Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

TDC Oracle integration #145

Merged
merged 7 commits into from
Oct 5, 2022
Merged

TDC Oracle integration #145

merged 7 commits into from
Oct 5, 2022

Conversation

jannisborn
Copy link
Contributor

@jannisborn jannisborn commented Oct 4, 2022

Closes #119
Closes #117

  • bumping tdc dependency which finally allows to relax the sklearn version

  • support for three more complex oracles. For details see here.

    • Two of them (ASKCOS and MoleculeOne) give synthesizability scores similar to RXN retroworkers. They need an api key or a the IP of the API endpoint to run. I created schemata to handle those
    • Third run is for docking. I simply populated the TDC interface that either allows to dock against an existing target (that is fetched automatically from their server) or against a user-provided target. In both cases, however, the user needs to install a lot of software manually before these properties work
    • No unit tests provided in all cases, since installation is either manual or requires authentification
  • I had to temporarily pin importlib_metadata since they just released v5 which comes with some errors, see here, original issue here

  • Unrelated: I fixed the legacy values of test_fraction in RT Trainer code

  • Unrelated: Renamed SIDER property to Sider in order to adhere to our styling

@cla-bot cla-bot bot added the cla-signed CLA has been signed label Oct 4, 2022
@jannisborn jannisborn added the enhancement New feature or request label Oct 4, 2022
@jannisborn jannisborn requested a review from drugilsberg October 4, 2022 16:05
@jannisborn jannisborn self-assigned this Oct 4, 2022
Copy link
Contributor

@drugilsberg drugilsberg left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Great job @jannisborn, I restarted the CI to make sure the failed test is due to some stochastic behaviour in one of the TorchDrug tests.

@jannisborn
Copy link
Contributor Author

My bad, I broke the test of the RT training pipeline when removing the legacy argument. It should work now

@jannisborn jannisborn merged commit eb6a99b into GT4SD:main Oct 5, 2022
@jannisborn jannisborn deleted the tdc branch October 5, 2022 09:16
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
cla-signed CLA has been signed enhancement New feature or request
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Relax sklearn version dependency caused by TDC TDC oracles based on API keys
2 participants