Nvim 0.11.5

.bash_prompt

@@ -2,9 +2,19 @@
 
 export PS1="\u@\h:\w\\$ "
 
-if [[ $HOSTNAME == "biowulf.nih.gov" ]] ; then
-    export PS1="\u@\[$(tput sgr0)\]\[\033[38;5;214m\]\h\[$(tput sgr0)\]:\w\\$ "
-fi
-if [[ $HOSTNAME == "helix.nih.gov" ]]; then
-    export PS1="\u@\[$(tput sgr0)\]\[\033[38;5;174m\]\h\[$(tput sgr0)\]:\w\\$ "
+# Only change prompt if running interactively
+if tty -s; then
+
+    # For colors, use colors.sh in the daler/dotfiles repo to easily show the
+    # color codes. E.g., in \033[38;5;214m\]\h, the 214 indicates an
+    # orange-yellow hostname.
+    #
+    # Or try https://bash-prompt-generator.org/ for more customization.
+    if [[ $HOSTNAME == "biowulf.nih.gov" ]] ; then
+
+        export PS1="\u@\[$(tput sgr0)\]\[\033[38;5;214m\]\h\[$(tput sgr0)\]:\w\\$ "
+    fi
+    if [[ $HOSTNAME == "helix.nih.gov" ]]; then
+        export PS1="\u@\[$(tput sgr0)\]\[\033[38;5;174m\]\h\[$(tput sgr0)\]:\w\\$ "
+    fi
 fi

.config/nvim/lazy-lock.json

@@ -1,49 +1,47 @@
 {
-  "LuaSnip": { "branch": "master", "commit": "33b06d72d220aa56a7ce80a0dd6f06c70cd82b9d" },
+  "LuaSnip": { "branch": "master", "commit": "3732756842a2f7e0e76a7b0487e9692072857277" },
   "accelerated-jk": { "branch": "master", "commit": "156c5158b72059404f6b8aaf15b59f87dd0aaa88" },
-  "aerial.nvim": { "branch": "master", "commit": "fd7fbe36772d7a955815c90ff9b58523bfdb410d" },
+  "aerial.nvim": { "branch": "master", "commit": "3c42785790d401731e7809a25f27f62dae2fec12" },
   "beacon.nvim": { "branch": "master", "commit": "5ab668c4123bc51269bf6f0a34828e68c142e764" },
-  "browsher.nvim": { "branch": "main", "commit": "4c0e5e37dd6ab9040a491acb3592ca38476a9a14" },
-  "bufferline.nvim": { "branch": "main", "commit": "261a72b90d6db4ed8014f7bda976bcdc9dd7ce76" },
-  "cmp-buffer": { "branch": "main", "commit": "3022dbc9166796b644a841a02de8dd1cc1d311fa" },
-  "cmp-nvim-lsp": { "branch": "main", "commit": "99290b3ec1322070bcfb9e846450a46f6efa50f0" },
-  "cmp-path": { "branch": "main", "commit": "91ff86cd9c29299a64f968ebb45846c485725f23" },
-  "cmp_luasnip": { "branch": "master", "commit": "98d9cb5c2c38532bd9bdb481067b20fea8f32e90" },
-  "conform.nvim": { "branch": "master", "commit": "f4e8837878fc5712d053ba3091a73d27d96a09e2" },
+  "blink-cmp-dictionary": { "branch": "master", "commit": "944b3b215b01303672d4213758db7c5c5a1e3c92" },
+  "blink.cmp": { "branch": "main", "commit": "b19413d214068f316c78978b08264ed1c41830ec" },
+  "browsher.nvim": { "branch": "main", "commit": "de87ffcdac45fc4fdd3f18882b81dbc002a2013d" },
+  "bufferline.nvim": { "branch": "main", "commit": "655133c3b4c3e5e05ec549b9f8cc2894ac6f51b3" },
+  "conform.nvim": { "branch": "master", "commit": "afce105eb47b0869dfafdac90d82f02ef2419d61" },
   "diffview.nvim": { "branch": "main", "commit": "4516612fe98ff56ae0415a259ff6361a89419b0a" },
-  "flash.nvim": { "branch": "main", "commit": "34c7be146a91fec3555c33fe89c7d643f6ef5cf1" },
-  "friendly-snippets": { "branch": "main", "commit": "efff286dd74c22f731cdec26a70b46e5b203c619" },
-  "gitsigns.nvim": { "branch": "main", "commit": "5f808b5e4fef30bd8aca1b803b4e555da07fc412" },
+  "flash.nvim": { "branch": "main", "commit": "fcea7ff883235d9024dc41e638f164a450c14ca2" },
+  "friendly-snippets": { "branch": "main", "commit": "572f5660cf05f8cd8834e096d7b4c921ba18e175" },
+  "gitsigns.nvim": { "branch": "main", "commit": "cdafc320f03f2572c40ab93a4eecb733d4016d07" },
   "gv.vim": { "branch": "master", "commit": "b6bb6664e2c95aa584059f195eb3a9f3cb133994" },
-  "indent-blankline.nvim": { "branch": "master", "commit": "259357fa4097e232730341fa60988087d189193a" },
-  "lazy.nvim": { "branch": "main", "commit": "7e6c863bc7563efbdd757a310d17ebc95166cef3" },
-  "lsp-progress.nvim": { "branch": "main", "commit": "f3df1df8f5ea33d082db047b5d2d2b83cc01cd8a" },
-  "lualine.nvim": { "branch": "master", "commit": "2a5bae925481f999263d6f5ed8361baef8df4f83" },
-  "mason.nvim": { "branch": "main", "commit": "e2f7f9044ec30067bc11800a9e266664b88cda22" },
-  "nightfox.nvim": { "branch": "main", "commit": "7557f26defd093c4e9bc17f28b08403f706f5a44" },
-  "nvim-cmp": { "branch": "main", "commit": "98e8b9d593a5547c126a39212d6f5e954a2d85dd" },
+  "indent-blankline.nvim": { "branch": "master", "commit": "005b56001b2cb30bfa61b7986bc50657816ba4ba" },
+  "indent-o-matic": { "branch": "master", "commit": "4d11e98f523d3c4500b1dc33f0d1a248a4f69719" },
+  "lazy.nvim": { "branch": "main", "commit": "85c7ff3711b730b4030d03144f6db6375044ae82" },
+  "lsp-progress.nvim": { "branch": "main", "commit": "ae52979ad412371ea6dc39ff70c8dfc681fb42b8" },
+  "lualine.nvim": { "branch": "master", "commit": "3946f0122255bc377d14a59b27b609fb3ab25768" },
+  "lush.nvim": { "branch": "main", "commit": "9c60ec2279d62487d942ce095e49006af28eed6e" },
+  "mason.nvim": { "branch": "main", "commit": "57e5a8addb8c71fb063ee4acda466c7cf6ad2800" },
   "nvim-colorizer.lua": { "branch": "master", "commit": "a065833f35a3a7cc3ef137ac88b5381da2ba302e" },
-  "nvim-lspconfig": { "branch": "master", "commit": "040001d85e9190a904d0e35ef5774633e14d8475" },
-  "nvim-tree.lua": { "branch": "master", "commit": "f7b76cd1a75615c8d6254fc58bedd2a7304eb7d8" },
-  "nvim-treesitter": { "branch": "master", "commit": "fa915a30c5cdf1d18129e9ef6ac2ee0fa799904f" },
-  "nvim-web-devicons": { "branch": "master", "commit": "0eb18da56e2ba6ba24de7130a12bcc4e31ad11cb" },
+  "nvim-lspconfig": { "branch": "master", "commit": "5bfcc89fd155b4ffc02d18ab3b7d19c2d4e246a7" },
+  "nvim-tree.lua": { "branch": "master", "commit": "3fb91e18a727ecc0385637895ec397dea90be42a" },
+  "nvim-treesitter": { "branch": "master", "commit": "42fc28ba918343ebfd5565147a42a26580579482" },
+  "nvim-web-devicons": { "branch": "master", "commit": "8dcb311b0c92d460fac00eac706abd43d94d68af" },
   "obsidian.nvim": { "branch": "main", "commit": "ae1f76a75c7ce36866e1d9342a8f6f5b9c2caf9b" },
-  "onedark.vim": { "branch": "main", "commit": "390b893d361c356ac1b00778d849815f2aa44ae4" },
-  "plenary.nvim": { "branch": "master", "commit": "2d9b06177a975543726ce5c73fca176cedbffe9d" },
-  "render-markdown.nvim": { "branch": "main", "commit": "0022a579ac7355966be5ade77699b88c76b6a549" },
-  "stickybuf.nvim": { "branch": "master", "commit": "183b9569bef78f44b17c078214f7d731f19cbefe" },
-  "telescope.nvim": { "branch": "master", "commit": "2eca9ba22002184ac05eddbe47a7fe2d5a384dfc" },
+  "onedark.vim": { "branch": "main", "commit": "68dca198f23ef979dc6a123ad50c598902117232" },
+  "plenary.nvim": { "branch": "master", "commit": "b9fd5226c2f76c951fc8ed5923d85e4de065e509" },
+  "render-markdown.nvim": { "branch": "main", "commit": "6e0e8902dac70fecbdd8ce557d142062a621ec38" },
+  "stickybuf.nvim": { "branch": "master", "commit": "0c1e5f1a3eb36eea2cea57083828269cc62c58e4" },
+  "telescope.nvim": { "branch": "master", "commit": "83a3a713d6b2d2a408491a1b959e55a7fa8678e8" },
   "toggleterm.nvim": { "branch": "main", "commit": "c80844fd52ba76f48fabf83e2b9f9b93273f418d" },
-  "trouble.nvim": { "branch": "main", "commit": "46cf952fc115f4c2b98d4e208ed1e2dce08c9bf6" },
+  "treesj": { "branch": "main", "commit": "4770492244ccecdc9b01e0e81fa8f2f6b4a23841" },
+  "trouble.nvim": { "branch": "main", "commit": "bd67efe408d4816e25e8491cc5ad4088e708a69a" },
   "vim-commentary": { "branch": "master", "commit": "64a654ef4a20db1727938338310209b6a63f60c9" },
   "vim-diff-enhanced": { "branch": "master", "commit": "8d161f1e97a5f5e64ea4219e6663f98a109df7b1" },
-  "vim-fugitive": { "branch": "master", "commit": "fcb4db52e7f65b95705aa58f0f2df1312c1f2df2" },
+  "vim-fugitive": { "branch": "master", "commit": "61b51c09b7c9ce04e821f6cf76ea4f6f903e3cf4" },
   "vim-mergetool": { "branch": "master", "commit": "0275a85256ad173e3cde586d54f66566c01b607f" },
-  "vim-python-pep8-indent": { "branch": "master", "commit": "baa647a70f1d6280a282a6cab425ef4094c9633d" },
-  "vim-sleuth": { "branch": "master", "commit": "be69bff86754b1aa5adcbb527d7fcd1635a84080" },
   "vim-surround": { "branch": "master", "commit": "3d188ed2113431cf8dac77be61b842acb64433d9" },
-  "vim-table-mode": { "branch": "master", "commit": "e4365bde024f73e205eefa2fb78e3029ddb92ea9" },
+  "vim-table-mode": { "branch": "master", "commit": "e156dbbedce0bbf61c0919db7678fa246fabd616" },
   "vis": { "branch": "master", "commit": "6a87efbfbd97238716b602c2b53564aa6329b5de" },
   "which-key.nvim": { "branch": "main", "commit": "0539da005b98b02cf730c1d9da82b8e8edb1c2d2" },
-  "zenburn.nvim": { "branch": "master", "commit": "821a84a57f0d87b553b563191239840d47052302" }
+  "zenburn.nvim": { "branch": "master", "commit": "0860da40c6f666dfff3381a8b0ee98e16e08ca66" },
+  "zenfade": { "branch": "main", "commit": "75284b99d9941bfee16ff5372f4b8205dd16f456" }
 }

.config/nvim/lua/plugins/conform.lua

@@ -17,7 +17,7 @@ return {
     opts = {
       formatters_by_ft = {
         lua = { "stylua" },
-        python = { "isort", "black" },
+        python = { "ruff", "black" },
         bash = { "shfmt" },
         sh = { "shfmt" },
       },

.config/nvim/lua/plugins/nvim-lspconfig.lua

@@ -1,8 +1,111 @@
 -- nvim-lspconfig allows convenient configuration of LSP clients
-return {
-  {
+
+-- nvim 0.11 changed the way lspconfig works, so we split the config based on
+-- version (hence the duplication)
+local post_v011 = vim.version().minor >= 11
+
+if post_v011 then
+  return {
+    "neovim/nvim-lspconfig",
+    version = "v2.5",
+    config = function()
+
+      -- Python language server
+      vim.lsp.config.pyright = {
+        cmd = { "pyright-langserver", "--stdio" },
+        filetypes = { "python" },
+        root_markers = {
+          "pyproject.toml",
+          "setup.py",
+          "setup.cfg",
+          "requirements.txt",
+          "Pipfile",
+          "pyrightconfig.json",
+          ".git",
+        },
+      }
+
+      -- ruff for Python as well
+      vim.lsp.config("ruff", {
+        init_options = {
+          settings = {
+            lint = {
+              preview = true,
+            },
+          },
+        },
+      })
+
+      -- Bash language server
+      vim.lsp.config.bashls = {
+        cmd = { "bash-language-server", "start" },
+        filetypes = { "sh", "bash" },
+        root_markers = { ".git" },
+      }
+
+      -- R language server
+      vim.lsp.config.r_language_server = {
+        cmd = { "R", "--slave", "-e", "languageserver::run()" },
+        filetypes = { "r", "rmd" },
+        root_markers = { ".git", "DESCRIPTION" },
+      }
+
+      -- Lua language server
+      vim.lsp.config.lua_ls = {
+        cmd = { "lua-language-server" },
+        filetypes = { "lua" },
+        root_markers = { ".luarc.json", ".luarc.jsonc", ".git" },
+        settings = {
+          Lua = {
+            runtime = { version = "LuaJIT" },
+            workspace = {
+              library = { vim.env.VIMRUNTIME },
+            },
+          },
+        },
+      }
+
+      -- By default show the virtual text.
+      vim.diagnostic.config({ virtual_text = true })
+
+      -- LSP keymaps
+      vim.api.nvim_create_autocmd("LspAttach", {
+        group = vim.api.nvim_create_augroup("UserLspConfig", {}),
+        callback = function(ev)
+          vim.keymap.set("n", "<leader>cv", function()
+            local current_config = vim.diagnostic.config()
+            vim.diagnostic.config({
+              virtual_text = not current_config.virtual_text,
+            })
+          end, { buffer = ev.buf, desc = "Toggle diagnostic virtual text" })
+          vim.keymap.set(
+            "n",
+            "<leader>ce",
+            vim.diagnostic.open_float,
+            { buffer = ev.buf, desc = "Open diagnostics/errors" }
+          )
+        end,
+      })
+    end,
+    keys = {
+      {
+        "<leader>cl",
+        function()
+          local clients = vim.lsp.get_clients({ bufnr = 0 })
+          if #clients > 0 then
+            vim.cmd("LspStop")
+          else
+            vim.cmd("LspStart")
+          end
+        end,
+        desc = "Toggle LSP",
+      },
+    },
+  }
+else
+  return {
     "neovim/nvim-lspconfig",
-    cmd = "LspStart",
+    version = "v2.5",
     init = function()
       local lspconfig = require("lspconfig")
 
@@ -22,46 +125,48 @@ return {
       -- Language server for Lua. These are the recommended options
       -- when mainly using Lua for Neovim
       lspconfig.lua_ls.setup({
-        autostart = false,
-        on_init = function(client)
-          local path = client.workspace_folders[1].name
-          if not vim.loop.fs_stat(path .. "/.luarc.json") and not vim.loop.fs_stat(path .. "/.luarc.jsonc") then
-            client.config.settings = vim.tbl_deep_extend("force", client.config.settings, {
-              Lua = {
-                runtime = { version = "LuaJIT" },
-                workspace = {
-                  checkThirdParty = false,
-                  library = {
-                    vim.env.VIMRUNTIME,
-                  },
-                },
-              },
-            })
-
-            client.notify("workspace/didChangeConfiguration", { settings = client.config.settings })
-          end
-        end,
+        settings = {
+          Lua = {
+            runtime = {
+              version = "LuaJIT",
+            },
+            workspace = {
+              library = { vim.env.VIMRUNTIME },
+            },
+          },
+        },
       })
 
       -- Use LspAttach autocommand to only map the following keys after
       -- the language server attaches to the current buffer
       vim.api.nvim_create_autocmd("LspAttach", {
         group = vim.api.nvim_create_augroup("UserLspConfig", {}),
         callback = function(ev)
-          vim.keymap.set("n", "<leader>cgd", vim.lsp.buf.definition, { buffer = ev.buf, desc = "Goto definition" })
+          vim.keymap.set("n", "<leader>cgd", vim.lsp.buf.definition, { buffer = ev.buf, desc = "Goto Definition" })
           vim.keymap.set("n", "<leader>cK", vim.lsp.buf.hover, { buffer = ev.buf, desc = "Hover help" })
           vim.keymap.set("n", "<leader>crn", vim.lsp.buf.rename, { buffer = ev.buf, desc = "Rename" })
-          vim.keymap.set("n", "<leader>cgr", vim.lsp.buf.references, { buffer = ev.buf, desc = "Goto references" })
-          vim.keymap.set("n", "<leader>ca", vim.lsp.buf.code_action, { buffer = ev.buf, desc = "Code action" })
+          vim.keymap.set("n", "<leader>cgr", vim.lsp.buf.references, { buffer = ev.buf, desc = "Goto References" })
+          vim.keymap.set("n", "<leader>ca", vim.lsp.buf.code_action, { buffer = ev.buf, desc = "Code Action" })
         end,
       })
     end,
     keys = {
-      -- Because autostart=false above, need to manually start the language server.
-      { "<leader>cl", "<cmd>LspStart<CR>", desc = "Start LSP" },
+      -- because autostart=false above, need to manually start the language server.
+      {
+        "<leader>cl",
+        function()
+          local clients = vim.lsp.get_clients({ bufnr = 0 })
+          if #clients > 0 then
+            vim.cmd("LspStop")
+          else
+            vim.cmd("LspStart")
+          end
+        end,
+        desc = "Toggle LSP",
+      },
       { "<leader>ce", vim.diagnostic.open_float, desc = "Open diagnostics/errors" },
       { "]d", vim.diagnostic.goto_next, desc = "Next diagnostic/error" },
       { "[d", vim.diagnostic.goto_prev, desc = "Prev diagnostic/error" },
     },
-  },
-}
+  }
+end

docs/changelog.rst

@@ -1,6 +1,28 @@
 Changelog
 =========
 
+2025-11-21
+----------
+
+**vim**
+
+- Bump installed nvim to v0.11.5, and update LSP configs accordingly
+
+nvim 0.11 added built-in LSP client support and some additional built-in
+keymaps. The LSP config here is backwards-compatible with the previously-used
+version v0.10.
+
+However if you re-install (i.e. ``setup.sh --install-neovim``) you'll get nvim
+0.11.5, which behaves a little differently with LSPs but is also now supported
+here. See :ref:`nvimlspconfig_ref` for details on these keymaps.
+
+**bash**
+
+Update ``.bash_prompt`` to only change prompts in an interactive session, which
+prevents the message ``tput: No value for $TERM and no -T specified`` when
+using non-interactive prompts like rsync or cron jobs. Also include some info
+on the colors and how to customize further.
+
 2025-10-27
 ----------
 

docs/nvim-plugins.rst

@@ -373,7 +373,14 @@ nvim's Language Server Protocol (LSP).
      ./setup.sh --install-npm  # install nodejs into conda env
 
 These keymaps start with :kbd:`c` (mnemonic: "code"). You need to start the
-language server with :kbd:`cl` to have access to any of the other keymaps.
+language server with :kbd:`cl` to have access to any of these keymaps.
+
+In nvim 0.11+, there are `default keymaps
+<https://neovim.io/doc/user/lsp.html#gra>`__ for LSP commands. These use the
+:kbd:`gr` prefix (presumably g for "global", but not sure what the mnemonic is
+for "r"). Otherwise, I'm using :kbd:`<leader>c` as the prefix for custom
+commands; mnemonic is "code".
+
 
 .. list-table::
     :header-rows: 1
@@ -384,20 +391,22 @@ language server with :kbd:`cl` to have access to any of the other keymaps.
     * - :kbd:`<leader>cl`
       - Start the LSP server for this buffer
     * - :kbd:`<leader>ce`
-      - Open diagnostic details
+      - Show details for the diagnostic
+    * - :kbd:`<leader>cv`
+      - Toggle virtual text diagnostics in buffer
     * - :kbd:`[d`
       - Prev diagnostic
     * - :kbd:`]d`
       - Next diagnostic
-    * - :kbd:`<leader>cgd`
+    * - :kbd:`grt`
       - Goto definition (e.g., when cursor is over a function)
-    * - :kbd:`<leader>cK`
+    * - :kbd:`K`
       - Hover help
-    * - :kbd:`<leader>crn`
+    * - :kbd:`grn`
       - Rename all instances of this symbol
-    * - :kbd:`<leader>cr`
+    * - :kbd:`grr`
       - Goto references
-    * - :kbd:`<leader>ca`
+    * - :kbd:`gra`
       - Code action (opens a menu if implemented)
 
 .. plugin-metadata::

setup.sh

@@ -22,7 +22,7 @@ set -eo pipefail
 # Change tool versions here
 VISIDATA_VERSION=2.11
 HUB_VERSION=2.14.2
-NVIM_VERSION=0.10.4
+NVIM_VERSION=0.11.5
 RG_VERSION=13.0.0
 BAT_VERSION=0.19.0
 JQ_VERSION=1.6