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AGENTS.md — Operational Rules for Autoprober Agents

Read this before using an AI agent or automation script with this project. The rules here are safety rules for physical machine control.

Absolute Safety Rules

1. Pn:P in GRBL status is not the safety endstop

The CNC controller probe input is not trusted for the optical endstop. Autoprober uses the real GRBL limit flags and an independent oscilloscope measurement instead.

  • <Idle|MPos:...|Pn:P|...> means the GRBL probe flag is active. Ignore it for safety decisions.
  • <Idle|MPos:...|Pn:X|...> means the X limit switch is active.
  • <Idle|MPos:...|Pn:Y|...> means the Y limit switch is active.
  • <Idle|MPos:...|Pn:Z|...> means the Z limit switch is active.
  • Pn:PX, Pn:PY, and Pn:PZ include a probe flag plus a real limit flag; use only the X, Y, or Z part as the real limit condition.

Any code that treats Pn:P as the optical endstop is wrong.

2. The independent endstop signal is oscilloscope Channel 4

The optical endstop is read as a voltage on Channel 4 through the oscilloscope wrapper. Configure the oscilloscope host and port with environment variables, not hardcoded lab addresses.

Required wiring:

  • Endstop OUT to Channel 4 probe tip.
  • Endstop GND to Channel 4 ground clip.
  • Endstop VCC to an external 5V supply.

Voltage interpretation:

Voltage Meaning Action
4.5V to 5.2V Healthy, clear slot OK
1.0V to 4.5V Ambiguous wiring or signal fault STOP
Less than 1.0V Optical beam broken / carriage compressed STOP immediately
Unreadable / disabled channel Scope configuration fault STOP

Use Scope.measure_mean(4) or Scope.read_endstop(channel=4).

3. Monitor Channel 4 continuously during motion

Checking Channel 4 once before a move is not enough. Motion must run with an EndstopMonitor polling in the background. A trigger during a move must issue feed hold immediately.

Example:

from autoprober.cnc import CNC
from autoprober.scope import Scope
from autoprober.safety import EndstopMonitor

scope = Scope(quiet=True)
cnc = CNC()

scope.connect()
cnc.connect()

monitor = EndstopMonitor(
    scope,
    threshold=1.0,
    poll_interval=0.1,
    hold_callback=cnc.feed_hold,
)
monitor.start()
try:
    cnc.move_relative(dx=5, feed=800)
    cnc.wait_for_idle()
finally:
    monitor.stop()

monitor.require_clear()

4. On trigger: stop, report, do not recover automatically

When Channel 4 triggers or faults:

  1. Stop motion with feed hold.
  2. Log what was running, the CNC position if available, and the Channel 4 voltage or error.
  3. Report the stop condition to the operator.
  4. Do not move again until a human operator explicitly clears the condition.

Do not automatically back off Z, jog away, retry, or continue scanning after a trigger. Those are still motion and require operator approval.

Startup Sequence

For a hardware session:

  1. Verify USB enumeration for the CNC and microscope.
  2. Run apps/preflight.py.
  3. Verify Channel 4 is clear with no motion.
  4. Home the CNC with apps/home.py or a monitored $H workflow.
  5. Run apps/calibrate.py over a feature-rich area before coordinate-based scan or probe work.

If USB devices disappear after a reboot, hub change, or controller reset, repeat the startup sequence. Do not trust prior runtime state.

Motion Rules

  • Use autoprober.cnc.CNC; do not open raw serial ports in app scripts.
  • Use autoprober.scope.Scope; do not open raw SCPI sockets in app scripts.
  • Use autoprober.microscope.Microscope; do not shell out for snapshots in app scripts.
  • Any script that moves the CNC must use EndstopMonitor.
  • A real X, Y, or Z limit pin is a stop condition.
  • A hard limit alarm is not a safety strategy. Stay inside the known travel envelope.
  • Homing must complete normally before absolute coordinate work.
  • If homing appears to complete too quickly or the machine position does not change, stop and investigate.

Recommended feed-rate ranges:

  • Clear travel: 1000 to 1500 mm/min.
  • Scan-step XY moves: 500 to 800 mm/min.
  • Z descent near contact: 100 to 200 mm/min.
  • Calibration moves: about 500 mm/min.

Use a Z hop for XY travel when the pogo pin or carriage could drag on a target:

cnc.move_relative(dz=+z_hop)
cnc.move_absolute(x=target_x, y=target_y)
cnc.move_relative(dz=-z_hop)

Calibration Rules

  • Calibration is runtime state, not source-controlled project data.
  • Read calibration from AUTOPROBER_RUNTIME_ROOT through the project helpers.
  • Run calibration after microscope remounting, refocus, meaningful Z changes, or any mechanical change that can affect field of view.
  • Do not save calibration from a blank or low-feature image.

Logging Rules

Use autoprober.logging.log() for meaningful actions. The log path is configured by AUTOPROBER_LOG_PATH.

Recommended log sources:

  • operator for manual/operator-driven script actions.
  • cnc for CNC wrapper commands and responses.
  • scope for oscilloscope wrapper activity.
  • microscope for microscope capture/stream activity.
  • calibrate, preflight, and dashboard for app-level events.
  • endstop-mon for safety monitor stop conditions.

Do not commit runtime logs.

Public Release Rules

  • Do not commit lab-specific IP addresses, hostnames, usernames, SSH aliases, credentials, or local filesystem paths.
  • Do not commit calibration files, flat-field images, microscope captures, stitched target maps, probe-review artifacts, or runtime logs unless they are explicitly prepared as public examples.
  • Keep hardware addresses configurable through environment variables.
  • Keep deployment instructions generic to a hardware host.
  • Keep CAD files limited to the intended public printable parts.

Current Public File Layout

apps/          Operator-facing scripts and dashboard backend
autoprober/    Reusable Python package for CNC, scope, microscope, safety, logs
dashboard/     Single-page dashboard frontend
docs/          Safety, architecture, device, and operations docs
cad/           Public printable STL files
config/        Example environment configuration

References

Read these public docs before running hardware:

  1. AGENTS.md
  2. README.md
  3. docs/safety.md
  4. docs/operations.md
  5. docs/architecture.md
  6. docs/devices/*.md