From 1fb3fe42431285e8890003598b39fa2bc46ca815 Mon Sep 17 00:00:00 2001 From: Laurent Guerard Date: Mon, 22 Jun 2026 16:21:56 +0200 Subject: [PATCH] =?UTF-8?q?feat:=20=E2=9C=A8=20bundle=20common=20bioio=20r?= =?UTF-8?q?eaders=20in=20the=20[bioio]=20extra?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 --- README.md | 6 +++--- pyproject.toml | 15 +++++++++++---- 2 files changed, 14 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 3f74985..f34c723 100644 --- a/README.md +++ b/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). --- diff --git a/pyproject.toml b/pyproject.toml index a46f202..c78b190 100644 --- a/pyproject.toml +++ b/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"]