feat: ✨ bundle common bioio readers in the [bioio] extra

Install bioio-nd2, bioio-ome-tiff, bioio-czi, bioio-tifffile and
bioio-lif automatically with patchworks[bioio] (alongside the
bioio-bioformats catch-all), so the common microscopy formats work
out of the box without picking readers by hand.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Author: lguerard

README.md

@@ -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).
 
 ---
 

pyproject.toml

@@ -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"]