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Fix PaccMann integration#447

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tereshchuk1 wants to merge 8 commits into
daisybio:developmentfrom
tereshchuk1:pr-388
Open

Fix PaccMann integration#447
tereshchuk1 wants to merge 8 commits into
daisybio:developmentfrom
tereshchuk1:pr-388

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@tereshchuk1

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This PR fixes the PaccMann implementation originally submitted in #388 by @gretag04, adapting it to work within the drevalpy framework.

Bug fixes

  • Removed top-level pytoda imports in paccmann_v2.py: import pytoda and from pytoda.smiles.transforms import AugmentTensor were imported at the top level but pytoda is not a drevalpy dependency. Imports are now lazy (inside the confidence=True branch only), using the bundled stub in PaccMann/pytoda/.
  • Fixed SMILES loading
  • Fixed gene list name

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⚠️ Please install the 'codecov app svg image' to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

❌ Patch coverage is 71.91011% with 125 lines in your changes missing coverage. Please review.
✅ Project coverage is 81.11%. Comparing base (7d24cd6) to head (3c2a22f).
⚠️ Report is 54 commits behind head on development.

Files with missing lines Patch % Lines
drevalpy/models/PaccMann/utils/interpret.py 12.50% 63 Missing ⚠️
drevalpy/models/PaccMann/utils/loss_functions.py 20.83% 19 Missing ⚠️
drevalpy/models/PaccMann/paccmann_v2.py 85.10% 14 Missing ⚠️
drevalpy/models/PaccMann/utils/layers.py 74.07% 14 Missing ⚠️
drevalpy/models/PaccMann/paccmann.py 95.03% 8 Missing ⚠️
drevalpy/models/PaccMann/utils/utils.py 75.00% 7 Missing ⚠️
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Additional details and impacted files
@@               Coverage Diff               @@
##           development     #447      +/-   ##
===============================================
+ Coverage        80.34%   81.11%   +0.77%     
===============================================
  Files              101      127      +26     
  Lines             8171    10057    +1886     
===============================================
+ Hits              6565     8158    +1593     
- Misses            1606     1899     +293     

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4 participants