2025-08-14 updates

.config/nvim/lua/config/autocmds.lua

@@ -95,6 +95,10 @@ vim.api.nvim_create_autocmd("FileType", {
       end,
       { desc = "Toggle render-markdown on an RMarkdown file" }
     )
+    vim.keymap.set({
+      "n",
+      "i",
+    }, "<leader>`", "<Esc>i```{r}<CR>```<Esc>O", { desc = "New fenced RMarkdown code block" })
   end,
 })
 

.config/nvim/lua/config/keymaps.lua

@@ -16,7 +16,6 @@ vim.keymap.set("t", "<Esc>", "<C-\\><C-n>") -- Fix <Esc> in terminal buffer
 vim.keymap.set("n", "<Leader>H", ":set hlsearch!<CR>", { desc = "Toggle search highlight" })
 vim.keymap.set("n", "<leader>W", ":%s/\\s\\+$//<cr>:let @/=''<CR>", { desc = "Clean trailing whitespace" })
 vim.keymap.set({ "n", "i" }, "<leader>R", "<Esc>:syntax sync fromstart<CR>", { desc = "Refresh syntax highlighting" })
-vim.keymap.set({ "n", "i" }, "<leader>`", "<Esc>i```{r}<CR>```<Esc>O", { desc = "New fenced RMarkdown code block" })
 vim.keymap.set(
   { "n", "i" },
   "<leader>ts",

.config/nvim/lua/config/options.lua

@@ -38,11 +38,11 @@ vim.opt.wildmenu = true -- Make tab completion for files/buffers act like bash
 vim.opt.wildmode="list:full" -- Show a list when pressing tab; complete first full match
 vim.opt.wildignore:append("*.swp,*.bak,*.pyc,*.class") -- Ignore these when autocompleting
 vim.opt.cursorline = true  -- Highlight line where the cursor is
-vim.opt.fillchars:append { diff = "╱" } -- in diffs, show deleted lines with slashes rather than dashes
+vim.opt.fillchars:append { diff = "·" } -- in diffs, show deleted lines with dots rather than dashes
 vim.opt.signcolumn = "yes" -- always show the signcolumn to minimize distraction of appearing and disappearing
 
--- vim.cmd(":autocmd InsertEnter * set cul") -- Color the current line in upon entering insert mode
--- vim.cmd(":autocmd InsertLeave * set nocul") -- Remove color upon existing insert mode
+-- vim.cmd(":autocmd InsertEnter * set nocul") -- Remove color when entering insert mode
+-- vim.cmd(":autocmd InsertLeave * set cul") -- Turn color back on when exiting insert mode
 -- vim.cmd("set guicursor=i:block") -- Always use block cursor. In some terminals and fonts (like iTerm), it can be hard to see the cursor when it changes to a line.
 
 -- Copy all yanked/deleted lines to the "+" buffer. Useful when you want to use

.config/nvim/lua/plugins/beacon.lua

@@ -15,7 +15,6 @@ return {
 
     end,
     keys = {
-      { "<S-k><S-j>", ":Beacon<CR>", desc = "Flash beacon" },
       { "N", "N:Beacon<CR>", desc = "Prev search hit and flash beacon" },
       { "n", "n:Beacon<CR>", desc = "Next search hit and flash beacon" },
       { "%", "%:Beacon<CR>", desc = "Go to matching bracket and flash beacon" },

.config/nvim/lua/plugins/blink.lua

@@ -0,0 +1,76 @@
+-- blink.cmp provides autocompletion
+
+-- Used below to detect if we're in a word or not
+local has_words_before = function()
+  local col = vim.api.nvim_win_get_cursor(0)[2]
+  if col == 0 then
+    return false
+  end
+  local line = vim.api.nvim_get_current_line()
+  return line:sub(col, col):match("%s") == nil
+end
+return {
+  "saghen/blink.cmp",
+  dependencies = {
+    "rafamadriz/friendly-snippets",
+    'Kaiser-Yang/blink-cmp-dictionary',
+    dependencies = { 'nvim-lua/plenary.nvim' }
+  },
+
+  -- using a release tag downloads pre-built binaries
+  version = "v1.*",
+
+  opts = {
+    keymap = {
+      -- At any time, <C-Space> to show menu, arrows to select, Enter to accept.
+      preset = 'default',
+
+      -- Additionally, this configures tab-completion to mimic what happens in bash:
+      --   * Tab shows selections if cursor is in or immediately after a word, and immediately fills in the first item
+      --   * Enter to select.
+      --   * Tab scrolls thru suggestions (or Shift-Tab to go back)
+      --
+      ['<Tab>'] = {
+        function(cmp)
+          if has_words_before() then
+            return cmp.show_and_insert()
+          end
+        end,
+        'snippet_forward',
+        'select_next',
+        'fallback',
+      },
+      -- Navigate to the previous suggestion or cancel completion if currently on the first one.
+      ['<S-Tab>'] = { 'snippet_backward', 'insert_prev' },
+      ['<CR>'] = { 'accept', 'fallback' },
+    },
+    sources = {
+      default = function()
+        local result = { 'lsp', 'path', 'snippets', 'buffer' }
+
+        -- turn on dictionary completion in non-code files
+        if vim.tbl_contains({ 'markdown', 'text', 'rst' }, vim.bo.filetype) then
+          table.insert(result, 'dictionary')
+        end
+        return result
+      end,
+      providers = {
+        dictionary = {
+          module = 'blink-cmp-dictionary',
+          name = 'Dict',
+          min_keyword_length = 3,
+          opts = {
+            -- This is the location of the word list on macOS and many Linux distributions
+            dictionary_files = { '/usr/share/dict/words' }
+          }
+        }
+      },
+    },
+    fuzzy = { implementation = "prefer_rust_with_warning" },
+    completion = {
+      menu = { auto_show = false },
+      trigger = { show_in_snippet = false },
+    },
+  },
+  opts_extend = { "sources.default" },
+}

.config/nvim/lua/plugins/browsher.lua

@@ -1,3 +1,4 @@
+-- browsher will copy a link to github/gitlab based on where you are in the code
 return {
   'claydugo/browsher.nvim',
   event = "VeryLazy",

.config/nvim/lua/plugins/zenburn.lua → .config/nvim/lua/plugins/colorschemes.lua

@@ -24,4 +24,5 @@ return {
     lazy = false,
     priority = 1000,
   },
+  { "daler/zenfade", dependencies = { "rktjmp/lush.nvim" }, lazy = false, priority = 1000 },
 }

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

@@ -18,9 +18,8 @@ return {
       formatters_by_ft = {
         lua = { "stylua" },
         python = { "isort", "black" },
-        javascript = { { "prettierd", "prettier" } },
-        bash = { { "shfmt" } },
-        sh = { { "shfmt" } },
+        bash = { "shfmt" },
+        sh = { "shfmt" },
       },
       formatters = {
         shfmt = {

.config/nvim/lua/plugins/indent-o-matic.lua

@@ -0,0 +1,4 @@
+-- indent-o-matic provides automatic detection of indentation settings
+return {
+  'Darazaki/indent-o-matic'
+}

.config/nvim/lua/plugins/lush.lua

@@ -0,0 +1,6 @@
+-- lush is used for colormaps and designing/modifying colormaps
+return {
+  priority=1000,
+  lazy=false,
+  "rktjmp/lush.nvim",
+}

.config/nvim/lua/plugins/render-markdown.lua

@@ -30,6 +30,9 @@ return {
           internal = { pattern = ".*", icon = "⛬ ", highlight = "RenderMarkdownLink" },
         },
       },
+      checkbox = {
+        checked = { icon = "✓" }
+      }
     },
   },
 }

.config/nvim/lua/plugins/treesj.lua

@@ -0,0 +1,12 @@
+-- treesj splits and joins nodes
+return {
+  'Wansmer/treesj',
+  lazy = false,
+  dependencies = { 'nvim-treesitter/nvim-treesitter' },
+  config = function()
+    require('treesj').setup({
+      use_default_keymaps = false,
+    })
+    vim.keymap.set('n', '<leader>j', require('treesj').toggle, { desc = "Toggle split/join nodes" })
+  end,
+}

Dockerfile

@@ -96,13 +96,13 @@ RUN ./setup.sh --install-npm
 # Additional for this container: asciinema for screen casts
 RUN source ~/.bashrc \
     && ca \
-    && mamba create -y -n asciinema asciinema \
+    && conda create -y -n asciinema asciinema \
     && ln -s $(conda info --base)/envs/asciinema/bin/asciinema ~/opt/bin
 
 # imagemagick for converting gifs
 RUN source ~/.bashrc \
     && ca \
-    && mamba create -y -n imagemagick imagemagick \
+    && conda create -y -n imagemagick imagemagick \
     && ln -s $(conda info --base)/envs/imagemagick/bin/convert ~/opt/bin
 
 # Install fonts for use by agg

docs/_static/plugin_metadata.css

@@ -0,0 +1,50 @@
+/* Styling for plugin metadata */
+.plugin-metadata {
+    background-color: #f5f5f5;
+    border-left: 3px solid #ccc;
+    padding: 10px;
+    margin-bottom: 15px;
+    font-size: 0.9em;
+}
+
+/* Style for commit hashes */
+.plugin-metadata code, .plugin-metadata tt {
+    background-color: #f0f0f0;
+    border: 1px solid #ddd;
+    padding: 0 3px;
+    font-size: 0.9em;
+    border-radius: 3px;
+    color: #666;
+    font-weight: bold;
+}
+
+/* Style for commit messages */
+.plugin-metadata em {
+    font-style: italic;
+    color: #444;
+}
+
+/* Style for the changes list */
+.plugin-metadata ul {
+    margin-left: 20px;
+    padding-left: 0;
+}
+
+.plugin-metadata li {
+    margin-bottom: 4px;
+}
+
+/* Style for definition lists */
+.plugin-metadata dl {
+    margin-bottom: 10px;
+}
+
+.plugin-metadata dt {
+    font-weight: bold;
+    color: #666;
+}
+
+.plugin-metadata dd {
+    margin-left: 20px;
+    margin-bottom: 5px;
+}

docs/changelog.rst

@@ -1,6 +1,44 @@
 Changelog
 =========
 
+2025-08-14
+----------
+
+**vim**
+
+- Replace vim-sleuth with indent-o-matic for better indentation detection
+- Replace nvim-cmp with blink.cmp for autocompletion (about the same features but with simplified config)
+- Update checkbox rendering in markdown files
+- Add zenfade colorscheme (not enabled by default)
+- Nicer diff deletion symbol
+- Add lush plugin
+- Add treesj plugin
+- Bump installed nvim version to 0.10.4
+
+**setup**
+
+- conda installation dir can be configured via env var ``CONDA_INSTALLATION_DIR``
+- dockerfile uses conda rather than mamba for testing
+
+**docs**
+
+Nvim documentation overhaul. This now includes a new sphinx extension which
+inspects the git history to create a changelog of a plugin. This looks for the
+plugin name in filenames, commit messages, and changed text in an attempt to be
+more transparent about changes over time.
+
+The updates also include splitting the vim plugins from the main vim docs and
+rewriting some supporting docs for vim.
+
+2025-05-16
+----------
+
+**setup**
+
+``--dotfiles`` now properly handles backups of existing files, using a manual
+copy approach rather than rsync (thanks @mitraak)
+
+
 2025-05-07
 ----------
 
@@ -15,8 +53,8 @@ Changelog
 
 - The previous changes (2024-11-19) for better Python code pasting did not work
   on all systems. IPython would sometimes have a lag using ``%cpaste``. So this
-  time, we use `bracketed paste <https://en.wikipedia.org/wiki/Bracketed-paste>
-  `__ when pasting into a running terminal. This seems to have better behavior
+  time, we use `bracketed paste <https://en.wikipedia.org/wiki/Bracketed-paste>`__
+  when pasting into a running terminal. This seems to have better behavior
   in general (including R) by reducing the noise of pasted lines.
 
 - new plugin, `browsher`, to construct a URL for github/gitlab that highlights

docs/conf.py

@@ -31,7 +31,8 @@
 sys.path.insert(0, ".")
 extensions = [
     "sphinx.ext.autosectionlabel",
-    "details_ext"
+    "details_ext",
+    "plugin_metadata_ext"
 ]
 
 # Add any paths that contain templates here, relative to this directory.