From 3e13941eae69ab031ba3181bd0badc2d6304a8ac Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Sat, 15 Jun 2024 19:26:42 +0200
Subject: [PATCH 01/27] nvim: Add mappings for inspecting treesitter

Simply invokes the `:Inspect` and `:InspectTree` commands, to have
quicker access, especially while tinkering with TS for the foreseeable
future.
---
 nvim/.config/nvim/lua/plugins/treesitter.lua | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/nvim/.config/nvim/lua/plugins/treesitter.lua b/nvim/.config/nvim/lua/plugins/treesitter.lua
index 5db7903..18e2e53 100644
--- a/nvim/.config/nvim/lua/plugins/treesitter.lua
+++ b/nvim/.config/nvim/lua/plugins/treesitter.lua
@@ -79,6 +79,10 @@ return {
 			"TSUpdate",
 			"TSUpdateSync",
 		},
+		keys = {
+			{ "<leader>si", "<cmd>Inspect<cr>", desc = "treesitter element", silent = true },
+			{ "<leader>sI", "<cmd>InspectTree<cr>", desc = "treesitter tree", silent = true },
+		},
 
 		-- show current cursor context at top of buffer
 		-- improves commenting plugin above by using ts

From 4f5445cc0ee610ef2aab28621076cc594109c70d Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Sun, 16 Jun 2024 16:40:10 +0200
Subject: [PATCH 02/27] nvim: Add function to cleanly unmap keys

Removes them from being active in vim as well as removing them from
being displayed in which-key.

Unfortunately the which-key implementation still seems broken, sometimes
removing them sometimes leaving them as-is.
---
 nvim/.config/nvim/lua/core/util.lua | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/nvim/.config/nvim/lua/core/util.lua b/nvim/.config/nvim/lua/core/util.lua
index d83d8f0..6279973 100644
--- a/nvim/.config/nvim/lua/core/util.lua
+++ b/nvim/.config/nvim/lua/core/util.lua
@@ -17,6 +17,17 @@ function T.get_plugin(plugin)
 	return nil
 end
 
+-- Remove the key from the vim keymap and from being displayed in which-key
+-- FIXME This does not consistently currently with which-key
+-- Every once in a while the maps are correctly hidden but other times they stay?
+function T.unmap_key(lhs, mode)
+	mode = mode or "n"
+	if T.is_available("which-key") then
+		vim.keymap.set(mode, lhs, "", { desc = "which_key_ignore", silent = true })
+	end
+	pcall(vim.keymap.del, mode, lhs)
+end
+
 -- from https://github.com/ray-x/navigator.lua/issues/247#issue-1465308677
 local function path_join(...)
 	return table.concat(vim.tbl_flatten({ ... }), "/")

From 0bac43eb915ce51e9630c0545a82da47602c6e6c Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Sun, 16 Jun 2024 16:44:02 +0200
Subject: [PATCH 03/27] nvim: Split python venv fetching into multiple

Now we can either fetch the python venv basefolder
(`require('core.util').get_python_venv_basefolder()`) or specifically
the python binary contained within (`.get_python_bin()`).

Additionally, the venv result should be cached for the duration of using
nvim so that we only have to fetch it once, regardless of how many
modules require it.
---
 nvim/.config/nvim/lua/core/util.lua          | 30 ++++++++++++++------
 nvim/.config/nvim/lua/plugins/config/lsp.lua |  4 +--
 2 files changed, 24 insertions(+), 10 deletions(-)

diff --git a/nvim/.config/nvim/lua/core/util.lua b/nvim/.config/nvim/lua/core/util.lua
index 6279973..2d336de 100644
--- a/nvim/.config/nvim/lua/core/util.lua
+++ b/nvim/.config/nvim/lua/core/util.lua
@@ -32,28 +32,42 @@ end
 local function path_join(...)
 	return table.concat(vim.tbl_flatten({ ... }), "/")
 end
+function T.get_python_venv_bin(workspace)
+	local pyenv = T.get_python_venv_basefolder(workspace)
+	if not pyenv then
+		-- Fallback to system Python.
+		return vim.fn.exepath("python3") or vim.fn.exepath("python") or "python"
+	end
+	return path_join(pyenv, "bin", "python")
+end
+-- cache path so we can call it multiple times
+local venv_path = ""
 -- return the current python environment path
-function T.get_python_venv(workspace)
+function T.get_python_venv_basefolder(workspace)
+	if venv_path and venv_path ~= "" then
+		return venv_path
+	end
+
 	-- Use activated virtualenv.
 	if vim.env.VIRTUAL_ENV then
-		return path_join(vim.env.VIRTUAL_ENV, "bin", "python")
+		venv_path = vim.env.VIRTUAL_ENV
+		return venv_path
 	end
 	-- Find and use virtualenv in workspace directory.
 	for _, pattern in ipairs({ "*", ".*" }) do
 		local match = vim.fn.glob(path_join(workspace, pattern, "pyvenv.cfg"))
 		if match ~= "" then
-			local py = path_join("bin", "python")
-			match = string.gsub(match, "pyvenv.cfg", py)
-			return match
+			match = string.gsub(match, "pyvenv.cfg", "")
+			venv_path = match
+			return venv_path
 		end
 		match = vim.fn.glob(path_join(workspace, pattern, "poetry.lock"))
 		if match ~= "" then
 			local venv_base_folder = vim.fn.trim(vim.fn.system("poetry env info -p"))
-			return path_join(venv_base_folder, "bin", "python")
+			venv_path = venv_base_folder
+			return venv_path
 		end
 	end
-	-- Fallback to system Python.
-	return vim.fn.exepath("python3") or vim.fn.exepath("python") or "python"
 end
 
 return T
diff --git a/nvim/.config/nvim/lua/plugins/config/lsp.lua b/nvim/.config/nvim/lua/plugins/config/lsp.lua
index e84244e..86f433c 100644
--- a/nvim/.config/nvim/lua/plugins/config/lsp.lua
+++ b/nvim/.config/nvim/lua/plugins/config/lsp.lua
@@ -167,7 +167,7 @@ local python_path
 lspconfig.basedpyright.setup({
 	on_attach = function(client, bufnr)
 		if python_path == nil then
-			python_path, _ = require("core.util").get_python_venv(client.config.root_dir)
+			python_path, _ = vim.fn.expand(require("core.util").get_python_venv_bin(client.config.root_dir))
 		end
 		-- print(string.format("[PYTHON VENV]: %s", vim.inspect(python_path)))
 		client.config.settings.python = {} or client.config.settings.python
@@ -179,7 +179,7 @@ lspconfig.ruff_lsp.setup({
 	on_attach = function(client, bufnr)
 		on_attach(client, bufnr)
 		if python_path == nil then
-			python_path, _ = require("core.util").get_python_venv(client.config.root_dir)
+			python_path, _ = vim.fn.expand(require("core.util").get_python_venv_bin(client.config.root_dir))
 		end
 		client.config.settings.python = {} or client.config.settings.python
 		client.config.settings.python.pythonPath = python_path

From 9dcd2f3d48a8a513c90fc366c12ca09395ead9fa Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Sun, 16 Jun 2024 17:41:18 +0200
Subject: [PATCH 04/27] nvim: Add direct python env set utility function

Added a simple 'set python environment' function to directly set the
correct python binary and update the PATH for python.
---
 nvim/.config/nvim/lua/core/util.lua             | 9 +++++++++
 nvim/.config/nvim/lua/plugins/data_analysis.lua | 4 ++--
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/nvim/.config/nvim/lua/core/util.lua b/nvim/.config/nvim/lua/core/util.lua
index 2d336de..1e81da0 100644
--- a/nvim/.config/nvim/lua/core/util.lua
+++ b/nvim/.config/nvim/lua/core/util.lua
@@ -32,6 +32,15 @@ end
 local function path_join(...)
 	return table.concat(vim.tbl_flatten({ ... }), "/")
 end
+function T.set_python_env(workspace)
+	local base = vim.fn.expand(require("core.util").get_python_venv_basefolder(workspace))
+	local p = vim.env.PATH or ""
+	if not base then
+		return
+	end
+	vim.g["python3_host_prog"] = vim.fn.expand(require("core.util").get_python_venv_bin())
+	vim.env.PATH = base .. "/bin:" .. p
+end
 function T.get_python_venv_bin(workspace)
 	local pyenv = T.get_python_venv_basefolder(workspace)
 	if not pyenv then
diff --git a/nvim/.config/nvim/lua/plugins/data_analysis.lua b/nvim/.config/nvim/lua/plugins/data_analysis.lua
index 0443e6a..aa3c1e0 100644
--- a/nvim/.config/nvim/lua/plugins/data_analysis.lua
+++ b/nvim/.config/nvim/lua/plugins/data_analysis.lua
@@ -9,12 +9,12 @@ return {
 			"nvim-treesitter/nvim-treesitter",
 		},
 		config = function()
+			require("core.util").set_python_env()
+
 			require("quarto").setup({
 				lspFeatures = {
 					enabled = true,
 					languages = { "r", "python", "julia", "bash" },
-					diagnostics = { enabled = false, triggers = { "BufWritePost" } },
-					completion = { enabled = true },
 				},
 				codeRunner = {
 					enabled = true,

From 849489afd6d47c1933c6594ad75e680aebc06090 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Sun, 16 Jun 2024 17:42:48 +0200
Subject: [PATCH 05/27] nvim: Move mini.bracketed comment to k suffix

Moved the mini bracketed comment following to use the ]k [k suffix. I am
not sure if this is completely taking since every now and again it seems
to still be overriding my own configured mapping.
---
 nvim/.config/nvim/lua/plugins/core.lua | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/nvim/.config/nvim/lua/plugins/core.lua b/nvim/.config/nvim/lua/plugins/core.lua
index 5544ca8..b1dd640 100644
--- a/nvim/.config/nvim/lua/plugins/core.lua
+++ b/nvim/.config/nvim/lua/plugins/core.lua
@@ -119,17 +119,17 @@ return {
 			require("mini.bracketed").setup({
 				{
 					buffer = { suffix = "b", options = {} },
-					comment = { suffix = "c", options = {} },
-					conflict = { suffix = "", options = {} },
+					comment = { suffix = "k", options = {} },
+					conflict = { suffix = "" }, -- disable to use git-conflict instead
 					diagnostic = { suffix = "d", options = {} },
-					file = { suffix = "f", options = {} },
-					indent = { suffix = "", options = {} }, -- disable since we use indentscope above
+					file = { suffix = "", options = {} },
+					indent = { suffix = "" }, -- disable since we use indentscope above
 					jump = { suffix = "j", options = {} },
 					location = { suffix = "l", options = {} },
 					oldfile = { suffix = "o", options = {} },
 					quickfix = { suffix = "q", options = {} },
 					treesitter = { suffix = "t", options = {} },
-					undo = { suffix = "", options = {} }, -- disable since I don't need it
+					undo = { suffix = "" }, -- disable since I don't need it
 					window = { suffix = "w", options = {} },
 					yank = { suffix = "y", options = {} },
 				},

From 63dc6fb88808c3d46ea9da96c028b7b8b29c83f3 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Sun, 16 Jun 2024 21:27:01 +0200
Subject: [PATCH 06/27] nvim: Set up quarto for interactive python work

---
 nvim/.config/nvim/after/ftplugin/quarto.lua   | 112 ++++--------------
 .../nvim/lua/plugins/data_analysis.lua        |  27 ++++-
 2 files changed, 49 insertions(+), 90 deletions(-)

diff --git a/nvim/.config/nvim/after/ftplugin/quarto.lua b/nvim/.config/nvim/after/ftplugin/quarto.lua
index 18d1d03..8840c65 100644
--- a/nvim/.config/nvim/after/ftplugin/quarto.lua
+++ b/nvim/.config/nvim/after/ftplugin/quarto.lua
@@ -6,14 +6,13 @@ local default_buffer_session = function()
 	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 default_buffer_session()
-	local path = require("core.util").get_python_venv()
+	local path = require("core.util").get_python_venv_bin()
 	vim.g["python3_host_prog"] = path
 
 	if vim.fn.executable("jupyter-console") ~= 1 then
@@ -41,92 +40,27 @@ vim.api.nvim_create_user_command("JupyterStart", function()
 	startsession()
 end, {})
 
-local map = vim.keymap.set
-
-local function molten_mappings_set()
-	-- Operate jupyter notebooks from within vim
-	map("n", "<localleader>cc", ":MoltenEvaluateLine<cr>", { silent = true })
-	map(
-		"n",
-		"<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>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,
+vim.api.nvim_create_autocmd({"InsertEnter", "BufEnter"}, {
+	callback = function()
+		if vim.b["sessionfile"] == nil then
+			local path = default_buffer_session()
+			vim.b["sessionfile"] = path
+			vim.schedule_wrap(startsession(path))
+		end
+	end,
 })
-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" })
-map(
-	"n",
-	"[e",
-	"<cmd>lua vim.diagnostic.goto_prev({severity = vim.diagnostic.severity.ERROR})<cr>",
-	{ buffer = bufnr, desc = "Previous error" }
-)
-map(
-	"n",
-	"]e",
-	"<cmd>lua vim.diagnostic.goto_next({severity = vim.diagnostic.severity.ERROR})<cr>",
-	{ buffer = bufnr, desc = "Next error" }
-)
+-- -- -- TODO find better way to enable lsp key mappings for quarto buffers
+-- -- local prefix = require("which-key").register
+-- -- prefix({ ["<localleader>l"] = { name = "+lsp" } })
+-- -- map("n", "<localleader>li", "<cmd>LspInfo<cr>", { buffer = bufnr, desc = "Lsp Info" })
+-- -- map("n", "<localleader>ld", "<cmd>lua vim.diagnostic.open_float()<cr>", { buffer = bufnr, desc = "Line diagnostics" })
+-- -- map("n", "<localleader>la", "<cmd>lua vim.lsp.buf.code_action()<cr>", { buffer = bufnr, desc = "Codeactions" })
+-- -- map("n", "<localleader>ln", "<cmd>lua vim.lsp.buf.rename()<cr>", { buffer = bufnr, desc = "Rename element" })
+-- -- map("n", "<localleader>lr", "<cmd>lua vim.lsp.buf.references()<cr>", { buffer = bufnr, desc = "References" })
+-- --
+-- -- map("n", "gD", "<cmd>lua vim.lsp.buf.declaration()<cr>", { buffer = bufnr, desc = "Declaration" })
+-- -- map("n", "gs", "<cmd>lua vim.lsp.buf.signature_help()<cr>", { buffer = bufnr, desc = "Signature help" })
+-- -- map("n", "gI", "<cmd>lua vim.lsp.buf.implementation()<cr>", { buffer = bufnr, desc = "Implementation" })
+-- -- map("n", "gt", "<cmd>lua vim.lsp.buf.type_definition()<cr>", { buffer = bufnr, desc = "Type definition" })
 
--- TODO find better way to enable lsp key mappings for quarto buffers
-local prefix = require("which-key").register
-prefix({ ["<localleader>l"] = { name = "+lsp" } })
-map("n", "<localleader>li", "<cmd>LspInfo<cr>", { buffer = bufnr, desc = "Lsp Info" })
-map("n", "<localleader>ld", "<cmd>lua vim.diagnostic.open_float()<cr>", { buffer = bufnr, desc = "Line diagnostics" })
-map("n", "<localleader>la", "<cmd>lua vim.lsp.buf.code_action()<cr>", { buffer = bufnr, desc = "Codeactions" })
-map("n", "<localleader>ln", "<cmd>lua vim.lsp.buf.rename()<cr>", { buffer = bufnr, desc = "Rename element" })
-map("n", "<localleader>lr", "<cmd>lua vim.lsp.buf.references()<cr>", { buffer = bufnr, desc = "References" })
-
-map("n", "K", "<cmd>lua vim.lsp.buf.hover()<cr>", { buffer = bufnr, desc = "Hover definition" })
-map("n", "gd", "<cmd>lua vim.lsp.buf.definition()<cr>", { buffer = bufnr, desc = "Definition" })
-map("n", "gD", "<cmd>lua vim.lsp.buf.declaration()<cr>", { buffer = bufnr, desc = "Declaration" })
-map("n", "gs", "<cmd>lua vim.lsp.buf.signature_help()<cr>", { buffer = bufnr, desc = "Signature help" })
-map("n", "gI", "<cmd>lua vim.lsp.buf.implementation()<cr>", { buffer = bufnr, desc = "Implementation" })
-map("n", "gt", "<cmd>lua vim.lsp.buf.type_definition()<cr>", { buffer = bufnr, desc = "Type definition" })
-
-if vim.b["sessionfile"] == nil then
-	local path = default_buffer_session()
-	vim.b["sessionfile"] = path
-	vim.schedule_wrap(startsession(path))
-end
+-- vim.g["python3_host_prog"] = vim.fn.expand(require("core.util").get_python_venv())
diff --git a/nvim/.config/nvim/lua/plugins/data_analysis.lua b/nvim/.config/nvim/lua/plugins/data_analysis.lua
index aa3c1e0..6d76169 100644
--- a/nvim/.config/nvim/lua/plugins/data_analysis.lua
+++ b/nvim/.config/nvim/lua/plugins/data_analysis.lua
@@ -1,4 +1,15 @@
 return {
+	{
+		"jmbuhr/otter.nvim",
+		config = function()
+			require("otter").setup({
+				buffers = {
+					set_filetype = true,
+					write_to_disk = false,
+				},
+			})
+		end,
+	},
 	{
 		"quarto-dev/quarto-nvim",
 		dependencies = {
@@ -7,6 +18,7 @@ return {
 			"vim-pandoc/vim-pandoc-syntax",
 			"hrsh7th/nvim-cmp",
 			"nvim-treesitter/nvim-treesitter",
+			{ "benlubas/molten-nvim", optional = true },
 		},
 		config = function()
 			require("core.util").set_python_env()
@@ -18,9 +30,22 @@ return {
 				},
 				codeRunner = {
 					enabled = true,
-					default_method = "molten",
+					default_method = "slime",
+					ft_runners = {
+						python = "molten",
+						quarto = "molten",
+					},
 				},
 			})
+			local map = vim.keymap.set
+			map("n", "<localleader>C", require("quarto.runner").run_cell, { desc = "run cell" })
+			map("n", "<localleader>ca", require("quarto.runner").run_above, { desc = "run cells above" })
+			map("n", "<localleader>cb", require("quarto.runner").run_below, { desc = "run cells below" })
+			map("n", "<localleader>cA", require("quarto.runner").run_all, { desc = "run all similar cells" })
+			map("n", "]c", "/^```{<cr>}:nohl<cr>", { desc = "Codecell forward" })
+			map("n", "[c", "?^```<cr>n}:nohl<cr>", { desc = "Codecell last" })
+			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,
 		ft = { "quarto" },
 	},

From e25aedd94b4bdee47735fdf6e2cc1247571bfd91 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Sun, 16 Jun 2024 21:29:34 +0200
Subject: [PATCH 07/27] nvim: Set up molten for interactive python repl

Set it up with extended options and keymaps. Will use an image provider
if it has been set externally (usually set by the 'image.nvim' setup
routine) or fall back to use the `wezterm.nvim` plugin to display it in
a wezterm pane. This display can be a little buggy so we should prefer
others.
---
 .../nvim/lua/plugins/data_analysis.lua        | 115 ++++++++++++++----
 1 file changed, 89 insertions(+), 26 deletions(-)

diff --git a/nvim/.config/nvim/lua/plugins/data_analysis.lua b/nvim/.config/nvim/lua/plugins/data_analysis.lua
index 6d76169..6eb80b2 100644
--- a/nvim/.config/nvim/lua/plugins/data_analysis.lua
+++ b/nvim/.config/nvim/lua/plugins/data_analysis.lua
@@ -50,7 +50,6 @@ return {
 		ft = { "quarto" },
 	},
 
-	-- REPL work
 	{
 		"3rd/image.nvim",
 		config = function()
@@ -71,41 +70,105 @@ return {
 		end,
 		ft = { "markdown", "vimwiki", "quarto" },
 	},
+	-- REPL work
 	{
 		"benlubas/molten-nvim",
+		dependencies = {
+			{ "willothy/wezterm.nvim", config = true },
+			{ "3rd/image.nvim", optional = true },
+		},
 		build = ":UpdateRemotePlugins",
 		config = function()
-			vim.g.molten_image_provider = "none" -- image integration does NOT work currently :-(
+			vim.g.molten_image_provider = vim.g.molten_image_provider or "wezterm"
 			vim.g.molten_auto_open_output = false
+			vim.g.molten_virt_text_output = true
+			if vim.fn.has("nvim-0.10") then
+				vim.g.molten_output_show_more = true
+			end
+			vim.api.nvim_create_autocmd("User", {
+				pattern = "MoltenInitPost",
+				callback = function()
+					local map = vim.keymap.set
+					if require("core.util").is_available("which-key") then
+						require("which-key").register({ ["<localleader>c"] = { name = "+codecells" } })
+					end
+					-- Operate jupyter notebooks from within vim
+					map(
+						"n",
+						"<localleader>cc",
+						":MoltenEvaluateOperator<cr>",
+						{ desc = "evaluate operator", silent = true }
+					)
+					map("n", "<localleader>cl", ":MoltenEvaluateLine<cr>", { desc = "evaluate line", silent = true })
+					map(
+						"x",
+						"<localleader>c",
+						":<C-u>MoltenEvaluateVisual<cr>",
+						{ desc = "evaluate visual", silent = true }
+					)
+					map(
+						"n",
+						"<localleader>cr",
+						":MoltenReevaluateCell<cr>",
+						{ desc = "reevaluate cell", silent = true }
+					)
+					map(
+						"n",
+						"<localleader>cp",
+						":noautocmd :MoltenEnterOutput<cr>",
+						{ silent = true, desc = "show output" }
+					)
+					map("n", "<localleader>cP", function()
+						vim.cmd("MoltenHideOutput")
+						vim.cmd("MoltenDelete")
+					end, { silent = true, desc = "hide output" })
+					map("n", "<localleader>co", ":MoltenImagePopup<cr>", { silent = true, desc = "open image" })
+					map("n", "<localleader>ci", ":MoltenInterrupt<cr>", { desc = "interrupt cell", silent = true })
+					map("n", "<localleader>cD", ":MoltenDeinit<cr>", { desc = "de-init molten", silent = true })
+					map("n", "<localleader>cR", ":MoltenRestart<cr>", { desc = "restart molten", silent = true })
+					-- FIXME: Works for toggling TO virt text but not back
+					local function toggle_virtual_text_output()
+						if vim.g.molten_virt_text_output then
+							vim.fn.MoltenUpdateOption("molten_virt_text_output", false)
+							return
+						end
+						vim.fn.MoltenUpdateOption("molten_virt_text_output", true)
+					end
+					map(
+						"n",
+						"<localleader>cV",
+						toggle_virtual_text_output,
+						{ desc = "toggle virtual output", silent = true }
+					)
+				end,
+			})
+			vim.api.nvim_create_autocmd("User", {
+				pattern = "MoltenDeinitPost",
+				callback = function()
+					local unmap = require("core.util").unmap_key
+					unmap("<localleader>cc")
+					unmap("<localleader>cl")
+					unmap("<localleader>c", "x")
+					unmap("<localleader>cr")
+					unmap("<localleader>cR")
+					unmap("<localleader>cp")
+					unmap("<localleader>cP")
+					unmap("<localleader>co")
+					unmap("<localleader>cD")
+					unmap("<localleader>ci")
+					unmap("<localleader>cV")
+					local map = vim.keymap.set
+					map("n", "<localleader>cI", ":MoltenInit<cr>", { desc = "init molten", silent = true })
+				end,
+			})
 		end,
-		cmd = {
-			"MoltenInfo",
-			"MoltenInit",
-			"MoltenDeinit",
-			"MoltenGoto",
-			"MoltenNext",
-			"MoltenPrev",
-			"MoltenEvaluateLine",
-			"MoltenEvaluateVisual",
-			"MoltenEvaluateOperator",
-			"MoltenEvaluateArgument",
-			"MoltenReevaluateCell",
-			"MoltenDelete",
-			"MoltenShowOutput",
-			"MoltenHideOutput",
-			"MoltenEnterOutput",
-			"MoltenInterrupt",
-			"MoltenRestart",
-			"MoltenSave",
-			"MoltenLoad",
-			"MoltenExportOutput",
-		},
-		ft = { "quarto", "python" },
-		lazy = false,
+		ft = { "norg", "quarto", "python" },
 		keys = {
 			{ "<leader>vn", ":MoltenInfo<cr>" },
+			{ "<localleader>ci", ":MoltenInit<cr>" },
 		},
 	},
+
 	-- Edit code blocks in md/quarto using whatever language is
 	{
 		"AckslD/nvim-FeMaco.lua",

From 0ec49583bd7cf73341f52ce56ddc6aa033a7ad15 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Sun, 16 Jun 2024 21:30:20 +0200
Subject: [PATCH 08/27] nvim: Set up image.nvim image display

Finally got image.nvim fully working on wezterm with the kitty backend
and auto-installed rock dependencies.
---
 nvim/.config/nvim/lazy-lock.json              |  2 +
 .../nvim/lua/plugins/data_analysis.lua        | 53 +++++++++++++------
 2 files changed, 40 insertions(+), 15 deletions(-)

diff --git a/nvim/.config/nvim/lazy-lock.json b/nvim/.config/nvim/lazy-lock.json
index 940af3f..1ed5022 100644
--- a/nvim/.config/nvim/lazy-lock.json
+++ b/nvim/.config/nvim/lazy-lock.json
@@ -38,6 +38,7 @@
   "lazy.nvim": { "branch": "main", "commit": "fafe1f7c640aed75e70a10e6649612cd96f39149" },
   "lsp-setup.nvim": { "branch": "main", "commit": "6e4e977512ce426d8b52c27f3b6e6aefc73e1452" },
   "lualine.nvim": { "branch": "master", "commit": "0a5a66803c7407767b799067986b4dc3036e1983" },
+  "luarocks.nvim": { "branch": "main", "commit": "1db9093915eb16ba2473cfb8d343ace5ee04130a" },
   "markmap.nvim": { "branch": "main", "commit": "5fb6755cf5434511cc23a4936c9eb76b9142fba5" },
   "mason-lspconfig.nvim": { "branch": "main", "commit": "9ae570e206360e47d30b4c35a4550c165f4ea7b7" },
   "mason-tool-installer.nvim": { "branch": "main", "commit": "c5e07b8ff54187716334d585db34282e46fa2932" },
@@ -84,6 +85,7 @@
   "vim-pandoc-syntax": { "branch": "master", "commit": "16939cda184ff555938cc895cc62477c172997f9" },
   "vim-scimark": { "branch": "master", "commit": "9b66a88fa4bb87b8baab3c4aecc43b985b32e7fd" },
   "vim-spellsync": { "branch": "master", "commit": "3d6dd50de9c4d953cc16638112a6ae196df41463" },
+  "wezterm.nvim": { "branch": "main", "commit": "f73bba23ab4becd146fa2d0a3a16a84b987eeaca" },
   "which-key.nvim": { "branch": "main", "commit": "0539da005b98b02cf730c1d9da82b8e8edb1c2d2" },
   "wrapping.nvim": { "branch": "master", "commit": "3a823200c297885b70515fa8d974e1763c578e26" },
   "zen-mode.nvim": { "branch": "main", "commit": "cb73b8bd0ef9d765b942db09dc762c603a89ae44" },
diff --git a/nvim/.config/nvim/lua/plugins/data_analysis.lua b/nvim/.config/nvim/lua/plugins/data_analysis.lua
index 6eb80b2..9d6e926 100644
--- a/nvim/.config/nvim/lua/plugins/data_analysis.lua
+++ b/nvim/.config/nvim/lua/plugins/data_analysis.lua
@@ -50,25 +50,48 @@ return {
 		ft = { "quarto" },
 	},
 
+	{
+		"vhyrro/luarocks.nvim",
+		priority = 1001, -- this plugin needs to run before anything else
+		opts = {
+			rocks = { "magick" },
+		},
+	},
+	-- image display
 	{
 		"3rd/image.nvim",
+		dependencies = { "luarocks.nvim" },
+		cond = vim.fn.executable("magick") == 1, -- only runs if imagemagick installed
 		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" },
-					},
-				},
-			})
+			local integrations = {}
+			if vim.treesitter.language.get_lang("markdown") then
+				integrations["markdown"] = {
+					enabled = true,
+					clear_in_insert_mode = true,
+					download_remote_images = true,
+					only_render_image_at_cursor = true,
+					filetypes = { "markdown", "vimwiki", "quarto" },
+				}
+			end
+			if vim.treesitter.language.get_lang("norg") then
+				integrations["neorg"] = {
+					enabled = true,
+					clear_in_insert_mode = true,
+					download_remote_images = true,
+					only_render_image_at_cursor = true,
+					filetypes = { "norg" },
+				}
+			end
+			if next(integrations) ~= nil then -- only set up if we have at least 1 TS parser
+				require("image").setup({
+					backend = "kitty",
+					integrations = integrations,
+				})
+				vim.g.molten_image_provider = "image.nvim"
+			end
 		end,
-		ft = { "markdown", "vimwiki", "quarto" },
+		ft = { "markdown", "vimwiki", "quarto", "norg", "python" },
+		priority = 51,
 	},
 	-- REPL work
 	{

From 4d8cc4d2af02ca1e438b14b50706e45252f5d4dc Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Sun, 16 Jun 2024 21:31:21 +0200
Subject: [PATCH 09/27] nvim: Add FeMaco codecell edit mapping

Added mapping to quickly edit any code cell in FeMaco, an extra buffer
which brings lsp functionality and similar with it. Can be used as a
fallback if otter.nvim is not working for the buffer, or when working on
a buffer which otter.nvim does not understand.
---
 nvim/.config/nvim/lua/plugins/data_analysis.lua | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/nvim/.config/nvim/lua/plugins/data_analysis.lua b/nvim/.config/nvim/lua/plugins/data_analysis.lua
index 9d6e926..90d04f7 100644
--- a/nvim/.config/nvim/lua/plugins/data_analysis.lua
+++ b/nvim/.config/nvim/lua/plugins/data_analysis.lua
@@ -203,8 +203,10 @@ return {
 		dependencies = {
 			"nvim-treesitter/nvim-treesitter",
 		},
+		keys = {
+			{ "<localleader>ce", ":FeMaco<cr>", desc = "edit codecell" },
+		},
 	},
-
 	-- MARKDOWN ONLY
 	-- Evaluate markdown code blocks
 	{

From 3b1a8748833c43efa526e00ff328702fc766876c Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Sun, 16 Jun 2024 21:32:56 +0200
Subject: [PATCH 10/27] nvim: Open ipynb files as quarto files

We can now open any ipynb file as if it were a quarto document by
leveraging the `jupytext.nvim` extension which works in the background
to convert everything. Will only work if `jupytext` program is actually
installed on the machine.

Allows normal editing of the file and will write any changes back to the
original notebook on save and exit!
---
 nvim/.config/nvim/lazy-lock.json              |  1 +
 .../nvim/lua/plugins/data_analysis.lua        | 23 +++++++++++++++++++
 2 files changed, 24 insertions(+)

diff --git a/nvim/.config/nvim/lazy-lock.json b/nvim/.config/nvim/lazy-lock.json
index 1ed5022..5712d06 100644
--- a/nvim/.config/nvim/lazy-lock.json
+++ b/nvim/.config/nvim/lazy-lock.json
@@ -35,6 +35,7 @@
   "glance.nvim": { "branch": "master", "commit": "51059bcf21016387b6233c89eed220cf47fca752" },
   "headlines.nvim": { "branch": "master", "commit": "618ef1b2502c565c82254ef7d5b04402194d9ce3" },
   "image.nvim": { "branch": "master", "commit": "da64ce69598875c9af028afe129f916b02ccc42e" },
+  "jupytext.nvim": { "branch": "main", "commit": "c8baf3ad344c59b3abd461ecc17fc16ec44d0f7b" },
   "lazy.nvim": { "branch": "main", "commit": "fafe1f7c640aed75e70a10e6649612cd96f39149" },
   "lsp-setup.nvim": { "branch": "main", "commit": "6e4e977512ce426d8b52c27f3b6e6aefc73e1452" },
   "lualine.nvim": { "branch": "master", "commit": "0a5a66803c7407767b799067986b4dc3036e1983" },
diff --git a/nvim/.config/nvim/lua/plugins/data_analysis.lua b/nvim/.config/nvim/lua/plugins/data_analysis.lua
index 90d04f7..803dae1 100644
--- a/nvim/.config/nvim/lua/plugins/data_analysis.lua
+++ b/nvim/.config/nvim/lua/plugins/data_analysis.lua
@@ -221,4 +221,27 @@ return {
 		},
 		lazy = false,
 	},
+
+	-- Open ipynb Jupyter notebooks as if they're quarto files
+	-- requires jupytext to be installed
+	{
+		"GCBallesteros/jupytext.nvim",
+		opts = {
+			style = "light",
+			custom_language_formatting = {
+				python = {
+					extension = "qmd",
+					style = "quarto",
+					force_ft = "quarto",
+				},
+				r = {
+					extension = "qmd",
+					style = "quarto",
+					force_ft = "quarto",
+				},
+			},
+		},
+		cond = vim.fn.executable("jupytext") == 1, -- only runs if imagemagick installed
+		lazy = false -- does not work in lazy mode
+	},
 }

From b2c64a092547ec23f55aba63e9da89751427be9e Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Sun, 16 Jun 2024 21:34:52 +0200
Subject: [PATCH 11/27] nvim: Allow pasting images into markup files

With the new `img-clip.nvim` extension we can copy any image anywhere
and simply paste it into a markdown/quarto/latex/typst/... document with
the right markup already.

Those can be from the web/locally. Also allows drag and drop from e.g.
web pages.

Mapped to `<leader>pp` currently, though we will have to find a better
mapping. Or invoked with `:ImagePaste`.
---
 nvim/.config/nvim/after/ftplugin/markdown.lua |  4 ++--
 nvim/.config/nvim/lazy-lock.json              |  1 +
 nvim/.config/nvim/lua/plugins/prose.lua       | 23 ++++++++++++++++++-
 3 files changed, 25 insertions(+), 3 deletions(-)

diff --git a/nvim/.config/nvim/after/ftplugin/markdown.lua b/nvim/.config/nvim/after/ftplugin/markdown.lua
index 7f2c06f..84ad5c0 100644
--- a/nvim/.config/nvim/after/ftplugin/markdown.lua
+++ b/nvim/.config/nvim/after/ftplugin/markdown.lua
@@ -35,9 +35,9 @@ if require("core.util").is_available("peek") then
 			peek.open()
 		end
 	end
-	map("n", "<leader>pp", togglePeek, { desc = "show md preview" })
+	map("n", "<leader>po", togglePeek, { desc = "show md preview" })
 else
-	map("n", "<leader>pp", "<Plug>MarkdownPreviewToggle", { desc = "show md preview" })
+	map("n", "<leader>po", "<Plug>MarkdownPreviewToggle", { desc = "show md preview" })
 end
 
 -- create mindmaps directly from markdown! requires external executable
diff --git a/nvim/.config/nvim/lazy-lock.json b/nvim/.config/nvim/lazy-lock.json
index 5712d06..56235ac 100644
--- a/nvim/.config/nvim/lazy-lock.json
+++ b/nvim/.config/nvim/lazy-lock.json
@@ -35,6 +35,7 @@
   "glance.nvim": { "branch": "master", "commit": "51059bcf21016387b6233c89eed220cf47fca752" },
   "headlines.nvim": { "branch": "master", "commit": "618ef1b2502c565c82254ef7d5b04402194d9ce3" },
   "image.nvim": { "branch": "master", "commit": "da64ce69598875c9af028afe129f916b02ccc42e" },
+  "img-clip.nvim": { "branch": "main", "commit": "fc30500c35663aa1762697f5aba31d43b86028f0" },
   "jupytext.nvim": { "branch": "main", "commit": "c8baf3ad344c59b3abd461ecc17fc16ec44d0f7b" },
   "lazy.nvim": { "branch": "main", "commit": "fafe1f7c640aed75e70a10e6649612cd96f39149" },
   "lsp-setup.nvim": { "branch": "main", "commit": "6e4e977512ce426d8b52c27f3b6e6aefc73e1452" },
diff --git a/nvim/.config/nvim/lua/plugins/prose.lua b/nvim/.config/nvim/lua/plugins/prose.lua
index d6c6327..7dfbbaa 100644
--- a/nvim/.config/nvim/lua/plugins/prose.lua
+++ b/nvim/.config/nvim/lua/plugins/prose.lua
@@ -1,4 +1,4 @@
-local writing_ft = { "quarto", "pandoc", "markdown", "text", "tex" }
+local writing_ft = { "quarto", "pandoc", "markdown", "text", "tex", "typst" }
 
 local prose_plugs = {
 	-- UI improvements
@@ -69,6 +69,26 @@ local prose_plugs = {
 		ft = writing_ft,
 	},
 
+	-- easy copy paste of images into markup files
+	{
+		"HakonHarnes/img-clip.nvim",
+		event = "VeryLazy",
+		opts = {
+			filetypes = {
+				quarto = {
+					url_encode_path = true,
+					template = "![$CURSOR]($FILE_PATH)",
+					download_images = false,
+				},
+			},
+		},
+		cmd = { "PasteImage" },
+		keys = {
+			{ "<leader>pp", "<cmd>PasteImage<cr>", desc = "Paste image from system clipboard" },
+		},
+		ft = writing_ft,
+	},
+
 	-- bring zettelkasten commands
 	{
 		"mickael-menu/zk-nvim",
@@ -111,6 +131,7 @@ local prose_plugs = {
 			"ZkOrphans",
 		},
 		keys = {
+			-- additional key instpirations https://github.com/al1-ce/MonolithVim/blob/master/after/ftplugin/markdown.lua
 			{ "<leader>ni", "<cmd>edit ~/documents/notes/index.md<cr>", desc = "open index", silent = true },
 			{ "<leader>nn", "<cmd>ZkNotes { sort = { 'modified' } }<cr>", desc = "note list" },
 			{

From ebee0042d860fa394f2894c32ff448283c9745ad Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Sun, 16 Jun 2024 21:36:18 +0200
Subject: [PATCH 12/27] nvim: Fix correct workspace propagation for python env

---
 nvim/.config/nvim/lua/core/util.lua | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nvim/.config/nvim/lua/core/util.lua b/nvim/.config/nvim/lua/core/util.lua
index 1e81da0..63b9c9d 100644
--- a/nvim/.config/nvim/lua/core/util.lua
+++ b/nvim/.config/nvim/lua/core/util.lua
@@ -38,7 +38,7 @@ function T.set_python_env(workspace)
 	if not base then
 		return
 	end
-	vim.g["python3_host_prog"] = vim.fn.expand(require("core.util").get_python_venv_bin())
+	vim.g["python3_host_prog"] = vim.fn.expand(require("core.util").get_python_venv_bin(workspace))
 	vim.env.PATH = base .. "/bin:" .. p
 end
 function T.get_python_venv_bin(workspace)

From fa1db974f0c320b6190ce6add09470358ab65d49 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Sun, 16 Jun 2024 21:38:05 +0200
Subject: [PATCH 13/27] nvim: Update plugins

---
 nvim/.config/nvim/lazy-lock.json | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/nvim/.config/nvim/lazy-lock.json b/nvim/.config/nvim/lazy-lock.json
index 56235ac..7384f80 100644
--- a/nvim/.config/nvim/lazy-lock.json
+++ b/nvim/.config/nvim/lazy-lock.json
@@ -31,13 +31,13 @@
   "friendly-snippets": { "branch": "main", "commit": "700c4a25caacbb4648c9a27972c2fe203948e0c2" },
   "fwatch.nvim": { "branch": "main", "commit": "a691f7349dc66285cd75a1a698dd28bca45f2bf8" },
   "git-conflict.nvim": { "branch": "main", "commit": "bfd9fe6fba9a161fc199771d85996236a0d0faad" },
-  "gitsigns.nvim": { "branch": "main", "commit": "76927d14d3fbd4ba06ccb5246e79d93b5442c188" },
+  "gitsigns.nvim": { "branch": "main", "commit": "0b04035bb7b3c83e999b9676e2fb46fd0aa9f910" },
   "glance.nvim": { "branch": "master", "commit": "51059bcf21016387b6233c89eed220cf47fca752" },
   "headlines.nvim": { "branch": "master", "commit": "618ef1b2502c565c82254ef7d5b04402194d9ce3" },
   "image.nvim": { "branch": "master", "commit": "da64ce69598875c9af028afe129f916b02ccc42e" },
   "img-clip.nvim": { "branch": "main", "commit": "fc30500c35663aa1762697f5aba31d43b86028f0" },
   "jupytext.nvim": { "branch": "main", "commit": "c8baf3ad344c59b3abd461ecc17fc16ec44d0f7b" },
-  "lazy.nvim": { "branch": "main", "commit": "fafe1f7c640aed75e70a10e6649612cd96f39149" },
+  "lazy.nvim": { "branch": "main", "commit": "c501b429cf995c645454539b924aaefae45bb9eb" },
   "lsp-setup.nvim": { "branch": "main", "commit": "6e4e977512ce426d8b52c27f3b6e6aefc73e1452" },
   "lualine.nvim": { "branch": "master", "commit": "0a5a66803c7407767b799067986b4dc3036e1983" },
   "luarocks.nvim": { "branch": "main", "commit": "1db9093915eb16ba2473cfb8d343ace5ee04130a" },
@@ -46,7 +46,7 @@
   "mason-tool-installer.nvim": { "branch": "main", "commit": "c5e07b8ff54187716334d585db34282e46fa2932" },
   "mason.nvim": { "branch": "main", "commit": "c43eeb5614a09dc17c03a7fb49de2e05de203924" },
   "mdeval.nvim": { "branch": "master", "commit": "2c32e2f3e7d8f222e7a4724989f218d036e1081d" },
-  "mini.nvim": { "branch": "main", "commit": "f24747266a047617d06605a2316aa6c071662fa2" },
+  "mini.nvim": { "branch": "main", "commit": "19e1584124cda35388d4fdb911eab7124014e541" },
   "molten-nvim": { "branch": "main", "commit": "df5ccef3b6fda3582f7746e45327ee031f668826" },
   "neogen": { "branch": "main", "commit": "0daffcec249bf42275e322361fe55b89a05ff278" },
   "neotest": { "branch": "master", "commit": "f30bab1faef13d47f3905e065215c96a42d075ad" },
@@ -56,7 +56,7 @@
   "nvim-colorizer.lua": { "branch": "master", "commit": "85855b38011114929f4058efc97af1059ab3e41d" },
   "nvim-coverage": { "branch": "main", "commit": "aa4b4400588e2259e87e372b1e4e90ae13cf5a39" },
   "nvim-lint": { "branch": "master", "commit": "941fa1220a61797a51f3af9ec6b7d74c8c7367ce" },
-  "nvim-lspconfig": { "branch": "master", "commit": "4d38bece98300e3e5cd24a9aa0d0ebfea4951c16" },
+  "nvim-lspconfig": { "branch": "master", "commit": "bd7c76375a511994c9ca8d69441f134dc10ae3bd" },
   "nvim-nio": { "branch": "master", "commit": "7969e0a8ffabdf210edd7978ec954a47a737bbcc" },
   "nvim-surround": { "branch": "main", "commit": "687ea2f33955df0042bf228853a82696265e7e2d" },
   "nvim-toggleterm.lua": { "branch": "main", "commit": "066cccf48a43553a80a210eb3be89a15d789d6e6" },
@@ -72,20 +72,19 @@
   "peek.nvim": { "branch": "master", "commit": "5820d937d5414baea5f586dc2a3d912a74636e5b" },
   "plenary.nvim": { "branch": "master", "commit": "50012918b2fc8357b87cff2a7f7f0446e47da174" },
   "popup.nvim": { "branch": "master", "commit": "b7404d35d5d3548a82149238289fa71f7f6de4ac" },
-  "quarto-nvim": { "branch": "main", "commit": "67e09027b5d8bd948907734fc6fb15028ffdcd28" },
+  "quarto-nvim": { "branch": "main", "commit": "a6e7452de5944f7f38a4b12f1d50e460c1dccd95" },
   "rainbow-delimiters.nvim": { "branch": "master", "commit": "12b1a1e095d968887a17ef791c2edb78d7595d46" },
   "smartcolumn.nvim": { "branch": "main", "commit": "d01b99355c7fab13233f48d0f28dc097e68a03f7" },
   "stickybuf.nvim": { "branch": "master", "commit": "2160fcd536d81f5fa43f7167dba6634e814e3154" },
   "telescope-fzf-native.nvim": { "branch": "main", "commit": "9ef21b2e6bb6ebeaf349a0781745549bbb870d27" },
   "telescope.nvim": { "branch": "master", "commit": "a0bbec21143c7bc5f8bb02e0005fa0b982edc026" },
-  "trouble.nvim": { "branch": "main", "commit": "3609bb9a82bbab1ef95cf2c27ce7e52267a7d40d" },
+  "trouble.nvim": { "branch": "main", "commit": "09380a8ed0694dbfbbcf59f9eaac499e259cb75c" },
   "twilight.nvim": { "branch": "main", "commit": "8bb7fa7b918baab1ca81b977102ddb54afa63512" },
   "undotree": { "branch": "main", "commit": "eab459ab87dd249617b5f7187bb69e614a083047" },
   "vifm.vim": { "branch": "master", "commit": "a8130c37d144b51d84bee19f0532abcd3583383f" },
   "vim-criticmarkup": { "branch": "master", "commit": "d15dc134eb177a170c79f6377f81eb02a9d20b02" },
   "vim-numbertoggle": { "branch": "main", "commit": "df9b1fe616507340718716204ba7f434125bdf7a" },
   "vim-pandoc-syntax": { "branch": "master", "commit": "16939cda184ff555938cc895cc62477c172997f9" },
-  "vim-scimark": { "branch": "master", "commit": "9b66a88fa4bb87b8baab3c4aecc43b985b32e7fd" },
   "vim-spellsync": { "branch": "master", "commit": "3d6dd50de9c4d953cc16638112a6ae196df41463" },
   "wezterm.nvim": { "branch": "main", "commit": "f73bba23ab4becd146fa2d0a3a16a84b987eeaca" },
   "which-key.nvim": { "branch": "main", "commit": "0539da005b98b02cf730c1d9da82b8e8edb1c2d2" },

From fae2d85cca05a08103a1652752ea0f4c29a81be7 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Sun, 16 Jun 2024 22:30:11 +0200
Subject: [PATCH 14/27] nvim: Fix crash on no python venv available

---
 nvim/.config/nvim/lua/core/util.lua | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nvim/.config/nvim/lua/core/util.lua b/nvim/.config/nvim/lua/core/util.lua
index 63b9c9d..93278d4 100644
--- a/nvim/.config/nvim/lua/core/util.lua
+++ b/nvim/.config/nvim/lua/core/util.lua
@@ -33,7 +33,8 @@ local function path_join(...)
 	return table.concat(vim.tbl_flatten({ ... }), "/")
 end
 function T.set_python_env(workspace)
-	local base = vim.fn.expand(require("core.util").get_python_venv_basefolder(workspace))
+	local base = require("core.util").get_python_venv_basefolder(workspace)
+	base = vim.fn.expand(base)
 	local p = vim.env.PATH or ""
 	if not base then
 		return

From 1a2e83ccb665123ad4269978593e99e9da5212bd Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Sun, 16 Jun 2024 22:30:49 +0200
Subject: [PATCH 15/27] nvim: Fix overlapping REPL key maps

---
 nvim/.config/nvim/lua/plugins/data_analysis.lua | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nvim/.config/nvim/lua/plugins/data_analysis.lua b/nvim/.config/nvim/lua/plugins/data_analysis.lua
index 803dae1..3eb3a05 100644
--- a/nvim/.config/nvim/lua/plugins/data_analysis.lua
+++ b/nvim/.config/nvim/lua/plugins/data_analysis.lua
@@ -145,8 +145,8 @@ return {
 						vim.cmd("MoltenHideOutput")
 						vim.cmd("MoltenDelete")
 					end, { silent = true, desc = "hide output" })
-					map("n", "<localleader>co", ":MoltenImagePopup<cr>", { silent = true, desc = "open image" })
-					map("n", "<localleader>ci", ":MoltenInterrupt<cr>", { desc = "interrupt cell", silent = true })
+					map("n", "<localleader>ci", ":MoltenImagePopup<cr>", { silent = true, desc = "open image" })
+					map("n", "<localleader>cI", ":MoltenInterrupt<cr>", { desc = "interrupt cell", silent = true })
 					map("n", "<localleader>cD", ":MoltenDeinit<cr>", { desc = "de-init molten", silent = true })
 					map("n", "<localleader>cR", ":MoltenRestart<cr>", { desc = "restart molten", silent = true })
 					-- FIXME: Works for toggling TO virt text but not back

From d8823d4661a2b518fccdeebd069e676f6c4953e0 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Mon, 17 Jun 2024 08:27:35 +0200
Subject: [PATCH 16/27] wezterm: Switch navigator and tab hiding maps around

Since I (almost) never use the navigator, it has been put behind
`<leader>T`. The tab-hiding I used a (little) more often so that now
lies behind `<leader>t`. Simple change.
---
 terminal/.config/wezterm/maps.lua | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/terminal/.config/wezterm/maps.lua b/terminal/.config/wezterm/maps.lua
index 40e1b43..a582345 100644
--- a/terminal/.config/wezterm/maps.lua
+++ b/terminal/.config/wezterm/maps.lua
@@ -52,7 +52,7 @@ local keys = {
 		mods = "LEADER",
 		action = act.ShowLauncherArgs({ flags = "FUZZY|WORKSPACES" }),
 	},
-	{ key = "t", mods = "LEADER", action = act.ShowTabNavigator },
+	{ key = "T", mods = "LEADER", action = act.ShowTabNavigator },
 	{ key = "[", mods = "LEADER", action = act.ActivateCopyMode },
 	{
 		key = "r",
@@ -100,7 +100,7 @@ local keys = {
 		action = act.EmitEvent("ActivatePaneDirection-Right"),
 	},
 	{ key = "a", mods = "CTRL|ALT", action = act.EmitEvent("toggle-leader") },
-	{ key = "T", mods = "CTRL", action = act.EmitEvent("toggle-tabbar") },
+	{ key = "t", mods = "LEADER", action = act.EmitEvent("toggle-tabbar") },
 }
 -- Leader + number to activate that tab
 for i = 1, 8 do

From c4f2522f2b8bccdfcbf803543805d7d8810ac2da Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Mon, 17 Jun 2024 08:30:06 +0200
Subject: [PATCH 17/27] wezterm: Ensure CTRL and SHIFT mods passed through

These bindings ensure that wezterm understands (and informs the shell)
that `<C-Return>` and `<S-Return>` are different key binds than just
`<Return>` on its own.

For example 'euporie' uses it to mimic the python notebook 'enter means
newline but ctrl-enter means execute' style of quick coding.
---
 terminal/.config/wezterm/maps.lua | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/terminal/.config/wezterm/maps.lua b/terminal/.config/wezterm/maps.lua
index a582345..b519d12 100644
--- a/terminal/.config/wezterm/maps.lua
+++ b/terminal/.config/wezterm/maps.lua
@@ -101,6 +101,8 @@ local keys = {
 	},
 	{ key = "a", mods = "CTRL|ALT", action = act.EmitEvent("toggle-leader") },
 	{ key = "t", mods = "LEADER", action = act.EmitEvent("toggle-tabbar") },
+	{ key = "Enter", mods = "CTRL", action = wezterm.action({ SendString = "\x1b[13;5u" }) },
+	{ key = "Enter", mods = "SHIFT", action = wezterm.action({ SendString = "\x1b[13;2u" }) },
 }
 -- Leader + number to activate that tab
 for i = 1, 8 do

From 543a149da21f015051ccfe9a42d8b7ebb212dca9 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Mon, 17 Jun 2024 10:31:39 +0200
Subject: [PATCH 18/27] nvim: Update treesitter dependencies

Moved rainbow delimiters into dependencies so that it runs with TS
instead of loading TS on its own. Made TS itself more lazy (only loading
on VeryLazy by default).

Run TSUpdate on each run instead of only each build step.
---
 nvim/.config/nvim/lua/plugins/treesitter.lua | 39 +++++++++-----------
 1 file changed, 18 insertions(+), 21 deletions(-)

diff --git a/nvim/.config/nvim/lua/plugins/treesitter.lua b/nvim/.config/nvim/lua/plugins/treesitter.lua
index 18e2e53..53306e2 100644
--- a/nvim/.config/nvim/lua/plugins/treesitter.lua
+++ b/nvim/.config/nvim/lua/plugins/treesitter.lua
@@ -1,7 +1,23 @@
 return {
 	{
 		"nvim-treesitter/nvim-treesitter",
-		build = ":TSUpdate",
+		run = ":TSUpdate",
+		-- show current cursor context at top of buffer
+		-- improves commenting plugin above by using ts
+		dependencies = {
+			{ "romgrk/nvim-treesitter-context", config = true },
+			"JoosepAlviste/nvim-ts-context-commentstring",
+			"RRethy/nvim-treesitter-textsubjects",
+			"windwp/nvim-ts-autotag",
+			"RRethy/nvim-treesitter-endwise",
+			-- rainbow brackets using treesitter
+			{
+				"HiPhish/rainbow-delimiters.nvim",
+				config = function()
+					require("rainbow-delimiters.setup").setup({})
+				end,
+			},
+		},
 		config = function()
 			require("nvim-treesitter.configs").setup({
 				-- one of "all", "maintained" (parsers with maintainers), or a list of languages
@@ -63,7 +79,7 @@ return {
 				filetype = "nu",
 			}
 		end,
-		event = { "BufReadPost", "BufNewFile", "BufWritePre", "VeryLazy" },
+		event = { "VeryLazy" },
 		cmd = {
 			"TSBufDisable",
 			"TSBufEnable",
@@ -83,24 +99,5 @@ return {
 			{ "<leader>si", "<cmd>Inspect<cr>", desc = "treesitter element", silent = true },
 			{ "<leader>sI", "<cmd>InspectTree<cr>", desc = "treesitter tree", silent = true },
 		},
-
-		-- show current cursor context at top of buffer
-		-- improves commenting plugin above by using ts
-		dependencies = {
-			{ "romgrk/nvim-treesitter-context", config = true },
-			"JoosepAlviste/nvim-ts-context-commentstring",
-			"RRethy/nvim-treesitter-textsubjects",
-			"windwp/nvim-ts-autotag",
-			"RRethy/nvim-treesitter-endwise",
-		},
-	},
-	-- rainbow brackets using treesitter
-	{
-		"https://gitlab.com/HiPhish/rainbow-delimiters.nvim",
-		lazy = false,
-		event = { "BufReadPost", "BufNewFile", "BufWritePre", "VeryLazy" },
-		config = function()
-			require("rainbow-delimiters.setup").setup({})
-		end,
 	},
 }

From 157fbc812c310d4516baaf1b5f54373049040f08 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Mon, 17 Jun 2024 10:42:12 +0200
Subject: [PATCH 19/27] nvim: Extraction completion setup into own module

As a first step to disentangle the ide.lua module into completion,
formatting, lsp (and maybe lint?), this separates the completion module
into its own file.
---
 nvim/.config/nvim/lazy-lock.json             |   2 +-
 nvim/.config/nvim/lua/plugins/completion.lua | 179 +++++++++++++++++++
 nvim/.config/nvim/lua/plugins/config/cmp.lua | 144 ---------------
 nvim/.config/nvim/lua/plugins/config/lsp.lua |   1 +
 nvim/.config/nvim/lua/plugins/ide.lua        |  33 ----
 5 files changed, 181 insertions(+), 178 deletions(-)
 create mode 100644 nvim/.config/nvim/lua/plugins/completion.lua
 delete mode 100644 nvim/.config/nvim/lua/plugins/config/cmp.lua

diff --git a/nvim/.config/nvim/lazy-lock.json b/nvim/.config/nvim/lazy-lock.json
index 7384f80..8de0f21 100644
--- a/nvim/.config/nvim/lazy-lock.json
+++ b/nvim/.config/nvim/lazy-lock.json
@@ -28,7 +28,7 @@
   "dressing.nvim": { "branch": "master", "commit": "572314728cb1ce012e825fd66331f52c94acac12" },
   "fidget.nvim": { "branch": "main", "commit": "ef99df04a1c53a453602421bc0f756997edc8289" },
   "flash.nvim": { "branch": "main", "commit": "7bb4a9c75d1e20cd24185afedeaa11681829ba23" },
-  "friendly-snippets": { "branch": "main", "commit": "700c4a25caacbb4648c9a27972c2fe203948e0c2" },
+  "friendly-snippets": { "branch": "main", "commit": "682157939e57bd6a2c86277dfd4d6fbfce63dbac" },
   "fwatch.nvim": { "branch": "main", "commit": "a691f7349dc66285cd75a1a698dd28bca45f2bf8" },
   "git-conflict.nvim": { "branch": "main", "commit": "bfd9fe6fba9a161fc199771d85996236a0d0faad" },
   "gitsigns.nvim": { "branch": "main", "commit": "0b04035bb7b3c83e999b9676e2fb46fd0aa9f910" },
diff --git a/nvim/.config/nvim/lua/plugins/completion.lua b/nvim/.config/nvim/lua/plugins/completion.lua
new file mode 100644
index 0000000..5988ef8
--- /dev/null
+++ b/nvim/.config/nvim/lua/plugins/completion.lua
@@ -0,0 +1,179 @@
+return {
+	-- completion setup
+	{
+		"hrsh7th/nvim-cmp",
+		branch = "main",
+		dependencies = {
+			"andersevenrud/cmp-tmux",
+			"cbarrete/completion-vcard",
+			"f3fora/cmp-spell",
+			"hrsh7th/cmp-nvim-lsp",
+			"hrsh7th/cmp-path",
+			"hrsh7th/cmp-buffer",
+			"hrsh7th/cmp-calc",
+			"hrsh7th/cmp-cmdline",
+			"hrsh7th/cmp-nvim-lua",
+			"hrsh7th/cmp-nvim-lsp-signature-help",
+			"dmitmel/cmp-digraphs",
+			"jc-doyle/cmp-pandoc-references",
+			"kdheepak/cmp-latex-symbols",
+			"lukas-reineke/cmp-rg",
+			"crispgm/cmp-beancount",
+			"ray-x/cmp-treesitter",
+			"saadparwaiz1/cmp_luasnip",
+			{
+				"L3MON4D3/LuaSnip",
+				dependencies = { "rafamadriz/friendly-snippets" },
+			},
+		},
+		config = function()
+			local luasnip = require("luasnip")
+			local cmp = require("cmp")
+
+			local has_words_before = function()
+				---@diagnostic disable-next-line:deprecated
+				local line, col = unpack(vim.api.nvim_win_get_cursor(0))
+				return col ~= 0
+					and vim.api.nvim_buf_get_lines(0, line - 1, line, true)[1]:sub(col, col):match("%s") == nil
+			end
+
+			local kind_icons = {
+				Text = "",
+				Method = "",
+				Function = "󰊕",
+				Constructor = "",
+				Field = "",
+				Variable = "",
+				Class = "",
+				Interface = "",
+				Module = "",
+				Property = "",
+				Unit = "",
+				Value = "V",
+				Enum = "",
+				Keyword = "",
+				Snippet = "",
+				Color = "",
+				File = "",
+				Reference = "",
+				Folder = "",
+				EnumMember = "",
+				Constant = "",
+				Struct = "",
+				Event = "",
+				Operator = "",
+				TypeParameter = "",
+			}
+
+			cmp.setup({
+				window = { documentation = cmp.config.window.bordered() },
+				snippet = {
+					expand = function(args)
+						require("luasnip").lsp_expand(args.body)
+					end,
+				},
+				sources = {
+					{ name = "nvim_lua" },
+					{
+						name = "beancount",
+						option = {
+							account = vim.env["HOME"] .. "/documents/records/budget/main.beancount", -- TODO implement dynamically
+						},
+					},
+					{ name = "otter" },
+					{ name = "nvim_lsp" },
+					{ name = "nvim_lsp_signature_help" },
+					{ name = "luasnip", keyword_length = 2 },
+					{ name = "pandoc_references" },
+					{ name = "calc" },
+					{ name = "path" },
+					{ name = "buffer", keyword_length = 3 },
+					{ name = "latex_symbols" },
+					{ name = "spell", keyword_length = 3 },
+					{ name = "tmux" }, -- { name = 'rg',           keyword_length = 5 },
+					{ name = "vCard" },
+					{ name = "digraphs", keyword_length = 2 },
+				},
+				mapping = cmp.mapping.preset.insert({
+					["<C-b>"] = cmp.mapping.scroll_docs(-4),
+					["<C-f>"] = cmp.mapping.scroll_docs(4),
+					["<CR>"] = cmp.mapping({
+						i = function(fallback)
+							if cmp.visible() and cmp.get_active_entry() then
+								cmp.confirm({
+									behavior = cmp.ConfirmBehavior.Replace,
+									select = false,
+								})
+							else
+								fallback()
+							end
+						end,
+						s = cmp.mapping.confirm({ select = true }),
+						c = cmp.mapping.confirm({
+							behavior = cmp.ConfirmBehavior.Replace,
+							select = false,
+						}), -- disable selection in cmd mode
+					}),
+					["<Tab>"] = cmp.mapping(function(fallback)
+						if cmp.visible() then
+							cmp.select_next_item()
+						-- You could replace the expand_or_jumpable() calls with expand_or_locally_jumpable()
+						-- they way you will only jump inside the snippet region
+						elseif luasnip.expand_or_jumpable() then
+							luasnip.expand_or_jump()
+						elseif has_words_before() then
+							cmp.complete()
+						else
+							fallback()
+						end
+					end, { "i", "s" }),
+					["<S-Tab>"] = cmp.mapping(function(fallback)
+						if cmp.visible() then
+							cmp.select_prev_item()
+						elseif luasnip.jumpable(-1) then
+							luasnip.jump(-1)
+						else
+							fallback()
+						end
+					end, { "i", "s" }),
+				}),
+				formatting = {
+					fields = { "kind", "abbr", "menu" },
+					format = function(entry, vim_item)
+						-- Kind icons, removing kind text leaving only icon
+						-- vim_item.kind = string.format('%s %s', kind_icons[vim_item.kind], vim_item.kind)
+						vim_item.kind = string.format("%s", kind_icons[vim_item.kind])
+
+						-- Source
+						vim_item.menu = ({
+							buffer = "",
+							calc = "󰃬",
+							digraphs = "∬",
+							latex_symbols = "𝓧",
+							luasnip = "",
+							nvim_lsp = "ℒ",
+							nvim_lua = "󰢱",
+							pandoc_references = "",
+							spell = "󰓆",
+							vCard = "󰛋",
+						})[entry.source.name]
+						return vim_item
+					end,
+				},
+			})
+			-- `/` cmdline setup.
+			cmp.setup.cmdline("/", {
+				mapping = cmp.mapping.preset.cmdline(),
+				sources = { { name = "buffer" } },
+			})
+			-- `:` cmdline setup.
+			cmp.setup.cmdline(":", {
+				mapping = cmp.mapping.preset.cmdline(),
+				sources = cmp.config.sources({ { name = "path" } }, {
+					{ name = "cmdline", option = { ignore_cmds = { "Man", "!" } } },
+				}),
+			})
+		end,
+		event = { "InsertEnter", "CmdlineEnter" },
+	},
+}
diff --git a/nvim/.config/nvim/lua/plugins/config/cmp.lua b/nvim/.config/nvim/lua/plugins/config/cmp.lua
deleted file mode 100644
index 49840cc..0000000
--- a/nvim/.config/nvim/lua/plugins/config/cmp.lua
+++ /dev/null
@@ -1,144 +0,0 @@
-local luasnip = require("luasnip")
-local cmp = require("cmp")
-
-local has_words_before = function()
-	local line, col = unpack(vim.api.nvim_win_get_cursor(0))
-	return col ~= 0 and vim.api.nvim_buf_get_lines(0, line - 1, line, true)[1]:sub(col, col):match("%s") == nil
-end
-
-local kind_icons = {
-	Text = "",
-	Method = "",
-	Function = "󰊕",
-	Constructor = "",
-	Field = "",
-	Variable = "",
-	Class = "",
-	Interface = "",
-	Module = "",
-	Property = "",
-	Unit = "",
-	Value = "V",
-	Enum = "",
-	Keyword = "",
-	Snippet = "",
-	Color = "",
-	File = "",
-	Reference = "",
-	Folder = "",
-	EnumMember = "",
-	Constant = "",
-	Struct = "",
-	Event = "",
-	Operator = "",
-	TypeParameter = "",
-}
-
-cmp.setup({
-	window = { documentation = cmp.config.window.bordered() },
-	snippet = {
-		expand = function(args)
-			require("luasnip").lsp_expand(args.body)
-		end,
-	},
-	sources = {
-		{ name = "nvim_lua" },
-		{
-			name = "beancount",
-			option = {
-				account = vim.env["HOME"] .. "/documents/records/budget/main.beancount", -- TODO implement dynamically
-			},
-		},
-		{ name = "otter" },
-		{ name = "nvim_lsp" },
-		{ name = "nvim_lsp_signature_help" },
-		{ name = "luasnip", keyword_length = 2 },
-		{ name = "pandoc_references" },
-		{ name = "calc" },
-		{ name = "path" },
-		{ name = "buffer", keyword_length = 3 },
-		{ name = "latex_symbols" },
-		{ name = "spell", keyword_length = 3 },
-		{ name = "tmux" }, -- { name = 'rg',           keyword_length = 5 },
-		{ name = "vCard" },
-		{ name = "digraphs", keyword_length = 2 },
-	},
-	mapping = cmp.mapping.preset.insert({
-		["<C-b>"] = cmp.mapping.scroll_docs(-4),
-		["<C-f>"] = cmp.mapping.scroll_docs(4),
-		["<CR>"] = cmp.mapping({
-			i = function(fallback)
-				if cmp.visible() and cmp.get_active_entry() then
-					cmp.confirm({
-						behavior = cmp.ConfirmBehavior.Replace,
-						select = false,
-					})
-				else
-					fallback()
-				end
-			end,
-			s = cmp.mapping.confirm({ select = true }),
-			c = cmp.mapping.confirm({
-				behavior = cmp.ConfirmBehavior.Replace,
-				select = false,
-			}), -- disable selection in cmd mode
-		}),
-		["<Tab>"] = cmp.mapping(function(fallback)
-			if cmp.visible() then
-				cmp.select_next_item()
-				-- You could replace the expand_or_jumpable() calls with expand_or_locally_jumpable()
-				-- they way you will only jump inside the snippet region
-			elseif luasnip.expand_or_jumpable() then
-				luasnip.expand_or_jump()
-			elseif has_words_before() then
-				cmp.complete()
-			else
-				fallback()
-			end
-		end, { "i", "s" }),
-		["<S-Tab>"] = cmp.mapping(function(fallback)
-			if cmp.visible() then
-				cmp.select_prev_item()
-			elseif luasnip.jumpable(-1) then
-				luasnip.jump(-1)
-			else
-				fallback()
-			end
-		end, { "i", "s" }),
-	}),
-	formatting = {
-		fields = { "kind", "abbr", "menu" },
-		format = function(entry, vim_item)
-			-- Kind icons, removing kind text leaving only icon
-			-- vim_item.kind = string.format('%s %s', kind_icons[vim_item.kind], vim_item.kind)
-			vim_item.kind = string.format("%s", kind_icons[vim_item.kind])
-
-			-- Source
-			vim_item.menu = ({
-				buffer = "",
-				calc = "󰃬",
-				digraphs = "∬",
-				latex_symbols = "𝓧",
-				luasnip = "",
-				nvim_lsp = "ℒ",
-				nvim_lua = "󰢱",
-				pandoc_references = "",
-				spell = "󰓆",
-				vCard = "󰛋",
-			})[entry.source.name]
-			return vim_item
-		end,
-	},
-})
--- `/` cmdline setup.
-cmp.setup.cmdline("/", {
-	mapping = cmp.mapping.preset.cmdline(),
-	sources = { { name = "buffer" } },
-})
--- `:` cmdline setup.
-cmp.setup.cmdline(":", {
-	mapping = cmp.mapping.preset.cmdline(),
-	sources = cmp.config.sources({ { name = "path" } }, {
-		{ name = "cmdline", option = { ignore_cmds = { "Man", "!" } } },
-	}),
-})
diff --git a/nvim/.config/nvim/lua/plugins/config/lsp.lua b/nvim/.config/nvim/lua/plugins/config/lsp.lua
index 86f433c..c67e77a 100644
--- a/nvim/.config/nvim/lua/plugins/config/lsp.lua
+++ b/nvim/.config/nvim/lua/plugins/config/lsp.lua
@@ -45,6 +45,7 @@ local servers = {
 
 -- TODO installed for conform/nvim-lint so should be sourced from there not here
 local to_mason =
+	---@diagnostic disable-next-line:deprecated
 	{ "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
diff --git a/nvim/.config/nvim/lua/plugins/ide.lua b/nvim/.config/nvim/lua/plugins/ide.lua
index f2b88a7..1dcec3d 100644
--- a/nvim/.config/nvim/lua/plugins/ide.lua
+++ b/nvim/.config/nvim/lua/plugins/ide.lua
@@ -195,39 +195,6 @@ return {
 		end,
 	},
 
-	-- completion setup
-	{
-		"hrsh7th/nvim-cmp",
-		branch = "main",
-		dependencies = {
-			"andersevenrud/cmp-tmux",
-			"cbarrete/completion-vcard",
-			"f3fora/cmp-spell",
-			"hrsh7th/cmp-nvim-lsp",
-			"hrsh7th/cmp-path",
-			"hrsh7th/cmp-buffer",
-			"hrsh7th/cmp-calc",
-			"hrsh7th/cmp-cmdline",
-			"hrsh7th/cmp-nvim-lua",
-			"hrsh7th/cmp-nvim-lsp-signature-help",
-			"dmitmel/cmp-digraphs",
-			"jc-doyle/cmp-pandoc-references",
-			"kdheepak/cmp-latex-symbols",
-			"lukas-reineke/cmp-rg",
-			"crispgm/cmp-beancount",
-			"ray-x/cmp-treesitter",
-			"saadparwaiz1/cmp_luasnip",
-			{
-				"L3MON4D3/LuaSnip",
-				dependencies = { "rafamadriz/friendly-snippets" },
-			},
-		},
-		config = function()
-			require("plugins.config.cmp")
-		end,
-		event = { "InsertEnter", "CmdlineEnter" },
-	},
-
 	-- useful quickfix-like buffer
 	{
 		"folke/trouble.nvim",

From c45d85922bc4930aa27bda04c853e7abb6366142 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Mon, 17 Jun 2024 13:13:15 +0200
Subject: [PATCH 20/27] nvim: Fix wrong lazy.nvim plugin spec options

Some options were left over from old plugin managers, some were just
used wrong.
---
 nvim/.config/nvim/lua/plugins/ide.lua        | 1 -
 nvim/.config/nvim/lua/plugins/treesitter.lua | 2 +-
 nvim/.config/nvim/lua/plugins/ui.lua         | 6 +++---
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/nvim/.config/nvim/lua/plugins/ide.lua b/nvim/.config/nvim/lua/plugins/ide.lua
index 1dcec3d..b4d3a05 100644
--- a/nvim/.config/nvim/lua/plugins/ide.lua
+++ b/nvim/.config/nvim/lua/plugins/ide.lua
@@ -99,7 +99,6 @@ return {
 			{ "WhoIsSethDaniel/mason-tool-installer.nvim" },
 		},
 		event = { "BufReadPost", "BufNewFile", "BufWritePre" },
-		after = { "nvim-cmp" },
 		config = function()
 			require("plugins.config.lsp")
 		end,
diff --git a/nvim/.config/nvim/lua/plugins/treesitter.lua b/nvim/.config/nvim/lua/plugins/treesitter.lua
index 53306e2..8ed1ff5 100644
--- a/nvim/.config/nvim/lua/plugins/treesitter.lua
+++ b/nvim/.config/nvim/lua/plugins/treesitter.lua
@@ -1,7 +1,7 @@
 return {
 	{
 		"nvim-treesitter/nvim-treesitter",
-		run = ":TSUpdate",
+		build = ":TSUpdate",
 		-- show current cursor context at top of buffer
 		-- improves commenting plugin above by using ts
 		dependencies = {
diff --git a/nvim/.config/nvim/lua/plugins/ui.lua b/nvim/.config/nvim/lua/plugins/ui.lua
index fbf0ed9..ab57b0b 100644
--- a/nvim/.config/nvim/lua/plugins/ui.lua
+++ b/nvim/.config/nvim/lua/plugins/ui.lua
@@ -2,7 +2,7 @@ return {
 	-- statusline
 	{
 		"nvim-lualine/lualine.nvim",
-		requires = { "nvim-tree/nvim-web-devicons", config = true },
+		dependencies = { { "nvim-tree/nvim-web-devicons", config = true } },
 		config = function()
 			-- FIXME: Errors out on no pynvim installed
 			-- local function molten()
@@ -58,10 +58,10 @@ return {
 			},
 		},
 		event = { "VeryLazy" },
-		cmd = {"Fidget"},
+		cmd = { "Fidget" },
 		keys = {
 			{ "<leader>sh", "<cmd>Fidget history<cr>", { silent = true, desc = "show notification history" } },
-		}
+		},
 	},
 	-- make all vim.ui interfaces prettyy
 	{ "stevearc/dressing.nvim", config = true, event = "VeryLazy" },

From a7aca62a15b36aa0996d85cbe624395eebf53024 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Mon, 17 Jun 2024 13:13:43 +0200
Subject: [PATCH 21/27] nvim: Extend lualine enabled extensions

Added more extensions for plugins that I use, all pre-defined.
---
 nvim/.config/nvim/lua/plugins/ui.lua | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/nvim/.config/nvim/lua/plugins/ui.lua b/nvim/.config/nvim/lua/plugins/ui.lua
index ab57b0b..7026909 100644
--- a/nvim/.config/nvim/lua/plugins/ui.lua
+++ b/nvim/.config/nvim/lua/plugins/ui.lua
@@ -40,7 +40,18 @@ return {
 					lualine_z = {},
 				},
 				tabline = {},
-				extensions = { "quickfix", "toggleterm" },
+				extensions = {
+					"aerial",
+					"lazy",
+					"man",
+					"mason",
+					"nvim-dap-ui",
+					"nvim-tree",
+					"oil",
+					"quickfix",
+					"toggleterm",
+					"trouble",
+				},
 			})
 		end,
 		event = { "VeryLazy" },

From 8dbfa2dd131ef04c33e7a2964754ca643335e680 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Mon, 17 Jun 2024 13:15:15 +0200
Subject: [PATCH 22/27] nvim: Extend snippet capability

Enabled snippet completion from the first letter (allowing single letter
snippet prefixes).
Extended the luasnip usage and added a telescope extension to show all
enabled snippets for the current buffer.
---
 nvim/.config/nvim/lazy-lock.json             |   1 +
 nvim/.config/nvim/lua/plugins/completion.lua |  30 +++++-
 nvim/.config/nvim/snippets/markdown.snippets |  80 +++++++++++++++
 nvim/.config/nvim/snippets/quarto.snippets   | 100 +++++++++++++++++++
 4 files changed, 206 insertions(+), 5 deletions(-)
 create mode 100644 nvim/.config/nvim/snippets/markdown.snippets
 create mode 100644 nvim/.config/nvim/snippets/quarto.snippets

diff --git a/nvim/.config/nvim/lazy-lock.json b/nvim/.config/nvim/lazy-lock.json
index 8de0f21..62fd9d9 100644
--- a/nvim/.config/nvim/lazy-lock.json
+++ b/nvim/.config/nvim/lazy-lock.json
@@ -77,6 +77,7 @@
   "smartcolumn.nvim": { "branch": "main", "commit": "d01b99355c7fab13233f48d0f28dc097e68a03f7" },
   "stickybuf.nvim": { "branch": "master", "commit": "2160fcd536d81f5fa43f7167dba6634e814e3154" },
   "telescope-fzf-native.nvim": { "branch": "main", "commit": "9ef21b2e6bb6ebeaf349a0781745549bbb870d27" },
+  "telescope-luasnip.nvim": { "branch": "master", "commit": "11668478677de360dea45cf2b090d34f21b8ae07" },
   "telescope.nvim": { "branch": "master", "commit": "a0bbec21143c7bc5f8bb02e0005fa0b982edc026" },
   "trouble.nvim": { "branch": "main", "commit": "09380a8ed0694dbfbbcf59f9eaac499e259cb75c" },
   "twilight.nvim": { "branch": "main", "commit": "8bb7fa7b918baab1ca81b977102ddb54afa63512" },
diff --git a/nvim/.config/nvim/lua/plugins/completion.lua b/nvim/.config/nvim/lua/plugins/completion.lua
index 5988ef8..cb5a3fc 100644
--- a/nvim/.config/nvim/lua/plugins/completion.lua
+++ b/nvim/.config/nvim/lua/plugins/completion.lua
@@ -3,6 +3,7 @@ return {
 	{
 		"hrsh7th/nvim-cmp",
 		branch = "main",
+		version = false,
 		dependencies = {
 			"andersevenrud/cmp-tmux",
 			"cbarrete/completion-vcard",
@@ -19,11 +20,30 @@ return {
 			"kdheepak/cmp-latex-symbols",
 			"lukas-reineke/cmp-rg",
 			"crispgm/cmp-beancount",
-			"ray-x/cmp-treesitter",
-			"saadparwaiz1/cmp_luasnip",
+			{ "ray-x/cmp-treesitter", dependencies = { "nvim-treesitter/nvim-treesitter" } },
 			{
-				"L3MON4D3/LuaSnip",
-				dependencies = { "rafamadriz/friendly-snippets" },
+				"saadparwaiz1/cmp_luasnip",
+				dependencies = {
+
+					{
+						"L3MON4D3/LuaSnip",
+						dependencies = {
+							"rafamadriz/friendly-snippets",
+							{
+								"benfowler/telescope-luasnip.nvim",
+								dependencies = { { "nvim-telescope/telescope.nvim", optional = true } },
+								config = function()
+									require("telescope").load_extension("luasnip")
+								end,
+							},
+						},
+						build = "make install_jsregexp",
+						config = function()
+							require("luasnip.loaders.from_vscode").lazy_load({ exclude = { "markdown", "quarto" } })
+							require("luasnip.loaders.from_snipmate").lazy_load()
+						end,
+					},
+				},
 			},
 		},
 		config = function()
@@ -83,7 +103,7 @@ return {
 					{ name = "otter" },
 					{ name = "nvim_lsp" },
 					{ name = "nvim_lsp_signature_help" },
-					{ name = "luasnip", keyword_length = 2 },
+					{ name = "luasnip", keyword_length = 1 },
 					{ name = "pandoc_references" },
 					{ name = "calc" },
 					{ name = "path" },
diff --git a/nvim/.config/nvim/snippets/markdown.snippets b/nvim/.config/nvim/snippets/markdown.snippets
new file mode 100644
index 0000000..d4b5709
--- /dev/null
+++ b/nvim/.config/nvim/snippets/markdown.snippets
@@ -0,0 +1,80 @@
+# Markdown snippets
+# Combination of snips from friendly-snippets and vim-snippets repos
+
+snippet h1 Heading level 1
+        # ${0}
+
+snippet h2 Heading level 2
+        ## ${0}
+
+snippet h3 Heading level 3
+        ### ${0}
+
+snippet h4 Heading level 4
+        #### ${0}
+
+snippet h5 Heading level 5
+        ##### ${0}
+
+snippet h6 Heading level 6
+        ##### ${0}
+
+snippet ] Link
+        [${1:text}](${2:link})
+
+snippet ]h Weblink
+        [${1:text}](https://${2:address})
+
+snippet ]c Link filled with clipboard contents
+        [${1:text}](${2:`@+`})
+
+snippet ]: Link reference style
+        [${1:id}]: ${2:text}
+
+snippet ]] Footnote
+        [^${1:id}]${0}
+
+        [^${1:id}]: ${2:text}
+
+snippet img Image link
+        ![${1:alt}](${2:link})
+
+snippet imgc Image link with clipboard content
+        ![${1:alt}](${2:`@+`})
+
+snippet ** Bold
+        **$0**
+snippet __ Bold
+        __$0__
+snippet --- Frontmatter
+        ---
+        $0
+        ---
+
+# codeblocks
+snippet `` Codeblock with language
+	    \`\`\`${1:language}
+	    ${2:code}
+	    \`\`\`
+
+# table
+snippet tb Simple table
+	    |  ${5:factors}      |    ${1:a}       |  ${2:b}   	|
+	    | ------------- |-------------  | ------- |
+	    |    ${3:f1}    |    ${0}          | N       |
+	    |    ${4:f2}    |    N          | N       |
+
+# tasklists
+snippet tl Tasklist item
+        - [ ] ${0:item}
+
+snippet tl3 Tasklist item
+        - [ ] ${1:item}
+        - [ ] ${2:item}
+        - [ ] ${0:item}
+
+# super/subscript - pandoc/extended markdown only
+snippet sub Subscript
+        ~${0}~
+snippet sup Superscript
+        ^${0}^
diff --git a/nvim/.config/nvim/snippets/quarto.snippets b/nvim/.config/nvim/snippets/quarto.snippets
new file mode 100644
index 0000000..47e9533
--- /dev/null
+++ b/nvim/.config/nvim/snippets/quarto.snippets
@@ -0,0 +1,100 @@
+# Quarto extensions to markdown
+
+extends markdown
+
+# definitions list
+snippet : Definition list
+        $1
+        : $0
+
+snippet `` Codecell with language
+        \`\`\`{${1:language}}
+        ${2:code}
+        \`\`\`
+
+snippet ``p Codecell with language
+        \`\`\`{python}
+        ${2:code}
+        \`\`\`
+
+snippet ``r Codecell with language
+        \`\`\`{r}
+        ${2:code}
+        \`\`\`
+
+snippet pyfig2 Sub-Figures from python codecell
+        \`\`\`{python}
+        #| label: fig-${1:label}
+        #| fig-cap: "${2:caption}"
+        #| fig-subcap:
+        #|   - "${3:subcap1}"
+        #|   - "${3:subcap2}"
+        #| layout-ncol: 2
+
+        ${0:code}
+        \`\`\`
+
+snippet pyfig Figure from python codecell
+        \`\`\`{python}
+        #| label: fig-${1:label}
+        #| fig-cap: "${2:caption}"
+
+        ${0:code}
+        \`\`\`
+
+snippet fig General figure
+        ![${1:caption}](${3:figure}){#fig-${2:label}}
+
+snippet pytab Figure from python codecell
+        \`\`\`{python}
+        #| label: tbl-${1:label}
+        #| tbl-cap: "${2:caption}"
+
+        ${0:code}
+        \`\`\`
+
+snippet fref Figure crossref
+        @fig-${1:label}
+snippet tref Table crossref
+        @tbl-${1:label}
+snippet sref Section crossref
+        @sec-${1:label}
+snippet eref Equation crossref
+        @eq-${1:label}
+
+snippet cite Citation
+        [@${1:bib-key}]
+
+snippet fn Footnote
+        [^${1:id}]
+
+        [^${1}]: ${2:text}
+
+snippet shortcode Shortcode
+        {{< $0 >}}
+
+snippet div Div block
+        ::: {.${1:class}}
+        $0
+        :::
+
+snippet note Callout note
+        ::: {.callout-note}
+        $0
+        :::
+snippet warn Callout warning
+        ::: {.callout-warning}
+        $0
+        :::
+snippet import Callout important
+        ::: {.callout-important}
+        $0
+        :::
+snippet tip Callout tip
+        ::: {.callout-tip}
+        $0
+        :::
+snippet caut Callout caution
+        ::: {.callout-caution}
+        $0
+        :::

From b2dfdfd5ffdcdc4d9e4377ac7ea8597dbe64db05 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Mon, 17 Jun 2024 13:33:31 +0200
Subject: [PATCH 23/27] nvim: Fix ruff lsp

We now make use of the ruff-inbuilt LSP offering since it just entered
beta.
We also disable all rules in pyright LSP that ruff takes care of, and in
turn disable hover capability in ruff since it's worse than pyright
(still).
More information here:
https://github.com/astral-sh/ruff/tree/main/crates/ruff_server#setup
and here:
https://github.com/astral-sh/ruff/blob/main/crates/ruff_server/docs/setup/NEOVIM.md
---
 nvim/.config/nvim/lua/plugins/config/lsp.lua | 22 ++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/nvim/.config/nvim/lua/plugins/config/lsp.lua b/nvim/.config/nvim/lua/plugins/config/lsp.lua
index c67e77a..080a7c6 100644
--- a/nvim/.config/nvim/lua/plugins/config/lsp.lua
+++ b/nvim/.config/nvim/lua/plugins/config/lsp.lua
@@ -34,7 +34,7 @@ local servers = {
 		filetypes = { "markdown", "quarto" },
 	},
 	basedpyright = {},
-	ruff_lsp = {},
+	ruff = {},
 	serve_d = {},
 	tailwindcss = {},
 	taplo = {},
@@ -54,7 +54,7 @@ require("mason-tool-installer").setup({
 	start_delay = 3000,
 })
 
-local function on_attach(client, bufnr)
+local function on_attach(_, bufnr)
 	local map = vim.keymap.set
 	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" })
@@ -167,21 +167,35 @@ local python_path
 -- ensure python virtualenv is determined automatically on lsp start
 lspconfig.basedpyright.setup({
 	on_attach = function(client, bufnr)
+		on_attach(client, bufnr)
 		if python_path == nil then
 			python_path, _ = vim.fn.expand(require("core.util").get_python_venv_bin(client.config.root_dir))
 		end
+		vim.g["python3_host_prog"] = python_path
 		-- print(string.format("[PYTHON VENV]: %s", vim.inspect(python_path)))
 		client.config.settings.python = {} or client.config.settings.python
 		client.config.settings.python.pythonPath = python_path
-		on_attach(client, bufnr)
 	end,
+	settings = {
+	    -- disable imports and linting since, we use ruff for that
+		pyright = {
+			disableOrganizeImports = true,
+		},
+		python = {
+			analysis = {
+				ignore = { "*" },
+			},
+		},
+	},
 })
-lspconfig.ruff_lsp.setup({
+lspconfig.ruff.setup({
 	on_attach = function(client, bufnr)
 		on_attach(client, bufnr)
+		client.server_capabilities.hoverProvider = false -- we use pyright for hover info
 		if python_path == nil then
 			python_path, _ = vim.fn.expand(require("core.util").get_python_venv_bin(client.config.root_dir))
 		end
+		vim.g["python3_host_prog"] = python_path
 		client.config.settings.python = {} or client.config.settings.python
 		client.config.settings.python.pythonPath = python_path
 	end,

From b4a9b5179f1eaca67e3ed981d2b4167d1b793166 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Mon, 17 Jun 2024 14:00:00 +0200
Subject: [PATCH 24/27] nvim: Automatically install linters and formatters

Switch out mason-tool-installer for mason-conform.nvim and
mason-nvim-lint as respective wrappers for automatically installing
formatters and linters.

Follows the same principle as mason-lspconfig.nvim (in fact, the repos
are mostly based on the same code) and apply the concept to the other
tools: Whatever is enabled in the respective plugins (lspconfig,
nvim-lint and conform.nvim) will automatically be installed by mason.

This is really neat and basically takes care of me ever having to
interact much with Mason itself or manually set up the tools to be
installed. All I have to make sure is that they're updated once in a
while.
---
 nvim/.config/nvim/lazy-lock.json             |   3 +-
 nvim/.config/nvim/lua/plugins/config/lsp.lua |  13 +-
 nvim/.config/nvim/lua/plugins/ide.lua        | 150 ++++++++++---------
 3 files changed, 84 insertions(+), 82 deletions(-)

diff --git a/nvim/.config/nvim/lazy-lock.json b/nvim/.config/nvim/lazy-lock.json
index 62fd9d9..3ed8b73 100644
--- a/nvim/.config/nvim/lazy-lock.json
+++ b/nvim/.config/nvim/lazy-lock.json
@@ -42,8 +42,9 @@
   "lualine.nvim": { "branch": "master", "commit": "0a5a66803c7407767b799067986b4dc3036e1983" },
   "luarocks.nvim": { "branch": "main", "commit": "1db9093915eb16ba2473cfb8d343ace5ee04130a" },
   "markmap.nvim": { "branch": "main", "commit": "5fb6755cf5434511cc23a4936c9eb76b9142fba5" },
+  "mason-conform.nvim": { "branch": "main", "commit": "abce2be529f3b4b336c56d0ba6336a9144e0fee6" },
   "mason-lspconfig.nvim": { "branch": "main", "commit": "9ae570e206360e47d30b4c35a4550c165f4ea7b7" },
-  "mason-tool-installer.nvim": { "branch": "main", "commit": "c5e07b8ff54187716334d585db34282e46fa2932" },
+  "mason-nvim-lint": { "branch": "main", "commit": "637a5b8f1b454753ec70289c4996d88a50808642" },
   "mason.nvim": { "branch": "main", "commit": "c43eeb5614a09dc17c03a7fb49de2e05de203924" },
   "mdeval.nvim": { "branch": "master", "commit": "2c32e2f3e7d8f222e7a4724989f218d036e1081d" },
   "mini.nvim": { "branch": "main", "commit": "19e1584124cda35388d4fdb911eab7124014e541" },
diff --git a/nvim/.config/nvim/lua/plugins/config/lsp.lua b/nvim/.config/nvim/lua/plugins/config/lsp.lua
index 080a7c6..3481a46 100644
--- a/nvim/.config/nvim/lua/plugins/config/lsp.lua
+++ b/nvim/.config/nvim/lua/plugins/config/lsp.lua
@@ -43,17 +43,6 @@ local servers = {
 	yamlls = {},
 }
 
--- TODO installed for conform/nvim-lint so should be sourced from there not here
-local to_mason =
-	---@diagnostic disable-next-line:deprecated
-	{ "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(_, bufnr)
 	local map = vim.keymap.set
 	map("n", "[d", "<cmd>lua vim.diagnostic.goto_prev()<cr>", { buffer = bufnr, desc = "Previous diagnostic" })
@@ -177,7 +166,7 @@ lspconfig.basedpyright.setup({
 		client.config.settings.python.pythonPath = python_path
 	end,
 	settings = {
-	    -- disable imports and linting since, we use ruff for that
+		-- disable imports and linting since, we use ruff for that
 		pyright = {
 			disableOrganizeImports = true,
 		},
diff --git a/nvim/.config/nvim/lua/plugins/ide.lua b/nvim/.config/nvim/lua/plugins/ide.lua
index b4d3a05..1fd191e 100644
--- a/nvim/.config/nvim/lua/plugins/ide.lua
+++ b/nvim/.config/nvim/lua/plugins/ide.lua
@@ -96,7 +96,6 @@ return {
 				"williamboman/mason-lspconfig.nvim",
 				cmd = { "LspInstall", "LspUninstall" },
 			},
-			{ "WhoIsSethDaniel/mason-tool-installer.nvim" },
 		},
 		event = { "BufReadPost", "BufNewFile", "BufWritePre" },
 		config = function()
@@ -104,7 +103,7 @@ return {
 		end,
 		keys = { { "<leader>vs", ":LspInfo<cr>", desc = "LspInfo" } },
 	},
-	-- very very pretty lsp 'peek' menus
+	-- pretty lsp 'peek' menus
 	{
 		"DNLHC/glance.nvim",
 		opts = { border = { enable = true }, theme = { enable = true, mode = "auto" } },
@@ -113,85 +112,98 @@ return {
 
 	-- linting setup
 	{
-		"mfussenegger/nvim-lint",
-		config = function()
-			require("lint").linters_by_ft = linters
-			vim.api.nvim_create_autocmd({ "BufWritePost", "InsertLeave" }, {
-				callback = function()
-					if not vim.g.disable_autolint then
-						require("lint").try_lint()
-					end
+		"rshkarin/mason-nvim-lint",
+		dependencies = {
+			{
+				"mfussenegger/nvim-lint",
+				config = function()
+					require("lint").linters_by_ft = linters
+					vim.api.nvim_create_autocmd({ "BufWritePost", "InsertLeave" }, {
+						callback = function()
+							if not vim.g.disable_autolint then
+								require("lint").try_lint()
+							end
+						end,
+					})
 				end,
-			})
-		end,
+				dependencies = { "williamboman/mason.nvim" },
+			},
+		},
 		event = { "BufReadPost", "BufNewFile", "BufWritePre" },
+		opts = {},
 	},
 
 	-- 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 }
+		"zapling/mason-conform.nvim",
+		dependencies = {
+			{
+				"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 = formatters,
+						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,
-				formatters_by_ft = formatters,
-				formatters = {
-					-- enable python isort functionality
-					ruff_fix = {
-						prepend_args = { "--select", "I" },
+				cmd = { "ConformInfo" },
+				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",
 					},
 				},
-			})
-			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 = { "BufReadPost", "BufNewFile", "BufWritePre" },
-		keys = {
-			{
-				"<localleader>ll",
-				function()
-					require("conform").format({ async = true, lsp_fallback = true })
+				init = function()
+					-- If you want the formatexpr, here is the place to set it
+					vim.o.formatexpr = "v:lua.require'conform'.formatexpr()"
 				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,
+		event = { "BufReadPost", "BufNewFile", "BufWritePre" },
+		opts = {},
 	},
 
 	-- useful quickfix-like buffer

From 2d513ad74b8e563c2ab107dc820124c865d31669 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Mon, 17 Jun 2024 14:32:24 +0200
Subject: [PATCH 25/27] nvim: Remove vale linter

It does not work right. I tried to set up the lsp instead, and that also
is giving me more trouble than I can troubleshoot right now.
---
 nvim/.config/nvim/lua/core/lazy.lua   | 2 +-
 nvim/.config/nvim/lua/plugins/ide.lua | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/nvim/.config/nvim/lua/core/lazy.lua b/nvim/.config/nvim/lua/core/lazy.lua
index 6c2c0d3..f57bf7b 100644
--- a/nvim/.config/nvim/lua/core/lazy.lua
+++ b/nvim/.config/nvim/lua/core/lazy.lua
@@ -36,7 +36,7 @@ require("lazy").setup({
 	defaults = { lazy = true, version = "*" },
 	performance = {
 		rtp = { disabled_plugins = { "netrw", "netrwPlugin" } },
-		cache = { enable = false },
+		cache = { enable = true },
 	},
 })
 vim.keymap.set("n", "<leader>vl", ":Lazy<cr>", { desc = "Lazy" })
diff --git a/nvim/.config/nvim/lua/plugins/ide.lua b/nvim/.config/nvim/lua/plugins/ide.lua
index 1fd191e..3adafec 100644
--- a/nvim/.config/nvim/lua/plugins/ide.lua
+++ b/nvim/.config/nvim/lua/plugins/ide.lua
@@ -3,11 +3,11 @@ local linters = {
 	bash = { "shellcheck" },
 	javascript = { "eslint_d" },
 	javascriptreact = { "eslint_d" },
-	markdown = { "markdownlint", "vale" },
-	quarto = { "markdownlint", "vale" },
+	markdown = { "markdownlint" },
+	quarto = { "markdownlint" },
 	sh = { "shellcheck" },
 	svelte = { "eslint_d" },
-	text = { "vale" },
+	text = {},
 	typescript = { "eslint_d" },
 	typescriptreact = { "eslint_d" },
 }

From 0f46dcad2851e2986550ef444e55faef4335a7c1 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Mon, 17 Jun 2024 15:28:09 +0200
Subject: [PATCH 26/27] nvim: Fix molten statusline icon

Fixed issue when pynvim did not exist in the environment but we tried to
invoke a molten-nvim command. Now we first fire up python to check for
pynvim existence. This takes a moment so we do it asynchronously and
cache the result for the rest of the program runtime.

Also we only show the molten icon if we are actually connected to a
running kernel.
---
 nvim/.config/nvim/lua/plugins/ui.lua | 37 +++++++++++++++++++---------
 1 file changed, 26 insertions(+), 11 deletions(-)

diff --git a/nvim/.config/nvim/lua/plugins/ui.lua b/nvim/.config/nvim/lua/plugins/ui.lua
index 7026909..73c1a4c 100644
--- a/nvim/.config/nvim/lua/plugins/ui.lua
+++ b/nvim/.config/nvim/lua/plugins/ui.lua
@@ -4,16 +4,31 @@ return {
 		"nvim-lualine/lualine.nvim",
 		dependencies = { { "nvim-tree/nvim-web-devicons", config = true } },
 		config = function()
-			-- FIXME: Errors out on no pynvim installed
-			-- local function molten()
-			-- 	if
-			-- 		require("core.util").is_available("molten.status")
-			-- 		and require("molten.status").initialized() ~= ""
-			-- 	then
-			-- 		return "󱪄"
-			-- 	end
-			-- 	return ""
-			-- end
+			local has_pynvim = -1
+			-- if molten exists, is initialized and connected to a kernel
+			-- show it in the statusline
+			local function molten()
+				local function checked_pynvim(_, exitcode)
+					if exitcode == 0 then
+						has_pynvim = 1
+					else
+						has_pynvim = 0
+					end
+				end
+				if has_pynvim == 0 then
+					return ""
+				elseif has_pynvim == -1 then
+					vim.fn.jobstart({ "python", "-c", "from neovim import VERSION" }, { on_exit = checked_pynvim })
+				end
+				if
+					has_pynvim == 1
+					and require("core.util").is_available("molten.status")
+					and require("molten.status").kernels() ~= ""
+				then
+					return "󱪄"
+				end
+				return ""
+			end
 			require("lualine").setup({
 				options = {
 					icons_enabled = true,
@@ -27,7 +42,7 @@ return {
 					lualine_a = { "mode" },
 					lualine_b = { "branch", "diff", "diagnostics" },
 					lualine_c = { "filename" },
-					lualine_x = { "encoding", "fileformat", "filetype", "molten" },
+					lualine_x = { "encoding", "fileformat", "filetype", molten },
 					lualine_y = { "progress" },
 					lualine_z = { "location" },
 				},

From 87ce74de403d6537dacbcca038aba2f7ccd326e5 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Mon, 17 Jun 2024 15:39:53 +0200
Subject: [PATCH 27/27] nvim: Show selection in lualine

Shows number of lines and characters selected in visual mode.
---
 nvim/.config/nvim/lua/plugins/ui.lua | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/nvim/.config/nvim/lua/plugins/ui.lua b/nvim/.config/nvim/lua/plugins/ui.lua
index 73c1a4c..9e829c3 100644
--- a/nvim/.config/nvim/lua/plugins/ui.lua
+++ b/nvim/.config/nvim/lua/plugins/ui.lua
@@ -29,6 +29,19 @@ return {
 				end
 				return ""
 			end
+
+            -- count number of selected lines and characters
+            -- stolen: https://github.com/chrisgrieser/.config/blob/8af1841ba24f7c81c513e12f853b52f530ef5b37/nvim/lua/plugins/lualine.lua#L80C1-L87C4
+			local function selectionCount()
+				local isVisualMode = vim.fn.mode():find("[Vv]")
+				if not isVisualMode then
+					return ""
+				end
+				local starts = vim.fn.line("v")
+				local ends = vim.fn.line(".")
+				local lines = starts <= ends and ends - starts + 1 or starts - ends + 1
+				return " " .. tostring(lines) .. "L " .. tostring(vim.fn.wordcount().visual_chars) .. "C"
+			end
 			require("lualine").setup({
 				options = {
 					icons_enabled = true,
@@ -44,7 +57,7 @@ return {
 					lualine_c = { "filename" },
 					lualine_x = { "encoding", "fileformat", "filetype", molten },
 					lualine_y = { "progress" },
-					lualine_z = { "location" },
+					lualine_z = { selectionCount, "location" },
 				},
 				inactive_sections = {
 					lualine_a = {},