PyScripts Overview

PyScripts are Pychron's built-in domain-specific language for scripting automated laboratory sequences. Rather than writing general Python, operators write scripts in a constrained vocabulary of commands that map directly to physical laboratory actions — opening valves, firing lasers, collecting ion beam signals, running peak centers. Scripts are stored as .py files in the MetaRepo and are referenced by name in the experiment queue, ensuring that the exact script used for each analysis is version-controlled alongside the data it produced.

Two script types

Type	Base class	File location in MetaRepo	Purpose
Extraction	ExtractionLinePyScript	scripts/extraction/	Controls the extraction line: valve sequencing, laser firing, furnace ramping, gas cleanup
Measurement	MeasurementPyScript	scripts/measurement/	Controls the spectrometer: multicollect sequences, peak center, baseline collection, equilibration waits

Scripts can call each other using gosub, allowing common sequences (e.g. a standard gas cleanup procedure) to be defined once and reused across many experiment types.

Command categories

Extraction scripts have access to:

• Valve commands: open, close, get_valve_state, cycle_valve
• Laser commands: extract, end_extract, set_laser_power, set_laser_temperature
• Timing: sleep, wait_for_condition
• Logging: info, warning
• Control flow: gosub, if/else (standard Python)

Measurement scripts have access to:

• Acquisition commands: multicollect, baselines, peak_center, coincidence
• Spectrometer control: set_deflection, set_integration_time, set_source_parameters
• Position: position_magnet
• Context variables: analysis_type, mass_spectrometer, extract_device, position
• Conditionals: add_termination, add_truncation, add_action, add_queue_condition

Where scripts live

Scripts are stored in the MetaRepo under a scripts/ directory:

<MetaRepoName>/
└── scripts/
    ├── extraction/
    │   ├── air.py
    │   ├── unknown.py
    │   └── blank_unknown.py
    ├── measurement/
    │   ├── argus.py
    │   ├── ngx_multicollect.py
    │   └── peak_center.py
    └── post_measurement/
        └── default.py

Each script in the experiment queue is referenced by its filename without the .py extension (e.g. argus or unknown). Pychron resolves this to the corresponding file in the MetaRepo at run time.

See also

• PyScript API Reference — full command reference
• Conditionals guide — add_termination, add_truncation, add_action (page coming soon)