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Fix Colab by using OF commit from pl_upgrades

Duplicate expansion support

Fixed a small typo in permutation unit test docstring

Update multi-chain permutation and permutation unittest 

Fixed a small typo in permutation unit test docstring

Without the break statement this function will fall back to setting the resolution to _reflns.d_resolution_high for most structures, which reflects the resolution limit in the raw data and not the final structure (see https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns.d_resolution_high.html and https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_refine.ls_d_res_high.html).

This adds workers=True to the Lightning seed_everything function which guarantees different random states across all processes in distributed training. Prior to that some processes on different GPUs with the same worker ID could share the same random state.

Note that this will break reproducibility between runs prior to and after this change.

Also removes the seed and supress_output modules that were not used anymore in OpenFold.