fix: enable full Quarto support when R is activated

Agent-Logs-Url: https://github.com/dwinkler1/np/sessions/8f21e9a2-22be-44c9-aa37-bc4fd64b20a3

Co-authored-by: dwinkler1 <22460147+dwinkler1@users.noreply.github.com>

.github/workflows/update.yml

@@ -22,6 +22,7 @@ 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

@@ -1,73 +0,0 @@
-# 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": 1778869304,
+        "lastModified": 1776877367,
-        "narHash": "sha256-30sZNZoA1cqF5JNO9fVX+wgiQYjB7HJqqJ4ztCDeBZE=",
+        "narHash": "sha256-EHq1/OX139R1RvBzOJ0aMRT3xnWyqtHBRUBuO1gFzjI=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "d233902339c02a9c334e7e593de68855ad26c4cb",
+        "rev": "0726a0ecb6d4e08f6adced58726b95db924cef57",
         "type": "github"
       },
       "original": {
@@ -45,19 +45,20 @@
           "nixpkgs"
         ],
         "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references",
-        "plugins-r": "plugins-r",
+        "plugins-r": [
-        "r-nvim-nix": "r-nvim-nix",
+          "plugins-r"
+        ],
         "rixpkgs": [
           "rixpkgs"
         ],
         "wrappers": "wrappers"
       },
       "locked": {
-        "lastModified": 1779362150,
+        "lastModified": 1776413627,
-        "narHash": "sha256-y3JTpxmNgtEYG1m21Ymvdmrul/WvJzOCX45AlV21aak=",
+        "narHash": "sha256-pU3u7T4MqpjUWxflNvd4i47FURp756L7nMRL8MV+QEw=",
         "owner": "dwinkler1",
         "repo": "nvimConfig",
-        "rev": "af6d975129768cce36ac4c46198ab2b3ebaafad3",
+        "rev": "2617face3b1be40534d2cae7f0a374a062b3710d",
         "type": "github"
       },
       "original": {
@@ -85,45 +86,20 @@
     "plugins-r": {
       "flake": false,
       "locked": {
-        "lastModified": 1776905071,
+        "lastModified": 1769881528,
-        "narHash": "sha256-dXox6qEs1VDE7vPNDoN8bY4g06uj1IEs6uki72w8lpA=",
+        "narHash": "sha256-oQSHHu6filJkAyH94yEvyTVuxA+5MU2dMOEAnsIjJKQ=",
         "owner": "R-nvim",
         "repo": "R.nvim",
-        "rev": "582f2af11290ac067e49018db38e12a511325556",
+        "rev": "958b472d763cb258927c7ef69af4fd9945cc5469",
         "type": "github"
       },
       "original": {
         "owner": "R-nvim",
-        "ref": "v0.99.4",
+        "ref": "v0.99.3",
         "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,
@@ -135,8 +111,8 @@
       },
       "original": {
         "owner": "dwinkler1",
+        "ref": "nixpkgs",
         "repo": "rixpkgs",
-        "rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e",
         "type": "github"
       }
     },
@@ -145,6 +121,7 @@
         "fran": "fran",
         "nixpkgs": "nixpkgs",
         "nvimConfig": "nvimConfig",
+        "plugins-r": "plugins-r",
         "rixpkgs": "rixpkgs"
       }
     },
@@ -156,11 +133,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1779297405,
+        "lastModified": 1776375800,
-        "narHash": "sha256-VFoBwH7ZjVxCnvZTb5ODRXt70sLtWMxstive0N+RS50=",
+        "narHash": "sha256-/SSAR77Brr9fbapsh1cb2K47JXCbvwS1GjM4yyDxle8=",
         "owner": "BirdeeHub",
         "repo": "nix-wrapper-modules",
-        "rev": "e7ed7a1205945befdf2e0d73ba7df91d935e5af1",
+        "rev": "f11469ca69068bac13d9e163b2bd268cc06dff57",
         "type": "github"
       },
       "original": {

templates/ed/flake.nix

@@ -7,8 +7,7 @@
     nvimConfig,
     ...
   } @ inputs: let
-    # ── Shared language support flags ──────────────────────────────
+    projectSettings = {pkgs}: {
-    # Used by both the neovim wrapper module and the devShell
       cats = {
         clickhouse = false;
         gitPlugins = false;
@@ -21,23 +20,12 @@
         r = false;
       };
 
-    # ── Language package lists ────────────────────────────────────
+      settings = let
-    # Shared between wrapper lang_packages and devShell toolchains.
+        # With `replace` packages are replaced otherwise they are merged with base packages
-    # Accept pkgs so they work inside forAllSystems for each system.
+        replace = pkgs.lib.mkForce;
-
+      in {
-    rPackages = pkgs:
+        lang_packages = {
-      (with pkgs.rpkgs.rPackages; [
+          python = replace (
-        fixest
-        # pkgs.extraRPackages.musicMetadata
-      ])
-      ++ (
-        if builtins.pathExists ./r-packages.nix
-        # p: with p.rPackages; [ ... ]
-        then import ./r-packages.nix pkgs.rpkgs
-        else []
-      );
-
-    pythonPackages = pkgs:
             (with pkgs.python3Packages; [
               duckdb
               polars
@@ -47,52 +35,44 @@
               # p: with p; [ ... ]
               then import ./python-packages.nix pkgs.python3Packages
               else []
+            )
           );
 
-    juliaPackages =
+          r = replace (
-      ["StatsBase"]
+            (with pkgs.rpkgs.rPackages; [
+              fixest
+              # pkgs.extraRPackages.musicMetadata
+            ])
+            ++ (
+              if builtins.pathExists ./r-packages.nix
+              # p: with p.rPackages; [ ... ]
+              then import ./r-packages.nix pkgs.rpkgs
+              else []
+            )
+          );
+
+          julia = replace ([
+              "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 = "nv";
+      binName = "vv";
 
       env = {
         IS_PROJECT_EDITOR = "1";
+        R_LIBS_USER = "./.nvimcom";
       };
 
-        runtimePkgs = with pkgs; [
+      extraPackages = with pkgs; [
         cowsay
       ];
 
@@ -108,83 +88,34 @@
         '';
       };
     };
-      evalResult = nvimConfig.inputs.wrappers.lib.evalModules {
+
-        modules = [
+    systems = nixpkgs.lib.systems.flakeExposed;
-          nvimConfig.wrapperModules.default
+    forAllSystems = nixpkgs.lib.genAttrs systems;
-          projectSettings
+    overlays = [inputs.nvimConfig.overlays.dependencies];
-        ];
-      };
   in {
-      default = evalResult.config.wrap {inherit pkgs;};
+    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;
     });
 
     devShells = forAllSystems (system: let
-      pkgs = import nixpkgs {
+      pkgs = import nixpkgs {inherit system overlays;};
-        inherit system overlays;
-        config = {allowUnfree = true;};
-      };
       nv = self.packages.${system}.default;
     in {
       default = pkgs.mkShell {
-        shellHook = ''
+        packages = [nv pkgs.updateR];
-          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/af2dd3f7b4b172077747c0869d4e30702fb71b0e";
+    rixpkgs.url = "github:dwinkler1/rixpkgs/nixpkgs";
     fran = {
       url = "github:dwinkler1/fran";
       inputs = {
@@ -197,7 +128,12 @@
         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;
+    };
   };
 }

templates/rde/flake.nix

@@ -185,6 +185,10 @@
                     julia = config.enabledLanguages.julia;
                     python = config.enabledLanguages.python;
                     r = config.enabledLanguages.r;
+                    # Enable markdown/quarto plugins whenever R is active so that
+                    # .qmd buffers get proper syntax highlighting and chunk
+                    # recognition via quarto-nvim and otter-nvim.
+                    markdown = config.enabledLanguages.r;
                     project = true;
                     gitPlugins = config.enabledPackages.gitPlugins;
                     background = config.theme.background;
@@ -202,11 +206,22 @@
     # Development shell configuration
     devShells = forSystems (system: let
       pkgs = import nixpkgs {inherit system;};
+      # When R is enabled, build an overlaid pkgs that includes the R-enhanced
+      # quarto (with knitr and other R packages baked in via extraRPackages).
+      # This ensures `quarto render` from the terminal also works correctly.
+      rPkgs =
+        if config.enabledLanguages.r
+        then
+          import nixpkgs {
+            inherit system;
+            overlays = [rixOverlay rOverlay];
+          }
+        else pkgs;
       # Language-specific packages that should be available in shell
-      languagePackages = with pkgs;
+      languagePackages =
         []
-        ++ (if config.enabledLanguages.r then [quarto] else [])
+        ++ (if config.enabledLanguages.r then [rPkgs.quarto] else [])
-        ++ (if config.enabledLanguages.python then [uv] else [])
+        ++ (if config.enabledLanguages.python then [pkgs.uv] else [])
         ++ (if config.enabledLanguages.julia then [] else []);
     in {
       default = pkgs.mkShell {

templates/rde/overlays/r.nix

@@ -18,8 +18,10 @@ final: prev: let
       broom         # Tidy model outputs
       data_table    # Fast data manipulation
       janitor       # Data cleaning helpers
+      knitr         # Required by Quarto to execute R code chunks
       languageserver # LSP for IDE support
       reprex        # Reproducible examples
+      rmarkdown     # Required by Quarto for R-based rendering
       styler        # Code formatting
       tidyverse     # Data science ecosystem
     ]