From 804c104146742dc9c4e83e83d4e8f64db7647703 Mon Sep 17 00:00:00 2001
From: Jannik Buhr <jannik.m.buhr@gmail.com>
Date: Fri, 17 May 2024 10:07:24 +0200
Subject: [PATCH 01/14] dev

---
 lua/plugins/completion.lua | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lua/plugins/completion.lua b/lua/plugins/completion.lua
index a9c102f..95199de 100644
--- a/lua/plugins/completion.lua
+++ b/lua/plugins/completion.lua
@@ -155,7 +155,7 @@ return {
 
   { -- gh copilot
     'zbirenbaum/copilot.lua',
-    enabled = false,
+    enabled = true,
     config = function()
       require('copilot').setup {
         suggestion = {

From edd78f62c08a3a3bb8d9d775fb1ec19ddac32bbf Mon Sep 17 00:00:00 2001
From: Jannik Buhr <jannik.m.buhr@gmail.com>
Date: Fri, 17 May 2024 15:42:11 +0200
Subject: [PATCH 02/14] feat: virtual text for dap

---
 lua/config/keymap.lua     |  6 +++++
 lua/plugins/debugging.lua | 49 +++++++++++++++++++++++++++++++++------
 2 files changed, 48 insertions(+), 7 deletions(-)

diff --git a/lua/config/keymap.lua b/lua/config/keymap.lua
index 16332a1..ddad173 100644
--- a/lua/config/keymap.lua
+++ b/lua/config/keymap.lua
@@ -285,8 +285,14 @@ wk.register({
     i = { new_terminal_ipython, 'new [i]python terminal' },
     j = { new_terminal_julia, 'new [j]ulia terminal' },
   },
+  e = {
+    name = '[e]dit',
+  },
   d = {
     name = '[d]ebug',
+    t = {
+      name = '[t]est',
+    },
   },
   f = {
     name = '[f]ind (telescope)',
diff --git a/lua/plugins/debugging.lua b/lua/plugins/debugging.lua
index 7ad09c2..fcb986d 100644
--- a/lua/plugins/debugging.lua
+++ b/lua/plugins/debugging.lua
@@ -27,22 +27,57 @@ return {
         'nvim-neotest/nvim-nio',
         'rcarriga/nvim-dap-ui',
         'mfussenegger/nvim-dap-python',
+        'theHamsta/nvim-dap-virtual-text',
       },
     },
     config = function()
       vim.fn.sign_define('DapBreakpoint', { text = '🦆', texthl = '', linehl = '', numhl = '' })
+      local dap = require 'dap'
+      local ui = require 'dapui'
       require('dapui').setup()
       require('dap-python').setup()
       require('dap.ext.vscode').load_launchjs 'launch.json'
+
+      require('nvim-dap-virtual-text').setup {
+        -- Hides tokens, secrets, and other sensitive information
+        -- From TJ DeVries' config
+        -- Not necessary, but also can't hurt
+        display_callback = function(variable)
+          local name = string.lower(variable.name)
+          local value = string.lower(variable.value)
+          if name:match 'secret' or name:match 'api' or value:match 'secret' or value:match 'api' then
+            return '*****'
+          end
+
+          if #variable.value > 15 then
+            return ' ' .. string.sub(variable.value, 1, 15) .. '... '
+          end
+
+          return ' ' .. variable.value
+        end,
+      }
+
+      dap.listeners.before.attach.dapui_config = function()
+        ui.open()
+      end
+      dap.listeners.before.launch.dapui_config = function()
+        ui.open()
+      end
+      dap.listeners.before.event_terminated.dapui_config = function()
+        ui.close()
+      end
+      dap.listeners.before.event_exited.dapui_config = function()
+        ui.close()
+      end
     end,
     keys = {
-      { '<leader>db', ":lua require'dap'.toggle_breakpoint()<cr>", desc = 'debug breakpoint' },
-      { '<leader>dc', ": lua require'dap'.continue()<cr>", desc = 'debug' },
-      { '<leader>do', ": lua require'dap'.step_over()<cr>", desc = 'debug over' },
-      { '<leader>dO', ": lua require'dap'.step_out()<cr>", desc = 'debug out' },
-      { '<leader>di', ": lua require'dap'.step_into()<cr>", desc = 'debug into' },
-      { '<leader>dr', ": lua require'dap'.repl_open()<cr>", desc = 'debug repl' },
-      { '<leader>du', ": lua require'dapui'.toggle()<cr>", desc = 'debug ui' },
+      { '<leader>db', ":lua require'dap'.toggle_breakpoint()<cr>", desc = 'debug [b]reakpoint' },
+      { '<leader>dc', ":lua require'dap'.continue()<cr>", desc = 'debug [c]ontinue' },
+      { '<leader>do', ":lua require'dap'.step_over()<cr>", desc = 'debug [o]ver' },
+      { '<leader>dO', ":lua require'dap'.step_out()<cr>", desc = 'debug [O]ut' },
+      { '<leader>di', ":lua require'dap'.step_into()<cr>", desc = 'debug [i]nto' },
+      { '<leader>dr', ":lua require'dap'.repl_open()<cr>", desc = 'debug [r]epl' },
+      { '<leader>du', ":lua require'dapui'.toggle()<cr>", desc = 'debug [u]i' },
     },
   },
 }

From 4e3e3abf7d267cfa109ad3d9e1a9cb9d7b52184a Mon Sep 17 00:00:00 2001
From: Jannik Buhr <jannik.m.buhr@gmail.com>
Date: Fri, 17 May 2024 15:42:25 +0200
Subject: [PATCH 03/14] feat: oil.nvim to edit the filesystem as a buffer

---
 lua/plugins/ui.lua | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/lua/plugins/ui.lua b/lua/plugins/ui.lua
index 5d41213..c7d0105 100644
--- a/lua/plugins/ui.lua
+++ b/lua/plugins/ui.lua
@@ -116,6 +116,26 @@ return {
     opts = { signs = false },
   },
 
+  { -- edit the file system as a buffer
+    'stevearc/oil.nvim',
+    opts = {
+      keymaps = {
+        ['<C-s>'] = false,
+        ['<C-h>'] = false,
+        ['<C-l>'] = false,
+      },
+      view_options = {
+        show_hidden = true,
+      },
+    },
+    dependencies = { 'nvim-tree/nvim-web-devicons' },
+    keys = {
+      { '-', ':Oil<cr>', desc = 'oil' },
+      { '<leader>ef', ':Oil<cr>', desc = 'edit [f]iles' },
+    },
+    cmd = 'Oil',
+  },
+
   { -- statusline
     -- PERF: I found this to slow down the editor
     'nvim-lualine/lualine.nvim',

From 8b7eb4276c4f903d2b923bfa55d06600b7f96d0d Mon Sep 17 00:00:00 2001
From: Jannik Buhr <jannik.m.buhr@gmail.com>
Date: Fri, 17 May 2024 16:16:26 +0200
Subject: [PATCH 04/14] test cute colorschemes

---
 lua/config/global.lua       |  3 +++
 lua/plugins/colorthemes.lua | 37 ++++++++++++++++++++++++++-----------
 2 files changed, 29 insertions(+), 11 deletions(-)

diff --git a/lua/config/global.lua b/lua/config/global.lua
index 284465b..0861819 100644
--- a/lua/config/global.lua
+++ b/lua/config/global.lua
@@ -5,6 +5,9 @@ local animals = require('misc.style').animals
 -- proper colors
 vim.opt.termguicolors = true
 
+-- show insert mode in terminal buffers
+vim.api.nvim_set_hl(0, 'TermCursor', { fg = '#A6E3A1', bg = '#A6E3A1' })
+
 -- disable fill chars (the ~ after the buffer)
 vim.o.fillchars = 'eob: '
 
diff --git a/lua/plugins/colorthemes.lua b/lua/plugins/colorthemes.lua
index cc30eeb..02cb21a 100644
--- a/lua/plugins/colorthemes.lua
+++ b/lua/plugins/colorthemes.lua
@@ -5,17 +5,7 @@ return {
   {
     'catppuccin/nvim',
     name = 'catppuccin',
-    -- using new default on nvim 0.10 now for a while to test
-    enabled = function()
-      -- only enabled catppuccin on lower versions
-      local has_new_default_theme = vim.fn.has 'nvim-0.10' == 1
-      if has_new_default_theme then
-        -- change cursor color for terminal insert mode
-        -- (because cursor shape does not change for now)
-        vim.api.nvim_set_hl(0, 'TermCursor', { fg = '#A6E3A1', bg = '#A6E3A1' })
-      end
-      return not has_new_default_theme
-    end,
+    enabled = false,
     lazy = false, -- make sure we load this during startup if it is your main colorscheme
     priority = 1000, -- make sure to load this before all the other start plugins
     config = function()
@@ -26,6 +16,31 @@ return {
       vim.api.nvim_set_hl(0, 'TermCursor', { fg = '#A6E3A1', bg = '#A6E3A1' })
     end,
   },
+
+  {
+    'oxfist/night-owl.nvim',
+    enabled = true,
+    lazy = false,
+    priority = 1000,
+    config = function()
+      -- load the colorscheme here
+      require('night-owl').setup()
+      vim.cmd.colorscheme 'night-owl'
+      vim.api.nvim_set_hl(0, 'TermCursor', { fg = '#A6E3A1', bg = '#A6E3A1' })
+    end,
+  },
+
+  {
+    'rebelot/kanagawa.nvim',
+    enabled = false,
+    lazy = false,
+    priority = 1000,
+    config = function()
+      vim.cmd.colorscheme 'kanagawa'
+      vim.api.nvim_set_hl(0, 'TermCursor', { fg = '#A6E3A1', bg = '#A6E3A1' })
+    end,
+  },
+
   {
     'olimorris/onedarkpro.nvim',
     enabled = false,

From bb01a8866102e87b73f997c7177d963fd66e3b4d Mon Sep 17 00:00:00 2001
From: Jannik Buhr <jannik.m.buhr@gmail.com>
Date: Fri, 17 May 2024 16:35:32 +0200
Subject: [PATCH 05/14] feat: kanagawa colorscheme

---
 lua/plugins/colorthemes.lua | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lua/plugins/colorthemes.lua b/lua/plugins/colorthemes.lua
index 02cb21a..71196e1 100644
--- a/lua/plugins/colorthemes.lua
+++ b/lua/plugins/colorthemes.lua
@@ -19,7 +19,7 @@ return {
 
   {
     'oxfist/night-owl.nvim',
-    enabled = true,
+    enabled = false,
     lazy = false,
     priority = 1000,
     config = function()
@@ -32,7 +32,7 @@ return {
 
   {
     'rebelot/kanagawa.nvim',
-    enabled = false,
+    enabled = true,
     lazy = false,
     priority = 1000,
     config = function()

From 7e80728f019d3be3a390c1635ffa4604fef48a95 Mon Sep 17 00:00:00 2001
From: Jannik Buhr <jannik.m.buhr@gmail.com>
Date: Fri, 17 May 2024 10:07:24 +0200
Subject: [PATCH 06/14] dev

---
 lua/plugins/completion.lua | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lua/plugins/completion.lua b/lua/plugins/completion.lua
index a9c102f..95199de 100644
--- a/lua/plugins/completion.lua
+++ b/lua/plugins/completion.lua
@@ -155,7 +155,7 @@ return {
 
   { -- gh copilot
     'zbirenbaum/copilot.lua',
-    enabled = false,
+    enabled = true,
     config = function()
       require('copilot').setup {
         suggestion = {

From 0470708f6db17398e16e130ff84c497cb0bfc5fc Mon Sep 17 00:00:00 2001
From: Jannik Buhr <jannik.m.buhr@gmail.com>
Date: Wed, 22 May 2024 00:19:50 +0200
Subject: [PATCH 07/14] remove signcolumn background color

---
 lua/plugins/colorthemes.lua | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/lua/plugins/colorthemes.lua b/lua/plugins/colorthemes.lua
index 71196e1..40ef99d 100644
--- a/lua/plugins/colorthemes.lua
+++ b/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,

From 887f7986091c386fba8d44f0414930250b4022d5 Mon Sep 17 00:00:00 2001
From: Jannik Buhr <jannik.m.buhr@gmail.com>
Date: Thu, 20 Jun 2024 11:49:03 +0200
Subject: [PATCH 08/14] feat: json ls

---
 lua/plugins/lsp.lua | 7 ++++++-
 lua/plugins/ui.lua  | 1 -
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/lua/plugins/lsp.lua b/lua/plugins/lsp.lua
index beb2a4b..387bdd0 100644
--- a/lua/plugins/lsp.lua
+++ b/lua/plugins/lsp.lua
@@ -144,12 +144,17 @@ return {
           yaml = {
             schemaStore = {
               enable = true,
-              url = '',
+              -- url = '',
             },
           },
         },
       }
 
+      lspconfig.jsonls.setup {
+        capabilities = capabilities,
+        flags = lsp_flags,
+      }
+
       lspconfig.dotls.setup {
         capabilities = capabilities,
         flags = lsp_flags,
diff --git a/lua/plugins/ui.lua b/lua/plugins/ui.lua
index 9ec17c0..9b8fcd8 100644
--- a/lua/plugins/ui.lua
+++ b/lua/plugins/ui.lua
@@ -51,7 +51,6 @@ return {
           vimgrep_arguments = vimgrep_arguments,
           file_ignore_patterns = {
             'node_modules',
-            '%_files/',
             '%_cache',
             '.git/',
             'site_libs',

From 7d455d0345995f2272b49576f0a0de35bd67dbd0 Mon Sep 17 00:00:00 2001
From: Jannik Buhr <jannik.m.buhr@gmail.com>
Date: Mon, 24 Jun 2024 15:04:14 +0200
Subject: [PATCH 09/14] use native gx

---
 lua/plugins/editing.lua | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lua/plugins/editing.lua b/lua/plugins/editing.lua
index 7d629bc..67a9409 100644
--- a/lua/plugins/editing.lua
+++ b/lua/plugins/editing.lua
@@ -88,6 +88,7 @@ return {
 
   {
     'chrishrb/gx.nvim',
+    enabled = false,
     keys = { { 'gx', '<cmd>Browse<cr>', mode = { 'n', 'x' } } },
     cmd = { 'Browse' },
     init = function()

From f08cba5449b58d7619b54617bdf43fb267b07b23 Mon Sep 17 00:00:00 2001
From: Jannik Buhr <jannik.m.buhr@gmail.com>
Date: Mon, 24 Jun 2024 15:05:06 +0200
Subject: [PATCH 10/14] ipython interactive snippet

---
 lua/plugins/lsp.lua        |  5 +++++
 snips/snippets/quarto.json | 12 ++++++++++++
 2 files changed, 17 insertions(+)

diff --git a/lua/plugins/lsp.lua b/lua/plugins/lsp.lua
index beb2a4b..d886aa7 100644
--- a/lua/plugins/lsp.lua
+++ b/lua/plugins/lsp.lua
@@ -248,6 +248,11 @@ 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
diff --git a/snips/snippets/quarto.json b/snips/snippets/quarto.json
index a78a9e1..83a400b 100644
--- a/snips/snippets/quarto.json
+++ b/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": [

From 77c96167260c6664e3a6a424af9f9b41ad86fb2c Mon Sep 17 00:00:00 2001
From: Jannik Buhr <jannik.m.buhr@gmail.com>
Date: Fri, 28 Jun 2024 12:38:54 +0200
Subject: [PATCH 11/14] need this url line

---
 lua/plugins/lsp.lua | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lua/plugins/lsp.lua b/lua/plugins/lsp.lua
index c327c7a..c002579 100644
--- a/lua/plugins/lsp.lua
+++ b/lua/plugins/lsp.lua
@@ -144,7 +144,7 @@ return {
           yaml = {
             schemaStore = {
               enable = true,
-              -- url = '',
+              url = '',
             },
           },
         },

From dbd2460d181f9a7c4b430bdfd0e14c2821328878 Mon Sep 17 00:00:00 2001
From: Jannik Buhr <jannik.m.buhr@gmail.com>
Date: Fri, 28 Jun 2024 20:33:10 +0200
Subject: [PATCH 12/14] wip

---
 init.lua               |  6 ++--
 lua/plugins/lsp.lua    | 65 +++++++++++++++++++++++++++++++-----------
 lua/plugins/quarto.lua |  2 +-
 lua/plugins/ui.lua     | 10 +------
 4 files changed, 53 insertions(+), 30 deletions(-)

diff --git a/init.lua b/init.lua
index 20e0803..18be247 100644
--- a/init.lua
+++ b/init.lua
@@ -10,6 +10,6 @@
 -- (may be outdated with newer versions of the plugins,
 -- check for yourself if you're interested in using them)
 
-require 'config.global'
-require 'config.lazy'
-require 'config.autocommands'
+require("config.global")
+require("config.lazy")
+require("config.autocommands")
diff --git a/lua/plugins/lsp.lua b/lua/plugins/lsp.lua
index c002579..87e4bed 100644
--- a/lua/plugins/lsp.lua
+++ b/lua/plugins/lsp.lua
@@ -1,9 +1,10 @@
 return {
+
   {
 
     -- for lsp features in code cells / embedded code
     'jmbuhr/otter.nvim',
-    dev = false,
+    dev = true,
     dependencies = {
       {
         'neovim/nvim-lspconfig',
@@ -37,7 +38,31 @@ 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()
@@ -73,13 +98,13 @@ return {
           ---@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')
@@ -93,8 +118,12 @@ return {
         allow_incremental_sync = true,
         debounce_text_changes = 150,
       }
+
+      local telescope_builtin = require 'telescope.builtin'
       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())
@@ -104,11 +133,11 @@ return {
       -- $home/.config/marksman/config.toml :
       -- [core]
       -- markdown.file_extensions = ["md", "markdown", "qmd"]
-      lspconfig.marksman.setup {
-        capabilities = capabilities,
-        filetypes = { 'markdown', 'quarto' },
-        root_dir = util.root_pattern('.git', '.marksman.toml', '_quarto.yml'),
-      }
+      -- lspconfig.marksman.setup {
+      --   capabilities = capabilities,
+      --   filetypes = { 'markdown', 'quarto' },
+      --   root_dir = util.root_pattern('.git', '.marksman.toml', '_quarto.yml'),
+      -- }
 
       lspconfig.r_language_server.setup {
         capabilities = capabilities,
@@ -201,16 +230,18 @@ 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,
             },
diff --git a/lua/plugins/quarto.lua b/lua/plugins/quarto.lua
index 7b33333..4489c3f 100644
--- a/lua/plugins/quarto.lua
+++ b/lua/plugins/quarto.lua
@@ -4,7 +4,7 @@ return {
     -- for complete functionality (language features)
     'quarto-dev/quarto-nvim',
     ft = { 'quarto' },
-    dev = false,
+    dev = true,
     opts = {
       lspFeatures = {
         languages = { 'r', 'python', 'julia', 'bash', 'lua', 'html', 'dot', 'javascript', 'typescript', 'ojs' },
diff --git a/lua/plugins/ui.lua b/lua/plugins/ui.lua
index 9b8fcd8..76c538a 100644
--- a/lua/plugins/ui.lua
+++ b/lua/plugins/ui.lua
@@ -333,15 +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
@@ -350,6 +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'

From d817c7e81b6e50c76fd8476814ae401b75fb4ee3 Mon Sep 17 00:00:00 2001
From: Jannik Buhr <jannik.m.buhr@gmail.com>
Date: Sat, 29 Jun 2024 14:43:03 +0200
Subject: [PATCH 13/14] disable treesitter textojects due to a bug

---
 lua/config/keymap.lua      |  4 +---
 lua/plugins/completion.lua |  2 +-
 lua/plugins/editing.lua    |  1 +
 lua/plugins/lsp.lua        | 18 ++++++++++--------
 lua/plugins/treesitter.lua |  8 +++++++-
 5 files changed, 20 insertions(+), 13 deletions(-)

diff --git a/lua/config/keymap.lua b/lua/config/keymap.lua
index ddad173..025cfc8 100644
--- a/lua/config/keymap.lua
+++ b/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' },
@@ -347,7 +345,7 @@ 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' },
diff --git a/lua/plugins/completion.lua b/lua/plugins/completion.lua
index 95199de..9a4752d 100644
--- a/lua/plugins/completion.lua
+++ b/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' },
diff --git a/lua/plugins/editing.lua b/lua/plugins/editing.lua
index 67a9409..53b958c 100644
--- a/lua/plugins/editing.lua
+++ b/lua/plugins/editing.lua
@@ -39,6 +39,7 @@ return {
         formatters_by_ft = {
           lua = { 'mystylua' },
           python = { 'isort', 'black' },
+          quarto = { 'injected' },
         },
         formatters = {
           mystylua = {
diff --git a/lua/plugins/lsp.lua b/lua/plugins/lsp.lua
index 87e4bed..ca9ee8e 100644
--- a/lua/plugins/lsp.lua
+++ b/lua/plugins/lsp.lua
@@ -87,10 +87,12 @@ 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')
@@ -110,6 +112,7 @@ return {
           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,
       })
@@ -119,11 +122,10 @@ return {
         debounce_text_changes = 150,
       }
 
-      local telescope_builtin = require 'telescope.builtin'
       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
+      -- 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())
@@ -133,11 +135,11 @@ return {
       -- $home/.config/marksman/config.toml :
       -- [core]
       -- markdown.file_extensions = ["md", "markdown", "qmd"]
-      -- lspconfig.marksman.setup {
-      --   capabilities = capabilities,
-      --   filetypes = { 'markdown', 'quarto' },
-      --   root_dir = util.root_pattern('.git', '.marksman.toml', '_quarto.yml'),
-      -- }
+      lspconfig.marksman.setup {
+        capabilities = capabilities,
+        filetypes = { 'markdown', 'quarto' },
+        root_dir = util.root_pattern('.git', '.marksman.toml', '_quarto.yml'),
+      }
 
       lspconfig.r_language_server.setup {
         capabilities = capabilities,
diff --git a/lua/plugins/treesitter.lua b/lua/plugins/treesitter.lua
index 82f6f58..e170a2d 100644
--- a/lua/plugins/treesitter.lua
+++ b/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()

From 03492ee193fbc3a0db7be735d9aef8cdd8707e5a Mon Sep 17 00:00:00 2001
From: Jannik Buhr <jannik.m.buhr@gmail.com>
Date: Sun, 30 Jun 2024 00:58:22 +0200
Subject: [PATCH 14/14] simplify

---
 init.lua               |  6 +++---
 lua/config/keymap.lua  |  9 +++++++--
 lua/plugins/lsp.lua    | 16 ++--------------
 lua/plugins/quarto.lua |  4 ++--
 4 files changed, 14 insertions(+), 21 deletions(-)

diff --git a/init.lua b/init.lua
index 18be247..20e0803 100644
--- a/init.lua
+++ b/init.lua
@@ -10,6 +10,6 @@
 -- (may be outdated with newer versions of the plugins,
 -- check for yourself if you're interested in using them)
 
-require("config.global")
-require("config.lazy")
-require("config.autocommands")
+require 'config.global'
+require 'config.lazy'
+require 'config.autocommands'
diff --git a/lua/config/keymap.lua b/lua/config/keymap.lua
index 025cfc8..5299f90 100644
--- a/lua/config/keymap.lua
+++ b/lua/config/keymap.lua
@@ -352,14 +352,19 @@ wk.register({
     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' },
diff --git a/lua/plugins/lsp.lua b/lua/plugins/lsp.lua
index ca9ee8e..bd350c4 100644
--- a/lua/plugins/lsp.lua
+++ b/lua/plugins/lsp.lua
@@ -4,26 +4,14 @@ return {
 
     -- for lsp features in code cells / embedded code
     'jmbuhr/otter.nvim',
-    dev = true,
+    dev = false,
     dependencies = {
       {
         '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 = {},
   },
 
   {
diff --git a/lua/plugins/quarto.lua b/lua/plugins/quarto.lua
index 4489c3f..3a2a946 100644
--- a/lua/plugins/quarto.lua
+++ b/lua/plugins/quarto.lua
@@ -4,10 +4,10 @@ return {
     -- for complete functionality (language features)
     'quarto-dev/quarto-nvim',
     ft = { 'quarto' },
-    dev = true,
+    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,