chore: Release Prep 2.5.0 (#128)

Author: sameeul

README.md

@@ -1,4 +1,4 @@
-# **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.4.10)
+# **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.5.0)
 
 [![Documentation Status](https://readthedocs.org/projects/bfio/badge/?version=latest)](https://bfio.readthedocs.io/en/latest/?badge=latest)
 [![PyPI](https://img.shields.io/pypi/v/bfio)](https://pypi.org/project/bfio/)
@@ -31,7 +31,7 @@ Docker containers with all necessary components are available (see
 
 ### Setting up Java
 
-**Note:** `bfio` can be used without Java, but only the `python` and `zarr`
+**Note:** `bfio` can be used without Java, but only the `python`, `zarr`, `zarr3`, and `tensorstore`
 backends will be usable. This means only files in tiled OME Tiff or OME Zarr format can be
 read/written.
 
@@ -50,15 +50,15 @@ be installed using pip:
 
 ## Docker
 
-### polusai/bfio:2.4.10
+### polusai/bfio:2.5.0
 
 Ubuntu based container with bfio and all dependencies (including Java).
 
-### polusai/bfio:2.4.10-imagej
+### polusai/bfio:2.5.0-imagej
 
 Same as above, except comes with ImageJ and PyImageJ.
 
-### polusai/bfio:2.4.10-tensorflow
+### polusai/bfio:2.5.0-tensorflow
 
 Tensorflow container with bfio installed.
 

docker/base/Dockerfile

@@ -49,11 +49,6 @@ RUN git apply --directory=bfio_src /bfio_src/docker/m2_repo.patch
 # Install using the new Python
 RUN python${PYTHON_VERSION} -m pip install /bfio_src --no-cache-dir
 
-# Apply jgo copy patch
-RUN git apply \
-    --directory=usr/local/lib/python${PYTHON_VERSION}/dist-packages \
-    /bfio_src/docker/jgo_copy.patch
-
 # clean up
 RUN rm -rf /bfio_src
 

docker/imagej/Dockerfile

@@ -44,11 +44,6 @@ RUN git apply --directory=bfio_src /bfio_src/docker/m2_repo.patch
 # Install
 RUN python3 -m pip install /bfio_src --no-cache-dir
 
-#Apply jgo copy patch
-RUN git apply \
-    --directory=usr/local/lib/python${PYTHON_VERSION}/site-packages \
-    /bfio_src/docker/jgo_copy.patch
-
 # Install packages
 ENV LIBRARY_PATH=/lib:/usr/lib
 

docker/tensorflow/Dockerfile

@@ -37,9 +37,6 @@ RUN git apply --directory=bfio_src /bfio_src/docker/m2_repo.patch
 # Install
 RUN pip3 install /bfio_src --no-cache-dir
 
-#Apply jgo copy patch
-RUN  git apply  --directory=usr/local/lib/python${PYTHON_VERSION}/dist-packages /bfio_src/docker/jgo_copy.patch
-
 # clean up
 RUN rm -rf /bfio_src
 

docs/source/Examples/Converter.rst

@@ -8,7 +8,7 @@ Introduction
 
 The bfio package is designed to make it easy to process arbitrarily sized images
 in a fast, scalable way. The two core classes, :doc:`/Reference/BioReader` and
-:doc:`/Reference/BioWriter`, can use one of three different backends depending
+:doc:`/Reference/BioWriter`, can use one of five different backends depending
 on the file type that will be read. Usually, the proper backend will be selected
 when opening a file. For cases where bfio fails to select the proper backend, the 
 ``backend`` parameter can be passed to the constructor. The following backends
@@ -20,10 +20,14 @@ are available in ``bfio``.
 2. ``backend="bioformats"`` can be used to read any
    `any format supported by Bio-Formats <https://docs.openmicroscopy.org/bio-formats/8.0.1/supported-formats.html>`_.
    The BioWriter with java backend will only save images as OME tiled tiff.
-3. ``backend="zarr"`` can be used to read/write a subset of Zarr files following
+3. ``backend="zarr"`` can be used to read/write a subset of Zarr v2 files following
    the `OME Zarr spec <https://ngff.openmicroscopy.org/latest/>`_.
+4. ``backend="zarr3"`` can be used to read/write Zarr v3 files following
+   the `OME Zarr spec <https://ngff.openmicroscopy.org/latest/>`_.
+5. ``backend="tensorstore"`` provides optimized reading/writing for both OME Tiff 
+   and OME Zarr (v2 and v3) files with enhanced performance.
 
-The advantage to using the ``python`` and ``zarr`` backends are speed and
+The advantage to using the ``python``, ``zarr``, ``zarr3``, and ``tensorstore`` backends are speed and
 scalability at the expense of a rigid file structure, while the ``bioformats`` backend
 provides broad access to a wide array of file types but is considerably slower.
 

docs/source/Installation.rst

@@ -13,7 +13,7 @@ A conda distribution is also available in the conda-forge channel. To install it
 
 Java and Bio-Formats
 -------------------
-``bfio`` can be used without Java, but only the ``python`` and ``zarr``
+``bfio`` can be used without Java, but only the ``python``, ``zarr``, ``zarr3``, and ``tensorstore``
 backends will be usable. This means only files in tiled OME Tiff or OME Zarr format can be
 read/written.
 

pyproject.toml

@@ -87,7 +87,7 @@ namespaces = false
 
 
 [tool.bumpversion]
-current_version = "2.4.10"
+current_version = "2.5.0"
 commit = true
 tag = true
 commit_args = "--no-verify"

requirements/requirements-base.txt

@@ -1 +1 @@
-bfio==2.4.10
+bfio==2.5.0

src/bfio/VERSION

@@ -1 +1 @@
-2.4.10
+2.5.0