Merge pull request #102 from sameeul/update_bioformat_8

Update to bioformats 8.0.0
PolusAI · Nov 12, 2024 · 0b45e4b · 0b45e4b
2 parents 8029048 + 58a3019
commit 0b45e4b
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diff --git a/docker/m2_repo.patch b/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:7.3.0")
+         scyjava.config.endpoints.append("ome:formats-gpl:8.0.0")
 +        scyjava.config.set_m2_repo("/etc/m2/")
 +        scyjava.config.set_cache_dir("/etc/m2/jgo_cache")
          scyjava.start_jvm()

diff --git a/docs/source/Examples/Converter.rst b/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/7.3.0/supported-formats.html>`_.
+   `any format supported by Bio-Formats <https://docs.openmicroscopy.org/bio-formats/8.0.0/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/>`_.

diff --git a/docs/source/Installation.rst b/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`` v7.3.0 .
+``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`` v8.0.0 .
diff --git a/src/bfio/utils.py b/src/bfio/utils.py
@@ -39,7 +39,7 @@ def start() -> str:
         """
 
         global JAR_VERSION
-        scyjava.config.endpoints.append("ome:formats-gpl:7.3.0")
+        scyjava.config.endpoints.append("ome:formats-gpl:8.0.0")
         scyjava.start_jvm()
         import loci
Original file line number	Diff line number	Diff line change
Expand Up		@@ -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`` v7.3.0 .
		``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`` v8.0.0 .