Labs · Liquid handling and fluidics

Fish Sorter pneumatic valve controller (Wago, Modbus TCP)

Fish Sorter pneumatic valve controller (Wago, Modbus TCP), adapted from czbiohub-sf/python-fish-sorter. It reads function_code and function_echo; sets draw_time_ms and expel_time_ms; runs set_pressure, set_vacuum, idle_atmospheric and safe_pneumatics. set_pressure: pressure on or off: writes the upstream press_on or press_off code and waits until the controller has taken it. A hardware driver: the market serves its fake backend, so no instrument is needed.

hardwareRisk R2BSD-3-Clausecontract_checkedserved on the fake backend
openai4s lab add labs/czbiohub-sf__python-fish-sorter

Install

Three ways to run this device. Each one serves its fake backend: no instrument, no simulator install and no upstream checkout.

OpenAI4S (one command)

shell
openai4s lab add labs/czbiohub-sf__python-fish-sorter

Installs the device into the OpenAI4S Lab on its fake backend and starts it. First time? See setup below.

Or, in the workbench, open the Lab tab → Market → Install.

Standalone MHS endpoint

shell
git clone --depth 1 https://github.com/PKU-YuanGroup/OpenMHS.git && cd OpenMHS
PYTHONPATH=MHS/sdk/src python3 -m mhs serve labs/czbiohub-sf__python-fish-sorter --port 7400
# in a second terminal, from the same directory:
PYTHONPATH=MHS/sdk/src python3 -m mhs describe --endpoint http://127.0.0.1:7400

Serves the device as an MHS endpoint on port 7400 from an OpenMHS clone (Python 3.10 or later, standard library only); describe prints what it offers.

Any MCP host (Claude Desktop, Cursor, …)

mcp configuration
{
  "mcpServers": {
    "python-fish-sorter": {
      "command": "python3",
      "args": [
        "-m",
        "mhs",
        "serve",
        "labs/czbiohub-sf__python-fish-sorter",
        "--mcp"
      ],
      "env": {
        "PYTHONPATH": "/path/to/OpenMHS/MHS/sdk/src"
      }
    }
  }
}

Add this server to the host's MCP configuration and replace /path/to/OpenMHS with the path of your OpenMHS clone. The host starts the server and talks to it on stdin and stdout.

What it does

Measures

  • function_code
  • function_echo

Adjusts

  • draw_time_ms
  • expel_time_ms

Actions

set_pressure
Pressure on or off: writes the upstream press_on or press_off code and waits until the controller has taken it
set_vacuum
Vacuum on or off: writes the upstream vac_on or vac_off code (the controller program sets or clears its Vacuum output) and waits until the controller has taken it
idle_atmospheric
Atmospheric idle: writes the upstream func_idle code and waits until the controller has taken it
safe_pneumatics
Safe-state stop path: writes the func_idle code and waits until the controller has taken it; takes no input

Names as the driver declares them. Units, limits and the safety declaration are in the package's REFERENCE.md.

First-time setup

The OpenAI4S workbench with the OpenMHS lab, from a source checkout:

shell
# OpenAI4S workbench with the OpenMHS lab (source checkout)
git clone --recursive https://github.com/PKU-YuanGroup/OpenAI4S.git
cd OpenAI4S && ./setup.sh && source .venv/bin/activate
openai4s lab add labs/czbiohub-sf__python-fish-sorter
openai4s serve        # open the Lab tab

The standalone endpoint and the MCP server need only an OpenMHS clone and Python 3.10 or later. More in the market's getting-started guide and on the OpenAI4S host page.

Source and evidence

Pinned commit
a8f2409fa692
Licence
BSD-3-Clause
Stars
3
Evidence
contract_checked on the fake backend
Backends
fake, hardware

The driver package MHS/drivers/labs/czbiohub-sf__python-fish-sorter wraps the upstream code at the pinned commit. Its REFERENCE.md documents the full contract: every value, action, unit, limit and the safety declaration.