v3.3.0

webknossos

Breaking Changes

• Renamed the existing webknossos.proofreading.agglomerate_graph.AgglomerateGraph to webknossos.proofreading.agglomerate_graph_data.AgglomerateGraphData. #1435
• Renamed the Annotation.get_agglomerate_graph to Annotation.get_agglomerate_graph_data. #1435
• Renamed RemoteDataset.download argument bbox to bounding_box. bbox is still available, but deprecated. #1435
• Moved the s3fs dependency to an optional extra. Install with webknossos[s3] or webknossos[all]. #1443
• The use_bioformats argument of Dataset.add_layer_from_images, Dataset.from_images and RemoteDataset.from_images is now False by default. None is not allowed anymore. #1446

Added

• Added RemoteDataset.add_layer_as_ref, RemoteLayer.add_mag_as_ref, RemoteAttachments.add_attachment_as_ref, RemoteAttachments.delete_attachment, RemoteAttachment.rename_attachment, Attachments.rename_attachments. #1438
• Added extend_layer_bounding_box kwarg with default True to RemoteLayer.add_mag_as_copy. #1438
• Added RemoteDataset.reopen method to allow reopening with a different access mode. #1438
• Added isVisible attribute to Skeleton.Tree #1442

Changed

• Rewrote the chunking of the tiff conversion. A non-user facing change. #1440
• Removed the proxay request recording/replaying functionality. All requests in the tests are now sent directly to the local WEBKNOSSOS instance. #1441
• Set more comfortable retries for s3 connections in the CLI commands. Call webknossos.utils.set_s3fs_retry_settings() for library use. #1443
• Swapped out pims for our fork scm-pims, which fixes issues with skimage. A non-user facing change. #1445