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Linting and updates#53

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a-r-j merged 116 commits intomaina-r-j/ProteinWorkshop:mainfrom ipmpa-r-j/ProteinWorkshop:ipmpCopy head branch name to clipboardDec 28, 2023

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Commits

Commits on Sep 1, 2023

• transfer less data to gpu

  

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Commits on Sep 16, 2023

• add rigid uitls

  

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Commits on Sep 17, 2023

• Merge remote-tracking branch 'origin' into ipmp

  

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Commits on Sep 19, 2023

• Merge branch 'main' into ipmp

  

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Commits on Sep 22, 2023

• Merge remote-tracking branch 'origin' into ipmp

  

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Commits on Sep 25, 2023

• add graph model hparams

  

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Commits on Sep 28, 2023

• add hparams

  

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Commits on Oct 23, 2023

• add support for loading hparam override

  

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• add optional hparam override to finetune run config

  

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• set in memory=True as default for cath and fold classification datasets

  

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• add torch geometric compile

  

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• fix scenario where only seq_pos_enc is a node feature

  

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• refactor logging to use a single logging call

  

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• remove duplicated entry

  

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• minor linting

  

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Commits on Oct 25, 2023

• formatting

  

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• add pre-trained inverse folding config

  

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• add EGNN pretraining config

  

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• add find graph encoder hparams

  

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• add baseline inverse folding config

  

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• add linters to toml

  

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• add pre-commit config

  

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• Add porject support for py311

  

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• Add cpu index url for torch for CI

  

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• add cpu torch source

  

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Commits on Oct 26, 2023

• rollback to max python 3.10 due to lack of torchdrug support

  

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• bump graphein to 1.7.4 for PyG 2.4+ support (and backwards compatibility

  

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• add warning log

  

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• add list to track processed files in case of overwrite

  

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Commits on Oct 27, 2023

• addmodel attribution script

  

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• update graphein version to 1.7.5+ and add captum dependency

  

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Commits on Oct 28, 2023

• add some more docstrings, clean up

  

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• add attribution to cli

  

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• update gitignore

  

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Commits on Nov 3, 2023

• Merge branch 'main' into ipmp

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  3c6f3e1

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• add DDP support #44

  

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  b7ffda0

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• update readme

  

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• Merge branch 'ipmp' of https://www.github.com/a-r-j/ProteinWorkshop into ipmp

  

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• update readme

  

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• ignore igfold dataset in overwrite test

  

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• add IGFold prediction datasets

  

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• Add igfold datamodule

  

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Commits on Nov 7, 2023

• fix binary graph classification config

  

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Commits on Nov 12, 2023

• add cdconv model

  

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• fix test fixture

  

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• update docs

  

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  e07cca2

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• linting

  

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• linting

  

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• add full model config for finetuning

  

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• linting

  

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Commits on Nov 13, 2023

• fix device request logging

  

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• add multihot label encoder

  

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Commits on Nov 16, 2023

• speed up positional encoding computation

  

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• fix device logging

  

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• add num_classes to GO datasets

  

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• lint cdconv config

  

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• add multilabel classification task configs

  

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• refactor f1_max for multilabel classif.

  

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  9270e44

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• add auprc to classification metrics, linting

  

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  4be174a

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• linting

  

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• set in_memory=True as default for GO datasets

  

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Commits on Nov 17, 2023

• clean up EC dataset

  

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  06364b2

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• clean up GO dataset

  

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  91cbc2f

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• improve instantiation test

  

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  40baf0c

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• set ec to in memory

  

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  d85c6f0

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• fix GO labelling

  

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Commits on Nov 18, 2023

• fix metrics memory leak

  

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Commits on Nov 19, 2023

• add ec_Reaction sweep

  

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Commits on Nov 20, 2023

• Ignore local Conda env in project directory

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• add missing mace ca_angles hparams

  

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• Merge branch 'ipmp' of https://www.github.com/a-r-j/ProteinWorkshop into ipmp

  

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Commits on Nov 21, 2023

• add addev config

  

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• A dataset loading script for antibody_developability.py

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• Merge branch 'ipmp' of https://github.com/a-r-j/ProteinWorkshop into ipmp

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Commits on Nov 22, 2023

• add esm BB config

  

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• Merge branch 'ipmp' of https://www.github.com/a-r-j/ProteinWorkshop into ipmp

  

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• Add ESM config for all feature schemes

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• add ppi prediction task updates

  

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• Merge branch 'ipmp' of https://www.github.com/a-r-j/ProteinWorkshop into ipmp

  

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• add ppi sweep config

  

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  f8ea13b

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• Update test script for masif_dataset.py

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• Update path for masif_site in test script

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• mask additional attributes in PPI site prediction

  

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  01caa96

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• resolve sequence tokenization

  

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Commits on Nov 23, 2023

• refactor chain identification

  

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• fix error in error fix

  

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  9d9994c

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• Fix fix of a fix

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• exclude erroneous examples

  

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• fix edge cases

  

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  e4b4d62

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• fix edge cases

  

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  eb44c49

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• Merge branch 'ipmp' of https://www.github.com/a-r-j/ProteinWorkshop into ipmp

  

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Commits on Nov 27, 2023

• add model io utils

  

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Commits on Nov 30, 2023

• standardise default features for train and finetune configs #61

  

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Commits on Dec 26, 2023

• refactor to new recommended jaxtyping/beartype syntax

  

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• typechecker refactor for esm

  

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• typechecker refactor for dataset base

  

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• lint

  

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• remove merge artifact from poetry.lock

  

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• fix beartype import

  

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• fix broken lock file

  

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• fix broken poetry.lock and update jaxtyping dependency

  

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• fix broken poetry.lock and update jaxtyping dependency

  

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• use mamba in test workflow

  

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• fix pyg wheel link for torch > 2.1.0

  

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• update tests

  

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• lint

  

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• fix test

  

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• set dummy labels on example_batch

  

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• fix zenodo url

  

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• fix zenodo url

  

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• fix beartype import name

  

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• add changelog

  

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• add attribution to toc

  

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Commits on Dec 28, 2023

• Update install instructions to PyTorch 2.1.2+, and sync docs with README.md line-by-line

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• fix malformed HTML in quickstart components

  

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• minor fixes to docs

  

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