Metadata-Version: 2.4
Name: automator-tsl
Version: 0.0.1
Summary: Automated imaging of microbial plates: Raspberry Pi controller, web UI, and reference assets
Author: Rohan R
Project-URL: Repository, https://github.com/rotsl/Automator
Project-URL: Documentation, https://rotsl.github.io/Automator/
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
License-File: LICENSE-MIT
License-File: LICENSE-CERN-OHL-S
License-File: LICENSE-CC-BY-4.0
License-File: documentation/ Third_Party_Notices.md
Requires-Dist: numpy==1.26.4
Requires-Dist: opencv-python==4.10.0.84
Requires-Dist: opencv-contrib-python==4.10.0.84
Requires-Dist: Pillow==11.3.0
Requires-Dist: Flask==3.0.3
Requires-Dist: werkzeug==3.0.3
Requires-Dist: Flask-SocketIO==5.5.1
Requires-Dist: python-socketio==5.14.2
Requires-Dist: eventlet==0.40.3
Requires-Dist: requests==2.32.4
Requires-Dist: python-dotenv==1.0.1
Requires-Dist: qrcode==8.0
Requires-Dist: segno==1.6.6
Requires-Dist: zxing-cpp==2.2.0
Requires-Dist: onnxruntime==1.18.0
Requires-Dist: pyserial==3.5
Requires-Dist: reportlab==4.2.0
Requires-Dist: huggingface_hub
Provides-Extra: pi
Requires-Dist: picamera2==0.3.31; extra == "pi"
Requires-Dist: RPi.GPIO==0.7.1; extra == "pi"
Requires-Dist: gpiozero==2.0.1; extra == "pi"
Dynamic: license-file

# Automator: automated imaging of microbial plates

Automator is an open-source system for real-time automated imaging, tracking, and analysis of microbial plates, integrating motion control, camera acquisition, and scheduling on Raspberry Pi hardware using Klipper, Moonraker, and a custom Python-based controller and web interface.

This package is the **installable distribution** of the Automator controller and its reference assets — for the full source repository, contributor guidelines, and changelog, see <https://github.com/rotsl/Automator>.

## Install on a new Raspberry Pi

### 1. System prerequisites (Raspberry Pi OS lite 64-bit)

```bash
sudo apt update
sudo apt install -y \
  python3 python3-venv python3-dev \
  libcamera-dev libcamera-apps v4l-utils \
  libjpeg-dev libpng-dev libatlas-base-dev
```

### 2. Create a virtual environment and install the package

```bash
python3 -m venv venv_clean
source venv_clean/bin/activate
pip install --upgrade pip
pip install automator-tsl[pi]
```

The `[pi]` extra pulls in the Raspberry-Pi-only hardware dependencies (`picamera2`, `RPi.GPIO`, `gpiozero`). Omit it if you're only inspecting the bundled documentation/templates on a non-Pi machine.

### 3. Fetch the plate-detection model

The YOLO ONNX model used for plate detection is not bundled in this package (to keep it small) — fetch it from Hugging Face after install:

```bash
automator-fetch-model
```

This downloads `bestnew.onnx` from [`rotsl/petri_dish_yolo`](https://huggingface.co/rotsl/petri_dish_yolo) and places it at `~/Automator/data/bestnew.onnx`.

### 4. Generate security keys, configure Klipper/Moonraker, and start the controller

Follow the full installation steps in [HandOver.md](https://github.com/rotsl/Automator/blob/main/documentation/HandOver.md), then start the controller:

```bash
python -m dev2.maincontroller
```

## Full documentation

The complete documentation site, including the step-by-step user guide, admin/maintainer handover, and run book, is published at:

<https://rotsl.github.io/Automator/>

## In this package

Alongside the Python code, this package installs a copy of the project's reference assets under `share/automator/` in your environment's install prefix:

- `share/automator/documentation/` — user and admin documentation (markdown + images)
- `share/automator/hardware/` — schematics, datasheets, and hardware images
- `share/automator/mechanical/` — assembly images, license, and mechanical guide
- `share/automator/data/` — `calibration.json`

## License

This package bundles software (MIT License), hardware design references (CERN Open Hardware Licence v2 - Strongly Reciprocal), and documentation (CC BY 4.0). See [LICENSE](https://github.com/rotsl/Automator/blob/main/LICENSE) for the full breakdown by component, and `LICENSE-MIT`, `LICENSE-CERN-OHL-S`, `LICENSE-CC-BY-4.0` for the individual license texts (all included with this package).

### Recommended citation

```bibtex
@software{R_Automator_Automated_Imaging_20252026,
author = {R, Rohan},
title = {{Automator: Automated Imaging of Microbial Plates}},
url = {https://github.com/rotsl/Automator},
year = {2025–2026}
}
```

## Institutional note

This package as part of the main repository represents research automation tooling developed at [The Sainsbury Laboratory, Norwich.](https://www.tsl.ac.uk)  
It is provided as-is for research and engineering use and is not a certified laboratory instrument unless approved by the institute.

Users are responsible for:

- validating the system for their experimental context  
- complying with local safety, electrical, and biological regulations  
- ensuring appropriate risk assessments are in place  

---
