Updating the examples files

[alexdepremia]

Proposed changes

Some of the example files are outdated. Some of them are not working anymore.

Types of changes

What types of changes does your code introduce?
Put an x in the boxes that apply

• [ x] Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)

Checklist

Put an x in the boxes that apply.

• Lint and unit tests pass locally with my changes
• I have added tests that prove my fix is effective or that my feature works

[alexdepremia]

When executing the examples notebooks, there are some problems. I solved the ones in the intrinsic dimension and the clustering notebooks. The information imbalance code gives me an error when dealing with periodic boundary conditions, but I think it is related to the cKDTree function in Scipy.
Error message:
File ckdtree.pyx:550, in scipy.spatial.ckdtree.cKDTree.init()
IndexError: invalid index to scalar variable.

Can someone check if you have the same error? My Scipy version is 1.7.1

[imacocco]

I just run the whole inf-imb notebook with both scipy 1.7.3 and scipy 1.8.1 and everything went smooth

[AldoGl]

They work for me too, I have scipy 1.6.1 and numpy 1.22.3

[AldoGl]

@alexdepremia if you agree I would merge all your changes excluding the changes to the intrinsic dimension notebook (because these conflict with some major improvements that @diegodoimo recently implemented). Let me know

[alexdepremia]

@AldoGl , yes sure. Go ahead!

[AldoGl]

@AldoGl , yes sure. Go ahead!

Done it, merging after the tests pass