Webknossos

webknossos
Added
- Added `apply_merger_mode.py` example. [592](https://github.com/scalableminds/webknossos-libs/pull/592)
- Added support for reading from multiple volume layers in annotations. If an annotation contains multiple volume layers, the layer name has to be provided when reading from a volume layer in an annotation (in `Annotation.save_volume_annotation()` and `Annotation.temporary_volume_annotation_layer_copy()`). Also, added the method `Annotation.get_volume_layer_names()` to see available volume layers. [588](https://github.com/scalableminds/webknossos-libs/pull/588)
Changed
- Dataset writes in higher mags do not increase the bounding box if the written data fits in the rounded up box. [595](https://github.com/scalableminds/webknossos-libs/pull/595)
Fixed
- Dataset down- & upload: [595](https://github.com/scalableminds/webknossos-libs/pull/595)
* Fixed download of higher mags.
* Bounding box after download is set correctly (was inflated before when downloading higher mags).
* The returned URL for uploads is corrected, this did not respect `new_dataset_name` before.

cluster-tools
Added
- Automatically detect when a multiprocessing context is set up without using an `if __name__ == "__main__"` guard in the main module. [598](https://github.com/scalableminds/webknossos-libs/pull/598)

webknossos
Fixed
- Skeleton: Fixed a bug when comparing `Graph` instances, this fixes failing loads which had the error message `Can only compare wk.Graph to another wk.Graph.` before. [593](https://github.com/scalableminds/webknossos-libs/pull/593)

webknossos
Added
- Added AnnotationInfo, Project and Task classes for handling annotation information and annotation project administration. [574](https://github.com/scalableminds/webknossos-libs/pull/574):

Changed
- Lifted the restriction that `BoundingBox` cannot have a negative topleft (introduced in v0.9.0). Also, negative size dimensions are flipped, so that the topleft <= bottomright,
e.g. `BoundingBox((10, 10, 10), (-5, 5, 5))` -> `BoundingBox((5, 10, 10), (5, 5, 5))`. [589](https://github.com/scalableminds/webknossos-libs/pull/589)

webknossos

Fixed
- `dataset.upload(layers_to_link=…)`: Fixed a bug where the upload did not complete if layers_to_link contained layers present in uploading dataset. [584](https://github.com/scalableminds/webknossos-libs/pull/584)

webknossos

Added
- A custom network request timeout can be set using `webknossos_context(…, timeout=300)` or `export WK_TIMEOUT="300"`. [577](https://github.com/scalableminds/webknossos-libs/pull/577)

Changed
- The default network request timeout changed from ½min to 30 min. [577](https://github.com/scalableminds/webknossos-libs/pull/577)

webknossos

Changed
- The signatures of `(Mag)View.for_each_chunk` and `(Mag)View.for_zipped_chunks` changed:
* The previous argument `work_on_chunk` is now called `func_per_chunk`.
* The various `chunk_size` arguments now have to be given in Mag(1). They now have default values.
- Deprecations in `(Mag)View.get_buffered_slice_reader/_writer` [564](https://github.com/scalableminds/webknossos-libs/pull/564):
* `(Mag)View.get_buffered_slice_reader`: using the parameters `offset` and `size` is deprecated.
Please use the parameter relative_bounding_box or absolute_bounding_box (both in Mag(1)) instead.
The old offset behavior was absolute for `MagView`s and relative for `View`s.
* `(Mag)View.get_buffered_slice_writer`: using the parameter `offset` is deprecated.
Please use the parameter relative_offset or absolute_offset (both in Mag(1)) instead.
The old offset behavior was absolute for `MagView`s and relative for `View`s.

wkcuber
Added
- Added `wkcuber.convert_zarr` tool to convert zarr files to wkw datasets. [549](https://github.com/scalableminds/webknossos-libs/pull/549)

Fixed
- Fixed automatic conversion of 3D tiff files which only have a single page. [575](https://github.com/scalableminds/webknossos-libs/pull/575)