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Add skeleton utilities #76

Merged
merged 3 commits into from
Apr 14, 2024
Merged

Add skeleton utilities #76

merged 3 commits into from
Apr 14, 2024

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talmo
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@talmo talmo commented Apr 14, 2024

  • Skeleton.add_node: Add a node by name or object.
  • Skeleton.add_edge: Add an edge by lists of names or objects.
  • Skeleton.add_symmetry: Add a symmetry edge by lists of names or objects.

Summary by CodeRabbit

  • New Features
    • Enhanced input flexibility for certain skeleton manipulation methods.
    • Introduced new capabilities to add nodes, edges, and symmetry relationships to skeletons.
    • Added test functions to verify the functionality of adding nodes, edges, and symmetries.

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coderabbitai bot commented Apr 14, 2024

Walkthrough

The recent updates to the sleap_io package enhance the Skeleton class with improved input flexibility and new methods for managing skeleton components. These changes bring added functionality and ensure robust testing for a more reliable skeleton implementation.

Changes

File Path Change Summary
sleap_io/model/skeleton.py Updated input types for index and __getitem__. Added methods add_node, add_edge, add_symmetry.
tests/model/test_skeleton.py Added tests for new methods in Skeleton: test_add_node, test_add_edge, test_add_symmetry.

Possibly related issues

🐰🌟
A hop, a skip, a code deploy,
With nodes and edges, oh what joy!
Adding symmetry, so sleek,
Now the skeleton's not so meek!
Cheers to changes, big and small,
Happy coding, one and all! 🎉
🌟🐰


Recent Review Details

Configuration used: CodeRabbit UI

Commits Files that changed from the base of the PR and between 578f6a4 and 6d14979.
Files selected for processing (1)
  • tests/model/test_skeleton.py (1 hunks)
Files skipped from review as they are similar to previous changes (1)
  • tests/model/test_skeleton.py

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Actionable comments posted: 4

@@ -183,7 +183,7 @@ def __len__(self) -> int:
"""Return the number of nodes in the skeleton."""
return len(self.nodes)

def index(self, node: Union[Node, str]) -> int:
def index(self, node: Node | str) -> int:
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Replace type comparison with isinstance() for better practice and readability in the index method.

- if type(node) == str:
+ if isinstance(node, str):
- elif type(node) == Node:
+ elif isinstance(node, Node):

Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.

Suggested change
def index(self, node: Node | str) -> int:
def index(self, node: Node | str) -> int:

@@ -192,11 +192,92 @@
else:
raise IndexError(f"Invalid indexing argument for skeleton: {node}")

def __getitem__(self, idx: Union[int, str]) -> Node:
def __getitem__(self, idx: int | str) -> Node:
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Replace type comparison with isinstance() for better practice and readability in the __getitem__ method.

- if type(idx) == int:
+ if isinstance(idx, int):
- elif type(idx) == str:
+ elif isinstance(idx, str):

Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.

Suggested change
def __getitem__(self, idx: int | str) -> Node:
def __getitem__(self, idx: int | str) -> Node:

Comment on lines +226 to +229
if edge.source not in self.nodes:
self.add_node(edge.source)
if edge.destination not in self.nodes:
self.add_node(edge.destination)
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Undefined variable edge used in add_edge. It seems you meant to use src instead.

- if edge.source not in self.nodes:
+ if src.source not in self.nodes:
- if edge.destination not in self.nodes:
+ if src.destination not in self.nodes:

Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.

Suggested change
if edge.source not in self.nodes:
self.add_node(edge.source)
if edge.destination not in self.nodes:
self.add_node(edge.destination)
if src.source not in self.nodes:
self.add_node(edge.source)
if src.destination not in self.nodes:
self.add_node(edge.destination)

Args:
node: A `Node` object or a string name to create a new node.
"""
if type(node) == str:
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Replace type comparison with isinstance() for better practice and readability in the add_node method.

- if type(node) == str:
+ if isinstance(node, str):

Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.

Suggested change
if type(node) == str:
if isinstance(node, str):

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codecov bot commented Apr 14, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.65%. Comparing base (65b5ac4) to head (6d14979).

Additional details and impacted files
@@            Coverage Diff             @@
##             main      #76      +/-   ##
==========================================
+ Coverage   94.45%   94.65%   +0.19%     
==========================================
  Files          13       13              
  Lines        1443     1497      +54     
==========================================
+ Hits         1363     1417      +54     
  Misses         80       80              

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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Actionable comments posted: 0

Actionable comments outside the diff hunks (1)
sleap_io/model/skeleton.py (1)

Line range hint 10-10: Remove unused import Union.

- from typing import Optional, Tuple, Union
+ from typing import Optional, Tuple

@talmo talmo merged commit 5d98c96 into main Apr 14, 2024
9 checks passed
@talmo talmo deleted the talmo/skeleton-utils branch April 14, 2024 01:57
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