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@jstriebel jstriebel released this 19 Jan 17:06
· 501 commits to master since this release
v0.9.0
ace3c1a

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
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