Dataset api restructuring (#331)

* WIP add initial documentation

* add documentation for dataset API

* fix linter errors

* fix lint error

* update pdoc

* implement PR feedback

* fix link to class

* fix path to class in documentation

* update changelog

* WIP: remove TiffDataset and TiledTiffDataset

* WIP: remove TiffDataset and TiledTiffDataset

* cleanup WKMagDataset

* rename WKDataset and WKMagDataset

* Implement get_view() to be safe

* update changelog

* fix downsampling

* fix bug in add_mag()

* fix MagView.for_each_chunk and implement PR feedback

* update changelog

* update changelog

Author: rschwanhold

Changelog.md

@@ -10,7 +10,20 @@ For upgrade instructions, please check the respective *Breaking Changes* section
 [Commits](https://github.com/scalableminds/webknossos-cuber/compare/v0.6.8...HEAD)
 
 ### Breaking Changes in Config & CLI
-
+- Refactoring of the dataset API: [#331](https://github.com/scalableminds/webknossos-cuber/pull/331)
+    - Tiff-support is now dropped (`TiffDataset` and `TiledTiffDataset` are now removed (alongside their corresponding `Layer` and `MagDataset` classes))
+    - Module names are now lowercase (previously: `wkcuber.api.Dataset`, `wkcuber.api.Layer`, `wkcuber.api.View`, `wkcuber.api.properties.DatasetProperties`, `wkcuber.api.properties.LayerProperties`, `wkcuber.api.properties.ResolutionProperties`)
+    - Some classes are renamed (`WKDataset` -> `Dataset`, `WKMagDataset` -> `MagView`)
+    - The "Layer types" (previously `Layer.COLOR` and `Layer.SEGMENTATION`) are now moved into their own class `wkcuber.api.layer.LayerTypes`. 
+    - `View` (in particular `get_view()`) is refactored to be safer (this is also a breaking change).
+      - The attribute `path_to_mag_dataset` was renamed to `path_to_mag_view`
+      - Changes for `View.get_view()` (these changes also apply for `MagView.get_view()` (previously `MagDataset.get_view()`)):
+        - The parameter `relative_offset` was renamed to `offset`.
+        - The parameter `is_bounded` was dropped (`View`s are now always bounded).
+        - The order of the parameters `size` and `offset` was changed, so that `offset` is now the first parameter.
+    - The shorthand `wkcuber.api.dataset.Dataset.get_view()` was removed.
+    - The flag `--write_tiff` of `convert_nifti` was removed.
+    
 ### Added
 
 ### Changed