Latest config changes

coc-settings.json

@@ -1,26 +0,0 @@
-{
-    "suggest.autoTrigger": "none", 
-    "suggest.timeout": 500,
-    "pyright.disableDocumentation":false,
-    "pyright.inlayHints.variableTypes":false,
-    "pyright.inlayHints.parameterTypes":false,
-    "pyright.inlayHints.functionReturnTypes":false,
-    "python.analysis.diagnosticSeverityOverrides":{
-        "reportUnboundVariable":"none"
-    },
-    "hover.target": "preview",
-    "clangd.path": "/usr/bin/clangd",
-    "python.formatting.provider": "black",
-    "python.formatting.blackArgs": ["-l","100"],
-    "coc.preferences.formatOnSaveFiletypes": ["python","java", "rust"],
-    "java.inlayHints.parameterNames.enabled": "none",
-    "java.format.settings.url": "/home/alex.selimov/RedTop.xml",
-    "workspace.ignoredFolders": [
-        "$HOME",
-        "$HOME/.cargo/**",
-        "$HOME/.rustup/**"
-    ],
-    "rust-analyzer.inlayHints.typeHints.enable": false,
-    "rust-analyzer.inlayHints.parameterHints.enable": false
-}
-

ftplugin/fortran.vim

@@ -1,13 +0,0 @@
-map <C-b> : w % <Bar> ! make <CR>
-
-"Some code snippets for filling in 
-inoremap ;d do<Space><CR>end<Space>do<Esc>O<Tab><++><Esc>kA
-inoremap ;i if<Space>()<Space>then<CR>end<Space>if<Esc>O<Tab><++><Esc>kF(a
-inoremap ;s select<Space>case(<++>)<CR>case(<++>)<CR><Tab><++><CR><Esc>4hicase(<++>)<CR><Tab><++><CR><Esc>4hiend<Space>select<CR><Esc>5kFsi
-inoremap ;ph print *, '------------------------------------------------------------'<CR>print *, ''<CR>print *, '------------------------------------------------------------'<Esc>kci'
-inoremap ;pr read(, *, iostat=iospara) <++><CR>if(iospara>0) then<CR>print *, "Error: Invalid read of <++> with error code", iospara<CR>call mpi_abort(mpi_comm_world, 1, ierr)<CR>end if<ESC>4k0f(a
-inoremap ;ptp print *, '[OK] - '<ESC>i
-inoremap ;ptf print *, '[FAILED] - '<ESC>i
-
-
-set colorcolumn=132

ftplugin/java.lua

@@ -0,0 +1 @@
+

ftplugin/java.vim

@@ -1,2 +1 @@
-set colorcolumn=120
 set tw=120

ftplugin/markdown.vim

@@ -1,22 +1,19 @@
-inoremap <Space><Space> <Esc>/<++><Enter>"_c4l
 set spell spellfile="~/.config/nvim/spell/wordlist"
 let g:markdown_fenced_languages = ['html', 'python', 'bash=sh', 'fortran']
-"set conceallevel=2
-"let g:vim_markdown_math = 1
-"let g:tex_conceal = "abdmg"
+set conceallevel=2
+let g:vim_markdown_math = 1
+let g:tex_conceal = "abdmg"
+let g:tex_superscripts= "[]"
+let g:tex_subscripts= "[]"
+let g:tex_conceal_frac=1
 hi clear Conceal
 map <C-b> : w % <Bar> AsyncRun md2pdf "%" <CR> 
 map <A-p> : w % <Bar> AsyncRun md2beamer "%" <CR> 
 map <A-b> : w % <Bar> AsyncRun md2docx %  <CR>
 map <C-z> : !zathura %:r.pdf & <CR>
-inoremap ;i ** <++><Esc>5hi
-inoremap ;b **** <++><Esc>6hi
-inoremap ;l [](<++>)<Esc>6hi
-inoremap ;I ![](<++>)<Esc>6hi
-inoremap ;pc  ```<CR>```<Esc>O
-inoremap ;cu - [ ]
-inoremap ;cc - [x]
-
-set tw=200
+inoremap ;b ****<esc>hi
+command Stab Tabularize /\s\+\zs\s/l1c0
+nnoremap ;t :Tabularize /\s\+\zs\s/l1c0<CR>
+set tw=1000
 set colorcolumn=
 

ftplugin/tex.vim

@@ -17,3 +17,5 @@ inoremap ;2t  \begin{table}[h!]<Enter>\begin{center}<Enter>\begin{tabular}{c c}<
 inoremap ;e \begin{equation}<Enter>\label{<++>}<Enter>\end{equation}<ESC>kO
 inoremap ;fw width=\textwidth<Esc>F\i
 inoremap ;fh height=\textheight<Esc>F\i
+
+set tw=5000

init.lua

@@ -0,0 +1,867 @@
+--  Specify the leader
+--  NOTE: Must happen before plugins are loaded (otherwise wrong leader will be used)
+vim.g.mapleader = ";"
+vim.g.maplocalleader = ";"
+
+-- [[ Setting options ]]
+-- Make line numbers default
+vim.opt.number = true
+vim.opt.relativenumber = true
+
+-- Disable mouse mode
+vim.opt.mouse = ""
+
+-- Don't show the mode, since it's already in status line
+vim.opt.showmode = false
+
+-- Case-insensitive searching UNLESS \C or capital in search
+vim.opt.ignorecase = true
+vim.opt.smartcase = true
+
+-- Keep signcolumn on by default
+vim.opt.signcolumn = "yes"
+
+-- Configure how new splits should be opened
+vim.opt.splitright = true
+vim.opt.splitbelow = true
+
+-- Sets how neovim will display certain whitespace in the editor.
+--  See :help 'list'
+--  and :help 'listchars'
+vim.opt.list = true
+vim.opt.listchars = { tab = "» ", trail = "·", nbsp = "␣" }
+
+-- Preview substitutions live, as you type!
+vim.opt.inccommand = "split"
+
+-- Show which line your cursor is on
+vim.opt.cursorline = true
+
+-- Minimal number of screen lines to keep above and below the cursor.
+-- vim.opt.scrolloff = 10
+
+-- General universal settings
+vim.opt.sw = 4
+vim.opt.ts = 4
+vim.opt.expandtab = true
+vim.opt.tw = 100
+vim.opt.colorcolumn = "+1"
+vim.opt.termguicolors = true
+vim.opt.pumheight = 5
+
+-- Disable semantic tokens
+vim.api.nvim_create_autocmd("LspAttach", {
+	callback = function(args)
+		local client = vim.lsp.get_client_by_id(args.data.client_id)
+		client.server_capabilities.semanticTokensProvider = nil
+	end,
+})
+
+-- Function to get work count in status line
+local function getWords()
+	-- the third string here is the string for visual-block mode (^V)
+	if vim.fn.mode() == "v" or vim.fn.mode() == "V" or vim.fn.mode() == "" then
+		return vim.fn.wordcount().visual_words .. ""
+	else
+		return vim.fn.wordcount().words .. ""
+	end
+end
+-- [[ Basic Keymaps ]]
+--  See `:help vim.keymap.set()`
+
+-- Set highlight on search, but clear on pressing <Esc> in normal mode
+vim.opt.hlsearch = true
+vim.keymap.set("n", "<Esc>", "<cmd>nohlsearch<CR>")
+
+-- Diagnostic keymaps
+vim.keymap.set("n", "[d", vim.diagnostic.goto_prev, { desc = "Go to previous [D]iagnostic message" })
+vim.keymap.set("n", "]d", vim.diagnostic.goto_next, { desc = "Go to next [D]iagnostic message" })
+vim.keymap.set("n", "<leader>e", vim.diagnostic.open_float, { desc = "Show diagnostic [E]rror messages" })
+vim.keymap.set("n", "<leader>q", vim.diagnostic.setloclist, { desc = "Open diagnostic [Q]uickfix list" })
+
+-- Keybinds to make split navigation easier.
+--  Use CTRL+<hjkl> to switch between windows
+--
+--  See `:help wincmd` for a list of all window commands
+vim.keymap.set("n", "<C-h>", "<C-w><C-h>", { desc = "Move focus to the left window" })
+vim.keymap.set("n", "<C-l>", "<C-w><C-l>", { desc = "Move focus to the right window" })
+vim.keymap.set("n", "<C-j>", "<C-w><C-j>", { desc = "Move focus to the lower window" })
+vim.keymap.set("n", "<C-k>", "<C-w><C-k>", { desc = "Move focus to the upper window" })
+-- Jump to the definition of the word under your cursor.
+--  This is where a variable was first declared, or where a function is defined, etc.
+--  To jump back, press <C-T>.
+vim.keymap.set("n", "gd", vim.lsp.buf.definition, { desc = "" })
+-- [[ Basic Autocommands ]]
+--  Go back to last edited line when reopening file
+vim.api.nvim_create_autocmd("BufRead", {
+	callback = function(opts)
+		vim.api.nvim_create_autocmd("BufWinEnter", {
+			once = true,
+			buffer = opts.buf,
+			callback = function()
+				local ft = vim.bo[opts.buf].filetype
+				local last_known_line = vim.api.nvim_buf_get_mark(opts.buf, '"')[1]
+				if
+					not (ft:match("gitcommit") and ft:match("gitrebase"))
+					and last_known_line > 1
+					and last_known_line <= vim.api.nvim_buf_line_count(opts.buf)
+				then
+					vim.api.nvim_feedkeys([[g`"]], "nx", false)
+				end
+			end,
+		})
+	end,
+})
+
+-- [[ Install `lazy.nvim` plugin manager ]]
+--    See `:help lazy.nvim.txt` or https://github.com/folke/lazy.nvim for more info
+local lazypath = vim.fn.stdpath("data") .. "/lazy/lazy.nvim"
+if not vim.loop.fs_stat(lazypath) then
+	local lazyrepo = "https://github.com/folke/lazy.nvim.git"
+	vim.fn.system({ "git", "clone", "--filter=blob:none", "--branch=stable", lazyrepo, lazypath })
+end ---@diagnostic disable-next-line: undefined-field
+vim.opt.rtp:prepend(lazypath)
+
+-- Get user dictionary
+local path = vim.fn.stdpath("config") .. "/spell/en.utf-8.add"
+local words = {}
+
+for word in io.open(path, "r"):lines() do
+	table.insert(words, word)
+end
+-- [[ Configure and install plugins ]]
+--
+--  To check the current status of your plugins, run
+--    :Lazy
+--
+--  You can press `?` in this menu for help. Use `:q` to close the window
+--
+--  To update plugins, you can run
+--    :Lazy update
+--
+--
+
+-- NOTE: Here is where you install your plugins.
+require("lazy").setup({
+
+	-- [[ Plugin Specs list ]]
+	-- NOTE: Plugins can be added with a link (or for a github repo: 'owner/repo' link).
+	{
+		"windwp/nvim-autopairs",
+		config = function()
+			local remap = vim.api.nvim_set_keymap
+			local npairs = require("nvim-autopairs")
+
+			npairs.setup({ map_bs = false, map_cr = false })
+
+			_G.MUtils = {}
+
+			MUtils.CR = function()
+				if vim.fn.pumvisible() ~= 0 then
+					if vim.fn.complete_info({ "selected" }).selected ~= -1 then
+						return npairs.esc("<c-y>")
+					else
+						return npairs.esc("<c-e>") .. npairs.autopairs_cr()
+					end
+				else
+					return npairs.autopairs_cr()
+				end
+			end
+			remap("i", "<cr>", "v:lua.MUtils.CR()", { expr = true, noremap = true })
+
+			MUtils.BS = function()
+				if vim.fn.pumvisible() ~= 0 and vim.fn.complete_info({ "mode" }).mode == "eval" then
+					return npairs.esc("<c-e>") .. npairs.autopairs_bs()
+				else
+					return npairs.autopairs_bs()
+				end
+			end
+			remap("i", "<bs>", "v:lua.MUtils.BS()", { expr = true, noremap = true })
+
+			-- put this to setup function and press <a-e> to use fast_wrap
+			npairs.setup({
+				fast_wrap = {},
+			})
+
+			-- change default fast_wrap
+			npairs.setup({
+				fast_wrap = {
+					map = "<M-e>",
+					chars = { "{", "[", "(", '"', "'" },
+					pattern = [=[[%'%"%>%]%)%}%,]]=],
+					end_key = "$",
+					before_key = "h",
+					after_key = "l",
+					cursor_pos_before = true,
+					keys = "qwertyuiopzxcvbnmasdfghjkl",
+					manual_position = true,
+					highlight = "Search",
+					highlight_grey = "Comment",
+				},
+			})
+
+			npairs.remove_rule("`")
+		end,
+	},
+	"christoomey/vim-tmux-navigator",
+	"kana/vim-textobj-user",
+	{
+		"GCBallesteros/vim-textobj-hydrogen",
+		dependencies = {
+			"kana/vim-textobj-user",
+		},
+	},
+	"godlygeek/tabular",
+	"tpope/vim-sleuth",
+	{
+		"codersauce/runst.nvim",
+		lazy = false,
+		opts = {},
+		config = function()
+			require("runst").setup()
+		end,
+	},
+	{
+		"Vigemus/iron.nvim",
+		ft = { "python" },
+		config = function()
+			local iron = require("iron.core")
+			local view = require("iron.view")
+
+			iron.setup({
+				config = {
+					-- Whether a repl should be discarded or not
+					scratch_repl = true,
+					-- Your repl definitions come here
+					repl_definition = {
+						python = {
+							-- Can be a table or a function that
+							-- returns a table (see below)
+							command = "ipython --no-autoindent",
+						},
+					},
+					-- How the repl window will be displayed
+					-- See below for more information
+					repl_open_cmd = require("iron.view").bottom(20),
+				},
+				-- Iron doesn't set keymaps by default anymore.
+				-- You can set them here or manually add keymaps to the functions in iron.core
+				keymaps = {
+					visual_send = "<leader>sc",
+					send_file = "<leader>sf",
+					send_line = "<leader>sl",
+					cr = "<leader>s<cr>",
+					interrupt = "<leader>s<space>",
+					exit = "<leader>sq",
+					clear = "<leader>cl",
+				},
+				-- If the highlight is on, you can change how it looks
+				-- For the available options, check nvim_set_hl
+				highlight = {
+					italic = true,
+				},
+				ignore_blank_lines = true, -- ignore blank lines when sending visual select lines
+			})
+			vim.keymap.set("n", ";rs", "<cmd>IronRepl<cr>")
+			vim.keymap.set("n", ";rr", "<cmd>IronRestart<cr>")
+			vim.keymap.set("n", ";rf", "<cmd>IronFocus<cr>")
+			vim.keymap.set("n", ";rh", "<cmd>IronHide<cr>")
+
+			repl_open_cmd = "horizontal bot 20 split"
+		end,
+	},
+	"ixru/nvim-markdown",
+	"KeitaNakamura/tex-conceal.vim",
+	"christoomey/vim-tmux-navigator",
+	"skywind3000/asyncrun.vim",
+	-- NOTE: Plugins can specify dependencies.
+	--
+	-- The dependencies are proper plugin specifications as well - anything
+	-- you do for a plugin at the top level, you can do for a dependency.
+	--
+	-- Use the `dependencies` key to specify the dependencies of a particular plugin
+	{ -- Fuzzy Finder (files, lsp, etc)
+		"nvim-telescope/telescope.nvim",
+		event = "VeryLazy",
+		branch = "0.1.x",
+		dependencies = {
+			"nvim-lua/plenary.nvim",
+			-- Useful for getting pretty icons, but requires special font.
+			--  If you already have a Nerd Font, or terminal set up with fallback fonts
+			--  you can enable this
+			{ "nvim-tree/nvim-web-devicons" },
+			{ "nvim-telescope/telescope-live-grep-args.nvim" },
+		},
+		config = function()
+			-- Telescope is a fuzzy finder that comes with a lot of different things that
+			-- it can fuzzy find! It's more than just a "file finder", it can search
+			-- many different aspects of Neovim, your workspace, LSP, and more!
+			--
+			-- The easiest way to use telescope, is to start by doing something like:
+			--  :Telescope help_tags
+			--
+			-- After running this command, a window will open up and you're able to
+			-- type in the prompt window. You'll see a list of help_tags options and
+			-- a corresponding preview of the help.
+			--
+			-- Two important keymaps to use while in telescope are:
+			--  - Insert mode: <c-/>
+			--  - Normal mode: ?
+			--
+			-- This opens a window that shows you all of the keymaps for the current
+			-- telescope picker. This is really useful to discover what Telescope can
+			-- do as well as how to actually do it!
+
+			-- [[ Configure Telescope ]]
+			-- See `:help telescope` and `:help telescope.setup()`
+			require("telescope").setup({
+				-- You can put your default mappings / updates / etc. in here
+				--  All the info you're looking for is in `:help telescope.setup()`
+				--
+				defaults = vim.tbl_extend("force", require("telescope.themes").get_ivy(), {
+					path_display = { "smart" },
+				}),
+			})
+
+			pcall(require("telescope").load_extension("live_grep_args"))
+			local builtin = require("telescope.builtin")
+			vim.keymap.set("n", "<C-g>", require("telescope").extensions.live_grep_args.live_grep_args)
+			vim.keymap.set(
+				"x",
+				"<C-g>",
+				"\"zy:lua require('telescope').extensions.live_grep_args.live_grep_args(require('telescope.themes').get_ivy({}))<cr><c-r>z"
+			)
+			vim.keymap.set("n", "<C-f>", builtin.find_files)
+		end,
+	},
+	{ -- LSP Configuration & Plugins
+		"neovim/nvim-lspconfig",
+		opts = {
+			autoformat = false,
+		},
+		dependencies = {
+			-- Automatically install LSPs and related tools to stdpath for neovim
+			"williamboman/mason.nvim",
+			"williamboman/mason-lspconfig.nvim",
+			"WhoIsSethDaniel/mason-tool-installer.nvim",
+
+			-- Useful status updates for LSP.
+			-- NOTE: `opts = {}` is the same as calling `require('fidget').setup({})`
+			{ "j-hui/fidget.nvim", opts = {} },
+		},
+		config = function()
+			vim.api.nvim_create_autocmd("LspAttach", {
+				group = vim.api.nvim_create_augroup("kickstart-lsp-attach", { clear = true }),
+				callback = function(event)
+					-- NOTE: Remember that lua is a real programming language, and as such it is possible
+					-- to define small helper and utility functions so you don't have to repeat yourself
+					-- many times.
+					--
+					-- In this case, we create a function that lets us more easily define mappings specific
+					-- for LSP related items. It sets the mode, buffer and description for us each time.
+					local map = function(keys, func, desc)
+						vim.keymap.set("n", keys, func, { buffer = event.buf, desc = "LSP: " .. desc })
+					end
+
+					-- Find references for the word under your cursor.
+					map("gr", require("telescope.builtin").lsp_references, "[G]oto [R]eferences")
+
+					-- Jump to the implementation of the word under your cursor.
+					--  Useful when your language has ways of declaring types without an actual implementation.
+					map("<leader>I", require("telescope.builtin").lsp_implementations, "[G]oto [I]mplementation")
+
+					-- Jump to the type of the word under your cursor.
+					--  Useful when you're not sure what type a variable is and you want to see
+					--  the definition of its *type*, not where it was *defined*.
+					map("<leader>D", require("telescope.builtin").lsp_type_definitions, "Type [D]efinition")
+
+					-- Fuzzy find all the symbols in your current document.
+					--  Symbols are things like variables, functions, types, etc.
+					map("<leader>ds", require("telescope.builtin").lsp_document_symbols, "[D]ocument [S]ymbols")
+
+					-- Fuzzy find all the symbols in your current workspace
+					--  Similar to document symbols, except searches over your whole project.
+					map(
+						"<leader>ws",
+						require("telescope.builtin").lsp_dynamic_workspace_symbols,
+						"[W]orkspace [S]ymbols"
+					)
+
+					-- Rename the variable under your cursor
+					--  Most Language Servers support renaming across files, etc.
+					map("<leader>rn", vim.lsp.buf.rename, "[R]e[n]ame")
+
+					-- Execute a code action, usually your cursor needs to be on top of an error
+					-- or a suggestion from your LSP for this to activate.
+					map("<leader>ca", vim.lsp.buf.code_action, "[C]ode [A]ction")
+
+					-- Opens a popup that displays documentation about the word under your cursor
+					--  See `:help K` for why this keymap
+					map("K", vim.lsp.buf.hover, "Hover Documentation")
+
+					-- WARN: This is not Goto Definition, this is Goto Declaration.
+					--  For example, in C this would take you to the header
+					map("gD", vim.lsp.buf.declaration, "[G]oto [D]eclaration")
+
+					-- The following two autocommands are used to highlight references of the
+					-- word under your cursor when your cursor rests there for a little while.
+					--    See `:help CursorHold` for information about when this is executed
+					--
+					-- When you move your cursor, the highlights will be cleared (the second autocommand).
+					local client = vim.lsp.get_client_by_id(event.data.client_id)
+					if client and client.server_capabilities.documentHighlightProvider then
+						vim.api.nvim_create_autocmd({ "CursorHold", "CursorHoldI" }, {
+							buffer = event.buf,
+							callback = vim.lsp.buf.document_highlight,
+						})
+
+						vim.api.nvim_create_autocmd({ "CursorMoved", "CursorMovedI" }, {
+							buffer = event.buf,
+							callback = vim.lsp.buf.clear_references,
+						})
+					end
+				end,
+			})
+
+			-- LSP servers and clients are able to communicate to each other what features they support.
+			--  By default, Neovim doesn't support everything that is in the LSP Specification.
+			--  When you add nvim-cmp, luasnip, etc. Neovim now has *more* capabilities.
+			--  So, we create new capabilities with nvim cmp, and then broadcast that to the servers.
+			local capabilities = vim.lsp.protocol.make_client_capabilities()
+			capabilities = vim.tbl_deep_extend("force", capabilities, require("cmp_nvim_lsp").default_capabilities())
+
+			-- Enable the following language servers
+			--  Feel free to add/remove any LSPs that you want here. They will automatically be installed.
+			--
+			--  Add any additional override configuration in the following tables. Available keys are:
+			--  - cmd (table): Override the default command used to start the server
+			--  - filetypes (table): Override the default list of associated filetypes for the server
+			--  - capabilities (table): Override fields in capabilities. Can be used to disable certain LSP features.
+			--  - settings (table): Override the default settings passed when initializing the server.
+			--        For example, to see the options for `lua_ls`, you could go to: https://luals.github.io/wiki/settings/
+			local servers = {
+				clangd = {
+					filetypes = {
+						"c",
+						"cpp",
+					},
+				},
+				yamlls = {},
+				-- gopls = {},
+				jdtls = {
+					filetypes = { "java" },
+					settings = {
+						java = {
+							format = {
+								settings = {
+									url = "~/RedTop.xml",
+								},
+							},
+						},
+					},
+				},
+				pyright = {},
+				fortls = {},
+				bashls = { dependencies = "shellcheck" },
+				rust_analyzer = {
+					settings = {
+						["rust-analyzer"] = {
+							check = {
+								command = "clippy",
+							},
+							rustfmt = {
+								extraArgs = { "+nightly" },
+							},
+						},
+					},
+				},
+				ltex = {
+					settings = {
+						ltex = {
+							enabled = { "latex", "tex", "bib", "markdown" },
+							language = "auto",
+							diagnosticSeverity = "information",
+							sentenceCacheSize = 2000,
+							latex = {
+								commands = {
+									["\\hypertarget"] = "dummy",
+								},
+							},
+							dictionary = (function()
+								-- For dictionary, search for files in the runtime to have
+								-- and include them as externals the format for them is
+								-- dict/{LANG}.txt
+								--
+								-- Also add dict/default.txt to all of them
+								local files = {}
+								for _, file in ipairs(vim.api.nvim_get_runtime_file("dict/*", true)) do
+									local lang = vim.fn.fnamemodify(file, ":t:r")
+									local fullpath = vim.fs.normalize(file, ":p")
+									files[lang] = { ":" .. fullpath }
+								end
+
+								if files.default then
+									for lang, _ in pairs(files) do
+										if lang ~= "default" then
+											vim.list_extend(files[lang], files.default)
+										end
+									end
+									files.default = nil
+								end
+								return files
+							end)(),
+						},
+					},
+				},
+				lua_ls = {
+					-- cmd = {...},
+					-- filetypes { ...},
+					-- capabilities = {},
+					settings = {
+						Lua = {
+							runtime = { version = "LuaJIT" },
+							workspace = {
+								checkThirdParty = false,
+								-- Tells lua_ls where to find all the Lua files that you have loaded
+								-- for your neovim configuration.
+								library = {
+									"${3rd}/luv/library",
+									unpack(vim.api.nvim_get_runtime_file("", true)),
+								},
+								-- If lua_ls is really slow on your computer, you can try this instead:
+								-- library = { vim.env.VIMRUNTIME },
+							},
+							-- You can toggle below to ignore Lua_LS's noisy `missing-fields` warnings
+							-- diagnostics = { disable = { 'missing-fields' } },
+						},
+					},
+				},
+			}
+
+			-- Ensure the servers and tools above are installed
+			--  To check the current status of installed tools and/or manually install
+			--  other tools, you can run
+			--    :Mason
+			--
+			--  You can press `g?` for help in this menu
+			require("mason").setup()
+
+			-- You can add other tools here that you want Mason to install
+			-- for you, so that they are available from within Neovim.
+			local ensure_installed = vim.tbl_keys(servers or {})
+			vim.list_extend(ensure_installed, {
+				"stylua", -- Used to format lua code
+				"black",
+				"clang-format",
+				"ormolu",
+				"beautysh",
+				"latexindent",
+				"prettier",
+			})
+			require("mason-tool-installer").setup({ ensure_installed = ensure_installed })
+
+			require("mason-lspconfig").setup({
+				handlers = {
+					function(server_name)
+						local server = servers[server_name] or {}
+						require("lspconfig")[server_name].setup({
+							cmd = server.cmd,
+							on_init = function(client)
+								client.offset_encoding = "utf-8"
+							end,
+							settings = server.settings,
+							filetypes = server.filetypes,
+							-- This handles overriding only values explicitly passed
+							-- by the server configuration above. Useful when disabling
+							-- certain features of an LSP (for example, turning off formatting for tsserver)
+							capabilities = vim.tbl_deep_extend("force", {}, capabilities, server.capabilities or {}),
+						})
+					end,
+				},
+			})
+		end,
+	},
+
+	{ -- Autoformat
+		"stevearc/conform.nvim",
+		setup = {
+			formatters = {
+				black = {
+					command = "black",
+					prepend_args = { "--line-length", "100" },
+				},
+			},
+		},
+		opts = {
+			notify_on_error = false,
+			format_on_save = {
+				timeout_ms = 500,
+				lsp_fallback = false,
+			},
+			formatters_by_ft = {
+				lua = { "stylua" },
+				-- Conform can also run multiple formatters sequentially
+				python = { "black" },
+				cpp = { "clang-format" },
+				c = { "clang-format" },
+				sh = { "beautysh" },
+				tex = { "latexindent" },
+				yaml = { "prettier" },
+			},
+		},
+	},
+
+	{ -- Autocompletion
+		"hrsh7th/nvim-cmp",
+		event = "InsertEnter",
+		dependencies = {
+			-- Snippet Engine & its associated nvim-cmp source
+			{
+				"L3MON4D3/LuaSnip",
+				build = (function()
+					-- Build Step is needed for regex support in snippets
+					-- This step is not supported in many windows environments
+					-- Remove the below condition to re-enable on windows
+					if vim.fn.has("win32") == 1 or vim.fn.executable("make") == 0 then
+						return
+					end
+					return "make install_jsregexp"
+				end)(),
+				config = function()
+					require("luasnip.loaders.from_snipmate").lazy_load({ paths = "./snippets" })
+					local ls = require("luasnip")
+					-- some shorthands...
+					local snip = ls.snippet
+					local node = ls.snippet_node
+					local text = ls.text_node
+					local insert = ls.insert_node
+					local func = ls.function_node
+					local choice = ls.choice_node
+					local dynamicn = ls.dynamic_node
+
+					ls.add_snippets(nil, {
+						python = {
+							snip({
+								trig = "imp",
+								namr = "Imports",
+								dscr = "Comments for imports",
+							}, {
+								text({ "# Core modules", "" }),
+								insert(1),
+								text({ "", "# Non-core modules", "" }),
+								insert(2),
+								text({ "", "# SEI modules", "" }),
+								insert(3),
+							}),
+						},
+						tex = {
+							snip({
+								trig = "input",
+								namr = "Input Cell",
+								dscr = "Cell for SEIInputTable",
+							}, {
+								text({ "\\hypertarget{" }),
+								insert(1),
+								text({ "}{" }),
+								insert(2),
+								text({ "} & \\SEICell{", "\t" }),
+								insert(3),
+								text({ "", "}\\\\", "" }),
+							}),
+						},
+						markdown = {
+							snip({
+								trig = "img",
+								namr = "image",
+								dscr = "Markdown img",
+							}, {
+								text({ "![" }),
+								insert(1),
+								text("]("),
+								insert(2),
+								text(")"),
+							}),
+						},
+					})
+				end,
+			},
+			"saadparwaiz1/cmp_luasnip",
+			"hrsh7th/cmp-nvim-lsp",
+			"hrsh7th/cmp-path",
+		},
+		config = function()
+			-- See `:help cmp`
+			local cmp = require("cmp")
+			local luasnip = require("luasnip")
+			luasnip.config.setup({})
+			cmp.setup({
+				snippet = {
+					expand = function(args)
+						luasnip.lsp_expand(args.body)
+					end,
+				},
+				completion = { completeopt = "menu,menuone,noinsert" },
+
+				-- For an understanding of why these mappings were
+				-- chosen, you will need to read `:help ins-completion`
+				--
+				-- No, but seriously. Please read `:help ins-completion`, it is really good!
+				mapping = cmp.mapping.preset.insert({
+					-- Select the [n]ext item
+					["<C-n>"] = cmp.mapping.select_next_item(),
+					-- Select the [p]revious item
+					["<C-p>"] = cmp.mapping.select_prev_item(),
+
+					-- Accept ([y]es) the completion.
+					--  This will auto-import if your LSP supports it.
+					--  This will expand snippets if the LSP sent a snippet.
+					["<C-y>"] = cmp.mapping.confirm({ select = true }),
+
+					["<leader>j"] = cmp.mapping(function()
+						if luasnip.expand_or_locally_jumpable() then
+							luasnip.expand_or_jump()
+						end
+					end, { "i", "s" }),
+					["<leader>k"] = cmp.mapping(function()
+						if luasnip.locally_jumpable(-1) then
+							luasnip.jump(-1)
+						end
+					end, { "i", "s" }),
+				}),
+				sources = {
+					{ name = "nvim_lsp" },
+					{ name = "luasnip" },
+					{ name = "path" },
+				},
+			})
+		end,
+		snippet = {
+			expand = function(args)
+				local luasnip = require("luasnip")
+				if not luasnip then
+					return
+				end
+				luasnip.lsp_expand(args.body)
+			end,
+		},
+	},
+
+	{ -- You can easily change to a different colorscheme.
+		-- Change the name of the colorscheme plugin below, and then
+		-- change the command in the config to whatever the name of that colorscheme is
+		--
+		-- If you want to see what colorschemes are already installed, you can use `:Telescope colorscheme`
+		"morhetz/gruvbox",
+		lazy = false, -- make sure we load this during startup if it is your main colorscheme
+		priority = 1000, -- make sure to load this before all the other start plugins
+		config = function()
+			-- Load the colorscheme here
+			vim.cmd.colorscheme("gruvbox")
+		end,
+	},
+
+	-- Highlight todo, notes, etc in comments
+	{ "folke/todo-comments.nvim", dependencies = { "nvim-lua/plenary.nvim" }, opts = { signs = false } },
+
+	{ -- Collection of various small independent plugins/modules
+		-- Simple and easy statusline.
+		--  You could remove this setup call if you don't like it,
+		--  and try some other statusline plugin
+		"echasnovski/mini.nvim",
+		config = function()
+			require("mini.statusline").setup({
+				content = {
+					active = function()
+						local mode, mode_hl = MiniStatusline.section_mode({ trunc_width = 120 })
+						local git = MiniStatusline.section_git({ trunc_width = 75 })
+						local diagnostics = MiniStatusline.section_diagnostics({ trunc_width = 75 })
+						local filename = MiniStatusline.section_filename({ trunc_width = 140 })
+						local fileinfo = MiniStatusline.section_fileinfo({ trunc_width = 120 })
+						local location = MiniStatusline.section_location({ trunc_width = 75 })
+						local search = MiniStatusline.section_searchcount({ trunc_width = 75 })
+						local words = getWords()
+						return MiniStatusline.combine_groups({
+
+							{ hl = mode_hl, strings = { mode } },
+							{ hl = "MiniStatuslineDevinfo", strings = { git, diagnostics } },
+							"%<", -- Mark general truncate point
+							{ hl = "MiniStatuslineFilename", strings = { filename } },
+							"%=", -- End left alignment
+							{ hl = "MiniStatuslineFileinfo", strings = { fileinfo } },
+							{ hl = "MiniStatuslineFileinfo", strings = { words } },
+							{ hl = mode_hl, strings = { search, location } },
+						})
+					end,
+				},
+			})
+		end,
+	},
+
+	{ -- Highlight, edit, and navigate code
+		"nvim-treesitter/nvim-treesitter",
+		build = ":TSUpdate",
+		config = function()
+			-- [[ Configure Treesitter ]] See `:help nvim-treesitter`
+
+			---@diagnostic disable-next-line: missing-fields
+			require("nvim-treesitter.configs").setup({
+				ensure_installed = { "bash", "c", "html", "lua", "markdown", "vim", "vimdoc" },
+				-- Autoinstall languages that are not installed
+				auto_install = true,
+				highlight = { enable = false },
+				indent = { enable = false },
+			})
+
+			-- There are additional nvim-treesitter modules that you can use to interact
+			-- with nvim-treesitter. You should go explore a few and see what interests you:
+			--
+			--    - Incremental selection: Included, see :help nvim-treesitter-incremental-selection-mod
+			--    - Show your current context: https://github.com/nvim-treesitter/nvim-treesitter-context
+			--    - Treesitter + textobjects: https://github.com/nvim-treesitter/nvim-treesitter-textobjects
+		end,
+	},
+	"airblade/vim-gitgutter",
+})
+--Set rustfmt command
+vim.g["rustfmt_command"] = "rustfmt +nightly"
+--Disable semantic highlights
+for _, group in ipairs(vim.fn.getcompletion("@lsp", "highlight")) do
+	vim.api.nvim_set_hl(0, group, {})
+end
+
+--Testing scorch highlighting
+vim.api.nvim_create_autocmd({ "BufRead", "BufNewFile" }, {
+	pattern = "*.scorch",
+	callback = function()
+		vim.bo.filetype = "scorch"
+	end,
+})
+
+-- Commands to disable formatting
+require("conform").setup({
+	format_on_save = function(bufnr)
+		-- Disable with a global or buffer-local variable
+		if vim.g.disable_autoformat or vim.b[bufnr].disable_autoformat then
+			return
+		end
+		return { timeout_ms = 500, lsp_fallback = true }
+	end,
+})
+
+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 autoformat-on-save",
+	bang = true,
+})
+vim.api.nvim_create_user_command("FormatEnable", function()
+	vim.b.disable_autoformat = false
+	vim.g.disable_autoformat = false
+end, {
+	desc = "Re-enable autoformat-on-save",
+})

init.vim

@@ -1,212 +0,0 @@
-" Plugins will be downloaded under the specified directory.
-call plug#begin('~/.vim/plugged')
-
-" Declare the list of plugins.
-Plug 'kana/vim-textobj-user'
-Plug 'godlygeek/tabular'
-Plug 'Vigemus/iron.nvim'
-Plug 'tpope/vim-markdown'
-Plug 'vim-airline/vim-airline'
-Plug 'vim-airline/vim-airline-themes'
-"Plug 'kien/ctrlp.vim'
-Plug 'morhetz/gruvbox'
-Plug 'skywind3000/asyncrun.vim'
-Plug 'norcalli/nvim-colorizer.lua'
-Plug 'nvim-lua/popup.nvim'
-Plug 'nvim-lua/plenary.nvim'
-Plug 'nvim-telescope/telescope.nvim'
-Plug 'neoclide/coc.nvim', {'branch': 'release'}
-Plug 'christoomey/vim-tmux-navigator'
-Plug 'GCBallesteros/vim-textobj-hydrogen'
-Plug 'nvim-telescope/telescope-live-grep-args.nvim'
-Plug 'folke/todo-comments.nvim'
-Plug 'windwp/nvim-autopairs'
-Plug 'nvim-treesitter/nvim-treesitter', {'do': ':TSUpdate'}
-
-" List ends here. Plugins become visible to Vim after this call.
-call plug#end()
-
-" All system-wide defaults are set in $VIMRUNTIME/debian.vim and sourced by
-" the call to :runtime you can find below.  If you wish to change any of those
-" settings, you should do it in this file (/etc/vim/vimrc), since debian.vim
-" will be overwritten everytime an upgrade of the vim packages is performed.
-" It is recommended to make changes after sourcing debian.vim since it alters
-" the value of the 'compatible' option.
-
-" This line should not be removed as it ensures that various options are
-" properly set to work with the Vim-related packages available in Debian.
-runtime! debian.vim
-
-" Vim will load $VIMRUNTIME/defaults.vim if the user does not have a vimrc.
-" This happens after /etc/vim/vimrc(.local) are loaded, so it will override
-" any settings in these files.
-" If you don't want that to happen, uncomment the below line to prevent
-" defaults.vim from being loaded.
-" let g:skip_defaults_vim = 1
-
-" Uncomment the next line to make Vim more Vi-compatible
-" NOTE: debian.vim sets 'nocompatible'.  Setting 'compatible' changes numerous
-" options, so any other options should be set AFTER setting 'compatible'.
-"set compatible
-
-" Vim5 and later versions support syntax highlighting. Uncommenting the next
-" line enables syntax highlighting by default.
-"if has("syntax")
-"  syntax on
-"endif
-
-" If using a dark background within the editing area and syntax highlighting
-" turn on this option as well
-set background=dark
-
-" Uncomment the following to have Vim jump to the last position when
-" reopening a file
-"if has("autocmd")
-"  au BufReadPost * if line("'\"") > 1 && line("'\"") <= line("$") | exe "normal! g'\"" | endif
-"endif
-
-" Uncomment the following to have Vim load indentation rules and plugins
-" according to the detected filetype.
-"if has("autocmd")
-"  filetype plugin indent on
-"endif
-
-" The following are commented out as they cause vim to behave a lot
-" differently from regular Vi. They are highly recommended though.
-"set showcmd		" Show (partial) command in status line.
-"set showmatch		" Show matching brackets.
-"set ignorecase		" Do case insensitive matching
-"set smartcase		" Do smart case matching
-"set incsearch		" Incremental search
-"set autowrite		" Automatically save before commands like :next and :make
-"set hidden		" Hide buffers when they are abandoned
-"set mouse=a		" Enable mouse usage (all modes)
-
-" Source a global configuration file if available
-if filereadable("/etc/vim/vimrc.local")
-  source /etc/vim/vimrc.local
-endif
-
-"Set the shell, required to make xclip work
-set shell=/bin/sh
-
-syntax enable
-set tabstop=4
-set softtabstop=4
-set shiftwidth=4
-set expandtab
-set shiftwidth=0
-set number
-set relativenumber
-set cursorline
-let g:airline_theme='gruvbox'
-let g:airline_powerline_fonts = 1
-colorscheme gruvbox
-
-"Filetype support
-filetype on 
-filetype plugin on 
-"Disable markdown cold folding
-let g:vim_markdown_folding_disabled = 1
-
-"Keybindings 
-map <C-s> :set spell spellfile=~/.config/nvim/spell/wordlist.utf-8.spl
-
-"Set up some Asyncrun commands
-let g:asyncrun_open=6
-"Set terminal for ipython setup
-let g:slime_target = "neovim"
-set splitbelow
-set splitright
-command! -nargs=* T split| resize 20 | terminal <args>
-
-"Use netrw instead of NerdTree
-let g:netrw_banner = 0
-let g:netrw_liststyle = 3
-let g:netrw_browse_split = 2
-let g:netrw_altv = 1
-let g:netrw_winsize = 25
-let g:NetrwIsOpen=0
-function! ToggleNetrw()
-    if g:NetrwIsOpen
-        let i = bufnr("$")
-        while (i >= 1)
-            if (getbufvar(i, "&filetype") == "netrw")
-                silent exe "bwipeout " . i 
-            endif
-            let i-=1
-        endwhile
-        let g:NetrwIsOpen=0
-    else
-        let g:NetrwIsOpen=1
-        silent Lexplore
-    endif
-endfunction
-noremap <silent> <C-t> :call ToggleNetrw()<CR>
-
-"Disable cold folding in markdown plugin, and other options
-let g:vim_markdown_folding_disabled=1
-
-"Set default fortran type
-let fortran_free_source=1
-
-"Add open command
-nnoremap gX :silent :execute
-            \ "!xdg-open" expand('%:p:h') . "/" . expand("<cfile>") " &"<cr>
- 
-
-map <S-u> <Nop>
-inoremap <C-u> <Nop>
-
-"calcurse commands
-autocmd BufRead,BufNewFile /tmp/calcurse* set filetype=markdown
-autocmd BufRead,BufNewFile ~/.calcurse/notes/* set filetype=markdown
-"hi Normal guibg=NONE ctermbg=NONE
-"Some autocommands
-"Clean up when Latex exits
-autocmd VimLeave *.tex ! cleanLatex %:r
-
-"Setup lua colorizer
-set termguicolors
-lua require'colorizer'.setup()
-
-"Set up telescope 
-lua require('telescope_settings')
-nnoremap <silent> <C-g> <cmd>lua require('telescope').extensions.live_grep_args.live_grep_args(require('telescope.themes').get_ivy({}))<cr>
-xnoremap <silent> <C-g> "zy:lua require('telescope').extensions.live_grep_args.live_grep_args(require('telescope.themes').get_ivy({}))<cr><c-r>z
-nnoremap <silent> <C-f> <cmd> Telescope find_files shorten_path=true theme=ivy<cr>
-nnoremap <silent> <A-g> <cmd> Telescope live_grep grep_open_files=true theme=ivy <cr>
-vnoremap <silent> <A-g> "zy:Telescope live_grep grep_open_files=true theme=ivy <cr><c-r>z
-" Change an option theme=ivy<cr>
-"
-"Some coc.nvim bindings
-nnoremap <silent> gd <cmd>call CocActionAsync('jumpDefinition')<cr>
-
-"Neomutt settings
-autocmd BufNewFile,BufRead /tmp/neomutt* set noautoindent filetype=mail wm=0 tw=0 nonumber nolist
-autocmd BufNewFile,BufRead ~/tmp/neomutt* set noautoindent filetype=mail wm=0 tw=0 nonumber  nolist
-
-set mouse=
-
-"Change from ctrl-w+key to ctrl-key
-nnoremap <C-J> <C-W><C-J>
-nnoremap <C-K> <C-W><C-K>
-nnoremap <C-L> <C-W><C-L>
-nnoremap <C-H> <C-W><C-H>
-
-
-"iron.nvim
-lua require('iron')
-set formatoptions-=o
-
-"autopair settings
-lua require('autopair')
-
-"todo-comments
-lua require("todo-comments").setup()
-"Default width for everything nonw
-set colorcolumn=100
-set tw=100
-
-"Some jumping
-inoremap ;<Space><Space> <Esc>/<++><Enter>"_c4l