Fix pandas 2.x API drift in top_network_plot helpers#390
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Two pandas API breaks were hitting top_network_plot() across panda, analyze_panda, lioness/analyze_lioness, and puma: 1. `DataFrame.drop(labels, 1)` — pandas 2.x requires `axis=1` as a keyword argument; the bare positional form raises `TypeError: DataFrame.drop() takes from 1 to 2 positional arguments but 3 were given`. 2. `self.export_panda_results[['force']] = self.lioness_results.iloc[:, index+2]` in AnalyzeLioness.top_network_plot — assigning a single-column Series to a single-element column list now raises `ValueError: Columns must be same length as key`. Use scalar key `self.export_panda_results["force"] = ...` instead. These came up while running the netbooks tutorials end-to-end against a fresh pandas 2.x install (pv2 Building_single-sample_LIONESS, pv3 Up_and_running_with_PANDA). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…cobra CI revealed two more sites breaking on the same pandas API change (Series integer subscript switching from positional to label-based): - netZooPy/condor/condor.py:308 in matrices(): `edge[1][N]` over a row Series with labels ['V1', 'V2', 'weight'] raised KeyError: 2 because the integer key is now treated as a label. Use `.iloc[N]` to keep positional semantics. - tests/test_cobra.py: `np.mean(X, axis=0)[i]` on a Series with column- label index raised KeyError: 0 for the same reason. Switch to `.iloc[i]`. Verified both test_cobra and test_condor pass under pandas 2.3.x. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #390 +/- ##
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Summary
Fix two pandas 2.x API drifts in the panda/lioness/puma top-network plotters. Both surfaced while running the netbooks tutorials end-to-end against a current pandas install.
DataFrame.drop(labels, 1)no longer accepts the bare positional axis in pandas 2.x — switch toaxis=1(4 call sites inpanda.py,analyze_panda.py,puma.py).self.export_panda_results[['force']] = seriesraisesValueError: Columns must be same length as keyin pandas 2.x — change to scalar["force"] = ...inAnalyzeLioness.top_network_plot.Test plan
panda_obj.top_network_plot(top=10, file="...")runs withoutTypeError(verified vianetbooks/netZooPy/Up_and_running_with_PANDA_and_netZooPy.ipynb)analyze_lioness_obj.top_network_plot(top=10, file="...")runs (verified vianetbooks/netZooPy/Building_single-sample_regulatory_networks_using_LIONESS_and_netZooPy.ipynb)puma.top_network_plot()— same change pattern, not exercised by a netbook but kept consistent with panda🤖 Generated with Claude Code