fix: Github actions workflows +, dependencies fix + cloudflare links

[wschuell]

I noticed Github actions have been failing at the setup phase for a few months, and made a few fixes to at least recover proper functioning of the workflows.

Changelogs

Actions fixes:

• install black[jupyter] in code-check
• remove fallback version dev (which is not a tag and probably the source of failure for the tests setup so far)
• added bioembeddings as an option for pip install (some pytests were failing and asking for it)
• hardcoded new cloudflare links for graphormer-pretrained (still looking for gs:// URLs)
• changed the gs:// URLs that were left in comments and notebooks

This leaves a few failures in pytest, but at least they are visible now