Logging

BioImageFlow uses the standard logging module under two logger names:

• bioimageflow — engine, registry, environment management, template resolution, tool loading.

• wetlands — worker process output (stdout/stderr from ProcessingTool.process_row runs).

BioImageFlow does not configure console logging during engine or workflow construction. Library users that want terminal progress can call bioimageflow.configure_logging() from the host application:

import bioimageflow

bioimageflow.configure_logging()

By default this sets the bioimageflow logger level to INFO and routes emitted DEBUG / INFO records to stdout and WARNING / ERROR / CRITICAL records to stderr, using the format %(asctime)s [%(name)s] %(message)s. Pass level=logging.DEBUG to emit debug records. Repeated calls are idempotent for BioImageFlow-owned console handlers; force=True replaces only those handlers and leaves unrelated user handlers in place.

configure_logging() also delegates Wetlands console setup to wetlands.logger.enable_console_logging. Wetlands 1.1.0 routes worker stdout to INFO / stdout and worker stderr to ERROR / stderr.

Adjusting verbosity

The standard logging API works:

import logging
logging.getLogger("bioimageflow").setLevel(logging.DEBUG)
logging.getLogger("wetlands").setLevel(logging.WARNING)

Routing to a file

Add your own handlers with the standard logging API:

import logging
handler = logging.FileHandler("bioimageflow.log")
handler.setFormatter(
    logging.Formatter("%(asctime)s [%(name)s] %(levelname)s: %(message)s")
)
logging.getLogger("bioimageflow").addHandler(handler)

Worker logs

Worker process output is forwarded to the wetlands logger by the Wetlands runtime. Wetlands owns its file logging through its environment manager; BioImageFlow does not duplicate or wrap that file logging behavior. Hosts that surface execution logs in a UI typically attach a custom handler to the wetlands logger and pump records onto a dispatch queue.

Specs.md §11 covers the contract end-to-end.