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.
For regular source development, set BIOIMAGEFLOW_CORE_SOURCE=/absolute/path/to/bioimageflow-core to validate and inject that project as an editable dependency without installing it into the orchestrator environment.
The accepted current configuration uses the explicit source path rather than a historical import-derived alias.
Any remaining alias retirement and complete implementation conformance are deferred to causal review C; this documentation change does not modify runtime behavior.
1 maintainer
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Release files for bioimageflow 0.9.5
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