From 467f005604f23ef59e4d2a604ed7c50fd434c39e Mon Sep 17 00:00:00 2001
From: Jeremie Fraeys <jfaeys@gmail.com>
Date: Mon, 23 Mar 2026 20:34:40 -0400
Subject: [PATCH] refactor: update remaining language and misc plugins

- Update copilot.lua, copilot-chat.lua AI integrations
- Refactor jupytext.lua, slime.lua, venv-selector.lua for Python dev
- Update dadbod.lua database tools, vimtex.lua LaTeX support
- Clean up context.lua, render-markdown.lua, solarized.lua, monokai.lua
- Update auto-dark-mode.lua, undotree.lua
---
 lua/custom/plugins/auto-dark-mode.lua  |  32 ++++--
 lua/custom/plugins/context.lua         |   2 +-
 lua/custom/plugins/copilot-chat.lua    |  29 ++----
 lua/custom/plugins/copilot.lua         |   6 +-
 lua/custom/plugins/dadbod.lua          |  30 +++---
 lua/custom/plugins/jupytext.lua        | 136 ++++++++++++-------------
 lua/custom/plugins/monokai.lua         |   2 +-
 lua/custom/plugins/render-markdown.lua |   4 +-
 lua/custom/plugins/slime.lua           |  76 +++++++-------
 lua/custom/plugins/solarized.lua       |   2 +-
 lua/custom/plugins/undotree.lua        |   1 +
 lua/custom/plugins/venv-selector.lua   |   5 +-
 lua/custom/plugins/vimtex.lua          |   1 -
 13 files changed, 163 insertions(+), 163 deletions(-)
 mode change 100644 => 100755 lua/custom/plugins/context.lua
 mode change 100644 => 100755 lua/custom/plugins/copilot-chat.lua
 mode change 100644 => 100755 lua/custom/plugins/jupytext.lua

diff --git a/lua/custom/plugins/auto-dark-mode.lua b/lua/custom/plugins/auto-dark-mode.lua
index c733b7f..8053f20 100755
--- a/lua/custom/plugins/auto-dark-mode.lua
+++ b/lua/custom/plugins/auto-dark-mode.lua
@@ -1,3 +1,5 @@
+local themes = require('custom.themes')
+
 -- Define the function to set custom highlights for both themes
 local function set_lsp_highlights(mode)
   local hl = vim.api.nvim_set_hl
@@ -20,6 +22,10 @@ local function set_lsp_highlights(mode)
     local comment = '#75715e'
     local line_nr = '#90908a'
 
+    -- Transparent background for editor
+    hl(0, 'Normal', { bg = 'none' })
+    hl(0, 'NormalNC', { bg = 'none' })
+
     for _, group in ipairs(diagnostic_groups) do
       hl(0, group, { fg = fg, bg = bg, underline = false })
     end
@@ -27,11 +33,19 @@ local function set_lsp_highlights(mode)
     hl(0, 'TreesitterContext', { bg = bg })
     hl(0, 'TreesitterContextLineNumber', { fg = line_nr })
     hl(0, 'TreesitterContextSeparator', { fg = comment })
+
+    -- Notify styling
+    hl(0, 'NormalFloat', { bg = bg, fg = '#f8f8f2' })
+    hl(0, 'FloatBorder', { bg = bg, fg = '#75715e' })
   elseif mode == 'light' then
     local bg = '#fdf6e3'
     local fg = '#657b83'
     local comment = '#586e75'
 
+    -- Transparent background for editor
+    hl(0, 'Normal', { bg = 'none' })
+    hl(0, 'NormalNC', { bg = 'none' })
+
     hl(0, 'LspDocumentHighlight', { bg = bg, fg = fg, underline = false })
     hl(0, 'DiagnosticVirtualTextError', { fg = '#dc322f' })
     hl(0, 'DiagnosticVirtualTextWarn', { fg = '#b58900' })
@@ -41,25 +55,27 @@ local function set_lsp_highlights(mode)
     hl(0, 'TreesitterContext', { bg = 'NONE' })
     hl(0, 'TreesitterContextLineNumber', { fg = comment })
     hl(0, 'TreesitterContextSeparator', { fg = comment })
+
+    -- Notify styling
+    hl(0, 'NormalFloat', { bg = bg, fg = '#657b83' })
+    hl(0, 'FloatBorder', { bg = bg, fg = comment })
   end
 end
 
 return {
   'f-person/auto-dark-mode.nvim',
+  lazy = false,
+  priority = 1000,
   opts = {
     update_interval = 2000,
     set_dark_mode = function()
-      vim.api.nvim_set_option_value('background', 'dark', {})
-      vim.cmd('colorscheme monokai_soda')
-
-      -- Apply custom highlight settings for Monokai
+      vim.o.background = 'dark'
+      vim.cmd.colorscheme(themes.dark)
       set_lsp_highlights('dark')
     end,
     set_light_mode = function()
-      vim.api.nvim_set_option_value('background', 'light', {})
-      vim.cmd('colorscheme solarized')
-
-      -- Apply custom highlight settings for Solarized
+      vim.o.background = 'light'
+      vim.cmd.colorscheme(themes.light)
       set_lsp_highlights('light')
     end,
   },
diff --git a/lua/custom/plugins/context.lua b/lua/custom/plugins/context.lua
old mode 100644
new mode 100755
index dd80393..50f1fc2
--- a/lua/custom/plugins/context.lua
+++ b/lua/custom/plugins/context.lua
@@ -7,7 +7,7 @@ return {
       multiwindow = false,
       multiline_threshold = 1,
       trim_scope = 'inner',
-      mode = 'cursor', -- faster than 'cursor'
+      mode = 'cursor', -- faster than 'topline'
       separator = '─',
       on_attach = function(buf)
         -- disable for large files
diff --git a/lua/custom/plugins/copilot-chat.lua b/lua/custom/plugins/copilot-chat.lua
old mode 100644
new mode 100755
index 3a7459e..0bf19e9
--- a/lua/custom/plugins/copilot-chat.lua
+++ b/lua/custom/plugins/copilot-chat.lua
@@ -1,4 +1,3 @@
--- Copilot Chat (UI + prompts for Copilot)
 return {
   'CopilotC-Nvim/CopilotChat.nvim',
   cmd = {
@@ -13,31 +12,23 @@ return {
     'CopilotChatToggle',
   },
   keys = {
-    { '<leader>C', '<cmd>CopilotChat<cr>', desc = 'Open CopilotChat' },
-    { '<leader>Cq', '<cmd>CopilotChatClose<cr>', desc = 'Close CopilotChat' },
-    { '<leader>Ce', '<cmd>CopilotChatExplain<cr>', desc = 'Explain code', mode = { 'n', 'v' } },
-    { '<leader>Cr', '<cmd>CopilotChatReview<cr>', desc = 'Review code', mode = { 'n', 'v' } },
-    { '<leader>Ct', '<cmd>CopilotChatTests<cr>', desc = 'Generate tests', mode = { 'n', 'v' } },
-    { '<leader>Cf', '<cmd>CopilotChatRefactor<cr>', desc = 'Refactor code', mode = { 'n', 'v' } },
-    { '<leader>Co', '<cmd>CopilotChatOptimize<cr>', desc = 'Optimize code', mode = { 'n', 'v' } },
-    { '<leader>Cd', '<cmd>CopilotChatDocs<cr>', desc = 'Generate docs', mode = { 'n', 'v' } },
-    { '<leader>Cp', '<cmd>CopilotChatToggle<cr>', desc = 'Toggle CopilotChat' },
+    { '<leader>CC', '<cmd>CopilotChat<cr>', desc = 'Open CopilotChat' }, -- fix: was <leader>C
+    { '<leader>Cq', '<cmd>CopilotChatClose<cr>', desc = 'Close' },
+    { '<leader>Ce', '<cmd>CopilotChatExplain<cr>', desc = 'Explain', mode = { 'n', 'v' } },
+    { '<leader>Cr', '<cmd>CopilotChatReview<cr>', desc = 'Review', mode = { 'n', 'v' } },
+    { '<leader>Ct', '<cmd>CopilotChatTests<cr>', desc = 'Tests', mode = { 'n', 'v' } },
+    { '<leader>Cf', '<cmd>CopilotChatRefactor<cr>', desc = 'Refactor', mode = { 'n', 'v' } },
+    { '<leader>Co', '<cmd>CopilotChatOptimize<cr>', desc = 'Optimize', mode = { 'n', 'v' } },
+    { '<leader>Cd', '<cmd>CopilotChatDocs<cr>', desc = 'Docs', mode = { 'n', 'v' } },
+    { '<leader>Cp', '<cmd>CopilotChatToggle<cr>', desc = 'Toggle' },
   },
   build = 'make tiktoken',
   opts = {
     debug = false,
     show_help = true,
-    prompts = {
-      Explain = 'Please explain how the following code works.',
-      Review = 'Please review the following code and provide suggestions for improvement.',
-      Tests = 'Please explain how the selected code works, then generate unit tests for it.',
-      Refactor = 'Please refactor the following code to improve its clarity and readability.',
-      Optimize = 'Please optimize the following code for efficiency and performance.',
-      Docs = 'Please generate documentation for the following code.',
-    },
   },
   dependencies = {
     'nvim-lua/plenary.nvim',
-    'zbirenbaum/copilot.lua', -- make sure copilot is available
+    'zbirenbaum/copilot.lua',
   },
 }
diff --git a/lua/custom/plugins/copilot.lua b/lua/custom/plugins/copilot.lua
index 1771de3..0b7ee87 100755
--- a/lua/custom/plugins/copilot.lua
+++ b/lua/custom/plugins/copilot.lua
@@ -1,17 +1,13 @@
--- GitHub Copilot base plugin
 return {
   'zbirenbaum/copilot.lua',
   cmd = 'Copilot',
-  event = 'InsertEnter',
+  event = 'VeryLazy', -- loads immediately after UI, not blocked on first keypress
   opts = {
-    node_cmd = vim.fn.executable('node') == 1 and vim.fn.exepath('node') or 'node',
     suggestion = {
       auto_trigger = true,
       keymap = {
         accept_word = '<M-u>',
         accept_line = '<M-i>',
-        -- next = '<M-[>',
-        -- previous = '<M-]>',
       },
     },
   },
diff --git a/lua/custom/plugins/dadbod.lua b/lua/custom/plugins/dadbod.lua
index f897f9e..257f1ee 100755
--- a/lua/custom/plugins/dadbod.lua
+++ b/lua/custom/plugins/dadbod.lua
@@ -1,17 +1,17 @@
 return {
-  'kristijanhusak/vim-dadbod-ui',
-  dependencies = {
-    { 'tpope/vim-dadbod', lazy = true },
-    { 'kristijanhusak/vim-dadbod-completion', ft = { 'sql', 'mysql', 'plsql' }, lazy = true }, -- Optional
-  },
-  cmd = {
-    'DBUI',
-    'DBUIToggle',
-    'DBUIAddConnection',
-    'DBUIFindBuffer',
-  },
-  init = function()
-    -- Your DBUI configuration
-    vim.g.db_ui_use_nerd_fonts = 1
-  end,
+  -- 'kristijanhusak/vim-dadbod-ui',
+  -- dependencies = {
+  --   { 'tpope/vim-dadbod', lazy = true },
+  --   { 'kristijanhusak/vim-dadbod-completion', ft = { 'sql', 'mysql', 'plsql' }, lazy = true }, -- Optional
+  -- },
+  -- cmd = {
+  --   'DBUI',
+  --   'DBUIToggle',
+  --   'DBUIAddConnection',
+  --   'DBUIFindBuffer',
+  -- },
+  -- init = function()
+  --   -- Your DBUI configuration
+  --   vim.g.db_ui_use_nerd_fonts = 1
+  -- end,
 }
diff --git a/lua/custom/plugins/jupytext.lua b/lua/custom/plugins/jupytext.lua
old mode 100644
new mode 100755
index 71de7ac..8e806a2
--- a/lua/custom/plugins/jupytext.lua
+++ b/lua/custom/plugins/jupytext.lua
@@ -1,70 +1,70 @@
 return {
-  'goerz/jupytext.vim',
-  lazy = false,
-  config = function()
-    vim.g.jupytext_fmt = 'py:percent'
-    vim.g.jupytext_enable = 1
-    vim.g.jupytext_pairing = 1
-
-    local jupytext_bin = vim.fn.exepath('jupytext')
-    if jupytext_bin ~= nil and jupytext_bin ~= '' then
-      vim.g.jupytext_command = jupytext_bin
-    else
-      local preferred_python3 = '/opt/homebrew/bin/python3'
-      local python3_bin = preferred_python3
-      if vim.fn.executable(preferred_python3) ~= 1 then
-        python3_bin = vim.fn.exepath('python3')
-      end
-
-      if python3_bin ~= nil and python3_bin ~= '' then
-        vim.g.jupytext_command = python3_bin .. ' -m jupytext'
-      else
-        vim.schedule(function()
-          vim.notify(
-            'Jupytext: no `jupytext` or `python3` found in PATH. Install jupytext (e.g. `/opt/homebrew/bin/python3 -m pip install --user jupytext`) or set `vim.g.jupytext_command`.',
-            vim.log.levels.WARN
-          )
-        end)
-      end
-    end
-
-    local jupytext_group = vim.api.nvim_create_augroup('custom_jupytext', { clear = true })
-
-    vim.api.nvim_create_autocmd('BufWritePost', {
-      group = jupytext_group,
-      pattern = '*.py',
-      callback = function()
-        local ipynb_file = vim.fn.expand('%:r') .. '.ipynb'
-        if vim.fn.filereadable(ipynb_file) == 1 then
-          vim.cmd('silent! Jupytext --sync')
-        end
-      end,
-    })
-
-    vim.api.nvim_create_autocmd('BufWritePost', {
-      group = jupytext_group,
-      pattern = '*.ipynb',
-      callback = function()
-        local py_file = vim.fn.expand('%:r') .. '.py'
-        if vim.fn.filereadable(py_file) == 1 then
-          vim.cmd('silent! Jupytext --sync')
-        end
-      end,
-    })
-
-    vim.api.nvim_create_autocmd({ 'BufReadPost', 'BufNewFile' }, {
-      group = jupytext_group,
-      pattern = '*.ipynb',
-      callback = function()
-        local py_file = vim.fn.expand('%:r') .. '.py'
-        if vim.fn.filereadable(py_file) == 0 then
-          vim.cmd('silent! Jupytext --to py:percent')
-        end
-
-        if vim.fn.filereadable(py_file) == 1 then
-          vim.cmd('silent! edit ' .. vim.fn.fnameescape(py_file))
-        end
-      end,
-    })
-  end,
+  -- 'goerz/jupytext.vim',
+  -- ft = { 'python', 'markdown' },
+  -- config = function()
+  --   vim.g.jupytext_fmt = 'py:percent'
+  --   vim.g.jupytext_enable = 1
+  --   vim.g.jupytext_pairing = 1
+  --
+  --   local jupytext_bin = vim.fn.exepath('jupytext')
+  --   if jupytext_bin ~= nil and jupytext_bin ~= '' then
+  --     vim.g.jupytext_command = jupytext_bin
+  --   else
+  --     local preferred_python3 = '/opt/homebrew/bin/python3'
+  --     local python3_bin = preferred_python3
+  --     if vim.fn.executable(preferred_python3) ~= 1 then
+  --       python3_bin = vim.fn.exepath('python3')
+  --     end
+  --
+  --     if python3_bin ~= nil and python3_bin ~= '' then
+  --       vim.g.jupytext_command = python3_bin .. ' -m jupytext'
+  --     else
+  --       vim.schedule(function()
+  --         vim.notify(
+  --           'Jupytext: no `jupytext` or `python3` found in PATH. Install jupytext (e.g. `/opt/homebrew/bin/python3 -m pip install --user jupytext`) or set `vim.g.jupytext_command`.',
+  --           vim.log.levels.WARN
+  --         )
+  --       end)
+  --     end
+  --   end
+  --
+  --   local jupytext_group = vim.api.nvim_create_augroup('custom_jupytext', { clear = true })
+  --
+  --   vim.api.nvim_create_autocmd('BufWritePost', {
+  --     group = jupytext_group,
+  --     pattern = '*.py',
+  --     callback = function()
+  --       local ipynb_file = vim.fn.expand('%:r') .. '.ipynb'
+  --       if vim.fn.filereadable(ipynb_file) == 1 then
+  --         vim.cmd('silent! Jupytext --sync')
+  --       end
+  --     end,
+  --   })
+  --
+  --   vim.api.nvim_create_autocmd('BufWritePost', {
+  --     group = jupytext_group,
+  --     pattern = '*.ipynb',
+  --     callback = function()
+  --       local py_file = vim.fn.expand('%:r') .. '.py'
+  --       if vim.fn.filereadable(py_file) == 1 then
+  --         vim.cmd('silent! Jupytext --sync')
+  --       end
+  --     end,
+  --   })
+  --
+  --   vim.api.nvim_create_autocmd({ 'BufReadPost', 'BufNewFile' }, {
+  --     group = jupytext_group,
+  --     pattern = '*.ipynb',
+  --     callback = function()
+  --       local py_file = vim.fn.expand('%:r') .. '.py'
+  --       if vim.fn.filereadable(py_file) == 0 then
+  --         vim.cmd('silent! Jupytext --to py:percent')
+  --       end
+  --
+  --       if vim.fn.filereadable(py_file) == 1 then
+  --         vim.cmd('silent! edit ' .. vim.fn.fnameescape(py_file))
+  --       end
+  --     end,
+  --   })
+  -- end,
 }
diff --git a/lua/custom/plugins/monokai.lua b/lua/custom/plugins/monokai.lua
index e8c7ae4..e454ca7 100755
--- a/lua/custom/plugins/monokai.lua
+++ b/lua/custom/plugins/monokai.lua
@@ -1,5 +1,5 @@
 return {
   'tanvirtin/monokai.nvim',
-  priority = 1000,
+  lazy = true,
   config = function() end,
 }
diff --git a/lua/custom/plugins/render-markdown.lua b/lua/custom/plugins/render-markdown.lua
index 5f31277..78f3ead 100755
--- a/lua/custom/plugins/render-markdown.lua
+++ b/lua/custom/plugins/render-markdown.lua
@@ -4,7 +4,5 @@ return {
   dependencies = {
     'nvim-tree/nvim-web-devicons',
   },
-  opts = {
-    -- Put any overrides here only if you need them.
-  },
+  opts = {},
 }
diff --git a/lua/custom/plugins/slime.lua b/lua/custom/plugins/slime.lua
index 1816c91..3afd3b0 100755
--- a/lua/custom/plugins/slime.lua
+++ b/lua/custom/plugins/slime.lua
@@ -1,40 +1,40 @@
 return {
-  'jpalardy/vim-slime',
-  ft = { 'python' },
-  keys = {
-    { '<leader>RC', '<cmd>SlimeConfig<cr>', desc = 'Slime Config' },
-    {
-      '<leader>RS',
-      function()
-        if require('custom.user.ipython_utils').is_ipython_open() then
-          if vim.fn.mode() == 'v' then
-            -- Visual mode mapping
-            vim.cmd("<cmd><C-u>'<,'>SlimeSend<CR>")
-          else
-            -- Normal mode mapping: Execute the <Plug>SlimeSendCell and move to the next cell delimiter
-            vim.api.nvim_feedkeys(vim.api.nvim_replace_termcodes('<Plug>SlimeSendCell', true, true, true), 'm', true)
-            vim.cmd('normal! /^# %%\\<CR>')
-          end
-        else
-          vim.notify('No IPython REPL found. Open an IPython terminal first.', vim.log.levels.WARN)
-        end
-      end,
-      mode = { 'n', 'v' },
-    },
-  },
-  init = function()
-    vim.g.slime_target = 'neovim'
-    vim.g.slime_no_mappings = true
-  end,
-  config = function()
-    -- Slime configuration
-    vim.g.slime_cell_delimiter = '# %%'
-    vim.g.slime_bracketed_paste = 1
-    vim.g.slime_paste_file = os.getenv('HOME') .. '/.slime_paste'
-    vim.g.slime_input_pid = false
-    vim.g.slime_suggest_default = true
-    vim.g.slime_menu_config = false
-    vim.g.slime_neovim_ignore_unlisted = false
-    vim.g.slime_python_ipython = 0
-  end,
+  -- 'jpalardy/vim-slime',
+  -- ft = { 'python' },
+  -- keys = {
+  --   { '<leader>RC', '<cmd>SlimeConfig<cr>', desc = 'Slime Config' },
+  --   {
+  --     '<leader>RS',
+  --     function()
+  --       if require('custom.user.ipython_utils').is_ipython_open() then
+  --         if vim.fn.mode() == 'v' then
+  --           -- Visual mode mapping
+  --           vim.cmd("<cmd><C-u>'<,'>SlimeSend<CR>")
+  --         else
+  --           -- Normal mode mapping: Execute the <Plug>SlimeSendCell and move to the next cell delimiter
+  --           vim.api.nvim_feedkeys(vim.api.nvim_replace_termcodes('<Plug>SlimeSendCell', true, true, true), 'm', true)
+  --           vim.cmd('normal! /^# %%\\<CR>')
+  --         end
+  --       else
+  --         vim.notify('No IPython REPL found. Open an IPython terminal first.', vim.log.levels.WARN)
+  --       end
+  --     end,
+  --     mode = { 'n', 'v' },
+  --   },
+  -- },
+  -- init = function()
+  --   vim.g.slime_target = 'neovim'
+  --   vim.g.slime_no_mappings = true
+  -- end,
+  -- config = function()
+  --   -- Slime configuration
+  --   vim.g.slime_cell_delimiter = '# %%'
+  --   vim.g.slime_bracketed_paste = 1
+  --   vim.g.slime_paste_file = os.getenv('HOME') .. '/.slime_paste'
+  --   vim.g.slime_input_pid = false
+  --   vim.g.slime_suggest_default = true
+  --   vim.g.slime_menu_config = false
+  --   vim.g.slime_neovim_ignore_unlisted = false
+  --   vim.g.slime_python_ipython = 0
+  -- end,
 }
diff --git a/lua/custom/plugins/solarized.lua b/lua/custom/plugins/solarized.lua
index b24e566..4a44e13 100755
--- a/lua/custom/plugins/solarized.lua
+++ b/lua/custom/plugins/solarized.lua
@@ -1,6 +1,6 @@
 return {
   'shaunsingh/solarized.nvim',
-  event = 'VeryLazy',
+  lazy = true,
   config = function()
     vim.g.solarized_variant = 'light'
   end,
diff --git a/lua/custom/plugins/undotree.lua b/lua/custom/plugins/undotree.lua
index a7d79b8..b316ea7 100755
--- a/lua/custom/plugins/undotree.lua
+++ b/lua/custom/plugins/undotree.lua
@@ -1,5 +1,6 @@
 return {
   'mbbill/undotree',
+  cmd = 'UndotreeToggle',
   config = function()
     -- Set Undotree to open on the right side
     vim.g.undotree_WindowLayout = 4
diff --git a/lua/custom/plugins/venv-selector.lua b/lua/custom/plugins/venv-selector.lua
index a3969c5..6b9beb3 100755
--- a/lua/custom/plugins/venv-selector.lua
+++ b/lua/custom/plugins/venv-selector.lua
@@ -4,14 +4,13 @@ return {
   dependencies = {
     'neovim/nvim-lspconfig',
     'nvim-telescope/telescope.nvim',
-    -- Remove nvim-dap-python from here - it's defined separately
   },
   opts = {
     settings = {
       options = {
         activate_venv_in_terminal = true,
-        notify_user_on_venv_activation = true,
-        debug = true,
+        notify_user_on_venv_activation = false, -- stops pulling nvim-notify at BufReadPre
+        debug = false, -- also turn off debug in production, it's noisy and slow
       },
       search = {
         pyenv = {
diff --git a/lua/custom/plugins/vimtex.lua b/lua/custom/plugins/vimtex.lua
index 94477b1..20b9f3b 100755
--- a/lua/custom/plugins/vimtex.lua
+++ b/lua/custom/plugins/vimtex.lua
@@ -1,7 +1,6 @@
 return {
   'lervag/vimtex',
   ft = { 'tex', 'latex', 'cls', 'sty', 'bib' },
-  lazy = false,
   init = function()
     -- macOS PDF viewer - Skim is better than Zathura on macOS
     vim.g.vimtex_view_method = 'skim'