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Adds Documentation and minor quality of life fixes #439

Merged
merged 114 commits into from
May 13, 2024
Merged

Adds Documentation and minor quality of life fixes #439

merged 114 commits into from
May 13, 2024

Commits on Sep 8, 2023

  1. Scripts from Lukas to be used in improved setup process

    @christinaflo
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Commits on Oct 6, 2023

  1. Add improved alignment-db creation script 

    - much faster due to the use of threading and mp
- also supports sharding
    @ljarosch
    ljarosch committed Oct 6, 2023
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Commits on Feb 8, 2024

  1. updates zero_to_fp32.py for new deepspeed version and import_weight b… 

    …ugfix
    @jnwei
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Commits on Feb 9, 2024

  1. Adjust weight conversion and add a script for converting checkpoints.

    @jnwei
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Commits on Feb 12, 2024

  1. bugfixes and adds a section to convert optim files

    @jnwei
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Commits on Feb 14, 2024

  1. Add log statement to weight conversion script

    @jnwei
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Commits on Feb 20, 2024

  1. changes reloading weights to account for possible state_dict headers.

    @jnwei
    jnwei committed Feb 20, 2024
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  2. Scripts from Lukas to be used in improved setup process

    @christinaflo
    christinaflo committed Feb 20, 2024
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  3. Add improved alignment-db creation script 

    - much faster due to the use of threading and mp
- also supports sharding
    @ljarosch @christinaflo
    ljarosch authored and christinaflo committed Feb 20, 2024
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  4. Merge branch 'setup-improvements' of https://github.com/aqlaboratory/… 

    …openfold into setup-improvements
    @christinaflo
    christinaflo committed Feb 20, 2024
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Commits on Feb 21, 2024

  1. Updates commit value for OpenFold notebook.

    @jnwei
    jnwei committed Feb 21, 2024
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  2. Merge weight-loading changes into setup-improvements

    @jnwei
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  3. removes outputs from OpenFold.ipynb

    @jnwei
    jnwei committed Feb 21, 2024
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Commits on Feb 22, 2024

  1. Changes resume_model_weights_only flag in train_openfold to reload we… 

    …ights only, without parsing a time step.
    @jnwei
    jnwei committed Feb 22, 2024
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Commits on Mar 13, 2024

  1. Adds experiment_config_json for setting custom configurations with … 

    …a json.
    @jnwei
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  2. adds config recording to wandb

    @jnwei
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Commits on Mar 19, 2024

  1. Improve type hints and formatting

    @ljarosch
    ljarosch committed Mar 19, 2024
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  2. Add default shard number

    @ljarosch
    ljarosch committed Mar 19, 2024
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Commits on Mar 20, 2024

  1. Add duplicate chain file support to alignment DB script 

    This makes it more straightforward to create an alignment database directly from the flattened RODA downloads
    @ljarosch
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  2. Add script for expanding the alignment dir with duplicates 

    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.
    @ljarosch
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  3. Initial commit for sphinx documentation.

    @jnwei
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Commits on Mar 21, 2024

  1. update license file

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Commits on Mar 29, 2024

  1. DNS: Local profiler changes

    @jnwei
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Commits on Apr 12, 2024

  1. changes required for pytorch2

    @jnwei
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Commits on Apr 17, 2024

  1. psivant local pl2 upgrades without mpi configuration

    @jnwei
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Commits on Apr 22, 2024

  1. clear up some space for docker ci

    @jnwei
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Commits on Apr 23, 2024

  1. run_pretrained_openfold.py: Change default paths of binary to be cond… 

    …a environment bin
    @jnwei
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Commits on Apr 29, 2024

  1. fix path error in scripts/utils.py and logging fix

    @jnwei
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Commits on May 2, 2024

  1. Scripts from Lukas to be used in improved setup process

    @christinaflo @jnwei
    christinaflo authored and jnwei committed May 2, 2024
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  2. Add improved alignment-db creation script 

    - much faster due to the use of threading and mp
- also supports sharding
    @ljarosch @jnwei
    ljarosch authored and jnwei committed May 2, 2024
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  3. Updates commit value for OpenFold notebook.

    @jnwei
    jnwei committed May 2, 2024
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  4. updates zero_to_fp32.py for new deepspeed version and import_weight b… 

    …ugfix
    @jnwei
    jnwei committed May 2, 2024
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  5. Adjust weight conversion and add a script for converting checkpoints.

    @jnwei
    jnwei committed May 2, 2024
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  6. bugfixes and adds a section to convert optim files

    @jnwei
    jnwei committed May 2, 2024
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  7. Add log statement to weight conversion script

    @jnwei
    jnwei committed May 2, 2024
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  8. changes reloading weights to account for possible state_dict headers.

    @jnwei
    jnwei committed May 2, 2024
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  9. removes outputs from OpenFold.ipynb

    @jnwei
    jnwei committed May 2, 2024
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  10. Changes resume_model_weights_only flag in train_openfold to reload we… 

    …ights only, without parsing a time step.
    @jnwei
    jnwei committed May 2, 2024
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  11. Adds experiment_config_json for setting custom configurations with … 

    …a json.
    @jnwei
    jnwei committed May 2, 2024
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  12. adds config recording to wandb

    @jnwei
    jnwei committed May 2, 2024
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  13. update license file

    @jnwei
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  14. DNS: Local profiler changes

    @jnwei
    jnwei committed May 2, 2024
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  15. changes required for pytorch2

    @jnwei
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  16. clear up some space for docker ci

    @jnwei
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  17. run_pretrained_openfold.py: Change default paths of binary to be cond… 

    …a environment bin
    @jnwei
    jnwei committed May 2, 2024
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  18. fix path error in scripts/utils.py and logging fix

    @jnwei
    jnwei committed May 2, 2024
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  19. Updates commit value for OpenFold notebook.

    @jnwei
    jnwei committed May 2, 2024
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  20. bugfixes and adds a section to convert optim files

    @jnwei
    jnwei committed May 2, 2024
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  21. Add log statement to weight conversion script

    @jnwei
    jnwei committed May 2, 2024
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  22. removes outputs from OpenFold.ipynb

    @jnwei
    jnwei committed May 2, 2024
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  23. Adds experiment_config_json for setting custom configurations with … 

    …a json.
    @jnwei
    jnwei committed May 2, 2024
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  24. adds config recording to wandb

    @jnwei
    jnwei committed May 2, 2024
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  25. DNS: Local profiler changes

    @jnwei
    jnwei committed May 2, 2024
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  26. changes required for pytorch2

    @jnwei
    jnwei committed May 2, 2024
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  27. adds deepspeed_evoformer flag to inference script.

    @jnwei
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  28. updates Bio.PDBData call and environment.yml

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  29. Merge branch 'setup-improvements' of https://github.com/aqlaboratory/… 

    …openfold into setup-improvements
    @jnwei
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  30. Removes OF copy of zero_to_fp32.py favoring deepspeed.util version

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  31. Removes OF copy of zero_to_fp32.py favoring deepspeed.util version

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  32. Updates organization of command line flags for pl.Trainer

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  33. Updates environment.yml to unpin wandb version

    @jnwei
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Commits on May 6, 2024

  1. adds mpi4py to environment and removes stray print statements from test

    @jnwei
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  2. Add more efficient script to generate all-seqs FASTA 

    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.
    @ljarosch
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  3. Give script more descriptive name

    @ljarosch
    ljarosch committed May 6, 2024
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  4. Slightly improve comment

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    ljarosch committed May 6, 2024
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  5. Set CLI description to more informative module docstring

    @ljarosch
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  6. Improve import formatting

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Commits on May 8, 2024

  1. Rough draft dump of docs and readthedocs build

    @jnwei
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  2. fix typo in readthedocs.yaml

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  3. replace doc environment pip dependencies with conda builds

    @jnwei
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  4. cleanup makefiles and original readme

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  5. updates to Inference.md

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  6. Add addtional inference pages

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  7. add convert v1 weights instructions

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  8. Adds FAQ section

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  9. creates link to FAQ in documentation

    @jnwei
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  10. small edits to main page

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  11. minor language edits

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Commits on May 9, 2024

  1. Hotfix to switch order of feature dict generation

    @christinaflo @jnwei
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  2. Added script for running decoy ranking experiments

    @sachinkadyan7 @jnwei
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  3. Fix distributed seeding behavior 

    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.
    @ljarosch @jnwei
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  4. Add LICENSE information to decoy ranking script

    @sachinkadyan7 @jnwei
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  5. Update README to include details for SoloSeq Embeddings

    @sachinkadyan7 @jnwei
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  6. Fix usage example in download_openfold_soloseq_params.sh

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  7. Add script to download embeddings for training SoloSeq

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  8. Fix resolution field in mmcif_parsing 

    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).
    @ljarosch @jnwei
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  9. Adds mkl version to environment.yml

    @jnwei
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  10. make space for docker CI

    @jnwei
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  11. Shorten README.md main page.

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  12. adds mmseqs2 to environment.yml for clustering

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Commits on May 10, 2024

  1. Update training OpenFold docs with correct paths.

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  2. Adds example directory

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Commits on May 11, 2024

  1. make sure padded asym_id won't affect permutation steps

    @dingquanyu @jnwei
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  2. fixed bugs in unittests for multi-chain permutation. now working on e… 

    …xtra subtests
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  3. remove unnecessary lines

    @dingquanyu @jnwei
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  4. restore to the verison on main

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  5. added typing hints and fixed some comments

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  6. make sure no padded features are going to be selected as anchors

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  7. fixed typing errors; added more comments

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  8. added comments

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  9. update comments;fixed typos

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  10. Update tests and comments

    @dingquanyu @jnwei
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  11. fixed typing error of anchor_gt_residue

    @dingquanyu @jnwei
    dingquanyu authored and jnwei committed May 11, 2024
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  12. Update test_permutation.py 

    Fixed a small typo in permutation unit test docstring
    @jnwei
    jnwei committed May 11, 2024
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  13. Merge branch 'docs' into setup-improvements

    @jnwei
    jnwei committed May 11, 2024
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Commits on May 13, 2024

  1. edits to inference documentation and script for parameters

    @jnwei
    jnwei committed May 13, 2024
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  2. fix typo in environment.yml

    @jnwei
    jnwei committed May 13, 2024
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  3. Merge pull request #419 from aqlaboratory/setup-improvements_addition… 

    …al-scripts

Duplicate expansion support
    @jnwei
    jnwei authored May 13, 2024
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  4. Merge branch 'main' into setup-improvements

    @jnwei
    jnwei authored May 13, 2024
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  5. small fix to docker-image ci workflow

    @jnwei
    jnwei committed May 13, 2024
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  6. Removes mpi4py from environment.yml -- not supported for Docker builds

    @jnwei
    jnwei committed May 13, 2024
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  7. updates biopython version to 1.80 in colab notebook

    @jnwei
    jnwei committed May 13, 2024
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  8. Updates biopython version to 1.83 in colab notebook, which seems to w… 

    …ork better
    @jnwei
    jnwei committed May 13, 2024
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  9. in scripts/utils.py account for case where no conda environment is sp… 

    …ecified.
    @jnwei
    jnwei committed May 13, 2024
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