Commits · 15b1bbd667652637ea334a9ddd6b71f393910a0e · OpenDAS / OpenFold

".github/vscode:/vscode.git/clone" did not exist on "0cd5d78350a434f7f56f2b7a50cdef1fd4c88ca4"

06 Feb, 2024 3 commits

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

Updates to setup.py and README · e94c97ec
Jennifer authored Feb 06, 2024

e94c97ec

02 Feb, 2024 6 commits
- Change parse_fasta to split on whitespace or '|' character · 790267e3
  Jennifer authored Feb 02, 2024
  
  790267e3
- remove nested definition of local_alignmnet_dir in run_pretrained_openfold.py · 0cf8b928
  Jennifer authored Feb 02, 2024
  
  0cf8b928
- readme and small updates for soloseq support on multimer · 26d555d5
  Jennifer authored Jan 29, 2024
  
  26d555d5
- Adds absolute error comparison function with better messaging. · 30195c4a
  Jennifer authored Jan 24, 2024
  
  30195c4a
- update deprecated jax.numpy.DeviceArray to jax.Array · 8f8b537d
  Jennifer authored Jan 23, 2024
  
  8f8b537d
- np type update in openfold.np.relax · 2120ce37
  Jennifer authored Jan 16, 2024
  
  2120ce37
23 Jan, 2024 1 commit
- Additional fix for multimer deepspeed test · 40d9e7d7
  Christina Floristean authored Jan 23, 2024
  
  40d9e7d7
17 Jan, 2024 2 commits
- Fix deepspeed test for multimer · 9a07b7f9
  Christina Floristean authored Jan 17, 2024
  
  9a07b7f9
- Merge pull request #396 from aqlaboratory/deepspeed-mean-test · 9e057b7a
  Christina Floristean authored Jan 17, 2024
```
Change test_compare_model in deepspeed test to use mean instead of max
```
  9e057b7a
11 Jan, 2024 1 commit
- Change test_compare_model in deepspeed test to use mean instead of max · 39f9958b
  jnwei authored Jan 11, 2024
  
  39f9958b
20 Dec, 2023 2 commits
- Merge pull request #389 from aqlaboratory/readme-changes · 561333f2
  Jennifer Wei authored Dec 20, 2023
```
Readme changes
```
  561333f2
- Adds an outline to the README · 40f98ff0
  jnwei authored Dec 20, 2023
  
  40f98ff0
19 Dec, 2023 2 commits
- Update README.md · f2005628
  Jennifer Wei authored Dec 19, 2023
```
small edits to headers
```
  f2005628
- [README] Updates inference section to highlight subsections. · cd54c029
  jnwei authored Dec 19, 2023
  
  cd54c029
18 Dec, 2023 1 commit
- Merge pull request #385 from dingquanyu/update-data-pipeline · a475ad11
  Christina Floristean authored Dec 18, 2023
```
Update data pipeline
```
  a475ad11
15 Dec, 2023 7 commits
- Update data_pipeline.py · 989f2d93
  Dingquan Yu authored Dec 15, 2023
  
  989f2d93
- get rid of parsing tar.gz2 files for now · 8d8584ac
  Dingquan Yu authored Dec 15, 2023
  
  8d8584ac
- added back cpu_count import · c5a69771
  Dingquan Yu authored Dec 14, 2023
  
  c5a69771
- remove unnecessary imports · ffa812e4
  Dingquan Yu authored Dec 14, 2023
  
  ffa812e4
- added steps of reading in compressed msa files · de28d842
  Dingquan Yu authored Dec 14, 2023
  
  de28d842
- added steps to read zipped msa files · e9287b49
  Dingquan Yu authored Dec 13, 2023
  
  e9287b49
- Fix missing import in tests · 9d6127cb
  Christina Floristean authored Dec 15, 2023
  
  9d6127cb
14 Dec, 2023 1 commit
- Bug fixes for multi-chain permutation alignment · fe8869c3
  Christina Floristean authored Dec 14, 2023
  
  fe8869c3
11 Dec, 2023 4 commits
- Added alignment indexing to multimer pipeline and fixed jackhmmer query return type · 4f38c826
  Christina Floristean authored Dec 11, 2023
  
  4f38c826
- Fix bug from deepspeed upgrade, do not use uniprot_hits in msa feats · bcabb8e3
  Christina Floristean authored Dec 11, 2023
  
  bcabb8e3
- Merge pull request #376 from dingquanyu/speedup-dataloader · f861ff39
  Christina Floristean authored Dec 11, 2023
```
Speed up data loading process 
```
  f861ff39
- Merge branch 'main' into multimer · 1606ac08
  Christina Floristean authored Dec 11, 2023
  
  1606ac08
08 Dec, 2023 4 commits
- Remove env restart from setup script · 67a00a6c
  Christina Floristean authored Dec 08, 2023
  
  67a00a6c
- Merge pull request #378 from aqlaboratory/deepspeed-evo-attention · a13c0ce5
  Christina Floristean authored Dec 08, 2023
```
Deepspeed evoformer attention
```
  a13c0ce5
- Minor change to tests · 40d76358
  Christina Floristean authored Dec 08, 2023
  
  40d76358
- Minor test and README changes · 336c899a
  Christina Floristean authored Dec 08, 2023
  
  336c899a
06 Dec, 2023 2 commits
- Updated DeepSpeed version, added inplace_safe for template offloading · cdd97841
  Christina Floristean authored Dec 06, 2023
  
  cdd97841
- Merge branch 'multimer' into speedup-dataloader · 6f26b0ad
  Dingquan Yu authored Dec 06, 2023
  
  6f26b0ad
05 Dec, 2023 4 commits
- Exclude uniprot hits from regular msa feature processing · 58d65692
  Christina Floristean authored Dec 05, 2023
  
  58d65692
- Merge pull request #375 from aqlaboratory/jackhmmer_query_update · 96f46b08
  Jennifer Wei authored Dec 05, 2023
```
Adds query_multiple to jackhammer.py
```
  96f46b08
- remove unnecessary imports and statements · 78ecfc64
  Dingquan Yu authored Dec 05, 2023
  
  78ecfc64
- reverse back to multimer branch version · 08bfb1ff
  Dingquan Yu authored Dec 05, 2023
  
  08bfb1ff