Merge branch 'dev'

lua/config/keymap.lua

@@ -299,13 +299,11 @@ wk.register({
     f = { '<cmd>Telescope find_files<cr>', '[f]iles' },
     h = { '<cmd>Telescope help_tags<cr>', '[h]elp' },
     k = { '<cmd>Telescope keymaps<cr>', '[k]eymaps' },
-    r = { '<cmd>Telescope lsp_references<cr>', '[r]eferences' },
     g = { '<cmd>Telescope live_grep<cr>', '[g]rep' },
     b = { '<cmd>Telescope current_buffer_fuzzy_find<cr>', '[b]uffer fuzzy find' },
     m = { '<cmd>Telescope marks<cr>', '[m]arks' },
     M = { '<cmd>Telescope man_pages<cr>', '[M]an pages' },
     c = { '<cmd>Telescope git_commits<cr>', 'git [c]ommits' },
-    s = { '<cmd>Telescope lsp_document_symbols<cr>', 'document [s]ymbols' },
     ['<space>'] = { '<cmd>Telescope buffers<cr>', '[ ] buffers' },
     d = { '<cmd>Telescope buffers<cr>', '[d] buffers' },
     q = { '<cmd>Telescope quickfix<cr>', '[q]uickfix' },
@@ -347,21 +345,26 @@ wk.register({
   },
   l = {
     name = '[l]anguage/lsp',
-    r = { '<cmd>Telescope lsp_references<cr>', '[r]eferences' },
+    r = { vim.lsp.buf.references, '[r]eferences' },
     R = { '[R]ename' },
     D = { vim.lsp.buf.type_definition, 'type [D]efinition' },
     a = { vim.lsp.buf.code_action, 'code [a]ction' },
     e = { vim.diagnostic.open_float, 'diagnostics (show hover [e]rror)' },
     d = {
       name = '[d]iagnostics',
-      d = { vim.diagnostic.disable, '[d]isable' },
+      d = {
+        function()
+          vim.diagnostic.enable(false)
+        end,
+        '[d]isable',
+      },
       e = { vim.diagnostic.enable, '[e]nable' },
     },
     g = { ':Neogen<cr>', 'neo[g]en docstring' },
   },
   o = {
     name = '[o]tter & c[o]de',
-    a = { require('otter').dev_setup, 'otter [a]ctivate' },
+    a = { require('otter').activate, 'otter [a]ctivate' },
     d = { require('otter').deactivate, 'otter [d]eactivate' },
     c = { 'O# %%<cr>', 'magic [c]omment code chunk # %%' },
     r = { insert_r_chunk, '[r] code chunk' },

lua/plugins/colorthemes.lua

@@ -36,6 +36,17 @@ return {
     lazy = false,
     priority = 1000,
     config = function()
+      require('kanagawa').setup {
+        colors = {
+          theme = {
+            all = {
+              ui = {
+                bg_gutter = 'none',
+              },
+            },
+          },
+        },
+      }
       vim.cmd.colorscheme 'kanagawa'
       vim.api.nvim_set_hl(0, 'TermCursor', { fg = '#A6E3A1', bg = '#A6E3A1' })
     end,

lua/plugins/completion.lua

@@ -120,7 +120,7 @@ return {
           },
         },
         sources = {
-          { name = 'otter' }, -- for code chunks in quarto
+          -- { name = 'otter' }, -- for code chunks in quarto
           { name = 'path' },
           { name = 'nvim_lsp' },
           { name = 'nvim_lsp_signature_help' },
@@ -155,7 +155,7 @@ return {
 
   { -- gh copilot
     'zbirenbaum/copilot.lua',
-    enabled = false,
+    enabled = true,
     config = function()
       require('copilot').setup {
         suggestion = {

lua/plugins/editing.lua

@@ -39,6 +39,7 @@ return {
         formatters_by_ft = {
           lua = { 'mystylua' },
           python = { 'isort', 'black' },
+          quarto = { 'injected' },
         },
         formatters = {
           mystylua = {
@@ -88,6 +89,7 @@ return {
 
   {
     'chrishrb/gx.nvim',
+    enabled = false,
     keys = { { 'gx', '<cmd>Browse<cr>', mode = { 'n', 'x' } } },
     cmd = { 'Browse' },
     init = function()

lua/plugins/lsp.lua

@@ -1,4 +1,5 @@
 return {
+
   {
 
     -- for lsp features in code cells / embedded code
@@ -8,21 +9,9 @@ return {
       {
         'neovim/nvim-lspconfig',
         'nvim-treesitter/nvim-treesitter',
-        'hrsh7th/nvim-cmp',
-      },
-    },
-    opts = {
-      lsp = {
-        hover = {
-          border = require('misc.style').border,
-        },
-      },
-      buffers = {
-        set_filetype = true,
-        write_to_disk = false,
       },
-      handle_leading_whitespace = true,
     },
+    opts = {},
   },
 
   {
@@ -37,7 +26,31 @@ return {
         enabled = false,
         opts = {},
       },
-      { 'folke/neodev.nvim', opts = {}, enabled = true },
+      {
+        {
+          'folke/lazydev.nvim',
+          ft = 'lua', -- only load on lua files
+          opts = {
+            library = {
+              -- See the configuration section for more details
+              -- Load luvit types when the `vim.uv` word is found
+              { path = 'luvit-meta/library', words = { 'vim%.uv' } },
+            },
+          },
+        },
+        { 'Bilal2453/luvit-meta', lazy = true }, -- optional `vim.uv` typings
+        { -- optional completion source for require statements and module annotations
+          'hrsh7th/nvim-cmp',
+          opts = function(_, opts)
+            opts.sources = opts.sources or {}
+            table.insert(opts.sources, {
+              name = 'lazydev',
+              group_index = 0, -- set group index to 0 to skip loading LuaLS completions
+            })
+          end,
+        },
+        -- { "folke/neodev.nvim", enabled = false }, -- make sure to uninstall or disable neodev.nvim
+      },
       { 'folke/neoconf.nvim', opts = {}, enabled = false },
     },
     config = function()
@@ -62,29 +75,32 @@ return {
       vim.api.nvim_create_autocmd('LspAttach', {
         group = vim.api.nvim_create_augroup('kickstart-lsp-attach', { clear = true }),
         callback = function(event)
-          local telescope = require 'telescope.builtin'
           local function map(keys, func, desc)
             vim.keymap.set('n', keys, func, { buffer = event.buf, desc = 'LSP: ' .. desc })
           end
+          local function vmap(keys, func, desc)
+            vim.keymap.set('v', keys, func, { buffer = event.buf, desc = 'LSP: ' .. desc })
+          end
 
           local client = vim.lsp.get_client_by_id(event.data.client_id)
           assert(client, 'LSP client not found')
 
           ---@diagnostic disable-next-line: inject-field
           client.server_capabilities.document_formatting = true
 
-          map('gS', telescope.lsp_document_symbols, '[g]o so [S]ymbols')
-          map('gD', telescope.lsp_type_definitions, '[g]o to type [D]efinition')
-          map('gd', telescope.lsp_definitions, '[g]o to [d]efinition')
-          map('K', '<cmd>lua vim.lsp.buf.hover()<CR>', '[K] hover documentation')
-          map('gh', '<cmd>lua vim.lsp.buf.signature_help()<CR>', '[g]o to signature [h]elp')
-          map('gI', telescope.lsp_implementations, '[g]o to [I]mplementation')
-          map('gr', telescope.lsp_references, '[g]o to [r]eferences')
+          map('gS', vim.lsp.buf.document_symbol, '[g]o so [S]ymbols')
+          map('gD', vim.lsp.buf.type_definition, '[g]o to type [D]efinition')
+          map('gd', vim.lsp.buf.definition, '[g]o to [d]efinition')
+          map('K', vim.lsp.buf.hover, '[K] hover documentation')
+          map('gh', vim.lsp.buf.signature_help, '[g]o to signature [h]elp')
+          map('gI', vim.lsp.buf.implementation, '[g]o to [I]mplementation')
+          map('gr', vim.lsp.buf.references, '[g]o to [r]eferences')
           map('[d', vim.diagnostic.goto_prev, 'previous [d]iagnostic ')
           map(']d', vim.diagnostic.goto_next, 'next [d]iagnostic ')
           map('<leader>ll', vim.lsp.codelens.run, '[l]ens run')
           map('<leader>lR', vim.lsp.buf.rename, '[l]sp [R]ename')
           map('<leader>lf', vim.lsp.buf.format, '[l]sp [f]ormat')
+          vmap('<leader>lf', vim.lsp.buf.format, '[l]sp [f]ormat')
           map('<leader>lq', vim.diagnostic.setqflist, '[l]sp diagnostic [q]uickfix')
         end,
       })
@@ -93,8 +109,11 @@ return {
         allow_incremental_sync = true,
         debounce_text_changes = 150,
       }
+
       vim.lsp.handlers['textDocument/hover'] = vim.lsp.with(vim.lsp.handlers.hover, { border = require('misc.style').border })
       vim.lsp.handlers['textDocument/signatureHelp'] = vim.lsp.with(vim.lsp.handlers.signature_help, { border = require('misc.style').border })
+      -- TODO: handle this
+      -- vim.lsp.handlers['textDocument/references'] = telescope_builtin.lsp_references
 
       local capabilities = vim.lsp.protocol.make_client_capabilities()
       capabilities = vim.tbl_deep_extend('force', capabilities, require('cmp_nvim_lsp').default_capabilities())
@@ -150,6 +169,11 @@ return {
         },
       }
 
+      lspconfig.jsonls.setup {
+        capabilities = capabilities,
+        flags = lsp_flags,
+      }
+
       lspconfig.dotls.setup {
         capabilities = capabilities,
         flags = lsp_flags,
@@ -196,16 +220,18 @@ return {
             },
             runtime = {
               version = 'LuaJIT',
-              plugin = lua_plugin_paths,
+              -- plugin = lua_plugin_paths,
             },
             diagnostics = {
-              globals = { 'vim', 'quarto', 'pandoc', 'io', 'string', 'print', 'require', 'table' },
               disable = { 'trailing-space' },
             },
             workspace = {
-              library = lua_library_files,
+              -- library = lua_library_files,
               checkThirdParty = false,
             },
+            doc = {
+              privateName = { '^_' },
+            },
             telemetry = {
               enable = false,
             },
@@ -248,6 +274,11 @@ return {
       --   }
       -- }
 
+      -- lspconfig.ruff_lsp.setup {
+      --   capabilities = capabilities,
+      --   flags = lsp_flags,
+      -- }
+
       -- See https://github.com/neovim/neovim/issues/23291
       -- disable lsp watcher.
       -- Too lags on linux for python projects

lua/plugins/quarto.lua

@@ -7,7 +7,7 @@ return {
     dev = false,
     opts = {
       lspFeatures = {
-        languages = { 'r', 'python', 'julia', 'bash', 'lua', 'html', 'dot', 'javascript', 'typescript', 'ojs' },
+        languages = { 'r', 'python', 'julia', 'bash', 'lua', 'html', 'dot', 'javascript', 'typescript', 'ojs', 'lua' },
       },
       codeRunner = {
         enabled = true,

lua/plugins/treesitter.lua

@@ -1,8 +1,14 @@
 return {
   {
     'nvim-treesitter/nvim-treesitter',
+    dev = false,
     dependencies = {
-      { 'nvim-treesitter/nvim-treesitter-textobjects' },
+      -- {
+      --   -- currently broken for R
+      --   'nvim-treesitter/nvim-treesitter-textobjects',
+      --   dev = false,
+      --   enabled = false,
+      -- },
     },
     run = ':TSUpdate',
     config = function()

lua/plugins/ui.lua

@@ -51,7 +51,6 @@ return {
           vimgrep_arguments = vimgrep_arguments,
           file_ignore_patterns = {
             'node_modules',
-            '%_files/',
             '%_cache',
             '.git/',
             'site_libs',
@@ -334,15 +333,6 @@ return {
     enabled = true,
     dev = false,
     ft = { 'markdown', 'quarto', 'vimwiki' },
-    dependencies = {
-      {
-        'vhyrro/luarocks.nvim',
-        priority = 1001, -- this plugin needs to run before anything else
-        opts = {
-          rocks = { 'magick' },
-        },
-      },
-    },
     config = function()
       -- Requirements
       -- https://github.com/3rd/image.nvim?tab=readme-ov-file#requirements
@@ -351,6 +341,7 @@ return {
       -- sudo apt install imagemagick
       -- sudo apt install libmagickwand-dev
       -- sudo apt install liblua5.1-0-dev
+      -- sudo apt install lua5.1
       -- sudo apt installl luajit
 
       local image = require 'image'

snips/snippets/quarto.json

@@ -1,4 +1,16 @@
 {
+  "ipython_interactive": {
+    "prefix": ["ipyinteractive"],
+    "body": [
+      "```{python}",
+      "from IPython.core.getipython import get_ipython",
+      "ip = get_ipython()",
+      "interactive = False",
+      "if ip is not None and 'interactiveshell.TerminalInteractiveShell' in str(ip):",
+      "  interactive = True",
+      "```"
+    ]
+  },
   "iframe": {
     "prefix": ["iframe"],
     "body": [