add get_agglomerate_graph to annotation (#1361)

* add get_agglomerate_graph to annotation

* ignore generated python code in ruff

* add type hints

* ignore type hints in ruff

* fix import and type

* add protobuf file

* update docs dependencies

* move _get_graph to abstract_api_client

* move generated files into own folder and update comments

* add generated code

* Apply suggestion from @fm3

Co-authored-by: Florian M <[email protected]>

* Apply suggestion from @fm3

Co-authored-by: Florian M <[email protected]>

* introduce _get_parsed_protobuf on the abstract_api_client. Add more comments. add changelog.

* reset symlink

* relax protobuf constraint

---------

Co-authored-by: valentin-pinkau <[email protected]>
Co-authored-by: Florian M <[email protected]>

Author: 3 people

docs/uv.lock

@@ -20,6 +20,8 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 - Dataset.add_layer_as_ref() now accepts RemoteLayer objects as well as Layer objects. [#1371](https://github.com/scalableminds/webknossos-libs/pull/1371])
 - RemoteDataset.annotation_id is now exposed, when available. [#1380](https://github.com/scalableminds/webknossos-libs/pull/1380)
 - RemoteDataset.open() now accepts an annotation url as well. [#1380](https://github.com/scalableminds/webknossos-libs/pull/1380)
+- RemoteAnnotation, now has a get_agglomerate_graph method, to make working with proofreading annotations easier. [#1361](https://github.com/scalableminds/webknossos-libs/pull/1361)
+
 ### Changed
 - Ported `test.sh` to `test.py`, run with `uv run test.py`. [#1379](https://github.com/scalableminds/webknossos-libs/pull/1379)
 - `Dataset.add_layer_as_ref(remote_layer.path)` does not work anymore. Please use `Dataset.add_layer_as_ref(remote_layer)` instead. [#1371](https://github.com/scalableminds/webknossos-libs/pull/1371])

webknossos/Changelog.md

@@ -45,6 +45,8 @@ dependencies = [
     "networkx ~=3.2.1",
     "numpy >=2.0.0,<3.0.0",
     "pims ~=0.7.0",
+    "protobuf<7,>=3.12.0",
+    "google-api-python-client >= 2.0.0",
     "psutil ~=6.0.0",
     "python-dateutil ~=2.8.0",
     "python-dotenv ~=1.0.1",
@@ -149,6 +151,8 @@ exclude = [
     "site-packages",
     "venv",
     "webknossos/dataset/_utils/vendor",
+    "webknossos/proofreading/generated/agglomerate_graph_pb2.py",
+    "webknossos/proofreading/generated/agglomerate_graph_pb2.pyi",
 ]
 
 # Same as Black.