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PR-1: Hydra-Powered YAML Configuration and run as Pip module #325

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YaoYinYing
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This is one of the separated PRs from #321 .

Full PR roadmap

id purpose # commits Affected
1 Hydra-Omegaconf and Pip module 6 Code, Config, Doc
2 BFD supports and MSA parallelism fixes 5 Code, Config, Case
3 Small molecule inputs and covalent bonds 4 Code, Case, Doc

Changelog:

Added

  • Configurability via YAML, supported by Hydra and OmegaConf.
  • New helixfold run command for performing inference.

Changed

  • Transitioned HelixFold3 to a pip-installable package.
  • Overrides now handled through CONFIG_DIFFS.
  • Replaced ml_collections.ConfigDict with DictConfig for better integration.

Fixed

  • Implemented automatic binary search within the PATH if not explicitly specified.

Removed

  • Deprecated requirements.txt in favor of direct pip installation dependencies.
  • Removed run_infer.sh script as functionality is now integrated into the main command interface.

YaoYinYing and others added 6 commits August 27, 2024 16:51
add override flag

fix: enable mutiple config overrides

feat: model config overriden

fix: imports

doc: merge to readme

fix:config

add configs
fix: maxit path

fix: maxit run with env
@RyanGarciaLI
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RyanGarciaLI commented Aug 28, 2024

@YaoYinYing It looks good to start, but it still needs further improvement. You can add my WeChat id "******", and we can discuss more details.

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