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zeming/bump-esm

zeming/esm-3.0.8

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zlin/esm3-readme-pin

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zlin/pip-install-pin

zlin/readme-fig2

zlin/readme-install-block

zlin/readme-install-pin

zlin/sdk-snippet-fix

zlin/sync-from-internal

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v3.0.0.post2

v3.0.1

v3.0.2

v3.0.3

v3.0.4

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v3.0.8

v3.1.0

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v3.2.1.post1

v3.2.2

v3.2.2.post2

v3.2.3

v3.2.4.a2-mga-folding-bridge

f652b471d2 release binder design notebook (#328) main Zeming Lin 2026-06-01 18:57:38 -04:00
b6b0e8815d Type max_inference_sigma as float | None to match downstream consumer (#314) Ben Viggiano 2026-05-30 08:09:06 -07:00
dc2b9827a1 Update README.md (#312) Samson Mataraso 2026-05-30 08:07:26 -07:00
975722d72d sync from internal (#323) Zeming Lin 2026-05-29 17:03:58 -04:00
d72119a3f6 sync from internal zlin/sync-from-internal Zeming Lin 2026-05-29 20:06:20 +00:00
af8ef5cead Fix Biohub Platform SDK snippets (ESMC + ESMFold2) and use carbonic anhydrase II (#311) Zeming Lin 2026-05-27 15:00:13 -04:00
8d9a67abc6 Fix Biohub Platform SDK snippets (ESMC + ESMFold2) and use carbonic anhydrase II zlin/sdk-snippet-fix Zeming Lin 2026-05-27 17:38:49 +00:00
d24395914c Show install block at top + fix Biohub Platform SDK snippets zlin/readme-install-block Zeming Lin 2026-05-27 16:48:19 +00:00
1a2c29d56b Show install block at the top of Running ESMC Locally (#310) Zeming Lin 2026-05-27 12:49:52 -04:00
81b3646c94 Add Figure 2 from ESMC blog post to README (#308) Zeming Lin 2026-05-27 11:38:04 -04:00
6d545fd68c Replace esmfold2_folding.png with Figure 2 (DockQ pass-rate panels) from ESMC blog zlin/readme-fig2 Zeming Lin 2026-05-27 15:14:10 +00:00
6ec3ff12be Pin tutorial pip-install lines + ESM3_README to commit SHA (#307) Zeming Lin 2026-05-27 08:42:00 -04:00
da603081f9 Pin tutorial pip-install lines + ESM3_README to commit SHA zlin/pip-install-pin Zeming Lin 2026-05-27 12:28:12 +00:00
17f2b00c57 Pin ESM3 quickstart pip install to commit SHA zlin/esm3-readme-pin Zeming Lin 2026-05-27 12:17:37 +00:00
8bbf3b5bc1 Pin ESM3 quickstart pip install to commit SHA zlin/readme-install-pin Zeming Lin 2026-05-27 12:16:55 +00:00
e2f7a1c1df Pin pip install esm to commit SHA (#305) Zeming Lin 2026-05-27 08:15:10 -04:00
18cd88d059 Pin pip install esm to commit SHA Zeming Lin 2026-05-27 12:12:18 +00:00
73ccb2d56e Update esm repo for ESMC paper zlin/esmc-paper-update Zeming Lin 2026-05-27 10:54:14 +00:00
c94ed8d763 Update esm repo for ESMC paper (#304) Zeming Lin 2026-05-27 07:41:49 -04:00
9baa94d56e mga esm v3.2.4.a2 v3.2.4.a2-mga-folding-bridge mga Ishaan Mathur 2026-05-11 17:16:00 +00:00
ee891c5239 add 6b sae name ishaan/sae Neil Thomas 2026-05-04 12:06:24 -05:00
3ba69f2397 add folding example ishaan/folding Neil Thomas 2026-03-19 01:07:32 +00:00
ddffe05768 add examples of getting sae features Neil Thomas 2026-03-17 18:16:52 -07:00
6596fc1f30 add sae Ishaan Mathur 2026-03-12 22:00:16 +00:00
453b2e2e71 Update README.md (#298) Neil Thomas 2026-01-26 11:44:52 -08:00
60bb1d19ec Update README.md esm-slack-invite-link Neil Thomas 2026-01-23 12:17:51 -08:00
95c3c0281d allow seqlen > 800 Ishaan Mathur 2025-11-24 20:53:20 +00:00
6e89bf7d12 sasa BOS/EOS fix (#286) Ishaan Mathur 2025-10-30 14:47:40 -04:00
6d82df34cd sasa BOS/EOS fix ishaan/sasa-fix Ishaan Mathur 2025-10-30 17:31:56 +00:00
e103c9c1c4 loosen version (#284) Ishaan Mathur 2025-10-22 16:54:07 -04:00
a3028bca88 loosen version ishaan/loosen_transformer_version Ishaan Mathur 2025-10-22 20:38:55 +00:00
232a1041d8 Ishaan/infer oxygen (#283) Ishaan Mathur 2025-10-22 12:19:25 -04:00
6e730a7bf6 update pixi lock ishaan/infer_oxygen Ishaan Mathur 2025-10-22 16:11:16 +00:00
e3220489fd updating version Ishaan Mathur 2025-10-22 16:10:24 +00:00
87e3bf28a4 infer oxygen in protein complex Ishaan Mathur 2025-10-22 14:28:24 +00:00
43c06f5863 addressing esm issue 279 and 265 Ishaan Mathur 2025-10-22 14:27:54 +00:00
709d3e603b write out plddt to mmcif Ishaan Mathur 2025-10-20 20:11:46 +00:00
2c104b454c folding Ishaan Mathur 2025-10-15 17:45:49 +00:00
23b084b94f syncing covalent bonds (#280) v3.2.3 Ishaan Mathur 2025-10-09 14:57:20 -04:00
a22356ca1c bump version ishaan/sync_again Ishaan Mathur 2025-10-09 18:46:47 +00:00
9e7e36876b syncing covalent bonds Ishaan Mathur 2025-10-09 18:30:46 +00:00
e8117a2f68 sync (#278) Ishaan Mathur 2025-10-07 15:32:35 -04:00
67861b681c sync ishaan/sync Ishaan Mathur 2025-10-07 17:50:39 +00:00
79c1208e96 Exposing pae in ESMProtein (#164) Ventura Rivera 2025-09-23 15:09:52 -07:00
3e109e2d1b 3.2.2.post2 (#276) v3.2.2.post2 Neil Thomas 2025-09-19 15:28:14 -07:00
38f50fb922 ruff checks release-3.2.2.post2_v2 Neil Thomas 2025-09-19 21:51:10 +00:00
64e1abeaed Merge branch 'main' into release-3.2.2.post2_v2 Neil Thomas 2025-09-19 21:47:59 +00:00
34c6638b58 Sync Neil Thomas 2025-09-19 21:46:14 +00:00
0382151104 Add none check for pyright Neil Thomas 2025-09-19 20:59:11 +00:00
c8969198c6 Enable running ESM on Mac silicon using MPS (#99) Imran Qureshi 2025-09-19 12:48:07 -07:00
1cfb08b424 3.2.2.post2 Neil Thomas 2025-09-19 19:27:16 +00:00
82e32db4ef update pixi lock release-3.2.2.post2 Neil Thomas 2025-09-19 19:02:01 +00:00
dc87f94e7e update pixi lock Neil Thomas 2025-09-19 18:51:15 +00:00
e488454d98 3.2.2.post2 Neil Thomas 2025-09-19 18:45:46 +00:00
97eb26b2fe pyright ignore flash_attn import because it is guarded (#274) Ishaan Mathur 2025-09-18 13:54:10 -04:00
e1477b826a fix oss test, bump pixi version ishaan/flash-attn-ignore Ishaan Mathur 2025-09-18 16:26:54 +00:00
55b3470850 pyright ignore flash_attn import because it is guarded Ishaan Mathur 2025-09-18 16:19:58 +00:00
d1155b25fb return flash attention james_scott/return_flash_attention James Scott 2025-09-17 17:14:24 -07:00
cbaccc1693 Revert "sync 3.2.2.post1 (#270)" (#272) Neil Thomas 2025-09-17 15:14:41 -07:00
7c7ecc933e Revert "sync 3.2.2.post1 (#270)" rollback-3.2.2.post1 Neil Thomas 2025-09-17 22:01:44 +00:00
bcc7b54327 Revert "sync 3.2.2.post1" sync-3.2.2.post1 Neil Thomas 2025-09-17 22:00:38 +00:00
c4e1c73b19 Update lockfile james_scott/update_pixi_lock James Scott 2025-09-17 14:49:41 -07:00
f4f97929b2 sync 3.2.2.post1 (#270) Neil Thomas 2025-09-17 14:24:07 -07:00
aaed83a018 sync 3.2.2.post1 Neil Thomas 2025-09-17 21:14:52 +00:00
7454c3d77b Remove flash attention (#269) v3.2.2 Zeming Lin 2025-09-15 10:06:42 -07:00
35c2088b75 Bump esm version - prepare for release (#268) Zeming Lin 2025-09-12 09:04:44 -07:00
d51cccd27e Bump esm version - prepare for release zeming/bump-esm Zeming Lin 2025-09-11 16:38:57 -04:00
95239e2d19 Sync over internal code to open source (#266) Ishaan Mathur 2025-08-18 17:34:56 -04:00
125166fe83 updating version in one more spot chore/fix-ci-testing Ishaan Mathur 2025-08-18 21:28:13 +00:00
4624158ebc removing python 3.10 and 3.11 as supported versions Ishaan Mathur 2025-08-18 21:16:27 +00:00
fe8aa273c2 updating token Ishaan Mathur 2025-08-18 19:36:36 +00:00
22f0642bd1 syncing oss Ishaan Mathur 2025-08-15 15:53:03 +00:00
6d29d92681 disable pixi cache, pytest coverage properly Steve Chan 2025-08-08 14:49:11 +00:00
9cf5e015db fail on pytest early Steve Chan 2025-08-08 14:40:13 +00:00
b2e5a5674b fix test imports Steve Chan 2025-08-08 14:25:18 +00:00
99d867c427 rearrange test tasks Steve Chan 2025-08-08 10:16:57 -04:00
7aee7e9d2e add precommit config Steve Chan 2025-08-08 09:43:58 -04:00
d8d04ecc92 proper placement for pytest stuff Steve Chan 2025-08-07 17:24:17 -04:00
87967f6dad chore: fix the ci to install the test requisites Steve Chan 2025-08-07 17:08:42 -04:00
a37c12c9d8 3.2.1.post1 branch v3.2.1.post1-branch Zeming Lin 2025-08-18 18:05:49 +00:00
9abce48184 Revert "chore: fix the ci to install the test requisites" (#264) v3.2.1.post1 Zeming Lin 2025-08-15 14:05:30 -07:00
5d0047ac73 Revert "chore: fix the ci to install the test requisites (#262)" revert-262-chore/fix-ci-testing Zeming Lin 2025-08-15 16:52:00 -04:00
7e0ebdb788 chore: fix the ci to install the test requisites (#262) Steve Chan 2025-08-15 13:01:43 -07:00
2a19c4edde fix(forge): various merge errors for the new binary encoding format (#261) Steve Chan 2025-08-15 09:27:24 -07:00
54fd0cc9f0 fix(forge): various merge errors for the new binary encoding format fix/merge-errors Steve Chan 2025-08-07 15:15:58 -04:00
b237fe781c adding CI that checks for linting, typechecking, and runs tests (#257) Ishaan Mathur 2025-07-14 16:45:31 -04:00
5e159aa938 adding CI that checks for linting, typechecking, and runs tests ishaan/CI-for-esm Ishaan Mathur 2025-07-11 18:31:26 +00:00
e0669a4a05 Revert "adding CI" Ishaan Mathur 2025-07-11 18:28:56 +00:00
ceacf4c199 adding CI Ishaan Mathur 2025-07-11 18:25:59 +00:00
be185fb05e Remove unused imports (#255) v3.2.1 santiag0m 2025-07-01 08:51:02 -05:00
28100a60fc Update to 3.2.1 (#254) santiag0m 2025-07-01 08:35:37 -05:00
32866c71c0 docs: update README TOC. (#244) s22chan 2025-05-29 11:16:30 -07:00
494e2e1d5c Remove tools notebooks upport v3.2.0 Neil Thomas 2025-04-08 00:52:47 +00:00
dc8d437db1 update np.array for numpy2 (#232) Neil Thomas 2025-04-04 14:13:26 -07:00
af5e95c951 update np.array for numpy2 neil/numpy-2 Neil Thomas 2025-04-04 21:07:53 +00:00
3fb1a6110d 3.2.0 - fix residue constants (#231) Neil Thomas 2025-04-04 10:55:40 -07:00
1e13b7b63f revert version neil/port-over-3.2.1 Neil Thomas 2025-04-04 17:47:49 +00:00
55843774c5 revert to 3.2.0 Neil Thomas 2025-04-04 17:46:48 +00:00
86811b7d2c 3.2.1 - fix residue constants Neil Thomas 2025-04-04 17:45:18 +00:00
6f3e9b1809 porting over 3.2.0 (#229) Chetan Mishra 2025-04-03 21:02:33 -04:00

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