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@github-actions github-actions released this 28 Oct 11:14
v3.0.0
e45dbf1

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
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