refactor package installation

README.md

@@ -0,0 +1,247 @@
+# nvimConfig
+
+Modular Neovim wrapper config. Defines a wrapped `vv` binary with per-category packages, plugins, and environment variables. Available as NixOS module, Home Manager module, or single-starflake import.
+
+## Quick start (imported into another flake)
+
+```nix
+{
+  inputs = {
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
+    rixpkgs.url = "github:dwinkler1/rixpkgs/af2dd3f7b4b172077747c0869d4e30702fb71b0e";
+    fran = {
+      url = "github:dwinkler1/fran";
+      inputs.nixpkgs.follows = "rixpkgs";
+    };
+    nvimConfig = {
+      url = "github:dwinkler1/nvimConfig";
+      inputs = {
+        nixpkgs.follows = "nixpkgs";
+        rixpkgs.follows = "rixpkgs";
+        fran.follows = "fran";
+      };
+    };
+  };
+
+  outputs = { self, nixpkgs, nvimConfig, ... } @ inputs: let
+    systems = ["aarch64-darwin" "x86_64-linux" "aarch64-linux"];
+    forAllSystems = nixpkgs.lib.genAttrs systems;
+  in {
+    packages = forAllSystems (system: let
+      pkgs = import nixpkgs {
+        inherit system;
+        config.allowUnfree = true;
+        overlays = [ nvimConfig.overlays.dependencies ];
+      };
+      evalResult = nvimConfig.inputs.wrappers.lib.evalModules {
+        modules = [
+          nvimConfig.wrapperModules.default
+          projectSettings  # see below
+        ];
+      };
+    in {
+      default = evalResult.config.wrap { inherit pkgs; };
+    });
+
+    devShells = forAllSystems (system: let
+      pkgs = import nixpkgs {
+        inherit system;
+        config.allowUnfree = true;
+        overlays = [ nvimConfig.overlays.dependencies ];
+      };
+      evalResult = nvimConfig.inputs.wrappers.lib.evalModules {
+        modules = [
+          nvimConfig.wrapperModules.default
+          projectSettings
+        ];
+      };
+      nv = evalResult.config.wrap { inherit pkgs; };
+    in {
+      default = pkgs.mkShell {
+        packages =
+          [ nv ]
+          ++ (evalResult.config.catPkgs.markdown or [])
+          ++ (evalResult.config.catPkgs.nix or []);
+      };
+    });
+  };
+}
+```
+
+## Home Manager module
+
+```nix
+{ inputs, ... }: {
+  home.packages = [
+    (inputs.nvimConfig.homeModules.default { inherit pkgs; })
+    # Or via the overlay:
+    # pkgs.vv
+  ];
+}
+```
+
+## NixOS module
+
+```nix
+{ inputs, ... }: {
+  environment.systemPackages = [
+    (inputs.nvimConfig.nixosModules.default { inherit pkgs; })
+  ];
+}
+```
+
+## Overriding settings
+
+Define a `projectSettings` attrset and pass it as the second module in `evalModules`. Every option in `nvimConfig.wrapperConfigs.default` can be overridden here.
+
+### Categories
+
+Enable only the cats you need. Defaults are listed in `modules/module/settings/cats.nix`.
+
+```nix
+projectSettings = {
+  cats = {
+    python = true;       # enable Python tooling
+    r = false;           # disable R
+    nix = true;
+    lua = false;
+    markdown = false;
+    optional = false;
+    gitPlugins = false;
+  };
+};
+```
+
+### Language packages (overlay extension)
+
+Add Python/R/Julia libraries that get appended to the overlay base packages.
+
+```nix
+projectSettings = {
+  settings.lang_packages = {
+    python = with pkgs.python3Packages; [ pandas numpy ];
+    r = with pkgs.rpkgs.rPackages; [ fixest data_table ];
+    julia = [ "StatsBase" "Plots" ];
+  };
+};
+```
+
+Use `lib.mkForce` to replace rather than append:
+
+```nix
+projectSettings = {
+  settings.lang_packages = {
+    python = pkgs.lib.mkForce (with pkgs.python3Packages; [ polars duckdb ]);
+  };
+};
+```
+
+### Runtime dependencies (per-cat packages)
+
+Override `catPkgs` to add tools that appear in both the wrapper PATH and the devShell. To add always-available packages not gated by any cat, use `runtimePkgs` directly (see next section).
+
+```nix
+projectSettings = {
+  catPkgs = {
+    nix = [ pkgs.nil pkgs.nixfmt ];
+    python = [
+      (pkgs.python3.withPackages (ps: [ ps.pandas ps.duckdb ]))
+      pkgs.ruff
+    ];
+  };
+};
+```
+
+### Direct runtimePkgs override (always-on)
+
+Add packages to `catPkgs.always` for tools that should always be available regardless of other cat toggles.
+
+```nix
+projectSettings = {
+  catPkgs = {
+    always = [ pkgs.git pkgs.curl pkgs.pre-commit ];
+  };
+};
+```
+
+### Runtime env vars
+
+```nix
+projectSettings = {
+  env = {
+    MY_PROJECT_VAR = "some-value";
+  };
+  envDefault = {
+    EDITOR = "vv";
+  };
+};
+```
+
+`env` values are forced; `envDefault` values can be overridden by the user's shell.
+
+### Neovim settings
+
+```nix
+projectSettings = {
+  settings = {
+    colorscheme = "kanagawa";
+    background = "dark";
+    wrapRc = true;
+    config_directory = ./nvim;  # path to init.lua + lua/ dir
+    aliases = [ "v" "nvim" ];   # extra binary names (default: [ "vvim" ])
+  };
+  binName = "nv";               # binary name (default: vv)
+};
+```
+
+## Adding plugins
+
+```nix
+projectSettings = {
+  specs = {
+    extraPlugins = {
+      data = with pkgs.vimPlugins; [
+        telescope-nvim
+        which-key-nvim
+      ];
+    };
+
+    extraLazy = {
+      lazy = true;
+      data = with pkgs.vimPlugins; [ dashboard-nvim ];
+    };
+
+    # Inject Lua config at startup
+    extraLua = {
+      data = pkgs.writeText "extra.lua" ''
+        vim.opt.number = true
+        vim.opt.relativenumber = true
+      '';
+      before = ["INIT_MAIN"];
+    };
+  };
+};
+```
+
+## Architecture
+
+```
+langPackages (flake.nix) ──► settings.lang_packages (module option)
+                                        │
+cats.nix ──► config.cats                │
+                  │                     │
+                  ▼                     ▼
+          cat-packages.nix ──► config.catPkgs.<cat>
+                  │                     │
+          ┌───────┘                     │
+          ▼                             ▼
+   deps.nix (runtimePkgs)       flake.nix (devShells)
+          │                             │
+          ▼                             ▼
+   wrapped vv PATH              nix develop PATH
+```
+
+- **Overlays** (`overlays/`) inject base packages into nixpkgs (rWrapper, quarto, baseRPackages, basePythonPackages).
+- **cat-packages.nix** is the single source of truth for per-category packages. Each list is gated by its cat toggle.
+- **deps.nix** wires `catPkgs` into the wrapper's runtime PATH.
+- **flake.nix** reads `catPkgs` for the devShell. `langPackages` feeds into `settings.lang_packages`.

flake.lock

@@ -74,20 +74,19 @@
         "nixpkgs": [
           "rixpkgs"
         ],
-        "rnvimsrc": [
+        "rnvimsrc": "rnvimsrc"
-          "plugins-r"
-        ]
       },
       "locked": {
-        "lastModified": 1778684156,
+        "lastModified": 1779438909,
-        "narHash": "sha256-Z4y1tQfkIsPK4NRxGn668HMDfWxnxNxSJ0CAOOXiIfY=",
+        "narHash": "sha256-1lvv0bdvSVyeCIgeZ7Ws7ffbDFurA5LJscS9dRLHzC8=",
         "owner": "dwinkler1",
         "repo": "r_nvim_nix",
-        "rev": "2f49dfee27886068e2f49cbd54558ce4cc424c82",
+        "rev": "ec17e22ab362a0ddfd6c2e9c5e95d43897a143be",
         "type": "github"
       },
       "original": {
         "owner": "dwinkler1",
+        "ref": "v0.99.4",
         "repo": "r_nvim_nix",
         "type": "github"
       }
@@ -108,6 +107,23 @@
         "type": "github"
       }
     },
+    "rnvimsrc": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1776905071,
+        "narHash": "sha256-dXox6qEs1VDE7vPNDoN8bY4g06uj1IEs6uki72w8lpA=",
+        "owner": "R-nvim",
+        "repo": "R.nvim",
+        "rev": "582f2af11290ac067e49018db38e12a511325556",
+        "type": "github"
+      },
+      "original": {
+        "owner": "R-nvim",
+        "ref": "v0.99.4",
+        "repo": "R.nvim",
+        "type": "github"
+      }
+    },
     "root": {
       "inputs": {
         "fran": "fran",

flake.nix

@@ -11,9 +11,12 @@
     };
     rixpkgs.url = "github:dwinkler1/rixpkgs/af2dd3f7b4b172077747c0869d4e30702fb71b0e";
 
-    r-nvim-nix.url = "github:dwinkler1/r_nvim_nix";
+    r-nvim-nix = {
-    r-nvim-nix.inputs.rnvimsrc.follows = "plugins-r";
+      url = "github:dwinkler1/r_nvim_nix/v0.99.4";
-    r-nvim-nix.inputs.nixpkgs.follows = "rixpkgs";
+      inputs = {
+        nixpkgs.follows = "rixpkgs";
+      };
+    };
 
     fran = {
       url = "github:dwinkler1/fran";
@@ -44,14 +47,15 @@
         duckdb
         polars
       ];
-      r = (with pkgs.rpkgs.rPackages; [
+      r =
+        (with pkgs.rpkgs.rPackages; [
           arrow
           broom
           data_table
           janitor
           styler
-        pkgs.nvimcom
+        ])
-      ]) ++ [ pkgs.nvimcom ];
+        ++ [pkgs.nvimcom];
       julia = [
         "DataFramesMeta"
         "QuackIO"
@@ -59,17 +63,6 @@
     };
 
     mkWrapperConfig = pkgs: {
-      cats = {
-        clickhouse = false;
-        gitPlugins = true;
-        julia = false;
-        lua = true;
-        markdown = true;
-        nix = true;
-        optional = false;
-        python = false;
-        r = true;
-      };
       settings = {
         lang_packages = langPackages pkgs;
       };
@@ -98,7 +91,11 @@
       import nixpkgs {
         inherit system;
         config = {allowUnfree = true;};
-        overlays = [ overlayDefs.dependencyOverlay ];
+        overlays = [
+          overlayDefs.dependencyOverlay
+          inputs.r-nvim-nix.overlays.default
+          inputs.fran.overlays.default
+        ];
       };
 
     module = (import ./modules/neovim.nix) inputs;
@@ -140,56 +137,21 @@
         pkgs = mkPkgs system;
         nvimPkg = wrapperSettings pkgs;
 
-        langPkgs = langPackages pkgs;
+        shellPackages = [nvimPkg]
-
+          ++ wrapper.config.catPkgs.always or []
-        pythonPackages = let
+          ++ wrapper.config.catPkgs.python or []
-          python_packages_fn =
+          ++ wrapper.config.catPkgs.r or []
-            if pkgs ? basePythonPackages
+          ++ wrapper.config.catPkgs.julia or []
-            then ps: pkgs.basePythonPackages ps ++ langPkgs.python
+          ++ wrapper.config.catPkgs.markdown or []
-            else _: langPkgs.python;
+          ++ wrapper.config.catPkgs.optional or []
-        in
+          ++ wrapper.config.catPkgs.external or []
-          with pkgs; [
+          ++ wrapper.config.catPkgs.nix or []
-            (python3.withPackages python_packages_fn)
+          ++ wrapper.config.catPkgs.lua or []
-            nodejs
+          ++ wrapper.config.catPkgs.clickhouse or [];
-            ruff
-            basedpyright
-            uv
-          ];
-
-        rPackages = let
-          r_packages = (pkgs.baseRPackages or []) ++ langPkgs.r;
-        in
-          with pkgs; [
-            (rWrapper.override {packages = r_packages;})
-            radianWrapper
-            (quarto.override {extraRPackages = r_packages;})
-            air-formatter
-            yaml-language-server
-            nvimcom
-            rnvimserver
-          ];
-
-        juliaPackages = let
-          julia_with_packages = pkgs.julia-bin.withPackages langPkgs.julia;
-        in [julia_with_packages];
-
-        markdownPackages = with pkgs; [
-          python313Packages.pylatexenc
-          quarto
-          zk
-        ];
-
-        shellPackages =
-          [nvimPkg]
-          ++ pkgs.lib.optionals wrapper.config.cats.python pythonPackages
-          ++ pkgs.lib.optionals wrapper.config.cats.r rPackages
-          ++ pkgs.lib.optionals wrapper.config.cats.julia juliaPackages
-          ++ pkgs.lib.optionals wrapper.config.cats.markdown markdownPackages;
       in {
         default = pkgs.mkShell {
           name = "vShell";
           packages = shellPackages;
-          nativeBuildInputs = pkgs.lib.optionals wrapper.config.cats.optional [ pkgs.devenv ];
           shellHook = ''
             echo 'I am a NixShell'
             export R_HOME=$(R RHOME)
@@ -223,9 +185,10 @@
             cat version_output.txt >> $out
           fi
         '';
-        module-eval =
+        module-eval = let
-          let _ = wrapper.config;
+          _ = wrapper.config;
-          in pkgs.runCommand "check-module-eval" {} ''
+        in
+          pkgs.runCommand "check-module-eval" {} ''
             echo "Module evaluation successful" > $out
           '';
       }

modules/module/settings/cat-packages.nix

@@ -0,0 +1,109 @@
+{
+  config,
+  pkgs,
+  lib,
+  ...
+}:
+let
+  maybe = cat: pkgsList:
+    lib.optionals (config.cats.${cat} or false) pkgsList;
+in
+{
+  options.catPkgs = lib.mkOption {
+    type = lib.types.attrsOf (lib.types.listOf lib.types.package);
+    description = "Per-cat package lists, gated by cat toggles. Single source of truth for runtimeDeps and devShells.";
+  };
+
+  config.catPkgs = {
+    always = maybe "always" (with pkgs; [ ]);
+
+    clickhouse = maybe "clickhouse" (with pkgs; [ clickhouse-lts ]);
+
+    external = maybe "external" (with pkgs; [
+      perl
+      ruby
+      shfmt
+      sqlfluff
+      tree-sitter
+    ]);
+
+    julia = maybe "julia" [
+      (pkgs.julia-bin.withPackages config.settings.lang_packages.julia)
+    ];
+
+    lua = maybe "lua" (with pkgs; [ lua-language-server ]);
+
+    markdown = maybe "markdown" (with pkgs; [
+      python313Packages.pylatexenc
+      quarto
+      zk
+    ]);
+
+    nix = maybe "nix" (with pkgs; [
+      alejandra
+      nix-doc
+      nixd
+    ]);
+
+    optional = maybe "optional" (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
+    ]);
+
+    python = maybe "python" (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 = 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
+      ]);
+
+    # cats without packages get empty lists
+    general = [ ];
+    gitPlugins = [ ];
+    treesitterParsers = [ pkgs.tree-sitter ];
+    utils = [ ];
+  };
+}

modules/module/settings/cats.nix

@@ -13,6 +13,7 @@
       Set a category to `false` to skip its dependency/plugin specs.
 
       Available categories:
+      - always: always-on packages (not gated by a toggle)
       - clickhouse: Clickhouse client and tools
       - external: external tools and integrations
       - general: core Neovim plugins/features
@@ -30,6 +31,7 @@
   };
 
   config.cats = {
+    always = lib.mkDefault true;
     clickhouse = lib.mkDefault false;
     external = lib.mkDefault true;
     general = lib.mkDefault true;

modules/module/settings/runtime-path.nix

@@ -1,33 +0,0 @@
-{
-  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.runtimePackages or [ ];
-        in
-        acc ++ lib.optionals (is_enabled && has_runtime_deps) packages
-      )
-      [ ];
-
-  prefix_packages = collect_runtime_packages "prefix";
-
-  to_path_specs = packages: [
-    {
-      data = [
-        "PATH"
-        ":"
-        "${lib.makeBinPath packages}"
-      ];
-    }
-  ];
-in
-{
-  config.prefixVar = lib.optionals (prefix_packages != [ ]) (to_path_specs prefix_packages);
-}

modules/module/specs/deps.nix

@@ -13,133 +13,69 @@
     };
   };
 
-  config.specs.external = {
+  config.specs.always = lib.mkIf (config.cats.always or true) {
+    data = lib.mkDefault null;
+    runtimeDeps = "prefix";
+    runtimePkgs = config.catPkgs.always;
+  };
+
+  config.specs.external = lib.mkIf (config.cats.external or true) {
     data = lib.mkDefault null;
     before = ["INIT_MAIN"];
     config = ''
       vim.o.shell = "${pkgs.zsh}/bin/zsh"
     '';
     runtimeDeps = "prefix";
-    runtimePkgs = with pkgs; [
+    runtimePkgs = config.catPkgs.external;
-      perl
-      ruby
-      shfmt
-      sqlfluff
-      tree-sitter
-    ];
   };
 
   config.specs.optional = lib.mkIf (config.cats.optional or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     before = ["INIT_MAIN"];
-    runtimePkgs = with pkgs; [
+    runtimePkgs = config.catPkgs.optional;
-      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
-    ];
   };
 
   config.specs.markdown = lib.mkIf (config.cats.markdown or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = with pkgs; [
+    runtimePkgs = config.catPkgs.markdown;
-      python313Packages.pylatexenc
-      quarto
-      zk
-    ];
   };
 
   config.specs.nix = lib.mkIf (config.cats.nix or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = with pkgs; [
+    runtimePkgs = config.catPkgs.nix;
-      alejandra
-      nix-doc
-      nixd
-    ];
   };
 
   config.specs.lua = lib.mkIf (config.cats.lua or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = with pkgs; [
+    runtimePkgs = config.catPkgs.lua;
-      lua-language-server
-    ];
   };
 
   config.specs.python = lib.mkIf (config.cats.python or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = let
+    runtimePkgs = config.catPkgs.python;
-      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
-      ];
   };
 
   config.specs.r = lib.mkIf (config.cats.r or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = let
+    runtimePkgs = config.catPkgs.r;
-      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
-      ];
   };
 
   config.specs.julia = lib.mkIf (config.cats.julia or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = let
+    runtimePkgs = config.catPkgs.julia;
-      julia_with_packages =
-        pkgs.julia-bin.withPackages config.settings.lang_packages.julia;
-    in [julia_with_packages];
   };
 
   config.specs.clickhouse = lib.mkIf (config.cats.clickhouse or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = with pkgs; [
+    runtimePkgs = config.catPkgs.clickhouse;
-      clickhouse-lts
-    ];
   };
 
   config.runtimePkgs = config.specCollect (acc: v: acc ++ (v.runtimePkgs or [])) [];

modules/neovim.nix

@@ -9,6 +9,7 @@ inputs:
 {
   imports = [
     wlib.wrapperModules.neovim
+    ./module/settings/cat-packages.nix
     ./module/specs/deps.nix
     ./module/specs/plugins.nix
     ./module/settings/core.nix
@@ -16,7 +17,6 @@ inputs:
     ./module/settings/env.nix
     ./module/settings/hosts.nix
     ./module/settings/lang-packages.nix
-    ./module/settings/runtime-path.nix
   ];
 
   options.nvim-lib.neovimPlugins = lib.mkOption {