Merge branch 'develop' into liezl/bump-to-1.4.1a3

.conda/meta.yaml

@@ -55,7 +55,7 @@ requirements:
     - conda-forge::seaborn
     - conda-forge::qudida
     - conda-forge::albumentations
-    - conda-forge::ndx-pose
+    - conda-forge::ndx-pose <0.2.0
     - conda-forge::importlib-metadata ==4.11.4
   run:
     - conda-forge::python ==3.7.12  # Run into _MAX_WINDOWS_WORKERS not found if <
@@ -90,7 +90,7 @@ requirements:
     - conda-forge::tensorflow-hub <0.14.0  # Causes pynwb conflicts on linux GH-1446
     - conda-forge::qudida
     - conda-forge::albumentations
-    - conda-forge::ndx-pose
+    - conda-forge::ndx-pose <0.2.0
     - conda-forge::importlib-metadata ==4.11.4
 
 # This no longer works so we have moved it to the build workflow

.conda_mac/meta.yaml

@@ -57,7 +57,7 @@ requirements:
     - conda-forge::seaborn
     - conda-forge::qudida
     - conda-forge::albumentations
-    - conda-forge::ndx-pose
+    - conda-forge::ndx-pose <0.2.0
 
   run:
     - conda-forge::python >=3.9.0, <3.10.0
@@ -89,7 +89,7 @@ requirements:
     # - conda-forge::tensorflow-hub  # pulls in tensorflow cpu from conda-forge
     - conda-forge::qudida
     - conda-forge::albumentations
-    - conda-forge::ndx-pose
+    - conda-forge::ndx-pose <0.2.0
 
 # test:
 #   imports:

environment.yml

@@ -40,7 +40,7 @@ dependencies:
     - conda-forge::tensorflow-hub  # Pinned in meta.yml, but no problems here... yet
     - conda-forge::qudida
     - conda-forge::albumentations
-    - conda-forge::ndx-pose
+    - conda-forge::ndx-pose <0.2.0
 
     # Packages required by tensorflow to find/use GPUs
     - conda-forge::cudatoolkit ==11.3.1

environment_mac.yml

@@ -39,6 +39,6 @@ dependencies:
     # - conda-forge::tensorflow-hub  # pulls in tensorflow cpu from conda-forge
     - conda-forge::qudida
     - conda-forge::albumentations
-    - conda-forge::ndx-pose
+    - conda-forge::ndx-pose <0.2.0
     - pip:
         - "--editable=.[conda_dev]"

environment_no_cuda.yml

@@ -41,7 +41,7 @@ dependencies:
     - conda-forge::tensorflow-hub
     - conda-forge::qudida
     - conda-forge::albumentations
-    - conda-forge::ndx-pose
+    - conda-forge::ndx-pose <0.2.0
 
     - pip:  
         - "--editable=.[conda_dev]"

pypi_requirements.txt

@@ -37,7 +37,7 @@ tensorflow>=2.6.3,<2.9; platform_machine != 'arm64'
 # tensorflow ==2.7.4; platform_machine != 'arm64'
 tensorflow-hub<=0.14.0
 albumentations
-ndx-pose
+ndx-pose<0.2.0
 # These dependencies are untested since we do not offer a wheel for apple silicon atm.
 tensorflow-macos==2.9.2; sys_platform == 'darwin' and platform_machine == 'arm64'
 tensorflow-metal==0.5.0; sys_platform == 'darwin' and platform_machine == 'arm64'

sleap/skeleton.py

@@ -18,7 +18,6 @@
 import attr
 import cattr
 import h5py
-import jsonpickle
 import networkx as nx
 import numpy as np
 from networkx.readwrite import json_graph
@@ -421,11 +420,30 @@ def encode(cls, data: Dict[str, Any]) -> str:
         Returns:
             json_str: The JSON string representation of the data.
         """
+
+        # This is required for backwards compatibility with SLEAP <=1.3.4
+        sorted_data = cls._recursively_sort_dict(data)
+
         encoder = cls()
-        encoded_data = encoder._encode(data)
+        encoded_data = encoder._encode(sorted_data)
         json_str = json.dumps(encoded_data)
         return json_str
 
+    @staticmethod
+    def _recursively_sort_dict(dictionary: Dict[str, Any]) -> Dict[str, Any]:
+        """Recursively sorts the dictionary by keys."""
+        sorted_dict = dict(sorted(dictionary.items()))
+        for key, value in sorted_dict.items():
+            if isinstance(value, dict):
+                sorted_dict[key] = SkeletonEncoder._recursively_sort_dict(value)
+            elif isinstance(value, list):
+                for i, item in enumerate(value):
+                    if isinstance(item, dict):
+                        sorted_dict[key][i] = SkeletonEncoder._recursively_sort_dict(
+                            item
+                        )
+        return sorted_dict
+
     def _encode(self, obj: Any) -> Any:
         """Recursively encodes the input object.
 
@@ -1477,7 +1495,7 @@ def to_json(self, node_to_idx: Optional[Dict[Node, int]] = None) -> str:
         Returns:
             A string containing the JSON representation of the skeleton.
         """
-        jsonpickle.set_encoder_options("simplejson", sort_keys=True, indent=4)
+
         if node_to_idx is not None:
             # Map Nodes to int
             indexed_node_graph = nx.relabel_nodes(G=self._graph, mapping=node_to_idx)

tests/test_skeleton.py

@@ -45,6 +45,18 @@ def test_decoded_encoded_Skeleton(skeleton_fixture_name, request):
     # Encode the graph as a json string to test .encode method
     encoded_json_str = SkeletonEncoder.encode(graph)
 
+    # Assert that the encoded json has keys in sorted order (backwards compatibility)
+    encoded_dict = json.loads(encoded_json_str)
+    sorted_keys = sorted(encoded_dict.keys())
+    assert list(encoded_dict.keys()) == sorted_keys
+    for key, value in encoded_dict.items():
+        if isinstance(value, dict):
+            assert list(value.keys()) == sorted(value.keys())
+        elif isinstance(value, list):
+            for item in value:
+                if isinstance(item, dict):
+                    assert list(item.keys()) == sorted(item.keys())
+
     # Get the skeleton from the encoded json string
     decoded_skeleton = Skeleton.from_json(encoded_json_str)