v3.0.1

webknossos

Fixed

• Fixed a bug where some tiff images could not be correctly converted to wkw/zarr, yielding KeyErrors. #1388

v3.0.0

webknossos

Breaking Changes

• The endpoint_url in UPath objects is now stored directly in the storage_options dict, instead of being stored in the storage_options["client_kwargs"] dict. #1365
• Removed Docker image scalableminds/webknossos-cli build. It will not be released further. #1376

Added

• Dataset.add_layer_as_ref() now accepts RemoteLayer objects as well as Layer objects. #1371
• RemoteDataset.annotation_id is now exposed, when available. #1380
• RemoteDataset.open() now accepts an annotation url as well. #1380
• RemoteAnnotation, now has a get_agglomerate_graph method, to make working with proofreading annotations easier. #1361

Changed

• Ported test.sh to test.py, run with uv run test.py. #1379
• Dataset.add_layer_as_ref(remote_layer.path) does not work anymore. Please use Dataset.add_layer_as_ref(remote_layer) instead. #1371
• Due to the refactoring, the imports of various classes have changed. Please update your code accordingly. #1371
• Deprecated a number of methods #1371:
  • Dataset.open_remote(), use RemoteDataset.open instead.
  • RemoteDatset.download_mesh(), use remote_segmentation_layer.download_mesh() instead.
  • Dataset.get_remote_datasets(), use RemoteDataset.list() instead.
  • Dataset.download(), use RemoteDataset.download() instead.
  • mag_view.is_foreign, use layer.is_mag_view_foreign(mag_view) instead.
  • Dataset.trigger_reload_in_datastore(), use RemoteDataset.trigger_reload_in_datastore() instead.
• Replaced pathlib.Path for upath.UPath internally. pathlib.Path is still supported for user-facing APIs. Adds support for universal_pathlib version 0.3.x. #1374
• Only use fs-based copy for mags on local file systems and S3. Other protocols, e.g. memory and HTTP, have caveats that break fs-based copying. #1365
• The add_* methods in Attachments now return the created attachment objects, similar to add_layer and add_mag. #1365
• The returned dataset ID from dataset exploration is now used. #1378
• Refactored the architecture, by introducing RemoteLayers, RemoteSegmentationLayers and their abstract base classes. #1371
• Updated the api version of the webknossos-api to 12. #1371
• Allowing RemoteDataset to align mags, when down- or upsampling #1382
• RemoteDatasets that use zarr streaming are no longer read-only. #1383
• Introduced transfer modes COPY, MOVE_AND_SYMLINK and HTTP for Dataset.upload() #1384

Fixed

• Fixed test.py to parse the command line arguments correctly. #1383

cluster_tools

Breaking Changes

• Deprecate the dask and kubernetes executors. They will be removed in a future version. #1375

v2.5.0

webknossos

Added

• Added context manager VolumeLayer.edit for creating and modifying volume annotations. #1340
• Added overwrite_existing flag to convert, convert-raw and convert-zarr CLI commands. Use with caution. #1372
• Added downsample, max-mag, interpolation-mode, sampling-mode args to convert, convert-raw and convert-zarr CLI commands, where it was missing, for consistency. #1372
• Added value rescaling to convert-raw CLI command through source-dtype and rescale-min-max args. #1372
• Added interpolation_mode and compress kwargs to Dataset.downsample method. #1372
• Added Team.get_by_id, Team.add_user and Team.delete methods. #1373
• Added RemoteFolder.get_root, RemoteFolder.get_subfolders, RemoteFolder.get_datasets, RemoteFolder.add_subfolder, RemoteFolder.move_to, RemoteFolder.delete methods and RemoteFolder.allowed_teams, RemoteFolder.name properties. #1373

Changed

• Team.add now returns the created team object. #1373
• Moved Team to webknossos.administration.team module. #1373

v2.4.12

webknossos

Changed

• Disabled conditional writes for S3 buckets in tensorstore. #1368

Fixed

• Fixed that some operations that need an authentication token didn’t ask for it but just failed. #1366

v2.4.11

webknossos

Breaking Changes

• All internal API client methods (webknossos.client) use keyword-only arguments. #1363
• The signature of Dataset.trigger_reload_on_datastore changed. dataset_name has been renamed to dataset_name_or_url. Alternatively, a dataset_id can be supplied. #1363

Changed

• Layer.add_mag_as_copy now automatically uses file-based copy, if possible. Therefore, Dataset.fs_copy_dataset, Dataset.add_fs_copy_layer and Layer.add_fs_copy_mag are deprecated. #1362
• The API methods now use v10 API version of Webknossos. Datasets are now referenced by ID instead of dataset name or directory name. #1363

v2.4.10

webknossos

Added

• Added support for remote datasets and annotations to webknossos export-as-tiff. #1356

v2.4.9

webknossos

Fixed

• Fixed a bug where paths of references mags were wrong, if the target dataset's path was a prefix of the source dataset's path. #1346

v2.4.8

webknossos

Added

• Added support for reading wkw datasets with the new "mag" key in datasource-properties.json, which replaces "wkwResolutions" for datasets written out by the webknossos server. #1349

v2.4.7

webknossos

Added

• Added MagView.rechunk methods to allow for rechunking of datasets. #1342
• Added the option to configure the codecs of Zarr3 datasets. Supply a Zarr3Config to the compress argument in Layer.add_mag or similar methods. codecs and chunk_key_encoding can be customized. #1343
• Added method download_mesh to the RemoteDataset and RemoteAnnotation classes to allow download of .stl files. #1307

Changed

• Enforces that chunk_shape and shard_shape have power-of-two values. This assumptions was used in the code previously, but not explicitly enforced. #1342
• The sharding_indexed codec is no longer used if chunk_shape == shard_shape. #1343

v2.4.6

Release for v2.4.6