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)

v0.8.26

GH Action for creating releases (#503)

* adds tools for changelog and release management

* use github token

* github_token is used by default, duh

* also check for already-existing higher versions

* workflow

* fixes

* pr feedback

* Update make_changelog.py

Co-authored-by: Philipp Otto <[email protected]>

Co-authored-by: Philipp Otto <[email protected]>

v0.8.25

Rename script-collection dir to script_collection (#505)

* rename script-collection dir to script_collection

* update changelog

v0.8.24

What's Changed

• Fix wkcuber --version in #494

Full Changelog: v0.8.23...v0.8.24

v0.8.23

webknossos

Breaking Changes

• wk.Graph now inherits from networkx.Graph directly. Therefore, the nx_graph attribute is removed. #481
• The class LayerCategories was removed. COLOR_TYPE and SEGMENTATION_TYPE were renamed to COLOR_CATEGORY and SEGMENTATION_CATEGORY and can now be imported directly. The type of many parameters were changed from str to the literal LayerCategoryType. #454

Added

• Added redownsample() method to Layer to recompute existing downsampled magnifications. #461
• Added globalize_floodfill.py script to globalize partially computed flood fill operations. #461

Changed

• Improved performance for calculations with Vec3Int and BoundingBox. #461
• Resolve path when symlinking layer and make_relative is False (instead of only making it absolute). #492

wkcuber

Added

• Added the flag --version to wkcuber. #471

v0.8.22

Breaking Changes

• Removed the organization parameter from the webknossos_context function. The organization will automatically be fetched using the token of the user. #470

Added

• Added a User class to the client that can be used to get meta-information of users or their logged time. The currently logged in user can be accessed, as well as all managed users. #470