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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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CLAassistant commented Sep 30, 2024

CLA assistant check
Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you all sign our Contributor License Agreement before we can accept your contribution.
0 out of 2 committers have signed the CLA.

❌ RyanGarciaLI
❌ YaoYinYing
You have signed the CLA already but the status is still pending? Let us recheck it.

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3 participants