v2.4.5

webknossos

Fixed

• Fixed an issue where the unit of the scale (voxel_size) was not considered when reading the NML. #1339

cluster_tools

Fixed

• Fixed that sometimes not all slurm jobs were canceled when an executor was killed. #1317
• Fixed that when multiple cluster executors were instantiated in the same process, the original SIGINT handler sometimes was no longer called, leading to the main application not shutting down correctly after a SIGINT signal. #1317

v2.4.4

webknossos

Added

• The function Dataset.announce_manual_upload now takes an additional optional parameter dataset_url to select the correct datastore in a multi-datastore setup. #1336

Changed

• Every file that sends logging messages has its own logger now. This can be used to selectively disable loggers. #1335

v2.4.3

webknossos

Changed

• Warnings regarding missing pims image readers are only printed once during conversion. Error messages regarding wk-libs version are not displayed in slurm environments. #1266

Fixed

• Fixed mag and attachment paths under Windows. #1329

v2.4.2

webknossos

Added

• Added operations for Project, Task and TaskType classes and objects: #1294
  • Added operations for Project class:
    • Project.create() for creating a new project.
    • my_project.delete() to delete a project object
  • Added my_project.update() to update priority, expected_time and is_blacklisted_from_report values of an existing project object.
  • Added operations for TaskType class:
    • TaskType.get_list() to get all TaskType objects.
    • TaskType.get_by_id() to get a TaskType by id.
    • TaskType.get_by_name() to get a TaskType by name.
    • TaskType.create() to create a new TaskType.
  • Added operations my_task_type.delete() method for TaskType objects.
  • Added Task.get_list()to get all Task objects.
  • Added operations for Task objects:
    • my_task.update() to update a Task object.
    • my_task.delete() to delete a Task object.
• Added TaskExperience class to store domain and value pair.
• The libs client now uses versioned datastore routes for improved compatibility across webknossos versions. #1328

Fixed

• Fixed the tests for the newest WEBKNOSSOS version. #1328

v2.4.1

webknossos

Changed

• Limit custom retries (e.g. additional to tensorstore internal retries) to certain network errors ("Too Many Requests", "GatewayTimeout"). #1330

v2.4.0

webknossos

Breaking Changes

• Dataset.shallow_copy_dataset does not symlink layers, mags and attachments anymore. Instead mags and attachments are referenced by their path. #1290
• Deprecated a number of methods #1290:
  • Dataset.add_symlink_layer, use Dataset.add_layer_as_ref instead.
  • Dataset.add_remote_layer, use Dataset.add_layer_as_ref instead (renamed).
  • Dataset.add_copy_layer, use Dataset.add_layer_as_copy instead (renamed).
  • Layer.add_symlink_mag, use Layer.add_mag_as_ref instead.
  • Layer.add_remote_mag, use Layer.add_mag_as_ref instead (renamed).
  • Layer.add_copy_mag, use Layer.add_mag_as_copy instead (renamed).
  • Attachments.add_symlink_attachments, use Attachments.add_attachment_as_ref instead (note the singular form).
  • Attachments.add_attachments, use Attachments.add_attachment_as_ref instead (note the singular form).
  • Attachments.add_copy_attachments, use Attachments.add_attachment_as_copy instead (note the singular form).
• Dataset.add_layer and Dataset.add_layer_like as well as derived methods do not eagerly create a folder for the layer anymore. Folders will be created, if necessary, when mags or attachments are added. #1290

Changed

• Changed the default path type to UPath #1326
• All mags now store their path in the datasource-properties.json file. This eliminates the need for symlinks and removes the need to check multiple possible mag paths (e.g. 1-1-1 or 1). It also unifies local and remote mags. #1290
• Dataset-local mags and attachments use the ./ prefix for their path in compliance with IETF RFC1808. #1290

v2.3.11

webknossos

Fixed

• Fixed excessive RAM consumption during downsampling by chunking the computation. #1325

v2.3.10

webknossos

Added

• Added layers_to_ignore argument to Dataset.copy_dataset. #1321

Changed

• Make number of retries and backoff factor configurable (mainly for tensorstore reads/writes). See DEFAULT_NUM_RETRIES and DEFAULT_BACKOFF_FACTOR environment variables. #1323

v2.3.9

webknossos

Added

• Added a feature to track attached files of a segmentation layer. Previously, these files were only auto-detected by WEBKNOSSOS based on the location in special folders. Attachments can be added, e.g. dataset.get_segmentation_layer("segmentation").attachments.add_mesh('path/to/meshfile.hdf5'). #1312
• Added a with_attachments parameter to Dataset.copy_dataset to copy attachments. #1312
• Added a get_segmentation_layer method to Dataset to get a correctly-typed segmentation layer by name. #1312
• Retry asynchronous tensorstore calls on failure to make operation on object storage datasets accessed via network more robust. #1319

Changed

• When adding a layer, the used dtype is only valid if it is supported by webknossos. #1316

Fixed

• Fixed an issue that creates an Error when add_mag() was called just with a chunk_shape. #1315

cluster_tools

Changed

• Use sacct to detect out of memory errors instead of seff for Slurm executor. #1297

v2.3.8

webknossos

Changed

• Made the folder_id parameter of Dataset.announce_manual_upload optional. #1313