flake.lock: Update

Flake lock file updates:

• Updated input 'nixpkgs':
    'github:NixOS/nixpkgs/d233902339c02a9c334e7e593de68855ad26c4cb?narHash=sha256-30sZNZoA1cqF5JNO9fVX%2BwgiQYjB7HJqqJ4ztCDeBZE%3D' (2026-05-15)
  → 'github:NixOS/nixpkgs/f83fc3c307e74bc5fd5adb7eb6b8b13ffd2a36e1?narHash=sha256-cCO8aTqss5x9Ky8GWkpY0Hy5fyTZEbtifSUV8QjSzic%3D' (2026-05-21)
• Updated input 'nvimConfig':
    'github:dwinkler1/nvimConfig/af6d975129768cce36ac4c46198ab2b3ebaafad3?narHash=sha256-y3JTpxmNgtEYG1m21Ymvdmrul/WvJzOCX45AlV21aak%3D' (2026-05-21)
  → 'github:dwinkler1/nvimConfig/15efa3299a488acff7065843c1824d3dbfbdc193?narHash=sha256-R/tHAUf5XVuykMNvuOjeBizk/m%2BlWI7m1U2tAYIqaJs%3D' (2026-05-23)
• Updated input 'nvimConfig/r-nvim-nix':
    'github:dwinkler1/r_nvim_nix/2f49dfee27886068e2f49cbd54558ce4cc424c82?narHash=sha256-Z4y1tQfkIsPK4NRxGn668HMDfWxnxNxSJ0CAOOXiIfY%3D' (2026-05-13)
  → 'github:dwinkler1/r_nvim_nix/a012c98b5cc6a8ce59d461825c71b4877f934056?narHash=sha256-OX3/QTVOq5o3DD6dNzNY8X2v/7ZtbQOM01Z8bVf5tHc%3D' (2026-05-22)
• Updated input 'nvimConfig/wrappers':
    'github:BirdeeHub/nix-wrapper-modules/e7ed7a1205945befdf2e0d73ba7df91d935e5af1?narHash=sha256-VFoBwH7ZjVxCnvZTb5ODRXt70sLtWMxstive0N%2BRS50%3D' (2026-05-20)
  → 'github:BirdeeHub/nix-wrapper-modules/8c90cbe3aaae094370b08f270682fc352fcbcb91?narHash=sha256-Y2S3mvEezyKL/A4XUkgVbhuvob9YKfnG25NuJDl8fuQ%3D' (2026-05-23)

.github/workflows/check.yml

@@ -1,6 +1,20 @@
 name: "Test RDE template"
 on:
   workflow_dispatch: # allows manual triggering
+  push:
+    paths:
+      - 'templates/rde/flake.lock'
+      - 'templates/rde/**/*.nix'
+      - 'templates/rde/**/*.sh'
+      - 'templates/rde/**/*.lua'
+      - '.github/workflows/check.yml'
+  pull_request:
+    paths:
+      - 'templates/rde/flake.lock'
+      - 'templates/rde/**/*.nix'
+      - 'templates/rde/**/*.sh'
+      - 'templates/rde/**/*.lua'
+      - '.github/workflows/check.yml'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true

.github/workflows/check_ed.yml

@@ -1,16 +1,9 @@
-name: "Test ed template"
+name: "Test ed template MacOS"
 on:
-  workflow_dispatch:
+  workflow_dispatch: # allows manual triggering
   push:
-    paths:
+    branches:
-      - 'templates/ed/**'
+      - 'update_rde'
-      - 'tests/ed/**'
-      - '.github/workflows/check_ed.yml'
-  pull_request:
-    paths:
-      - 'templates/ed/**'
-      - 'tests/ed/**'
-      - '.github/workflows/check_ed.yml'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -19,105 +12,15 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest]
+        os: [macos-latest, ubuntu-latest]
     steps:
     - uses: actions/checkout@v6
     - uses: cachix/install-nix-action@v31
       with:
-        github_access_token: ${{ github.token }}
+        github_access_token: ${{ secrets.GITHUB_TOKEN }}
     - uses: cachix/cachix-action@v17
       with:
         name: rde
         authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
         extraPullNames: rstats-on-nix, nix-community
-
+    - run: nix build ./templates/ed
-    - name: Build template
-      run: nix build ./templates/ed
-
-    - name: Test R script
-      env:
-        NO_NUSHELL: '1'
-      run: |
-        cd templates/ed
-        nix develop --command bash -c "Rscript ${{ github.workspace }}/tests/ed/test.R"
-
-    - name: Test Python script (disabled by default)
-      env:
-        NO_NUSHELL: '1'
-      run: |
-        cd templates/ed
-        nix develop --command bash -c "python3 ${{ github.workspace }}/tests/ed/test.py" || echo "SKIP: Python packages not enabled"
-
-  test-with-python:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v6
-    - uses: cachix/install-nix-action@v31
-      with:
-        github_access_token: ${{ github.token }}
-    - uses: cachix/cachix-action@v17
-      with:
-        name: rde
-        authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
-        extraPullNames: rstats-on-nix, nix-community
-
-    - name: Setup test directory with Python enabled
-      run: |
-        TEST_DIR=$(mktemp -d)
-        cp -r templates/ed/. "$TEST_DIR/"
-        cd "$TEST_DIR"
-        sed -i 's/python[[:space:]]*=[[:space:]]*false;/python = true;/' flake.nix
-        grep -q "python[[:space:]]*=[[:space:]]*true;" flake.nix || {
-          echo "Error: Failed to enable Python in flake.nix"
-          exit 1
-        }
-        echo "TEST_DIR=$TEST_DIR" >> $GITHUB_ENV
-
-    - name: Build with Python enabled
-      run: |
-        cd "$TEST_DIR"
-        nix build
-
-    - name: Test Python packages
-      env:
-        NO_NUSHELL: '1'
-      run: |
-        cd "$TEST_DIR"
-        nix develop --command bash -c "python3 ${{ github.workspace }}/tests/ed/test.py"
-
-  test-with-julia:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v6
-    - uses: cachix/install-nix-action@v31
-      with:
-        github_access_token: ${{ github.token }}
-    - uses: cachix/cachix-action@v17
-      with:
-        name: rde
-        authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
-        extraPullNames: rstats-on-nix, nix-community
-
-    - name: Setup test directory with Julia enabled
-      run: |
-        TEST_DIR=$(mktemp -d)
-        cp -r templates/ed/. "$TEST_DIR/"
-        cd "$TEST_DIR"
-        sed -i 's/julia[[:space:]]*=[[:space:]]*false;/julia = true;/' flake.nix
-        grep -q "julia[[:space:]]*=[[:space:]]*true;" flake.nix || {
-          echo "Error: Failed to enable Julia in flake.nix"
-          exit 1
-        }
-        echo "TEST_DIR=$TEST_DIR" >> $GITHUB_ENV
-
-    - name: Build with Julia enabled
-      run: |
-        cd "$TEST_DIR"
-        nix build
-
-    - name: Test Julia packages
-      env:
-        NO_NUSHELL: '1'
-      run: |
-        cd "$TEST_DIR"
-        # nix develop --command bash -c "julia ${{ github.workspace }}/tests/ed/test.jl"

.github/workflows/check_macos.yml

@@ -3,7 +3,7 @@ on:
   workflow_dispatch: # allows manual triggering
   push:
     branches:
-      - 'update_ed'
+      - 'update_rde'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -23,4 +23,5 @@ jobs:
         name: rde
         authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
         extraPullNames: rstats-on-nix, nix-community
+    - run: nix build ./templates/rde
     - run: nix build ./templates/ed

.github/workflows/update.yml

@@ -26,7 +26,7 @@ jobs:
         uses: DeterminateSystems/update-flake-lock@v28
         with:
           token: ${{ secrets.GH_TOKEN_FOR_UPDATES }}
-          branch: update_ed
+          branch: update_rde
           path-to-flake-dir: "templates/ed"
           pr-title: "Update RDE flake.lock" # Title of PR to be created
           pr-labels: |                  # Labels to be set on the PR

templates/ed/.gitignore

@@ -1,2 +1 @@
 .nvimcom
-.commandcode/

templates/ed/flake.lock

@@ -22,15 +22,15 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1779560665,
+        "lastModified": 1779357205,
-        "narHash": "sha256-tpyBcxPpcQb8ukyNF7DoCwfSY3VPsxHoYwj00Cayv5o=",
+        "narHash": "sha256-cCO8aTqss5x9Ky8GWkpY0Hy5fyTZEbtifSUV8QjSzic=",
-        "owner": "nixos",
+        "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "64c08a7ca051951c8eae34e3e3cb1e202fe36786",
+        "rev": "f83fc3c307e74bc5fd5adb7eb6b8b13ffd2a36e1",
         "type": "github"
       },
       "original": {
-        "owner": "nixos",
+        "owner": "NixOS",
         "ref": "nixos-unstable",
         "repo": "nixpkgs",
         "type": "github"
@@ -45,6 +45,7 @@
           "nixpkgs"
         ],
         "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references",
+        "plugins-r": "plugins-r",
         "r-nvim-nix": "r-nvim-nix",
         "rixpkgs": [
           "rixpkgs"
@@ -52,11 +53,11 @@
         "wrappers": "wrappers"
       },
       "locked": {
-        "lastModified": 1779544872,
+        "lastModified": 1779519005,
-        "narHash": "sha256-AnuNQ9nbXrDYmL97TOejAds/FQOgD6FEOHABp/8dmsU=",
+        "narHash": "sha256-R/tHAUf5XVuykMNvuOjeBizk/m+lWI7m1U2tAYIqaJs=",
         "owner": "dwinkler1",
         "repo": "nvimConfig",
-        "rev": "aec9110e709e1aa50d78f06293c4bde14974b23f",
+        "rev": "15efa3299a488acff7065843c1824d3dbfbdc193",
         "type": "github"
       },
       "original": {
@@ -81,25 +82,44 @@
         "type": "github"
       }
     },
+    "plugins-r": {
+      "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"
+      }
+    },
     "r-nvim-nix": {
       "inputs": {
         "nixpkgs": [
           "nvimConfig",
           "rixpkgs"
         ],
-        "rnvimsrc": "rnvimsrc"
+        "rnvimsrc": [
+          "nvimConfig",
+          "plugins-r"
+        ]
       },
       "locked": {
-        "lastModified": 1779438909,
+        "lastModified": 1779439280,
-        "narHash": "sha256-1lvv0bdvSVyeCIgeZ7Ws7ffbDFurA5LJscS9dRLHzC8=",
+        "narHash": "sha256-OX3/QTVOq5o3DD6dNzNY8X2v/7ZtbQOM01Z8bVf5tHc=",
         "owner": "dwinkler1",
         "repo": "r_nvim_nix",
-        "rev": "ec17e22ab362a0ddfd6c2e9c5e95d43897a143be",
+        "rev": "a012c98b5cc6a8ce59d461825c71b4877f934056",
         "type": "github"
       },
       "original": {
         "owner": "dwinkler1",
-        "ref": "v0.99.4",
         "repo": "r_nvim_nix",
         "type": "github"
       }
@@ -120,23 +140,6 @@
         "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",
@@ -153,11 +156,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1779297405,
+        "lastModified": 1779512817,
-        "narHash": "sha256-VFoBwH7ZjVxCnvZTb5ODRXt70sLtWMxstive0N+RS50=",
+        "narHash": "sha256-Y2S3mvEezyKL/A4XUkgVbhuvob9YKfnG25NuJDl8fuQ=",
         "owner": "BirdeeHub",
         "repo": "nix-wrapper-modules",
-        "rev": "e7ed7a1205945befdf2e0d73ba7df91d935e5af1",
+        "rev": "8c90cbe3aaae094370b08f270682fc352fcbcb91",
         "type": "github"
       },
       "original": {

templates/ed/flake.nix

@@ -6,36 +6,9 @@
     nixpkgs,
     nvimConfig,
     ...
-  }: let
+  } @ inputs: let
-    systems = ["aarch64-darwin" "x86_64-linux" "aarch64-linux"];
+    # ── Shared language support flags ──────────────────────────────
-    forAllSystems = nixpkgs.lib.genAttrs systems;
+    # Used by both the neovim wrapper module and the devShell
-
-    mkPkgs = system:
-      import nixpkgs {
-        inherit system;
-        config.allowUnfree = true;
-        overlays = [nvimConfig.overlays.dependencies];
-      };
-
-    projectModule = pkgs: let
-      baseConfig = nvimConfig.wrapperConfigs.default {inherit pkgs;};
-      extraRPackages =
-        if builtins.pathExists ./r-packages.nix
-        then import ./r-packages.nix pkgs.rpkgs
-        else [];
-
-      extraPythonPackages =
-        if builtins.pathExists ./python-packages.nix
-        then import ./python-packages.nix pkgs.python3Packages
-        else [];
-
-      extraJuliaPackages =
-        if builtins.pathExists ./julia-packages.nix
-        then import ./julia-packages.nix
-        else [];
-
-      projectName = builtins.baseNameOf (toString self.outPath);
-    in {
     cats = {
       clickhouse = false;
       gitPlugins = false;
@@ -45,115 +18,184 @@
       nix = true;
       optional = false;
       python = false;
-        r = true;
+      r = false;
     };
 
-      settings = {
+    # ── Language package lists ────────────────────────────────────
-        lang_packages = {
+    # Shared between wrapper lang_packages and devShell toolchains.
-          python = with pkgs.python3Packages;
+    # Accept pkgs so they work inside forAllSystems for each system.
-            [
-              requests
-            ]
-            ++ extraPythonPackages;
 
-          r =
+    rPackages = pkgs:
       (with pkgs.rpkgs.rPackages; [
-              arrow
-              data_table
         fixest
-              pkgs.nvimcom
+        # pkgs.extraRPackages.musicMetadata
       ])
-            ++ extraRPackages;
+      ++ (
+        if builtins.pathExists ./r-packages.nix
+        # p: with p.rPackages; [ ... ]
+        then import ./r-packages.nix pkgs.rpkgs
+        else []
+      );
 
-          julia =
+    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"]
-            ++ extraJuliaPackages;
+      ++ (
-        };
+        if builtins.pathExists ./julia-packages.nix
+        # [ ... ]
+        then import ./julia-packages.nix
+        else []
+      );
 
-        colorscheme = "tokyonight"; #"kanagawa";
+    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";
 
-      env.IS_PROJECT_EDITOR = "1";
+        env = {
-
+          IS_PROJECT_EDITOR = "1";
-      catPkgs = {
-        always = [
-          pkgs.git
-          pkgs.pre-commit
-          pkgs.cowsay
-        ];
-
-        nix = [
-          pkgs.nil
-          pkgs.nixfmt
-        ];
         };
 
-      specs.extraLua = {
+        runtimePkgs = with pkgs; [
+          cowsay
+        ];
+
+        specs.extraLua = let
+          name = builtins.baseNameOf (builtins.toString ./.);
+        in {
+          data = pkgs.vimPlugins.mini-notify;
           before = ["INIT_MAIN"];
-        data = pkgs.writeText "project-startup.lua" ''
+          config = ''
             require("mini.notify").setup()
             vim.notify = MiniNotify.make_notify()
-          vim.notify("Welcome to ${projectName}!")
+            vim.notify("Welcome to ${name}!")
           '';
         };
       };
-  in {
+      evalResult = nvimConfig.inputs.wrappers.lib.evalModules {
-    formatter = forAllSystems (system: (mkPkgs system).nixfmt-tree);
+        modules = [
-
+          nvimConfig.wrapperModules.default
-    packages = forAllSystems (system: let
+          projectSettings
-      pkgs = mkPkgs system;
+        ];
-    in {
-      default = nvimConfig.lib.mkWrapper {
-        inherit pkgs;
-        modules = [(projectModule pkgs)];
       };
+    in {
+      default = evalResult.config.wrap {inherit pkgs;};
     });
 
     devShells = forAllSystems (system: let
-      pkgs = mkPkgs system;
+      pkgs = import nixpkgs {
-      evalResult = nvimConfig.lib.eval {
+        inherit system overlays;
-        inherit pkgs;
+        config = {allowUnfree = true;};
-        modules = [(projectModule pkgs)];
       };
-      nv = evalResult.config.wrap {inherit pkgs;};
+      nv = self.packages.${system}.default;
     in {
       default = pkgs.mkShell {
+        shellHook = ''
+          exec nu
+          alias gst='git status'
+          alias glol='git log --oneline --graph --decorate'
+          alias gc='git commit'
+          alias gl='git pull'
+          alias gp='git push'
+        '';
         packages =
           [
             nv
+            pkgs.git
+            pkgs.pre-commit
             pkgs.nushell
           ]
-          ++ nvimConfig.lib.devShellPackages evalResult.config;
+          # ── R toolchain (R REPL, quarto, LSP, formatter) ─────
-        shellHook =
+          ++ pkgs.lib.optionals cats.r (let
-          nvimConfig.lib.shellHook evalResult.config
+            r_packages = (pkgs.baseRPackages or []) ++ rPackages pkgs;
-          + ''
+          in [
-            if [ -z "''${NO_NUSHELL:-}" ]; then
+            (pkgs.rWrapper.override {packages = r_packages;})
-              exec nu
+            pkgs.radianWrapper
-            fi
+            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";
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
-
     rixpkgs.url = "github:dwinkler1/rixpkgs/af2dd3f7b4b172077747c0869d4e30702fb71b0e";
-
     fran = {
       url = "github:dwinkler1/fran";
-      inputs.nixpkgs.follows = "rixpkgs";
+      inputs = {
+        nixpkgs.follows = "rixpkgs";
+      };
     };
-
     nvimConfig = {
       url = "github:dwinkler1/nvimConfig";
       inputs = {
-        nixpkgs.follows = "nixpkgs";
         rixpkgs.follows = "rixpkgs";
+        nixpkgs.follows = "nixpkgs";
         fran.follows = "fran";
       };
     };

tests/ed/test.R

@@ -1,29 +0,0 @@
-#!/usr/bin/env Rscript
-
-packages <- c("arrow", "data.table", "fixest", "nvimcom")
-failed <- character(0)
-
-for (pkg in packages) {
-  ok <- tryCatch(
-    {
-      # nvimcom requires Neovim; skip loading but check it's installed
-      if (pkg == "nvimcom") {
-        requireNamespace(pkg, quietly = TRUE)
-      } else {
-        library(pkg, character.only = TRUE, quietly = TRUE)
-      }
-      TRUE
-    },
-    error = function(e) FALSE
-  )
-  if (!ok) {
-    failed <- c(failed, pkg)
-  }
-}
-
-if (length(failed) > 0) {
-  cat(sprintf("FAIL: %s\n", paste(failed, collapse = ", ")))
-  quit(status = 1)
-}
-
-cat("PASS: all packages loaded\n")

tests/ed/test.jl

@@ -1,19 +0,0 @@
-#!/usr/bin/env julia
-
-packages = ["StatsBase"]
-failed = String[]
-
-for pkg in packages
-    try
-        @eval using $pkg
-    catch
-        push!(failed, pkg)
-    end
-end
-
-if !isempty(failed)
-    @error "FAIL: $(join(failed, ", "))"
-    exit(1)
-end
-
-println("PASS: all packages loaded")

tests/ed/test.py

@@ -1,17 +0,0 @@
-#!/usr/bin/env python3
-import sys
-
-packages = ["requests"]
-failed = []
-
-for pkg in packages:
-    try:
-        __import__(pkg)
-    except ImportError:
-        failed.append(pkg)
-
-if failed:
-    sys.stderr.write(f"FAIL: {', '.join(failed)}\n")
-    sys.exit(1)
-
-print("PASS: all packages loaded")