v0.9.5

webknossos

Fixed

• Skeleton: Fixed a bug when comparing Graph instances, this fixes failing loads which had the error message Can only compare wk.Graph to another wk.Graph. before. #593

v0.9.4

webknossos

Added

• Added AnnotationInfo, Project and Task classes for handling annotation information and annotation project administration. #574:

Changed

• Lifted the restriction that BoundingBox cannot have a negative topleft (introduced in v0.9.0). Also, negative size dimensions are flipped, so that the topleft <= bottomright,
  e.g. BoundingBox((10, 10, 10), (-5, 5, 5)) -> BoundingBox((5, 10, 10), (5, 5, 5)). #589

v0.9.3

webknossos

Fixed

• dataset.upload(layers_to_link=…): Fixed a bug where the upload did not complete if layers_to_link contained layers present in uploading dataset. #584

v0.9.2

webknossos

Added

• A custom network request timeout can be set using webknossos_context(…, timeout=300) or export WK_TIMEOUT="300". #577

Changed

• The default network request timeout changed from ½min to 30 min. #577

v0.9.1

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:
  • (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 MagViews and relative for Views.
  • (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 MagViews and relative for Views.

wkcuber

Added

• Added wkcuber.convert_zarr tool to convert zarr files to wkw datasets. #549

Fixed

• Fixed automatic conversion of 3D tiff files which only have a single page. #575

v0.9.0

webknossos

Breaking Changes

• Various changes in View & MagView signatures #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_boxor 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

Fixed

• Fixed the dataset download of private datasets which need a token. #562

wkcuber

Added

• wkcuber.upload for uploading local datasets to webKnossos. #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

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

v0.8.30

Release for v0.8.30

v0.8.29

Release for v0.8.29

v0.8.28

Release for v0.8.28

v0.8.27

Prepare changelog for 0.8.27 (#512)