More robust shell setup with nu

Update RDE flake.lock

.github/workflows/update.yml

@@ -22,7 +22,6 @@ jobs:
           name: rde
           authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
           extraPullNames: rstats-on-nix, nix-community
-      - run: cd templates/rde/ && nix develop -c p-updateDeps
       - name: Update ed flake.lock
         uses: DeterminateSystems/update-flake-lock@v28
         with:

templates/ed/README.md

@@ -0,0 +1,73 @@
+# Project Editor
+
+A per-project Neovim wrapper built with [nix-wrapper-modules](https://birdeehub.github.io/nix-wrapper-modules/) and [nvimConfig](https://github.com/dwinkler1/nvimConfig).
+
+## Setup
+
+The flake provides two entry points:
+
+| Command | What you get |
+|---|---|
+| `direnv allow` / `nix develop` | **(Recommended)** A shell with `nv` and all enabled language toolchains (R, Python, Julia, Quarto) on `PATH`. |
+| `nix run` | Launches only the `nv` editor. Language toolchains (R, Python, etc.) are **not** on `PATH`. |
+
+### With direnv (recommended)
+
+```bash
+direnv allow   # enter the devShell automatically
+nv             # launch the pre-configured Neovim
+R              # R REPL is available (if enabled in flake.nix)
+```
+
+### Without direnv
+
+```bash
+nix develop    # enter the devShell manually
+nv             # launch Neovim
+R              # R REPL is available (if enabled in flake.nix)
+```
+
+> **Why `nix run` only gives the editor:** The flake's `packages.default` is the wrapped Neovim binary. Language toolchains (R, radian, quarto, etc.) live in `devShells.default`. Use `nix develop` (or `direnv allow`) to get the full environment.
+
+## Configuration
+
+The `flake.nix` is the single source of truth. Key knobs:
+
+| Option | What it controls |
+|---|---|
+| `cats` | Toggle language support (nix, r, python, julia, etc.) |
+| `settings.lang_packages.<lang>` | Language-specific packages installed in the wrapper |
+| `settings.colorscheme` | Neovim colorscheme |
+| `settings.background` | `"dark"` or `"light"` |
+| `settings.wrapRc` | When `true`, init.lua is embedded (rebuild to change); when `false`, init.lua is external (reload without rebuild) |
+| `binName` | The wrapper binary name (`nv` by default) |
+| `env` | Environment variables set in the wrapper |
+| `extraPackages` | Extra system packages available in the wrapper's PATH |
+| `specs.extraLua` | Inject lazy.nvim plugin specs |
+
+### Adding packages without editing flake.nix
+
+Create any of these optional files in the project root to add dependencies without modifying `flake.nix`:
+
+- **`python-packages.nix`** — receives `python3Packages`, return a list of packages:
+  ```nix
+  p: with p; [ numpy scipy ]
+  ```
+
+- **`r-packages.nix`** — receives `rpkgs` (includes `rPackages`), return a list:
+  ```nix
+  p: with p.rPackages; [ ggplot2 data.table ]
+  ```
+
+- **`julia-packages.nix`** — no arguments, return a list of package name strings:
+  ```nix
+  [ "DataFrames" "Plots" ]
+  ```
+
+## Formatting
+
+```bash
+nix fmt
+```
+
+Uses `nixfmt-rfc-style` pinned via the flake's `formatter` output.

templates/ed/flake.lock

@@ -22,11 +22,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1776877367,
-        "narHash": "sha256-EHq1/OX139R1RvBzOJ0aMRT3xnWyqtHBRUBuO1gFzjI=",
+        "lastModified": 1778869304,
+        "narHash": "sha256-30sZNZoA1cqF5JNO9fVX+wgiQYjB7HJqqJ4ztCDeBZE=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "0726a0ecb6d4e08f6adced58726b95db924cef57",
+        "rev": "d233902339c02a9c334e7e593de68855ad26c4cb",
         "type": "github"
       },
       "original": {
@@ -45,20 +45,19 @@
           "nixpkgs"
         ],
         "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references",
-        "plugins-r": [
-          "plugins-r"
-        ],
+        "plugins-r": "plugins-r",
+        "r-nvim-nix": "r-nvim-nix",
         "rixpkgs": [
           "rixpkgs"
         ],
         "wrappers": "wrappers"
       },
       "locked": {
-        "lastModified": 1776413627,
-        "narHash": "sha256-pU3u7T4MqpjUWxflNvd4i47FURp756L7nMRL8MV+QEw=",
+        "lastModified": 1779362150,
+        "narHash": "sha256-y3JTpxmNgtEYG1m21Ymvdmrul/WvJzOCX45AlV21aak=",
         "owner": "dwinkler1",
         "repo": "nvimConfig",
-        "rev": "2617face3b1be40534d2cae7f0a374a062b3710d",
+        "rev": "af6d975129768cce36ac4c46198ab2b3ebaafad3",
         "type": "github"
       },
       "original": {
@@ -86,20 +85,45 @@
     "plugins-r": {
       "flake": false,
       "locked": {
-        "lastModified": 1769881528,
-        "narHash": "sha256-oQSHHu6filJkAyH94yEvyTVuxA+5MU2dMOEAnsIjJKQ=",
+        "lastModified": 1776905071,
+        "narHash": "sha256-dXox6qEs1VDE7vPNDoN8bY4g06uj1IEs6uki72w8lpA=",
         "owner": "R-nvim",
         "repo": "R.nvim",
-        "rev": "958b472d763cb258927c7ef69af4fd9945cc5469",
+        "rev": "582f2af11290ac067e49018db38e12a511325556",
         "type": "github"
       },
       "original": {
         "owner": "R-nvim",
-        "ref": "v0.99.3",
+        "ref": "v0.99.4",
         "repo": "R.nvim",
         "type": "github"
       }
     },
+    "r-nvim-nix": {
+      "inputs": {
+        "nixpkgs": [
+          "nvimConfig",
+          "rixpkgs"
+        ],
+        "rnvimsrc": [
+          "nvimConfig",
+          "plugins-r"
+        ]
+      },
+      "locked": {
+        "lastModified": 1778684156,
+        "narHash": "sha256-Z4y1tQfkIsPK4NRxGn668HMDfWxnxNxSJ0CAOOXiIfY=",
+        "owner": "dwinkler1",
+        "repo": "r_nvim_nix",
+        "rev": "2f49dfee27886068e2f49cbd54558ce4cc424c82",
+        "type": "github"
+      },
+      "original": {
+        "owner": "dwinkler1",
+        "repo": "r_nvim_nix",
+        "type": "github"
+      }
+    },
     "rixpkgs": {
       "locked": {
         "lastModified": 1771303851,
@@ -111,8 +135,8 @@
       },
       "original": {
         "owner": "dwinkler1",
-        "ref": "nixpkgs",
         "repo": "rixpkgs",
+        "rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e",
         "type": "github"
       }
     },
@@ -121,7 +145,6 @@
         "fran": "fran",
         "nixpkgs": "nixpkgs",
         "nvimConfig": "nvimConfig",
-        "plugins-r": "plugins-r",
         "rixpkgs": "rixpkgs"
       }
     },
@@ -133,11 +156,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1776375800,
-        "narHash": "sha256-/SSAR77Brr9fbapsh1cb2K47JXCbvwS1GjM4yyDxle8=",
+        "lastModified": 1779297405,
+        "narHash": "sha256-VFoBwH7ZjVxCnvZTb5ODRXt70sLtWMxstive0N+RS50=",
         "owner": "BirdeeHub",
         "repo": "nix-wrapper-modules",
-        "rev": "f11469ca69068bac13d9e163b2bd268cc06dff57",
+        "rev": "e7ed7a1205945befdf2e0d73ba7df91d935e5af1",
         "type": "github"
       },
       "original": {

templates/ed/flake.nix

@@ -7,7 +7,8 @@
     nvimConfig,
     ...
   } @ inputs: let
-    projectSettings = {pkgs}: {
+    # ── Shared language support flags ──────────────────────────────
+    # Used by both the neovim wrapper module and the devShell
     cats = {
       clickhouse = false;
       gitPlugins = false;
@@ -20,25 +21,11 @@
       r = false;
     };
 
-      settings = let
-        # With `replace` packages are replaced otherwise they are merged with base packages
-        replace = pkgs.lib.mkForce;
-      in {
-        lang_packages = {
-          python = replace (
-            (with pkgs.python3Packages; [
-              duckdb
-              polars
-            ])
-            ++ (
-              if builtins.pathExists ./python-packages.nix
-              # p: with p; [ ... ]
-              then import ./python-packages.nix pkgs.python3Packages
-              else []
-            )
-          );
+    # ── Language package lists ────────────────────────────────────
+    # Shared between wrapper lang_packages and devShell toolchains.
+    # Accept pkgs so they work inside forAllSystems for each system.
 
-          r = replace (
+    rPackages = pkgs:
       (with pkgs.rpkgs.rPackages; [
         fixest
         # pkgs.extraRPackages.musicMetadata
@@ -48,31 +35,64 @@
         # p: with p.rPackages; [ ... ]
         then import ./r-packages.nix pkgs.rpkgs
         else []
-            )
       );
 
-          julia = replace ([
-              "StatsBase"
-            ]
+    pythonPackages = pkgs:
+      (with pkgs.python3Packages; [
+        duckdb
+        polars
+      ])
+      ++ (
+        if builtins.pathExists ./python-packages.nix
+        # p: with p; [ ... ]
+        then import ./python-packages.nix pkgs.python3Packages
+        else []
+      );
+
+    juliaPackages =
+      ["StatsBase"]
       ++ (
         if builtins.pathExists ./julia-packages.nix
         # [ ... ]
         then import ./julia-packages.nix
         else []
-            ));
+      );
+
+    systems = ["aarch64-darwin" "x86_64-linux" "aarch64-linux"];
+    forAllSystems = nixpkgs.lib.genAttrs systems;
+    overlays = [inputs.nvimConfig.overlays.dependencies];
+  in {
+    formatter = forAllSystems (system: nixpkgs.legacyPackages.${system}.nixfmt-rfc-style);
+
+    packages = forAllSystems (system: let
+      pkgs = import nixpkgs {
+        inherit system overlays;
+        config = {allowUnfree = true;};
+      };
+      # Plain attrset — pkgs is captured from the surrounding scope,
+      # so the module system does not need lazy _module.args resolution.
+      projectSettings = {
+        inherit cats;
+        settings = let
+          # With `replace` packages are replaced otherwise they are merged with base packages
+          replace = pkgs.lib.mkForce;
+        in {
+          lang_packages = {
+            python = replace (pythonPackages pkgs);
+            r = replace (rPackages pkgs);
+            julia = replace juliaPackages;
           };
           colorscheme = "kanagawa";
           background = "dark";
           wrapRc = true;
         };
-      binName = "vv";
+        binName = "nv";
 
         env = {
           IS_PROJECT_EDITOR = "1";
-        R_LIBS_USER = "./.nvimcom";
         };
 
-      extraPackages = with pkgs; [
+        runtimePkgs = with pkgs; [
           cowsay
         ];
 
@@ -88,34 +108,83 @@
           '';
         };
       };
-
-    systems = nixpkgs.lib.systems.flakeExposed;
-    forAllSystems = nixpkgs.lib.genAttrs systems;
-    overlays = [inputs.nvimConfig.overlays.dependencies];
+      evalResult = nvimConfig.inputs.wrappers.lib.evalModules {
+        modules = [
+          nvimConfig.wrapperModules.default
+          projectSettings
+        ];
+      };
     in {
-    packages = forAllSystems (system: let
-      pkgs = import nixpkgs {inherit system overlays;};
-      baseNvim = nvimConfig.packages.${system}.default;
-
-      nvim = (baseNvim.eval (projectSettings {inherit pkgs;})).config.wrapper;
-      default = nvim;
-    in {
-      default = nvim;
+      default = evalResult.config.wrap {inherit pkgs;};
     });
 
     devShells = forAllSystems (system: let
-      pkgs = import nixpkgs {inherit system overlays;};
+      pkgs = import nixpkgs {
+        inherit system overlays;
+        config = {allowUnfree = true;};
+      };
       nv = self.packages.${system}.default;
     in {
       default = pkgs.mkShell {
-        packages = [nv pkgs.updateR];
+        shellHook = ''
+          exec nu
+          alias gst='git status'
+          alias glol='git log --oneline --graph --decorate'
+          alias gc='git commit'
+          alias gl='git pull'
+          alias gp='git push'
+        '';
+        packages =
+          [
+            nv
+            pkgs.git
+            pkgs.pre-commit
+            pkgs.nushell
+          ]
+          # ── R toolchain (R REPL, quarto, LSP, formatter) ─────
+          ++ pkgs.lib.optionals cats.r (let
+            r_packages = (pkgs.baseRPackages or []) ++ rPackages pkgs;
+          in [
+            (pkgs.rWrapper.override {packages = r_packages;})
+            pkgs.radianWrapper
+            pkgs.air-formatter
+            pkgs.yaml-language-server
+            pkgs.nvimcom
+            pkgs.rnvimserver
+          ])
+          # ── Python toolchain (interpreter, LSP, formatter) ────
+          ++ pkgs.lib.optionals cats.python [
+            (pkgs.python3.withPackages (ps: pkgs.basePythonPackages ps ++ pythonPackages pkgs))
+            pkgs.nodejs
+            pkgs.ruff
+            pkgs.basedpyright
+            pkgs.uv
+          ]
+          # ── Julia toolchain ───────────────────────────────────
+          ++ pkgs.lib.optionals cats.julia [
+            pkgs.julia-bin.withPackages
+            juliaPackages
+          ]
+          # ── Markdown toolchain (quarto, zk) ───────────────────
+          ++ (let
+            r_packages = (pkgs.baseRPackages or []) ++ rPackages pkgs;
+            quarto =
+              if cats.r
+              then pkgs.quarto.override {extraRPackages = r_packages;}
+              else pkgs.quarto;
+          in
+            pkgs.lib.optionals cats.markdown [
+              pkgs.python313Packages.pylatexenc
+              quarto
+              pkgs.zk
+            ]);
       };
     });
   };
 
   inputs = {
     nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
-    rixpkgs.url = "github:dwinkler1/rixpkgs/nixpkgs";
+    rixpkgs.url = "github:dwinkler1/rixpkgs/af2dd3f7b4b172077747c0869d4e30702fb71b0e";
     fran = {
       url = "github:dwinkler1/fran";
       inputs = {
@@ -128,12 +197,7 @@
         rixpkgs.follows = "rixpkgs";
         nixpkgs.follows = "nixpkgs";
         fran.follows = "fran";
-        "plugins-r".follows = "plugins-r";
       };
     };
-    "plugins-r" = {
-      url = "github:R-nvim/R.nvim/v0.99.3";
-      flake = false;
-    };
   };
 }