BFG Repo-Cleaner

If you did not take with your .gitignore or just used git add . you might have by accident committed large files. This might lead to an error like

remote: error: See https://gh.io/lfs for more information.
remote: error: File reports/gemini-pro/.langchain.db is 123.01 MB; this exceeds GitHub's file size limit of 100.00 MB
remote: error: GH001: Large files detected. You may want to try Git Large File Storage - https://git-lfs.github.com.
To github.com:lamalab-org/chem-bench.git
 ! [remote rejected]     kjappelbaum/issue258 -> kjappelbaum/issue258 (pre-receive hook declined)
error: failed to push some refs to 'github.com:lamalab-org/chem-bench.git'

To fix this, you need to remove the large files. A convenient tool for doing this is BFG.

Once you download the file you can run it using something like

java -jar ~/Downloads/bfg-1.14.0.jar --strip-blobs-bigger-than 100M --no-blob-protection

to remove large files.

Note that this here uses --no-blob-protection as BFG defaults to not touching the last commit.

After the BFG run, it will prompt you to run something like

git reflog expire --expire=now --all && git gc --prune=now --aggressive

Guo, Jeff, and Philippe Schwaller. 2024. “It Takes Two to Tango: Directly Optimizing for Constrained Synthesizability in Generative Molecular Design.” arXiv. https://doi.org/10.48550/ARXIV.2410.11527.

Landrum, Gregory A., Jessica Braun, Paul Katzberger, Marc T. Lehner, and Sereina Riniker. 2024. “Lwreg: A Lightweight System for Chemical Registration and Data Storage.” Journal of Chemical Information and Modeling 64 (16): 6247–52. https://doi.org/10.1021/acs.jcim.4c01133.

Orsi, Markus, and Jean-Louis Reymond. 2024. “One Chiral Fingerprint to Find Them All.” Journal of Cheminformatics 16 (1): 53.