Webknossos

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)

webknossos
Breaking Changes
- Various changes in View & MagView signatures [553](https://github.com/scalableminds/webknossos-libs/pull/553):
- **Breaking Changes**:
* `MagView.read`: if nothing is supplied and the layer does not start at (0, 0, 0),
the default behaviour changes from starting at absolute (0, 0, 0) to the layer's bounding box
* `MagView.write`: if no offset is supplied and the layer does not start at (0, 0, 0),
the default behaviour changes from starting at absolute (0, 0, 0) to the layer's bounding box
* `(Mag)View.get_view`: read_only is a keyword-only argument now
* `MagView.get_bounding_boxes_on_disk()` now returns an iterator yielding bounding boxes in Mag(1)
- **Deprecations**
The following usages are marked as deprecated with warnings and will be removed in future releases:
* Using the `offset` parameter for `read`/`write`/`get_view` in MagView and View is deprecated.
There are new counterparts `absolute_offset` and `relative_offset` which have to be specified in Mag(1),
whereas `offset` previously was specified in the Mag of the respective View.
Also, for `read`/`get_view` only using `size` is deprecated, since it used to refer to the size in the View's Mag.
Instead, `size` should always be used together with `absolute_offset` or `relative_offset`. Then it is interpreted in Mag(1).
* The (Mag)View attributes `view.global_offset` and `view.size` are deprecated now, which were in the Mag of the respective View.
Please use `view.bounding_box` instead, which is in Mag(1).
* `read_bbox` on the (Mag)View is deprecated as well, please use `read` with the `absolute_bounding_box`or `relative_bounding_box` parameter instead. You'll have to pass the bounding box in Mag(1) then.


Added
- Added a check for dataset name availability before attempting to upload. [555](https://github.com/scalableminds/webknossos-libs/pull/555)

Fixed
- Fixed the dataset download of private datasets which need a token. [562](https://github.com/scalableminds/webknossos-libs/pull/562)

wkcuber
Added
- `wkcuber.upload` for uploading local datasets to webKnossos. [544](https://github.com/scalableminds/webknossos-libs/pull/544)

Changed
- Logging is now set to log level `INFO` by default. `DEBUG` logging can be enabled with the `--verbose` flag. Consequently, the `--silent` flag has been removed. [544](https://github.com/scalableminds/webknossos-libs/pull/544)

cluster-tools
Added
- Allow to configure the MaxArraySize and MaxSubmitJobs slurm limits via the `SLURM_MAX_ARRAY_SIZE` and `SLURM_MAX_SUBMIT_JOBS` environment variables. If the environment variables are not specified, the limits are determined automatically. [554](https://github.com/scalableminds/webknossos-libs/pull/554)