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feat: bundle common bioio readers in [bioio] extra #11

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Merged
lguerard merged 1 commit into from
Jun 22, 2026
Merged

feat: bundle common bioio readers in [bioio] extra #11

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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -39,9 +39,9 @@ pip install "patchworks[napari]" # interactive napari viewer plugin
pip install "patchworks[all]" # Everything (except napari GUI)
```

> `bioio` reads CZI/LIF/ND2/OME-TIFF/… — it ships with `bioio-bioformats`, the
> Bio-Formats catch-all reader (needs a JVM). Add faster native readers where
> you want them (e.g. `bioio-ome-tiff`, `bioio-czi`, `bioio-lif`, `bioio-nd2`).
> `bioio` reads CZI/LIF/ND2/OME-TIFF/… The `[bioio]` extra bundles the common
> native readers (`bioio-nd2`, `bioio-ome-tiff`, `bioio-czi`, `bioio-tifffile`,
> `bioio-lif`) plus `bioio-bioformats`, the Bio-Formats catch-all reader (JVM).

---

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15 changes: 11 additions & 4 deletions pyproject.toml
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Expand Up @@ -43,10 +43,17 @@ io = ["psutil", "tqdm"]
cellpose = ["cellpose>=3.0"]
gpu = ["nvidia-ml-py"]
# bioio enables converting any image format (CZI, LIF, ND2, OME-TIFF, …) to
# OME-ZARR. bioio-bioformats is the Bio-Formats catch-all reader (needs a JVM);
# add narrower native readers too where you want them (bioio-ome-tiff,
# bioio-czi, bioio-lif, bioio-nd2) as they are faster than going through Java.
bioio = ["bioio", "bioio-bioformats"]
# OME-ZARR. Ships the common native readers (faster than going through Java)
# plus bioio-bioformats, the Bio-Formats catch-all reader (needs a JVM).
bioio = [
"bioio",
"bioio-bioformats",
"bioio-nd2",
"bioio-ome-tiff",
"bioio-czi",
"bioio-tifffile",
"bioio-lif",
]
# napari enables the interactive viewer plugin (GUI-heavy, kept out of [all]).
napari = ["napari[all]"]
dev = ["pytest", "pytest-cov", "scikit-image", "psutil", "tqdm"]
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