[ds-api] Dataset api properties refactoring (#374)

* WIP: starting to remove parallel properties structure

* use cattrs to (de)serialize the properties

* cleanup

* remove redundant properties

* reformat properties in testdata

* fix linter/typecheck/format errors

* don't export the properties after a dataset is opened

* fix bug in get_view

* fix upsampling test case

* implement PR feedback

* Discard magnifications from the properties which do not exist on disk

* format code

* replace get_bounding_box and set_bounding_box with the property 'bounding_box'

* fix merge error

Author: rschwanhold

Changelog.md

@@ -10,7 +10,12 @@ For upgrade instructions, please check the respective *Breaking Changes* section
 [Commits](https://github.com/scalableminds/webknossos-cuber/compare/v0.8.12...HEAD)
 
 ### Breaking Changes in Config & CLI
-
+- Replaced the old properties classes of the Dataset API with attr-classes.
+  - The `Layer.rename()` function is now replaced with the setter of `Layer.name`.
+  - The functions `Layer.get_view_configuration` and `Layer.set_view_conficuration` are replaced by the property `Layer.default_view_configuration`. (Same applies to `Dataset.get_view_configuration` and `Dataset.set_view_configuration`)
+  - Moved `LayerViewConfiguration` and `DatasetViewConfiguration` into `properties.py`
+  - Removed `Layer.set_bounding_box_offset` and `Layer.set_bounding_box_size`.
+  - Renamed `Layer.get_bounding_box()` to the property `Layer.bounding_box`. The method `Layer.set_bounding_box` is replaced with the setter of the property `Layer.bounding_box`.
 ### Added
 - The API documentation is now hosted on a publicwebpage. [#392](https://github.com/scalableminds/webknossos-cuber/pull/392)
 

poetry.lock

@@ -22,6 +22,8 @@ scikit-learn = "^0.24.0"
 tifffile = "^2020.11.26"
 imagecodecs = "^2020.5.30"
 czifile = "^2019.7.2"
+attrs = "^21.1.0"
+cattrs = "1.7.1"
 
 [tool.poetry.dev-dependencies]
 pylint = "^2.6.0"

pyproject.toml

@@ -4,7 +4,7 @@
         "team": ""
     },
     "scale": [
-        1
+        1, 1, 1
     ],
     "defaultViewConfiguration": {
         "position": [
@@ -19,7 +19,7 @@
             "name": "color",
             "category": "color",
             "elementClass": "uint24",
-            "num_channels": 3,
+            "numChannels": 3,
             "boundingBox": {
                 "topLeft": [
                     0,