large refactor

modules/module/settings/cat-packages.nix

@@ -70,7 +70,6 @@ in
       tokei
       wget
       yq
-      zathura
     ]);
 
     python = maybe "python" (let
@@ -90,15 +89,14 @@ in
 
     r = maybe "r" (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
-        rnvimserver
-      ]);
+    in [
+      (pkgs.rpkgs.rWrapper.override { packages = r_packages; })
+      pkgs.rpkgs.radianWrapper
+      (pkgs.rpkgs.quarto.override { extraRPackages = r_packages; })
+      pkgs.air-formatter
+      pkgs.yaml-language-server
+      pkgs.rnvimserver
+    ]);
 
     # cats without packages get empty lists
     general = [ ];

modules/module/settings/core.nix

@@ -16,7 +16,7 @@
 
   # Lua packages available to neovim (for :lua require())
   config.settings.nvim_lua_env = lp:
-    lib.optionals (config.cats.general or true) [ lp.tiktoken_core ];
+    lib.optionals (config.cats.general or false) [ lp.tiktoken_core ];
 
   # Binary name for the wrapper
   config.binName = lib.mkDefault "vv";

modules/module/settings/env.nix

@@ -7,21 +7,21 @@
   # Environment variables set for the wrapper.
   # These are available when running neovim.
   config.env = lib.mkMerge [
-    (lib.mkIf (config.cats.python or true) {
+    (lib.mkIf (config.cats.python or false) {
       UV_PYTHON_DOWNLOADS = "never";
       UV_PYTHON = pkgs.python.interpreter;
     })
-    (lib.mkIf (config.cats.r or true) {
+    (lib.mkIf (config.cats.r or false) {
       RNVIM_COMPLDIR = "$PWD/.r-compl";
-      R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.Rlibs";
+      R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.r-libs";
       TMPDIR = "$PWD/.r-tmp";
     })
   ];
 
   # Environment variables with defaults (can be overridden by user)
   config.envDefault = lib.mkMerge [
-    (lib.mkIf (config.cats.r or true) {
-      R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.Rlibs";
+    (lib.mkIf (config.cats.r or false) {
+      R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.r-libs";
     })
   ];
 }

modules/module/settings/hosts.nix

@@ -29,7 +29,7 @@
         ];
       };
     }
-    (lib.mkIf (config.cats.julia or true) {
+    (lib.mkIf (config.cats.julia or false) {
       jl = {
         nvim-host.enable = true;
         nvim-host.package = "${pkgs.julia-bin}/bin/julia";
@@ -39,10 +39,10 @@
         ];
       };
     })
-    (lib.mkIf (config.cats.python or true) {
+    (lib.mkIf (config.cats.python or false) {
       python3.nvim-host.enable = true;
     })
-    (lib.mkIf (config.cats.r or true) {
+    (lib.mkIf (config.cats.r or false) {
       r = {
         nvim-host.enable = true;
         nvim-host.package = "${pkgs.rWrapper}/bin/R";

modules/module/settings/lang-packages.nix

@@ -1,5 +1,6 @@
 {
   config,
+  pkgs,
   lib,
   ...
 }:
@@ -26,14 +27,29 @@
     };
     default = { };
     description = ''
-      Language-specific package overrides appended to each language spec's runtimePackages.
-      Intended for flake.nix overrides via wrapper.config.wrap.
+      Language-specific package defaults and downstream overrides appended to each
+      language spec's runtime packages.
     '';
   };
 
   config.settings.lang_packages = {
-    python = lib.mkDefault [ ];
-    r = lib.mkDefault [ ];
-    julia = lib.mkDefault [ ];
+    python = lib.mkDefault (with pkgs.python3Packages; [
+      duckdb
+      polars
+    ]);
+    r = lib.mkDefault (
+      (with pkgs.rpkgs.rPackages; [
+        arrow
+        broom
+        data_table
+        janitor
+        styler
+      ])
+      ++ [pkgs.nvimcom]
+    );
+    julia = lib.mkDefault [
+      "DataFramesMeta"
+      "QuackIO"
+    ];
   };
 }

modules/module/specs/deps.nix

@@ -13,13 +13,13 @@
     };
   };
 
-  config.specs.always = lib.mkIf (config.cats.always or true) {
+  config.specs.always = lib.mkIf (config.cats.always or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     runtimePkgs = config.catPkgs.always;
   };
 
-  config.specs.external = lib.mkIf (config.cats.external or true) {
+  config.specs.external = lib.mkIf (config.cats.external or false) {
     data = lib.mkDefault null;
     before = ["INIT_MAIN"];
     config = ''
@@ -29,50 +29,50 @@
     runtimePkgs = config.catPkgs.external;
   };
 
-  config.specs.optional = lib.mkIf (config.cats.optional or true) {
+  config.specs.optional = lib.mkIf (config.cats.optional or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     before = ["INIT_MAIN"];
     runtimePkgs = config.catPkgs.optional;
   };
 
-  config.specs.markdown = lib.mkIf (config.cats.markdown or true) {
+  config.specs.markdown = lib.mkIf (config.cats.markdown or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     runtimePkgs = config.catPkgs.markdown;
   };
 
-  config.specs.nix = lib.mkIf (config.cats.nix or true) {
+  config.specs.nix = lib.mkIf (config.cats.nix or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     runtimePkgs = config.catPkgs.nix;
   };
 
-  config.specs.lua = lib.mkIf (config.cats.lua or true) {
+  config.specs.lua = lib.mkIf (config.cats.lua or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     runtimePkgs = config.catPkgs.lua;
   };
 
-  config.specs.python = lib.mkIf (config.cats.python or true) {
+  config.specs.python = lib.mkIf (config.cats.python or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     runtimePkgs = config.catPkgs.python;
   };
 
-  config.specs.r = lib.mkIf (config.cats.r or true) {
+  config.specs.r = lib.mkIf (config.cats.r or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     runtimePkgs = config.catPkgs.r;
   };
 
-  config.specs.julia = lib.mkIf (config.cats.julia or true) {
+  config.specs.julia = lib.mkIf (config.cats.julia or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     runtimePkgs = config.catPkgs.julia;
   };
 
-  config.specs.clickhouse = lib.mkIf (config.cats.clickhouse or true) {
+  config.specs.clickhouse = lib.mkIf (config.cats.clickhouse or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     runtimePkgs = config.catPkgs.clickhouse;

modules/module/specs/plugins.nix

@@ -4,11 +4,11 @@
   lib,
   ...
 }: {
-  config.specs.gitPlugins = lib.mkIf (config.cats.gitPlugins or true) {
+  config.specs.gitPlugins = lib.mkIf (config.cats.gitPlugins or false) {
     data = [];
   };
 
-  config.specs.r = lib.mkIf (config.cats.r or true) {
+  config.specs.r = lib.mkIf (config.cats.r or false) {
     data = with pkgs.vimPlugins; [
       pkgs.r-nvim
       quarto-nvim
@@ -19,14 +19,14 @@
     ];
   };
 
-  config.specs.markdown-lazy = lib.mkIf (config.cats.markdown or true) {
+  config.specs.markdown-lazy = lib.mkIf (config.cats.markdown or false) {
     lazy = true;
     data = [
       config.nvim-lib.neovimPlugins.cmp-pandoc-references
     ];
   };
 
-  config.specs.general = lib.mkIf (config.cats.general or true) {
+  config.specs.general = lib.mkIf (config.cats.general or false) {
     data = with pkgs.vimPlugins; [
       lze
       lzextras
@@ -79,7 +79,7 @@
     ];
   };
 
-  config.specs.lua = lib.mkIf (config.cats.lua or true) {
+  config.specs.lua = lib.mkIf (config.cats.lua or false) {
     data = with pkgs.vimPlugins; [
       luvit-meta
       {
@@ -89,7 +89,7 @@
     ];
   };
 
-  config.specs.markdown = lib.mkIf (config.cats.markdown or true) {
+  config.specs.markdown = lib.mkIf (config.cats.markdown or false) {
     data = with pkgs.vimPlugins; [
       quarto-nvim
       render-markdown-nvim
@@ -104,7 +104,7 @@
     ];
   };
 
-  config.specs.utils = lib.mkIf (config.cats.utils or true) {
+  config.specs.utils = lib.mkIf (config.cats.utils or false) {
     data = with pkgs.vimPlugins; [
       blink-cmp
       nvim-lspconfig
@@ -119,7 +119,7 @@
     ];
   };
 
-  config.specs.treesitterParsers = lib.mkIf (config.cats.treesitterParsers or true) {
+  config.specs.treesitterParsers = lib.mkIf (config.cats.treesitterParsers or false) {
     data = with pkgs.vimPlugins.nvim-treesitter-parsers; [
       bash
       c
@@ -158,7 +158,7 @@
     ];
   };
 
-  config.specs.utils-lazy = lib.mkIf (config.cats.utils or true) {
+  config.specs.utils-lazy = lib.mkIf (config.cats.utils or false) {
     lazy = true;
     data = with pkgs.vimPlugins; [
       blink-compat
@@ -175,7 +175,7 @@
     ];
   };
 
-  config.specs.gitPlugins-lazy = lib.mkIf (config.cats.gitPlugins or true) {
+  config.specs.gitPlugins-lazy = lib.mkIf (config.cats.gitPlugins or false) {
     lazy = true;
     data = [];
   };