julia test not working

.github/workflows/check.yml

@@ -1,20 +1,6 @@
 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

@@ -1,9 +1,16 @@
-name: "Test ed template MacOS"
+name: "Test ed template"
 on:
-  workflow_dispatch: # allows manual triggering
+  workflow_dispatch:
   push:
-    branches:
+    paths:
-      - 'update_rde'
+      - 'templates/ed/**'
+      - '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
@@ -12,15 +19,105 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-latest, ubuntu-latest]
+        os: [ubuntu-latest]
     steps:
     - uses: actions/checkout@v6
     - uses: cachix/install-nix-action@v31
       with:
-        github_access_token: ${{ secrets.GITHUB_TOKEN }}
+        github_access_token: ${{ github.token }}
     - uses: cachix/cachix-action@v17
       with:
         name: rde
         authToken: '${{ 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_rde'
+      - 'update_ed'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -23,5 +23,4 @@ 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_rde
+          branch: update_ed
           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 +1,2 @@
 .nvimcom
+.commandcode/

templates/ed/flake.lock

@@ -22,15 +22,15 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1778869304,
+        "lastModified": 1779357205,
-        "narHash": "sha256-30sZNZoA1cqF5JNO9fVX+wgiQYjB7HJqqJ4ztCDeBZE=",
+        "narHash": "sha256-cCO8aTqss5x9Ky8GWkpY0Hy5fyTZEbtifSUV8QjSzic=",
-        "owner": "NixOS",
+        "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "d233902339c02a9c334e7e593de68855ad26c4cb",
+        "rev": "f83fc3c307e74bc5fd5adb7eb6b8b13ffd2a36e1",
         "type": "github"
       },
       "original": {
-        "owner": "NixOS",
+        "owner": "nixos",
         "ref": "nixos-unstable",
         "repo": "nixpkgs",
         "type": "github"
@@ -45,7 +45,6 @@
           "nixpkgs"
         ],
         "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references",
-        "plugins-r": "plugins-r",
         "r-nvim-nix": "r-nvim-nix",
         "rixpkgs": [
           "rixpkgs"
@@ -53,11 +52,11 @@
         "wrappers": "wrappers"
       },
       "locked": {
-        "lastModified": 1779362150,
+        "lastModified": 1779544872,
-        "narHash": "sha256-y3JTpxmNgtEYG1m21Ymvdmrul/WvJzOCX45AlV21aak=",
+        "narHash": "sha256-AnuNQ9nbXrDYmL97TOejAds/FQOgD6FEOHABp/8dmsU=",
         "owner": "dwinkler1",
         "repo": "nvimConfig",
-        "rev": "af6d975129768cce36ac4c46198ab2b3ebaafad3",
+        "rev": "aec9110e709e1aa50d78f06293c4bde14974b23f",
         "type": "github"
       },
       "original": {
@@ -82,44 +81,25 @@
         "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": 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"
       }
@@ -140,6 +120,23 @@
         "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",

templates/ed/flake.nix

@@ -6,196 +6,154 @@
     nixpkgs,
     nvimConfig,
     ...
-  } @ inputs: let
+  }: 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;
-    };
-
-    # ── 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"];
     forAllSystems = nixpkgs.lib.genAttrs systems;
-    overlays = [inputs.nvimConfig.overlays.dependencies];
+
+    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;
+        julia = false;
+        lua = false;
+        markdown = false;
+        nix = true;
+        optional = false;
+        python = false;
+        r = true;
+      };
+
+      settings = {
+        lang_packages = {
+          python = with pkgs.python3Packages;
+            [
+              requests
+            ]
+            ++ extraPythonPackages;
+
+          r =
+            (with pkgs.rpkgs.rPackages; [
+              arrow
+              data_table
+              fixest
+              pkgs.nvimcom
+            ])
+            ++ extraRPackages;
+
+          julia =
+            ["StatsBase"]
+            ++ extraJuliaPackages;
+        };
+
+        colorscheme = "tokyonight"; #"kanagawa";
+        background = "dark";
+        wrapRc = true;
+      };
+
+      binName = "nv";
+
+      env.IS_PROJECT_EDITOR = "1";
+
+      catPkgs = {
+        always = [
+          pkgs.git
+          pkgs.pre-commit
+          pkgs.cowsay
+        ];
+
+        nix = [
+          pkgs.nil
+          pkgs.nixfmt
+        ];
+      };
+
+      specs.extraLua = {
+        before = ["INIT_MAIN"];
+        data = pkgs.writeText "project-startup.lua" ''
+          require("mini.notify").setup()
+          vim.notify = MiniNotify.make_notify()
+          vim.notify("Welcome to ${projectName}!")
+        '';
+      };
+    };
   in {
-    formatter = forAllSystems (system: nixpkgs.legacyPackages.${system}.nixfmt-rfc-style);
+    formatter = forAllSystems (system: (mkPkgs system).nixfmt-tree);
 
     packages = forAllSystems (system: let
-      pkgs = import nixpkgs {
+      pkgs = mkPkgs system;
-        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";
-        };
-
-        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
-        ];
-      };
     in {
-      default = evalResult.config.wrap {inherit pkgs;};
+      default = nvimConfig.lib.mkWrapper {
+        inherit pkgs;
+        modules = [(projectModule pkgs)];
+      };
     });
 
     devShells = forAllSystems (system: let
-      pkgs = import nixpkgs {
+      pkgs = mkPkgs system;
-        inherit system overlays;
+      evalResult = nvimConfig.lib.eval {
-        config = {allowUnfree = true;};
+        inherit pkgs;
+        modules = [(projectModule pkgs)];
       };
-      nv = self.packages.${system}.default;
+      nv = evalResult.config.wrap {inherit pkgs;};
     in {
       default = pkgs.mkShell {
-        shellHook = ''
-          exec nu
-          alias gst='git status'
-          alias glol='git log --oneline --graph --decorate'
-          alias gc='git commit'
-          alias gl='git pull'
-          alias gp='git push'
-        '';
         packages =
           [
             nv
-            pkgs.git
-            pkgs.pre-commit
             pkgs.nushell
           ]
-          # ── R toolchain (R REPL, quarto, LSP, formatter) ─────
+          ++ nvimConfig.lib.devShellPackages evalResult.config;
-          ++ pkgs.lib.optionals cats.r (let
+        shellHook =
-            r_packages = (pkgs.baseRPackages or []) ++ rPackages pkgs;
+          nvimConfig.lib.shellHook evalResult.config
-          in [
+          + ''
-            (pkgs.rWrapper.override {packages = r_packages;})
+            if [ -z "''${NO_NUSHELL:-}" ]; then
-            pkgs.radianWrapper
+              exec nu
-            pkgs.air-formatter
+            fi
-            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 = {
+      inputs.nixpkgs.follows = "rixpkgs";
-        nixpkgs.follows = "rixpkgs";
-      };
     };
+
     nvimConfig = {
       url = "github:dwinkler1/nvimConfig";
       inputs = {
-        rixpkgs.follows = "rixpkgs";
         nixpkgs.follows = "nixpkgs";
+        rixpkgs.follows = "rixpkgs";
         fran.follows = "fran";
       };
     };

tests/ed/test.R

@@ -0,0 +1,29 @@
+#!/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

@@ -0,0 +1,19 @@
+#!/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

@@ -0,0 +1,17 @@
+#!/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")