Define, validate, run, and log multi-step BioLM protocol workflows.
Protocols chain model calls and data transforms in YAML; use these commands to scaffold files, check schema compliance, inspect definitions, and send results to MLflow.
Usage
biolm protocol [OPTIONS] COMMAND [ARGS]...
biolm protocol init
Create a new protocol YAML file from a blank template or bundled example.
Generated files can be validated immediately with biolm protocol validate.
Usage
biolm protocol init [OPTIONS] [FILENAME]
Options
- -o, --output <output>
Output file path (default: protocol.yaml)
- -e, --example <example>
Use an example template
- --list-examples
List available example templates
- -f, --force
Overwrite existing file
- -i, --interactive
Interactive mode to select example
Arguments
- FILENAME
Optional argument
biolm protocol list
List protocols registered on the BioLM platform (platform listing coming soon).
Today, inspect local YAML files with biolm protocol show or validate them with
biolm protocol validate.
Usage
biolm protocol list [OPTIONS]
biolm protocol log
Log protocol run results to MLflow using the protocol outputs configuration.
Creates or updates an experiment at account/workspace/protocol and records metrics,
parameters, and artifacts from a results file.
Usage
biolm protocol log [OPTIONS] RESULTS
Options
- --outputs <outputs>
Outputs config YAML or protocol YAML file
- --account <account>
Required Account name (experiment path: account/workspace/protocol)
- --workspace <workspace>
Required Workspace name (experiment path: account/workspace/protocol)
- --protocol <protocol_slug>
Required Protocol name/slug (experiment path: account/workspace/protocol)
- --dry-run
Prepare data without logging to MLflow
- --mlflow-uri <mlflow_uri>
MLflow tracking URI
- --aggregate-over <aggregate_over>
Compute aggregates over selected rows or all rows
- Options:
selected | all
- --protocol-name <protocol_name>
Protocol display name for metadata (default: from protocol YAML)
- --protocol-version <protocol_version>
Protocol version for metadata
Arguments
- RESULTS
Required argument
biolm protocol run
Execute a protocol defined in a YAML file (execution support coming soon).
Validates the file path today; full remote execution will run the task graph on the platform.
Usage
biolm protocol run [OPTIONS] PROTOCOL_FILE
Arguments
- PROTOCOL_FILE
Required argument
biolm protocol show
Show a formatted report for a protocol from a local YAML file or platform ID.
Displays tasks, dependencies, inputs/outputs, and configuration in a readable layout.
Usage
biolm protocol show [OPTIONS] [PROTOCOL_SOURCE]
Arguments
- PROTOCOL_SOURCE
Optional argument
biolm protocol validate
Validate a protocol YAML file against the JSON schema and internal rules.
Checks YAML syntax, task references, circular dependencies, and template expressions.
Usage
biolm protocol validate [OPTIONS] PROTOCOL_FILE
Options
- --json
Output results in JSON format
Arguments
- PROTOCOL_FILE
Required argument