init wrapper-module config

modules/module/settings/cats.nix

@@ -0,0 +1,51 @@
+{
+  config,
+  lib,
+  ...
+}:
+{
+  options.cats = lib.mkOption {
+    type = lib.types.attrsOf lib.types.bool;
+    description = ''
+      Category toggles used to enable/disable specs by name.
+
+      Keys map directly to specs (e.g., `python` controls `specs.python`).
+      Set a category to `false` to skip its dependency/plugin specs.
+
+      Available categories:
+      - clickhouse: Clickhouse client and tools
+      - customPlugins: local plugin specs
+      - external: external tools and integrations
+      - general: core Neovim plugins/features
+      - gitPlugins: git-related plugins
+      - julia: Julia tooling and packages
+      - lua: Lua tooling and LSPs
+      - markdown: markdown tooling and plugins
+      - nix: Nix tooling and plugins
+      - optional: optional tools and utilities
+      - python: Python tooling and plugins
+      - r: R tooling and plugins
+      - test: test-only tooling (disabled by default)
+      - treesitterParsers: Treesitter parsers
+      - utils: general utilities
+    '';
+  };
+
+  config.cats = {
+    clickhouse = lib.mkDefault false;
+    customPlugins = lib.mkDefault true;
+    external = lib.mkDefault true;
+    general = lib.mkDefault true;
+    gitPlugins = lib.mkDefault true;
+    julia = lib.mkDefault false;
+    lua = lib.mkDefault false;
+    markdown = lib.mkDefault false;
+    nix = lib.mkDefault false;
+    optional = lib.mkDefault false;
+    python = lib.mkDefault false;
+    r = lib.mkDefault false;
+    test = lib.mkDefault false;
+    treesitterParsers = lib.mkDefault true;
+    utils = lib.mkDefault true;
+  };
+}

modules/module/settings/core.nix

@@ -0,0 +1,35 @@
+{
+  config,
+  lib,
+  ...
+}:
+{
+  # Point to the directory containing init.lua, plugin/, lua/, etc.
+  config.settings.config_directory = ../../..;
+
+  # Default colorscheme and background
+  config.settings.colorscheme = "kanagawa";
+  config.settings.background = "dark";
+
+  # Enable RC wrapping (allows neovim to find the config)
+  config.settings.wrapRc = true;
+
+  # Lua packages available to neovim (for :lua require())
+  config.settings.nvim_lua_env = lp:
+    lib.optionals (config.cats.general or false) [ lp.tiktoken_core ];
+
+  # Binary name for the wrapper
+  config.binName = "n";
+
+  # Prevent neovim from loading system-wide config
+  config.settings.block_normal_config = true;
+
+  # Don't symlink the config (we wrap it instead)
+  config.settings.dont_link = false;
+
+  # Create additional aliases for the binary
+  config.settings.aliases = [ "vim" ];
+
+  # Enable wrapper handling of spec runtimeDeps (template pattern).
+  config.settings.autowrapRuntimeDeps = true;
+}

modules/module/settings/env.nix

@@ -0,0 +1,27 @@
+{
+  config,
+  pkgs,
+  lib,
+  ...
+}:
+{
+  # Environment variables set for the wrapper.
+  # These are available when running neovim.
+  config.env = lib.mkMerge [
+    (lib.mkIf (config.cats.r or false) {
+      R_LIBS_USER = "./.Rlibs";
+    })
+    (lib.mkIf (config.cats.python or false) {
+      UV_PYTHON_DOWNLOADS = "never";
+      UV_PYTHON = pkgs.python.interpreter;
+    })
+    (lib.mkIf (config.cats.test or false) {
+      TESTVAR = "It worked!";
+    })
+  ];
+
+  # Environment variables with defaults (can be overridden by user)
+  config.envDefault = lib.mkIf (config.cats.test or false) {
+    TESTVAR2 = "It worked again!";
+  };
+}

modules/module/settings/hosts.nix

@@ -0,0 +1,57 @@
+{
+  config,
+  pkgs,
+  lib,
+  ...
+}:
+{
+  config.hosts = lib.mkMerge [
+    {
+      node.nvim-host.enable = true;
+      perl.nvim-host.enable = true;
+      ruby.nvim-host.enable = true;
+
+      g = {
+        nvim-host.enable = true;
+        nvim-host.package = "${pkgs.neovide}/bin/neovide";
+        nvim-host.argv0 = "neovide";
+        nvim-host.flags."--neovim-bin" = "${placeholder "out"}/bin/${config.binName}";
+      };
+
+      m = {
+        nvim-host.enable = false;
+        nvim-host.package = "${pkgs.uv}/bin/uv";
+        nvim-host.argv0 = "uv";
+        nvim-host.addFlag = [
+          "run"
+          "marimo"
+          "edit"
+        ];
+      };
+    }
+    (lib.mkIf (config.cats.julia or true) {
+      jl = {
+        nvim-host.enable = true;
+        nvim-host.package = "${pkgs.julia-bin}/bin/julia";
+        nvim-host.argv0 = "julia";
+        nvim-host.addFlag = [
+          "--project=@."
+        ];
+      };
+    })
+    (lib.mkIf (config.cats.python or true) {
+      python3.nvim-host.enable = true;
+    })
+    (lib.mkIf (config.cats.r or true) {
+      r = {
+        nvim-host.enable = true;
+        nvim-host.package = "${pkgs.rWrapper}/bin/R";
+        nvim-host.argv0 = "R";
+        nvim-host.addFlag = [
+          "--no-save"
+          "--no-restore"
+        ];
+      };
+    })
+  ];
+}

modules/module/settings/lang-packages.nix

@@ -0,0 +1,39 @@
+{
+  config,
+  lib,
+  ...
+}:
+{
+  options.settings.lang_packages = lib.mkOption {
+    type = lib.types.submodule {
+      options = {
+        python = lib.mkOption {
+          type = lib.types.listOf lib.types.package;
+          default = [ ];
+          description = "Additional Python-related packages appended to the python spec (overlay defaults remain).";
+        };
+        r = lib.mkOption {
+          type = lib.types.listOf lib.types.package;
+          default = [ ];
+          description = "Additional R-related packages appended to the r spec (overlay defaults remain).";
+        };
+        julia = lib.mkOption {
+          type = lib.types.listOf lib.types.str;
+          default = [ ];
+          description = "Additional Julia packages (names) passed to julia-bin.withPackages.";
+        };
+      };
+    };
+    default = { };
+    description = ''
+      Language-specific package overrides appended to each language spec's extraPackages.
+      Intended for flake.nix overrides via wrapper.config.wrap.
+    '';
+  };
+
+  config.settings.lang_packages = {
+    python = lib.mkDefault [ ];
+    r = lib.mkDefault [ ];
+    julia = lib.mkDefault [ ];
+  };
+}

modules/module/settings/runtime-path.nix

@@ -0,0 +1,35 @@
+{
+  config,
+  lib,
+  ...
+}:
+let
+  collect_runtime_packages = runtime_deps_type:
+    config.specCollect
+      (acc: spec:
+        let
+          is_enabled = if spec ? enable then spec.enable else true;
+          has_runtime_deps = (spec.runtimeDeps or false) == runtime_deps_type;
+          packages = spec.extraPackages or [ ];
+        in
+        acc ++ lib.optionals (is_enabled && has_runtime_deps) packages
+      )
+      [ ];
+
+  prefix_packages = collect_runtime_packages "prefix";
+  suffix_packages = collect_runtime_packages "suffix";
+
+  to_path_specs = packages: [
+    {
+      data = [
+        "PATH"
+        ":"
+        "${lib.makeBinPath packages}"
+      ];
+    }
+  ];
+in
+{
+  config.prefixVar = lib.optionals (prefix_packages != [ ]) (to_path_specs prefix_packages);
+  config.suffixVar = lib.optionals (suffix_packages != [ ]) (to_path_specs suffix_packages);
+}

modules/module/specs/cats-enable.nix

@@ -0,0 +1,51 @@
+{ config, lib, ... }:
+{
+  # This module implements category-based enabling of specs.
+  # It runs early (order 200) so other specMaps can see the enable flags.
+  #
+  # How it works:
+  # 1. For each spec, extract its name (removing -lazy suffix if present)
+  # 2. Check if there's a corresponding cats.<name> toggle
+  # 3. Set spec.value.enable based on the cats toggle (default: true)
+  # 4. This allows specs to be conditionally included based on config.cats settings
+  #
+  # Example: If config.cats.python = false, then specs.python.enable = false
+
+  config.specMaps = lib.mkOrder 200 [
+    {
+      name = "CATS_ENABLE";
+      data =
+        list:
+        map (
+          v:
+          if v.type == "spec" || v.type == "parent" then
+            let
+              # Extract spec name, handling lazy specs (remove -lazy suffix)
+              specName =
+                if v.name == null then
+                  null
+                else if lib.hasSuffix "-lazy" v.name then
+                  lib.removeSuffix "-lazy" v.name
+                else
+                  v.name;
+
+              # Check if this spec has a corresponding cat toggle
+              catEnabled =
+                if specName != null && builtins.hasAttr specName config.cats then
+                  config.cats.${specName}
+                else
+                  true;  # Default to enabled if no cat toggle exists
+            in
+            v
+            // {
+              value = v.value // {
+                # Use explicit enable if set, otherwise use cat toggle
+                enable = if v.value ? enable then v.value.enable else catEnabled;
+              };
+            }
+          else
+            v
+        ) list;
+    }
+  ];
+}

modules/module/specs/deps.nix

@@ -0,0 +1,188 @@
+{
+  config,
+  pkgs,
+  lib,
+  wlib,
+  ...
+}: {
+  # ============================================================================
+  # SPEC MODULE DEFAULTS
+  # ============================================================================
+  # Define default options available to all specs
+
+  config.specMods = {parentSpec ? null, ...}: {
+    options.extraPackages = lib.mkOption {
+      type = lib.types.listOf wlib.types.stringable;
+      default = [];
+      description = "a extraPackages spec field to put packages to suffix to the PATH";
+    };
+  };
+
+  # ============================================================================
+  # EXTERNAL TOOLS SPEC
+  # ============================================================================
+  # Core system tools and utilities
+
+  config.specs.external = {
+    data = lib.mkDefault null;
+    before = ["INIT_MAIN"];
+    config = ''
+      vim.o.shell = "${pkgs.zsh}/bin/zsh"
+    '';
+    runtimeDeps = "prefix";
+    extraPackages = with pkgs; [
+      perl
+      ruby
+      shfmt
+      sqlfluff
+      tree-sitter
+    ];
+  };
+
+  # ============================================================================
+  # OPTIONAL TOOLS SPEC
+  # ============================================================================
+
+  config.specs.optional = lib.mkIf (config.cats.optional or true) {
+    data = lib.mkDefault null;
+    runtimeDeps = "prefix";
+    before = ["INIT_MAIN"];
+    extraPackages = with pkgs; [
+      bat
+      broot
+      devenv
+      dust
+      fd
+      fzf
+      gawk
+      gh
+      git
+      hunspell
+      hunspellDicts.de-at
+      hunspellDicts.en-us
+      ispell
+      jq
+      just
+      lazygit
+      man
+      ncdu
+      pigz
+      poppler
+      ripgrep
+      tokei
+      wget
+      yq
+      zathura
+    ];
+  };
+
+  # ============================================================================
+  # MARKDOWN SPEC
+  # ============================================================================
+
+  config.specs.markdown = lib.mkIf (config.cats.markdown or true) {
+    data = lib.mkDefault null;
+    runtimeDeps = "prefix";
+    extraPackages = with pkgs; [
+      python313Packages.pylatexenc
+      quarto
+      zk
+    ];
+  };
+
+  # ============================================================================
+  # NIX SPEC
+  # ============================================================================
+
+  config.specs.nix = lib.mkIf (config.cats.nix or true) {
+    data = lib.mkDefault null;
+    runtimeDeps = "prefix";
+    extraPackages = with pkgs; [
+      alejandra
+      nix-doc
+      nixd
+    ];
+  };
+
+  # ============================================================================
+  # LUA SPEC
+  # ============================================================================
+
+  config.specs.lua = lib.mkIf (config.cats.lua or true) {
+    data = lib.mkDefault null;
+    runtimeDeps = "prefix";
+    extraPackages = with pkgs; [
+      lua-language-server
+    ];
+  };
+
+  # ============================================================================
+  # PYTHON SPEC
+  # ============================================================================
+
+  config.specs.python = lib.mkIf (config.cats.python or true) {
+    data = lib.mkDefault null;
+    runtimeDeps = "prefix";
+    extraPackages = let
+      python_packages_fn =
+        if pkgs ? basePythonPackages
+        then ps: pkgs.basePythonPackages ps ++ config.settings.lang_packages.python
+        else _: config.settings.lang_packages.python;
+      python_with_packages = pkgs.python3.withPackages python_packages_fn;
+    in
+      with pkgs; [
+        python_with_packages
+        nodejs
+        ruff
+        basedpyright
+        uv
+      ];
+  };
+
+  # ============================================================================
+  # R SPEC
+  # ============================================================================
+
+  config.specs.r = lib.mkIf (config.cats.r or true) {
+    data = lib.mkDefault null;
+    runtimeDeps = "prefix";
+    extraPackages = let
+      r_packages = (pkgs.baseRPackages or []) ++ config.settings.lang_packages.r;
+    in
+      with pkgs; [
+        (rWrapper.override {packages = r_packages;})
+        radianWrapper
+        (quarto.override {extraRPackages = r_packages;})
+        air-formatter
+        yaml-language-server
+        updateR
+      ];
+  };
+
+  # ============================================================================
+  # JULIA SPEC
+  # ============================================================================
+
+  config.specs.julia = lib.mkIf (config.cats.julia or true) {
+    data = lib.mkDefault null;
+    runtimeDeps = "prefix";
+    extraPackages = let
+      julia_with_packages =
+        pkgs.julia-bin.withPackages config.settings.lang_packages.julia;
+    in [julia_with_packages];
+  };
+
+  # ============================================================================
+  # CLICKHOUSE SPEC
+  # ============================================================================
+
+  config.specs.clickhouse = lib.mkIf (config.cats.clickhouse or true) {
+    data = lib.mkDefault null;
+    runtimeDeps = "prefix";
+    extraPackages = with pkgs; [
+      clickhouse-lts
+    ];
+  };
+
+  config.extraPackages = config.specCollect (acc: v: acc ++ (v.extraPackages or [])) [];
+}

modules/module/specs/plugins.nix

@@ -0,0 +1,183 @@
+{
+  config,
+  pkgs,
+  lib,
+  ...
+}:
+{
+  config.specs.gitPlugins = {
+    data = [ ];
+  };
+
+  config.specs.r = {
+    data = [
+      config.nvim-lib.neovimPlugins.r
+    ];
+  };
+
+  config.specs.markdown-lazy = {
+    lazy = true;
+    data = [
+      config.nvim-lib.neovimPlugins.cmp-pandoc-references
+    ];
+  };
+
+  config.specs.r-lazy = {
+    lazy = true;
+    data = [
+      config.nvim-lib.neovimPlugins.cmp-r
+    ];
+  };
+
+  config.specs.general = {
+    data = with pkgs.vimPlugins; [
+      lze
+      lzextras
+      plenary-nvim
+      neogit
+      {
+        data = mini-nvim;
+        pname = "mini.nvim";
+      }
+      {
+        data = cyberdream-nvim;
+        pname = "cyberdream";
+      }
+      {
+        data = onedark-nvim;
+        pname = "onedark";
+      }
+      {
+        data = tokyonight-nvim;
+        pname = "tokyonight";
+      }
+      {
+        data = kanagawa-nvim;
+        pname = "kanagawa";
+      }
+      {
+        data = gruvbox-nvim;
+        pname = "gruvbox";
+      }
+      {
+        data = nord-nvim;
+        pname = "nord";
+      }
+      {
+        data = dracula-nvim;
+        pname = "dracula";
+      }
+      {
+        data = vscode-nvim;
+        pname = "vscode";
+      }
+      {
+        data = nightfox-nvim;
+        pname = "nightfox";
+      }
+      {
+        data = catppuccin-nvim;
+        pname = "catppuccin";
+      }
+    ];
+  };
+
+  config.specs.lua = {
+    data = with pkgs.vimPlugins; [
+      luvit-meta
+      {
+        data = lazydev-nvim;
+        pname = "lazydev";
+      }
+    ];
+  };
+
+  config.specs.markdown = {
+    data = with pkgs.vimPlugins; [
+      quarto-nvim
+      render-markdown-nvim
+      {
+        data = otter-nvim;
+        pname = "otter";
+      }
+      {
+        data = zk-nvim;
+        pname = "zk";
+      }
+    ];
+  };
+
+  config.specs.utils = {
+    data = with pkgs.vimPlugins; [
+      blink-cmp
+      nvim-lspconfig
+      nvim-treesitter-context
+      nvim-treesitter-textobjects
+      {
+        data = pkgs.codecompanion-nvim;
+        pname = "codecompanion";
+      }
+    ];
+  };
+
+  config.specs.treesitterParsers = {
+    data = with pkgs.vimPlugins.nvim-treesitter-parsers; [
+      bash
+      c
+      cpp
+      csv
+      diff
+      dockerfile
+      git_config
+      git_rebase
+      gitattributes
+      gitcommit
+      gitignore
+      html
+      javascript
+      json
+      julia
+      latex
+      lua
+      luadoc
+      make
+      markdown
+      markdown_inline
+      nix
+      python
+      query
+      r
+      rnoweb
+      regex
+      sql
+      toml
+      vim
+      vimdoc
+      xml
+      yaml
+      zig
+    ];
+  };
+
+  config.specs.utils-lazy = {
+    lazy = true;
+    data = with pkgs.vimPlugins; [
+      blink-compat
+      blink-copilot
+      cmp-cmdline
+      colorful-menu-nvim
+      conform-nvim
+      copilot-lua
+      nvim-dap
+      nvim-dap-ui
+      nvim-dap-virtual-text
+      nvim-lint
+      vim-slime
+    ];
+  };
+
+  config.specs.gitPlugins-lazy = {
+    lazy = true;
+    data = [ ];
+  };
+}