cellmap_flow.cli.yaml_cli
YAML-based CLI for running multiple models. Similar to cli_v2 but uses YAML configuration files for batch processing.
This dynamically discovers ModelConfig subclasses just like cli_v2, making it easy to add new model types without modifying this file.
Attributes
Functions
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Submit multiple model inference jobs. |
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Run multiple model inference jobs from a YAML configuration file. |
Module Contents
- cellmap_flow.cli.yaml_cli.logger
- cellmap_flow.cli.yaml_cli.run_multiple(models: List[cellmap_flow.models.models_config.ModelConfig], dataset_path: str, charge_group: str, queue: str, wrap_raw: bool = True) None
Submit multiple model inference jobs.
- Parameters:
models – List of ModelConfig instances to run
dataset_path – Base path to the dataset
charge_group – Billing/chargeback group
queue – Job queue name
- cellmap_flow.cli.yaml_cli.main(config_path: str, log_level: str, list_types: bool, validate_only: bool)
Run multiple model inference jobs from a YAML configuration file.
The YAML file should have the following structure:
data_path: /path/to/data charge_group: my_group queue: gpu_h100 # optional, defaults to gpu_h100 json_data: /path/to/config.json # optional models:
- my_model:
type: dacapo run_name: my_run iteration: 100
- fly_model:
type: fly checkpoint: /path/to/checkpoint.ts classes: [mito, er, nucleus] resolution: [4, 4, 4]
The model keys (my_model, fly_model) become the model names.
Model types are automatically discovered from ModelConfig subclasses. Use –list-types to see all available types.
Examples:
cellmap_flow_yaml config.yaml cellmap_flow_yaml config.yaml –log-level DEBUG cellmap_flow_yaml –list-types cellmap_flow_yaml config.yaml –validate-only