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Graphs from cogex #70

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@kkaris kkaris commented Sep 30, 2025 •
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This PR does the following:

  • Update net_functions.py:
    • For more modern python
    • Updates necessary for new network search dumping pathway
    • Hide pybel imports to silo that dependency
  • Update graph generation tests
  • Allow setting AWS buckets via config (used for dockerization in downstream apps). This includes the commits from Allow to set AWS buckets in config #67 in this repository.
  • Cleaned up logic and added comments in statistics.py

Supersedes #67.

kkaris added 24 commits September 26, 2025 14:17
@kkaris
Allow to set AWS buckets in config
09f93c7
@kkaris
Update logic to check if file exists before recalculating
807b34f
@kkaris
Handle filenames and use pathlib.Path
a580f31
@kkaris
Make inputs optional if just loading result
ecfc7a2
@kkaris
Update z-score weigth setting functions
479bfdc
@kkaris
Set z-scores and correlation weights on sif df directly
ae824b9
@kkaris
Use better parameter name
998f193
@kkaris
Restore mesh_id_dict for now
a202e40
@kkaris
Update ontology edge addition
b2aefef
@kkaris
Set dtype for weight to avoid mixing types
f16a661
@kkaris
Make date optional
e60f2de
@kkaris
Update docstring
9bdaf50
@kkaris
Add clarifying comment in doctstring
6397d4b
@kkaris
Fix add logger messages
8272fe3
@kkaris
Setup numpy version agnostic longfloat
fe6d039
@kkaris
Update helpers getting sif and hash-mesh map data
b488db7
@kkaris
Hide Pybel usage to make network search tests run easier
c2ed6b9
@kkaris
Add logp to SIF dictionary and update edge assertions
658ed08
@kkaris
Add function to set edge level corr weight for DiGraphs
93a6486
@kkaris
Update belief and correlation weights in graph processing
7ecb058
@kkaris
Remove any pandas <NA> in sif position column
85d19b0
@kkaris
Add residue/position to test SIF, add check of corr_weight assert log…
9a26c51 
…p not in statements dict
@kkaris
Restore file permissions
f4d6ff2
@kkaris
Add position/residue to test sif in tests/__init__.py
6962aa6
This was referenced Sep 30, 2025
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@kkaris