nvim: Update +show mode mappings and descriptions

Mappings preceded by <leader>s 'show' something so removed a lot of the 'toggle'
wording from their descriptions.

Subsumed the toggleterm toggles under this menu since they 'show' a term window
(lazygit or ipython).
Changed Aerial mappings to show navigator by default (`<leader>so`) and the
sidebar outline only on capital version (`<leader>sO`) since this mapping is
used less often.

Removed broken molten-image setup.

nvim/.config/nvim/after/ftplugin/quarto.lua

@@ -1,6 +1,18 @@
+local default_buffer_session = function()
+	local buffer_path = vim.api.nvim_buf_get_name(0) or vim.fn.tempname()
+	local temp_path = vim.fn.stdpath("run") .. "/molten-sessions" .. buffer_path .. ".json"
+
+	local dir = vim.fn.fnamemodify(temp_path, ":p:h")
+	if vim.fn.getftype(dir) ~= "dir" then
+		vim.fn.mkdir(dir, "p")
+	end
+
+	return temp_path
+end
+
 -- Start quarto session
 local startsession = function(file, args)
-	file = file or "/tmp/jupyter-magma-session.json"
+	file = file or default_buffer_session()
 	local path = require("util").get_python_venv()
 	vim.g["python3_host_prog"] = path
 
@@ -15,9 +27,8 @@ local startsession = function(file, args)
 	vim.fn.jobstart({ "jupyter", "console", "-f", file }, {
 		on_stdout = function(_)
 			if not once then
-			    vim.cmd("MoltenInit " .. file)
+				vim.cmd("MoltenInit " .. file)
-			    -- vim.cmd("JupyterAttach " .. file)
+			end
-		    end
 			once = true
 		end,
 		on_exit = function(_)
@@ -31,39 +42,63 @@ vim.api.nvim_create_user_command("JupyterStart", function()
 end, {})
 
 local map = vim.keymap.set
--- filetype mappings
--- PLUGIN: magma-nvim
--- Operate jupyter notebooks from within vim
-map("n", "<localleader>cc", ":MoltenEvaluateLine<cr>", { silent = true })
-map(
-	"n",
-	"<localleader>C",
-	"?^```{<cr>jV/```<cr>k:<C-u>MoltenEvaluateVisual<cr>",
-	{ silent = true, desc = "Evaluate current code cell" }
-)
-map("x", "<localleader>c", ":<C-u>MoltenEvaluateVisual<cr>", { silent = true })
-map(
-	"n",
-	"<localleader>c",
-	"nvim_exec('MoltenEvaluateOperator', v:true)",
-	{ expr = true, silent = true, desc = "+code-evaluation" }
-)
-map("n", "<localleader>cr", ":MoltenReevaluateCell<cr>", { silent = true })
-map("n", "<localleader>cu", ":MoltenShowOutput<cr>", { silent = true })
-map("n", "<localleader>cU", ":noautocmd :MoltenEnterOutput<cr>", { silent = true, desc = "Molten enter output" })
-map("n", "<localleader>cd", ":MoltenDelete<cr>", { silent = true })
-map("n", "<localleader>cs", ":MoltenInterrupt<cr>")
-map("n", "<localleader>ci", ":MoltenInit ")
-map("n", "<localleader>cD", ":MoltenDeinit<cr>")
-map("n", "<localleader>cR", ":MoltenRestart<cr>")
 
--- jump to beginning of previous/ next cell code
+local function molten_mappings_set()
-map("n", "]c", "/^```{<cr>}:nohl<cr>", { desc = "Next quarto cell" })
+	-- Operate jupyter notebooks from within vim
-map("n", "[c", "?^```<cr>n}:nohl<cr>", { desc = "Previous quarto cell" })
+	map("n", "<localleader>cc", ":MoltenEvaluateLine<cr>", { silent = true })
--- insert cell header above/below
+	map(
-map("n", "<localleader>co", "o```{python}<cr><cr>```<esc>k", { desc = "Insert quarto cell below" })
+		"n",
-map("n", "<localleader>cO", "O```{python}<cr><cr>```<esc>k", { desc = "Insert quarto cell above" })
+		"<localleader>C",
+		require("quarto.runner").run_cell,
+		{ silent = true, desc = "Evaluate current code cell" }
+	)
+	map("x", "<localleader>c", ":<C-u>MoltenEvaluateVisual<cr>", { silent = true })
+	map(
+		"n",
+		"<localleader>c",
+		"nvim_exec('MoltenEvaluateOperator', v:true)",
+		{ expr = true, silent = true, desc = "+code-evaluation" }
+	)
+	map("n", "<localleader>cr", ":MoltenReevaluateCell<cr>", { silent = true })
+	map("n", "<localleader>cu", ":MoltenShowOutput<cr>", { silent = true })
+	map("n", "<localleader>cU", ":noautocmd :MoltenEnterOutput<cr>", { silent = true, desc = "Molten enter output" })
+	map("n", "<localleader>cd", ":MoltenDelete<cr>", { silent = true })
+	map("n", "<localleader>ci", ":MoltenInterrupt<cr>")
+	map("n", "<localleader>cI", ":MoltenInfo<cr>")
+	map("n", "<localleader>cN", ":MoltenInit ")
+	map("n", "<localleader>cD", ":MoltenDeinit<cr>")
+	map("n", "<localleader>cR", ":MoltenRestart<cr>")
+	map(
+		"n",
+		"<localleader>cA",
+		require("quarto.runner").run_all,
+		{ silent = true, desc = "Evaluate all code cells" }
+	)
+	map(
+		"n",
+		"<localleader>ca",
+		require("quarto.runner").run_above,
+		{ silent = true, desc = "Evaluate cells above current" }
+	)
+	map(
+		"n",
+		"<localleader>cb",
+		require("quarto.runner").run_below,
+		{ silent = true, desc = "Evaluate cells below current" }
+	)
 
+	-- jump to beginning of previous/ next cell code
+	map("n", "]c", "/^```{<cr>}:nohl<cr>", { desc = "Next quarto cell" })
+	map("n", "[c", "?^```<cr>n}:nohl<cr>", { desc = "Previous quarto cell" })
+	-- insert cell header above/below
+	map("n", "<localleader>co", "o```{python}<cr><cr>```<esc>k", { desc = "Insert quarto cell below" })
+	map("n", "<localleader>cO", "O```{python}<cr><cr>```<esc>k", { desc = "Insert quarto cell above" })
+end
+
+vim.api.nvim_create_autocmd("User", {
+	pattern = "MoltenInitPost",
+	callback = molten_mappings_set,
+})
 local bufnr = 0
 map("n", "[d", "<cmd>lua vim.diagnostic.goto_prev()<cr>", { buffer = bufnr, desc = "Previous diagnostic" })
 map("n", "]d", "<cmd>lua vim.diagnostic.goto_next()<cr>", { buffer = bufnr, desc = "Next diagnostic" })
@@ -97,6 +132,7 @@ map("n", "gI", "<cmd>lua vim.lsp.buf.implementation()<cr>", { buffer = bufnr, de
 map("n", "gt", "<cmd>lua vim.lsp.buf.type_definition()<cr>", { buffer = bufnr, desc = "Type definition" })
 
 if vim.b["sessionfile"] == nil then
-	vim.b["sessionfile"] = vim.fn.tempname() .. ".json"
+	local path = default_buffer_session()
-	startsession(vim.b["sessionfile"])
+	vim.b["sessionfile"] = path
+	vim.schedule_wrap(startsession(path))
 end

nvim/.config/nvim/lazy-lock.json

@@ -32,7 +32,6 @@
   "gitsigns.nvim": { "branch": "main", "commit": "6ef8c54fb526bf3a0bc4efb0b2fe8e6d9a7daed2" },
   "headlines.nvim": { "branch": "master", "commit": "e3d7bfdf40e41a020d966d35f8b48d75b90367d2" },
   "image.nvim": { "branch": "master", "commit": "c40215d7d7d1d8c823ee9a77be1a894d5c8df41b" },
-  "jupyter-kernel.nvim": { "branch": "main", "commit": "5772fa8932f2c73736a777082656f1bfe0287076" },
   "lazy.nvim": { "branch": "main", "commit": "96584866b9c5e998cbae300594d0ccfd0c464627" },
   "lightspeed.nvim": { "branch": "main", "commit": "fcc72d8a4d5f4ebba62d8a3a0660f88f1b5c3b05" },
   "lsp-setup.nvim": { "branch": "main", "commit": "7276e54faf4af909b6ea171975fd4179ebe65cec" },

nvim/.config/nvim/lua/core/mappings.lua

@@ -195,19 +195,21 @@ map("n", "<localleader>ZD", ":setlocal spell! spelllang=de_de<cr>", { desc = "To
 map("i", "<c-z>", "<C-G>u<Esc>[s1z=`]a<C-G>u")
 map("n", "<localleader>z", "ms[s1z=`s", { desc = "Fix last spell error" })
 
+prefix({ ["<leader>s"] = { name = "+show" } })
 -- Set vim to distraction free prose mode
 map("n", "<leader>sz", ":ZenMode<cr>", { silent = true })
 -- PLUGIN: mini.nvim
-prefix({ ["<leader>s"] = { name = "+show" } })
+map("n", "<leader>sm", ":lua MiniMap.toggle()<cr>", { silent = true, desc = "minimap" })
-map("n", "<leader>sm", ":lua MiniMap.toggle()<cr>", { silent = true, desc = "toggle minimap" })
+map("n", "<leader>ss", ":lua MiniStarter.open()<cr>", { desc = "startpage" })
-map("n", "<leader>ss", ":lua MiniStarter.open()<cr>", { desc = "show startpage" })
 
 -- PLUGIN: symbols-outline.nvim
-map("n", "<leader>so", "<cmd>AerialToggle<cr>", { silent = true, desc = "toggle symbol outline" })
+map("n", "<leader>so", "<cmd>AerialNavToggle<cr>", { silent = true, desc = "symbol navigator" })
-map("n", "<leader>sn", "<cmd>AerialNavToggle<cr>", { silent = true, desc = "toggle symbol navigator" })
+map("n", "<leader>sO", "<cmd>AerialToggle<cr>", { silent = true, desc = "symbol outline" })
+
+-- PLUGIN: nvim-tree
+map("n", "<leader>se", "<cmd>NvimTreeToggle<cr>", { silent = true, desc = "filetree" })
 
 -- PLUGIN: nvim-tree
-map("n", "<leader>se", "<cmd>NvimTreeToggle<cr>", { silent = true, desc = "toggle filetree" })
 map("n", "<leader>sd", "<cmd>Trouble workspace_diagnostics<cr>", { silent = true, desc = "diagnostics workspace" })
 map("n", "<leader>sD", "<cmd>Trouble document_diagnostics<cr>", { silent = true, desc = "diagnostics document" })
 
@@ -257,11 +259,10 @@ map("v", "<localleader>nf", ":ZkMatch<cr>", { desc = "find note from selection"
 -- PLUGIN: toggleterm.nvim
 -- create a lazygit or python window, set up in toggleterm settings
 -- TODO create ability to go into python environment when in poetry venv and/or euporie/jupyter notebook
-prefix({ ["<localleader>t"] = { name = "+term" } })
+map("n", "<leader>sg", ":Lazygit<cr>")
-map("n", "<leader>tg", ":Lazygit<cr>")
+map("n", "<leader>sG", ":Lazygit!<cr>")
-map("n", "<leader>tG", ":Lazygit!<cr>")
+map("n", "<leader>sp", ":Pythonterm<cr>")
-map("n", "<leader>tp", ":Pythonterm<cr>")
+map("n", "<leader>sP", ":Pythonterm!<cr>")
-map("n", "<leader>tP", ":Pythonterm!<cr>")
 
 prefix({ ["<localleader>s"] = { name = "+set" } })
 -- PLUGIN: wrapping.nvim

nvim/.config/nvim/lua/plugins/data_analysis.lua

@@ -12,31 +12,20 @@ return {
 			require("quarto").setup({
 				lspFeatures = {
 					enabled = true,
-					languages = { "r", "python", "julia" },
+					languages = { "r", "python", "julia", "bash" },
-					diagnostics = { enabled = true, triggers = { "BufWrite" } },
+					diagnostics = { enabled = true, triggers = { "BufWritePost" } },
 					completion = { enabled = true },
 				},
+				codeRunner = {
+					enabled = true,
+					default_method = "molten",
+				},
 			})
 		end,
 		lazy = false,
 		ft = "quarto",
 	},
 
-	{
-		"lkhphuc/jupyter-kernel.nvim",
-		config = true,
-		cmd = "JupyterAttach",
-		build = ":UpdateRemotePlugins",
-		keys = {
-			{
-				"<localleader>ck",
-				"<Cmd>JupyterInspect<CR>",
-				desc = "Inspect object in kernel",
-			},
-		},
-		lazy = false,
-	},
-
 	-- REPL work
 	{
 		"3rd/image.nvim",
@@ -62,7 +51,7 @@ return {
 		"benlubas/molten-nvim",
 		build = ":UpdateRemotePlugins",
 		config = function()
-			vim.g.molten_image_provider = "image_nvim"
+			vim.g.molten_image_provider = "none" -- image integration does NOT work currently :-(
 			vim.g.molten_auto_open_output = false
 		end,
 		cmd = {