Commits · 09e74c7613d2f1ff29c16d9544b12d42eb59000b · OpenDAS / OpenFold

29 Apr, 2024 1 commit
- fix path error in scripts/utils.py and logging fix · 09e74c76
  Jennifer authored Apr 29, 2024
  
  09e74c76
23 Apr, 2024 1 commit
- run_pretrained_openfold.py: Change default paths of binary to be conda environment bin · cb3ff410
  jnwei authored Apr 23, 2024
  
  cb3ff410
22 Apr, 2024 1 commit
- clear up some space for docker ci · 81c847b1
  Jennifer authored Apr 22, 2024
  
  81c847b1
17 Apr, 2024 1 commit
- psivant local pl2 upgrades without mpi configuration · bbf989a7
  Jennifer authored Apr 16, 2024
  
  bbf989a7
12 Apr, 2024 1 commit
- changes required for pytorch2 · ce000c60
  Jennifer Wei authored Apr 12, 2024
  
  ce000c60
29 Mar, 2024 1 commit
- DNS: Local profiler changes · d8418293
  Jennifer authored Mar 29, 2024
  
  d8418293
21 Mar, 2024 1 commit
- update license file · fdd4e1d8
  jnwei authored Mar 21, 2024
  
  fdd4e1d8
13 Mar, 2024 2 commits
- adds config recording to wandb · 6ba0a594
  Jennifer authored Mar 13, 2024
  
  6ba0a594
- Adds `experiment_config_json` for setting custom configurations with a json. · d1fe024b
  Jennifer authored Mar 13, 2024
  
  d1fe024b
22 Feb, 2024 1 commit
- Changes resume_model_weights_only flag in train_openfold to reload weights... · f4df7217
  Jennifer authored Feb 22, 2024
```
Changes resume_model_weights_only flag in train_openfold to reload weights only, without parsing a time step.
```
  f4df7217
21 Feb, 2024 3 commits
- removes outputs from OpenFold.ipynb · f1cd1381
  jnwei authored Feb 21, 2024
  
  f1cd1381
- Merge weight-loading changes into setup-improvements · 9776b696
  jnwei authored Feb 21, 2024
  
  9776b696
- Updates commit value for OpenFold notebook. · 9f346d35
  jnwei authored Feb 21, 2024
  
  9f346d35
20 Feb, 2024 4 commits
- Merge branch 'setup-improvements' of https://github.com/aqlaboratory/openfold... · 11952997
  Christina Floristean authored Feb 20, 2024
```
Merge branch 'setup-improvements' of https://github.com/aqlaboratory/openfold into setup-improvements
```
  11952997
- Add improved alignment-db creation script · 70918209
  Lukas Jarosch authored Oct 06, 2023
```
- much faster due to the use of threading and mp
- also supports sharding
```
  70918209
- Scripts from Lukas to be used in improved setup process · 50949b9a
  Christina Floristean authored Sep 08, 2023
  
  50949b9a
- changes reloading weights to account for possible state_dict headers. · ddfccd56
  Jennifer authored Feb 14, 2024
  
  ddfccd56
14 Feb, 2024 1 commit
- Add log statement to weight conversion script · e31e0378
  Jennifer authored Feb 13, 2024
  
  e31e0378
12 Feb, 2024 1 commit
- bugfixes and adds a section to convert optim files · 775f77dd
  Jennifer authored Feb 12, 2024
  
  775f77dd
09 Feb, 2024 1 commit
- Adjust weight conversion and add a script for converting checkpoints. · 260592e0
  Jennifer authored Feb 09, 2024
  
  260592e0
08 Feb, 2024 2 commits
- updates zero_to_fp32.py for new deepspeed version and import_weight bugfix · 1df591b0
  Jennifer authored Feb 08, 2024
  
  1df591b0
- Merge pull request #405 from aqlaboratory/multimer · bb3f51e5
  Christina Floristean authored Feb 07, 2024
```
Full multimer merge
```
  bb3f51e5
07 Feb, 2024 14 commits
- Merge branch 'main' into multimer · c33a0bd6
  Christina Floristean authored Feb 07, 2024
  
  c33a0bd6
- Fixed learning rate scheduler issue, returned to original msa file parsing · 6275091c
  Christina Floristean authored Feb 07, 2024
  
  6275091c
- Merge pull request #404 from jnwei/multimer-small-edits · bc075004
  Jennifer Wei authored Feb 07, 2024
```
Type fixes and README changes for multimer branch
```
  bc075004
- Merge branch 'multimer' into multimer-small-edits · a2adb147
  jnwei authored Feb 07, 2024
  
  a2adb147
- edit starting sequence in notebook · 1165d9eb
  jnwei authored Feb 07, 2024
  
  1165d9eb
- Adding multimer support to OpenFold notebook · d4acbe6e
  jnwei authored Jan 30, 2024
  
  d4acbe6e
- Update README.md · 81d817fe
  Jennifer Wei authored Jan 31, 2024
```
fixed a typo in the readme for soloseq params path
```
  81d817fe
- edit starting sequence in notebook · 5e0616b6
  jnwei authored Feb 07, 2024
  
  5e0616b6
- Adding multimer support to OpenFold notebook · 94a3b18e
  jnwei authored Jan 30, 2024
  
  94a3b18e
- update setup.py file for version number · 3c5233bd
  jnwei authored Feb 07, 2024
  
  3c5233bd
- adds cutlass directory to .gitignore · 396fd44a
  Jennifer authored Feb 07, 2024
  
  396fd44a
- Add fixes to permutation test after refactor · 0fe5ea31
  Jennifer authored Feb 07, 2024
  
  0fe5ea31
- fix deepspeed_evo_attention to work in both monomer and multimer settings. · 0aa69474
  Jennifer authored Feb 07, 2024
  
  0aa69474
- create separate test configs for multimer and monomer · 204ed191
  Jennifer authored Feb 07, 2024
  
  204ed191
06 Feb, 2024 4 commits

debugging for permutation test · bf8788c7
Jennifer authored Feb 06, 2024

bf8788c7
Fix Miniforge3 download link in Dockerfile · de12c0ea
controny authored Feb 05, 2024

de12c0ea
suporting newer numpy · 15b1bbd6
yoel shoshan authored Apr 23, 2023

15b1bbd6

Bump actions/setup-python from 4 to 5 · 51d6a41d

dependabot[bot] authored Dec 06, 2023

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4...v5

)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>

51d6a41d