Merge pull request #1 from AD-SDL/clean_make

Remove Makefile

.gitignore

@@ -168,3 +168,6 @@ cython_debug/
 
 # Ruff
 .ruff_cache
+
+# Outputs
+experiment_output.jpg

README.md

@@ -4,33 +4,25 @@ This is a template Workcell repository for the [Workcell Execution Interface](ht
 
 ## Dependencies
 
-- This template uses GNU make and a handful of makefiles for configuration and as a command runner. You can run `make help` for a complete list of supported `make` commands and a brief description of what they do.
 - You'll need [docker installed](https://docs.docker.com/engine/install/)
-    - Make sure to follow the [post installation steps](https://docs.docker.com/engine/install/linux-postinstall/) to enable non-root user access
+    - Make sure on Linux to follow the [post installation steps](https://docs.docker.com/engine/install/linux-postinstall/) to enable non-root user access
+- You'll need Python 3.8 or greater installed to run the Example Application.
 
 ## Configuration
 
 As much as possible, this workcell is designed to be configured declaratively. This is done with:
 
-- Build rules and targets defined in the `Makefile` and included makefiles in the `make/` subdirectory.
-- A `.env` file, generated by `make` based on configuration declared in `make/config.mk`
+- A `.env` file, which you can create by copying `example.env` (`cp example.env .env` on Linux).
 - The `compose.yaml` docker compose file, which defines a "stack" of containers that control your workcell
-    - Note: whenever you see `${SOME_VARIABLE_NAME}` in the compose file, this value is being taken from the `.env` generated by `make`
-- The `Dockerfile` in `example_app/`, which allows you to customize your experiment applications container (e.g. you can add any software or python packages that your code depends on in here)
+    - Note: whenever you see `${SOME_VARIABLE_NAME}` in the compose file, this value is being taken from the `.env`
 - The Workcell Config in `workcell_defs/example_workcell.yaml`, which allows you to define WEI specific configuration for your workcell
 
-## Building, Running, and Managing your Workcell and Experiment Application
+## Building, Running, and Managing your Workcell
 
-Here are some common commands you can use to manage this workcell:
+- `docker compose up` to start your workcell (`docker compose up -d` starts it in the background)
+- `docker compose down` to stop a workcell
+- `docker compose logs -f` to view the output
 
-- `make build`: build the workcell, incorporating any changes as needed
-- `make start`: start just the containers, but don't run the experiment application
-- `make run`: run your experiment application (run `make start` first)
-- `make exec`: opens a terminal inside your application container
-- `make stop`: stops the workcell and any currently running applications
+## Experiment Application
 
-For a complete list of supported commands, you can run `make` or `make help`.
-
-## Using Diaspora
-
-To use Diaspora for logging events, you can change `USE_DIASPORA` to `true` in the `Makefile` or run `make <subcommand> USE_DIASPORA=true`
+See `example_app/README.md` for info on installing and running the example application using your workcell.

compose.yaml

@@ -1,22 +1,6 @@
 name: example_workcell
+include: ['wei.compose.yaml']
 services:
-  ############
-  # Your app #
-  ############
-  example_app:
-    container_name: ${APP_NAME}
-    build:
-      context: ./example_app
-      dockerfile: ${DOCKERFILE}
-    volumes:
-      - ./example_app:/home/app/example_app # Mount your app code, so you can edit it without rebuilding the image
-      - ${WEI_DATA_DIR}:/home/app/.wei # Mount the wei data directory
-      - diaspora_config:/home/app/.diaspora
-    command: python example_app/example_app.py
-    env_file:
-      - .env
-    profiles: [example_app]
-
   ###########
   # Modules #
   ###########
@@ -38,52 +22,3 @@ services:
     command: python webcam_module/src/webcam_rest_node.py --port 2001
     env_file:
       - .env
-
-  #####################
-  # WEI Core Services #
-  #####################
-  wei_server:
-    image: ghcr.io/ad-sdl/wei
-    container_name: wei_server
-    ports:
-      - 8000:8000
-    volumes:
-      - ${WORKCELLS_DIR}:/workcell_defs
-      - ${WEI_DATA_DIR}:/home/app/.wei
-      - diaspora_config:/home/app/.diaspora
-    command: python3 -m wei.server --workcell /workcell_defs/${WORKCELL_FILENAME} --use_diaspora ${USE_DIASPORA}
-    env_file:
-      - .env
-    depends_on:
-      - wei_redis
-  wei_engine:
-    image: ghcr.io/ad-sdl/wei
-    container_name: wei_engine
-    volumes:
-      - ${WORKCELLS_DIR}:/workcell_defs
-      - ${WEI_DATA_DIR}:/home/app/.wei
-    env_file:
-      - .env
-    command: python3 -m wei.engine --workcell /workcell_defs/${WORKCELL_FILENAME} --use_diaspora ${USE_DIASPORA}
-    environment:
-     - PYTHONUNBUFFERED=1 # Fix weird bug with empty logging
-    depends_on:
-      - wei_redis
-      - wei_server
-      - sleep_node
-      - webcam_node
-  wei_redis:
-    image: redis
-    container_name: wei_redis
-    ports:
-      - 6379:6379
-    volumes:
-      - ${REDIS_DIR}:/data
-    command: redis-server --save 60 1 --loglevel warning
-
-################
-# Data Storage #
-################
-volumes:
-  diaspora_config:
-    driver: local

example.env

@@ -0,0 +1,8 @@
+# Copy this file and rename to `.env` to set environment variables for docker-compose
+USER_ID=
+GROUP_ID=
+PROJECT_DIR=~/workspace/wei_template_workcell
+WEI_DATA_DIR=~/.wei
+REDIS_DIR=~/.wei/redis
+WORKCELL_FILENAME=example_workcell.yaml
+WORKCELLS_DIR=${PROJECT_DIR}/workcell_defs

example_app/README.md

@@ -1 +1,11 @@
 # Example App
+
+In the `example_app` directory:
+
+```
+python -m venv .venv
+source .venv/bin/activate
+pip install -e .
+# After starting the workcell:
+python example_app.py
+```

example_app/example_app.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-"""Runs an example of a WEI workflow"""
+"""Example experiment application that uses the WEI client to run a workflow."""
 
 import json
 from pathlib import Path
@@ -9,12 +9,12 @@
 
 def main() -> None:
     """Runs an example WEI workflow"""
+    # This defines the Experiment object that will communicate with the WEI server
+    exp = ExperimentClient("localhost", "8000", "Example_Program")
+
     # The path to the Workflow definition yaml file
     wf_path = Path(__file__).parent / "workflows" / "example_workflow.yaml"
 
-    # This defines the Experiment object that will communicate with the WEI server
-    exp = ExperimentClient("wei_server", "8000", "Example_Program")
-
     # This runs the workflow
     flow_info = exp.start_run(
         wf_path.resolve(),
@@ -28,7 +28,7 @@ def main() -> None:
     # The below line can be used to fetch the result and save it in our local directory
     exp.get_file(
         flow_info["hist"]["Take Picture"]["action_msg"],
-        "/home/app/.wei/experiment_output.jpg",
+        "experiment_output.jpg",
     )
 
 

example_app/pyproject.toml

@@ -4,9 +4,7 @@ version = "1.0.0"
 description = "A simple example WEI application that waits for a set amount of time, then takes a picture with a webcam."
 authors = [{name = "Ryan D. Lewis", email="[email protected]"}]
 dependencies = [
-    # "fastapi>=0.103",
-    # "uvicorn>=0.14.0",
-    # "ad_sdl.wei",
+    "ad_sdl.wei",
 ]
 requires-python = ">=3.8.1"
 readme = "README.md"

example_app/workflows/example_workflow.yaml

@@ -11,17 +11,25 @@ modules:
 flowdef:
   #This defines a step in the workflow. Each step represents an action on a single module
   #This is a human legible name for the step
-  - name: Sleep workcell for t seconds
+  # - name: Sleep workcell for t seconds
   #This defines which module the action will run on, in this case, a test node that simply sleeps for t seconds
-    module: sleeper
+    # module: sleeper
   #This tells the module which action in its library to run, in this case grabbing a wellplate from one of the storage tower
-    action: sleep
+    # action: sleep
   #These arguments specify the parameters for the action above, in this case, which tower the arm will pull a plate from.
+    # args:
+      # t: "payload.wait_time"
+  #This represents checks that will take place before the system runs, in this case, there are none specified
+    # checks: null
+  #This is a place for additional notes
+    # comment: Sleep for 5 seconds before we take a picture
+
+  - name: Sleep workcell for t seconds
+    module: sleeper
+    action: sleep
     args:
       t: "payload.wait_time"
-  #This represents checks that will take place before the system runs, in this case, there are none specified
     checks: null
-  #This is a place for additional notes
     comment: Sleep for 5 seconds before we take a picture
 
   - name: Take Picture