Update pl_upgrades to use numpy 2 and update other dependencies#533
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This makes it more straightforward to create an alignment database directly from the flattened RODA downloads
This adds support for duplicate chain expansion for the alignment dir format. This script can be run on the flattened non-redundant RODA alignments to add explicit directories for all of the duplicate chains in the duplicate_chains file, symlinked to their representative chain alignment directory.
The commit used so far now fails with Colab's numpy. (Commit from current main does not work either.)
The previous data_dir_to_fasta.py script is very slow and requires fully reparsing mmCIF files. This new script is much faster and uses the sequence information from the alignment data instead. Note that this will not include chains for which alignments could not be generated, but we can't use those during training anyways.
…all-docs docs: Add env var instructions to install guide
…ahadams/install-docs Revert "docs: Add env var instructions to install guide "
docs: Add env var to install guide
…te-script Fix RODA flatten script
Minor typo fix in Installation.md
merge changes from upstream pl_upgrades
small fix to spacing
small fix to spacing
jaewshin
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Mar 7, 2026
Update pl_upgrades to use numpy 2 and update other dependencies
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Noteable updates include: