update

lazy-lock.json

@@ -1,65 +1,68 @@
 {
-  "LuaSnip": { "branch": "master", "commit": "2dbef19461198630b3d7c39f414d09fb07d1fdd2" },
+  "LuaSnip": { "branch": "master", "commit": "a7a4b4682c4b3e2ba82b82a4e6e5f5a0e79dec32" },
   "bufresize.nvim": { "branch": "master", "commit": "3b19527ab936d6910484dcc20fb59bdb12322d8b" },
   "cellular-automaton.nvim": { "branch": "main", "commit": "b7d056dab963b5d3f2c560d92937cb51db61cb5b" },
-  "chezmoi.nvim": { "branch": "refactor", "commit": "4fbd33d7510e4a9697fa8b60181b9066b19399a1" },
+  "chezmoi.nvim": { "branch": "refactor", "commit": "a0fd6e164493b9d16137ee362c6b2106e5c32fa3" },
   "chezmoi.vim": { "branch": "main", "commit": "a35b426db9d83f8fcf43981f299ad3145d001af2" },
   "cloak.nvim": { "branch": "main", "commit": "9abe4e986e924fc54a972c1b0ff52b65a0622624" },
   "cmp-nvim-lsp": { "branch": "main", "commit": "5af77f54de1b16c34b23cba810150689a3a90312" },
-  "conform.nvim": { "branch": "master", "commit": "c0e0e80f0c233cb3a249f719a44324c660163a3f" },
+  "conform.nvim": { "branch": "master", "commit": "34b81e70da83e26c048290204de44268eb59814e" },
-  "copilot.vim": { "branch": "release", "commit": "315c6d2b16e018cb8020f20aaa7081ebc4070828" },
+  "copilot.vim": { "branch": "release", "commit": "57a0115908895f465eb3476f03a0aaa7096e8fe1" },
-  "everforest": { "branch": "main", "commit": "63ea67d948ddbc9915055a815ca0686930dc73d5" },
+  "everforest": { "branch": "main", "commit": "eedb19079c6bf9d162f74a5c48a6d2759f38cc76" },
   "focus.nvim": { "branch": "master", "commit": "4135f976afe5d6e1fe66dff121db9d06643f439f" },
+  "fzf": { "branch": "master", "commit": "507089d7b235b602f2f400be34c79a895e8c10dc" },
+  "fzf.vim": { "branch": "master", "commit": "8ea9574b3ebdc44fbe3dc6381a13f9ce0c290e2f" },
   "gitsigns.nvim": { "branch": "main", "commit": "2c2463dbd82eddd7dbab881c3a62cfbfbe3c67ae" },
   "glow.nvim": { "branch": "main", "commit": "238070a686c1da3bccccf1079700eb4b5e19aea4" },
   "harpoon": { "branch": "master", "commit": "ccae1b9bec717ae284906b0bf83d720e59d12b91" },
-  "image.nvim": { "branch": "master", "commit": "77df64af37ff68a1f593aa4f79b42b1388479239" },
+  "image.nvim": { "branch": "master", "commit": "0dd8bdbb8855bc98c534a902c91dc9eddb8155b1" },
-  "indent-blankline.nvim": { "branch": "master", "commit": "12e92044d313c54c438bd786d11684c88f6f78cd" },
+  "indent-blankline.nvim": { "branch": "master", "commit": "821a7acd88587d966f7e464b0b3031dfe7f5680c" },
   "lazy.nvim": { "branch": "main", "commit": "28126922c9b54e35a192ac415788f202c3944c9f" },
-  "lsp-zero.nvim": { "branch": "v3.x", "commit": "abac76482ec3012a2b359ba956a74e2ffd33d46f" },
+  "lsp-zero.nvim": { "branch": "v3.x", "commit": "8cce56f62f3b67a44b71106bc687e13e53ff95b0" },
-  "lualine.nvim": { "branch": "master", "commit": "7d131a8d3ba5016229e8a1d08bf8782acea98852" },
+  "lualine.nvim": { "branch": "master", "commit": "8b56462bfb746760465264de41b4907310f113ec" },
-  "mason-lspconfig.nvim": { "branch": "main", "commit": "0954d7730e749d606ddf8d7ae8846848be435d53" },
+  "mason-lspconfig.nvim": { "branch": "main", "commit": "21d33d69a81f6351e5a5f49078b2e4f0075c8e73" },
-  "mason-tool-installer.nvim": { "branch": "main", "commit": "bf0f4f8062d3acbe0afcc61db01a4d19d96310e4" },
+  "mason-tool-installer.nvim": { "branch": "main", "commit": "1212fb6082b7177dde17ea65e429e027835aeb40" },
-  "mason.nvim": { "branch": "main", "commit": "c43eeb5614a09dc17c03a7fb49de2e05de203924" },
+  "mason.nvim": { "branch": "main", "commit": "3b5068f0fc565f337d67a2d315d935f574848ee7" },
   "meh": { "branch": "master", "commit": "e2962284bbd53db5cbe2db39efaa3ea74ade0fb1" },
   "mini.bufremove": { "branch": "main", "commit": "931a3bb514147d9e812767275c4beba6b779b1d3" },
-  "mini.comment": { "branch": "main", "commit": "68a1e9de2ea47268205503ab1dcd48ff79648251" },
+  "mini.comment": { "branch": "main", "commit": "a4b7e46deb9ad2feb8902cc5dbf087eced112ee5" },
   "nabla.nvim": { "branch": "master", "commit": "27a6ea9ed7452bb9e0b19eb0942b5bcf7d051b2f" },
-  "neo-tree.nvim": { "branch": "v3.x", "commit": "e578fe7a5832421b0d2c5b3c0a7a1e40e0f6a47a" },
+  "neo-tree.nvim": { "branch": "v3.x", "commit": "459c60317cc1d251f6eb3b6f010d015d5d24b806" },
-  "nui.nvim": { "branch": "main", "commit": "35da9ca1de0fc4dda96c2e214d93d363c145f418" },
+  "nui.nvim": { "branch": "main", "commit": "fbb139c6f14896b434d0229099e1acd863ae6bec" },
-  "nvim-bqf": { "branch": "main", "commit": "bdc2a4e5bb670b3c0e33ada9c0eec636d93a0748" },
+  "nvim-bqf": { "branch": "main", "commit": "b51a37fcd808edafd52511458467c8c9a701ea8d" },
   "nvim-cmp": { "branch": "main", "commit": "04e0ca376d6abdbfc8b52180f8ea236cbfddf782" },
-  "nvim-lint": { "branch": "master", "commit": "966ab3dc37eee3e413692264b44a3011b05a6060" },
+  "nvim-lint": { "branch": "master", "commit": "e824adb9bc01647f71e55457353a68f0f37f9931" },
-  "nvim-lspconfig": { "branch": "master", "commit": "e655c96cf00f7b783871b3787187ed3fa25ff64e" },
+  "nvim-lspconfig": { "branch": "master", "commit": "9ad7021267c6caeb01f839c91ad8f15fb608807e" },
-  "nvim-spectre": { "branch": "master", "commit": "6a0785ef64c839d935a2f92e20988e962fb6537e" },
+  "nvim-spectre": { "branch": "master", "commit": "3712ff0cdf4f9f877d9ca708d835a877d9a0abaf" },
-  "nvim-surround": { "branch": "main", "commit": "703ec63aa798e5e07d309b35e42def34bebe0174" },
+  "nvim-surround": { "branch": "main", "commit": "d47001f8ddf9646c24f16d2732d4d0255acd2121" },
-  "nvim-treesitter": { "branch": "master", "commit": "10e8dffb7961fae98cf83efa0e170c22ae2cd33a" },
+  "nvim-treesitter": { "branch": "master", "commit": "cc6b108ea1251bd361f091b7d5a0dd41c04f8611" },
-  "nvim-treesitter-context": { "branch": "master", "commit": "f2ef98cd18fca352448756d3feb6e58d82583274" },
+  "nvim-treesitter-context": { "branch": "master", "commit": "b8b7e52c1517d401d7c519787d5dc4528c41291a" },
-  "nvim-treesitter-textobjects": { "branch": "master", "commit": "dd0b2036c3a27cb6e6486f8bd24188c6ca43af0b" },
+  "nvim-treesitter-textobjects": { "branch": "master", "commit": "b7a0bfa3e93697ca5b61b15df633404bf8f45883" },
   "nvim-ts-context-commentstring": { "branch": "main", "commit": "7ab799a9792f7cf3883cf28c6a00ad431f3d382a" },
-  "nvim-web-devicons": { "branch": "master", "commit": "7f30f2da3c3641841ceb0e2c150281f624445e8f" },
+  "nvim-web-devicons": { "branch": "master", "commit": "4adea17610d140a99c313e3f79a9dc01825d59ae" },
-  "oil.nvim": { "branch": "master", "commit": "bf753c3e3f8736939ad5597f92329dfe7b1df4f5" },
+  "oil.nvim": { "branch": "master", "commit": "18dfd2458dc741fea683357a17aaa95870b25a3c" },
   "playground": { "branch": "master", "commit": "ba48c6a62a280eefb7c85725b0915e021a1a0749" },
   "plenary.nvim": { "branch": "master", "commit": "4f71c0c4a196ceb656c824a70792f3df3ce6bb6d" },
   "rasmus": { "branch": "main", "commit": "f824de95d446686e479781c0c2b778c177da528f" },
   "readline.nvim": { "branch": "main", "commit": "5cb27349bc01cdcdb3d3494e5337d8b3834aef1a" },
-  "refactoring.nvim": { "branch": "master", "commit": "fb4990a0546c59136930ea624b8640d07957f281" },
+  "refactoring.nvim": { "branch": "master", "commit": "93d69cce9f0cbee8afae5b2380b296323792645f" },
-  "rose-pine": { "branch": "main", "commit": "f01ce3a71748a92997d266cfe2c985decd18c601" },
+  "rose-pine": { "branch": "main", "commit": "a29b09d15a9ef5cd575fbe5ae2a3cfb854876caf" },
-  "smart-splits.nvim": { "branch": "master", "commit": "36bfe63246386fc5ae2679aa9b17a7746b7403d5" },
+  "smart-splits.nvim": { "branch": "master", "commit": "1ae8794e9e7fbdf0ec4074f2d0e056556a834f75" },
+  "snakemake": { "branch": "main", "commit": "2887604ebe8a1e4c9c226780129312f556150dca" },
   "symbols-outline.nvim": { "branch": "master", "commit": "564ee65dfc9024bdde73a6621820866987cbb256" },
-  "telescope-fzf-native.nvim": { "branch": "main", "commit": "6c921ca12321edaa773e324ef64ea301a1d0da62" },
+  "telescope-fzf-native.nvim": { "branch": "main", "commit": "9ef21b2e6bb6ebeaf349a0781745549bbb870d27" },
-  "telescope.nvim": { "branch": "master", "commit": "0f865f17af4f9bc1587a0132414cdfd32d91852e" },
+  "telescope.nvim": { "branch": "master", "commit": "dc1ea28cc2a02cd1cebb9d80e967807d668f78f8" },
   "todo-comments.nvim": { "branch": "main", "commit": "833d8dd8b07eeda37a09e99460f72a02616935cb" },
-  "tree-sitter-just": { "branch": "main", "commit": "4f5d53b52a65771f9695df3f1a294d5c80b916fb" },
+  "tree-sitter-just": { "branch": "main", "commit": "43f2c5efb96e51bbd8e64284662911b60849df00" },
   "trouble.nvim": { "branch": "main", "commit": "f1168feada93c0154ede4d1fe9183bf69bac54ea" },
   "undotree": { "branch": "master", "commit": "9dbbf3b7d19dda0d22ceca461818e4739ad8154d" },
   "venn.nvim": { "branch": "main", "commit": "e4d68341a73dd56c64955058821a58295fb337b1" },
-  "vim-dispatch": { "branch": "master", "commit": "b84d00f11567abfcfec82a6838c7d41dfa49a447" },
+  "vim-dispatch": { "branch": "master", "commit": "4c695bc052cad2ae6b980aebbe48d046466e27ae" },
-  "vim-fugitive": { "branch": "master", "commit": "9f92ff14d9d1169e08f197a2250fcaea88e9c767" },
+  "vim-fugitive": { "branch": "master", "commit": "41beedabc7e948c787ea5696e04c3544c3674e23" },
   "vim-illuminate": { "branch": "master", "commit": "305bf07b919ac526deb5193280379e2f8b599926" },
-  "vim-startuptime": { "branch": "master", "commit": "ab5acd23f39347bab04904df2177e114bffb97a8" },
+  "vim-startuptime": { "branch": "master", "commit": "308b0088a864c4711a96e45b6734cf9294074f65" },
   "vim-tmux-navigator": { "branch": "master", "commit": "38b1d0402c4600543281dc85b3f51884205674b6" },
-  "vimtex": { "branch": "master", "commit": "9df79e15bf035d1cfb32c11fffed38dd7b6a0501" },
+  "vimtex": { "branch": "master", "commit": "a77d14b2e4391c0d3e860708bb1fd56161ab68eb" },
   "which-key.nvim": { "branch": "main", "commit": "4433e5ec9a507e5097571ed55c02ea9658fb268a" },
   "zen-mode.nvim": { "branch": "main", "commit": "78557d972b4bfbb7488e17b5703d25164ae64e6a" }
 }

lua/rayandrew/autocmds.lua

@@ -90,11 +90,17 @@ autocmd({ "BufWritePre" }, {
   end,
 })
 
-autocmd({ "BufWritePre" }, {
+-- autocmd({ "BufWritePre" }, {
-  group = augroup("remove_trailing_whitespace"),
+--   group = augroup("remove_trailing_whitespace"),
-  pattern = "*",
+--   pattern = "*",
-  command = [[%s/\s\+$//e]],
+--   callback = function()
-})
+--     if vim.b.disable_whitespace or vim.g.disable_whitespace then
+--       return
+--     end
+--     vim.cmd([[%s/\s\+$//e]])
+--   end,
+--   -- command = [[%s/\s\+$//e]],
+-- })
 
 -- vim.api.nvim_create_autocmd({ "WinNew", "WinClosed", "WinEnter" }, {
 --   group = vim.api.nvim_create_augroup("on_demand_wrap", {}),
@@ -110,14 +116,12 @@ autocmd({ "VimLeave" }, {
   end,
 })
 
--- translate vimscript below into nvim lua api
+-- set *.smk and Snakefile to filetype=snakemake
--- autocmd BufWritePost ~/.local/share/chezmoi/* ! chezmoi apply --source-path "%"
+autocmd({ "BufRead", "BufNewFile" }, {
--- autocmd({ "BufWritePost" }, {
+  group = augroup("snakemake_filetype"),
---   group = augroup("chezmoi_apply"),
+  pattern = { "*.smk", "Snakefile" },
---   pattern = "~/.local/share/chezmoi/*",
+  callback = function()
---   callback = function(event)
+    vim.bo.filetype = "snakemake"
---     print("chezmoi apply --source-path " .. event.match)
+    vim.bo.commentstring = "# %s"
---     -- vim.fn.jobstart("chezmoi apply --source-path " .. event.match, { detach = true })
+  end,
---   end,
+})
---   -- command = [[! chezmoi apply --source-path "%"]],
--- })

lua/rayandrew/commands.lua

@@ -1,3 +1,5 @@
+--- [[ Conform ]] commands
+
 -- https://github.com/stevearc/conform.nvim/blob/master/doc/recipes.md#lazy-loading-with-lazynvim
 vim.api.nvim_create_user_command("FormatDisable", function(args)
   if args.bang then
@@ -31,3 +33,24 @@ vim.api.nvim_create_user_command("Format", function(args)
   end
   require("conform").format({ async = true, lsp_fallback = true, range = range })
 end, { range = true })
+
+--- [[ WhiteSpace ]] commands
+
+-- vim.api.nvim_create_user_command("RemoveWhiteSpaceEnable", function()
+--   vim.b.disable_whitespace = false
+--   vim.g.disable_whitespace = false
+-- end, {
+--   desc = "Re-enable whitespace removal on save",
+-- })
+--
+-- vim.api.nvim_create_user_command("RemoveWhiteSpaceDisable", function(args)
+--   if args.bang then
+--     -- RemoveWhiteSpaceDisable! will disable whitespace removal just for this buffer
+--     vim.b.disable_whitespace = true
+--   else
+--     vim.g.disable_whitespace = true
+--   end
+-- end, {
+--   desc = "Disable whitespace removal on save",
+--   bang = true,
+-- })

lua/rayandrew/plugins/editor.lua

@@ -214,4 +214,12 @@ return {
       })
     end,
   },
+
+  {
+    "snakemake/snakemake",
+    ft = "snakemake",
+    config = function(plugin)
+      vim.opt.rtp:append(plugin.dir .. "/misc/vim")
+    end,
+  },
 }

lua/rayandrew/plugins/general.lua

@@ -1,5 +1,5 @@
 return {
-  { "folke/lazy.nvim",       version = "*" },
+  { "folke/lazy.nvim", version = "*" },
   { "nvim-lua/plenary.nvim", lazy = true },
 
   {
@@ -37,9 +37,11 @@ return {
     name = "everforest",
     opts = {
       background = "hard",
-    }
+    },
   },
 
+  { "junegunn/fzf.vim", dependencies = { "junegunn/fzf" } },
+
   -- {
   --   "f-person/auto-dark-mode.nvim",
   --   config = {

lua/rayandrew/plugins/lsp.lua

@@ -71,7 +71,7 @@ return {
         lsp_zero.on_attach(function(client, bufnr)
           -- see :help lsp-zero-keybindings
           -- to learn the available actions
-          lsp_zero.default_keymaps({ buffer = bufnr })
+          lsp_zero.default_keymaps({ buffer = bufnr, preserve_mappings = false })
         end)
 
         require("mason-lspconfig").setup({
@@ -211,7 +211,7 @@ return {
       }
       lint.linters["editorconfig-checker"].args = {
         "-no-color",
-        "-disable-max-line-length",          -- only rule of thumb
+        "-disable-max-line-length", -- only rule of thumb
         "-disable-trim-trailing-whitespace", -- will be formatted anyway
       }
     end,

lua/rayandrew/tools.lua

@@ -5,7 +5,6 @@ local lsps = {
   python = { "pyright" },
 }
 
-
 -- https://github.com/chrisgrieser/.config/blob/7dc36c350976010b32ece078edd581687634811a/nvim/lua/plugins/linter-formatter.lua#L214-L234
 M.linters = {
   lua = { "selene" },
@@ -50,7 +49,7 @@ M.formatters = {
   sh = { "shellcheck", "shfmt" },
   bib = { "trim_whitespace", "bibtex-tidy" },
   ["_"] = { "trim_whitespace", "trim_newlines", "squeeze_blanks" },
-  ["*"] = { "codespell" },
+  -- ["*"] = { "codespell" },
 }
 
 M.debuggers = {}