CLI Reference¶

GGE provides a comprehensive command-line interface for running evaluations.

Basic Usage¶

gge --real <real_data.h5ad> --generated <generated_data.h5ad> --conditions <columns> --output <dir>

Arguments¶

Required Arguments¶

Argument	Short	Description
`--real`	`-r`	Path to real data file (h5ad format)
`--generated`	`-g`	Path to generated data file (h5ad format)
`--conditions`	`-c`	One or more condition columns for matching
`--output`	`-o`	Output directory for results

Optional Arguments¶

Argument	Default	Description
`--split-column`	None	Column name for train/test split
`--splits`	all	Which splits to evaluate (e.g., "test")
`--metrics`	all	Which metrics to compute
`--n-genes`	all	Number of genes to evaluate (random subset)
`--seed`	42	Random seed for reproducibility
`--verbose`	False	Print detailed progress
`--version`	-	Show version and exit

Examples¶

Basic Evaluation¶

gge --real real.h5ad --generated generated.h5ad \
    --conditions perturbation \
    --output results/

Multiple Conditions¶

gge --real real.h5ad --generated generated.h5ad \
    --conditions perturbation cell_type dose \
    --output results/

Test Set Only¶

gge --real real.h5ad --generated generated.h5ad \
    --conditions perturbation \
    --split-column split \
    --splits test \
    --output results/

Specific Metrics¶

gge --real real.h5ad --generated generated.h5ad \
    --conditions perturbation \
    --metrics pearson spearman wasserstein_1 \
    --output results/

Subset of Genes¶

gge --real real.h5ad --generated generated.h5ad \
    --conditions perturbation \
    --n-genes 1000 \
    --seed 42 \
    --output results/

Verbose Output¶

gge --real real.h5ad --generated generated.h5ad \
    --conditions perturbation \
    --verbose \
    --output results/

Available Metrics¶

Use these names with --metrics:

pearson - Pearson correlation
spearman - Spearman correlation
wasserstein_1 - Wasserstein-1 distance
wasserstein_2 - Wasserstein-2 distance
mmd - Maximum Mean Discrepancy
energy - Energy distance

Exit Codes¶

Code	Meaning
0	Success
1	Error (invalid arguments, file not found, etc.)

Environment Variables¶

Variable	Description
`GGE_SEED`	Default random seed
`GGE_VERBOSE`	Default verbosity (0 or 1)