
+    no_underline = false, -- Force no underline
+    styles = { -- Handles the styles of general hi groups (see `:h highlight-args`):
+        comments = { "italic" }, -- Change the style of comments
+        conditionals = { "italic" },
+        loops = {},
+        functions = {},
+        keywords = {},
+        strings = {},
+        variables = {},
+        numbers = {},
+        booleans = {},
+        properties = {},
+        types = {},
+        operators = {},
+        -- miscs = {}, -- Uncomment to turn off hard-coded styles
+    },
+    lsp_styles = { -- Handles the style of specific lsp hl groups (see `:h lsp-highlight`).
+        virtual_text = {
+            errors = { "italic" },
+            hints = { "italic" },
+            warnings = { "italic" },
+            information = { "italic" },
+            ok = { "italic" },
+        },
+        underlines = {
+            errors = { "underline" },
+            hints = { "underline" },
+            warnings = { "underline" },
+            information = { "underline" },
+            ok = { "underline" },
+        },
+        inlay_hints = {
+            background = true,
+        },
+    },
+    color_overrides = {},
+    custom_highlights = {},
+    default_integrations = true,
+    auto_integrations = false,
+    integrations = {
+        cmp = true,
+        gitsigns = true,
+        nvimtree = true,
+        notify = false,
+        mini = {
+            enabled = true,
+            indentscope_color = "",
+        },
+        telescope = {
+            enabled = true,
+        },
+        lsp_trouble = true,
+    },
+})
+
+vim.cmd.colorscheme "catppuccin"

apps/neovim/cmp.lua

@@ -0,0 +1,86 @@
+-- https://github.com/hrsh7th/nvim-cmp
+local cmp = require'cmp'
+
+cmp.setup({
+  snippet = {
+    -- REQUIRED - you must specify a snippet engine
+    expand = function(args)
+      vim.fn["vsnip#anonymous"](args.body) -- For `vsnip` users.
+      -- require('luasnip').lsp_expand(args.body) -- For `luasnip` users.
+      -- require('snippy').expand_snippet(args.body) -- For `snippy` users.
+      -- vim.fn["UltiSnips#Anon"](args.body) -- For `ultisnips` users.
+      -- vim.snippet.expand(args.body) -- For native neovim snippets (Neovim v0.10+)
+
+      -- For `mini.snippets` users:
+      -- local insert = MiniSnippets.config.expand.insert or MiniSnippets.default_insert
+      -- insert({ body = args.body }) -- Insert at cursor
+      -- cmp.resubscribe({ "TextChangedI", "TextChangedP" })
+      -- require("cmp.config").set_onetime({ sources = {} })
+    end,
+  },
+  window = {
+    completion = cmp.config.window.bordered(),
+    documentation = cmp.config.window.bordered(),
+  },
+  mapping = cmp.mapping.preset.insert({
+    ['<C-b>'] = cmp.mapping.scroll_docs(-4),
+    ['<C-f>'] = cmp.mapping.scroll_docs(4),
+    ['<C-j>'] = cmp.mapping.complete(),
+    ['<C-e>'] = cmp.mapping.abort(),
+    ['<CR>'] = cmp.mapping.confirm({ select = true }), -- Accept currently selected item. Set `select` to `false` to only confirm explicitly selected items.
+  }),
+  sources = cmp.config.sources({
+    { name = 'nvim_lsp' },
+    { name = 'vsnip' }, -- For vsnip users.
+    -- { name = 'luasnip' }, -- For luasnip users.
+    -- { name = 'ultisnips' }, -- For ultisnips users.
+    -- { name = 'snippy' }, -- For snippy users.
+  }, {
+    { name = 'buffer' },
+  })
+})
+
+-- To use git you need to install the plugin petertriho/cmp-git and uncomment lines below
+-- Set configuration for specific filetype.
+--[[ cmp.setup.filetype('gitcommit', {
+  sources = cmp.config.sources({
+    { name = 'git' },
+  }, {
+    { name = 'buffer' },
+  })
+)
+require("cmp_git").setup() ]]-- 
+
+-- Use buffer source for `/` and `?` (if you enabled `native_menu`, this won't work anymore).
+cmp.setup.cmdline({ '/', '?' }, {
+  mapping = cmp.mapping.preset.cmdline(),
+  sources = {
+    { name = 'buffer' }
+  }
+})
+
+-- Use cmdline & path source for ':' (if you enabled `native_menu`, this won't work anymore).
+cmp.setup.cmdline(':', {
+  mapping = cmp.mapping.preset.cmdline(),
+  sources = cmp.config.sources({
+    { name = 'path' }
+  }, {
+    { name = 'cmdline' }
+  }),
+  matching = { disallow_symbol_nonprefix_matching = false }
+})
+
+-- Set up lspconfig.
+local capabilities = require('cmp_nvim_lsp').default_capabilities()
+
+function config_and_enable_lsp(language, extra_config)
+  --lsp_config = { capabilities = capabilities }
+  --vim.lsp.config(language, lsp_config)
+  vim.lsp.enable(language)
+end
+
+vim.lsp.config('*', {
+  capabilities = capabilities
+})
+
+

apps/neovim/default.nix

@@ -0,0 +1,113 @@
+{ config, pkgs, inputs, my-r,... }:
+let
+  nvim-config-store = builtins.filterSource (path: type: baseNameOf path != "default.nix") ./.;
+  nvim-config-files = builtins.attrNames (builtins.readDir nvim-config-store);
+  nvim-config-lis = map (path: builtins.readFile "${nvim-config-store}/${path}") (nvim-config-files);
+  nvim-config = builtins.concatStringsSep "\n" nvim-config-lis;
+
+in
+{
+  programs.neovim = {
+    enable = true;
+    defaultEditor = true;
+
+    plugins = with pkgs.vimPlugins; [
+      nvim-treesitter.withAllGrammars
+      nvim-lspconfig
+      telescope-nvim
+      nvim-cmp
+      cmp-nvim-lsp
+      nvim-tree-lua
+      which-key-nvim
+      trouble-nvim
+      kanagawa-nvim
+      lazygit-nvim
+      quarto-nvim
+      otter-nvim
+      otter-nvim
+      image-nvim
+      molten-nvim
+      toggleterm-nvim
+      markdown-preview-nvim
+      lualine-nvim
+      gitsigns-nvim
+      indent-blankline-nvim
+      guess-indent-nvim
+      nvim-autopairs
+      catppuccin-nvim
+    ];
+
+    extraLuaConfig = nvim-config;
+
+
+    extraPackages = with pkgs; [
+      #quarto
+      pyright
+      ripgrep
+      lua-language-server
+      rust-analyzer
+      lazygit
+      tectonic
+      imagemagick
+      jupyter
+      pnglatex
+      nil
+      nixfmt
+
+      rustc
+      cargo
+      rustfmt
+      clippy
+      rust-analyzer
+    ];
+
+    extraLuaPackages = p: with p; [
+      magick
+    ];
+
+    
+    extraPython3Packages = ps: with ps; [
+      pynvim
+      jupyter-client
+      cairosvg
+      pnglatex
+      plotly
+      pyperclip
+      ipython
+      nbformat
+    ];
+
+
+
+  };
+
+  xdg.dataFile."jupyter/kernels/ir-nix/kernel.json".text = ''
+    {
+      "argv": [
+        "${my-r.env}/bin/R",
+        "--slave",
+        "-e",
+        "IRkernel::main()",
+        "--args",
+        "{connection_file}"
+      ],
+      "display_name": "R (nix)",
+      "language": "R"
+    }
+  '';
+
+  home.file.".Rprofile".text = ''
+graphics::par(bg = "white")
+options(
+  jupyter.rich_display      = TRUE,
+  #jupyter.display_mimetypes = c("text/plain", "image/png", "text/latex"),
+  jupyter.display_mimetypes = c("text/plain", "image/png"),
+  jupyter.plot_mimetypes    = "image/png"
+)
+ '';
+
+  #sessionVariables = {
+  #  EDITOR = "nvim";
+  #  VISUAL = "nvim";
+  #};
+}

apps/neovim/diagnostic.lua

@@ -0,0 +1,21 @@
+local sign = function(opts)
+  vim.fn.sign_define(opts.name, {
+    texthl = opts.name,
+    text = opts.text,
+    numhl = ''
+  })
+end
+
+sign({name = 'DiagnosticSignError', text = '✘'})
+sign({name = 'DiagnosticSignWarn', text = '▲'})
+sign({name = 'DiagnosticSignHint', text = '⚑'})
+sign({name = 'DiagnosticSignInfo', text = '»'})
+
+vim.diagnostic.config({
+  virtual_text = false,
+  severity_sort = true,
+  float = {
+    border = 'rounded',
+    source = 'always',
+  },
+})

apps/neovim/gitsigns.lua

@@ -0,0 +1,66 @@
+require('gitsigns').setup{
+  on_attach = function(bufnr)
+    local gitsigns = require('gitsigns')
+
+    local function map(mode, l, r, opts)
+      opts = opts or {}
+      opts.buffer = bufnr
+      vim.keymap.set(mode, l, r, opts)
+    end
+
+    -- Navigation
+    map('n', ']c', function()
+      if vim.wo.diff then
+        vim.cmd.normal({']c', bang = true})
+      else
+        gitsigns.nav_hunk('next')
+      end
+    end)
+
+    map('n', '[c', function()
+      if vim.wo.diff then
+        vim.cmd.normal({'[c', bang = true})
+      else
+        gitsigns.nav_hunk('prev')
+      end
+    end)
+
+    -- Actions
+    map('n', '<leader>hs', gitsigns.stage_hunk)
+    map('n', '<leader>hr', gitsigns.reset_hunk)
+
+    map('v', '<leader>hs', function()
+      gitsigns.stage_hunk({ vim.fn.line('.'), vim.fn.line('v') })
+    end)
+
+    map('v', '<leader>hr', function()
+      gitsigns.reset_hunk({ vim.fn.line('.'), vim.fn.line('v') })
+    end)
+
+    map('n', '<leader>hS', gitsigns.stage_buffer)
+    map('n', '<leader>hR', gitsigns.reset_buffer)
+    map('n', '<leader>hp', gitsigns.preview_hunk)
+    map('n', '<leader>hi', gitsigns.preview_hunk_inline)
+
+    map('n', '<leader>hb', function()
+      gitsigns.blame_line({ full = true })
+    end)
+
+    map('n', '<leader>hd', gitsigns.diffthis)
+
+    map('n', '<leader>hD', function()
+      gitsigns.diffthis('~')
+    end)
+
+    map('n', '<leader>hQ', function() gitsigns.setqflist('all') end)
+    map('n', '<leader>hq', gitsigns.setqflist)
+
+    -- Toggles
+    map('n', '<leader>tb', gitsigns.toggle_current_line_blame)
+    map('n', '<leader>tw', gitsigns.toggle_word_diff)
+
+
+    -- Text object
+    map({'o', 'x'}, 'ih', gitsigns.select_hunk)
+  end
+}

apps/neovim/guess-indent.lua

@@ -0,0 +1 @@
+require("guess-indent").setup {}

apps/neovim/ibl.lua

@@ -0,0 +1,10 @@
+require("ibl").setup {
+  indent = {
+    char = "",
+    highlight = "IblIndent",
+  }
+}
+--│, ┆, ⋅, ╎
+
+-- Use very subtle color
+vim.api.nvim_set_hl(0, "IblIndent", { fg = "#3a3a3a" })

apps/neovim/init.lua

@@ -0,0 +1,61 @@
+vim.g.mapleader = ' '
+vim.g.maplocalleader = ' '
+
+vim.g.have_nerd_font = true
+
+vim.o.number = true
+
+vim.o.mouse = 'a'
+
+--vim.o.showmode = false
+
+vim.schedule(function()
+  vim.o.clipboard = 'unnamedplus'
+end)
+
+
+vim.o.breakindent = true
+vim.o.undofile = true
+
+vim.o.ignorecase = true
+vim.o.smartcase = true
+
+vim.o.signcolumn = 'yes'
+
+vim.o.colorcolumn = "80"
+
+vim.o.updatetime = 250
+
+vim.o.timeoutlen = 300
+
+vim.o.splitright = true
+vim.o.splitbelow = true
+
+vim.o.list = true
+vim.opt.listchars = { tab = '» ', trail = '·', nbsp = '␣' }
+
+vim.o.inccommand = 'split'
+
+vim.o.cursorline = true
+
+vim.o.scrolloff = 15
+
+vim.o.confirm = true
+
+vim.keymap.set('i', 'jk', '<Escape>')
+vim.keymap.set('i', 'kj', '<Escape>')
+--vim.keymap.set('i', 'jf', '<Escape>')
+
+
+--  See `:help wincmd` for a list of all window commands
+vim.keymap.set('n', '<C-h>', '<C-w><C-h>', { desc = 'Move focus to the left window' })
+vim.keymap.set('n', '<C-l>', '<C-w><C-l>', { desc = 'Move focus to the right window' })
+vim.keymap.set('n', '<C-j>', '<C-w><C-j>', { desc = 'Move focus to the lower window' })
+vim.keymap.set('n', '<C-k>', '<C-w><C-k>', { desc = 'Move focus to the upper window' })
+
+
+
+vim.o.tabstop = 2
+vim.o.smartindent = true
+vim.o.shiftwidth = 2
+vim.o.expandtab = true

apps/neovim/lazygit.lua

@@ -0,0 +1,14 @@
+vim.g.lazygit_floating_window_winblend = 0 -- transparency of floating window
+vim.g.lazygit_floating_window_scaling_factor = 0.9 -- scaling factor for floating window
+vim.g.lazygit_floating_window_border_chars = {'╭','─', '╮', '│', '╯','─', '╰', '│'} -- customize lazygit popup window border characters
+vim.g.lazygit_floating_window_use_plenary = 0 -- use plenary.nvim to manage floating window if available
+vim.g.lazygit_use_neovim_remote = 1 -- fallback to 0 if neovim-remote is not installed
+
+vim.g.lazygit_use_custom_config_file_path = 0 -- config file path is evaluated if this value is 1
+vim.g.lazygit_config_file_path = '' -- custom config file path
+-- OR
+vim.g.lazygit_config_file_path = {} -- table of custom config file paths
+
+vim.g.lazygit_on_exit_callback = nil -- optional function callback when exiting lazygit (useful for example to refresh some UI elements after lazy git has made some changes)
+
+vim.keymap.set("n", "<Leader>gg", ":LazyGit<CR>", { desc = "LazyGit" })

apps/neovim/lsp.lua

@@ -0,0 +1,101 @@
+local lspconfig = require('lspconfig')
+
+vim.lsp.config('lua_ls', { cmd = { 'lua-language-server' },
+  settings = {
+    Lua = {
+      runtime = {
+        version = 'LuaJIT',
+        path = vim.split(package.path, ';'),
+      },
+      diagnostics = {
+        globals = { 'vim' },
+      },
+    },
+  },
+})
+
+vim.lsp.config('rust_analyzer', {
+  settings = {
+    ['rust-analyzer'] = {
+      diagnostics = {
+        enable = true;
+      };
+    };
+  }
+})
+
+
+
+local languages = {
+  'rust_analyzer',
+  'r_language_server',
+  'lua_ls',
+  'quarto',
+  'nil_ls',
+  'pyright'
+}
+
+for _, language in ipairs(languages) do
+  vim.lsp.enable(language)
+end
+
+vim.diagnostic.config {
+  severity_sort = true,
+  float = { border = 'rounded', source = 'if_many' },
+  underline = { severity = vim.diagnostic.severity.ERROR },
+  signs = vim.g.have_nerd_font and {
+    text = {
+      [vim.diagnostic.severity.ERROR] = '󰅚 ',
+      [vim.diagnostic.severity.WARN] = '󰀪 ',
+      [vim.diagnostic.severity.INFO] = '󰋽 ',
+      [vim.diagnostic.severity.HINT] = '󰌶 ',
+    },
+  } or {},
+  virtual_text = {
+    source = 'if_many',
+    spacing = 2,
+    format = function(diagnostic)
+      local diagnostic_message = {
+        [vim.diagnostic.severity.ERROR] = diagnostic.message,
+        [vim.diagnostic.severity.WARN] = diagnostic.message,
+        [vim.diagnostic.severity.INFO] = diagnostic.message,
+        [vim.diagnostic.severity.HINT] = diagnostic.message,
+      }
+      return diagnostic_message[diagnostic.severity]
+    end,
+  },
+} 
+
+vim.api.nvim_create_autocmd("LspAttach", {
+  callback = function(event)
+    local buf = event.buf
+    local opts = function(desc)
+      return { buffer = buf, desc = desc }
+    end
+
+    -- Jumping + finding
+    vim.keymap.set("n", "gd", vim.lsp.buf.definition, opts("[G]oto Definition"))
+    vim.keymap.set("n", "gD", vim.lsp.buf.declaration, opts("Goto [D]eclaration"))
+    vim.keymap.set("n", "gi", vim.lsp.buf.implementation, opts("[G]oto [I]mplementation"))
+    vim.keymap.set("n", "gr", vim.lsp.buf.references, opts("[G]oto [R]eferences"))
+
+    -- Info + documentation
+    vim.keymap.set("n", "K", vim.lsp.buf.hover, opts("Hover Documentation"))
+    vim.keymap.set("n", "<C-k>", vim.lsp.buf.signature_help, opts("Signature Help"))
+
+    -- Actions + rename
+    vim.keymap.set("n", "<leader>rn", vim.lsp.buf.rename, opts("[R]e[n]ame"))
+    vim.keymap.set({ "n", "v" }, "<leader>ca", vim.lsp.buf.code_action, opts("[C]ode [A]ction"))
+
+    -- Diagnostics navigation
+    vim.keymap.set("n", "[d", vim.diagnostic.goto_prev, opts("Prev Diagnostic"))
+    vim.keymap.set("n", "]d", vim.diagnostic.goto_next, opts("Next Diagnostic"))
+    vim.keymap.set("n", "<leader>e", vim.diagnostic.open_float, opts("Show Error"))
+    vim.keymap.set("n", "<leader>q", vim.diagnostic.setloclist, opts("Diagnostic Quickfix"))
+
+    -- Formatting
+    vim.keymap.set("n", "<leader>f", function()
+      vim.lsp.buf.format({ async = true })
+    end, opts("[F]ormat Buffer"))
+  end,
+})

apps/neovim/lua-line.lua

@@ -0,0 +1,54 @@
+require('lualine').setup {
+  options = {
+    icons_enabled = true,
+    theme = 'auto',
+    component_separators = { left = '', right = ''},
+    section_separators = { left = '', right = ''},
+    disabled_filetypes = {
+      statusline = {},
+      winbar = {},
+    },
+    ignore_focus = {},
+    always_divide_middle = true,
+    always_show_tabline = true,
+    globalstatus = false,
+    refresh = {
+      statusline = 1000,
+      tabline = 1000,
+      winbar = 1000,
+      refresh_time = 16, -- ~60fps
+      events = {
+        'WinEnter',
+        'BufEnter',
+        'BufWritePost',
+        'SessionLoadPost',
+        'FileChangedShellPost',
+        'VimResized',
+        'Filetype',
+        'CursorMoved',
+        'CursorMovedI',
+        'ModeChanged',
+      },
+    }
+  },
+  sections = {
+    lualine_a = {'mode'},
+    lualine_b = {'branch', 'diff', 'diagnostics'},
+    lualine_c = {'filename'},
+    lualine_x = {'encoding', 'fileformat', 'filetype'},
+    lualine_y = {'progress'},
+    lualine_z = {'location'}
+  },
+  inactive_sections = {
+    lualine_a = {},
+    lualine_b = {},
+    lualine_c = {'filename'},
+    lualine_x = {'location'},
+    lualine_y = {},
+    lualine_z = {}
+  },
+  tabline = {},
+  winbar = {},
+  inactive_winbar = {},
+  extensions = {}
+}

apps/neovim/molten.lua

@@ -0,0 +1,48 @@
+vim.g.molten_auto_open_output = true
+vim.g.molten_wrap_output = true
+vim.g.molten_output_show_exec_time = true
+vim.g.molten_output_win_hide_on_leave = false
+vim.g.molten_use_border_highlights = true
+vim.g.molten_virt_text_output = true
+vim.g.molten_image_provider = "image.nvim"
+vim.g.molten_image_location = "both"
+vim.g.molten_output_virt_lines = true
+vim.g.molten_cover_empty_lines = true
+vim.g.molten_output_truncate = "bottom" 
+vim.g.molten_virt_text_max_lines = 20
+--vim.g.molten_output = "pane"
+
+vim.api.nvim_set_hl(0, "NormalFloat", { bg = "#1e1e2e" })
+vim.api.nvim_set_hl(0, "FloatBorder", { bg = "#1e1e2e" })
+-- vim.api.nvim_set_hl(0, "MoltenVirtualText", {
+--     bg = "#ae0606",
+--     fg = "#ffd787",
+--     italic = true,
+-- })
+
+require("image").setup({
+  editor = {
+    -- force a visible background for plots
+    background = "white",      -- or "#ffffff" or "black"
+    inline = {
+      enable = true,
+    };
+  },
+})
+
+vim.keymap.set("n", "<localleader>mi", ":MoltenInit<CR>",
+    { silent = true, desc = "Initialize the plugin" })
+vim.keymap.set("n", "<localleader>e", ":MoltenEvaluateOperator<CR>",
+    { silent = true, desc = "run operator selection" })
+vim.keymap.set("n", "<localleader>rl", ":MoltenEvaluateLine<CR>",
+    { silent = true, desc = "evaluate line" })
+vim.keymap.set("n", "<localleader>rr", ":MoltenReevaluateCell<CR>",
+    { silent = true, desc = "re-evaluate cell" })
+vim.keymap.set("v", "<localleader>r", ":<C-u>MoltenEvaluateVisual<CR>gv",
+    { silent = true, desc = "evaluate visual selection" }) 
+vim.keymap.set("n", "<localleader>rd", ":MoltenDelete<CR>",
+    { silent = true, desc = "molten delete cell" })
+vim.keymap.set("n", "<localleader>oh", ":MoltenHideOutput<CR>",
+    { silent = true, desc = "hide output" })
+vim.keymap.set("n", "<localleader>os", ":noautocmd MoltenEnterOutput<CR>",
+    { silent = true, desc = "show/enter output" })

apps/neovim/nvim-tree.lua

@@ -0,0 +1,25 @@
+-- disable netrw at the very start of your init.lua
+vim.g.loaded_netrw = 1
+vim.g.loaded_netrwPlugin = 1
+
+-- optionally enable 24-bit colour
+vim.opt.termguicolors = true
+
+
+-- OR setup with some options
+require("nvim-tree").setup({
+  sort = {
+    sorter = "case_sensitive",
+  },
+  view = {
+    width = 30,
+  },
+  renderer = {
+    group_empty = true,
+  },
+  filters = {
+    dotfiles = true,
+  },
+})
+
+vim.keymap.set('n', '<Leader>d', ':NvimTreeToggle<CR>', { desc = 'Open or close the tree' })

apps/neovim/otter.lua

@@ -0,0 +1,5 @@
+require("otter").setup({
+  buffers = {
+    write_to_disk = true,
+  },
+})

apps/neovim/quarto.lua

@@ -0,0 +1,37 @@
+local quarto = require('quarto')
+require('quarto').setup{
+  debug = true,
+  lspFeatures = {
+    enabled = true,
+    hover = true,
+    chunks = "curly",
+    languages = { "r", "python", "julia", "bash", "html" },
+    diagnostics = {
+      enabled = false,
+      lint_cache = false,
+      triggers = { "BufWritePost" },
+    },
+    completion = {
+      enabled = true,
+    },
+  },
+  codeRunner = {
+    enabled = true,
+    default_method = "molten", -- "molten", "slime", "iron" or <function>
+    ft_runners = { r = "molten", python = "molten" }, -- filetype to runner, ie. `{ python = "molten" }`.
+    -- Takes precedence over `default_method`
+    never_run = { 'yaml' }, -- filetypes which are never sent to a code runner
+  },
+}
+
+vim.keymap.set('n', '<leader>qp', quarto.quartoPreview, { silent = true, noremap = true })
+
+local runner = require("quarto.runner")
+vim.keymap.set("n", "<localleader>rr", runner.run_cell,  { desc = "run cell", silent = true })
+vim.keymap.set("n", "<localleader>ra", runner.run_above, { desc = "run cell and above", silent = true })
+vim.keymap.set("n", "<localleader>rR", runner.run_all,   { desc = "run all cells", silent = true })
+vim.keymap.set("n", "<localleader>rl", runner.run_line,  { desc = "run line", silent = true })
+vim.keymap.set("v", "<localleader>r",  runner.run_range, { desc = "run visual range", silent = true })
+vim.keymap.set("n", "<localleader>RA", function()
+  runner.run_all(true)
+end, { desc = "run all cells of all languages", silent = true })

apps/neovim/telescope.lua

@@ -0,0 +1,36 @@
+local builtin = require('telescope.builtin')
+vim.keymap.set('n', '<leader>ff', builtin.find_files, { desc = 'Telescope find files' })
+vim.keymap.set('n', '<leader>fg', builtin.live_grep, { desc = 'Telescope live grep' })
+vim.keymap.set('n', '<leader>fb', builtin.buffers, { desc = 'Telescope buffers' })
+vim.keymap.set('n', '<leader>fh', builtin.help_tags, { desc = 'Telescope help tags' })
+
+require('telescope').setup{
+  defaults = {
+    -- Default configuration for telescope goes here:
+    -- config_key = value,
+    mappings = {
+      i = {
+        -- map actions.which_key to <C-h> (default: <C-/>)
+        -- actions.which_key shows the mappings for your picker,
+        -- e.g. git_{create, delete, ...}_branch for the git_branches picker
+        ["<C-h>"] = "which_key"
+      }
+    }
+  },
+  pickers = {
+    -- Default configuration for builtin pickers goes here:
+    -- picker_name = {
+    --   picker_config_key = value,
+    --   ...
+    -- }
+    -- Now the picker_config_key will be applied every time you call this
+    -- builtin picker
+  },
+  extensions = {
+    -- Your extension configuration goes here:
+    -- extension_name = {
+    --   extension_config_key = value,
+    -- }
+    -- please take a look at the readme of the extension you want to configure
+  }
+}

apps/neovim/toggleterm.lua

@@ -0,0 +1,5 @@
+require("toggleterm").setup()
+
+vim.keymap.set("n", "<Leader>tt", '<cmd>ToggleTerm direction=float<CR>', { noremap = ture, silent = true })
+vim.keymap.set("n", "<Leader>tv", '<cmd>ToggleTerm direction=vertical<CR>', { noremap = ture, silent = true })
+vim.keymap.set("n", "<Leader>th", '<cmd>ToggleTerm direction=horizontal<CR>', { noremap = ture, silent = true })

apps/neovim/treesitter.lua

@@ -0,0 +1,23 @@
+vim.api.nvim_create_autocmd("FileType", {
+  pattern = "*",
+  callback = function()
+    local ft = vim.bo.filetype
+    local lang = vim.treesitter.language.get_lang(ft)
+
+    if not lang or not vim.treesitter.language.add(lang) then
+      return
+    end
+
+    vim.treesitter.start()
+
+    -- Set folding if available
+    if vim.treesitter.query.get(lang, "folds") then
+      vim.wo.foldexpr = "v:lua.vim.treesitter.foldexpr()"
+    end
+
+    -- Set indentation if available (overrides traditional indent)
+    if vim.treesitter.query.get(lang, "indents") then
+      vim.bo.indentexpr = "nvim_treesitter#indent()"
+    end
+  end
+})

apps/neovim/trouble.lua

@@ -0,0 +1,204 @@
+---@class trouble.Mode: trouble.Config,trouble.Section.spec
+---@field desc? string
+---@field sections? string[]
+
+---@class trouble.Config
+---@field mode? string
+---@field config? fun(opts:trouble.Config)
+---@field formatters? table<string,trouble.Formatter> custom formatters
+---@field filters? table<string, trouble.FilterFn> custom filters
+---@field sorters? table<string, trouble.SorterFn> custom sorters
+local defaults = {
+  auto_close = false, -- auto close when there are no items
+  auto_open = false, -- auto open when there are items
+  auto_preview = true, -- automatically open preview when on an item
+  auto_refresh = true, -- auto refresh when open
+  auto_jump = false, -- auto jump to the item when there's only one
+  focus = false, -- Focus the window when opened
+  restore = true, -- restores the last location in the list when opening
+  follow = true, -- Follow the current item
+  indent_guides = true, -- show indent guides
+  max_items = 200, -- limit number of items that can be displayed per section
+  multiline = true, -- render multi-line messages
+  pinned = false, -- When pinned, the opened trouble window will be bound to the current buffer
+  warn_no_results = true, -- show a warning when there are no results
+  open_no_results = false, -- open the trouble window when there are no results
+  ---@type trouble.Window.opts
+  win = {}, -- window options for the results window. Can be a split or a floating window.
+  -- Window options for the preview window. Can be a split, floating window,
+  -- or `main` to show the preview in the main editor window.
+  ---@type trouble.Window.opts
+  preview = {
+    type = "main",
+    -- when a buffer is not yet loaded, the preview window will be created
+    -- in a scratch buffer with only syntax highlighting enabled.
+    -- Set to false, if you want the preview to always be a real loaded buffer.
+    scratch = true,
+  },
+  -- Throttle/Debounce settings. Should usually not be changed.
+  ---@type table<string, number|{ms:number, debounce?:boolean}>
+  throttle = {
+    refresh = 20, -- fetches new data when needed
+    update = 10, -- updates the window
+    render = 10, -- renders the window
+    follow = 100, -- follows the current item
+    preview = { ms = 100, debounce = true }, -- shows the preview for the current item
+  },
+  -- Key mappings can be set to the name of a builtin action,
+  -- or you can define your own custom action.
+  ---@type table<string, trouble.Action.spec|false>
+  keys = {
+    ["?"] = "help",
+    r = "refresh",
+    R = "toggle_refresh",
+    q = "close",
+    o = "jump_close",
+    ["<esc>"] = "cancel",
+    ["<cr>"] = "jump",
+    ["<2-leftmouse>"] = "jump",
+    ["<c-s>"] = "jump_split",
+    ["<c-v>"] = "jump_vsplit",
+    -- go down to next item (accepts count)
+    -- j = "next",
+    ["}"] = "next",
+    ["]]"] = "next",
+    -- go up to prev item (accepts count)
+    -- k = "prev",
+    ["{"] = "prev",
+    ["[["] = "prev",
+    dd = "delete",
+    d = { action = "delete", mode = "v" },
+    i = "inspect",
+    p = "preview",
+    P = "toggle_preview",
+    zo = "fold_open",
+    zO = "fold_open_recursive",
+    zc = "fold_close",
+    zC = "fold_close_recursive",
+    za = "fold_toggle",
+    zA = "fold_toggle_recursive",
+    zm = "fold_more",
+    zM = "fold_close_all",
+    zr = "fold_reduce",
+    zR = "fold_open_all",
+    zx = "fold_update",
+    zX = "fold_update_all",
+    zn = "fold_disable",
+    zN = "fold_enable",
+    zi = "fold_toggle_enable",
+    gb = { -- example of a custom action that toggles the active view filter
+      action = function(view)
+        view:filter({ buf = 0 }, { toggle = true })
+      end,
+      desc = "Toggle Current Buffer Filter",
+    },
+    s = { -- example of a custom action that toggles the severity
+      action = function(view)
+        local f = view:get_filter("severity")
+        local severity = ((f and f.filter.severity or 0) + 1) % 5
+        view:filter({ severity = severity }, {
+          id = "severity",
+          template = "{hl:Title}Filter:{hl} {severity}",
+          del = severity == 0,
+        })
+      end,
+      desc = "Toggle Severity Filter",
+    },
+  },
+  ---@type table<string, trouble.Mode>
+  modes = {
+    -- sources define their own modes, which you can use directly,
+    -- or override like in the example below
+    lsp_references = {
+      -- some modes are configurable, see the source code for more details
+      params = {
+        include_declaration = true,
+      },
+    },
+    -- The LSP base mode for:
+    -- * lsp_definitions, lsp_references, lsp_implementations
+    -- * lsp_type_definitions, lsp_declarations, lsp_command
+    lsp_base = {
+      params = {
+        -- don't include the current location in the results
+        include_current = false,
+      },
+    },
+    -- more advanced example that extends the lsp_document_symbols
+    symbols = {
+      desc = "document symbols",
+      mode = "lsp_document_symbols",
+      focus = false,
+      win = { position = "right" },
+      filter = {
+        -- remove Package since luals uses it for control flow structures
+        ["not"] = { ft = "lua", kind = "Package" },
+        any = {
+          -- all symbol kinds for help / markdown files
+          ft = { "help", "markdown" },
+          -- default set of symbol kinds
+          kind = {
+            "Class",
+            "Constructor",
+            "Enum",
+            "Field",
+            "Function",
+            "Interface",
+            "Method",
+            "Module",
+            "Namespace",
+            "Package",
+            "Property",
+            "Struct",
+            "Trait",
+          },
+        },
+      },
+    },
+  },
+  -- stylua: ignore
+  icons = {
+    ---@type trouble.Indent.symbols
+    indent = {
+      top           = "│ ",
+      middle        = "├╴",
+      last          = "└╴",
+      -- last          = "-╴",
+      -- last       = "╰╴", -- rounded
+      fold_open     = " ",
+      fold_closed   = " ",
+      ws            = "  ",
+    },
+    folder_closed   = " ",
+    folder_open     = " ",
+    kinds = {
+      Array         = " ",
+      Boolean       = "󰨙 ",
+      Class         = " ",
+      Constant      = "󰏿 ",
+      Constructor   = " ",
+      Enum          = " ",
+      EnumMember    = " ",
+      Event         = " ",
+      Field         = " ",
+      File          = " ",
+      Function      = "󰊕 ",
+      Interface     = " ",
+      Key           = " ",
+      Method        = "󰊕 ",
+      Module        = " ",
+      Namespace     = "󰦮 ",
+      Null          = " ",
+      Number        = "󰎠 ",
+      Object        = " ",
+      Operator      = " ",
+      Package       = " ",
+      Property      = " ",
+      String        = " ",
+      Struct        = "󰆼 ",
+      TypeParameter = " ",
+      Variable      = "󰀫 ",
+    },
+  },
+}
+

apps/neovim/which-key.lua

@@ -0,0 +1 @@
+local wk = require("which-key")