refactor dataset, remote_dataset, and layer

[valentin-pinkau]

Description:

• This PR refactors the Dataset, Layer, MagView architecture, by introducing remote variants.
• In addition, the new upload method allows to upload directly to the underlying storage.
• Breaking changes are documented in the changelog.
• Docs and examples need to be updated.

Todos:

Make sure to delete unnecessary points or to check all before merging:

• Updated Changelog
• Updated Documentation
• Added / Updated Tests
• Considered adding this to the Examples

[normanrz]

Great work! Just minor comments. Maybe you can check that the abstract classes only have functions that multiple subclasses need. And, please make the layer-linking more ergonomic, as discussed.

[github-actions]

☂️ Python Coverage

current status: ✅

Overall Coverage

Lines	Covered	Coverage	Threshold	Status
9946	8358	84%	80%	🟢

New Files

File	Coverage	Status
webknossos/webknossos/dataset/abstract_dataset.py	91%	🟢
webknossos/webknossos/dataset/layer/_init_.py	100%	🟢
webknossos/webknossos/dataset/layer/abstract_layer.py	94%	🟢
webknossos/webknossos/dataset/layer/layer_to_link.py	77%	🟢
webknossos/webknossos/dataset/layer/remote_layer.py	86%	🟢
webknossos/webknossos/dataset/layer/segmentation_layer/init.py	100%	🟢
webknossos/webknossos/dataset/layer/segmentation_layer/abstract_segmentation_layer.py	91%	🟢
webknossos/webknossos/dataset/layer/segmentation_layer/attachments/init.py	100%	🟢
webknossos/webknossos/dataset/layer/segmentation_layer/attachments/attachment.py	93%	🟢
webknossos/webknossos/dataset/layer/segmentation_layer/remote_segmentation_layer.py	47%	🟢
webknossos/webknossos/dataset/layer/segmentation_layer/segmentation_layer.py	100%	🟢
webknossos/webknossos/dataset/layer/view/_init_.py	100%	🟢
webknossos/webknossos/dataset/remote_dataset.py	84%	🟢
webknossos/webknossos/dataset_properties/init.py	100%	🟢
webknossos/webknossos/dataset_properties/dataset_properties.py	96%	🟢
webknossos/webknossos/dataset_properties/structuring.py	98%	🟢
webknossos/webknossos/ssl_context.py	100%	🟢
TOTAL	92%	🟢

Modified Files

File	Coverage	Status
webknossos/webknossos/_init_.py	72%	🟢
webknossos/webknossos/_nml/parameters.py	98%	🟢
webknossos/webknossos/administration/task.py	81%	🟢
webknossos/webknossos/annotation/annotation.py	79%	🟢
webknossos/webknossos/annotation/volume_layer.py	98%	🟢
webknossos/webknossos/cli/convert.py	96%	🟢
webknossos/webknossos/cli/convert_knossos.py	37%	🟢
webknossos/webknossos/cli/convert_raw.py	67%	🟢
webknossos/webknossos/cli/convert_zarr.py	35%	🟢
webknossos/webknossos/cli/copy_dataset.py	100%	🟢
webknossos/webknossos/cli/download.py	84%	🟢
webknossos/webknossos/cli/export_as_tiff.py	56%	🟢
webknossos/webknossos/client/_init_.py	100%	🟢
webknossos/webknossos/client/_download_dataset.py	95%	🟢
webknossos/webknossos/client/_upload_dataset.py	86%	🟢
webknossos/webknossos/client/api_client/_abstract_api_client.py	94%	🟢
webknossos/webknossos/client/api_client/_serialization.py	96%	🟢
webknossos/webknossos/client/api_client/datastore_api_client.py	90%	🟢
webknossos/webknossos/client/api_client/models.py	100%	🟢
webknossos/webknossos/client/api_client/wk_api_client.py	86%	🟢
webknossos/webknossos/dataset/_init_.py	100%	🟢
webknossos/webknossos/dataset/_utils/infer_bounding_box_existing_files.py	100%	🟢
webknossos/webknossos/dataset/_utils/pims_images.py	87%	🟢
webknossos/webknossos/dataset/_utils/segmentation_recognition.py	91%	🟢
webknossos/webknossos/dataset/dataset.py	76%	🟢
webknossos/webknossos/dataset/defaults.py	100%	🟢
webknossos/webknossos/dataset/ome_metadata.py	95%	🟢
webknossos/webknossos/dataset/remote_dataset_registry.py	93%	🟢
webknossos/webknossos/dataset/remote_folder.py	86%	🟢
webknossos/webknossos/skeleton/skeleton.py	92%	🟢
webknossos/webknossos/utils.py	73%	🟢
TOTAL	85%	🟢

updated for commit: d81a14b by action🐍