Try turning mincount to 1e-6 or something else suitably small, and I think you will figure out the issue.

I'll close because I don't think there is an error here. Please discuss at https://discourse.matplotlib.org if you would like more explanation. Thanks!

Thanks for your answer ! Although, I believe there might still be something more to say @jklymak. From the hexbin documentation it is said :

mincnt > 0, default: None
    If not None, only display cells with more than mincnt number of points in the cell.

Hence the mincnt should, to my understanding of the docstring, not depend on any of the variables (not x,y, or C). It should be the minimum number of points landing in the hexagon no ? This might be an English related problem though...

Right maybe the documentation could be clearer. Apparently when c is provided it modifies the count (or weight) of each data point. In this case you are making those counts be less than 1, and falling below the threshold.

OK if I pick this one up? I can see how an improvement to the mincnt part of the docstring would help here.

@RebeccaWPerry we don't assign PRs, so if an issue doesn't have a linked PR, anyone is welcome to work on it. If there is a linked PR, please try and work in the confines of that PR.

I looked into this more and realized it wasn't actually a documentation-only issue. I included more details in PR #21381, but for for the same of completeness here is an example that shows even when "scaling" by 1 and reducing with sum the bug persists.

import numpy as np
import matplotlib.pyplot as plt

npts = int(2e4)

# Create a random distribution and another one as it perturbation
y = np.random.randint(0, 100, npts)
# Y axis variable
x = np.random.normal(loc=0, scale=2, size=npts)

# Plot
fig, axes = plt.subplots(2,1)

#C not specified
ax = axes[0]
res1 = ax.hexbin(x, y, mincnt=1, extent=[-8,8,0,100], gridsize=150)

#adding weights of 1 and specifying reduce as sum should be identical to no weights
ax = axes[1]
res2 = ax.hexbin(x, y, C=np.ones(len(x)), mincnt=1, extent=[-8,8,0,100], gridsize=150,
                 reduce_C_function = np.sum)

c1 = res1.get_array()                
c2 = res2.get_array()

print('points binned in plot1: ', sum(c1))
print('points binned in plot2: ', sum(c2))

fig.savefig(f"hexbin_weights.png")
plt.show()

With v3.8.0 and main, the code from the OP gives me

So I think this is fixed, probably by #26113.