DeprecationWarning with numpy 1.25: Conversion of an array with ndim > 0 to a scalar is deprecated

[GianlucaFicarelli]

With numpy 1.25 and libsonata 0.1.21, this code causes a DeprecationWarning:

import numpy as np
import libsonata
cc = libsonata.CircuitConfig.from_file("tests/data/config/circuit_config.json")
pop = cc.edge_population("edges-AB")
ids = np.asarray([1])
pop.afferent_edges(ids)

Result:

<ipython-input-1-d0433371129e>:6: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
  pop.afferent_edges(ids)
Selection([(0, 1), (2, 4)])

While these calls don't cause any warning:

In [2]: ids = [1]
   ...: pop.afferent_edges(ids)
   ...: 
Selection([(0, 1), (2, 4)])

In [3]: ids = 1
   ...: pop.afferent_edges(ids)
Selection([(0, 1), (2, 4)])

[mgeplf]

Thanks for the repro, I can generate the same error.

I will look into it.

[mgeplf]

It's an ordering issue when creating the bindings; because the scalar version is registered first, it is used. I guess previously, auto-coercion would happen from the single element array, to a scalar (since this came first), where we would change it back into a vector...

I need to check where else we may be doing this.