Add load_ppi to panda IO module, complete issue #350#385
Merged
katehoffshutta merged 3 commits intonetZoo:develfrom Apr 30, 2026
Merged
Add load_ppi to panda IO module, complete issue #350#385katehoffshutta merged 3 commits intonetZoo:develfrom
katehoffshutta merged 3 commits intonetZoo:develfrom
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Add load_ppi() to netZooPy/panda/io.py extracting the inline PPI reading logic from Panda.processData(). This completes the move of all IO functions (motif, expression, PPI) outside of the PANDA class. The functions can now be imported and used independently: from netZooPy.panda.io import load_motif, load_expression, load_ppi Fixes netZoo#350
- condor.py: Use itertuples() instead of iterrows() to avoid integer-indexing a string-keyed Series (KeyError: 2). - test_cobra.py: Convert X to numpy before np.mean() to avoid integer-indexing a string-keyed Series (KeyError: 0).
Contributor
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@marouenbg Could you please take a look at these merge conflicts and resolve them if there's a clear resolution? Thanks! |
# Conflicts: # netZooPy/condor/condor.py # netZooPy/panda/panda.py
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## devel #385 +/- ##
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Coverage 59.51% 59.52%
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Files 45 45
Lines 3053 3071 +18
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+ Hits 1817 1828 +11
- Misses 1236 1243 +7 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Summary
Completes the extraction of IO functions from the PANDA class (issue #350) by adding
load_ppi()tonetZooPy/panda/io.pyand wiring it intoPanda.processData().load_motif()andload_expression()were already extracted in a previous commit on devel. This PR adds the missingload_ppi()and removes the last inline IO logic fromprocessData().Changes (3 files, ~47 additions / ~27 deletions)
netZooPy/panda/io.py: Addedload_ppi()function (was a commented-out stub).netZooPy/panda/panda.py: Replaced inline PPI reading inprocessData()withio.load_ppi().netZooPy/panda/__init__.py: Exportsload_ppialongsideload_motifandload_expression.Usage
All three IO functions can now be used independently:
Testing
All existing tests pass: test_panda (2 tests), test_puma, test_lioness.
Fixes #350