Peter Cock

It looks like we all forgot about this PR :( At very least, the proposed LaTeX chapter in the tutorial would now need converting to RST (using pandoc would probably...

Probably overdue for deprecation rather than updating if there is not good current use age: https://biopython.org/wiki/Deprecation_policy

Adding a new wrapper for the SCOP JSON based REST API sounds good in principle. We could go ahead and deprecate the HTML returning legacy API wrapper too.

I don't know - I've never used SCOP. This module has been without a direct owner for many years - the vast majority of changes have been code style/maintenance, deprecation...

Noting the online SCOP test are currently failing with a timeout, currently the entire scop.mrc-lmb.cam.ac.uk domain is unavailable. The site was up and running at of 16 April according to...

The old site now redirects to https://www.ebi.ac.uk/pdbe/scop/ and there doesn't seem to be an equivalent to the legacy search. There is a free text search, and the REST API though....

e.g. https://ci.appveyor.com/project/biopython/biopython/builds/49747521/job/ys3k706a2g1ma0nm seemed to time out at the end uploading coverage

The old function didn't explicitly handle U either: ```python def GC(seq): """Calculate G+C content (DEPRECATED). Use Bio.SeqUtils.gc_fraction instead. """ warnings.warn( "GC is deprecated; please use gc_fraction instead.", BiopythonDeprecationWarning, ) gc...

Good detective work! I was working on something else at the time and didn't dig into this. We might try a best efforts attempt to parse them anyway with a...

Thank you! That's great to hear. Let's leave this open a bit longer, and recheck the ``NC_*`` versions in a little while in the expectation they get fixed soon.