Feature/pipettor

.devcontainer/Dockerfile

@@ -1,23 +1,21 @@
 FROM --platform=linux/amd64 althack/ros2:humble-full
-
 # ** [Optional] Uncomment this section to install additional packages. **
 ENV DEBIAN_FRONTEND=noninteractive
 RUN apt-get update \
-        && apt-get -y install --no-install-recommends \
-        python3-pip \
-        python3.10-venv \
-        ros-${ROS_DISTRO}-rclpy \
-        ros-${ROS_DISTRO}-ur \
-        ros-${ROS_DISTRO}-moveit\
-        build-essential \
-        python3-colcon-common-extensions \
-        libopencv-dev \
-        python3-opencv \
-        # Clean up
-        && apt-get autoremove -y \
-        && apt-get clean -y \
-        && rm -rf /var/lib/apt/lists/*
-
+ && apt-get -y install --no-install-recommends \
+ python3-pip \
+ python3.10-venv \
+ ros-${ROS_DISTRO}-rclpy \
+ ros-${ROS_DISTRO}-ur \
+ ros-${ROS_DISTRO}-moveit\
+ build-essential \
+ python3-colcon-common-extensions \
+ libopencv-dev \
+ python3-opencv \
+# Clean up
+ && apt-get autoremove -y \
+ && apt-get clean -y \
+ && rm -rf /var/lib/apt/lists/*
 ENV DEBIAN_FRONTEND=dialog
 
 # Set up auto-source of workspace for ros user
@@ -30,5 +28,19 @@ RUN curl -fsSL https://pixi.sh/install.sh | sh
 RUN echo 'export PATH="/home/ros/.pixi/bin:$PATH"' >> /home/ros/.bashrc
 RUN echo 'eval "$(pixi completion --shell bash)"' >> /home/ros/.bashrc
 
-# Bring the default user back to root for unit test or other admin tasks
+# Copy entire repo and run setup script
 USER root
+WORKDIR ${WORKSPACE}
+COPY . .
+
+# Run setup script to install dependencies
+RUN chmod +x setup.sh && \
+    sed -i 's/sudo //g' setup.sh && \
+    ./setup.sh && \
+    apt-get autoremove -y && \
+    apt-get clean -y && \
+    rm -rf /var/lib/apt/lists/*
+
+# Bring the default user back to root for unit test or other admin tasks
+WORKDIR ${WORKSPACE}
+USER root

.github/workflows/docker-build.yaml

@@ -0,0 +1,49 @@
+name: Build and Push Docker Image to GHCR
+on:
+  push:
+    tags:
+      - 'v*'
+  workflow_dispatch:
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=semver,pattern={{major}}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: ./.devcontainer/Dockerfile
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/ros.yaml

@@ -2,9 +2,9 @@ name: ROS C++ Testing and Linting
 
 on:
   push:
-    branches: [main, humble]
+    branches: [main, humble, feature/*]
   pull_request:
-    branches: [main, humble]
+    branches: [main, humble, feature/*]
   workflow_dispatch:
 
 jobs:

.github/workflows/ruff.yml

@@ -2,9 +2,9 @@ name: Check Code Style - Ruff
 
 on:
   push:
-    branches: [main, humble]
+    branches: [main, humble, feature/*]
   pull_request:
-    branches: [main, humble]
+    branches: [main, humble, feature/*]
   workflow_dispatch:
 
 jobs:

.github/workflows/super-linter.yml

@@ -8,9 +8,9 @@ name: Lint Code Base (Super-Linter)
 
 on:
   push:
-    branches: [main, humble]
+    branches: [main, humble, feature/*]
   pull_request:
-    branches: [main, humble]
+    branches: [main, humble, feature/*]
 jobs:
   run-lint:
     runs-on: ubuntu-latest

.gitignore

@@ -4,6 +4,12 @@ log
 site
 erobs.code-workspace
 
+# Packages being handled by vcs
+src/end_effectors/pipettor
+src/end_effectors/robotiq_hande
+src/end_effectors/ros2_epick_gripper
+src/end_effectors/serial
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

README.md

@@ -1,6 +1,6 @@
 # Extensible Robotic Beamline Scientist
 
-Project repository for building extensible robotic beamline scientists at NSLS-II.
+Project repository for building extensible robotic beamline scientists at NSLS-II. ROS 2 Humble with Ubuntu 22.04 LTS
 
 ## Contents
 
@@ -31,33 +31,76 @@ Each manifest in the [docker](./docker) directory is a container image that can
 
 ### Docker Contents
 
-We use Podman throughout this work, but have named the container images with Docker in mind.
+**⚠️ The `docker/` directory and `scripts/pdf-launch-scripts/` are DEPRECATED. See below for the active deployment workflow.**
 
-- [erobs-common-img](./docker/erobs-common-img): Common container image for running the majority of applications herein, including: UR robot driver, gripper service, MoveIt service, and the pdf_beamtime_server (primary `Action` server).
-- [bsui](./docker/bsui): Container image for running the Bluesky User Interface with mounts at NSLS-II.
-- [azure-kinect](./docker/azure-kinect): Container image for running the Azure Kinect ROS2 driver.
-- Other auxiliary container images that are not used in the main application, but are useful for development and testing:
-  - [ursim](./docker/ursim): Container image for running a simulated UR3e robot arm with a teach pendant.
-  - [ur-driver](./docker/ur-driver): Container image for running the UR3e robot arm ROS2 driver.
-  - [ur-moveit](./docker/ur-moveit): Container image for running MoveIt with the UR3e robot arm.
-  - [ur-example](./docker/ur-example): Container image for running a simple action with the UR3e robot arm.
-  - [erobs-hello-moveit](./docker/erobs-hello-moveit): Container image for running a simple action with the UR3e robot arm.
+#### Active Deployment Workflow
 
+For development and deployment
+
+- **Development**: Use [.devcontainer/Dockerfile](./.devcontainer/Dockerfile) with VSCode devcontainer for local development
+- **CI/CD**: Automated builds via [.github/workflows/docker-build.yaml](./.github/workflows/docker-build.yaml)
+  - Push a version tag to trigger automatic build and publish to GitHub Container Registry (GHCR)
+- **Deployment**: Pull the unified container image from GHCR at `ghcr.io/<your-org>/<your-repo>:latest`
+  - All dependencies are pre-installed (no apt install required at deployment)
+  - Launch ROS2 nodes using `ros2 launch` commands directly from the container
+
+#### Deprecated Docker Contents (For Reference Only)
+
+The following directories contain legacy container configurations and are **no longer maintained**:
+
+- [docker/](./docker/): Legacy multi-container Dockerfiles - See [docker/DEPRECATED.md](./docker/DEPRECATED.md)
+- [scripts/pdf-launch-scripts/](./scripts/pdf-launch-scripts/): Legacy deployment scripts referencing gatekept GHCR images - See [scripts/pdf-launch-scripts/DEPRECATED.md](./scripts/pdf-launch-scripts/DEPRECATED.md)
+
+These can be used for learning purposes but should not be used for active development or deployment.
 
 ### Hello Moveit
 
-Demonstrations using a combination of the MoveIt tutorials and some UR specific tools, to show how to make simple actions
-that can deploy MoveIt using the MoveGroupInterface.
+Demonstrations using a combination of the MoveIt tutorials and some UR specific tools, to show how to make simple actions that can deploy MoveIt using the MoveGroupInterface.
 
 ### Bluesky ROS
 
 Ongoing developments of integrating ROS2 and Bluesky. Currently targeted towards integrating Ophyd Objects as ROS2 Action Clients.
 
-## Using Containers to Run the Full Applicaiton Suite
+## Development Setup
+
+### Local Development with VSCode
+
+1. Install VSCode with the Remote-Containers extension
+2. Open this repository in VSCode
+3. VSCode will prompt to "Reopen in Container" - accept this
+4. The devcontainer will automatically build using `.devcontainer/Dockerfile`
+5. Once inside the container, build the workspace:
+   ```bash
+   colcon build --symlink-install
+   source install/setup.bash
+   ```
+
+### Deployment
+
+For production deployment:
+
+1. **Automated Build**: Push a version tag to trigger GitHub Actions
+   ```bash
+   git tag v1.0.0
+   git push origin v1.0.0
+   ```
+
+2. **Pull from GHCR**: On your deployment machine
+   ```bash
+   podman pull ghcr.io/<your-org>/<your-repo>:latest
+   ```
+
+3. **Run containers**: Launch ROS2 nodes with appropriate environment variables
+   ```bash
+   podman run -it --network host --ipc=host \
+     --env ROS_DOMAIN_ID=10 \
+     ghcr.io/<your-org>/<your-repo>:latest \
+     ros2 launch <package> <launch_file>
+   ```
 
-The complete application uses a 1-node-per-container model. The containers are currently orchestrated by bash scripts detailed in the READMEs of each container image. Specifically, the full application is detailed in [erobs-common-img](./docker/erobs-common-img/README.md).
+## Running Example Applications (Legacy - For Learning Only)
 
-## Running some example applications
+**⚠️ The following examples use deprecated docker configurations. See above for current deployment workflow.**
 
 In order to run the `ur-example` with Docker, follow this procedure:
 

build.sh

@@ -4,16 +4,17 @@ set -e
 # Set the default build type
 BUILD_TYPE=RelWithDebInfo
 
-source /opt/ros/${ROS_DISTRO}/setup.bash && colcon build \
-        --merge-install \
-        --symlink-install \
-        --packages-select ur3e_hande_robot_description serial robotiq_driver pdf_beamtime_interfaces \
-        --cmake-args "-DCMAKE_BUILD_TYPE=$BUILD_TYPE" "-DCMAKE_EXPORT_COMPILE_COMMANDS=On" \
-        --cmake-args "-DCMAKE_CXX_FLAGS=-Wall -Wextra -Wpedantic"
+# source /opt/ros/${ROS_DISTRO}/setup.bash && colcon build 
+#         --merge-install \
+#         --symlink-install \
+#         --packages-select ur3e_hande_robot_description serial robotiq_driver pdf_beamtime_interfaces \
+#         --cmake-args "-DCMAKE_BUILD_TYPE=$BUILD_TYPE" "-DCMAKE_EXPORT_COMPILE_COMMANDS=On" \
+#         --cmake-args "-DCMAKE_CXX_FLAGS=-Wall -Wextra -Wpedantic"
 
 colcon build \
         --merge-install \
         --symlink-install \
         --executor sequential \
         --cmake-args "-DCMAKE_BUILD_TYPE=$BUILD_TYPE" "-DCMAKE_EXPORT_COMPILE_COMMANDS=On" \
-        -Wall -Wextra -Wpedantic
+        -Wall -Wextra -Wpedantic \
+        --packages-skip epick_moveit_studio epick_config

docker/DEPRECATED.md

@@ -0,0 +1,26 @@
+# ⚠️ DEPRECATED
+
+**This directory is deprecated and should not be used for new development.**
+
+## Why is this deprecated?
+
+The container images in this directory are being deprecated because:
+
+1. **CI/CD uses devcontainer**: The GitHub Actions workflows use `.devcontainer/Dockerfile` for testing and building
+2. **Different source dependencies**: These images will soon depend on different source code
+3. **Inconsistent with development workflow**: The devcontainer approach provides better integration with modern development tools
+
+## What should you use instead?
+
+For development and deployment, use:
+- **Development**: `.devcontainer/Dockerfile` for VSCode devcontainer development
+- **Deployment**: Container images published to GitHub Container Registry (GHCR) built from the devcontainer
+- **CI/CD**: Automated workflows in `.github/workflows/`
+
+## Timeline
+
+This directory will be removed or archived in a future release.
+
+## Questions?
+
+See the main [README.md](../README.md) for current deployment instructions.

docker/README.md

@@ -1,4 +1,10 @@
-# To run the demo contianers
+# ⚠️ DEPRECATED - See [DEPRECATED.md](./DEPRECATED.md)
+
+**This directory is deprecated. Use `.devcontainer/Dockerfile` and GHCR images instead.**
+
+---
+
+# To run the demo contianers for Learning purposes
 
 ```bash
 cd docker/ursim

scripts/pdf-launch-scripts/DEPRECATED.md

@@ -0,0 +1,41 @@
+# ⚠️ DEPRECATED
+
+**This directory is deprecated and should not be used for new development or deployment.**
+
+## Why is this deprecated?
+
+The container launch scripts in this directory are being deprecated because:
+
+1. **Gatekept container images**: These scripts reference GHCR images behind other accounts that you cannot control:
+   - `ghcr.io/chandimafernando/erobs-common-img:latest` (personal account)
+   - `ghcr.io/nsls2/erobs-ur-driver:latest`
+   - `ghcr.io/nsls2/ur-hande-draft:latest`
+   - `ghcr.io/nsls2/erobs-bsui:latest`
+
+2. **Old architecture**: These containers use the deprecated `docker/` directory approach that clones and builds source code inside the container at build time
+
+3. **Inconsistent with CI/CD**: The GitHub Actions workflows now use `.devcontainer/Dockerfile` for building and publishing to GHCR
+
+## What should you use instead?
+
+For deployment, use the new unified container workflow:
+
+### Development
+- Use `.devcontainer/Dockerfile` with VSCode devcontainer for local development
+
+### Deployment
+1. **Pull from GHCR**: The GitHub Actions workflow automatically builds and publishes container images to your repository's GHCR when you push version tags
+2. **Run containers**: Launch ROS2 nodes directly from the unified container image using `ros2 launch` commands
+3. **See the main README**: Refer to [../../README.md](../../README.md) for current deployment instructions
+
+### CI/CD
+- Automated builds are configured in `.github/workflows/docker-build.yaml`
+- Push a version tag (e.g., `v1.0.0`) to trigger automated builds
+
+## Timeline
+
+This directory will be removed or archived in a future release.
+
+## Questions?
+
+See the main [README.md](../../README.md) for current deployment instructions.

scripts/pdf-launch-scripts/README.md

@@ -1,3 +1,9 @@
+# ⚠️ DEPRECATED - See [DEPRECATED.md](./DEPRECATED.md)
+
+**This directory is deprecated. Use `.devcontainer/Dockerfile` and GHCR images instead.**
+
+---
+
 # File Contents
 Docker launch scripts for ROS2 at the PDF beamline. Detailed documentation on building and deploying containers at NSLS-II
 can be found in our [documentation](https://docs.nsls2.bnl.gov/docs/how-to/containers.html).