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.
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Release files for bioimageflow 0.9.3
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Source distribution (sdist)
| File | Size | Uploaded | |
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| bioimageflow-0.9.3.tar.gz | 435.5 kB | Details |
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| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| bioimageflow-0.9.3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 983.0 kB
Release files / bioimageflow-0.9.3.tar.gz
| Download URL | bioimageflow-0.9.3.tar.gz |
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| Size | 435.5 kB |
| Tags | Source |
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Release files / bioimageflow-0.9.3-py3-none-any.whl
| Download URL | bioimageflow-0.9.3-py3-none-any.whl |
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| Size | 547.5 kB |
| Tags | Python 3 |
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uv/0.10.9 {"installer":{"name":"uv","version":"0.10.9","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
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