bioimageflow
Main-process orchestrator for BioImageFlow workflows.
This package builds workflow DAGs, resolves column bindings, executes tools, and publishes cache records and run views.
Worker-safe tool authoring primitives live in bioimageflow-core; optional domain tools live in separate bioimageflow-*-tools packages.
Install:
pip install bioimageflow
Install the optional distributed runtime when using ParslEngine:
pip install "bioimageflow[parsl]"
Install the PSI/J cluster orchestrator launcher with Parsl:
pip install "bioimageflow[parsl,psij]"
For workspace development, use the repository root:
uv sync
uv run pytest packages/bioimageflow tests
Wetlands worker environments install bioimageflow-core independently from the orchestrator environment.
By default WetlandsEnvManager injects bioimageflow-core==<installed version> for reproducible runtime environments.
Set BIOIMAGEFLOW_USE_LOCAL_CORE=1 while developing from a source checkout to inject the local editable bioimageflow-core project into newly created worker environments.
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