Minor nvim configuration

CHANGELOG.md

@@ -1,5 +1,13 @@
 # CHANGELOG
 
+## 2025-04-29
+
+## 2025-04-29
+
+- Changed nvim Python LSP from `basedpyright` to disabled by default
+- Set shell to `fish` in nvim configuration
+- Added ToggleTerm plugin for improved terminal management in nvim
+
 ## 2025-03-25
 
 - Switch to LazyVim from kickstarter for nvim config.
@@ -21,9 +29,6 @@
 - Update bash configuration with simplified aliases
 - Remove old/unused scripts
 - Remove Linux-specific apt packages file
-
-## 2025-03-09
-
 - Replace nvim config with lua version
 - Add ghostty config
 - Remove iterm config

docker-compose.yml

@@ -1,7 +1,5 @@
 ---
-version: "3.9"
 services:
-
   # Format markdown and yml files.
   prettier:
     build:

ncbi/get_species_tax_id.py

@@ -1,4 +1,10 @@
-#!/usr/bin/env python3
+#!/usr/bin/env -S uv run --script
+# /// script
+# requires-python = ">=3.12"
+# dependencies = [
+# "requests",
+# ]
+# ///
 
 import requests
 from xml.etree import ElementTree as ET

nvim/lua/config/options.lua

@@ -2,8 +2,11 @@
 -- Default options that are always set: https://github.com/LazyVim/LazyVim/blob/main/lua/lazyvim/config/options.lua
 -- Add any additional options here
 
-vim.g.lazyvim_python_lsp = "basedpyright"
+-- Can set this to have type warnings, however this usually creates too much noise
+-- vim.g.lazyvim_python_lsp = "basedpyright"
 
 -- Venv for neovim plugins
 -- These are managed by ansible in the dotfiles setup
 vim.env.PATH = vim.env.PATH .. ":" .. vim.fn.expand("~/.venvs/nvim/bin")
+
+vim.o.shell = "fish"

nvim/lua/plugins/disabled.lua

@@ -0,0 +1,2 @@
+-- disabled lazyvim plugins here
+return {}

nvim/lua/plugins/toggleterm.lua

@@ -0,0 +1,100 @@
+return {
+  "akinsho/toggleterm.nvim",
+  version = "*",
+  config = function()
+    local toggleterm = require("toggleterm")
+
+    toggleterm.setup({
+      -- Terminal window size
+      size = function(term)
+        if term.direction == "horizontal" then
+          return 15
+        elseif term.direction == "vertical" then
+          return vim.o.columns * 0.4
+        end
+      end,
+
+      -- Default terminal direction
+      direction = "horizontal",
+
+      -- Terminal window settings
+      open_mapping = [[<c-\>]], -- Ctrl+\ to toggle terminal
+      hide_numbers = true, -- Hide line numbers in terminal
+      shade_filetypes = {},
+      shade_terminals = true,
+      shading_factor = 2, -- degree of terminal window shading
+      start_in_insert = true, -- start terminal in insert mode
+      insert_mappings = true, -- allow toggling terminal in insert mode
+      persist_size = true,
+      close_on_exit = false, -- close terminal when process exits
+      shell = vim.o.shell, -- use your default shell
+    })
+
+    -- Set up key mappings for terminals
+    vim.keymap.set("n", "<leader>tt", "<cmd>ToggleTerm<CR>", { desc = "[T]oggle [T]erminal" })
+    vim.keymap.set("n", "<leader>tf", "<cmd>ToggleTerm direction=float<CR>", { desc = "[T]oggle [F]loating terminal" })
+    vim.keymap.set(
+      "n",
+      "<leader>tv",
+      "<cmd>ToggleTerm direction=vertical<CR>",
+      { desc = "[T]oggle [V]ertical terminal" }
+    )
+    vim.keymap.set(
+      "n",
+      "<leader>th",
+      "<cmd>ToggleTerm direction=horizontal<CR>",
+      { desc = "[T]oggle [H]orizontal terminal" }
+    )
+
+    -- Send text to terminal
+    vim.keymap.set("n", "<leader>tl", function()
+      local term_id = vim.v.count > 0 and vim.v.count or 1
+
+      -- Get terminal by ID and toggle it if closed
+      local term = require("toggleterm.terminal").get(term_id)
+      if term and not term:is_open() then
+        term:toggle()
+      end
+
+      -- Send the current line
+      require("toggleterm").send_lines_to_terminal("single_line", true, { args = term_id })
+    end, { desc = "[T]erminal send [L]ine" })
+
+    vim.keymap.set("v", "<leader>ts", function()
+      local term_id = vim.v.count > 0 and vim.v.count or 1
+
+      -- Get terminal by ID and toggle it if closed
+      local term = require("toggleterm.terminal").get(term_id)
+      if term and not term:is_open() then
+        term:toggle()
+      end
+
+      -- Send the visual selection
+      require("toggleterm").send_lines_to_terminal("visual_selection", true, { args = term_id })
+    end, { desc = "[T]erminal [S]end visual selection" })
+
+    -- Terminal navigation keymaps
+    function _G.set_terminal_keymaps()
+      local opts = { buffer = 0 }
+      vim.keymap.set("t", "<esc>", [[<C-\><C-n>]], opts)
+      vim.keymap.set("t", "jk", [[<C-\><C-n>]], opts)
+      vim.keymap.set("t", "<C-h>", [[<Cmd>wincmd h<CR>]], opts)
+      vim.keymap.set("t", "<C-j>", [[<Cmd>wincmd j<CR>]], opts)
+      vim.keymap.set("t", "<C-k>", [[<Cmd>wincmd k<CR>]], opts)
+      vim.keymap.set("t", "<C-l>", [[<Cmd>wincmd l<CR>]], opts)
+      vim.keymap.set("t", "<C-w>", [[<C-\><C-n><C-w>]], opts)
+    end
+
+    -- Auto-apply terminal keymaps when opening a terminal
+    vim.cmd("autocmd! TermOpen term://* lua set_terminal_keymaps()")
+  end,
+  keys = {
+    { "<c-\\>", desc = "Toggle terminal" },
+    { "<leader>tt", desc = "Toggle terminal" },
+    { "<leader>tf", desc = "Toggle floating terminal" },
+    { "<leader>tv", desc = "Toggle vertical terminal" },
+    { "<leader>th", desc = "Toggle horizontal terminal" },
+    { "<leader>ts", desc = "Send visual selection to terminal", mode = "v" },
+    { "<leader>tl", desc = "Send line to terminal" },
+  },
+}