nvim: Update spellfile

Will automatically add function end tags for a bunch of languages, most importantly
for me to lua and bash.

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
 
@@ -11,10 +23,13 @@ local startsession = function(file, args)
 	if args then
 		file = args[0]
 	end
+	local once = false
 	vim.fn.jobstart({ "jupyter", "console", "-f", file }, {
 		on_stdout = function(_)
-			vim.cmd("MagmaInit " .. file)
+			if not once then
-			vim.cmd("JupyterAttach " .. file)
+				vim.cmd("MoltenInit " .. file)
+			end
+			once = true
 		end,
 		on_exit = function(_)
 			vim.notify(string.format("jupyter kernel stopped: %s", file), vim.log.levels.INFO)
@@ -27,31 +42,49 @@ vim.api.nvim_create_user_command("JupyterStart", function()
 end, {})
 
 local map = vim.keymap.set
--- filetype mappings
+
--- PLUGIN: magma-nvim
+local function molten_mappings_set()
 	-- Operate jupyter notebooks from within vim
-map("n", "<localleader>cc", ":MagmaEvaluateLine<cr>", { silent = true })
+	map("n", "<localleader>cc", ":MoltenEvaluateLine<cr>", { silent = true })
 	map(
 		"n",
 		"<localleader>C",
-	"?^```{<cr>jV/```<cr>k:<C-u>MagmaEvaluateVisual<cr>",
+		require("quarto.runner").run_cell,
 		{ silent = true, desc = "Evaluate current code cell" }
 	)
-map("x", "<localleader>c", ":<C-u>MagmaEvaluateVisual<cr>", { silent = true })
+	map("x", "<localleader>c", ":<C-u>MoltenEvaluateVisual<cr>", { silent = true })
 	map(
 		"n",
 		"<localleader>c",
-	"nvim_exec('MagmaEvaluateOperator', v:true)",
+		"nvim_exec('MoltenEvaluateOperator', v:true)",
 		{ expr = true, silent = true, desc = "+code-evaluation" }
 	)
-map("n", "<localleader>cr", ":MagmaReevaluateCell<cr>", { silent = true })
+	map("n", "<localleader>cr", ":MoltenReevaluateCell<cr>", { silent = true })
-map("n", "<localleader>cu", ":MagmaShowOutput<cr>", { silent = true })
+	map("n", "<localleader>cu", ":MoltenShowOutput<cr>", { silent = true })
-map("n", "<localleader>cU", ":noautocmd :MagmaEnterOutput<cr>", { silent = true, desc = "MagmaEnterOutput" })
+	map("n", "<localleader>cU", ":noautocmd :MoltenEnterOutput<cr>", { silent = true, desc = "Molten enter output" })
-map("n", "<localleader>cd", ":MagmaDelete<cr>", { silent = true })
+	map("n", "<localleader>cd", ":MoltenDelete<cr>", { silent = true })
-map("n", "<localleader>cs", ":MagmaInterrupt<cr>")
+	map("n", "<localleader>ci", ":MoltenInterrupt<cr>")
-map("n", "<localleader>ci", ":MagmaInit ")
+	map("n", "<localleader>cN", ":MoltenInit ")
-map("n", "<localleader>cD", ":MagmaDeinit<cr>")
+	map("n", "<localleader>cD", ":MoltenDeinit<cr>")
-map("n", "<localleader>cR", ":MagmaRestart<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" })
@@ -59,7 +92,12 @@ 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" })
@@ -93,6 +131,7 @@ 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/init.lua

@@ -10,7 +10,6 @@ for _, source in ipairs({
 	"core.autocmds",
 	"core.mappings",
 	"core.look",
-	"personal",
 }) do
 	local status_ok, fault = pcall(require, source)
 	if not status_ok then

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

@@ -1,8 +1,8 @@
 {
-  "Arduino.nvim": { "branch": "main", "commit": "1e986040861e77dd7107abfecc473c60ccd97d3f" },
+  "Arduino.nvim": { "branch": "main", "commit": "fad71572bf7a79b88da38167a756259b03d0c3ef" },
   "BetterLua.vim": { "branch": "master", "commit": "d2d6c115575d09258a794a6f20ac60233eee59d5" },
   "FixCursorHold.nvim": { "branch": "master", "commit": "1900f89dc17c603eec29960f57c00bd9ae696495" },
-  "LuaSnip": { "branch": "master", "commit": "0b4950a237ce441a6a3a947d501622453f6860ea" },
+  "LuaSnip": { "branch": "master", "commit": "118263867197a111717b5f13d954cd1ab8124387" },
   "Navigator.nvim": { "branch": "master", "commit": "91d86506ac2a039504d5205d32a1d4bc7aa57072" },
   "aerial.nvim": { "branch": "master", "commit": "63ec2bfc3d9b8ce1fd943fff14781504d8ee250e" },
   "bats.vim": { "branch": "master", "commit": "6a5d2ef22b0ede503d867770afd02ebb1f97b709" },
@@ -23,69 +23,71 @@
   "cmp-treesitter": { "branch": "master", "commit": "b8bc760dfcc624edd5454f0982b63786a822eed9" },
   "cmp_luasnip": { "branch": "master", "commit": "05a9ab28b53f71d1aece421ef32fee2cb857a843" },
   "completion-vcard": { "branch": "master", "commit": "2220fd517a985ececed1adcf0e5be8f2815564c7" },
+  "conform.nvim": { "branch": "master", "commit": "ce95e6b2a072d81fd312ff213f241cacab1eccef" },
   "dial.nvim": { "branch": "master", "commit": "54b503f906bc9e5ab85288414840a1b86d40769f" },
-  "dressing.nvim": { "branch": "master", "commit": "59fe7ef1aeeed499b983614fcfff89206bf0d5ce" },
+  "dressing.nvim": { "branch": "master", "commit": "8b7ae53d7f04f33be3439a441db8071c96092d19" },
   "fidget.nvim": { "branch": "main", "commit": "0ba1e16d07627532b6cae915cc992ecac249fb97" },
-  "friendly-snippets": { "branch": "main", "commit": "43727c2ff84240e55d4069ec3e6158d74cb534b6" },
+  "friendly-snippets": { "branch": "main", "commit": "53d3df271d031c405255e99410628c26a8f0d2b0" },
   "fwatch.nvim": { "branch": "main", "commit": "a691f7349dc66285cd75a1a698dd28bca45f2bf8" },
   "git-conflict.nvim": { "branch": "main", "commit": "4e0191c9a0ae05d7fbdcdc7f15cd358f56d23bfb" },
-  "gitsigns.nvim": { "branch": "main", "commit": "bb808fc7376ed7bac0fbe8f47b83d4bf01738167" },
+  "gitsigns.nvim": { "branch": "main", "commit": "6ef8c54fb526bf3a0bc4efb0b2fe8e6d9a7daed2" },
-  "headlines.nvim": { "branch": "master", "commit": "74a083a3c32a08be24f7dfcc6f448ecf47857f46" },
+  "headlines.nvim": { "branch": "master", "commit": "e3d7bfdf40e41a020d966d35f8b48d75b90367d2" },
-  "jupyter-kernel.nvim": { "branch": "main", "commit": "5b409598033884a3d819e2a3bcd1fe340bc8d783" },
+  "image.nvim": { "branch": "master", "commit": "c40215d7d7d1d8c823ee9a77be1a894d5c8df41b" },
-  "lazy.nvim": { "branch": "main", "commit": "1c16e4236f0937e8955865a0e5e046c7dafbc4b5" },
+  "lazy.nvim": { "branch": "main", "commit": "96584866b9c5e998cbae300594d0ccfd0c464627" },
-  "lightspeed.nvim": { "branch": "main", "commit": "299eefa6a9e2d881f1194587c573dad619fdb96f" },
+  "lightspeed.nvim": { "branch": "main", "commit": "fcc72d8a4d5f4ebba62d8a3a0660f88f1b5c3b05" },
   "lsp-setup.nvim": { "branch": "main", "commit": "7276e54faf4af909b6ea171975fd4179ebe65cec" },
-  "lualine.nvim": { "branch": "master", "commit": "45e27ca739c7be6c49e5496d14fcf45a303c3a63" },
+  "lualine.nvim": { "branch": "master", "commit": "2248ef254d0a1488a72041cfb45ca9caada6d994" },
-  "magma-nvim-goose": { "branch": "main", "commit": "9a626aab63361d027541d023707f82e28d7f872c" },
   "markdown-preview.nvim": { "branch": "master", "commit": "9becceee5740b7db6914da87358a183ad11b2049" },
   "markmap.nvim": { "branch": "main", "commit": "3befc2a54c2448a16c30c1c7762aab263f22946a" },
-  "mason-lspconfig.nvim": { "branch": "main", "commit": "397273083f988c1a17acf3816947cd198338e700" },
+  "mason-lspconfig.nvim": { "branch": "main", "commit": "4eb8e15e3c0757303d4c6dea64d2981fc679e990" },
-  "mason-null-ls.nvim": { "branch": "main", "commit": "ae0c5fa57468ac65617f1bf821ba0c3a1e251f0c" },
+  "mason-tool-installer.nvim": { "branch": "main", "commit": "8b70e7f1e0a4119c1234c3bde4a01c241cabcc74" },
-  "mason.nvim": { "branch": "main", "commit": "cd7835b15f5a4204fc37e0aa739347472121a54c" },
+  "mason.nvim": { "branch": "main", "commit": "41e75af1f578e55ba050c863587cffde3556ffa6" },
   "mdeval.nvim": { "branch": "master", "commit": "2654caf8ecaad702b50199d18e39cff23d81e0ba" },
-  "mini.nvim": { "branch": "main", "commit": "707dca4f4152c2d9c9b4c5e02635f78dfd33db50" },
+  "mini.nvim": { "branch": "main", "commit": "b5645ac6eefce8e7af9d7dd4e5e296a81cba8a10" },
-  "neotest": { "branch": "master", "commit": "6fd61fe665381939a6d70eb08ef1959a10af369e" },
+  "molten-nvim": { "branch": "main", "commit": "93f2f168e77cbd82a881e07030cdbd45a48ed070" },
+  "neotest": { "branch": "master", "commit": "009328955066ae6c170d24bb0de5f168d8760ff8" },
   "neotest-python": { "branch": "master", "commit": "81d2265efac717bb567bc15cc652ae10801286b3" },
-  "null-ls.nvim": { "branch": "main", "commit": "0010ea927ab7c09ef0ce9bf28c2b573fc302f5a7" },
+  "nvim-FeMaco.lua": { "branch": "main", "commit": "6af458f0196215f397db31a6e1fb2df795811693" },
-  "nvim-FeMaco.lua": { "branch": "main", "commit": "c4e9c71c9ca595772a360435bdf91bee3f9d32b1" },
   "nvim-base16": { "branch": "master", "commit": "96e308958625a84940d5e443475465abf99c7bd9" },
-  "nvim-cmp": { "branch": "main", "commit": "5dce1b778b85c717f6614e3f4da45e9f19f54435" },
+  "nvim-cmp": { "branch": "main", "commit": "0b751f6beef40fd47375eaf53d3057e0bfa317e4" },
   "nvim-colorizer.lua": { "branch": "master", "commit": "dde3084106a70b9a79d48f426f6d6fec6fd203f7" },
-  "nvim-coverage": { "branch": "main", "commit": "fd6f94781c94958d1c26353d0d43a82ea5572b31" },
+  "nvim-coverage": { "branch": "main", "commit": "cf4b5c61dfac977026a51a2bcad9173c272986ce" },
-  "nvim-lspconfig": { "branch": "master", "commit": "8f3ddc448769f563248654a5099c943c7139137e" },
+  "nvim-lint": { "branch": "master", "commit": "849ccb610de3f6ce1a239ea1e68568ef1a53d5df" },
+  "nvim-lspconfig": { "branch": "master", "commit": "cf3dd4a290084a868fac0e2e876039321d57111c" },
   "nvim-notify": { "branch": "master", "commit": "ea9c8ce7a37f2238f934e087c255758659948e0f" },
-  "nvim-surround": { "branch": "main", "commit": "0d6882635817a2677749a330127d12ac30a4f3c8" },
+  "nvim-surround": { "branch": "main", "commit": "703ec63aa798e5e07d309b35e42def34bebe0174" },
   "nvim-toggleterm.lua": { "branch": "main", "commit": "faee9d60428afc7857e0927fdc18daa6c409fa64" },
-  "nvim-tree.lua": { "branch": "master", "commit": "aaee4cd896b74f85a81bed7eef2db7869960c4d0" },
+  "nvim-tree.lua": { "branch": "master", "commit": "7d1760f892951dd6a118dae1d7a1d8df5f029edf" },
   "nvim-treesitter": { "branch": "master", "commit": "63260da18bf273c76b8e2ea0db84eb901cab49ce" },
-  "nvim-treesitter-context": { "branch": "master", "commit": "4cf64264c049c55f256550ad247b606f3e53bc77" },
+  "nvim-treesitter-context": { "branch": "master", "commit": "bf4d15ee4e96ff5201f16a4ed14443670662eb90" },
-  "nvim-treesitter-textsubjects": { "branch": "master", "commit": "48b3bf54e32f23e2299c59ff76fa3b0599565b39" },
+  "nvim-treesitter-endwise": { "branch": "master", "commit": "4c344ffc8d54d7e1ba2cefaaa2c10ea93aa1cc2d" },
+  "nvim-treesitter-textsubjects": { "branch": "master", "commit": "011c09784f1a95cf469a48c1993b664190440391" },
   "nvim-ts-autotag": { "branch": "main", "commit": "6be1192965df35f94b8ea6d323354f7dc7a557e4" },
-  "nvim-ts-context-commentstring": { "branch": "main", "commit": "92e688f013c69f90c9bbd596019ec10235bc51de" },
+  "nvim-ts-context-commentstring": { "branch": "main", "commit": "1277b4a1f451b0f18c0790e1a7f12e1e5fdebfee" },
   "nvim-ts-rainbow2": { "branch": "master", "commit": "b3120cd5ae9ca524af9cb602f41e12e301fa985f" },
-  "nvim-web-devicons": { "branch": "master", "commit": "3af745113ea537f58c4b1573b64a429fefad9e07" },
+  "nvim-web-devicons": { "branch": "master", "commit": "5efb8bd06841f91f97c90e16de85e96d57e9c862" },
-  "otter.nvim": { "branch": "main", "commit": "2752dd199d73342f13a1bd599a99822505e2803f" },
+  "otter.nvim": { "branch": "main", "commit": "9a3db06bf3abadafb93279648317984ca789b888" },
-  "playground": { "branch": "master", "commit": "ba48c6a62a280eefb7c85725b0915e021a1a0749" },
   "plenary.nvim": { "branch": "master", "commit": "50012918b2fc8357b87cff2a7f7f0446e47da174" },
   "popup.nvim": { "branch": "master", "commit": "b7404d35d5d3548a82149238289fa71f7f6de4ac" },
-  "quarto-nvim": { "branch": "main", "commit": "b349b7e54f5f5543b6104bfbad0e7d09d4f7c564" },
+  "quarto-nvim": { "branch": "main", "commit": "0a35b3890e9d723b730506d7d8b3ba3d0d6aae2e" },
   "smartcolumn.nvim": { "branch": "main", "commit": "d01b99355c7fab13233f48d0f28dc097e68a03f7" },
   "stickybuf.nvim": { "branch": "master", "commit": "e3db41f2c1bb2df3ee6ff964ee74fe991f6f9566" },
   "telescope-fzf-native.nvim": { "branch": "main", "commit": "6c921ca12321edaa773e324ef64ea301a1d0da62" },
-  "telescope.nvim": { "branch": "master", "commit": "7011eaae0ac1afe036e30c95cf80200b8dc3f21a" },
+  "telescope.nvim": { "branch": "master", "commit": "d90956833d7c27e73c621a61f20b29fdb7122709" },
+  "trouble.nvim": { "branch": "main", "commit": "f1168feada93c0154ede4d1fe9183bf69bac54ea" },
   "twilight.nvim": { "branch": "main", "commit": "8bb7fa7b918baab1ca81b977102ddb54afa63512" },
-  "undotree": { "branch": "main", "commit": "41f56b30cc774ad26c4945c7e10673453893e7ad" },
+  "undotree": { "branch": "main", "commit": "a88c8ab7f780bc14ab9356c2311c44f49213d47c" },
   "vifm.vim": { "branch": "master", "commit": "a8130c37d144b51d84bee19f0532abcd3583383f" },
   "vim-criticmarkup": { "branch": "master", "commit": "d15dc134eb177a170c79f6377f81eb02a9d20b02" },
   "vim-easy-align": { "branch": "master", "commit": "0db4ea6132110631ec678a99a82aa49a0686ae65" },
   "vim-exchange": { "branch": "master", "commit": "784d63083ad7d613aa96f00021cd0dfb126a781a" },
   "vim-numbertoggle": { "branch": "main", "commit": "df9b1fe616507340718716204ba7f434125bdf7a" },
   "vim-oscyank": { "branch": "main", "commit": "ffe827a27dae98aa826e2295336c650c9a434da0" },
-  "vim-pandoc-syntax": { "branch": "master", "commit": "4268535e1d33117a680a91160d845cd3833dfe28" },
+  "vim-pandoc-syntax": { "branch": "master", "commit": "16939cda184ff555938cc895cc62477c172997f9" },
   "vim-spellsync": { "branch": "master", "commit": "3d6dd50de9c4d953cc16638112a6ae196df41463" },
-  "which-key.nvim": { "branch": "main", "commit": "bf09a25bdc9a83bcc69d2cf078e680368676513b" },
+  "which-key.nvim": { "branch": "main", "commit": "ce741eb559c924d72e3a67d2189ad3771a231414" },
   "wrapping.nvim": { "branch": "master", "commit": "5e87f1424c86c50d3bc205830aa56ed1cad45467" },
   "zen-mode.nvim": { "branch": "main", "commit": "cb73b8bd0ef9d765b942db09dc762c603a89ae44" },
   "zettelkasten.nvim": { "branch": "main", "commit": "0e77624689b470410f5355b613d45219c9350264" },
-  "zk-nvim": { "branch": "main", "commit": "e9e5e21dbeacd0e753728c7ea45b7a7582d9080a" }
+  "zk-nvim": { "branch": "main", "commit": "142625638d2fad464939c6ee1775571aba6379c6" }
 }

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

@@ -137,7 +137,6 @@ map(
 	{ desc = "colorschemes" }
 )
 map("n", "<leader>vl", ":Lazy<cr>", { desc = "Lazy" })
-map("n", "<leader>vm", ":Mason<cr>", { desc = "Mason" })
 
 -- PLUGIN: Telescope GLOBAL FUZZY FINDING
 -- buffers and files in current workdir
@@ -178,16 +177,11 @@ map("n", "<localleader>q", "gqap", { silent = true, desc = "Format current parag
 map("x", "<localleader>q", "gq", { silent = true, desc = "Format {motion}" })
 map("n", "<localleader>Q", "vapJgqap", { silent = true, desc = "Unformat then format paragraph" })
 
--- FORMAT code with
--- PLUGIN: formatter.nvim
-map("n", "<localleader>f", ":FormatLock<cr>")
-map("n", "<localleader>F", ":FormatWriteLock<cr>")
-
 -- SPELL CHECKING
 -- Move to the prev/next spelling error with [S ]S
 -- Move to the prev/next spelling error or suggestion with [s ]s
 prefix({ ["<localleader>Z"] = { name = "+Spelling" } })
-map("n", "<localleader>ZZ", ":setlocal spell! spelllang=en_us,en_uk,de_de<cr>", { desc = "Toggle spellcheck" })
+map("n", "<localleader>ZZ", ":setlocal spell! spelllang=en_us,en_gb,de_de<cr>", { desc = "Toggle spellcheck" })
 map("n", "<localleader>ZE", ":setlocal spell! spelllang=en_us<cr>", { desc = "Toggle EN_US spellcheck" })
 map("n", "<localleader>ZB", ":setlocal spell! spelllang=en_gb<cr>", { desc = "Toggle EN_GB spellcheck" })
 map("n", "<localleader>ZD", ":setlocal spell! spelllang=de_de<cr>", { desc = "Toggle DE_DE spellcheck" })
@@ -195,19 +189,23 @@ 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 = "toggle filetree" })
+map("n", "<leader>se", "<cmd>NvimTreeToggle<cr>", { silent = true, desc = "filetree" })
+
+-- PLUGIN: nvim-tree
+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" })
 
 -- PLUGIN: easy-align
 -- Start interactive EasyAlign in visual mode (e.g. vipga)
@@ -255,11 +253,10 @@ 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
@@ -277,5 +274,3 @@ map(
 	'<cmd>lua require("colorizer").attach_to_buffer(0, {mode = "background"} )<cr>',
 	{ silent = true, desc = "colorize background" }
 )
-
-map("n", "<leader>sa", "<cmd>FormatOnSave<cr>", { silent = true, desc = "toggle format on save" })

nvim/.config/nvim/lua/core/settings.lua

@@ -84,7 +84,7 @@ local globals = {
 	maplocalleader = ",",
 	tex_flavor = "latex",
 
-	format_on_save = false, -- from personal toggle function
+	disable_autoformat = true, -- only format files manually
 }
 
 for o, v in pairs(globals) do

nvim/.config/nvim/lua/personal/format_on_save_toggle.lua

@@ -1,33 +0,0 @@
-local function stop_formatting()
-	vim.api.nvim_del_augroup_by_name("LspFormat")
-end
-
-local function start_formatting()
-	for _, client in pairs(vim.lsp.get_active_clients()) do
-		require("lsp-setup.utils").format_on_save(client)
-	end
-end
-
-local function _toggle(opts)
-	if opts.args == "" then
-		vim.g.format_on_save = not vim.g.format_on_save
-	elseif opts.args == "on" or opts.args == "1" then
-		vim.g.format_on_save = true
-	elseif opts.args == "off" or opts.args == "0" then
-		vim.g.format_on_save = false
-	else
-		vim.notify("Please provide arguments 'on' or 'off' or non arguments to toggle.")
-	end
-
-	if vim.g.format_on_save == true then
-		start_formatting()
-	else
-		stop_formatting()
-	end
-end
-
-vim.api.nvim_create_user_command(
-	"FormatOnSave",
-	_toggle,
-	{ desc = "toggle automatically formatting on save", nargs = "?" }
-)

nvim/.config/nvim/lua/personal/init.lua

@@ -1 +0,0 @@
-require("personal.format_on_save_toggle")

nvim/.config/nvim/lua/plugins/config/lsp.lua

@@ -17,6 +17,7 @@ local servers = {
 	docker_compose_language_service = {},
 	dockerls = {},
 	emmet_ls = {},
+	eslint = {},
 	gopls = {},
 	julials = {},
 	lua_ls = {
@@ -42,6 +43,16 @@ local servers = {
 	yamlls = {},
 }
 
+-- TODO installed for conform/nvim-lint so should be sourced from there not here
+local to_mason =
+	{ "stylua", "shellcheck", "shfmt", "markdownlint", "bibtex-tidy", "jq", "prettier", "ruff", unpack(servers) }
+require("mason-tool-installer").setup({
+	-- a list of all tools you want to ensure are installed upon
+	-- start
+	ensure_installed = to_mason,
+	start_delay = 3000,
+})
+
 local function on_attach(client, bufnr)
 	local map = vim.keymap.set
 	map("n", "[d", "<cmd>lua vim.diagnostic.goto_prev()<cr>", { buffer = bufnr, desc = "Previous diagnostic" })
@@ -59,8 +70,7 @@ local function on_attach(client, bufnr)
 		{ buffer = bufnr, desc = "Next error" }
 	)
 
-	require("which-key").register({ ["<localleader>l"] = { name = "+lsp" } })
+	require("which-key").register({ ["<localleader>l"] = { name = "+language" } })
-	map("n", "<localleader>li", "<cmd>LspInfo<cr>", { buffer = bufnr, desc = "Lsp Info" })
 	map(
 		"n",
 		"<localleader>ld",
@@ -100,7 +110,6 @@ local function on_attach(client, bufnr)
 			{ buffer = bufnr, desc = "Implementation" }
 		)
 	end
-	map("n", "<localleader>ll", "<cmd>lua vim.lsp.buf.format()<CR>", { buffer = bufnr, desc = "Format document" })
 	map("n", "K", "<cmd>lua vim.lsp.buf.hover()<cr>", { buffer = bufnr, desc = "Hover definition" })
 	map("n", "<localleader>lc", "<cmd>lua vim.lsp.buf.declaration()<cr>", { buffer = bufnr, desc = "Declaration" })
 	map(
@@ -116,16 +125,20 @@ local function on_attach(client, bufnr)
 			vim.diagnostic.disable(0)
 		end
 	end, { buffer = bufnr, desc = "Disable buffer diagnostics" })
-
-	if vim.g.format_on_save then
-		require("lsp-setup.utils").format_on_save(client)
-	end
 end
 
 -- Display diagnostics as virtual text only if not in insert mode
 -- https://lr.artemislena.eu/r/neovim/comments/12inp4c/disable_diagnostics_virtual_text_when_in_insert/jqqifwk/
-vim.api.nvim_create_autocmd("InsertEnter", { callback = function() vim.diagnostic.config({ virtual_text = false, }) end })
+vim.api.nvim_create_autocmd("InsertEnter", {
-vim.api.nvim_create_autocmd("InsertLeave", { callback = function() vim.diagnostic.config({ virtual_text = true, }) end })
+	callback = function()
+		vim.diagnostic.config({ virtual_text = false })
+	end,
+})
+vim.api.nvim_create_autocmd("InsertLeave", {
+	callback = function()
+		vim.diagnostic.config({ virtual_text = true })
+	end,
+})
 
 lsp.setup({
 	default_mappings = false,
@@ -137,6 +150,7 @@ lsp.setup({
 })
 
 local lspconfig = require("lspconfig")
+lspconfig.nushell.setup({})
 
 local python_path
 -- ensure python virtualenv is determined automatically on lsp start
@@ -152,12 +166,11 @@ lspconfig.pyright.setup({
 })
 lspconfig.ruff_lsp.setup({
 	on_attach = function(client, bufnr)
+		on_attach(client, bufnr)
 		if python_path == nil then
 			python_path, _ = require("util").get_python_venv(client.config.root_dir)
 		end
-		-- print(string.format("[PYTHON VENV]: %s", vim.inspect(python_path)))
 		client.config.settings.python.pythonPath = python_path
-		on_attach(client, bufnr)
 	end,
 })
 
@@ -167,45 +180,3 @@ if require("util").is_available("arduino") then
 		on_new_config = require("arduino").on_new_config,
 	})
 end
-
-local null_ls = require("null-ls")
-null_ls.setup({})
-require("mason-null-ls").setup({
-	ensure_installed = { "black", "prettier", "shfmt", "eslint-lsp", "stylua", "jq", "vale", "markdownlint" },
-	automatic_installation = false,
-	handlers = {
-		shfmt = function(_, _)
-			null_ls.register(null_ls.builtins.formatting.shfmt.with({
-				extra_filetypes = { "bash", "zsh" },
-			}))
-		end,
-		prettier = function(_, _)
-			null_ls.register(null_ls.builtins.formatting.prettier.with({
-				extra_filetypes = { "astro" },
-				disabled_filetypes = { "markdown" },
-				timeout = 7000,
-			}))
-		end,
-		eslint = function(_, _)
-			null_ls.register(null_ls.builtins.diagnostics.eslint.with({
-				extra_filetypes = { "astro" },
-			}))
-			null_ls.register(null_ls.builtins.code_actions.eslint.with({
-				extra_filetypes = { "astro" },
-			}))
-		end,
-		markdownlint = function(_, _)
-			null_ls.register(null_ls.builtins.diagnostics.markdownlint.with({
-				extra_filetypes = { "quarto" },
-			}))
-		end,
-		vale = function(_, _)
-			null_ls.register(null_ls.builtins.diagnostics.vale.with({
-				condition = function(utils)
-					return (utils.root_has_file({ ".vale.ini", "_vale.ini" }) and utils.root_has_file({ "styles/" }))
-				end,
-			}))
-		end,
-	},
-})
-

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

@@ -12,48 +12,74 @@ 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" },
-		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
 	{
-		"WhiteBlackGoose/magma-nvim-goose",
+		"3rd/image.nvim",
+		config = function()
+			-- Example for configuring Neovim to load user-installed installed Lua rocks:
+			package.path = package.path .. ";" .. vim.fn.expand("$HOME") .. "/.luarocks/share/lua/5.1/?/init.lua;"
+			package.path = package.path .. ";" .. vim.fn.expand("$HOME") .. "/.luarocks/share/lua/5.1/?.lua;"
+			require("image").setup({
+				backend = "kitty",
+				integrations = {
+					markdown = {
+						enabled = true,
+						download_remote_images = true,
+						only_render_image_at_cursor = true,
+						filetypes = { "markdown", "vimwiki", "quarto" },
+					},
+				},
+			})
+		end,
+		ft = { "markdown", "vimwiki", "quarto" },
+	},
+	{
+		"benlubas/molten-nvim",
 		build = ":UpdateRemotePlugins",
 		config = function()
-			vim.g.magma_image_provider = "kitty"
+			vim.g.molten_image_provider = "none" -- image integration does NOT work currently :-(
-			vim.g.magma_automatically_open_output = false
+			vim.g.molten_auto_open_output = false
 		end,
 		cmd = {
-			"MagmaInit",
+			"MoltenInfo",
-			"MagmaEvaluateOperator",
+			"MoltenInit",
-			"MagmaEvaluateLine",
+			"MoltenDeinit",
-			"MagmaEvaluateVisual",
+			"MoltenGoto",
-			"MagmaRestart",
+			"MoltenNext",
+			"MoltenPrev",
+			"MoltenEvaluateLine",
+			"MoltenEvaluateVisual",
+			"MoltenEvaluateOperator",
+			"MoltenEvaluateArgument",
+			"MoltenReevaluateCell",
+			"MoltenDelete",
+			"MoltenShowOutput",
+			"MoltenHideOutput",
+			"MoltenEnterOutput",
+			"MoltenInterrupt",
+			"MoltenRestart",
+			"MoltenSave",
+			"MoltenLoad",
+			"MoltenExportOutput",
 		},
 		ft = { "quarto", "python" },
 		lazy = false,
+		keys = {
+			{ "<leader>vn", ":MoltenInfo<cr>" },
+		},
 	},
 
 	-- MARKDOWN ONLY
@@ -73,9 +99,9 @@ return {
 	{
 		"AckslD/nvim-FeMaco.lua",
 		cmd = {
-	        "FeMaco"
+			"FeMaco",
 		},
 		ft = { "markdown" },
-	    config = true
+		config = true,
-	}
+	},
 }

nvim/.config/nvim/lua/plugins/ide.lua

@@ -47,25 +47,162 @@ return {
 					"MasonUpdate",
 				},
 				build = ":MasonUpdate",
+				keys = {
+					{ "<leader>vm", ":Mason<cr>", desc = "Mason" },
+				},
 			},
 			{
 				"williamboman/mason-lspconfig.nvim",
 				cmd = { "LspInstall", "LspUninstall" },
 			},
 			{
-				"jose-elias-alvarez/null-ls.nvim",
+				"WhoIsSethDaniel/mason-tool-installer.nvim",
-				dependencies = {
-					"nvim-lua/plenary.nvim",
-					"jay-babu/mason-null-ls.nvim",
-				},
-				event = "VeryLazy",
 			},
 		},
-		event = "BufReadPost",
+		event = { "BufRead", "BufNewFile", "InsertEnter" },
+		after = { "nvim-cmp" },
 		config = function()
 			require("plugins.config.lsp")
 		end,
+		keys = { {
+			"<leader>vs",
+			":LspInfo<cr>",
+			desc = "LspInfo",
+		} },
 	},
+
+	-- linting setup
+	{
+		"mfussenegger/nvim-lint",
+		config = function()
+			local linters = {
+				astro = {},
+				bash = {},
+				javascript = {},
+				javascriptreact = {},
+				markdown = {},
+				quarto = {},
+				sh = {},
+				svelte = {},
+				text = {},
+				typescript = {},
+				typescriptreact = {},
+			}
+			local per_cmd = function(cmd, ft_table)
+				if vim.fn.executable(cmd) == 1 then
+					for _, v in pairs(ft_table) do
+						table.insert(v, cmd)
+					end
+				end
+			end
+			per_cmd("markdownlint", { linters.markdown, linters.quarto })
+			per_cmd("vale", { linters.markdown, linters.text, linters.quarto })
+			per_cmd("shellcheck", { linters.sh, linters.bash })
+			per_cmd("eslint_d", {
+				linters.astro,
+				linters.javascript,
+				linters.javascriptreact,
+				linters.svelte,
+				linters.typescript,
+				linters.typescriptreact,
+			})
+			require("lint").linters_by_ft = linters
+			vim.api.nvim_create_autocmd({ "BufWritePost", "InsertLeave" }, {
+				callback = function()
+					require("lint").try_lint()
+				end,
+			})
+		end,
+		event = { "BufReadPost", "BufNewFile" },
+	},
+
+	-- formatting setup
+	{
+		"stevearc/conform.nvim",
+		config = function()
+			require("conform").setup({
+				lsp_fallback = true,
+				format_after_save = function(bufnr)
+					if vim.g.disable_autoformat or vim.b[bufnr].disable_autoformat then
+						return
+					end
+					return { lsp_fallback = true }
+				end,
+				formatters_by_ft = {
+					angular = { { "prettierd", "prettier" } },
+					astro = { { "prettierd", "prettier" } },
+					bash = { "shfmt" },
+					bib = { "bibtex-tidy" },
+					css = { { "prettierd", "prettier" } },
+					graphql = { { "prettierd", "prettier" } },
+					html = { { "prettierd", "prettier" } },
+					javascript = { { "prettierd", "prettier" } },
+					javascriptreact = { { "prettierd", "prettier" } },
+					json = { "jq" },
+					lua = { "stylua" },
+					python = { "ruff_fix", "ruff_format" },
+					sh = { "shfmt" },
+					svelte = { { "prettierd", "prettier" } },
+					typescript = { { "prettierd", "prettier" } },
+					typescriptreact = { { "prettierd", "prettier" } },
+					vue = { { "prettierd", "prettier" } },
+					yaml = { { "prettierd", "prettier" } },
+					zsh = { "shfmt" },
+				},
+				formatters = {
+					-- enable python isort functionality
+					ruff_fix = {
+						prepend_args = { "--select", "I" },
+					},
+				},
+			})
+			vim.api.nvim_create_user_command("FormatDisable", function(args)
+				if args.bang then
+					-- FormatDisable! will disable formatting just for this buffer
+					vim.b.disable_autoformat = true
+				else
+					vim.g.disable_autoformat = true
+				end
+			end, {
+				desc = "Disable formatting on save",
+				bang = true,
+			})
+			vim.api.nvim_create_user_command("FormatEnable", function()
+				vim.b.disable_autoformat = false
+				vim.g.disable_autoformat = false
+			end, {
+				desc = "Enable formatting on save",
+			})
+		end,
+		cmd = { "ConformInfo" },
+		event = { "BufReadPre" },
+		keys = {
+			{
+				"<localleader>ll",
+				function()
+					require("conform").format({ async = true, lsp_fallback = true })
+				end,
+				desc = "Format buffer",
+			},
+			{
+				"<localleader>lL",
+				function()
+					vim.g.disable_autoformat = not vim.g.disable_autoformat
+				end,
+				desc = "Toggle AutoFormat",
+			},
+			{
+				"<leader>vf",
+				":ConformInfo<cr>",
+				desc = "ConformInfo",
+			},
+		},
+		init = function()
+			-- If you want the formatexpr, here is the place to set it
+			vim.o.formatexpr = "v:lua.require'conform'.formatexpr()"
+		end,
+	},
+
 	-- completion setup
 	{
 		"hrsh7th/nvim-cmp",
@@ -96,12 +233,25 @@ return {
 		config = function()
 			require("plugins.config.cmp")
 		end,
-		event = { "InsertEnter", "CmdlineEnter", "VeryLazy" },
+		event = { "InsertEnter", "CmdlineEnter" },
 	},
 
 	-- loading animations for some LSP
 	{ "j-hui/fidget.nvim", config = true, tag = "legacy", event = "VeryLazy" },
 
+	-- useful quickfix-like buffer
+	{
+		"folke/trouble.nvim",
+		dependencies = { "nvim-tree/nvim-web-devicons" },
+		opts = {},
+		cmd = {
+			"Trouble",
+			"TroubleRefresh",
+			"TroubleToggle",
+			"TroubleClose",
+		},
+	},
+
 	-- testing setup
 	{
 		"nvim-neotest/neotest",

nvim/.config/nvim/lua/plugins/prose.lua

@@ -3,9 +3,7 @@ local writing_ft = { "quarto", "pandoc", "markdown", "text", "tex" }
 local prose_plugs = {
 	-- UI improvements
 	-- provide distraction free writing
-	{ "folke/zen-mode.nvim", config = true, event = "VeryLazy" },
+	{ "folke/zen-mode.nvim", config = true, cmd = { "ZenMode" }, dependencies = { "folke/twilight.nvim" } },
-	-- provide even distraction free-er writing (lowlight paragraphs)
-	{ "folke/twilight.nvim", event = "VeryLazy" },
 	{
 		"andrewferrier/wrapping.nvim",
 		config = function()

nvim/.config/nvim/lua/plugins/treesitter.lua

@@ -7,11 +7,21 @@ return {
 			require("nvim-treesitter.configs").setup({
 				-- one of "all", "maintained" (parsers with maintainers), or a list of languages
 				ensure_installed = "all",
+				auto_install = true,
 				highlight = {
 					enable = true,
+					language_tree = true,
 					disable = function(_, bufnr)
-						return vim.api.nvim_buf_line_count(bufnr) > 7000
+						if
+							vim.api.nvim_buf_line_count(bufnr) > 1000
+							or vim.fn.strwidth(vim.fn.getline(".")) > 300
+							or vim.fn.getfsize(vim.fn.expand("%")) > 1024 * 1024
+						then
+							return true
+						end
+						return false
 					end,
+					additional_vim_regex_highlighting = false,
 				},
 				incremental_selection = { enable = true },
 				textobjects = { enable = true },
@@ -24,11 +34,6 @@ return {
 					strategy = { rainbow.strategy.global },
 				},
 
-				-- for improved commentstrings, needs corresponding plugin
-				context_commentstring = {
-					enable = true,
-					enable_autocmd = false, -- since we run it as a hook from the mini.comment plugin
-				},
 				-- allows using . and ; to target treesitter branches
 				textsubjects = {
 					enable = true,
@@ -37,7 +42,33 @@ return {
 						[";"] = "textsubjects-container-outer",
 					},
 				},
+
+                endwise = {
+                    enable = true
+                }
 			})
+
+			-- for improved commentstrings, needs corresponding plugin
+			require("ts_context_commentstring").setup({
+				enable = true,
+				enable_autocmd = false, -- since we run it as a hook from the mini.comment plugin
+				languages = {
+					nu = "# %s",
+				},
+			})
+
+			-- treesitter parser for nushell. To fully get e.g. syntax highlight
+			-- working you need a highlight file too. For now I installed manually, see:
+			-- https://github.com/nushell/tree-sitter-nu/blob/main/installation/neovim.md
+			local parser_config = require("nvim-treesitter.parsers").get_parser_configs()
+			parser_config.nu = {
+				install_info = {
+					url = "https://github.com/nushell/tree-sitter-nu",
+					files = { "src/parser.c" },
+					branch = "main",
+				},
+				filetype = "nu",
+			}
 		end,
 		event = "BufReadPost",
 		cmd = {
@@ -63,11 +94,10 @@ return {
 			"https://gitlab.com/HiPhish/nvim-ts-rainbow2.git",
 			{ "romgrk/nvim-treesitter-context", config = true },
 			"JoosepAlviste/nvim-ts-context-commentstring",
-			{
 			"RRethy/nvim-treesitter-textsubjects",
-			},
 			"windwp/nvim-ts-autotag",
+			"RRethy/nvim-treesitter-endwise",
 		},
 	},
-	{ "nvim-treesitter/playground", cmd = "TSPlaygroundToggle" }, -- interactively view and query the treesitter tree
 }
+

nvim/.config/nvim/spell/en.utf-8.add

@@ -8,7 +8,7 @@ FDI
 Farole
 Fordism
 Fordist
-Gramsci's
+Gramsci
 JIT
 Kyrgyzstan
 Kyūshū
@@ -196,3 +196,13 @@ programmatically
 TUI
 Lemmy
 cli
+Pareto
+decarbonise
+Gini
+Familia
+Bolsa
+ppts
+ppt
+Programo
+Urbano
+redistributional

scripts/.local/bin/py

@@ -0,0 +1,43 @@
+#!/usr/bin/env bash
+
+molten_session_dir="/run/user/$UID/molten-sessions"
+cur_dir=$(pwd)
+search_dir="${molten_session_dir}${cur_dir}"
+
+if [ "$1" == "-c" ]; then
+    cmd=$(echo -e "euporie-console\njupyter-console\nptipython\nipython\npython" | fzf)
+fi
+
+# set normal command first
+if [ -z "$cmd" ]; then
+    if exist ptipython; then
+        cmd=ptipython
+    elif exist ipython; then
+        cmd=ipython
+    elif exist python; then
+        cmd=python
+    else
+        echo "No python found on system, please install." 1>&2
+        exit 1
+    fi
+fi
+
+# search for molten session for current dir
+if [ -n "$(ls -A "${search_dir}" 2>/dev/null)" ]; then
+    res=$(find "$search_dir" -maxdepth 1 -type f -name "*.json")
+    if [ "$(echo "$res" | wc -l)" -gt 1 ]; then
+        session=$(echo "$res" | fzf --prompt "Molten session> ")
+    fi
+fi
+
+# attach to kernel
+if [ -n "${session}" ]; then
+    if exist euporie-console || [ "$cmd" == "euporie-console" ]; then
+        euporie-console --edit-mode vi --connection-file "$session"
+    elif exist jupyter-console || [ "$cmd" == "jupyter-console" ]; then
+        jupyter-console --existing "$session"
+    fi
+# or just run normal python
+else
+    $cmd
+fi

sh/.config/sh/alias

@@ -106,15 +106,6 @@ else
     done
 fi
 
-# python
-if exist ptipython; then
-    alias py=ptipython
-elif exist ipython; then
-    alias py=ipython
-elif exist python; then
-    alias py=python
-fi
-
 # distrobox
 if exist distrobox; then
     alias db=distrobox