API Reference

This page summarizes the runtime knobs users most often need when launching FedGWAS through Flower.

CLI entry point

Most local simulations should start from the packaged CLI:

fedgwas-sim --help

The command creates a local simulation project, configures examples and presets, runs readiness checks, launches Flower, and evaluates or collects outputs. See the main fedgwas-sim CLI documentation for the complete command reference.

Flower run config

Key	Type	Default	Purpose
simulation	boolean	true	Selects simulation-aware client behavior and output layout.
num-server-rounds	integer	300	Maximum Flower rounds. The strategy stops earlier when it reaches done.
config_path	string	experiments/correctness/tiny_even/configs	Directory containing server/config.yaml and center_x/config.yaml files.
default-partition-by	string	samples	Default partitioning mode for client initialization.
server_output_dir	string	unset	Optional explicit server output directory override.
chunk_size / server_chunk_size	integer	experiment server.chunk_size or 1000	Chunk size sent during init_chunks and init_chunks_lr.
lr_pad_to	integer	experiment server.lr_pad_to or 0	Optional padding target for privacy-preserving tokens in local association filtering.
phenotype_fix_missing_to_case	boolean	false	Creates a derived PLINK prefix with missing phenotypes recoded for toy runs.

Example:

flwr run . local-simulation --stream --run-config \
  'simulation=true num-server-rounds=100 config_path="experiments/correctness/tiny_even/configs"'

Center config files

Each center_x/config.yaml contains:

Section	Purpose
input_data	PLINK prefix and input type.
output	Per-center intermediate and log directories.
parameters	Chunk sizes, run tags, and anonymization offsets.
thresholds	Federated QC, relatedness screening, and association screening thresholds.
flower	Deployment address and nominal round count.
participation	Per-stage opt-in flags.

Server config file

The server config is required at <config_path>/server/config.yaml unless server_output_dir is provided. It must define output.log_dir or output.intermediate_dir.

Main Python entry points

File	Role
pipeline/client_app.py	Flower ClientApp; creates FedLRClient and routes stages.
pipeline/server_app.py	Flower ServerApp; resolves config and creates the strategy.
pipeline/cli/sim.py	Typer application behind the fedgwas-sim command.
pipeline/server/strategy_strict.py	Stage machine and encrypted relay orchestration.
pipeline/clients/base_client.py	PLINK chunking, anonymization, phenotype helpers.
pipeline/server/aggregator_king.py	Server-side KING chunk reconstruction and PLINK2 execution.
pipeline/server/aggregator_lr.py	Server-side LR chunk reconstruction and PLINK execution.