Metadata-Version: 2.4
Name: bioimageflow
Version: 0.5.0
Summary: Python library for orchestrating bioimage analysis workflows
Project-URL: Homepage, https://github.com/Inria-SAIRPICO/bioimageflow
Project-URL: Documentation, https://bioimageflow.readthedocs.io/latest/
Project-URL: Repository, https://github.com/Inria-SAIRPICO/bioimageflow
Project-URL: Issues, https://github.com/Inria-SAIRPICO/bioimageflow/issues
Author: BioImageFlow Contributors
License-Expression: BSD-4-Clause
License-File: LICENSE
Keywords: bioimage-analysis,bioimageflow,microscopy,workflow
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.10
Requires-Dist: bioimageflow-core<0.3,>=0.2.1
Requires-Dist: numpy>=1.23.5
Requires-Dist: pandas>=2.0.0
Requires-Dist: pyarrow>=12.0.0
Requires-Dist: pydantic>=2.0.0
Requires-Dist: wetlands<3,>=2.0.0
Provides-Extra: parsl
Requires-Dist: parsl<2026.6,>=2026.5.25; extra == 'parsl'
Provides-Extra: psij
Requires-Dist: psij-python<0.10,>=0.9.11; extra == 'psij'
Description-Content-Type: text/markdown

# 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:

```bash
pip install bioimageflow
```

Install the optional distributed runtime when using `ParslEngine`:

```bash
pip install "bioimageflow[parsl]"
```

Install the PSI/J cluster orchestrator launcher with Parsl:

```bash
pip install "bioimageflow[parsl,psij]"
```

For workspace development, use the repository root:

```bash
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.
