Sort encoded `Skeleton` dictionary for backwards compatibility

Description

In #1970, we created our own SkeletonEncoder class to move away from using jsonpickle.encode. And, while the SkeletonEncoder paired with the SkeletonDecoder works perfectly fine, we get some strange behavior when trying to load Skeleton jsons across versions of SLEAP (that still use jsonpickle.decode).

The only difference seemed to be the ordering of the keys in the dictionaries; thus, this PR sorts the Skeleton dictionaries before encoding them - which has proven to do the trick with some manual testing across versions.

Unsorted skeleton (breaks backwards compatibility)

{"directed": true, "multigraph": true, "graph": {"name": "Skeleton-0", "num_edges_inserted": 46}, "nodes": [{"id": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["head", 1.0]}}}, {"id": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["thorax", 1.0]}}}, {"id": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["abdomen", 1.0]}}}, {"id": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["wingL", 1.0]}}}, {"id": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["wingR", 1.0]}}}, {"id": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["forelegL4", 1.0]}}}, {"id": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["forelegR4", 1.0]}}}, {"id": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["midlegL4", 1.0]}}}, {"id": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["midlegR4", 1.0]}}}, {"id": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["hindlegL4", 1.0]}}}, {"id": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["hindlegR4", 1.0]}}}, {"id": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["eyeL", 1.0]}}}, {"id": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["eyeR", 1.0]}}}], "links": [{"edge_insert_idx": 44, "type": {"py/reduce": [{"py/type": "sleap.skeleton.EdgeType"}, {"py/tuple": [1]}]}, "source": {"py/id": 1}, "target": {"py/id": 12}, "key": 0}, {"edge_insert_idx": 45, "type": {"py/id": 14}, "source": {"py/id": 1}, "target": {"py/id": 13}, "key": 0}, {"edge_insert_idx": 34, "type": {"py/id": 14}, "source": {"py/id": 2}, "target": {"py/id": 1}, "key": 0}, {"edge_insert_idx": 35, "type": {"py/id": 14}, "source": {"py/id": 2}, "target": {"py/id": 3}, "key": 0}, {"edge_insert_idx": 36, "type": {"py/id": 14}, "source": {"py/id": 2}, "target": {"py/id": 4}, "key": 0}, {"edge_insert_idx": 37, "type": {"py/id": 14}, "source": {"py/id": 2}, "target": {"py/id": 5}, "key": 0}, {"edge_insert_idx": 38, "type": {"py/id": 14}, "source": {"py/id": 2}, "target": {"py/id": 6}, "key": 0}, {"edge_insert_idx": 39, "type": {"py/id": 14}, "source": {"py/id": 2}, "target": {"py/id": 7}, "key": 0}, {"edge_insert_idx": 40, "type": {"py/id": 14}, "source": {"py/id": 2}, "target": {"py/id": 8}, "key": 0}, {"edge_insert_idx": 41, "type": {"py/id": 14}, "source": {"py/id": 2}, "target": {"py/id": 9}, "key": 0}, {"edge_insert_idx": 42, "type": {"py/id": 14}, "source": {"py/id": 2}, "target": {"py/id": 10}, "key": 0}, {"edge_insert_idx": 43, "type": {"py/id": 14}, "source": {"py/id": 2}, "target": {"py/id": 11}, "key": 0}]}

Sorted skeleton (backwards compatible)

{"directed": true, "graph": {"name": "Skeleton-0", "num_edges_inserted": 46}, "links": [{"edge_insert_idx": 44, "key": 0, "source": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["head", 1.0]}}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["eyeL", 1.0]}}, "type": {"py/reduce": [{"py/type": "sleap.skeleton.EdgeType"}, {"py/tuple": [1]}]}}, {"edge_insert_idx": 45, "key": 0, "source": {"py/id": 1}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["eyeR", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 34, "key": 0, "source": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["thorax", 1.0]}}, "target": {"py/id": 1}, "type": {"py/id": 3}}, {"edge_insert_idx": 35, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["abdomen", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 36, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["wingL", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 37, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["wingR", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 38, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["forelegL4", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 39, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["forelegR4", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 40, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["midlegL4", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 41, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["midlegR4", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 42, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["hindlegL4", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 43, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["hindlegR4", 1.0]}}, "type": {"py/id": 3}}], "multigraph": true, "nodes": [{"id": {"py/id": 1}}, {"id": {"py/id": 5}}, {"id": {"py/id": 6}}, {"id": {"py/id": 7}}, {"id": {"py/id": 8}}, {"id": {"py/id": 9}}, {"id": {"py/id": 10}}, {"id": {"py/id": 11}}, {"id": {"py/id": 12}}, {"id": {"py/id": 13}}, {"id": {"py/id": 14}}, {"id": {"py/id": 2}}, {"id": {"py/id": 4}}]}

v1.3.3 Skeleton

{"directed": true, "graph": {"name": "Skeleton-0", "num_edges_inserted": 46}, "links": [{"edge_insert_idx": 44, "key": 0, "source": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["head", 1.0]}}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["eyeL", 1.0]}}, "type": {"py/reduce": [{"py/type": "sleap.skeleton.EdgeType"}, {"py/tuple": [1]}]}}, {"edge_insert_idx": 45, "key": 0, "source": {"py/id": 1}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["eyeR", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 34, "key": 0, "source": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["thorax", 1.0]}}, "target": {"py/id": 1}, "type": {"py/id": 3}}, {"edge_insert_idx": 35, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["abdomen", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 36, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["wingL", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 37, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["wingR", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 38, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["forelegL4", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 39, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["forelegR4", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 40, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["midlegL4", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 41, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["midlegR4", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 42, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["hindlegL4", 1.0]}}, "type": {"py/id": 3}}, {"edge_insert_idx": 43, "key": 0, "source": {"py/id": 5}, "target": {"py/object": "sleap.skeleton.Node", "py/state": {"py/tuple": ["hindlegR4", 1.0]}}, "type": {"py/id": 3}}], "multigraph": true, "nodes": [{"id": {"py/id": 1}}, {"id": {"py/id": 5}}, {"id": {"py/id": 6}}, {"id": {"py/id": 7}}, {"id": {"py/id": 8}}, {"id": {"py/id": 9}}, {"id": {"py/id": 10}}, {"id": {"py/id": 11}}, {"id": {"py/id": 12}}, {"id": {"py/id": 13}}, {"id": {"py/id": 14}}, {"id": {"py/id": 2}}, {"id": {"py/id": 4}}]}

Types of changes

[x] Bugfix
[ ] New feature
[ ] Refactor / Code style update (no logical changes)
[ ] Build / CI changes
[ ] Documentation Update
[ ] Other (explain)

Does this address any currently open issues?

1972
1970
1961
1841

Outside contributors checklist

[ ] Review the guidelines for contributing to this repository
[ ] Read and sign the CLA and add yourself to the authors list
[ ] Make sure you are making a pull request against the develop branch (not main). Also you should start your branch off develop
[ ] Add tests that prove your fix is effective or that your feature works
[ ] Add necessary documentation (if appropriate)

Thank you for contributing to SLEAP!

:heart:

Summary by CodeRabbit

New Features
- Introduced a method to sort dictionary keys recursively during the encoding process for improved data consistency.
Bug Fixes
- Enhanced the encoding process to ensure compatibility with earlier versions of the SLEAP framework.
Tests
- Added assertions to verify that encoded JSON keys are sorted, improving robustness and compatibility.

Walkthrough

The changes in this pull request involve modifications to the SkeletonEncoder class in the sleap/skeleton.py file. A new static method, _recursively_sort_dict, is introduced to sort dictionaries recursively by their keys, which is called within the encode method to ensure sorted data for backward compatibility with earlier SLEAP versions. Additionally, a test in tests/test_skeleton.py is updated to verify that the keys in the encoded JSON string are sorted, enhancing the robustness of the encoding process.

Changes

File	Change Summary
sleap/skeleton.py	- Added method: `_recursively_sort_dict(dictionary: Dict[str, Any])` in `SkeletonEncoder`. - Updated method: `encode(cls, data: Dict[str, Any])` to include sorting step. - Removed unnecessary line for setting `jsonpickle` options.
tests/test_skeleton.py	- Updated `test_decoded_encoded_Skeleton` to assert that keys in the encoded JSON are sorted, including nested dictionaries and lists.

Possibly related PRs

#1970: The introduction of the SkeletonEncoder class in this PR directly relates to the modifications made to the SkeletonEncoder class in the main PR, as both involve changes to the encoding process within sleap/skeleton.py.

Suggested reviewers

talmo

Poem

In the land where data hops,
A rabbit sorts and never stops.
With keys aligned in perfect rows,
Compatibility is how it grows!
Encoding magic, swift and bright,
In SLEAP's world, all feels just right! 🐇✨

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talmolab / sleap