Webknossos

webknossos

Changed
- Added `layer_name` as optional argument to `Dataset.from_images` method. If the created dataset contains only a single layer, `layer_name` is used, otherwise the given `layer_name` is a common prefix for all layers. [1054](https://github.com/scalableminds/webknossos-libs/pull/1054)
- The context variable of View.get_buffered_slice_writer() is a BufferedSliceWriter now instead of a Generator. Interaction with the SliceWriter does not change, but updating the offset after first initialization is possible now. [1052](https://github.com/scalableminds/webknossos-libs/pull/1052)

webknossos

Changed
- Updated ruff to v0.4.0 [1047](https://github.com/scalableminds/webknossos-libs/pull/1047)
- Added NIfTI suffix .nii to list of supported bioformats suffixes. [1048](https://github.com/scalableminds/webknossos-libs/pull/1048)


cluster_tools

Changed
- Array jobs are spawned faster now, because common meta data is not serialized for each subjob. The performance improvement is especially big, when custom logging code is configured for array jobs. [1042](https://github.com/scalableminds/webknossos-libs/pull/1042)
- Updated ruff to v0.4.0 [1047](https://github.com/scalableminds/webknossos-libs/pull/1047)

webknossos

Changed
- Removed special CLI command for cubing Nifti files. Use regular conversion command instead. Further, moved Python dependencies for examples and dev dependcies into optional groups which are not installed by default. Install with `poetry install --with dev --with examples`. [1024](https://github.com/scalableminds/webknossos-libs/pull/1024)


cluster_tools

Changed
- Moved the dependencies for Kubernetes and Dask support into optional extras that need to be installed separately. Either with `poetry install --all-extras or pip install -e "all"`. [1024](https://github.com/scalableminds/webknossos-libs/pull/1024)

webknossos

Fixed
- Fixed a bug, where using an unaligned topleft value for `add_layer_from_images` leads to corrupted data. [1036](https://github.com/scalableminds/webknossos-libs/pull/1036)

webknossos

Changed
- The characters `` and `$` are allowed within layer names now. [1034](https://github.com/scalableminds/webknossos-libs/pull/1034)

webknossos

Added
- Add CLI tool for offline merging of zip annotations with fallback datasets. [996](https://github.com/scalableminds/webknossos-libs/pull/996)
- Added support for converting new file formats such as DICOM, using the bioformats reader. [1014](https://github.com/scalableminds/webknossos-libs/pull/1014)

Changed
- The rules for naming the layers have been tightened to match the allowed layer names on webknossos. [1016](https://github.com/scalableminds/webknossos-libs/pull/1016)
- Replaced PyLint linter + black formatter with Ruff for development. [1013](https://github.com/scalableminds/webknossos-libs/pull/1013)
- The remote operations now use the WEBKNOSSOS API version 6. [1018](https://github.com/scalableminds/webknossos-libs/pull/1018)
- The conversion of 4D Tiff files to a Zarr3 Dataset is possible. NDBoundingBoxes and VecInt classes are introduced to support working with more than 3 dimensions. [966](https://github.com/scalableminds/webknossos-libs/pull/966)


cluster_tools

Changed
- Replaced black+isort formatters and pylint linter with ruff. [1023](https://github.com/scalableminds/webknossos-libs/pull/1023)