Update openfold to use pytorch 2 and other updated dependencies#534

Merged

jnwei merged 116 commits into

mainfrom

Apr 26, 2025

Commits on Jan 12, 2024

initial compatibility changes for upgrading multimer
jnwei
committed

Commits on Jan 16, 2024

np type update in openfold.np.relax
jnwei
committed

Commits on Jan 24, 2024

Additional fix for multimer deepspeed test

christinaflo
authored and
jnwei
committed

Commits on Jan 26, 2024

first pass changes to run with pl 2.1
jnwei
committed

Commits on Mar 19, 2024

Commits on Mar 21, 2024

superimposition fix from Aymen
jnwei
committed

Commits on Mar 25, 2024

seed workers fix and validation_epoch_end extra argument
jnwei
committed

Commits on Mar 27, 2024

add metric logging to progress bar.
jnwei
committed

Commits on Apr 1, 2024

more logging changes
jnwei
committed

Commits on Apr 2, 2024

Commits on Apr 11, 2024

adds reload_dataloaders_every_n_epochs flag
jnwei
committed

Commits on Apr 17, 2024

change message for test_model.py compare
jnwei
committed

Commits on Apr 20, 2024

Commits on May 2, 2024

Remove nvcc compute capability 37 which caused kernel build issues
jnwei
committed

Commits on May 6, 2024

Commits on May 11, 2024

Update docker-image.yml
jnwei
authored

Commits on May 13, 2024

make sure padded asym_id won't affect permutation steps

dingquanyu
authored and
jnwei
committed
fixed bugs in unittests for multi-chain permutation. now working on extra subtests

dingquanyu
authored and
jnwei
committed
remove unnecessary lines

dingquanyu
authored and
jnwei
committed
restore to the verison on main

dingquanyu
authored and
jnwei
committed
added typing hints and fixed some comments

dingquanyu
authored and
jnwei
committed
make sure no padded features are going to be selected as anchors

dingquanyu
authored and
jnwei
committed
fixed typing errors; added more comments

dingquanyu
authored and
jnwei
committed
added comments

dingquanyu
authored and
jnwei
committed
update comments;fixed typos

dingquanyu
authored and
jnwei
committed
Update tests and comments

dingquanyu
authored and
jnwei
committed
fixed typing error of anchor_gt_residue

dingquanyu
authored and
jnwei
committed
Update test_permutation.py
jnwei
committed
Initial commit for sphinx documentation.
jnwei
committed
Rough draft dump of docs and readthedocs build
jnwei
committed
fix typo in readthedocs.yaml
jnwei
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replace doc environment pip dependencies with conda builds
jnwei
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cleanup makefiles and original readme
jnwei
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updates to Inference.md
jnwei
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Add addtional inference pages
jnwei
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add convert v1 weights instructions
jnwei
committed
Adds FAQ section
jnwei
committed
creates link to FAQ in documentation
jnwei
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small edits to main page
jnwei
committed
minor language edits
jnwei
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Adds mkl version to environment.yml
jnwei
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make space for docker CI
jnwei
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Shorten README.md main page.
jnwei
committed
adds mmseqs2 to environment.yml for clustering
jnwei
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Update training OpenFold docs with correct paths.
jnwei
committed
Adds example directory
jnwei
committed
Update docker-image.yml
jnwei
authored
Update docker-image.yml
jnwei
authored
Merge branch 'main' into pl_upgrades
jnwei
authored
fix typo in environment.yml
jnwei
committed
remove mpipy from pip install requirements
jnwei
committed
in scripts/utils.py account for case where no conda environment is specified.
jnwei
committed
Merge pull request #438 from jnwei/pl_upgrades
jnwei
authored

Commits on Oct 22, 2024

Fix pl_upgrades enwironment (numpy, cuda, gcc)
vaclavhanzl
committed

Commits on Nov 7, 2024

Merge pull request #496 from vaclavhanzl/vh-fix-pl_upgrades-env
jnwei
authored

Commits on Apr 23, 2025

Commits on Apr 26, 2025