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Update pandas dependency.py #45

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Merged
eusimeo merged 2 commits into from
Jul 8, 2026
Merged

Update pandas dependency.py #45

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a1c21ed
Update pandas dependency.py
eusimeo Jul 8, 2026
d6fae25
Clean up grid.py by removing commented debug code
jgwalkup Jul 8, 2026
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11 changes: 8 additions & 3 deletions src/grid.py
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Original file line number Diff line number Diff line change
Expand Up @@ -709,9 +709,14 @@ def reinitialization(self,initialization,microbes_pp,output,mode,pulse,*args):
# calculate frequency of every taxon
frequencies = cum_abundance/cum_abundance.sum()
frequencies = frequencies.fillna(0)

frequencies = frequencies.clip(lower=0, upper=1) # guard against any stray negative/over-1 values (sum of 1)
frequencies = frequencies / frequencies.sum() if frequencies.sum() > 0 else frequencies # renormalize to exactly 1

# last: assign microbes to each grid box randomly based on prior densities
choose_taxa = np.zeros((self.n_taxa,self.gridsize), dtype='int8')
for i in range(self.n_taxa):
choose_taxa[i,:] = np.random.binomial(1, frequencies[i], self.gridsize)
self.Microbes.loc[np.ravel(choose_taxa,order='F')==0] = np.float32(0) # NOTE order='F'
freq=np.float64(frequencies.iloc[1]) #working independent of indexing (based on location not index labels)
p_vec = np.array([freq, 1.0 - freq], dtype=np.float64) #solve numoy issues
p_vec = p_vec / p_vec.sum()
choose_taxa[i,:] = np.random.choice([1,0], self.gridsize, replace=True, p=p_vec)
self.Microbes.loc[np.ravel(choose_taxa,order='F')==0] = np.float32(0) # NOTE order='F'
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