Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Import latest changes in main #2

Open
wants to merge 122 commits into
base: main
Choose a base branch
from
Open

Import latest changes in main #2

wants to merge 122 commits into from

Conversation

amorehead
Copy link
Owner

No description provided.

Augustin-Zidek and others added 30 commits February 8, 2022 01:27
@Augustin-Zidek @copybara-github
Remove unused code.
b5ed6b7 
PiperOrigin-RevId: 427128482
Change-Id: I31134f7b0675260c79c799f14626140d74d745d4
@tomhennigan @copybara-github
Add split_rng=False (current default) to sharded_map.
929b188 
Haiku plans to make split_rng a required argument to hk.vmap in an upcoming
release. This change updates AlphaFold to preserve the current behaviour. We
also handle the case where users are using a release of Haiku without the
split_rng option, for these users split_rng=False is implied.

PiperOrigin-RevId: 428429472
Change-Id: I3292396eb330ffabf2f36f5364aa0ae1bc74cf71
@mfigurnov @copybara-github
Improve support for num_recycle=0.
2cd61ad 
Previously, setting num_recycle=0 in a pretrained recycling model skipped creating some Linears and LayerNorms. This meant that the the offsets of these modules were not applied leading to a degraded performance in that case.

PiperOrigin-RevId: 429075328
Change-Id: I9257f859521799f45e2deef3803c249311051225
@rich12321 @copybara-github
Enable multiple seeds per model for AlphaFold-Multimer.
eb49d15 
PiperOrigin-RevId: 429318717
Change-Id: Ib07df7ecd4bc52feea80a66c585ce51f332ac7a1
@rich12321 @copybara-github
Fix random_seed overflow when seeds per model > 1.
b787ca2 
PiperOrigin-RevId: 429520386
Change-Id: Ic1ba2b31e25a0511fefe5d0d462fc5a218641a56
@rich12321 @copybara-github
Remove prokaryotic pairing from AFOS.
89a6875 
PiperOrigin-RevId: 429521382
Change-Id: Ib9bfce50834bb129af0dbd3508cd0b92856a9bb1
@copybara-github
Remove unused bias arg in GlobalAttention.
16bab4d 
PiperOrigin-RevId: 430053169
Change-Id: Ia7461bc23d6e0c94f5bef8c1ded1c8306193e67e
@andycowie @copybara-github
Simplify mounting of files.
552586e 
PiperOrigin-RevId: 430450270
Change-Id: Ie9f30b253d1cabf6b20e596732b9bab4963dc776
@tomwardio @copybara-github
No longer use runtime=nvidia to expose GPUs to the container.
5f37a5a 
Instead use `DeviceRequest`, which is equivalent to running with `--gpu all`.

PiperOrigin-RevId: 431933575
Change-Id: Iee9f70ae8f291d16850e4f58349559d9468ef4d8
@sbodenstein @copybara-github
Remove unused function casp_model_names.
189f7d8 
PiperOrigin-RevId: 431956393
Change-Id: I1d97992967b8c276dfa978b91bc5066efdd3b62c
@sbodenstein @copybara-github
Update multimer models to v2.
eba82a6 
PiperOrigin-RevId: 432150462
Change-Id: I508371123adf9dad20f4fe1082c7a6c7cd6815d4
@rich12321 @copybara-github
Update change-log to briefly describe the change in AlphaFold-Multime…
3e046ad 
…r models.

PiperOrigin-RevId: 432931310
Change-Id: I19acd7eb7f3a63922481d9db3bc8d881efbbf550
@rich12321 @copybara-github
Update open source between_residue_clash_loss to take into account mu…
481b8be 
…ltiple chains.

PiperOrigin-RevId: 432934821
Change-Id: If5decaf654823a37c4270151039a12606f526f7a
@sbodenstein @copybara-github
Add instructions for using multimer v1 model weights.
918434f 
PiperOrigin-RevId: 433187350
Change-Id: Ibb524ead7290d7fa0cbf609c5e2df105de5a5fc3
@copybara-github
Add info for getting in touch via email to colab and readme.
8cdec53 
PiperOrigin-RevId: 435031203
Change-Id: Ib3fdb9931219f3a139b324e751914a00f425fe2c
@copybara-github
Fix readme wording.
0007c35 
PiperOrigin-RevId: 435113747
Change-Id: I8ca82eab2b88c1e5709abc479d5cb876af983c11
@Augustin-Zidek @copybara-github
Do not reuse the temporary output directory in run_alphafold_test.
b85ffe1 
PiperOrigin-RevId: 435373710
Change-Id: I52c46cdfaccf73a456dfad52a2e3a103791653f4
@rchen152 @copybara-github
Silence some pytype errors.
ed0886c 
PiperOrigin-RevId: 436161190
Change-Id: Ia10df42f5f3f638a7a5b7b804c593a1e28a4ef44
@Augustin-Zidek
Mention the workaround for the Nvidia public key issue in the README.
c42a96f 
PiperOrigin-RevId: 449223429
Change-Id: Iaa59e839fe3822cc319a2ae5600ed36ee4d6777c
@Augustin-Zidek @copybara-github
Fix AlphaFold version in setup.py.
197bd19 
PiperOrigin-RevId: 450934613
Change-Id: I2b5f7a740a3d9b87ccd495a65bcf8b4605c72585
@Augustin-Zidek @copybara-github
Fix jax.tree_multimap deprecation warning.
d9e5e1d 
PiperOrigin-RevId: 451994826
Change-Id: I4573baf61d33010c75de717d3b49f47bc9c6a8ac
@tomwardio @copybara-github
Add support for CUDA patch versions.
55c948c 
PiperOrigin-RevId: 452008235
Change-Id: Ic6ae00a207d3b0eb809b039b5df9e7bebdaee558
@Augustin-Zidek @copybara-github
Clarify that AlphaFold works only under Linux.
c9a9e87 
PiperOrigin-RevId: 453397654
Change-Id: I7e7d7dfc54a4c76b6a28b47630567677f35ecb30
@Augustin-Zidek @copybara-github
Pin protobuf version to 3.20.1.
0f7ab13 
PiperOrigin-RevId: 454545752
Change-Id: I80656e917ee799fbf808002260634d2b1c38dca0
@Augustin-Zidek @copybara-github
Bump AlphaFold version to 2.2.1.
623cc11 
PiperOrigin-RevId: 454568110
Change-Id: Icd82696dacc250cfc3b7b71fc71d9fcd7669d032
@tomwardio @copybara-github
Replace period with hyphens in place, instead of declaring environmen…
ab10514 
…t variable.

PiperOrigin-RevId: 454618760
Change-Id: Ia6501f62ff3769a591497ac3413dc7526b31d1cc
@Augustin-Zidek @copybara-github
Bump AlphaFold version to v2.2.2.
b0b7afa 
PiperOrigin-RevId: 454626138
Change-Id: I9a6061ff7411e187ad7c5a94b6eebd8f3663d450
@tomwardio @copybara-github
Remove unused type hint from run_alphafold script.
157c0ea 
PiperOrigin-RevId: 454817469
Change-Id: I677ee0cabbcf64b4682a0f4b218c23daf95ac13e
@tomwardio @copybara-github
Move disable_v2_behaviour() to setUp to enable running tests in t…
5f4a9cc 
…est suites.

PiperOrigin-RevId: 454823596
Change-Id: I893dc051a5f21d53905acee45a4dcb5c5609daf9
@tomwardio @copybara-github
Add matplotlib test dependency so we can run notebook_utils_test.
725e79a 
PiperOrigin-RevId: 454823630
Change-Id: I9903ca5eb2284c8775631e2ffaf452869c7d4d7c
DeepMind and others added 30 commits August 18, 2023 07:26
@copybara-github
Fix: return correct renaming mask.
bbe8a84 
PiperOrigin-RevId: 558140222
Change-Id: I7fb69e8a7c9ce95a26d0816fb8c1c02cba68f660
@Augustin-Zidek @copybara-github
Remove unused imports.
c9431c4 
PiperOrigin-RevId: 562507313
Change-Id: Ic82f113455c0be50c0af1e9df4498991072e554c
@Augustin-Zidek @copybara-github
Add a cast to prevent future Pandas typing issues.
22f6919 
PiperOrigin-RevId: 563001314
Change-Id: I441729e337e5bf782f70beeb92d8cf0c870bc98a
@copybara-github
Replace deprecated PRNGKeyArray isinstance checks
a8875a9 
For details, see jax-ml/jax#17297

PiperOrigin-RevId: 565705637
Change-Id: I88c4a3003166580e28111c4e410c8412c23ccb9d
@copybara-github
Add assertion to aid type checking.
bbc133b 
PiperOrigin-RevId: 568220760
Change-Id: Ied9e33692bbd7fb8c02b039f64688cc31f005885
@Augustin-Zidek @copybara-github
Update wwPDB paths from ftp.wwpdb.org to files.wwpdb.org.
f78c589 
See https://www.wwpdb.org/news/news?year=2022#6303be3b707ecd4f63b3d3d9 for the wwPDB announcement.

PiperOrigin-RevId: 575762003
Change-Id: If25ea2777c33b03f03b27d54046c71753cb33038
@Augustin-Zidek @copybara-github
Revert a change that is not compatible with JAX 0.3.25.
f715f01 
PiperOrigin-RevId: 578486539
Change-Id: Id0e535ebf75916b5179791d093ca714e343ccb69
@hawkinsp @copybara-github
[JAX] Replace uses of jax.devices("cpu") with jax.local_devices(backe…
1fa9200 
…nd="cpu").

An upcoming change to JAX will include non-local (addressable) CPU devices in jax.devices() when JAX is used multicontroller-style, where there are multiple Python processes.

This change preserves the current behavior by replacing uses of jax.devices("cpu"), which previously only returned local devices, with jax.local_devices("cpu"), which will return local devices both now and in the future.

This change is always be safe (i.e., it should always preserve the previous behavior) but it may sometimes be unnecessary if code is never used in a multicontroller setting.

PiperOrigin-RevId: 582680953
Change-Id: I614739de052185c42932ddb91d1d464751442f65
@mattjj @copybara-github
Loosen overly tight numerical tolerances to allow for one-time random…
4f44731 
… value

change from jax-ml/jax#18480

PiperOrigin-RevId: 591243740
Change-Id: I86457bfcaae65771ccb4e39d3e4d929335d71652
@Htomlinson14 @copybara-github
Uninstall keras in notebook to avoid the keras initializer fault.
632ef57 
PiperOrigin-RevId: 603012242
Change-Id: Icf0120e1baf1278862ea62402a86c9eac5932710
@Htomlinson14 @copybara-github
Update conda to 24.1.2.
032e2f2 
PiperOrigin-RevId: 611404763
Change-Id: Icc7d637e1de9fa82da76aa8dccd9b9dce8be6246
@Augustin-Zidek @copybara-github
Fix how we extract mmCIF resolution (fix ordering issue).
6d95d19 
Thanks to @ljarosch for reporting and suggesting a fix in #915.

PiperOrigin-RevId: 617817805
Change-Id: I46738b248a054d06fe902626cff161fe521e99f1
@Htomlinson14 @copybara-github
Update jax, haiku and chex versions.
5208f1b 
PiperOrigin-RevId: 623469847
Change-Id: I64a812e00e099f6503b9aa1e0cfde1133ea8a774
@Htomlinson14 @copybara-github
Remove deprecated PRNGKeyArray.
7e7de59 
PiperOrigin-RevId: 623494831
Change-Id: Ie15c1d517fd7b34662d69d05205151d9c7021da4
@Htomlinson14 @copybara-github
Update requirements:
dbe2a43 
- Ubuntu to 20.04
- Cuda to 12.2.2
- Tensorflow to 2.16.1
- Jax to 0.4.26
- Openmm to 8.0.0

PiperOrigin-RevId: 624094170
Change-Id: I49391c3f721e93ac8ccd5a4483cdb6f2ec61cd3b
@Htomlinson14 @copybara-github
Update openmm in AlphaFold colab.
4d4a1ae 
PiperOrigin-RevId: 625019041
Change-Id: If6e5b23edeb1f06bd91b4daf1c449d12ed407895
@Augustin-Zidek @copybara-github
Add documentation for AlphaFold Server JSON file format.
f251de6 
PiperOrigin-RevId: 631787106
Change-Id: Ib58c166a2945d459c1555dd1920963887b8d7c16
@copybara-github
Replace deprecated jax.tree_* functions with jax.tree.*
5b0e1f2 
The top-level `jax.tree_*` aliases have long been deprecated, and will soon be removed. Alternate APIs are in `jax.tree_util`, with shorter aliases in the `jax.tree` submodule, added in JAX version 0.4.25.

PiperOrigin-RevId: 633878846
Change-Id: I282e177b3c9026b805d6eb5e5d6e6b1287f87e55
@Augustin-Zidek @copybara-github
Inline SCOPData to be compatible with future Biopython versions.
93a9a04 
PiperOrigin-RevId: 648368396
Change-Id: Icfd8135c5602ca81007dd6074a3258d5ae0187ee
@hawkinsp @copybara-github
[numpy] Fix users of NumPy APIs that are removed in NumPy 2.0.
692c01c 
This change migrates users of APIs removed in NumPy 2.0 to their recommended replacements (https://numpy.org/devdocs/numpy_2_0_migration_guide.html).

PiperOrigin-RevId: 655904142
Change-Id: Idcf2384de70cb27cb92e3f421dc8e0a9a6466507
@Augustin-Zidek @copybara-github
Pin setuptools on a version smaller than 72.0.0.
a2217f0 
PiperOrigin-RevId: 660325717
Change-Id: I11b5cf0b0b7cc8bfa48de170a1653e013d7734a1
@Augustin-Zidek @copybara-github
Make apt output log-friendly by adding the --quiet flag.
85e0be3 
PiperOrigin-RevId: 665259372
Change-Id: I516c7780b8a821065bf19fe3c79dba604f2c917c
@Augustin-Zidek @copybara-github
Update the disclaimer to match AlphaFold 3 + run mdformat.
d95a92a 
PiperOrigin-RevId: 696460542
Change-Id: I42defc0a687207ee57801b0aeba78fe1e63b03e6
@copybara-github
Automated Code Change: Suppress pytype errors
bbd8300 
PiperOrigin-RevId: 700257299
Change-Id: If6ce01bd60ab0422eca10578db8d58b1a3137b40
@Augustin-Zidek @copybara-github
Update Conda to 24.11.1 to fix Docker build failure and small improve…
6350ddd 
…ments to the Dockerfile.

PiperOrigin-RevId: 707479885
Change-Id: Ic3c71229bcf3a935cae86aee64ee7c02220e1085
@copybara-github
jax.numpy.clip: update use of deprecated arguments.
fa0c526 
- a is now positional-only
- a_min is now min
- a_max is now max

The old argument names have been deprecated since JAX v0.4.27.

PiperOrigin-RevId: 715343439
Change-Id: I50b086b249360c142f42ed4d8e50d48692c11dfa
@Augustin-Zidek @copybara-github
Bump Python in Colab to 3.11.
11a991e 
PiperOrigin-RevId: 718812632
Change-Id: I54b901e7a361a63a2c3f366535dbe2cd3e792b99
@Augustin-Zidek @copybara-github
Do not use jnp.clip arguments which are not supported in the pinned J…
93e024b 
…AX version.

PiperOrigin-RevId: 719259712
Change-Id: I7eb76868275c862201cc7eb26fede8c987e5b760
@copybara-github
Update JSON format docs with new template on/off, cutoff date fields.
24fbdfc 
PiperOrigin-RevId: 720186008
Change-Id: I53b84c0b52509f93e85cc8705aeba4888398f5bb
@dlasecki @copybara-github
Deprecate the AlphaFold 2 notebook
2ca41b1 
PiperOrigin-RevId: 720951827
Change-Id: Ie30be1252f6e6dc4038be6b307395f45e638d5ad
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.