From 1075366382f679629cab39fbc6b7b84606d8bfb5 Mon Sep 17 00:00:00 2001
From: dlond <dlond@me.com>
Date: Mon, 13 Oct 2025 17:19:19 +1300
Subject: [PATCH 1/2] feat: Enhanced Jupyter notebook support
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- Improved Molten configuration with better cell handling
- Added Jupytext for .ipynb ↔ .py conversion
- Added image.nvim for inline plot display
- Smart cell execution with <leader>mc
- Auto-detection of notebook files
- Cell navigation with [c and ]c

Addresses #57

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>
---
 lua/plugins/config/image.lua    |  47 +++++++++++
 lua/plugins/config/jupytext.lua | 141 ++++++++++++++++++++++++++++++++
 lua/plugins/config/molten.lua   |  99 +++++++++++++++++++---
 lua/plugins/spec/image.lua      |   8 ++
 lua/plugins/spec/jupytext.lua   |  12 +++
 lua/plugins/spec/molten.lua     |  19 +++++
 6 files changed, 315 insertions(+), 11 deletions(-)
 create mode 100644 lua/plugins/config/image.lua
 create mode 100644 lua/plugins/config/jupytext.lua
 create mode 100644 lua/plugins/spec/image.lua
 create mode 100644 lua/plugins/spec/jupytext.lua
 create mode 100644 lua/plugins/spec/molten.lua

diff --git a/lua/plugins/config/image.lua b/lua/plugins/config/image.lua
new file mode 100644
index 0000000..f3216c9
--- /dev/null
+++ b/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_curser_mode = 'popup',
+        floating_windows = false,
+        filetypes = { 'markdown', 'vimwiki' },
+      },
+      neog = {
+        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
diff --git a/lua/plugins/config/jupytext.lua b/lua/plugins/config/jupytext.lua
new file mode 100644
index 0000000..0fad9f1
--- /dev/null
+++ b/lua/plugins/config/jupytext.lua
@@ -0,0 +1,141 @@
+-- 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
+        
+        for _, line in ipairs(first_lines) do
+          if line:match("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
\ No newline at end of file
diff --git a/lua/plugins/config/molten.lua b/lua/plugins/config/molten.lua
index 7dc4eb5..93d6ccf 100644
--- a/lua/plugins/config/molten.lua
+++ b/lua/plugins/config/molten.lua
@@ -1,18 +1,95 @@
+-- Molten (Jupyter) configuration
 local M = {}
 
 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' })
+  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()
+  -- Tell Molten about cell delimiters
+  vim.g.molten_cell_delimiter = '^# %%'
+
+  setup_keymaps()
+  setup_autocmds()
+end
+
+-- Initialize
+M.setup()
+
 return M
+
diff --git a/lua/plugins/spec/image.lua b/lua/plugins/spec/image.lua
new file mode 100644
index 0000000..8d2f9c5
--- /dev/null
+++ b/lua/plugins/spec/image.lua
@@ -0,0 +1,8 @@
+-- Render images in neovim
+return {
+  '3rd/image.nvim',
+  build = false,
+  opts = {
+    processor = 'magick_cli',
+  },
+}
diff --git a/lua/plugins/spec/jupytext.lua b/lua/plugins/spec/jupytext.lua
new file mode 100644
index 0000000..da401d5
--- /dev/null
+++ b/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
+}
\ No newline at end of file
diff --git a/lua/plugins/spec/molten.lua b/lua/plugins/spec/molten.lua
new file mode 100644
index 0000000..0abec4b
--- /dev/null
+++ b/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,
+}

From 539f9e6b61d50291c0c490ae75d1ec1a096f2bb4 Mon Sep 17 00:00:00 2001
From: dlond <dlond@me.com>
Date: Thu, 2 Apr 2026 11:17:16 +1300
Subject: [PATCH 2/2] fix: ready for testing

---
 lua/plugins/config/image.lua    |  4 ++--
 lua/plugins/config/jupytext.lua | 10 +++++++---
 lua/plugins/config/molten.lua   |  5 ++---
 lua/plugins/spec/image.lua      |  6 +++---
 lua/plugins/spec/jupytext.lua   |  4 ++--
 5 files changed, 16 insertions(+), 13 deletions(-)

diff --git a/lua/plugins/config/image.lua b/lua/plugins/config/image.lua
index f3216c9..807a5e5 100644
--- a/lua/plugins/config/image.lua
+++ b/lua/plugins/config/image.lua
@@ -11,11 +11,11 @@ function M.setup()
         clear_in_insert_mode = false,
         download_remote_images = true,
         only_render_image_at_cursor = false,
-        only_render_image_at_curser_mode = 'popup',
+        only_render_image_at_cursor_mode = 'popup',
         floating_windows = false,
         filetypes = { 'markdown', 'vimwiki' },
       },
-      neog = {
+      neorg = {
         enabled = true,
         filetypes = { 'norg' },
       },
diff --git a/lua/plugins/config/jupytext.lua b/lua/plugins/config/jupytext.lua
index 0fad9f1..9687ece 100644
--- a/lua/plugins/config/jupytext.lua
+++ b/lua/plugins/config/jupytext.lua
@@ -45,9 +45,13 @@ function M.setup()
         -- 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:") and line:match("formats:") then
+          if line:match("jupytext") then
+            saw_jupytext = true
+          end
+          if saw_jupytext and line:match("formats:") then
             has_pairing = true
             break
           end
@@ -138,4 +142,4 @@ end
 -- Run setup
 M.setup()
 
-return M
\ No newline at end of file
+return M
diff --git a/lua/plugins/config/molten.lua b/lua/plugins/config/molten.lua
index 93d6ccf..db7fe0d 100644
--- a/lua/plugins/config/molten.lua
+++ b/lua/plugins/config/molten.lua
@@ -1,8 +1,8 @@
 -- Molten (Jupyter) configuration
 local M = {}
 
-function M.setup()
-  -- Keybindings
+-- Keybindings
+local function setup_keymaps()
   local keymap = vim.keymap.set
 
   -- Basic operations
@@ -92,4 +92,3 @@ end
 M.setup()
 
 return M
-
diff --git a/lua/plugins/spec/image.lua b/lua/plugins/spec/image.lua
index 8d2f9c5..be5bf33 100644
--- a/lua/plugins/spec/image.lua
+++ b/lua/plugins/spec/image.lua
@@ -2,7 +2,7 @@
 return {
   '3rd/image.nvim',
   build = false,
-  opts = {
-    processor = 'magick_cli',
-  },
+  config = function()
+    require('plugins.config.image').setup()
+  end,
 }
diff --git a/lua/plugins/spec/jupytext.lua b/lua/plugins/spec/jupytext.lua
index da401d5..52d4cf3 100644
--- a/lua/plugins/spec/jupytext.lua
+++ b/lua/plugins/spec/jupytext.lua
@@ -8,5 +8,5 @@ return {
   end,
   config = function()
     require('plugins.config.jupytext')
-  end
-}
\ No newline at end of file
+  end,
+}