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>
2026-05-22 21:23:31 -04:00 · 2026-04-29 06:25:26 +00:00
6 changed files with 130 additions and 272 deletions
--- a/.github/workflows/update.yml
+++ b/.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:
--- a/templates/ed/README.md
+++ b/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.
--- a/templates/ed/flake.lock
+++ b/templates/ed/flake.lock
@ -22,11 +22,11 @@
    },
    "nixpkgs": {
      "locked": {
-        "lastModified": 1778869304,
-        "narHash": "sha256-30sZNZoA1cqF5JNO9fVX+wgiQYjB7HJqqJ4ztCDeBZE=",
+        "lastModified": 1776877367,
+        "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",
-        "r-nvim-nix": "r-nvim-nix",
+        "plugins-r": [
+          "plugins-r"
+        ],
        "rixpkgs": [
          "rixpkgs"
        ],
        "wrappers": "wrappers"
      },
      "locked": {
-        "lastModified": 1779362150,
-        "narHash": "sha256-y3JTpxmNgtEYG1m21Ymvdmrul/WvJzOCX45AlV21aak=",
+        "lastModified": 1776413627,
+        "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,
-        "narHash": "sha256-dXox6qEs1VDE7vPNDoN8bY4g06uj1IEs6uki72w8lpA=",
+        "lastModified": 1769881528,
+        "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,
-        "narHash": "sha256-VFoBwH7ZjVxCnvZTb5ODRXt70sLtWMxstive0N+RS50=",
+        "lastModified": 1776375800,
+        "narHash": "sha256-/SSAR77Brr9fbapsh1cb2K47JXCbvwS1GjM4yyDxle8=",
        "owner": "BirdeeHub",
        "repo": "nix-wrapper-modules",
-        "rev": "e7ed7a1205945befdf2e0d73ba7df91d935e5af1",
+        "rev": "f11469ca69068bac13d9e163b2bd268cc06dff57",
        "type": "github"
      },
      "original": {
--- a/templates/ed/flake.nix
+++ b/templates/ed/flake.nix
@ -7,184 +7,115 @@
    nvimConfig,
    ...
  } @ inputs: let
-    # ── Shared language support flags ──────────────────────────────
-    # Used by both the neovim wrapper module and the devShell
-    cats = {
-      clickhouse = false;
-      gitPlugins = false;
-      julia = false;
-      lua = false;
-      markdown = false;
-      nix = true;
-      optional = false;
-      python = false;
-      r = false;
+    projectSettings = {pkgs}: {
+      cats = {
+        clickhouse = false;
+        gitPlugins = false;
+        julia = false;
+        lua = false;
+        markdown = false;
+        nix = true;
+        optional = false;
+        python = false;
+        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 []
+            )
+          );
+
+          r = replace (
+            (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 []
+            ));
+        };
+        colorscheme = "kanagawa";
+        background = "dark";
+        wrapRc = true;
+      };
+      binName = "vv";
+
+      env = {
+        IS_PROJECT_EDITOR = "1";
+        R_LIBS_USER = "./.nvimcom";
+      };
+
+      extraPackages = with pkgs; [
+        cowsay
+      ];
+
+      specs.extraLua = let
+        name = builtins.baseNameOf (builtins.toString ./.);
+      in {
+        data = pkgs.vimPlugins.mini-notify;
+        before = ["INIT_MAIN"];
+        config = ''
+          require("mini.notify").setup()
+          vim.notify = MiniNotify.make_notify()
+          vim.notify("Welcome to ${name}!")
+        '';
+      };
    };

-    # ── Language package lists ────────────────────────────────────
-    # Shared between wrapper lang_packages and devShell toolchains.
-    # Accept pkgs so they work inside forAllSystems for each system.
-
-    rPackages = pkgs:
-      (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 []
-      );
-
-    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"];
+    systems = nixpkgs.lib.systems.flakeExposed;
    forAllSystems = nixpkgs.lib.genAttrs systems;
    overlays = [inputs.nvimConfig.overlays.dependencies];
  in {
-    formatter = forAllSystems (system: nixpkgs.legacyPackages.${system}.nixfmt-rfc-style);
-
    packages = forAllSystems (system: let
-      pkgs = import nixpkgs {
-        inherit system overlays;
-        config = {allowUnfree = true;};
-      };
-      # Plain attrset — pkgs is captured from the surrounding scope,
-      # so the module system does not need lazy _module.args resolution.
-      projectSettings = {
-        inherit cats;
-        settings = let
-          # With `replace` packages are replaced otherwise they are merged with base packages
-          replace = pkgs.lib.mkForce;
-        in {
-          lang_packages = {
-            python = replace (pythonPackages pkgs);
-            r = replace (rPackages pkgs);
-            julia = replace juliaPackages;
-          };
-          colorscheme = "kanagawa";
-          background = "dark";
-          wrapRc = true;
-        };
-        binName = "nv";
+      pkgs = import nixpkgs {inherit system overlays;};
+      baseNvim = nvimConfig.packages.${system}.default;

-        env = {
-          IS_PROJECT_EDITOR = "1";
-        };
-
-        runtimePkgs = with pkgs; [
-          cowsay
-        ];
-
-        specs.extraLua = let
-          name = builtins.baseNameOf (builtins.toString ./.);
-        in {
-          data = pkgs.vimPlugins.mini-notify;
-          before = ["INIT_MAIN"];
-          config = ''
-            require("mini.notify").setup()
-            vim.notify = MiniNotify.make_notify()
-            vim.notify("Welcome to ${name}!")
-          '';
-        };
-      };
-      evalResult = nvimConfig.inputs.wrappers.lib.evalModules {
-        modules = [
-          nvimConfig.wrapperModules.default
-          projectSettings
-        ];
-      };
+      nvim = (baseNvim.eval (projectSettings {inherit pkgs;})).config.wrapper;
+      default = nvim;
    in {
-      default = evalResult.config.wrap {inherit pkgs;};
+      default = nvim;
    });

    devShells = forAllSystems (system: let
-      pkgs = import nixpkgs {
-        inherit system overlays;
-        config = {allowUnfree = true;};
-      };
+      pkgs = import nixpkgs {inherit system overlays;};
      nv = self.packages.${system}.default;
    in {
      default = pkgs.mkShell {
-        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
-            ]);
+        packages = [nv pkgs.updateR];
      };
    });
  };

  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;
+    };
  };
 }
--- a/templates/rde/flake.nix
+++ b/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.python then [uv] else [])
+        ++ (if config.enabledLanguages.r then [rPkgs.quarto] else [])
+        ++ (if config.enabledLanguages.python then [pkgs.uv] else [])
        ++ (if config.enabledLanguages.julia then [] else []);
    in {
      default = pkgs.mkShell {
--- a/templates/rde/overlays/r.nix
+++ b/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
    ]