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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

Commits on Sep 1, 2023

  1. transfer less data to gpu

    Arian Jamasb committed Sep 1, 2023
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Commits on Sep 16, 2023

  1. add rigid uitls

    Jamasb committed Sep 16, 2023
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Commits on Sep 17, 2023

  1. Merge remote-tracking branch 'origin' into ipmp

    Jamasb committed Sep 17, 2023
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Commits on Sep 19, 2023

  1. Merge branch 'main' into ipmp

    Jamasb committed Sep 19, 2023
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Commits on Sep 22, 2023

  1. Merge remote-tracking branch 'origin' into ipmp

    Jamasb committed Sep 22, 2023
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Commits on Sep 25, 2023

  1. add graph model hparams

    Jamasb committed Sep 25, 2023
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Commits on Sep 28, 2023

  1. add hparams

    Jamasb committed Sep 28, 2023
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Commits on Oct 23, 2023

  1. add support for loading hparam override

    Jamasb committed Oct 23, 2023
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  2. add optional hparam override to finetune run config

    Jamasb committed Oct 23, 2023
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  3. set in memory=True as default for cath and fold classification datasets

    Jamasb committed Oct 23, 2023
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  4. add torch geometric compile

    Jamasb committed Oct 23, 2023
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  5. fix scenario where only seq_pos_enc is a node feature

    Jamasb committed Oct 23, 2023
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  6. refactor logging to use a single logging call

    Jamasb committed Oct 23, 2023
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  7. remove duplicated entry

    Jamasb committed Oct 23, 2023
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  8. minor linting

    Jamasb committed Oct 23, 2023
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Commits on Oct 25, 2023

  1. formatting

    Jamasb committed Oct 25, 2023
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  2. add pre-trained inverse folding config

    Jamasb committed Oct 25, 2023
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  3. add EGNN pretraining config

    Jamasb committed Oct 25, 2023
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  4. add find graph encoder hparams

    Jamasb committed Oct 25, 2023
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  5. add baseline inverse folding config

    Jamasb committed Oct 25, 2023
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  6. add linters to toml

    Jamasb committed Oct 25, 2023
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  7. add pre-commit config

    Jamasb committed Oct 25, 2023
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  8. Add porject support for py311

    Jamasb committed Oct 25, 2023
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  9. Add cpu index url for torch for CI

    Jamasb committed Oct 25, 2023
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  10. add cpu torch source

    Jamasb committed Oct 25, 2023
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Commits on Oct 26, 2023

  1. rollback to max python 3.10 due to lack of torchdrug support

    Jamasb committed Oct 26, 2023
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  2. bump graphein to 1.7.4 for PyG 2.4+ support (and backwards compatibility

    Jamasb committed Oct 26, 2023
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  3. add warning log

    Jamasb committed Oct 26, 2023
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  4. add list to track processed files in case of overwrite

    Jamasb committed Oct 26, 2023
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Commits on Oct 27, 2023

  1. addmodel attribution script

    Jamasb committed Oct 27, 2023
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  2. update graphein version to 1.7.5+ and add captum dependency

    Jamasb committed Oct 27, 2023
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Commits on Oct 28, 2023

  1. add some more docstrings, clean up

    Jamasb committed Oct 28, 2023
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  2. add attribution to cli

    Jamasb committed Oct 28, 2023
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  3. update gitignore

    Jamasb committed Oct 28, 2023
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Commits on Nov 3, 2023

  1. Merge branch 'main' into ipmp

    @a-r-j
    a-r-j authored Nov 3, 2023
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  2. add DDP support #44

    Jamasb committed Nov 3, 2023
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  3. update readme

    Jamasb committed Nov 3, 2023
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  4. Merge branch 'ipmp' of https://www.github.com/a-r-j/ProteinWorkshop i… 

    …nto ipmp
    Jamasb committed Nov 3, 2023
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  5. update readme

    Jamasb committed Nov 3, 2023
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  6. ignore igfold dataset in overwrite test

    Jamasb committed Nov 3, 2023
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  7. add IGFold prediction datasets

    Jamasb committed Nov 3, 2023
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  8. Add igfold datamodule

    Jamasb committed Nov 3, 2023
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Commits on Nov 7, 2023

  1. fix binary graph classification config

    Jamasb committed Nov 7, 2023
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Commits on Nov 12, 2023

  1. add cdconv model

    Jamasb committed Nov 12, 2023
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  2. fix test fixture

    Jamasb committed Nov 12, 2023
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  3. update docs

    Jamasb committed Nov 12, 2023
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  4. linting

    Jamasb committed Nov 12, 2023
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  5. linting

    Jamasb committed Nov 12, 2023
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  6. add full model config for finetuning

    Jamasb committed Nov 12, 2023
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  7. linting

    Jamasb committed Nov 12, 2023
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Commits on Nov 13, 2023

  1. fix device request logging

    Jamasb committed Nov 13, 2023
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  2. add multihot label encoder

    Jamasb committed Nov 13, 2023
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Commits on Nov 16, 2023

  1. speed up positional encoding computation

    Jamasb committed Nov 16, 2023
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  2. fix device logging

    Jamasb committed Nov 16, 2023
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  3. add num_classes to GO datasets

    Jamasb committed Nov 16, 2023
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  4. lint cdconv config

    Jamasb committed Nov 16, 2023
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  5. add multilabel classification task configs

    Jamasb committed Nov 16, 2023
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  6. refactor f1_max for multilabel classif.

    Jamasb committed Nov 16, 2023
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  7. add auprc to classification metrics, linting

    Jamasb committed Nov 16, 2023
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  8. linting

    Jamasb committed Nov 16, 2023
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  9. set in_memory=True as default for GO datasets

    Jamasb committed Nov 16, 2023
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Commits on Nov 17, 2023

  1. clean up EC dataset

    Jamasb committed Nov 17, 2023
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  2. clean up GO dataset

    Jamasb committed Nov 17, 2023
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  3. improve instantiation test

    Jamasb committed Nov 17, 2023
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  4. set ec to in memory

    Jamasb committed Nov 17, 2023
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  5. fix GO labelling

    Jamasb committed Nov 17, 2023
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Commits on Nov 18, 2023

  1. fix metrics memory leak

    Jamasb committed Nov 18, 2023
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Commits on Nov 19, 2023

  1. add ec_Reaction sweep

    Jamasb committed Nov 19, 2023
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Commits on Nov 20, 2023

  1. Ignore local Conda env in project directory

    @amorehead
    amorehead committed Nov 20, 2023
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  2. add missing mace ca_angles hparams

    Jamasb committed Nov 20, 2023
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  3. Merge branch 'ipmp' of https://www.github.com/a-r-j/ProteinWorkshop i… 

    …nto ipmp
    Jamasb committed Nov 20, 2023
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Commits on Nov 21, 2023

  1. add addev config

    Jamasb committed Nov 21, 2023
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  2. A dataset loading script for antibody_developability.py

    @amorehead
    amorehead committed Nov 21, 2023
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  3. Merge branch 'ipmp' of https://github.com/a-r-j/ProteinWorkshop into … 

    …ipmp
    @amorehead
    amorehead committed Nov 21, 2023
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Commits on Nov 22, 2023

  1. add esm BB config

    Jamasb committed Nov 22, 2023
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  2. Merge branch 'ipmp' of https://www.github.com/a-r-j/ProteinWorkshop i… 

    …nto ipmp
    Jamasb committed Nov 22, 2023
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  3. Add ESM config for all feature schemes

    @amorehead
    amorehead committed Nov 22, 2023
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  4. add ppi prediction task updates

    Jamasb committed Nov 22, 2023
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  5. Merge branch 'ipmp' of https://www.github.com/a-r-j/ProteinWorkshop i… 

    …nto ipmp
    Jamasb committed Nov 22, 2023
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  6. add ppi sweep config

    Jamasb committed Nov 22, 2023
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  7. Update test script for masif_dataset.py

    @amorehead
    amorehead committed Nov 22, 2023
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  8. Update path for masif_site in test script

    @amorehead
    amorehead committed Nov 22, 2023
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  9. mask additional attributes in PPI site prediction

    Jamasb committed Nov 22, 2023
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  10. resolve sequence tokenization

    Jamasb committed Nov 22, 2023
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Commits on Nov 23, 2023

  1. refactor chain identification

    Jamasb committed Nov 23, 2023
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  2. fix error in error fix

    Jamasb committed Nov 23, 2023
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  3. Fix fix of a fix

    @amorehead
    amorehead committed Nov 23, 2023
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  4. exclude erroneous examples

    Jamasb committed Nov 23, 2023
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  5. fix edge cases

    Jamasb committed Nov 23, 2023
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  6. fix edge cases

    Jamasb committed Nov 23, 2023
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  7. Merge branch 'ipmp' of https://www.github.com/a-r-j/ProteinWorkshop i… 

    …nto ipmp
    Jamasb committed Nov 23, 2023
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Commits on Nov 27, 2023

  1. add model io utils

    Jamasb committed Nov 27, 2023
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Commits on Nov 30, 2023

  1. standardise default features for train and finetune configs #61

    Jamasb committed Nov 30, 2023
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Commits on Dec 26, 2023

  1. refactor to new recommended jaxtyping/beartype syntax

    Jamasb committed Dec 26, 2023
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  2. typechecker refactor for esm

    Jamasb committed Dec 26, 2023
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  3. typechecker refactor for dataset base

    Jamasb committed Dec 26, 2023
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  4. lint

    Jamasb committed Dec 26, 2023
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  5. remove merge artifact from poetry.lock

    Jamasb committed Dec 26, 2023
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  6. fix beartype import

    Jamasb committed Dec 26, 2023
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  7. fix broken lock file

    Jamasb committed Dec 26, 2023
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  8. fix broken poetry.lock and update jaxtyping dependency

    Jamasb committed Dec 26, 2023
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  9. fix broken poetry.lock and update jaxtyping dependency

    Jamasb committed Dec 26, 2023
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  10. use mamba in test workflow

    Jamasb committed Dec 26, 2023
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  11. fix pyg wheel link for torch > 2.1.0

    Jamasb committed Dec 26, 2023
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  12. update tests

    Jamasb committed Dec 26, 2023
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  13. lint

    Jamasb committed Dec 26, 2023
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  14. fix test

    Jamasb committed Dec 26, 2023
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  15. set dummy labels on example_batch

    Jamasb committed Dec 26, 2023
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  16. fix zenodo url

    Jamasb committed Dec 26, 2023
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  17. fix zenodo url

    Jamasb committed Dec 26, 2023
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  18. fix beartype import name

    Jamasb committed Dec 26, 2023
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  19. add changelog

    Jamasb committed Dec 26, 2023
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  20. add attribution to toc

    Jamasb committed Dec 26, 2023
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Commits on Dec 28, 2023

  1. Update install instructions to PyTorch 2.1.2+, and sync docs with REA… 

    …DME.md line-by-line
    @amorehead
    amorehead committed Dec 28, 2023
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  2. fix malformed HTML in quickstart components

    Arian Jamasb committed Dec 28, 2023
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  3. minor fixes to docs

    Arian Jamasb committed Dec 28, 2023
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