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Merged
jgwalkup merged 2 commits into from
Jul 16, 2026
+4 −5
Merged

Debugging and making code faster #51

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9178c1a
Update grid.py
eusimeo Jul 16, 2026
d1aab8d
Update utility.py
eusimeo Jul 16, 2026
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1 change: 0 additions & 1 deletion src/grid.py
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Original file line number Diff line number Diff line change
Expand Up @@ -717,7 +717,6 @@ def reinitialization(self,initialization,microbes_pp,output,mode,pulse,*args):
# 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)
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()
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8 changes: 4 additions & 4 deletions src/utility.py
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Expand Up @@ -10,7 +10,7 @@
import numpy as np
import pandas as pd
import pickle
from scipy.stats import distributions
from scipy.stats import uniform, norm # instead of calling the whole distributions package (heavy) we call only the needed objects


def LHS(n,loc,upc,dist):
Expand All @@ -34,9 +34,9 @@ def LHS(n,loc,upc,dist):

scale = upc - loc
if dist == 'uniform':
rv = distributions.uniform(loc=loc, scale=scale)
rv = uniform(loc=loc, scale=scale)
elif dist == 'normal':
rv = distributions.norm(loc=loc, scale=scale)
rv = norm(loc=loc, scale=scale)

lhs = rv.ppf(points)

Expand Down Expand Up @@ -87,4 +87,4 @@ def export(output,site,name):
"""

with open(site + "_" + str(name) + ".pickle", "wb") as f:
pickle.dump(output, f, pickle.HIGHEST_PROTOCOL)
pickle.dump(output, f, pickle.HIGHEST_PROTOCOL)
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