Python API¶

CytoScnPy exposes a minimal Python API to invoke the analyzer programmatically.

cytoscnpy module¶

run(args: List[str]) -> int¶

Executes the CytoScnPy analyzer with the provided command-line arguments.

Parameters:

• args: A list of strings representing command-line arguments (e.g., [".", "--json"]).

Returns:

• int: Exit code (0 for success, non-zero for failure/findings).

Example:

import cytoscnpy
import sys

# Run analysis on current directory and output JSON
args = [".", "--json", "--quiet"]
exit_code = cytoscnpy.run(args)

if exit_code != 0:
    print("Issues found!")

Note: The run function writes output directly to standard output/error, similar to running the CLI. To capture output, you may need to redirect stdout.