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Linting and updates #53

Merged
merged 116 commits into from
Dec 28, 2023
Merged

Linting and updates #53

merged 116 commits into from
Dec 28, 2023

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a-r-j
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@a-r-j a-r-j commented Oct 25, 2023 •
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Arian Jamasb and others added 25 commits September 1, 2023 17:55
transfer less data to gpu
53c8fa3
add rigid uitls
f0b43bc
Merge remote-tracking branch 'origin' into ipmp
fb8b62a
Merge branch 'main' into ipmp
8cf1eb9
Merge remote-tracking branch 'origin' into ipmp
437d2f2
add graph model hparams
c97391d
add hparams
a5d0eaa
add support for loading hparam override
fd43446
add optional hparam override to finetune run config
c2c8b01
set in memory=True as default for cath and fold classification datasets
c2dcbee
add torch geometric compile
d041a3e
fix scenario where only seq_pos_enc is a node feature
d83c62e
refactor logging to use a single logging call
eedc9e5
remove duplicated entry
005db26
minor linting
f184773
formatting
90835ea
add pre-trained inverse folding config
282c6c3
add EGNN pretraining config
eec1308
add find graph encoder hparams
02abcd8
add baseline inverse folding config
1847379
add linters to toml
881efee
add pre-commit config
034268a
Add porject support for py311
cdfcdb8
Add cpu index url for torch for CI
ff44a34
add cpu torch source
bbcfab7
@amorehead
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LGTM. Nice to see pre-commit making its way into the project

@a-r-j
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a-r-j commented Oct 26, 2023

@amorehead I suspect tests are failing because the test_train_fast_dev_run is exceeding the resource usage allowance on the runner. Any ideas how to mitigate this? This test has passed previously

Jamasb and others added 28 commits November 22, 2023 17:41
fix edge cases
e4b4d62
fix edge cases
eb44c49
Merge branch 'ipmp' of https://www.github.com/a-r-j/ProteinWorkshop i…
76aa0b5 
…nto ipmp
add model io utils
758a292
standardise default features for train and finetune configs #61
595b5ac
refactor to new recommended jaxtyping/beartype syntax
381040c
typechecker refactor for esm
9fbc041
typechecker refactor for dataset base
69d0474
lint
248478b
remove merge artifact from poetry.lock
e7123f6
fix beartype import
5173259
fix broken lock file
a0a775a
fix broken poetry.lock and update jaxtyping dependency
6be97aa
fix broken poetry.lock and update jaxtyping dependency
3d39e27
use mamba in test workflow
d7d22b9
fix pyg wheel link for torch > 2.1.0
be5dd40
update tests
735640b
lint
8d32aa2
fix test
b15bdf2
set dummy labels on example_batch
a0782c4
fix zenodo url
cc4364e
fix zenodo url
cefcb8b
fix beartype import name
c322df6
add changelog
3e735c8
add attribution to toc
19dd12d
@amorehead
Update install instructions to PyTorch 2.1.2+, and sync docs with REA…
22fca65 
…DME.md line-by-line
fix malformed HTML in quickstart components
3014dc3
minor fixes to docs
a46c4ed
@a-r-j a-r-j merged commit 03b66ad into main Dec 28, 2023
2 checks passed
@amorehead amorehead deleted the ipmp branch December 28, 2023 19:21
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Torch 2.0.1 unsupported by Poetry
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@a-r-j @amorehead