chore: Release Prep v2.4.7 (#107)

* Restrict zarr version upper bound, update bioformats version

* Bump version: 2.4.6 → 2.4.7-dev0

* Bump version: 2.4.7-dev0 → 2.4.7

Author: sameeul

README.md

@@ -1,4 +1,4 @@
-# **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.4.6)
+# **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.4.7)
 
 [![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/)
@@ -50,15 +50,15 @@ be installed using pip:
 
 ## Docker
 
-### polusai/bfio:2.4.6
+### polusai/bfio:2.4.7
 
 Ubuntu based container with bfio and all dependencies (including Java).
 
-### polusai/bfio:2.4.6-imagej
+### polusai/bfio:2.4.7-imagej
 
 Same as above, except comes with ImageJ and PyImageJ.
 
-### polusai/bfio:2.4.6-tensorflow
+### polusai/bfio:2.4.7-tensorflow
 
 Tensorflow container with bfio installed.
 

docker/m2_repo.patch

@@ -5,7 +5,7 @@ index 954d682..cb88332 100644
 @@ -40,6 +40,8 @@ try:
 
          global JAR_VERSION
-         scyjava.config.endpoints.append("ome:formats-gpl:8.0.0")
+         scyjava.config.endpoints.append("ome:formats-gpl:8.0.1")
 +        scyjava.config.set_m2_repo("/etc/m2/")
 +        scyjava.config.set_cache_dir("/etc/m2/jgo_cache")
          scyjava.start_jvm()

docs/source/Examples/Converter.rst

@@ -18,7 +18,7 @@ are available in ``bfio``.
    Tiled tiff is the preferred file format for reading/writing arbitrarily sized
    images.
 2. ``backend="bioformats"`` can be used to read any
-   `any format supported by Bio-Formats <https://docs.openmicroscopy.org/bio-formats/8.0.0/supported-formats.html>`_.
+   `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
    the `OME Zarr spec <https://ngff.openmicroscopy.org/latest/>`_.

docs/source/Installation.rst

@@ -26,4 +26,4 @@ Here are some info on installing Maven on various OS (`Windows <https://phoenixn
 
 
 NOTE: ``Bio-Formats`` is licensed under GPL, while ``bfio`` is licensed under MIT. This may have consequences when packaging any software that uses
-``bfio`` as a dependency. During the first invocation of ``bfio``, ``scyjava`` will try to download ``Bio-Formats`` package from the Maven repository. The current version of ``bfio`` uses ``Bio-Formats`` v8.0.0 .
+``bfio`` as a dependency. During the first invocation of ``bfio``, ``scyjava`` will try to download ``Bio-Formats`` package from the Maven repository. The current version of ``bfio`` uses ``Bio-Formats`` v8.0.1 .

pyproject.toml

@@ -7,7 +7,7 @@ requires = [
   "imagecodecs>=2021.2.26",
   "numpy",
   "ome-types>=0.4.2",
-  "zarr>=2.6.1",
+  "zarr>=2.6.1,<3",
   "scyjava",
   "jpype1",
   "tifffile>=2022.8.12",
@@ -23,7 +23,7 @@ dependencies = [
     "imagecodecs>=2021.2.26",
     "numpy",
     "ome-types>=0.4.2",
-    "zarr>=2.6.1",
+    "zarr>=2.6.1,<3",
     "scyjava",
     "jpype1",
     "tifffile>=2022.8.12",
@@ -87,7 +87,7 @@ namespaces = false
 
 
 [tool.bumpversion]
-current_version = "2.4.6"
+current_version = "2.4.7"
 commit = true
 tag = true
 commit_args = "--no-verify"

requirements/requirements-base.txt

@@ -1 +1 @@
-bfio==2.4.6
+bfio==2.4.7

src/bfio/VERSION

@@ -1 +1 @@
-2.4.6
+2.4.7

src/bfio/utils.py

@@ -39,7 +39,7 @@ def start() -> str:
         """
 
         global JAR_VERSION
-        scyjava.config.endpoints.append("ome:formats-gpl:8.0.0")
+        scyjava.config.endpoints.append("ome:formats-gpl:8.0.1")
         scyjava.start_jvm()
         import loci