triplets_correct with networkx #273
Conversation
…/treedata/nx.digraph. backend logic uses nx.digraphs. added helper functions working on nx.digraphs to critique_utilities.py. added tests in compare_tree_test.py for the new triplets_correct function
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## 3.0.0 #273 +/- ##
==========================================
+ Coverage 84.94% 86.91% +1.96%
==========================================
Files 76 76
Lines 5773 5922 +149
==========================================
+ Hits 4904 5147 +243
+ Misses 869 775 -94
🚀 New features to boost your workflow:
|
mattjones315
left a comment
mattjones315
left a comment
There was a problem hiding this comment.
Great job @gloriayma! Left a few comments that we should resolve.
High level comment is that there are a lot of helper functions that we can reduce and refactorize. Also worthwhile to use pre-existing implementations rather than manually implement things like DFS/BFS. In general we can clean up things this way - writing way less code. Check out William's pycea implementation of get_depth, for example: https://github.com/YosefLab/pycea/blob/main/src/pycea/pp/setup_tree.py
… old unedited files
…_digraph function
…ers for docstrings for critique_utilities helper functions
…nstances in compare.py with new collapse_unifurcations from utils.py
… to use networkx native node depth function
colganwi
left a comment
colganwi
left a comment
There was a problem hiding this comment.
Getting close @gloriayma! Most of my comments are formatting and removing redundant code.
ChatGPT is excellent at doing this! Try copy and pasting this code and asking for a cleaned up and simplified version. You probably won't want to use its output directly but it will give you some ideas of where to trim.
….py) to remove redundant code. other minor edits to function names in critique_utilities.py
for more information, see https://pre-commit.ci
No description provided.