CI failures with pytest 8

[RMeli]

For a few days, CI has been failing consistently. Different platforms, different molecular I/O library, different network libraries.

The most notable difference between the last green CI and the failing CI is pytest, gone from 7.4.4 to 8.0.0.

Looking at the failure, it appears that the error message raised and the one captured by pytest do not match:

E       Failed: DID NOT WARN. No warnings of type (<class 'UserWarning'>,) matching the regex were emitted.
E        Regex: No atomic number information stored on nodes.
E        Emitted warnings: [ UserWarning('No atomic property information stored on nodes. Node matching is not performed...')].

It appears that some of the error messages were not updated in #64. However, this failed silently because of pytest-dev/pytest#9288.

Since pyrest=8.0.0, warns() [...] re-emits unmatched warnings when the context closes – previously it would consume all warnings, hiding those that were not matched by the function.