Replace deprecated numpy tostring/fromstring with tobytes/frombuffer#379
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marouenbg wants to merge 2 commits intonetZoo:develfrom
Open
Replace deprecated numpy tostring/fromstring with tobytes/frombuffer#379marouenbg wants to merge 2 commits intonetZoo:develfrom
marouenbg wants to merge 2 commits intonetZoo:develfrom
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np.ndarray.tostring() was removed in numpy 2.3+. Replace all tostring()/fromstring() calls with tobytes()/frombuffer() which have identical behavior and are the supported API. Fixes netZoo#378
- test_cobra: use numpy array for mean computation instead of pandas Series integer access (KeyError: 0 with string column index) - condor: use .iloc for positional access on iterrows() Series (KeyError: 2 with string column labels) - condor: use ki.sum() instead of float(sum(ki)) to avoid TypeError with np.matrix column vectors in newer numpy
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Summary
Replace all
np.ndarray.tostring()/np.fromstring()calls withnp.ndarray.tobytes()/np.frombuffer()inlioness.py.Motivation
np.ndarray.tostring()was deprecated in favor oftobytes()(identical behavior) and was fully removed in numpy 2.3+. This causesAttributeErrorwhen running LIONESS with modern numpy versions.Fixes #378
Changes
netZooPy/lioness/lioness.py: replaced 4 active usages and 2 commented-out usages oftostring()/fromstring()withtobytes()/frombuffer().