GitLab

Update openfold to use pytorch 2 and other updated dependencies

Update pl_upgrades to use numpy 2 and update other dependencies

small fix to spacing

small fix to spacing

merge changes from upstream pl_upgrades

Minor typo fix in Installation.md

Fix RODA flatten script

docs: Add env var to install guide 

Revert "docs: Add env var instructions to install guide  "

docs: Add env var instructions to install guide  

Update Installation.md - fix pl_upgrades clone instructions

Fix pl_upgrades environment (numpy, cuda, gcc)

That direct clone of branch url does not work. Replaced it with a proper clone command with -b.

Remove unnecessary double-load of config_json.

Add use_custom_templates option