added latex support and reorg ftplugins

after/queries/markdown/highlights.scm

@@ -0,0 +1,2 @@
+;extend
+

after/queries/markdown/textobjects.scm

@@ -0,0 +1,6 @@
+;extends
+
+(fenced_code_block (code_fence_content) @class.inner) @class.outer
+
+(paragraph) @function.outer @function.inner
+

after/queries/markdown_inline/highlights.scm

@@ -0,0 +1,13 @@
+;extends
+
+[
+  (shortcut_link)
+] @nospell
+
+(strikethrough
+(emphasis_delimiter)
+(strikethrough
+  (emphasis_delimiter)
+  (emphasis_delimiter))
+(emphasis_delimiter))@markup.doublestrikethrough
+

after/queries/norg/injections.scm

@@ -0,0 +1,12 @@
+; Injection for code blocks
+(ranged_verbatim_tag (tag_name) @_tagname (tag_parameters .(tag_param) @injection.language) (ranged_verbatim_tag_content) @injection.content (#any-of? @_tagname "code" "embed"))
+(ranged_verbatim_tag (tag_name) @_tagname (tag_parameters)? (ranged_verbatim_tag_content) @injection.content (#eq? @_tagname "math") (#set! injection.language "latex"))
+
+(
+    (inline_math) @injection.content
+    (#offset! @injection.content 0 1 0 -1)
+    (#set! injection.language "latex")
+)
+
+(ranged_verbatim_tag (tag_name) @_tagname (ranged_verbatim_tag_content) @injection.content (#eq? @_tagname "document.meta") (#set! injection.language "norg_meta"))
+

after/queries/python/highlights.scm

@@ -0,0 +1,12 @@
+;extends
+(
+(comment) @comment
+(#match? @comment "^\\#\\|")
+) @text.literal
+
+
+(
+(comment) @content
+(#match? @content "^\\# ?\\%\\%")
+) @class.outer @text.literal
+

after/queries/python/textobjects.scm

@@ -0,0 +1,7 @@
+;extends
+
+(
+(comment) @content1
+(#match? @content1 "^\\# ?\\%\\%")
+) @class.inner
+

after/queries/r/highlights.scm

@@ -0,0 +1,6 @@
+;extends
+(
+(comment) @comment
+(#match? @comment "^\\#\\|")
+) @text.literal
+

after/queries/r/textobjects.scm

@@ -0,0 +1,7 @@
+;extends
+
+(
+(comment) @content1
+(#match? @content1 "^\\# ?\\%\\%")
+) @class.inner
+

after/queries/rust/injections.scm

@@ -0,0 +1,15 @@
+;extends
+(macro_invocation
+(scoped_identifier
+path: (identifier) @path (#eq? @path "sqlx")
+name: (identifier) @name (#match? @name "^query.*")
+)
+
+(token_tree
+(raw_string_literal) @injection.content
+(#set! injection.language "sql")
+(#set! injection.include-children)
+)
+(#offset! @injection.content 0 3 0 -2)
+)
+

ftplugin/lua.lua

@@ -1,6 +1,6 @@
 vim.opt.expandtab = true
-vim.opt.shiftwidth = 2
+vim.opt.shiftwidth = 4
-vim.opt.tabstop = 2
+vim.opt.tabstop = 4
 vim.opt.expandtab = true
 
 vim.opt_local.formatoptions:remove('o')

init.lua

@@ -13,6 +13,8 @@ if not vim.loop.fs_stat(lazypath) then
 end
 vim.opt.rtp:prepend(vim.env.LAZY or lazypath)
 
+vim.cmd('filetype plugin on')
+
 vim.g.mapleader = ' '
 vim.g.maplocalleader = ' '
 
@@ -23,4 +25,3 @@ require('config.mappings')
 require('config.utils')
 require('config.themes')
 
-vim.cmd('filetype plugin on')

lua/config/autocmds.lua

@@ -64,3 +64,29 @@ vim.cmd([[
   autocmd TermOpen * tnoremap <Esc> <C-\><C-n>
 ]])
 
+-- Open PDF in the background when a .tex file is opened
+vim.api.nvim_create_autocmd("BufEnter", {
+  pattern = "*.tex",
+  callback = function()
+    -- Construct an absolute path to the PDF file
+    local pdf_path = vim.fn.expand('%:p:h') .. "/output/" .. vim.fn.expand('%:t:r') .. '.pdf'
+    if vim.fn.filereadable(pdf_path) == 1 then
+      -- Start Zathura asynchronously in the background with an absolute path
+      vim.fn.jobstart({ 'nohup', 'zathura', pdf_path, '>/dev/null', '2>&1', '&' }, { detach = true })
+    else
+      print("PDF file not found: " .. pdf_path)
+    end
+  end,
+})
+
+-- Close Zathura gracefully when leaving Neovim
+vim.api.nvim_create_autocmd("VimLeavePre", {
+  callback = function()
+    -- Attempt to terminate Zathura gracefully with a grace period
+    vim.fn.system({ 'pkill', '-TERM', '-f', 'zathura' })
+    vim.defer_fn(function()
+      vim.fn.system({ 'pkill', '-KILL', '-f', 'zathura' })
+    end, 2000) -- Wait for 2 seconds before force killing if necessary
+  end,
+})
+

lua/config/mappings.lua

@@ -37,6 +37,10 @@ vim.keymap.set('n', '<leader>bs', '<cmd>split<CR>', { desc = 'Openn Buf Horizont
 vim.keymap.set('n', '<leader>bv', '<cmd>vsp<CR>', { desc = 'Open Buf Vertical Split' })
 vim.keymap.set('n', '<leader>bt', '<cmd>terminal<CR>')
 
+-- -- open terminal for R and Python
+-- vim.keymap.set('n', '<leader>bR', '<cmd>terminal R<CR>', { desc = 'Open R Terminal' })
+-- vim.keymap.set('n', '<leader>bP', '<cmd>terminal python<CR>', { desc = 'Open Python Terminal' })
+
 -- Editing Keymaps
 vim.keymap.set('x', '<leader>p', [["_dP"]], { desc = 'Paste without register' })
 vim.keymap.set({ 'n', 'v' }, '<leader>d', [["_d"]], { desc = 'Delete without register' })
@@ -45,16 +49,16 @@ vim.keymap.set('n', '<leader>Y', '"+Y')
 -- replace current word in current scope
 vim.keymap.set(
   'n',
-  '<leader>r',
+  '<leader>rw',
   ':%s/\\<<C-r><C-w>\\>/<C-r><C-w>/gI<Left><Left><Left>',
-  { desc = '[R]eplace Current Word in Current Scope' }
+  { desc = '[R]eplace Current [W]ord in Current Scope' }
 )
 -- replace current word in file scope
 vim.keymap.set(
   'n',
-  '<leader>R',
+  '<leader>rW',
   ':%s/\\<<C-r><C-w>\\>/<C-r><C-w>/gI<Left><Left><Left>',
-  { desc = '[R]eplace Current Word in File Scope' }
+  { desc = '[R]eplace Current [W]ord in File Scope' }
 )
 
 -- Open vertical split pane
@@ -87,7 +91,7 @@ vim.keymap.set({ 'n', 'v' }, '<leader>sw', function()
 end, { desc = '[S]earch current [W]ord' })
 vim.keymap.set('n', '<leader>sp', function()
   require('telescope.builtin').grep_string({ search = vim.fn.input('Grep Search > ') })
-end, { desc = '[S]search [P]roject' })
+end, { desc = '[S]earch [P]roject' })
 vim.keymap.set('n', '<leader>sG', require('telescope.builtin').live_grep, { desc = '[S]earch by [G]rep' })
 vim.keymap.set('n', '<leader>sg', ':LiveGrepGitRoot<cr>', { desc = '[S]earch by [G]rep on Git Root' })
 vim.keymap.set('n', '<leader>sd', require('telescope.builtin').diagnostics, { desc = '[S]earch [D]iagnostics' })
@@ -97,13 +101,43 @@ vim.keymap.set('n', '<leader>sr', require('telescope.builtin').resume, { desc =
 -- Diagnostic keymaps
 vim.keymap.set('n', '[d', vim.diagnostic.goto_prev, { desc = 'Go to previous diagnostic message' })
 vim.keymap.set('n', ']d', vim.diagnostic.goto_next, { desc = 'Go to next diagnostic message' })
-vim.keymap.set('n', '<leader>e', vim.diagnostic.open_float, { desc = 'Open floating diagnostic message' })
+-- vim.keymap.set('n', '<leader>ef', vim.diagnostic.open_float, { desc = 'Open floating diagnostic message' })
--- vim.keymap.set('n', '<leader>vd', function()
+-- vim.keymap.set('n', '<leader>ee', function()
 --   vim.diagnostic.setloclist()
 --   vim.cmd('lopen')
 -- end, { desc = 'Open the diagnostics location list' })
 
--- Refactoring Keymaps
+-- local runner = require("quarto.runner")
+-- vim.keymap.set('n', '<leader>qrc', runner.run_cell, { desc = '[R]un [C]ell', silent = true })
+-- vim.keymap.set('n', '<leader>qra', runner.run_above, { desc = '[R]un cell and [A]bove', silent = true })
+-- vim.keymap.set('n', "<leader>qrA", runner.run_all, { desc = "run all cells", silent = true })
+-- vim.keymap.set('n', "<leader>qrl", runner.run_line, { desc = "run line", silent = true })
+-- vim.keymap.set('v', '<leader>qr', runner.run_range, { desc = "run visual range", silent = true })
+-- vim.keymap.set('n', '<leader>qRA', function()
+--   runner.run_all(true)
+-- end, { desc = "run all cells of all languages", silent = true })
+
+-- Latex-specific Keymaps
+-- Keybinding to compile LaTeX to PDF using xelatex with latexmk and output to the "output" directory
+vim.keymap.set('n', '<leader>ll', ':!mkdir -p output && latexmk -pdf -xelatex -output-directory=output -synctex=1 %<CR>',
+  {
+    desc = 'Compile LaTeX to PDF using xelatex with SyncTeX in the output directory',
+    noremap = true,
+    silent = true
+  })
+
+
+-- Keybinding to view the compiled PDF in Zathura from the output directory
+vim.keymap.set('n', '<leader>lv', function()
+  local pdf_path = vim.fn.expand('%:p:h') .. '/output/' .. vim.fn.expand('%:t:r') .. '.pdf'
+  vim.cmd(':silent !nohup zathura ' .. pdf_path .. ' >/dev/null 2>&1 &')
+end, {
+  desc = 'View PDF in Zathura from the output directory',
+  noremap = true,
+  silent = true
+})
+
+-- -- Refactoring Keymaps
 -- vim.keymap.set({ "x" }, "<leader>re", [[<Esc><Cmd>lua require('refactoring').refactor('Extract Function')<CR>]],
 --   { noremap = true, silent = true, expr = false, desc = "Extract Function" })
 -- vim.keymap.set({ "x" }, "<leader>rf", [[<Esc><Cmd>lua require('refactoring').refactor('Extract Function To File')<CR>]],

lua/config/utils.lua

@@ -1,6 +1,5 @@
-return {
 -- Function to get the current visual selection
-  get_visual_selection = function()
+local function get_visual_selection()
   vim.cmd 'noau normal! "vy"'
   local text = vim.fn.getreg 'v'
   vim.fn.setreg('v', {})
@@ -11,13 +10,18 @@ return {
   else
     return ''
   end
-  end,
+end
 
 -- Function to get the current search query
-  get_search_query = function()
+local function get_search_query()
   local word_under_cursor = vim.fn.expand '<cword>'
   local visual_selection = require('config.utils').get_visual_selection()
 
   return visual_selection ~= '' and visual_selection or word_under_cursor
-  end,
+end
+
+return {
+  get_visual_selection = get_visual_selection,
+  get_search_query = get_search_query,
 }
+

lua/custom/plugins/cmp.lua

@@ -21,15 +21,19 @@ return {
     -- Set completion options
     vim.opt.completeopt = { 'menu', 'menuone', 'noselect' }
 
-    -- Lazy load snippets from friendly-snippets
-    require('luasnip.loaders.from_vscode').lazy_load()
-
     -- Import required modules
     local cmp = require('cmp')
     local luasnip = require('luasnip')
 
     -- Setup luasnip
-    luasnip.config.setup({})
+    luasnip.config.setup({
+      history = true,
+      updateevents = 'TextChanged,TextChangedI',
+    })
+
+    -- Lazy load snippets from friendly-snippets and custom snippets
+    require('luasnip.loaders.from_vscode').lazy_load()
+    require('luasnip.loaders.from_vscode').load(vim.fn.stdpath('config') .. '/snippets')
 
     -- Setup nvim-cmp
     cmp.setup({
@@ -90,12 +94,6 @@ return {
       }),
     })
 
-    -- Additional luasnip configuration
-    luasnip.config.set_config({
-      history = true,
-      updateevents = 'TextChanged,TextChangedI',
-    })
-
     -- Setup for SQL filetype with vim-dadbod-completion
     cmp.setup.filetype('sql', {
       sources = cmp.config.sources({

lua/custom/plugins/formatting.lua

@@ -16,6 +16,10 @@ return {
         end
       end,
       go = { 'gofumpt', 'goimports' },
+      yaml = { 'prettier' },       -- Added YAML formatter
+      bash = { 'shfmt' },          -- Added Bash formatter
+      rust = { 'rustfmt' },        -- Added Rust formatter
+      dockerfile = { 'hadolint' }, -- Added Dockerfile formatter
     }
 
     require('conform').setup({
@@ -28,12 +32,15 @@ return {
 
     require('mason-tool-installer').setup({
       ensure_installed = {
-        'stylua',
+        'stylua',    -- Lua
-        'ruff',
+        'ruff',      -- Python
-        'isort',
+        'isort',     -- Python
-        'black',
+        'black',     -- Python
-        'gofumpt',
+        'gofumpt',   -- Go
-        'goimports',
+        'goimports', -- Go
+        'prettier',  -- YAML, JSON, etc.
+        'shfmt',     -- Bash
+        'hadolint',  -- Dockerfile
       },
     })
   end,

lua/custom/plugins/fugitive.lua

@@ -1,47 +1,46 @@
 return {
   'tpope/vim-fugitive',
   config = function()
-    vim.keymap.set('n', '<leader>gs', vim.cmd.Git)
+    -- General key mappings for Fugitive
+    vim.keymap.set('n', '<leader>gs', vim.cmd.Git, { desc = 'Open Git status' })
 
-    local jfraeys_fugitive = vim.api.nvim_create_augroup('jfraeys_fugitive', {})
+    -- Create an autocommand group for Fugitive-specific settings
+    local fugitive_augroup = vim.api.nvim_create_augroup('fugitive', { clear = true })
 
-    local autocmd = vim.api.nvim_create_autocmd
+    -- Set up autocommands for Fugitive buffers
-    autocmd('BufWinEnter', {
+    vim.api.nvim_create_autocmd('BufWinEnter', {
-      group = jfraeys_fugitive,
+      group = fugitive_augroup,
       pattern = '*',
       callback = function()
-        if vim.bo.ft ~= 'fugitive' then
+        if vim.bo.ft ~= 'fugitive' then return end
-          return
-        end
 
         local bufnr = vim.api.nvim_get_current_buf()
         local opts = { buffer = bufnr, remap = false }
 
-        vim.keymap.set('n', '<leader>p', function()
+        -- Key mappings specific to Fugitive buffers
-          vim.cmd.Git 'push'
+        vim.keymap.set('n', '<leader>p', function() vim.cmd.Git('push') end, opts)
-        end, opts)
+        vim.keymap.set('n', '<leader>P', function() vim.cmd.Git('pull --rebase') end, opts)
-
-        -- rebase always
-        vim.keymap.set('n', '<leader>P', function()
-          vim.cmd.Git { 'pull', '--rebase' }
-        end, opts)
-
-        -- NOTE: It allows me to easily set the branch I am pushing and any tracking
-        -- needed if I did not set the branch up correctly
         vim.keymap.set('n', '<leader>t', ':Git push -u origin ', opts)
       end,
     })
 
-    vim.keymap.set('n', 'gu', '<cmd>diffget //2<CR>')
+    -- Additional key mappings outside of Fugitive buffers
-    vim.keymap.set('n', 'gh', '<cmd>diffget //3<CR>')
+    vim.keymap.set('n', 'gu', '<cmd>diffget //2<CR>', { desc = 'Get diff for version 2' })
+    vim.keymap.set('n', 'gh', '<cmd>diffget //3<CR>', { desc = 'Get diff for version 3' })
+
+    -- Set up a faster command for Fugitive in Lua
+    local function git_command(args)
+      local cmd = 'Git ' .. args
+      vim.cmd(cmd)
+    end
+
+    vim.api.nvim_create_user_command('Git', function(params)
+      git_command(params.args)
+    end, { nargs = '*' })
   end,
   cond = function()
-    -- Function to check if the current directory is a Git repository
+    -- Efficient Git repository check
-    local is_git_repo = function()
+    return vim.fn.isdirectory('.git') == 1
-      local git_dir = vim.fn.finddir('.git', '.;')
-      return git_dir and #git_dir > 0
-    end
-    return is_git_repo()
   end,
 }
 

lua/custom/plugins/images.lua

@@ -0,0 +1,104 @@
+return {
+  -- {
+  --   'vhyrro/luarocks.nvim',
+  --   priority = 1001,
+  --   opts = {
+  --     rocks = { 'magick' },
+  --   },
+  --   event = 'VeryLazy', -- Adjust this based on your needs
+  -- },
+  -- {
+  --   'willothy/wezterm.nvim',
+  --   config = true,
+  --   event = 'BufWinEnter', -- Or another appropriate event
+  -- },
+  -- {
+  --   '3rd/image.nvim',
+  --   enabled = true,
+  --   commit = 'deb158d',
+  --   dev = false,
+  --   ft = { 'markdown', 'quarto', 'vimwiki' },
+  --   config = function()
+  --     local image = require 'image'
+  --     image.setup {
+  --       backend = 'wezterm',
+  --       integrations = {
+  --         markdown = {
+  --           enabled = true,
+  --           only_render_image_at_cursor = true,
+  --           filetypes = { 'markdown', 'vimwiki', 'quarto' },
+  --         },
+  --       },
+  --       editor_only_render_when_focused = false,
+  --       window_overlap_clear_enabled = true,
+  --       tmux_show_only_in_active_window = true,
+  --       window_overlap_clear_ft_ignore = { 'cmp_menu', 'cmp_docs', 'scrollview', 'scrollview_sign' },
+  --       max_width = nil,
+  --       max_height = nil,
+  --       max_width_window_percentage = nil,
+  --       max_height_window_percentage = 30,
+  --       kitty_method = 'normal',
+  --     }
+  --
+  --     local function clear_all_images()
+  --       local bufnr = vim.api.nvim_get_current_buf()
+  --       local images = image.get_images { buffer = bufnr }
+  --       for _, img in ipairs(images) do
+  --         img:clear()
+  --       end
+  --     end
+  --
+  --     local function get_image_at_cursor(buf)
+  --       local images = image.get_images { buffer = buf }
+  --       local row = vim.api.nvim_win_get_cursor(0)[1] - 1
+  --       for _, img in ipairs(images) do
+  --         if img.geometry ~= nil and img.geometry.y == row then
+  --           local og_max_height = img.global_state.options.max_height_window_percentage
+  --           img.global_state.options.max_height_window_percentage = nil
+  --           return img, og_max_height
+  --         end
+  --       end
+  --       return nil
+  --     end
+  --
+  --     local create_preview_window = function(img, og_max_height)
+  --       local buf = vim.api.nvim_create_buf(false, true)
+  --       local win_width = vim.api.nvim_get_option_value('columns', {})
+  --       local win_height = vim.api.nvim_get_option_value('lines', {})
+  --       local win = vim.api.nvim_open_win(buf, true, {
+  --         relative = 'editor',
+  --         style = 'minimal',
+  --         width = win_width,
+  --         height = win_height,
+  --         row = 0,
+  --         col = 0,
+  --         zindex = 1000,
+  --       })
+  --       vim.keymap.set('n', 'q', function()
+  --         vim.api.nvim_win_close(win, true)
+  --         img.global_state.options.max_height_window_percentage = og_max_height
+  --       end, { buffer = buf })
+  --       return { buf = buf, win = win }
+  --     end
+  --
+  --     local handle_zoom = function(bufnr)
+  --       local img, og_max_height = get_image_at_cursor(bufnr)
+  --       if img == nil then
+  --         return
+  --       end
+  --
+  --       local preview = create_preview_window(img, og_max_height)
+  --       image.hijack_buffer(img.path, preview.win, preview.buf)
+  --     end
+  --
+  --     vim.keymap.set('n', '<leader>io', function()
+  --       local bufnr = vim.api.nvim_get_current_buf()
+  --       handle_zoom(bufnr)
+  --     end, { buffer = true, desc = 'image [o]pen' })
+  --
+  --     vim.keymap.set('n', '<leader>ic', clear_all_images, { desc = 'image [c]lear' })
+  --   end,
+  -- },
+  --
+}
+

lua/custom/plugins/linting.lua

@@ -6,14 +6,21 @@ return {
     'BufNewFile',
   },
   config = function()
+    -- Linter configurations based on file type
     require('lint').linters_by_ft = {
       python = { 'ruff' },
       go = { 'golangcilint' },
       yaml = { 'yamllint' },
+      bash = { 'shellcheck' },
+      lua = { 'luacheck' },        -- Added Lua linter
+      rust = { 'clippy' },         -- Use `clippy` for Rust linting
+      dockerfile = { 'hadolint' }, -- Added Dockerfile linter
     }
 
+    -- Autocommand group for triggering linting
     local lint_augroup = vim.api.nvim_create_augroup('lint', { clear = true })
 
+    -- Trigger linting on buffer enter, write, and insert leave
     vim.api.nvim_create_autocmd({ 'BufEnter', 'BufWritePost', 'InsertLeave' }, {
       group = lint_augroup,
       callback = function()
@@ -21,17 +28,23 @@ return {
       end,
     })
 
+    -- Keybinding to manually lint the current buffer
     vim.keymap.set('n', '<leader>l', function()
       require('lint').try_lint()
     end, { desc = 'Lint the current buffer' })
 
+    -- Mason tool installer setup
     require('mason-tool-installer').setup({
       ensure_installed = {
-        'ruff',
+        'ruff',          -- Python
-        -- 'mypy',
+        -- 'mypy',       -- Uncomment if needed for additional Python linting
-        'golangci-lint',
+        'golangci-lint', -- Go
-        'yamllint',
+        'yamllint',      -- YAML
+        'shellcheck',    -- Bash
+        'luacheck',      -- Lua
+        'hadolint',      -- Dockerfile
       },
     })
   end,
 }
+

lua/custom/plugins/lsp-config.lua

@@ -1,7 +1,6 @@
 return {
   'neovim/nvim-lspconfig',
   dependencies = {
-    -- Automatically install LSPs to stdpath for neovim
     { 'williamboman/mason.nvim', config = true },
     'williamboman/mason-lspconfig.nvim',
     'WhoIsSethDaniel/mason-tool-installer.nvim',
@@ -13,19 +12,119 @@ return {
       opts = {},
     },
 
-    -- Additional lua configuration, makes nvim stuff amazing!
+    -- Additional Lua configuration
     'folke/neodev.nvim',
   },
   config = function()
-    local on_attach = function(client, bufnr)
+    -- General capabilities for LSP servers
-      local nmap = function(keys, func, desc)
+    local capabilities = vim.lsp.protocol.make_client_capabilities()
+    local has_cmp, cmp_nvim_lsp = pcall(require, 'cmp_nvim_lsp')
+    if has_cmp then
+      capabilities = cmp_nvim_lsp.default_capabilities()
+    end
+
+    -- LSP server configurations
+    local servers = {
+      bashls = { filetypes = { 'sh', 'bash' } },
+      clangd = {},
+      gopls = {
+        settings = {
+          gopls = {
+            gofumpt = true,
+            staticcheck = true,
+            completeUnimported = true,
+            usePlaceholders = true,
+            analyses = {
+              unusedparams = true,
+            },
+          },
+        },
+      },
+      ruff_lsp = { filetypes = { 'python' } },
+      pyright = {
+        filetypes = { 'python' },
+        settings = {
+          python = {
+            analysis = {
+              autoSearchPaths = false,
+              diagnosticMode = 'workspace',
+              useLibraryCodeForTypes = true,
+              typeCheckingMode = 'off',
+            },
+          },
+        },
+      },
+      rust_analyzer = { cmd = { 'rustup', 'run', 'stable', 'rust-analyzer' } },
+      texlab = {
+        flags = {
+          debounce_text_changes = 150,
+        },
+        settings = {
+          texlab = {
+            build = {
+              executable = "latexmk",
+              args = { "-pdf", "-xelatex", "-output-directory=output", "-interaction=nonstopmode", "-synctex=1", "%f" },
+              onSave = true,
+            },
+            forwardSearch = {
+              executable = "zathura",
+              args = { "--synctex-forward", "%l:1:%f", "%p" },
+            },
+          },
+        },
+      },
+      lua_ls = {
+        filetypes = { 'lua' },
+        settings = {
+          Lua = {
+            runtime = { version = 'LuaJIT', path = vim.split(package.path, ';') },
+            diagnostics = { globals = { 'vim' } },
+            workspace = {
+              library = vim.api.nvim_get_runtime_file('', true),
+              checkThirdParty = false,
+            },
+            telemetry = { enable = false },
+          },
+        },
+      },
+      yamlls = {
+        filetypes = { 'yaml' },
+        settings = {
+          yaml = {
+            schemas = {
+              ['https://json.schemastore.org/github-workflow.json'] = '/.github/workflows/*.{yml,yaml}',
+            },
+          },
+        },
+      },
+      taplo = { filetypes = { 'toml' } },
+      dockerls = { filetypes = { 'Dockerfile' } },
+    }
+
+    -- Setup LSP servers via mason-lspconfig
+    require('mason-lspconfig').setup({
+      ensure_installed = vim.tbl_keys(servers),
+      handlers = {
+        function(server_name)
+          require('lspconfig')[server_name].setup({
+            capabilities = capabilities,
+          })
+        end,
+      },
+    })
+
+    -- Setup specific LSP servers with custom configuration
+    for server, config in pairs(servers) do
+      require('lspconfig')[server].setup(vim.tbl_extend('force', {
+        capabilities = capabilities,
+        on_attach = function(client, bufnr)
+          local function nmap(keys, func, desc)
             if desc then
               desc = 'LSP: ' .. desc
             end
             vim.keymap.set('n', keys, func, { buffer = bufnr, desc = desc })
           end
 
-      -- Key mappings for LSP features
           nmap('<leader>rn', vim.lsp.buf.rename, '[R]e[n]ame')
           nmap('<leader>ca', function()
             vim.lsp.buf.code_action(require('telescope.themes').get_dropdown({
@@ -43,156 +142,11 @@ return {
 
           nmap('K', vim.lsp.buf.hover, 'Hover Documentation')
           nmap('<C-k>', vim.lsp.buf.signature_help, 'Signature Documentation')
-
+        end,
-      nmap('gD', vim.lsp.buf.declaration, '[G]oto [D]eclaration')
+      }, config))
-      nmap('gv', ':vsplit<CR>:lua vim.lsp.buf.declaration()<CR>', '[G]oto [V]irtual Text')
-      nmap('<leader>wa', vim.lsp.buf.add_workspace_folder, '[W]orkspace [A]dd Folder')
-      nmap('<leader>wr', vim.lsp.buf.remove_workspace_folder, '[W]orkspace [R]emove Folder')
-      nmap('<leader>wl', function()
-        print(vim.inspect(vim.lsp.buf.list_workspace_folders()))
-      end, '[W]orkspace [L]ist Folders')
-    end
-
-    local capabilities = vim.lsp.protocol.make_client_capabilities()
-    if pcall(require, 'cmp_nvim_lsp') then
-      capabilities = require('cmp_nvim_lsp').default_capabilities()
-    end
-
-    require('neodev').setup({
-      library = {
-        plugins = { 'nvim-dap-ui' },
-        types = true,
-      },
-    })
-
-    local servers = {
-      clangd = {},
-      gopls = {
-        settings = {
-          gopls = {
-            completeUnimported = true,
-            usePlaceholders = true,
-            analysis = {
-              unusedParams = true,
-            },
-          },
-        },
-      },
-      htmx = {
-        filetypes = { 'html' },
-      },
-      ruff_lsp = {
-        filetypes = { 'python' },
-      },
-      pyright = {
-        filetypes = { 'python' },
-        settings = {
-          python = {
-            analysis = {
-              autoSearchPaths = false,
-              diagnosticMode = 'workspace',
-              useLibraryCodeForTypes = true,
-              typeCheckingMode = 'off',
-            },
-          },
-        },
-      },
-      rust_analyzer = {
-        cmd = { 'rustup', 'run', 'stable', 'rust-analyzer' },
-      },
-      lua_ls = {
-        filetypes = { 'lua' },
-        settings = {
-          Lua = {
-            runtime = {
-              version = 'LuaJIT',
-              path = vim.split(package.path, ';'),
-            },
-            diagnostics = {
-              globals = { 'vim' },
-            },
-            workspace = {
-              library = vim.api.nvim_get_runtime_file('', true),
-              checkThirdParty = false,
-            },
-            telemetry = {
-              enable = false,
-            },
-          },
-        },
-      },
-      ocamllsp = {
-        manual_install = true,
-        filetypes = { 'ocaml', 'ocaml.interface', 'ocaml.cram', 'ocaml.menhir' },
-        settings = {
-          codelens = { enabled = true },
-          inlayHints = { enable = true },
-        },
-      },
-      yamlls = {
-        filetypes = { 'yaml' },
-        settings = {
-          yaml = {
-            schemas = {
-              ['https://json.schemasstore.org/github-workflow.json'] = '/.github/workflows/*.{yml,yaml}',
-            },
-          },
-        },
-      },
-      taplo = {
-        filetypes = { 'toml' },
-      },
-      dockerls = {
-        filetypes = { 'Dockerfile' },
-      },
-    }
-
-    local ensure_installed = vim.tbl_filter(function(key)
-      local t = servers[key]
-      if type(t) == 'table' then
-        return not t.manual_install
-      else
-        return t
-      end
-    end, vim.tbl_keys(servers))
-
-    require('mason').setup({
-      ui = {
-        icons = {
-          package_installed = '✓',
-          package_pending = '➜',
-          package_uninstalled = '✗',
-        },
-      },
-    })
-
-    local mason_lspconfig = require('mason-lspconfig')
-    mason_lspconfig.setup({
-      ensure_installed = ensure_installed,
-    })
-
-    for name, config in pairs(servers) do
-      if config then
-        require('lspconfig')[name].setup({
-          capabilities = capabilities,
-          on_attach = on_attach,
-          settings = config.settings,
-          filetypes = config.filetypes,
-          cmd = config.cmd,
-        })
-      end
-    end
-
-    require('cmp')
-
-    local sign = function(opts)
-      vim.fn.sign_define(opts.name, {
-        texthl = opts.name,
-        text = opts.text,
-        numhl = '',
-      })
     end
 
+    -- Diagnostics configuration
     vim.diagnostic.config({
       underline = true,
       severity_sort = true,
@@ -202,19 +156,34 @@ return {
         spacing = 2,
       },
       float = {
-        source = 'if_many',
+        Source = 'if_many',
         border = 'rounded',
       },
     })
 
+    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.lsp.handlers['textDocument/hover'] = vim.lsp.with(vim.lsp.handlers.hover, { border = 'rounded' })
+    -- Fidget configuration (LSP progress)
-    vim.lsp.handlers['textDocument/signatureHelp'] =
+    require('fidget').setup({})
-      vim.lsp.with(vim.lsp.handlers.signature_help, { border = 'rounded' })
+
+    -- Neodev setup for improved Lua development
+    require('neodev').setup({
+      library = {
+        plugins = { 'nvim-dap-ui' },
+        types = true,
+      },
+    })
   end,
 }
 

lua/custom/plugins/markdown-preview.lua

@@ -0,0 +1,4 @@
+return {
+  'iamcco/markdown-preview.nvim',
+}
+

lua/custom/plugins/quarto.lua

@@ -0,0 +1,72 @@
+return {
+  -- -- Quarto support for data science
+  -- {
+  --   'quarto-dev/quarto-nvim',
+  --   ft = { 'quarto' },
+  --   opts = {
+  --     codeRunner = {
+  --       enabled = true,
+  --       default_method = "molten",
+  --     },
+  --   },
+  --   dependencies = {
+  --     'jmbuhr/otter.nvim',               -- For language features in code cells
+  --     'nvim-treesitter/nvim-treesitter', -- Syntax highlighting and code understanding
+  --   },
+  -- },
+  --
+  -- -- Jupytext integration for working with Jupyter notebooks
+  -- {
+  --   'GCBallesteros/jupytext.nvim',
+  --   opts = {
+  --     custom_language_formatting = {
+  --       python = { extension = 'qmd', style = 'quarto', force_ft = 'quarto' },
+  --       r = { extension = 'qmd', style = 'quarto', force_ft = 'quarto' },
+  --     },
+  --   },
+  -- },
+  --
+  -- -- Image management and clipboard integration
+  -- {
+  --   'HakonHarnes/img-clip.nvim',
+  --   event = 'BufEnter',
+  --   ft = { 'markdown', 'quarto', 'latex' },
+  --   opts = {
+  --     default = { dir_path = 'img' },
+  --     filetypes = {
+  --       markdown = { url_encode_path = true, template = '![$CURSOR]($FILE_PATH)' },
+  --       quarto = { url_encode_path = true, template = '![$CURSOR]($FILE_PATH)' },
+  --     },
+  --   },
+  --   config = function(_, opts)
+  --     require('img-clip').setup(opts)
+  --     vim.keymap.set('n', '<leader>ii', ':PasteImage<cr>', { desc = 'Insert image from clipboard' })
+  --   end,
+  -- },
+  --
+  -- -- Equation preview in markdown/quarto files
+  -- {
+  --   'jbyuki/nabla.nvim',
+  --   keys = {
+  --     { '<leader>qm', ':lua require"nabla".toggle_virt()<cr>', { desc = 'Toggle math equations' } },
+  --   },
+  -- },
+  --
+  -- -- Molten for interactive code execution
+  -- {
+  --   'benlubas/molten-nvim',
+  --   enabled = true,
+  --   build = ':UpdateRemotePlugins',
+  --   init = function()
+  --     vim.g.molten_image_provider = 'image.nvim'
+  --     vim.g.molten_output_win_max_height = 20
+  --     vim.g.molten_auto_open_output = false
+  --   end,
+  --   keys = {
+  --     { 'n', '<leader>mi', ':MoltenInit<cr>',                { desc = 'Molten init' } },
+  --     { 'v', '<leader>mv', ':<C-u>MoltenEvaluateVisual<cr>', { desc = 'Evaluate visual selection' } },
+  --     { 'n', '<leader>mr', ':MoltenReevaluateCell<cr>',      { desc = 'Re-evaluate cell' } },
+  --   },
+  -- },
+}
+

lua/custom/plugins/refactoring.lua

@@ -15,7 +15,7 @@ return {
   },
   config = function()
     require('refactoring').setup({
-      show_success_message = false,
+      show_success_message = true,
     })
   end,
 }

lua/custom/plugins/tree-sitter.lua

@@ -4,7 +4,6 @@ return {
   dependencies = {
     'nvim-treesitter/nvim-treesitter-textobjects',
     'https://github.com/apple/pkl-neovim.git',
-    'windwp/nvim-ts-autotag',
   },
   build = ':TSUpdate',
   config = function()
@@ -12,7 +11,8 @@ return {
     local ts = require('nvim-treesitter.configs')
     ts.setup({
       ensure_installed = {
-        'c', 'cpp', 'lua', 'python', 'go', 'rust', 'vimdoc', 'vim'
+        'bash', 'c', 'cpp', 'lua', 'python', 'go', 'markdown', 'markdown_inline', 'r', 'rust', 'vimdoc', 'vim', 'yaml',
+        'query'
       },
       ignore_install = { '' },
       highlight = {
@@ -23,10 +23,10 @@ return {
       incremental_selection = {
         enable = true,
         keymaps = {
-          init_selection = '<c-space>',
+          init_selection = 'gnn',
-          node_incremental = '<c-space>',
+          node_incremental = 'grn',
-          scope_incremental = '<c-s>',
+          scope_incremental = 'grc',
-          node_decremental = '<M-space>',
+          node_decremental = 'grm',
         },
       },
       textobjects = {
@@ -73,16 +73,6 @@ return {
         },
       },
     })
-
-    -- Autotag setup
-    require('nvim-ts-autotag').setup({
-      enable = true,
-    })
   end,
-  opts = {
-    autotag = {
-      enable = true,
-    },
-  },
 }
 

queries/markdown/textobjects.scm

@@ -0,0 +1,15 @@
+; (atx_heading
+;   heading_content: (_) @class.inner) @class.outer
+;
+; (setext_heading
+;   heading_content: (_) @class.inner) @class.outer
+;
+; (thematic_break) @class.outer
+
+(fenced_code_block (code_fence_content) @block.inner) @block.outer
+
+[
+  (paragraph)
+  (list)
+] @block.outer
+

queries/r/textobjects.scm

@@ -0,0 +1,50 @@
+; block
+; call
+(call) @call.outer
+
+(arguments) @call.inner
+
+; class
+; comment
+(comment) @comment.outer
+
+; conditional
+(if_statement
+  condition: (_)? @conditional.inner) @conditional.outer
+
+; function
+[
+  (function_definition)
+] @function.outer
+
+(function_definition
+  [
+    (call)
+    (binary_operator)
+  ] @function.inner) @function.outer
+
+
+; loop
+[
+  (while_statement)
+  (for_statement)
+  (repeat_statement)
+] @loop.outer
+
+(while_statement
+  body: (_) @loop.inner)
+
+(repeat_statement
+  body: (_) @loop.inner)
+
+(for_statement
+  body: (_) @loop.inner)
+
+; statement
+
+(program
+  (_) @statement.outer)
+
+; number
+(float) @number.inner
+