jupyter improvements

lua/plugins/config/image.lua

@@ -0,0 +1,47 @@
+local M = {}
+
+function M.setup()
+  local image = require 'image'
+  image:setup {
+    backend = 'kitty',
+    processor = 'magick_cli',
+    integrations = {
+      markdown = {
+        enabled = true,
+        clear_in_insert_mode = false,
+        download_remote_images = true,
+        only_render_image_at_cursor = false,
+        only_render_image_at_cursor_mode = 'popup',
+        floating_windows = false,
+        filetypes = { 'markdown', 'vimwiki' },
+      },
+      neorg = {
+        enabled = true,
+        filetypes = { 'norg' },
+      },
+      typst = {
+        enabled = true,
+        filetypes = { 'typst' },
+      },
+      html = {
+        enabled = false,
+      },
+      css = {
+        enabled = false,
+      },
+    },
+    max_width = 100,
+    max_height = 12,
+    max_width_window_percentage = math.huge,
+    max_height_window_percentage = math.huge,
+    scale_factor = 1.0,
+    window_overlap_clear_enabled = true,
+    -- window_overlap_clear_ft_ignore = { 'cmp_menu', 'cmp_docs', 'snacks_notif', 'scrollview', 'scrollview_sign' },
+    window_overlap_clear_ft_ignore = { 'cmp_menu', 'cmp_docs', '' },
+    editor_only_render_when_focused = false,
+    tmux_show_only_in_active_window = false,
+    hijack_file_patterns = { '*.png', '*.jpg', '*.jpeg', '*.gif', '*.webp', '*.avif' },
+  }
+end
+
+return M

lua/plugins/config/jupytext.lua

@@ -0,0 +1,145 @@
+-- Jupytext configuration
+local M = {}
+
+function M.setup()
+  -- Basic settings
+  vim.g.jupytext_fmt = 'py:percent'
+  vim.g.jupytext_command = 'jupytext'
+
+  -- Create user commands
+  local function create_commands()
+    vim.api.nvim_create_user_command('JupytextSync', function()
+      vim.cmd('!jupytext --sync %')
+      vim.notify("Notebook synced", vim.log.levels.INFO)
+    end, { desc = "Sync current file with its notebook pair" })
+
+    vim.api.nvim_create_user_command('JupytextPair', function()
+      vim.cmd('!jupytext --set-formats ipynb,py:percent %')
+      vim.notify("Notebook paired with .py file", vim.log.levels.INFO)
+    end, { desc = "Pair notebook with Python file" })
+
+    vim.api.nvim_create_user_command('JupytextConvert', function(opts)
+      local format = opts.args ~= "" and opts.args or "py:percent"
+      vim.cmd('!jupytext --to ' .. format .. ' %')
+      vim.notify("Converted to " .. format, vim.log.levels.INFO)
+    end, { 
+      nargs = '?',
+      desc = "Convert notebook to format (default: py:percent)",
+      complete = function()
+        return { 'py:percent', 'md', 'py:light', 'py:sphinx', 'jl:percent', 'r:percent' }
+      end
+    })
+  end
+
+  -- Setup auto-sync for paired files
+  local function setup_autosync()
+    local augroup = vim.api.nvim_create_augroup("JupytextSync", { clear = true })
+
+    vim.api.nvim_create_autocmd("BufWritePost", {
+      group = augroup,
+      pattern = { "*.py", "*.ipynb", "*.md", "*.jl", "*.r" },
+      callback = function()
+        local file = vim.fn.expand('%:p')
+        local bufnr = vim.api.nvim_get_current_buf()
+
+        -- Check if file has jupytext pairing metadata
+        local first_lines = vim.api.nvim_buf_get_lines(bufnr, 0, 15, false)
+        local has_pairing = false
+        local saw_jupytext = false
+
+        for _, line in ipairs(first_lines) do
+          if line:match("jupytext") then
+            saw_jupytext = true
+          end
+          if saw_jupytext and line:match("formats:") then
+            has_pairing = true
+            break
+          end
+        end
+
+        if has_pairing then
+          -- Run sync in background
+          vim.fn.jobstart({'jupytext', '--sync', file}, {
+            on_exit = function(_, exit_code)
+              if exit_code == 0 then
+                vim.schedule(function()
+                  vim.notify("Jupytext: Synced with notebook", vim.log.levels.INFO)
+                end)
+              end
+            end
+          })
+        end
+      end,
+      desc = "Auto-sync Jupytext paired files"
+    })
+  end
+
+  -- Setup keymaps
+  local function setup_keymaps()
+    -- Only set these in relevant filetypes
+    vim.api.nvim_create_autocmd("FileType", {
+      pattern = { "python", "markdown", "julia", "r" },
+      callback = function()
+        local opts = { buffer = true, silent = true }
+        vim.keymap.set("n", "<leader>js", ":JupytextSync<CR>", 
+          vim.tbl_extend("force", opts, { desc = "Sync with notebook" }))
+        vim.keymap.set("n", "<leader>jp", ":JupytextPair<CR>", 
+          vim.tbl_extend("force", opts, { desc = "Pair with notebook" }))
+        vim.keymap.set("n", "<leader>jc", ":JupytextConvert ", 
+          vim.tbl_extend("force", opts, { desc = "Convert to format" }))
+      end
+    })
+  end
+
+  -- Integration with Molten
+  local function setup_molten_integration()
+    -- When opening .ipynb files, offer to convert
+    vim.api.nvim_create_autocmd({"BufRead", "BufNewFile"}, {
+      pattern = "*.ipynb",
+      callback = function()
+        local file = vim.fn.expand('%:p')
+        local py_file = file:gsub('%.ipynb$', '.py')
+
+        -- Check if .py version exists
+        if vim.fn.filereadable(py_file) == 1 then
+          -- Close the current buffer and open the .py version
+          vim.cmd('buffer #')  -- Go to alternate buffer
+          vim.cmd('bdelete! #')  -- Delete the ipynb buffer
+          vim.cmd('edit ' .. py_file)
+          vim.notify("Opened paired .py file instead of .ipynb", vim.log.levels.INFO)
+        else
+          -- Offer to convert
+          vim.schedule(function()
+            vim.ui.select(
+              { "Convert to .py", "Keep as JSON" },
+              { prompt = "Convert notebook to Python?" },
+              function(choice)
+                if choice == "Convert to .py" then
+                  local result = vim.fn.system('jupytext --to py:percent "' .. file .. '"')
+                  if vim.v.shell_error == 0 then
+                    vim.cmd('edit! ' .. py_file)
+                    vim.notify("Converted and opened as .py", vim.log.levels.INFO)
+                  else
+                    vim.notify("Failed to convert: " .. result, vim.log.levels.ERROR)
+                  end
+                end
+              end
+            )
+          end)
+        end
+      end,
+      desc = "Handle .ipynb files with Jupytext"
+    })
+  end
+
+  -- Initialize all components
+  create_commands()
+  setup_autosync()
+  setup_keymaps()
+  setup_molten_integration()
+end
+
+-- Run setup
+M.setup()
+
+return M

lua/plugins/config/molten.lua

@@ -1,18 +1,94 @@
+-- Molten (Jupyter) configuration
 local M = {}
 
+-- Keybindings
+local function setup_keymaps()
+  local keymap = vim.keymap.set
+
+  -- Basic operations
+  keymap('n', '<leader>mi', ':MoltenInit<CR>', { desc = 'Molten Init', silent = true })
+  keymap('n', '<leader>ml', ':MoltenEvaluateLine<CR>', { desc = 'Evaluate Line', silent = true })
+  keymap('n', '<leader>mr', ':MoltenReevaluateCell<CR>', { desc = 'Re-evaluate Cell', silent = true })
+  keymap('v', '<leader>mv', ':<C-u>MoltenEvaluateVisual<CR>gv', { desc = 'Evaluate Visual', silent = true })
+
+  -- Additional useful keymaps
+  keymap('n', '<leader>md', ':MoltenDelete<CR>', { desc = 'Delete Cell', silent = true })
+  keymap('n', '<leader>mh', ':MoltenHideOutput<CR>', { desc = 'Hide Output', silent = true })
+  keymap('n', '<leader>mo', ':noautocmd MoltenEnterOutput<CR>', { desc = 'Enter Output', silent = true })
+
+  -- Better cell execution that always works
+  keymap('n', '<leader>mc', function()
+    -- Always use the operator approach for consistency
+    -- This finds cell boundaries based on # %% markers
+    vim.cmd 'MoltenEvaluateOperator'
+
+    -- Send 'ip' (inner paragraph) which respects the cell markers
+    local keys = vim.api.nvim_replace_termcodes('ip', true, false, true)
+    vim.api.nvim_feedkeys(keys, 'n', false)
+  end, { desc = 'Run Cell', silent = true })
+
+  -- Alternative: Run and move to next cell
+  keymap('n', '<leader>mn', function()
+    vim.cmd 'MoltenEvaluateOperator'
+    local keys = vim.api.nvim_replace_termcodes('ip', true, false, true)
+    vim.api.nvim_feedkeys(keys, 'n', false)
+    -- Move to next cell
+    vim.fn.search('^# %%', 'W')
+  end, { desc = 'Run Cell and Next', silent = true })
+
+  -- Cell navigation
+  keymap('n', ']c', ':MoltenNext<CR>', { desc = 'Next Cell', silent = true })
+  keymap('n', '[c', ':MoltenPrev<CR>', { desc = 'Previous Cell', silent = true })
+end
+
+-- Setup autocommands
+local function setup_autocmds()
+  local augroup = vim.api.nvim_create_augroup('MoltenConfig', { clear = true })
+
+  -- Auto-initialize for Python files
+  vim.api.nvim_create_autocmd('FileType', {
+    group = augroup,
+    pattern = { 'python' },
+    callback = function()
+      vim.keymap.set('n', '<leader>ms', function()
+        vim.cmd 'MoltenInit python3'
+        vim.notify('Molten kernel started', vim.log.levels.INFO)
+      end, { buffer = true, desc = 'Start Python Kernel' })
+
+      -- Auto-detect notebook files with cell markers
+      vim.schedule(function()
+        local lines = vim.api.nvim_buf_get_lines(0, 0, -1, false)
+        for _, line in ipairs(lines) do
+          if line:match '^# %%' then
+            vim.notify('Notebook detected. Use <leader>ms to start kernel', vim.log.levels.INFO)
+            break
+          end
+        end
+      end)
+    end,
+  })
+
+  -- Better notebook file handling
+  vim.api.nvim_create_autocmd('BufRead', {
+    group = augroup,
+    pattern = { '*.ipynb' },
+    callback = function()
+      -- Consider using jupytext for better .ipynb handling
+      vim.notify('Notebook file detected. Use :MoltenInit to start kernel', vim.log.levels.INFO)
+    end,
+  })
+end
+
+-- Main setup function
 function M.setup()
-  -- Keybindings
-  local map = vim.keymap.set
-
-  map('n', '<leader>Mi', ':MoltenInit<CR>', { desc = 'Molten: Initialize' })
-  map('n', '<leader>Me', ':MoltenEvaluateOperator<CR>', { desc = 'Molten: Evaluate operator' })
-  map('v', '<leader>Me', ':<C-u>MoltenEvaluateVisual<CR>gv', { desc = 'Molten: Evaluate visual' })
-  map('n', '<leader>Ml', ':MoltenEvaluateLine<CR>', { desc = 'Molten: Evaluate line' })
-  map('n', '<leader>Mr', ':MoltenReevaluateCell<CR>', { desc = 'Molten: Re-evaluate cell' })
-  map('n', '<leader>Md', ':MoltenDelete<CR>', { desc = 'Molten: Delete cell' })
-  map('n', '<leader>Mo', ':MoltenShowOutput<CR>', { desc = 'Molten: Show output' })
-  map('n', '<leader>Mh', ':MoltenHideOutput<CR>', { desc = 'Molten: Hide output' })
-  map('n', '<leader>Mx', ':MoltenInterrupt<CR>', { desc = 'Molten: Interrupt kernel' })
+  -- Tell Molten about cell delimiters
+  vim.g.molten_cell_delimiter = '^# %%'
+
+  setup_keymaps()
+  setup_autocmds()
 end
 
+-- Initialize
+M.setup()
+
 return M

lua/plugins/spec/image.lua

@@ -0,0 +1,8 @@
+-- Render images in neovim
+return {
+  '3rd/image.nvim',
+  build = false,
+  config = function()
+    require('plugins.config.image').setup()
+  end,
+}

lua/plugins/spec/jupytext.lua

@@ -0,0 +1,12 @@
+-- Jupytext - Jupyter notebook as plain text
+return {
+  'goerz/jupytext.vim',
+  ft = { 'ipynb', 'python', 'markdown', 'julia', 'r' },
+  build = function()
+    -- Ensure jupytext is installed
+    vim.fn.system('pip install jupytext')
+  end,
+  config = function()
+    require('plugins.config.jupytext')
+  end,
+}

lua/plugins/spec/molten.lua

@@ -0,0 +1,19 @@
+-- Molten - Jupyter notebook support in Neovim
+return {
+  'benlubas/molten-nvim',
+  version = '^1.0.0',
+  dependencies = { '3rd/image.nvim' },
+  build = ':UpdateRemotePlugins',
+  init = function()
+    -- Basic settings
+    vim.g.molten_image_provider = 'image.nvim'
+    vim.g.molten_output_win_max_height = 20
+    vim.g.molten_auto_open_output = true
+    vim.g.molten_wrap_output = true
+    vim.g.molten_virt_text_output = true
+  end,
+  config = function()
+    -- Delegate to config file for complex setup
+    require('plugins.config.molten')
+  end,
+}