wip plugins: configure environment for quarto

- Installs and configures the nvim-quarto plugin.
- Adds needed plugins and configuration from diving in the quarto
  kickstart configuration, which is damn huge.
- Adds the marksman parser for markdown, with its configuration.
- Adds the quarto filetype to the pandoc pluging.
- Loads the markdown snippets for the quarto filetype.
- Adds language support for treesitter.
- Installs and configure vim-slime plugin in order to execute emmbedded
  code (but it doesn't work as it misses a LOT of configuration).
- Documents very shortly the added plugins in the README.

Co-Authored-by: iGor milhit <igor@milhit.ch>

README.md

@@ -102,6 +102,10 @@ I won't provide links for each of these plugins as they are easily to be found.
 - `rainbow-csv.nvim` to manage CSV files.
 - `venv-selector.nvim` to ease python virtual env.
 - `vim-grammalecte` to get a good grammar checker for French.
+- Quarto:
+  - `nvim-quarto` to add quarto environment configuration.
+  - `otter` for the embedded code completion.
+  - `vim-slime` for the embedded code execution.
 
 <!-- references -->
 

lua/core/options.lua

@@ -1,3 +1,7 @@
+-- Temporary setting needed to make otter working
+--   https://github.com/jmbuhr/otter.nvim/issues/179
+vim.treesitter.language.register("markdown", { "quarto", "rmd" })
+
 -- Search and replace
 --  Ignore case except when using a capital case
 --  Highlight found occurrences

lua/plugins/lsp/mason.lua

@@ -17,6 +17,8 @@ return {
     -- Import lspconfig
     local lspconfig = require("lspconfig")
 
+    local util = require("lspconfig.util")
+
     -- Import mason-tool-installer 
     local mason_tool_installer = require("mason-tool-installer")
 
@@ -51,6 +53,7 @@ return {
         "html",
         "jsonls",
         "lua_ls",
+        "marksman",
         "pylsp",
         "yamlls",
       },
@@ -105,7 +108,7 @@ return {
         end,
 
         jsonls = function()
-            lspconfig.lua_ls.setup({
+            lspconfig.jsonls.setup({
               settings = {
                 json = {
                   schemas = require("schemastore").json.schemas(),
@@ -113,6 +116,22 @@ return {
                 }
               }
             })
+        end,
+
+        marksman = function()
+          lspconfig.marksman.setup({
+            setting = {
+              filetypes = {
+                "markdown",
+                "quarto",
+              },
+            root_dir = util.root_pattern(
+              '.git',
+              '.marksman.toml',
+              '_quarto.yml'
+              ),
+            }
+          })
         end
       },
     })

lua/plugins/markdown/pandoc.lua

@@ -39,9 +39,10 @@ return {
   {
     "vim-pandoc/vim-pandoc",
     ft = {
-		  'markdown',
+		  "markdown",
-			'pandoc',
+			"pandoc",
-			'pandoc.markdown'
+			"pandoc.markdown",
+      "quarto",
 		},
     lazy = true,
   },

lua/plugins/markdown/zotcite.lua

@@ -1,25 +0,0 @@
--- Install and configure zotcite
---  https://github.com/jalvesaq/zotcite
-
-return {
-  "jalvesaq/zotcite",
-  dependencies = {
-    "nvim-treesitter/nvim-treesitter",
-    -- Add completion for zotcite
-    "jalvesaq/cmp-zotcite",
-  },
-  config = function ()
-    require("zotcite").setup({
-      -- waiting for zotcite options
-    })
-    require("cmp_zotcite").setup({
-      -- Add the pandoc filetype
-      filetypes = {
-        "pandoc",
-        "markdown",
-        "rmd",
-        "quarto",
-      }
-    })
-  end
-}

lua/plugins/nvim-cmp.lua

@@ -28,6 +28,9 @@ return {
     "hrsh7th/cmp-emoji",
     -- vs-code pictrograms
     "onsails/lspkind.nvim",
+
+    -- Completion source for code emmbedded in other documents
+    "jmbuh/otter.nvim",
   },
 
   -- Configure nvim-cmp
@@ -40,16 +43,17 @@ return {
 
     luasnip.config.setup {
       -- Extend markdown snippets to pandoc filetype
-      --   https://github.com/L3MON4D3/LuaSnip/issues/132#issuecomment-1101710309
+      --   https://github.com/L3MON4D3/LuaSnip/issues/132#issuecomment-1101731222
       snippets = {
         markdown = {},
       },
       luasnip.filetype_extend("pandoc", {"markdown"}),
+      luasnip.filetype_extend("quarto", {"markdown"}),
     }
 
     -- Load snippets from ~/.config/nvim/my_snippets/
     require("luasnip.loaders.from_lua").lazy_load(
-      {paths = "~/.config/nvim/my_snippets/"}
+      { paths = "~/.config/nvim/my_snippets/" }
     )
     require("luasnip.loaders.from_vscode").lazy_load()
 

lua/plugins/quarto.lua

@@ -0,0 +1,16 @@
+-- Install and configure `quarto-nvim`
+--   https://github.com/quarto-dev/quarto-nvim
+
+return {
+  {
+    "quarto-dev/quarto-nvim",
+    lazy = true,
+    ft = {
+      "quarto",
+    },
+    dependencies = {
+      "jmbuhr/otter.nvim",
+      "nvim-treesitter/nvim-treesitter",
+    },
+  },
+}

lua/plugins/treesitter.lua

@@ -39,6 +39,7 @@ return {
 
 	-- Configure treesitter
 	config = function()
+    ---@diagnostic disable-next-line: missing-fields
 		local config = require("nvim-treesitter.configs")
 
 		config.setup({
@@ -55,26 +56,28 @@ return {
 			-- Installed and configured languages 
 			ensure_installed = {
 				"bash",
+				"css",
 				"dot",
 				"gitignore",
 				"html",
+				"javascript",
 				"json",
+        "julia",
 				"latex",
 				"lua",
+        "markdown",
+        "markdown_inline",
+        "mermaid",
+        "norg",
 				"python",
+				"query",
+        "r",
+        "typescript",
 				"vim",
+				"vimdoc",
 				"yaml",
 			},
 
-      -- Empty option, to avoid warning
-      modules = {},
-
-      -- List of parsers to ignore installing 
-      ignore_install = {
-        "markdown",
-        "markdown_inline"
-      },
-
 			-- Do not install parses synchronously
 			sync_install = false,
 

lua/plugins/vim-slime.lua

@@ -0,0 +1,50 @@
+-- Install and configure vim-slime
+--   https://github.com/jpalardy/vim-slime
+
+return {
+  'jpalardy/vim-slime',
+  dev = false,
+  init = function()
+    vim.b['quarto_is_python_chunk'] = false
+    Quarto_is_in_python_chunk = function()
+      require('otter.tools.functions').is_otter_language_context 'python'
+    end
+
+    vim.cmd [[
+      let g:slime_dispatch_ipython_pause = 100
+      function SlimeOverride_EscapeText_quarto(text)
+      call v:lua.Quarto_is_in_python_chunk()
+      if exists('g:slime_python_ipython') && len(split(a:text,"\n")) > 1 && b:quarto_is_python_chunk && !(exists('b:quarto_is_r_mode') && b:quarto_is_r_mode)
+      return ["%cpaste -q\n", g:slime_dispatch_ipython_pause, a:text, "--", "\n"]
+      else
+      if exists('b:quarto_is_r_mode') && b:quarto_is_r_mode && b:quarto_is_python_chunk
+      return [a:text, "\n"]
+      else
+      return [a:text]
+      end
+      end
+      endfunction
+      ]]
+
+    vim.g.slime_target = 'neovim'
+    vim.g.slime_no_mappings = true
+    vim.g.slime_python_ipython = 1
+  end,
+  config = function()
+    vim.g.slime_input_pid = false
+    vim.g.slime_suggest_default = true
+    vim.g.slime_menu_config = false
+    vim.g.slime_neovim_ignore_unlisted = true
+
+    local function mark_terminal()
+      local job_id = vim.b.terminal_job_id
+      vim.print('job_id: ' .. job_id)
+    end
+
+    local function set_terminal()
+      vim.fn.call('slime#config', {})
+    end
+    vim.keymap.set('n', '<leader>cm', mark_terminal, { desc = '[m]ark terminal' })
+    vim.keymap.set('n', '<leader>cs', set_terminal, { desc = '[s]et terminal' })
+  end
+}