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Add Drug-Target Interaction dataset#100

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csjackson0 wants to merge 74 commits intoOpenBioML:mainOpenBioML/chemnlp:mainfrom csjackson0:Add-Drug-Target-Interaction-datasetcsjackson0/chemnlp:Add-Drug-Target-Interaction-datasetCopy head branch name to clipboard

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Commits on Mar 11, 2023

• initial commit for Drug_target_interaction dataset

  

  Cody Jackson

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• remove data

  

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Commits on Mar 13, 2023

• deleted .DS_store

  

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• update metadata file type field to continuous

  

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• [pre-commit.ci] auto fixes from pre-commit.com hooks

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• feat: Add uris field for identifiers (OpenBioML#103)

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Commits on Mar 14, 2023

• docs: add submodule advice (OpenBioML#105)

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• feat: add initial env script

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• feat: separate install scripts

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• fix: add branch for main when cloning

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• Merge pull request OpenBioML#106 from jackapbutler/update-submodule-branch

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• docs: add cluster readme for script

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• fix: update paths used in env script

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• fix: add graceful fail to env creation

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• chore: rename linux to stability

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• Revert "feat: Add uris field for identifiers (OpenBioML#103)"

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• feat: Add uris field for identifiers (OpenBioML#103)

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• fix: force env creation (for each experiment)

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• make env creation user-specific

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Commits on Mar 15, 2023

• feat: add ability to run same script from slurm

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• feat: add pos arg for env dir

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• fix: remove duplicate lines

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• docs: update readme with additional info

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• feat: add second arg instead of username

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• docs: update docs

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• Merge pull request OpenBioML#107 from jackapbutler/add-cluster-env-script

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Commits on Mar 16, 2023

• delete bindingdb_kd and data_original

  

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• Merge branch 'Add-Drug-Target-Interaction-dataset' of https://github.com/strubeyj/chemnlp into Add-Drug-Target-Interaction-dataset

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• delete bindingdb_kd and data_original

  

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• remove .DS_Store

  

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• changed type to continous

  

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• [pre-commit.ci] auto fixes from pre-commit.com hooks

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• chore: run pre-commit in CI, rework datasets (OpenBioML#98)

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• Fix model docstrings (OpenBioML#119)

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Commits on Mar 17, 2023

• docs: update dataset & readme docs (OpenBioML#104)

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Commits on Mar 19, 2023

• add splits

  

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Commits on Mar 21, 2023

• feat: transform.py cleanup to create nice meta.yaml files (OpenBioML#121)

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• feat: add cluster train script (OpenBioML#112)

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• Change url for gpt-neox submodule

  

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• Merge pull request OpenBioML#126 from maw501/update-submodule-url

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Commits on Mar 22, 2023

• fix: flashpoint smiles column name in capital letters. (OpenBioML#125)

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Commits on Mar 23, 2023

• feat: add wandb logging to pipeline configuration (OpenBioML#123)

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• feat: implement benchmark field 2 (OpenBioML#128)

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Commits on Mar 26, 2023

• chore: disable pre-commit autocommit (OpenBioML#131)

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Commits on Mar 28, 2023

• docs: update contribution guide to reflect schema changes (OpenBioML#135)

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• add benchmarks

  

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• Merge branch 'Add-Drug-Target-Interaction-dataset' of https://github.com/strubeyj/chemnlp into Add-Drug-Target-Interaction-dataset

  

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• remove file

  

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• fixed long lines

  

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• initial commit for Drug_target_interaction dataset

  

  Cody Jackson

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• remove data

  

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• deleted .DS_store

  

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• update metadata file type field to continuous

  

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• delete bindingdb_kd and data_original

  

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• [pre-commit.ci] auto fixes from pre-commit.com hooks

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• delete bindingdb_kd and data_original

  

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• remove .DS_Store

  

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• changed type to continous

  

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• add splits

  

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• add benchmarks

  

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• remove file

  

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• fixed long lines

  

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• Merge branch 'Add-Drug-Target-Interaction-dataset' of github.com:strubeyj/chemnlp into Add-Drug-Target-Interaction-dataset

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• feat: cleanup transform.py and meta.yaml

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• feat: change dir name to lowercase

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• feat: cleanup identifiers

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• feat: target type to continuous

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• feat: target type to continuous also in meta.yaml

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• feat: rerun pre-commit on meta.yaml

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• feat: add name field for other targets

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