Add permissions block to ED workflow for security

Co-authored-by: dwinkler1 <22460147+dwinkler1@users.noreply.github.com>
Update README with ED template documentation
2026-07-07 17:28:23 -04:00 · 2026-02-16 00:10:00 +00:00 · 2026-02-16 00:07:47 +00:00 · 2026-02-16 00:06:34 +00:00 · 2026-02-16 00:04:18 +00:00
14 changed files with 692 additions and 332 deletions
--- a/.github/workflows/check.yml
+++ b/.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
@ -18,7 +32,7 @@ jobs:
    - uses: cachix/install-nix-action@v31
      with:
        github_access_token: ${{ secrets.GITHUB_TOKEN }}
-    - uses: cachix/cachix-action@v17
+    - uses: cachix/cachix-action@v16
      with:
        name: rde
        authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
@ -111,7 +125,7 @@ jobs:
    - uses: cachix/install-nix-action@v31
      with:
        github_access_token: ${{ secrets.GITHUB_TOKEN }}
-    - uses: cachix/cachix-action@v17
+    - uses: cachix/cachix-action@v16
      with:
        name: rde
        authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
@ -167,7 +181,7 @@ jobs:
    - uses: cachix/install-nix-action@v31
      with:
        github_access_token: ${{ secrets.GITHUB_TOKEN }}
-    - uses: cachix/cachix-action@v17
+    - uses: cachix/cachix-action@v16
      with:
        name: rde
        authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
--- a/.github/workflows/check_ed.yml
+++ b/.github/workflows/check_ed.yml
@ -1,19 +1,21 @@
-name: "Test ed template"
+name: "Test ED template"
 on:
-  workflow_dispatch:
+  workflow_dispatch: # allows manual triggering
  push:
    paths:
-      - 'templates/ed/**'
-      - 'tests/ed/**'
+      - 'templates/ed/flake.lock'
+      - 'templates/ed/**/*.nix'
      - '.github/workflows/check_ed.yml'
  pull_request:
    paths:
-      - 'templates/ed/**'
-      - 'tests/ed/**'
+      - 'templates/ed/flake.lock'
+      - 'templates/ed/**/*.nix'
      - '.github/workflows/check_ed.yml'
 concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true
+permissions:
+  contents: read
 jobs:
  tests:
    runs-on: ${{ matrix.os }}
@ -22,102 +24,257 @@ jobs:
        os: [ubuntu-latest]
    steps:
    - uses: actions/checkout@v6
+    - uses: wimpysworld/nothing-but-nix@main
+      with:
+        hatchet-protocol: 'carve'
    - uses: cachix/install-nix-action@v31
      with:
-        github_access_token: ${{ github.token }}
-    - uses: cachix/cachix-action@v17
+        github_access_token: ${{ secrets.GITHUB_TOKEN }}
+    - uses: cachix/cachix-action@v16
      with:
        name: rde
        authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
        extraPullNames: rstats-on-nix, nix-community
-
+    
+    # Build and basic checks
    - name: Build template
      run: nix build ./templates/ed
-
-    - name: Test R script
-      env:
-        NO_NUSHELL: '1'
+    - name: Run flake check
+      run: nix flake check ./templates/ed
+    
+    # Test development shell functionality
+    - name: Test dev shell enters successfully
      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'
+        nix develop --command bash -c "echo 'Dev shell works'"
+    
+    # Test Neovim functionality (custom binary name: vv)
+    - name: Test vv command is available
      run: |
        cd templates/ed
-        nix develop --command bash -c "python3 ${{ github.workspace }}/tests/ed/test.py" || echo "SKIP: Python packages not enabled"
-
+        nix develop --command bash -c "which vv"
+    
+    - name: Test vv launches in headless mode
+      run: |
+        cd templates/ed
+        nix develop --command bash -c "vv --headless --version"
+    
+    # Test utility commands
+    - name: Test updateR command is available
+      run: |
+        cd templates/ed
+        nix develop --command bash -c "which updateR"
+    
+    # Test extra packages
+    - name: Test cowsay is available
+      run: |
+        cd templates/ed
+        nix develop --command bash -c "which cowsay"
+    
+    - name: Test cowsay works
+      run: |
+        cd templates/ed
+        nix develop --command bash -c "cowsay 'ED template test'"
+    
+    # Test that package is built correctly
+    - name: Test default package can be run
+      run: |
+        cd templates/ed
+        nix run . -- --headless --version
+    
+    # Test Neovim configuration
+    - name: Test mini-notify plugin loads
+      run: |
+        cd templates/ed
+        # Check that the welcome notification config is present
+        nix develop --command bash -c "vv --headless -c 'lua print(vim.inspect(require(\"mini.notify\")))' -c 'quit' 2>&1 | grep -q 'table'"
+  
  test-with-python:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v6
+    - uses: wimpysworld/nothing-but-nix@main
+      with:
+        hatchet-protocol: 'carve'
    - uses: cachix/install-nix-action@v31
      with:
-        github_access_token: ${{ github.token }}
-    - uses: cachix/cachix-action@v17
+        github_access_token: ${{ secrets.GITHUB_TOKEN }}
+    - uses: cachix/cachix-action@v16
      with:
        name: rde
        authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
        extraPullNames: rstats-on-nix, nix-community
-
+    
+    # Create a temporary directory with Python enabled
    - name: Setup test directory with Python enabled
      run: |
        TEST_DIR=$(mktemp -d)
        cp -r templates/ed/. "$TEST_DIR/"
        cd "$TEST_DIR"
+        # Enable Python in the config
        sed -i 's/python[[:space:]]*=[[:space:]]*false;/python = true;/' flake.nix
+        # Verify the change was successful
        grep -q "python[[:space:]]*=[[:space:]]*true;" flake.nix || {
          echo "Error: Failed to enable Python in flake.nix"
          exit 1
        }
-        echo "TEST_DIR=$TEST_DIR" >> $GITHUB_ENV
-
+        echo "TEST_PYTHON_DIR=$TEST_DIR" >> $GITHUB_ENV
+    
    - name: Build with Python enabled
      run: |
-        cd "$TEST_DIR"
+        cd "$TEST_PYTHON_DIR"
        nix build
-
-    - name: Test Python packages
-      env:
-        NO_NUSHELL: '1'
+    
+    - name: Test Python packages are available
      run: |
-        cd "$TEST_DIR"
-        nix develop --command bash -c "python3 ${{ github.workspace }}/tests/ed/test.py"
-
-  test-with-julia:
+        cd "$TEST_PYTHON_DIR"
+        nix develop --command bash -c "python3 -c 'import duckdb; import polars; print(\"Python packages loaded\")'"
+    
+    - name: Test Python can execute code
+      run: |
+        cd "$TEST_PYTHON_DIR"
+        nix develop --command bash -c "python3 -c 'print(1+1)'"
+  
+  test-with-r:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v6
+    - uses: wimpysworld/nothing-but-nix@main
+      with:
+        hatchet-protocol: 'carve'
    - uses: cachix/install-nix-action@v31
      with:
-        github_access_token: ${{ github.token }}
-    - uses: cachix/cachix-action@v17
+        github_access_token: ${{ secrets.GITHUB_TOKEN }}
+    - uses: cachix/cachix-action@v16
      with:
        name: rde
        authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
        extraPullNames: rstats-on-nix, nix-community
-
+    
+    # Create a temporary directory with R enabled
+    - name: Setup test directory with R enabled
+      run: |
+        TEST_DIR=$(mktemp -d)
+        cp -r templates/ed/. "$TEST_DIR/"
+        cd "$TEST_DIR"
+        # Enable R in the config
+        sed -i 's/r[[:space:]]*=[[:space:]]*false;/r = true;/' flake.nix
+        # Verify the change was successful
+        grep -q "r[[:space:]]*=[[:space:]]*true;" flake.nix || {
+          echo "Error: Failed to enable R in flake.nix"
+          exit 1
+        }
+        echo "TEST_R_DIR=$TEST_DIR" >> $GITHUB_ENV
+    
+    - name: Build with R enabled
+      run: |
+        cd "$TEST_R_DIR"
+        nix build
+    
+    - name: Test R launches
+      run: |
+        cd "$TEST_R_DIR"
+        nix develop --command bash -c "R --version"
+    
+    - name: Test R packages are available
+      run: |
+        cd "$TEST_R_DIR"
+        nix develop --command bash -c "R -e 'library(fixest); print(\"R package fixest loaded\")'"
+    
+    - name: Test R can execute code
+      run: |
+        cd "$TEST_R_DIR"
+        nix develop --command bash -c "R -e 'print(1+1)'"
+  
+  test-with-julia:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v6
+    - uses: wimpysworld/nothing-but-nix@main
+      with:
+        hatchet-protocol: 'carve'
+    - uses: cachix/install-nix-action@v31
+      with:
+        github_access_token: ${{ secrets.GITHUB_TOKEN }}
+    - uses: cachix/cachix-action@v16
+      with:
+        name: rde
+        authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
+        extraPullNames: rstats-on-nix, nix-community
+    
+    # Create a temporary directory with Julia enabled
    - name: Setup test directory with Julia enabled
      run: |
        TEST_DIR=$(mktemp -d)
        cp -r templates/ed/. "$TEST_DIR/"
        cd "$TEST_DIR"
+        # Enable Julia in the config
        sed -i 's/julia[[:space:]]*=[[:space:]]*false;/julia = true;/' flake.nix
+        # Verify the change was successful
        grep -q "julia[[:space:]]*=[[:space:]]*true;" flake.nix || {
          echo "Error: Failed to enable Julia in flake.nix"
          exit 1
        }
-        echo "TEST_DIR=$TEST_DIR" >> $GITHUB_ENV
-
+        echo "TEST_JULIA_DIR=$TEST_DIR" >> $GITHUB_ENV
+    
    - name: Build with Julia enabled
      run: |
-        cd "$TEST_DIR"
+        cd "$TEST_JULIA_DIR"
        nix build
-
-    - name: Test Julia packages
-      env:
-        NO_NUSHELL: '1'
+    
+    - name: Test Julia launches
      run: |
+        cd "$TEST_JULIA_DIR"
+        nix develop --command bash -c "julia --version"
+    
+    - name: Test Julia can execute code
+      run: |
+        cd "$TEST_JULIA_DIR"
+        nix develop --command bash -c "julia -e 'println(1+1)'"
+  
+  test-with-multiple-languages:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v6
+    - uses: wimpysworld/nothing-but-nix@main
+      with:
+        hatchet-protocol: 'carve'
+    - uses: cachix/install-nix-action@v31
+      with:
+        github_access_token: ${{ secrets.GITHUB_TOKEN }}
+    - uses: cachix/cachix-action@v16
+      with:
+        name: rde
+        authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
+        extraPullNames: rstats-on-nix, nix-community
+    
+    # Create a temporary directory with multiple languages enabled
+    - name: Setup test directory with all languages enabled
+      run: |
+        TEST_DIR=$(mktemp -d)
+        cp -r templates/ed/. "$TEST_DIR/"
        cd "$TEST_DIR"
-        # nix develop --command bash -c "julia ${{ github.workspace }}/tests/ed/test.jl"
+        # Enable all languages in the config
+        sed -i 's/python[[:space:]]*=[[:space:]]*false;/python = true;/' flake.nix
+        sed -i 's/r[[:space:]]*=[[:space:]]*false;/r = true;/' flake.nix
+        sed -i 's/julia[[:space:]]*=[[:space:]]*false;/julia = true;/' flake.nix
+        # Verify the changes were successful
+        grep -q "python[[:space:]]*=[[:space:]]*true;" flake.nix || exit 1
+        grep -q "r[[:space:]]*=[[:space:]]*true;" flake.nix || exit 1
+        grep -q "julia[[:space:]]*=[[:space:]]*true;" flake.nix || exit 1
+        echo "TEST_MULTI_DIR=$TEST_DIR" >> $GITHUB_ENV
+    
+    - name: Build with all languages enabled
+      run: |
+        cd "$TEST_MULTI_DIR"
+        nix build
+    
+    - name: Test all languages work together
+      run: |
+        cd "$TEST_MULTI_DIR"
+        nix develop --command bash -c "python3 --version && R --version && julia --version"
+    
+    - name: Test all language packages are available
+      run: |
+        cd "$TEST_MULTI_DIR"
+        nix develop --command bash -c "python3 -c 'import duckdb' && R -e 'library(fixest)' && julia -e 'using StatsBase'"
--- a/.github/workflows/check_macos.yml
+++ b/.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
@ -18,9 +18,28 @@ jobs:
    - uses: cachix/install-nix-action@v31
      with:
        github_access_token: ${{ secrets.GITHUB_TOKEN }}
-    - uses: cachix/cachix-action@v17
+    - uses: cachix/cachix-action@v16
      with:
        name: rde
        authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
        extraPullNames: rstats-on-nix, nix-community
-    - run: nix build ./templates/ed
+    
+    # Test RDE template
+    - name: Build RDE template
+      run: nix build ./templates/rde
+    - name: Check RDE flake
+      run: nix flake check ./templates/rde
+    - name: Test RDE dev shell
+      run: |
+        cd templates/rde
+        nix develop --command bash -c "p --headless --version"
+    
+    # Test ED template
+    - name: Build ED template
+      run: nix build ./templates/ed
+    - name: Check ED flake
+      run: nix flake check ./templates/ed
+    - name: Test ED dev shell
+      run: |
+        cd templates/ed
+        nix develop --command bash -c "vv --headless --version"
--- a/.github/workflows/update.yml
+++ b/.github/workflows/update.yml
@ -17,16 +17,18 @@ jobs:
      - uses: cachix/install-nix-action@v31
        with:
          github_access_token: ${{ secrets.GITHUB_TOKEN }}
-      - uses: cachix/cachix-action@v17
+      - uses: cachix/cachix-action@v16
        with:
          name: rde
          authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
          extraPullNames: rstats-on-nix, nix-community
-      - name: Update ed flake.lock
+      - run: cd templates/rde/ && nix develop -c p-updateDeps
+      - run: cd templates/ed/ && nix develop -c updateR
+      - name: Update n flake.lock
        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
--- a/README.md
+++ b/README.md
@ -4,9 +4,32 @@ A collection of Nix flake templates for reproducible development environments.

 ## Templates

+### ED (Editor)
+
+A simple Neovim-based development environment with optional language support.
+
+**Quick start:**
+```bash
+nix flake init -t github:dwinkler1/np#ed
+nix develop
+vv  # Launch Neovim (custom binary name)
+```
+
+**Features:**
+- ✨ Lightweight Neovim configuration
+- 🔧 Configurable language support (Python, R, Julia, Nix)
+- 📦 Reproducible with Nix
+- 🎨 Custom theming (Kanagawa by default)
+- 🔔 Mini-notify plugin for notifications
+
+**Default configuration:**
+- Nix support enabled
+- Custom binary: `vv`
+- Includes: cowsay, updateR utility
+
 ### RDE (Research Development Environment)

-The default template for data science and research projects with support for R, Python, and Julia.
+A comprehensive template for data science and research projects with support for R, Python, and Julia.

 **Quick start:**
 ```bash
@ -34,12 +57,63 @@ All templates are automatically tested to ensure functionality:

 ### CI Workflows

- `.github/workflows/check.yml` - Comprehensive functionality tests (Ubuntu)
- `.github/workflows/check_macos.yml` - macOS compatibility tests
+**RDE Template:**
+- `.github/workflows/check.yml` - Comprehensive functionality tests for RDE (Ubuntu)
+  - Basic build and flake checks
+  - Dev shell functionality
+  - R command availability and functionality
+  - Neovim integration
+  - Utility commands (p-initProject, p-updateDeps)
+  - Separate jobs for Python and Julia configurations
+
+**ED Template:**
+- `.github/workflows/check_ed.yml` - Comprehensive functionality tests for ED (Ubuntu)
+  - Basic build and flake checks
+  - Dev shell functionality
+  - Neovim (vv) command tests
+  - updateR utility tests
+  - Extra packages (cowsay) verification
+  - Separate jobs for Python, R, Julia, and multi-language configurations
+
+**Cross-platform:**
+- `.github/workflows/check_macos.yml` - macOS compatibility tests for both templates
 - `.github/workflows/update.yml` - Automated dependency updates

 ## Usage

+### ED Template
+
+1. **Initialize a new project:**
+   ```bash
+   nix flake init -t github:dwinkler1/np#ed
+   ```
+
+2. **Enter development environment:**
+   ```bash
+   nix develop
+   # or with direnv
+   echo "use flake" > .envrc && direnv allow
+   ```
+
+3. **Start editing:**
+   ```bash
+   vv              # Launch Neovim
+   updateR         # Update R packages (when R is enabled)
+   cowsay "Hello!" # Fun utility included
+   ```
+
+4. **Enable languages:**
+   Edit `flake.nix` and change `false` to `true` in the `cats` section:
+   ```nix
+   cats = {
+     python = true;  # Enable Python support
+     r = true;       # Enable R support
+     julia = true;   # Enable Julia support
+   };
+   ```
+
+### RDE Template
+
 1. **Initialize a new project:**
   ```bash
   nix flake init -t github:dwinkler1/np#rde
--- a/templates/ed/.gitignore
+++ b/templates/ed/.gitignore
@ -1,2 +1 @@
 .nvimcom
-.commandcode/
--- a/templates/ed/README.md
+++ b/templates/ed/README.md
@ -1,73 +1,284 @@
-# Project Editor
+# ED Template - Simple Editor Environment

-A per-project Neovim wrapper built with [nix-wrapper-modules](https://birdeehub.github.io/nix-wrapper-modules/) and [nvimConfig](https://github.com/dwinkler1/nvimConfig).
+A lightweight, customizable Neovim-based development environment with optional language support for Python, R, Julia, and Nix.

-## Setup
+## Features

-The flake provides two entry points:
+- ✨ **Lightweight**: Minimal configuration, fast startup
+- 🔧 **Configurable**: Enable only the languages you need
+- 📦 **Reproducible**: Nix-based environment management
+- 🎨 **Themed**: Beautiful Kanagawa colorscheme (customizable)
+- 🔔 **Notifications**: Mini-notify plugin for user feedback

-| 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)
+## Quick Start

 ```bash
-direnv allow   # enter the devShell automatically
-nv             # launch the pre-configured Neovim
-R              # R REPL is available (if enabled in flake.nix)
+# Initialize a new project with the ED template
+nix flake init -t github:dwinkler1/np#ed
+
+# Enter the development environment
+nix develop
+
+# Launch Neovim
+vv
 ```

-### 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:
+The ED template uses a centralized configuration structure at the top of `flake.nix`:

-| 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
+```nix
+cats = {
+  clickhouse = false;
+  gitPlugins = false;
+  julia = false;
+  lua = false;
+  markdown = false;
+  nix = true;        # Enabled by default
+  optional = false;
+  python = false;
+  r = false;
+};
 ```

-Uses `nixfmt-rfc-style` pinned via the flake's `formatter` output.
+### Enabling Languages
+
+To enable support for a specific language, edit `flake.nix` and set the corresponding cat to `true`:
+
+#### Python
+```nix
+cats = {
+  python = true;
+  # ... other settings
+};
+```
+
+Includes: Python 3, duckdb, polars packages by default
+
+#### R
+```nix
+cats = {
+  r = true;
+  # ... other settings
+};
+```
+
+Includes: fixest package by default
+
+#### Julia
+```nix
+cats = {
+  julia = true;
+  # ... other settings
+};
+```
+
+Includes: StatsBase package by default
+
+### Custom Package Files
+
+You can specify additional packages by creating these files in your project:
+
+- `python-packages.nix` - Additional Python packages
+  ```nix
+  p: with p; [
+    numpy
+    pandas
+    # ... more packages
+  ]
+  ```
+
+- `r-packages.nix` - Additional R packages
+  ```nix
+  p: with p.rPackages; [
+    ggplot2
+    dplyr
+    # ... more packages
+  ]
+  ```
+
+- `julia-packages.nix` - Additional Julia packages
+  ```nix
+  [
+    "DataFrames"
+    "Plots"
+    # ... more packages
+  ]
+  ```
+
+## Available Commands
+
+### Neovim
+- `vv` - Launch Neovim (custom binary name)
+- `vv --headless` - Run Neovim in headless mode for scripting
+
+### Utilities
+- `updateR` - Update R package snapshots from rstats-on-nix
+- `cowsay` - Fun ASCII art text formatter (included as example)
+
+## Customization
+
+### Binary Name
+
+The default binary name is `vv`. To change it, edit the `binName` in `flake.nix`:
+
+```nix
+binName = "myeditor";  # Changes command from 'vv' to 'myeditor'
+```
+
+### Colorscheme
+
+Change the colorscheme in the settings section:
+
+```nix
+settings = {
+  colorscheme = "kanagawa";  # or "gruvbox", "tokyonight", etc.
+  background = "dark";        # or "light"
+  # ...
+};
+```
+
+### Extra Packages
+
+Add more system packages in the `extraPackages` section:
+
+```nix
+extraPackages = with pkgs; [
+  cowsay
+  ripgrep
+  fd
+  # ... more packages
+];
+```
+
+### Welcome Message
+
+The template includes a welcome notification. Customize it in the `specs.extraLua` section:
+
+```nix
+config = ''
+  require("mini.notify").setup()
+  vim.notify = MiniNotify.make_notify()
+  vim.notify("Welcome to ${name}!")
+'';
+```
+
+## Environment Variables
+
+The template sets the following environment variables:
+
+- `IS_PROJECT_EDITOR=1` - Indicates you're in the project editor environment
+- `R_LIBS_USER=./.nvimcom` - Project-local R package directory
+
+## Language Package Management
+
+### Replace vs Merge
+
+By default, language packages are **replaced** rather than merged with base packages. This is controlled by:
+
+```nix
+let
+  replace = pkgs.lib.mkForce;
+in {
+  lang_packages = {
+    python = replace ([...]);  # Replaces base packages
+    r = replace ([...]);       # Replaces base packages
+    julia = replace ([...]);   # Replaces base packages
+  };
+}
+```
+
+To **merge** with base packages instead, remove the `replace` wrapper:
+
+```nix
+lang_packages = {
+  python = (with pkgs.python3Packages; [...]);
+  # ...
+};
+```
+
+## Development Shell
+
+The development shell provides access to the Neovim package plus additional utilities:
+
+```bash
+nix develop  # Enter the dev shell
+```
+
+Available in dev shell:
+- `vv` - The configured Neovim
+- `updateR` - Update R packages (when R support is enabled)
+- All packages listed in `extraPackages`
+
+## Testing
+
+The ED template has comprehensive CI/CD tests:
+
+### Automated Tests (`.github/workflows/check_ed.yml`)
+
+1. **Basic Tests** (Ubuntu)
+   - Build verification
+   - Flake check
+   - Dev shell entry
+   - Neovim launch and version check
+   - Utility commands availability
+
+2. **Language-Specific Tests**
+   - Python configuration: Package imports, code execution
+   - R configuration: Package loading, code execution
+   - Julia configuration: Version check, code execution
+   - Multi-language: All languages enabled together
+
+3. **macOS Tests** (`.github/workflows/check_macos.yml`)
+   - Build verification on macOS
+   - Basic functionality tests
+
+## Tips
+
+1. **Use direnv for automatic environment loading:**
+   ```bash
+   echo "use flake" > .envrc
+   direnv allow
+   ```
+
+2. **Pin specific package versions** by editing `flake.lock`:
+   ```bash
+   nix flake update  # Update all inputs
+   nix flake lock --update-input nixpkgs  # Update specific input
+   ```
+
+3. **Check what's included in your build:**
+   ```bash
+   nix path-info -Sh ./result
+   ```
+
+4. **Build for different platforms:**
+   ```bash
+   nix build .#packages.x86_64-linux.default
+   nix build .#packages.aarch64-darwin.default
+   ```
+
+## Comparison with RDE Template
+
+| Feature | ED Template | RDE Template |
+|---------|-------------|--------------|
+| **Complexity** | Lightweight | Comprehensive |
+| **Binary Name** | `vv` | `p` |
+| **Project Structure** | Manual | `p-initProject` command |
+| **Language Support** | Optional (Python, R, Julia, Nix) | Built-in (R default, Python/Julia optional) |
+| **Research Tools** | None | Quarto, Marimo, Pluto.jl |
+| **Package Management** | updateR | p-updateDeps (comprehensive) |
+| **Use Case** | Simple editing, lightweight projects | Research, data science, complex projects |
+
+## Contributing
+
+When modifying the ED template, please ensure:
+
+1. All tests pass in `.github/workflows/check_ed.yml`
+2. The template builds on both Linux and macOS
+3. Documentation is updated to reflect changes
+4. Changes follow the existing code patterns
+
+## License
+
+See [LICENSE](../../LICENSE) file for details.
--- a/templates/ed/flake.lock
+++ b/templates/ed/flake.lock
@ -7,11 +7,11 @@
        ]
      },
      "locked": {
-        "lastModified": 1776413584,
-        "narHash": "sha256-xqqv46MTveuT4yJH2YihmbHGy5mdLnnLFDebVmUws/E=",
+        "lastModified": 1771133455,
+        "narHash": "sha256-DvHfkW3DctWV+YnigY4+5Stn9NgI38JqR2IScXDX8z8=",
        "owner": "dwinkler1",
        "repo": "fran",
-        "rev": "da09626e4dd8f0f57078b3a04e0443a8c20defa1",
+        "rev": "68b189ab981adae06590ee1929a70c8b86afd2b8",
        "type": "github"
      },
      "original": {
@ -22,16 +22,16 @@
    },
    "nixpkgs": {
      "locked": {
-        "lastModified": 1779560665,
-        "narHash": "sha256-tpyBcxPpcQb8ukyNF7DoCwfSY3VPsxHoYwj00Cayv5o=",
-        "owner": "nixos",
+        "lastModified": 1771043024,
+        "narHash": "sha256-O1XDr7EWbRp+kHrNNgLWgIrB0/US5wvw9K6RERWAj6I=",
+        "owner": "NixOS",
        "repo": "nixpkgs",
-        "rev": "64c08a7ca051951c8eae34e3e3cb1e202fe36786",
+        "rev": "3aadb7ca9eac2891d52a9dec199d9580a6e2bf44",
        "type": "github"
      },
      "original": {
-        "owner": "nixos",
-        "ref": "nixos-unstable",
+        "owner": "NixOS",
+        "ref": "nixos-25.11",
        "repo": "nixpkgs",
        "type": "github"
      }
@ -45,18 +45,18 @@
          "nixpkgs"
        ],
        "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references",
-        "r-nvim-nix": "r-nvim-nix",
+        "plugins-r": "plugins-r",
        "rixpkgs": [
          "rixpkgs"
        ],
        "wrappers": "wrappers"
      },
      "locked": {
-        "lastModified": 1779544872,
-        "narHash": "sha256-AnuNQ9nbXrDYmL97TOejAds/FQOgD6FEOHABp/8dmsU=",
+        "lastModified": 1770172480,
+        "narHash": "sha256-gem34C89cocBGuWLj7cdrAS5WkrOBp6V+ycQM/RhcCw=",
        "owner": "dwinkler1",
        "repo": "nvimConfig",
-        "rev": "aec9110e709e1aa50d78f06293c4bde14974b23f",
+        "rev": "8f5c05252e914cb3738039a7ec13eb7d5955227a",
        "type": "github"
      },
      "original": {
@ -81,59 +81,35 @@
        "type": "github"
      }
    },
-    "r-nvim-nix": {
-      "inputs": {
-        "nixpkgs": [
-          "nvimConfig",
-          "rixpkgs"
-        ],
-        "rnvimsrc": "rnvimsrc"
-      },
+    "plugins-r": {
+      "flake": false,
      "locked": {
-        "lastModified": 1779438909,
-        "narHash": "sha256-1lvv0bdvSVyeCIgeZ7Ws7ffbDFurA5LJscS9dRLHzC8=",
-        "owner": "dwinkler1",
-        "repo": "r_nvim_nix",
-        "rev": "ec17e22ab362a0ddfd6c2e9c5e95d43897a143be",
+        "lastModified": 1769736135,
+        "narHash": "sha256-T4QgcBL+LCXvrEiRE2JW4jtUKl8DKzFHk8czGUO1jgY=",
+        "owner": "R-nvim",
+        "repo": "R.nvim",
+        "rev": "2701ec64f5485e17c0e057081a9ae2058d776464",
        "type": "github"
      },
      "original": {
-        "owner": "dwinkler1",
-        "ref": "v0.99.4",
-        "repo": "r_nvim_nix",
+        "owner": "R-nvim",
+        "repo": "R.nvim",
        "type": "github"
      }
    },
    "rixpkgs": {
      "locked": {
-        "lastModified": 1771303851,
-        "narHash": "sha256-tgveHozOJ2D/mi3LxVy/FcmLFDlM5XKZxsNB2XpvzaM=",
-        "owner": "dwinkler1",
-        "repo": "rixpkgs",
-        "rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e",
+        "lastModified": 1770035835,
+        "narHash": "sha256-Pi8f3LPTFmG7SZeAJEAamOWly1SZhEofT92uBqS4atY=",
+        "owner": "rstats-on-nix",
+        "repo": "nixpkgs",
+        "rev": "0d3fe7afce51d2126fdccf0b717d8048b90e4781",
        "type": "github"
      },
      "original": {
-        "owner": "dwinkler1",
-        "repo": "rixpkgs",
-        "rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e",
-        "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",
+        "owner": "rstats-on-nix",
+        "ref": "2026-02-02",
+        "repo": "nixpkgs",
        "type": "github"
      }
    },
@ -153,11 +129,11 @@
        ]
      },
      "locked": {
-        "lastModified": 1779297405,
-        "narHash": "sha256-VFoBwH7ZjVxCnvZTb5ODRXt70sLtWMxstive0N+RS50=",
+        "lastModified": 1769745458,
+        "narHash": "sha256-Fq6THKEiAKx+wWQ4wTg9HvOAyD6i8JkWfHVQDZH7Byo=",
        "owner": "BirdeeHub",
        "repo": "nix-wrapper-modules",
-        "rev": "e7ed7a1205945befdf2e0d73ba7df91d935e5af1",
+        "rev": "cc5e052dd1e93ae75dc06e3fabf46f0820c272f2",
        "type": "github"
      },
      "original": {
--- a/templates/ed/flake.nix
+++ b/templates/ed/flake.nix
@ -6,36 +6,8 @@
    nixpkgs,
    nvimConfig,
    ...
-  }: let
-    systems = ["aarch64-darwin" "x86_64-linux" "aarch64-linux"];
-    forAllSystems = nixpkgs.lib.genAttrs systems;
-
-    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 {
+  } @ inputs: let
+    projectSettings = {pkgs}: {
      cats = {
        clickhouse = false;
        gitPlugins = false;
@ -45,115 +17,116 @@
        nix = true;
        optional = false;
        python = false;
-        r = true;
+        r = false;
      };

-      settings = {
+      settings = let
+        # With `replace` packages are replaced otherwise they are merged with base packages
+        replace = pkgs.lib.mkForce;
+      in {
        lang_packages = {
-          python = with pkgs.python3Packages;
-            [
-              requests
-            ]
-            ++ extraPythonPackages;
-
-          r =
-            (with pkgs.rpkgs.rPackages; [
-              arrow
-              data_table
-              fixest
-              pkgs.nvimcom
+          python = replace (
+            (with pkgs.python3Packages; [
+              duckdb
+              polars
            ])
-            ++ extraRPackages;
+            ++ (
+              if builtins.pathExists ./python-packages.nix
+              # p: with p; [ ... ]
+              then import ./python-packages.nix pkgs.python3Packages
+              else []
+            )
+          );

-          julia =
-            ["StatsBase"]
-            ++ extraJuliaPackages;
+          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 = "tokyonight"; #"kanagawa";
+        colorscheme = "kanagawa";
        background = "dark";
        wrapRc = true;
      };
+      binName = "vv";

-      binName = "nv";
-
-      env.IS_PROJECT_EDITOR = "1";
-
-      catPkgs = {
-        always = [
-          pkgs.git
-          pkgs.pre-commit
-          pkgs.cowsay
-        ];
-
-        nix = [
-          pkgs.nil
-          pkgs.nixfmt
-        ];
+      env = {
+        IS_PROJECT_EDITOR = "1";
+        R_LIBS_USER = "./.nvimcom";
      };

-      specs.extraLua = {
+      extraPackages = 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 {
-    formatter = forAllSystems (system: (mkPkgs system).nixfmt-tree);

+    systems = nixpkgs.lib.systems.flakeExposed;
+    forAllSystems = nixpkgs.lib.genAttrs systems;
+    overlays = [inputs.nvimConfig.overlays.dependencies];
+  in {
    packages = forAllSystems (system: let
-      pkgs = mkPkgs system;
+      pkgs = import nixpkgs {inherit system overlays;};
+      baseNvim = nvimConfig.packages.${system}.default;
+
+      nvim = (baseNvim.eval (projectSettings {inherit pkgs;})).config.wrapper;
+      default = nvim;
    in {
-      default = nvimConfig.lib.mkWrapper {
-        inherit pkgs;
-        modules = [(projectModule pkgs)];
-      };
+      default = nvim;
    });

    devShells = forAllSystems (system: let
-      pkgs = mkPkgs system;
-      evalResult = nvimConfig.lib.eval {
-        inherit pkgs;
-        modules = [(projectModule pkgs)];
-      };
-      nv = evalResult.config.wrap {inherit pkgs;};
+      pkgs = import nixpkgs {inherit system overlays;};
+      nv = self.packages.${system}.default;
    in {
      default = pkgs.mkShell {
-        packages =
-          [
-            nv
-            pkgs.nushell
-          ]
-          ++ nvimConfig.lib.devShellPackages evalResult.config;
-        shellHook =
-          nvimConfig.lib.shellHook evalResult.config
-          + ''
-            if [ -z "''${NO_NUSHELL:-}" ]; then
-              exec nu
-            fi
-          '';
+        packages = [nv pkgs.updateR];
      };
    });
  };

  inputs = {
-    nixpkgs.url = "github:nixos/nixpkgs/nixos-unstable";
-
-    rixpkgs.url = "github:dwinkler1/rixpkgs/af2dd3f7b4b172077747c0869d4e30702fb71b0e";
-
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-25.11";
+    rixpkgs.url = "github:dwinkler1/rixpkgs/nixpkgs";
    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";
      };
    };
--- a/templates/rde/flake.lock
+++ b/templates/rde/flake.lock
@ -7,11 +7,11 @@
        ]
      },
      "locked": {
-        "lastModified": 1776413584,
-        "narHash": "sha256-xqqv46MTveuT4yJH2YihmbHGy5mdLnnLFDebVmUws/E=",
+        "lastModified": 1771133455,
+        "narHash": "sha256-DvHfkW3DctWV+YnigY4+5Stn9NgI38JqR2IScXDX8z8=",
        "owner": "dwinkler1",
        "repo": "fran",
-        "rev": "da09626e4dd8f0f57078b3a04e0443a8c20defa1",
+        "rev": "68b189ab981adae06590ee1929a70c8b86afd2b8",
        "type": "github"
      },
      "original": {
@ -73,11 +73,11 @@
    },
    "nixpkgs": {
      "locked": {
-        "lastModified": 1777077449,
-        "narHash": "sha256-AIiMJiqvGrN4HyLEbKAoCSRRYn0rnlW5VbKNIMIYqm4=",
+        "lastModified": 1771043024,
+        "narHash": "sha256-O1XDr7EWbRp+kHrNNgLWgIrB0/US5wvw9K6RERWAj6I=",
        "owner": "nixos",
        "repo": "nixpkgs",
-        "rev": "a4bf06618f0b5ee50f14ed8f0da77d34ecc19160",
+        "rev": "3aadb7ca9eac2891d52a9dec199d9580a6e2bf44",
        "type": "github"
      },
      "original": {
@ -138,16 +138,16 @@
    },
    "rixpkgs": {
      "locked": {
-        "lastModified": 1776958221,
-        "narHash": "sha256-cOHLrMWifj8HQMIG6gMhGowwPAkyX/kijDx38wK8kUM=",
+        "lastModified": 1770035835,
+        "narHash": "sha256-Pi8f3LPTFmG7SZeAJEAamOWly1SZhEofT92uBqS4atY=",
        "owner": "rstats-on-nix",
        "repo": "nixpkgs",
-        "rev": "db90c554b7172188324b84deea35ed5975e20e44",
+        "rev": "0d3fe7afce51d2126fdccf0b717d8048b90e4781",
        "type": "github"
      },
      "original": {
        "owner": "rstats-on-nix",
-        "ref": "2026-04-22",
+        "ref": "2026-02-02",
        "repo": "nixpkgs",
        "type": "github"
      }
--- a/templates/rde/flake.nix
+++ b/templates/rde/flake.nix
@ -219,7 +219,7 @@
    });
  };
  inputs = {
-    rixpkgs.url = "github:rstats-on-nix/nixpkgs/2026-04-22";
+    rixpkgs.url = "github:rstats-on-nix/nixpkgs/2026-02-02";
    nixpkgs.url = "github:nixos/nixpkgs/nixos-25.11";
    nixCats = {
      url = "github:dwinkler1/nixCatsConfig";
--- a/tests/ed/test.R
+++ b/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")
--- a/tests/ed/test.jl
+++ b/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")
--- a/tests/ed/test.py
+++ b/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")
Author	SHA1	Message	Date
copilot-swe-agent[bot]	3c52f6b820	Add permissions block to ED workflow for security Co-authored-by: dwinkler1 <22460147+dwinkler1@users.noreply.github.com>	2026-02-16 00:10:00 +00:00
copilot-swe-agent[bot]	5ac0c775ef	Update README with ED template documentation Co-authored-by: dwinkler1 <22460147+dwinkler1@users.noreply.github.com>	2026-02-16 00:07:47 +00:00
copilot-swe-agent[bot]	0e20fe6229	Add comprehensive test workflow for ED template Co-authored-by: dwinkler1 <22460147+dwinkler1@users.noreply.github.com>	2026-02-16 00:06:34 +00:00
copilot-swe-agent[bot]	503b6534ae	Initial plan	2026-02-16 00:04:18 +00:00