Commits · f94ee668e52a67b7de056dd10a50ed885569bca7 · OpenDAS / OpenFold

"examples/vscode:/vscode.git/clone" did not exist on "b82dca0db25073d2b7c1f3e34b9f9e20ffdf6e81"

02 Nov, 2023 1 commit
- Fixes for inference alignment generation · f94ee668
  Christina Floristean authored Nov 02, 2023
  
  f94ee668
30 Oct, 2023 5 commits
- Merge branch 'main' into multimer · 5eacd8b6
  Christina Floristean authored Oct 30, 2023
  
  5eacd8b6
- Added multimer inference to README · 15850092
  Christina Floristean authored Oct 30, 2023
  
  15850092
- Merge pull request #365 from aqlaboratory/dependabot/github_actions/actions/setup-python-4 · 2338b896
  Jennifer Wei authored Oct 30, 2023
```
Bump actions/setup-python from 2 to 4
```
  2338b896
- Bump actions/setup-python from 2 to 4 · dcd809d9
  dependabot[bot] authored Oct 30, 2023
```
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 4.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v2...v4

)

---
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>
```
  dcd809d9
- Merge pull request #366 from aqlaboratory/dependabot/github_actions/actions/checkout-4 · 51472e75
  Jennifer Wei authored Oct 30, 2023
```
Bump actions/checkout from 2 to 4
```
  51472e75
27 Oct, 2023 6 commits

Bump actions/checkout from 2 to 4 · 13728b12

dependabot[bot] authored Oct 27, 2023

Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v2...v4

)

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

13728b12

Merge pull request #360 from aqlaboratory/installation-updates · f7dba95f
Jennifer Wei authored Oct 27, 2023
```
Merging installation updates and updates
```
f7dba95f
Adds KMP_AFFINITY to conda environment. · e3716118
Jennifer Wei authored Oct 27, 2023

e3716118

Merge branch 'installation-updates' of... · 6df89c76

Jennifer Wei authored Oct 27, 2023

Merge branch 'installation-updates' of https://github.com/aqlaboratory/openfold into installation-updates

6df89c76

Adds libgcc and pytorch::pytorch to environment.yml · 13f0f6fe
Jennifer Wei authored Oct 27, 2023

13f0f6fe
Merge branch 'main' into multimer · d7c11537
Christina Floristean authored Oct 27, 2023

d7c11537

25 Oct, 2023 2 commits
- README: Small improvements, info regarding templates · 9e32781f
  Sachin Kadyan authored Oct 25, 2023
  
  9e32781f
- Update readme, also reset flash attention version to 0.2.1 in environment.yml · f68a6c69
  jnwei authored Oct 25, 2023
  
  f68a6c69
24 Oct, 2023 12 commits
- Test docker image nvidia/11.7.1-cudnn8-devel-ubuntu18.04 · a5c69a79
  jnwei authored Oct 24, 2023
  
  a5c69a79
- Change docker image to use cudnn devel environment · e2bb3c4b
  jnwei authored Oct 24, 2023
  
  e2bb3c4b
- Test nvidia image 11.4.3-cudnn8-runtime-unbuntu18.04 · 6fe34248
  jnwei authored Oct 24, 2023
  
  6fe34248
- Fix export statement · 5efba442
  jnwei authored Oct 24, 2023
  
  5efba442
- Update Dockerfile to add conda path to $LD_LIBRARY_PATH · 3817d940
  jnwei authored Oct 24, 2023
  
  3817d940
- update flash-attention-version · a5a86d43
  jnwei authored Oct 24, 2023
  
  a5a86d43
- Add git to environment.yml · f06657fe
  Jennifer Wei authored Oct 24, 2023
  
  f06657fe
- README: Update details about SoloSeq and inference-time embedding generation. · 2d4fe4f4
  Sachin Kadyan authored Oct 24, 2023
  
  2d4fe4f4
- Test flash-attention v0.2.1 on docker CI · a90da395
  jnwei authored Oct 24, 2023
  
  a90da395
- Separate out input parsing code in `EmbeddingGenerator` · 86b990d6
  Sachin Kadyan authored Oct 24, 2023
```
Bugfix: Corrected paths for just-in-time embedding generation
```
  86b990d6
- Just-in-time embedding generation for the SoloSeq model · 8185c307
  Sachin Kadyan authored Oct 24, 2023
  
  8185c307
- README: Add details about using the bulk embedding generation script · 4c8e3764
  Sachin Kadyan authored Oct 23, 2023
  
  4c8e3764
23 Oct, 2023 9 commits
- Merge remote-tracking branch 'mattwthompson/ci' into installation-updates · 5f5c8f2a
  jnwei authored Oct 23, 2023
  
  5f5c8f2a
- Use conventional "short hash" style · 7666c802
  Matthew W. Thompson authored Oct 23, 2023
  
  7666c802
- Update name to `pytorch-lightning` · 58210350
  Matthew W. Thompson authored Oct 23, 2023
  
  58210350
- Add Dependabot for Actions · 736d6687
  Matthew W. Thompson authored Oct 23, 2023
  
  736d6687
- Update checkout action · 32c11376
  Matthew W. Thompson authored Oct 23, 2023
  
  32c11376
- Switch to Miniforge3 · f86d42f4
  Matthew W. Thompson authored Oct 23, 2023
  
  f86d42f4
- Update environment YAML · 6bf5c8ce
  Matthew W. Thompson authored Oct 23, 2023
  
  6bf5c8ce
- More cleaning of bulk embedding generation script · 92835fd5
  Sachin Kadyan authored Oct 23, 2023
  
  92835fd5
- Cleaned up `precompute_embeddings.py`. · 0026173e
  Sachin Kadyan authored Oct 22, 2023
  
  0026173e
21 Oct, 2023 1 commit
- New script for generating ESM embeddings in bulk · bcc6d97b
  Sachin Kadyan authored Oct 09, 2023
  
  bcc6d97b
20 Oct, 2023 4 commits
- Update BibTex · 0c20e3c9
  Gustaf Ahdritz authored Oct 19, 2023
  
  0c20e3c9
- Remove conda env config setting and update to README · d6ae9f58
  jnwei authored Oct 20, 2023
  
  d6ae9f58
- Updates Dockerfile to not use OpenMM patches. · b3a118fc
  Jennifer Wei authored Oct 20, 2023
  
  b3a118fc
- Merge branch 'installation-updates' of... · 2893fd93
  Jennifer Wei authored Oct 20, 2023
```
Merge branch 'installation-updates' of https://github.com/aqlaboratory/openfold into installation-updates

Merging changes from different systems
```
  2893fd93