Improve template with setup documentation and best practices

- Add setup checklist and ghcr.io visibility documentation to README
- Document minimal vs full base image options in Dockerfile
- Add Git LFS checkout to CI and release workflows
- Add .gitattributes template for Git LFS configuration
- Document common system dependencies for R package compilation

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: fnaji

.gitattributes

@@ -0,0 +1,18 @@
+# Git LFS tracking for large files commonly used in operators
+# Uncomment the file types you need to track with LFS
+# Note: Only use LFS for files that are truly large (>1MB)
+
+# Data files (uncomment as needed)
+# *.rds filter=lfs diff=lfs merge=lfs -text
+# *.RDS filter=lfs diff=lfs merge=lfs -text
+# *.csv filter=lfs diff=lfs merge=lfs -text
+# *.tsv filter=lfs diff=lfs merge=lfs -text
+
+# Binary/media files (uncomment as needed)
+# *.pdf filter=lfs diff=lfs merge=lfs -text
+# *.png filter=lfs diff=lfs merge=lfs -text
+# *.jpg filter=lfs diff=lfs merge=lfs -text
+# *.jpeg filter=lfs diff=lfs merge=lfs -text
+
+# Example: Track specific large files
+# data/large_reference.rds filter=lfs diff=lfs merge=lfs -text

.github/workflows/ci.yml

@@ -22,6 +22,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+        with:
+          lfs: true
 
       - name: Log in to the Container registry
         uses: docker/login-action@v3.3.0

.github/workflows/release.yml

@@ -21,6 +21,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+        with:
+          lfs: true
 
       - name: Update container in operator.json
         run: |

Dockerfile

@@ -1,5 +1,18 @@
+# =============================================================================
+# BASE IMAGE OPTIONS
+# =============================================================================
+# Option A: Full runtime (default) - larger image, most dependencies included
 FROM tercen/runtime-r44:4.4.3-8
 
+# Option B: Minimal runtime - smaller image, faster pulls
+# Uncomment the lines below and comment out Option A above to use minimal image
+# FROM tercen/runtime-r44-minimal:4.4.3-2
+# RUN apk update && apk add --no-cache \
+#     gcc g++ musl-dev make gfortran \
+#     curl-dev openssl-dev git pkgconfig
+# # Uncomment if your R packages have Rust dependencies (e.g., stringi, gifski):
+# #   cargo rust
+
 COPY . /operator
 WORKDIR /operator
 

README.md

@@ -11,6 +11,67 @@ The `Template R Operator` is a template repository for the creation of R operato
 
 Detailed information can be found in the [Tercen developer's guide](https://tercen.github.io/developers_guide/).
 
+## Setup Checklist
+
+After creating your operator from this template, complete the following steps:
+
+- [ ] Update `operator.json`:
+  - Change `name` and `description`
+  - Update `authors` to your organization
+  - Update `container` to match your repo: `ghcr.io/YOUR_ORG/YOUR_REPO:main`
+  - Update `urls` similarly
+  - Configure `properties` for your operator's parameters
+- [ ] If using minimal base image, uncomment and configure the Dockerfile accordingly
+- [ ] Run `renv::init()` locally and commit `renv.lock`
+- [ ] Push your changes to trigger the CI workflow
+- [ ] **Important**: Make the Docker package publicly accessible (see below)
+
+## GitHub Container Registry Visibility
+
+By default, GitHub Container Registry (ghcr.io) packages inherit the repository's visibility settings. If your repository is **private**, the Docker image will also be private, and Tercen/BioNavigator will fail to pull it with an error like:
+
+```
+Error response from daemon: denied
+```
+
+**To fix this**, you have two options:
+
+1. **Make the package public** (recommended if repo stays private):
+   - Go to `https://github.com/orgs/YOUR_ORG/packages`
+   - Find your operator package
+   - Click "Package settings"
+   - Under "Danger Zone", click "Change visibility" and select "Public"
+
+2. **Make the repository public**:
+   - This automatically makes associated packages public
+
+## Dockerfile Options
+
+This template provides two base image options:
+
+| Option | Base Image | Use Case |
+|--------|------------|----------|
+| **Full runtime** (default) | `tercen/runtime-r44:4.4.3-8` | Most dependencies included, easier setup |
+| **Minimal runtime** | `tercen/runtime-r44-minimal:4.4.3-2` | Smaller image, requires adding build dependencies |
+
+If using the minimal runtime, uncomment the relevant lines in the Dockerfile and add any system dependencies your R packages require. Common dependencies:
+
+- `gcc g++ musl-dev make` - C/C++ compilation (most R packages)
+- `gfortran` - Fortran compiler (statistical packages, linear algebra)
+- `curl-dev openssl-dev` - HTTP/SSL support
+- `cargo rust` - Rust toolchain (some modern R packages)
+
+## Git LFS
+
+This template includes a `.gitattributes` file with commented-out LFS tracking rules for common large file types (`.rds`, `.csv`, `.pdf`, images). If your operator requires large data files:
+
+1. Install Git LFS: `git lfs install`
+2. Uncomment the relevant lines in `.gitattributes` for file types you need to track
+3. Run `git lfs track` to verify your patterns
+4. Commit the updated `.gitattributes` before adding large files
+
+---
+
 Below is the operator README standard structure.
 
 ### Description
@@ -21,12 +82,12 @@ The `Template R operator` is a template repository for the creation of R operato
 
 Input|.
 ---|---
-`x-axis`        | type, description 
-`y-axis`        | type, description 
-`row`           | type, description 
-`column`        | type, description 
-`colors`        | type, description 
-`labels`        | type, description 
+`x-axis`        | type, description
+`y-axis`        | type, description
+`row`           | type, description
+`column`        | type, description
+`colors`        | type, description
+`labels`        | type, description
 
 Settings|.
 ---|---