MADSci Experiments Skill

MADSci Experiments

MADSci provides four experiment modalities, all built on ExperimentBase which uses MadsciClientMixin (composition, not RestNode inheritance). Choose the right modality for your use case, then implement run_experiment().

Key Files

| File | Purpose | |------|---------| | src/madsci_experiment_application/madsci/experiment_application/experiment_base.py | Base class, lifecycle, context manager | | src/madsci_experiment_application/madsci/experiment_application/experiment_script.py | Simple run-once modality | | src/madsci_experiment_application/madsci/experiment_application/experiment_notebook.py | Jupyter notebook modality | | src/madsci_experiment_application/madsci/experiment_application/experiment_tui.py | Terminal UI modality | | src/madsci_experiment_application/madsci/experiment_application/experiment_node.py | REST server modality | | src/madsci_common/madsci/common/types/experiment_types.py | ExperimentDesign, Experiment, ExperimentStatus | | src/madsci_client/madsci/client/experiment_client.py | Experiment Manager HTTP client | | src/madsci_client/madsci/client/client_mixin.py | MadsciClientMixin with 7 lazy client properties | | src/madsci_common/madsci/common/bundled_templates/experiment/ | Templates for all 4 modalities |

Choosing a Modality

| Modality | Best For | Entry Point | Interactive? | |----------|----------|-------------|-------------| | ExperimentScript | Batch processing, automated pipelines | run() or main() | No | | ExperimentNotebook | Exploratory analysis, Jupyter workflows | start() / end() | Yes (cell-by-cell) | | ExperimentTUI | Operator-attended experiments needing pause/cancel | run_tui() | Yes (terminal) | | ExperimentNode | Remote-controlled experiments via REST API | start_server() | Via HTTP |

Architecture

ExperimentBase (MadsciClientMixin)
  ├── ExperimentScript     # run() -> manage_experiment() -> run_experiment()
  ├── ExperimentNotebook   # start() / end() with Rich display
  ├── ExperimentTUI        # Textual TUI with threading.Event pause/cancel
  └── ExperimentNode       # Wraps RestNode internally, exposes run_experiment as action

Key design choice: ExperimentBase uses composition (MadsciClientMixin), not inheritance from RestNode. Only ExperimentNode creates a RestNode internally when it needs server capabilities.

ExperimentDesign vs Experiment

ExperimentDesign: Template/blueprint. Defines experiment_name, description, resource_conditions. Reusable across runs. Can be loaded from YAML.
Experiment: Runtime instance. Has experiment_id (ULID), status, timestamps, ownership. Created by start_experiment_run().

from madsci.common.types.experiment_types import ExperimentDesign

design = ExperimentDesign(
    experiment_name="Synthesis Optimization",
    experiment_description="Optimize reaction conditions for compound X",
)

# Or load from YAML
design = ExperimentDesign.from_yaml("experiment_design.yaml")

ExperimentScript (Simplest Modality)

from madsci.experiment_application.experiment_script import ExperimentScript
from madsci.common.types.experiment_types import ExperimentDesign

class SynthesisExperiment(ExperimentScript):
    experiment_design = ExperimentDesign(
        experiment_name="Synthesis Run",
        experiment_description="Automated synthesis workflow",
    )

    def run_experiment(self, sample_id: str = "default", cycles: int = 3) -> dict:
        """Core experiment logic. Called within manage_experiment() context."""
        results = []
        for i in range(cycles):
            result = self.workcell_client.run_workflow(
                "synthesis", parameters={"sample_id": sample_id, "cycle": i}
            )
            results.append(result)
            self.logger.info("Cycle completed", cycle=i, result=result)

        return {"sample_id": sample_id, "results": results}

if __name__ == "__main__":
    SynthesisExperiment.main(sample_id="ABC123", cycles=5)

Entry points:

run(*args, **kwargs): Instance method. Merges config args with passed args.
main(*args, **kwargs): Class method. Creates instance and calls run().

Config class: ExperimentScriptConfig adds run_args and run_kwargs fields for CLI/env configuration.

ExperimentNotebook (Jupyter)

Designed for cell-by-cell interactive use in Jupyter notebooks.

# Cell 1: Setup
from my_experiment import MyNotebookExperiment
exp = MyNotebookExperiment()

# Cell 2: Start
exp.start(run_name="Exploration Run 1")

# Cell 3: Execute
result = exp.run_workflow("characterize", parameters={"sample": "S1"})

# Cell 4: Visualize
exp.display(result, title="Characterization Results")

# Cell 5: End
exp.end()

Or use as context manager:

with MyNotebookExperiment() as exp:
    result = exp.run_workflow("synthesis")
    exp.display(result, title="Results")

Key methods:

start(run_name, run_description): Starts experiment, displays status. Returns self.
end(status): Ends experiment, displays summary. Returns self.
run_workflow(workflow_name, parameters, display_result): Convenience wrapper for workcell_client.run_workflow().
display(data, title): Rich-formatted display (falls back to plain print).

Config class: ExperimentNotebookConfig adds rich_output: bool = True and auto_display_results: bool = True.

ExperimentTUI (Terminal UI)

Interactive terminal interface with pause/cancel controls via Textual.

from madsci.experiment_application.experiment_tui import ExperimentTUI
from madsci.common.types.experiment_types import ExperimentDesign

class OperatorExperiment(ExperimentTUI):
    experiment_design = ExperimentDesign(
        experiment_name="Operator-Assisted Synthesis",
    )

    def run_experiment(self) -> dict:
        results = []
        for step in range(10):
            self.check_experiment_status()  # Handles pause/cancel locally
            result = self.workcell_client.run_workflow("step", parameters={"n": step})
            results.append(result)
        return {"steps_completed": len(results)}

if __name__ == "__main__":
    OperatorExperiment().run_tui()

Thread-safe controls:

request_pause() / request_resume() / request_cancel(): Called from TUI thread
check_experiment_status(): Called in experiment thread. Uses threading.Event (no server round-trips). Raises ExperimentCancelledError if cancelled. Blocks while paused.

Config class: ExperimentTUIConfig adds refresh_interval: float = 1.0 and show_logs: bool = True.

Requires: pip install textual (optional dependency).

ExperimentNode (REST Server)

Exposes run_experiment() as a node action, controllable via the workcell manager.

from madsci.experiment_application.experiment_node import ExperimentNode
from madsci.common.types.experiment_types import ExperimentDesign

class RemoteExperiment(ExperimentNode):
    experiment_design = ExperimentDesign(
        experiment_name="Remote Synthesis",
    )

    def run_experiment(self, sample_id: str, temperature: float = 25.0) -> dict:
        return self.workcell_client.run_workflow(
            "process", parameters={"sample_id": sample_id, "temp": temperature}
        )

if __name__ == "__main__":
    RemoteExperiment().start_server()

Internals: Creates a RestNode instance internally. Wraps run_experiment as a non-blocking action inside manage_experiment() context.

Config class: ExperimentNodeConfig adds server_host: str = "0.0.0.0", server_port: int = 6000, cors_enabled: bool = True.

Lifecycle and Context Manager

`manage_experiment()` (Recommended)

with self.manage_experiment(run_name="Run 1") as exp:
    # Experiment started, logging context established
    result = exp.workcell_client.run_workflow("my_workflow")
    # On success: end_experiment(COMPLETED) called automatically
    # On exception: handle_exception() called, then re-raised

The context manager:

Calls start_experiment_run() -> registers with Experiment Manager
Sets up hierarchical logging context (experiment_id, experiment_name, run_name, experiment_type)
Yields self
On success: end_experiment(COMPLETED)
On exception: handle_exception() then re-raises

Manual lifecycle

exp.start_experiment_run(run_name="Manual Run")
try:
    exp.run_experiment()
    exp.end_experiment(status=ExperimentStatus.COMPLETED)
except Exception as e:
    exp.handle_exception(e)
    raise

Exception handling

Override handle_exception() for custom behavior:

def handle_exception(self, exception: Exception) -> None:
    if isinstance(exception, RecoverableError):
        self.logger.warning("Recoverable error, retrying", error=str(exception))
        return  # Don't end experiment
    super().handle_exception(exception)  # Logs error + ends with FAILED

ExperimentStatus

class ExperimentStatus(str, Enum):
    IN_PROGRESS = "in_progress"
    PAUSED = "paused"
    COMPLETED = "completed"
    FAILED = "failed"
    CANCELLED = "cancelled"
    UNKNOWN = "unknown"

Exception Types

from madsci.common.exceptions import (
    ExperimentCancelledError,    # Raised when experiment cancelled externally
    ExperimentFailedError,       # Raised when experiment fails externally
    ExperimentPauseTimeoutError, # Raised when pause exceeds max_pause_wait
)

Client Access (via MadsciClientMixin)

All experiment modalities provide 7 lazy-initialized client properties:

self.event_client       # EventClient - logging and events
self.logger             # Alias for event_client
self.resource_client    # ResourceClient - inventory
self.data_client        # DataClient - data storage
self.experiment_client  # ExperimentClient - experiment lifecycle
self.workcell_client    # WorkcellClient - workflow execution
self.location_client    # LocationClient - locations
self.lab_client         # LabClient - lab coordination

Clients are created on first access. URLs resolved from config or lab context (service discovery).

Configuration

All configs inherit from ExperimentBaseConfig (MadsciBaseSettings, env prefix EXPERIMENT_):

# Common fields (ExperimentBaseConfig):
lab_server_url: Optional[AnyUrl]         # Lab manager for service discovery
event_server_url: Optional[AnyUrl]       # Override Event Manager URL
experiment_server_url: Optional[AnyUrl]  # Override Experiment Manager URL
workcell_server_url: Optional[AnyUrl]    # Override Workcell Manager URL
data_server_url: Optional[AnyUrl]        # Override Data Manager URL
resource_server_url: Optional[AnyUrl]    # Override Resource Manager URL
location_server_url: Optional[AnyUrl]    # Override Location Manager URL
max_pause_wait: Optional[float]          # Max seconds to wait while paused (None = forever)

Config files searched via walk-up: settings.yaml, experiment.settings.yaml, .env, experiment.env.

Creating Experiments from Templates

madsci new experiment
# Choose modality: script, notebook, tui, node
# Provide: experiment_name, description

Templates in src/madsci_common/madsci/common/bundled_templates/experiment/:

script/ -> {name}.py
notebook/ -> {name}.ipynb
tui/ -> {name}_tui.py
node/ -> {name}_node.py

Checking Experiment Status (Pause/Cancel)

Call check_experiment_status() at natural checkpoints in long-running experiments:

def run_experiment(self):
    for batch in batches:
        self.check_experiment_status()  # Blocks if paused, raises if cancelled
        process(batch)

ExperimentTUI behavior: Uses local threading.Event (no network calls). Other modalities: Polls Experiment Manager with exponential backoff (5s -> 60s). Logs "Still waiting" every 5 minutes.

Common Pitfalls

Override run_experiment(), not run(): run() handles lifecycle; run_experiment() is your logic
Use manage_experiment() context manager: Ensures proper start/end and exception handling
ULID not UUID: Use new_ulid_str() for any IDs you generate
Notebook start/end: Must call start() before run_workflow() and end() when done
TUI requires textual: pip install textual or it raises ImportError
ExperimentApplication is deprecated: Use the 4 modalities above instead (removal in v0.8.0)
Client URLs: Set via config, env vars (EXPERIMENT_EVENT_SERVER_URL), or lab context (service discovery via lab_server_url)
AnyUrl trailing slash: Pydantic's AnyUrl always adds a trailing slash

Agent Skills: MADSci Experiments

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