From b304b663d7902108747a63c2bb5253de37bcfa41 Mon Sep 17 00:00:00 2001 From: FranCDoc Date: Wed, 10 Jun 2026 22:52:39 -0300 Subject: [PATCH 1/2] docs: clarify updating an existing AlphaFold checkout The update instructions currently mention `git fetch origin main`, but `git fetch` only downloads updates and does not update the working tree. Use `git checkout main` followed by `git pull --ff-only origin main` so users explicitly update their local checkout without creating a merge commit. Fixes #654. --- README.md | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index e0d1aa10..8735a80a 100644 --- a/README.md +++ b/README.md @@ -268,8 +268,15 @@ update that will be significantly faster but will require a bit more work. Make sure you follow these steps in the exact order they are listed below: 1. **Update the code.** - * Go to the directory with the cloned AlphaFold repository and run `git - fetch origin main` to get all code updates. + * Go to the directory with the cloned AlphaFold repository and run: + + ```bash + git checkout main + git pull --ff-only origin main + ``` + + This updates the local checkout to the latest `main` branch without + creating a merge commit. 1. **Update the UniProt, UniRef, MGnify and PDB seqres databases.** * Remove `/uniprot`. * Run `scripts/download_uniprot.sh `. From 0601ba8405bb3a6e9df5b24a4f4e9508b1345714 Mon Sep 17 00:00:00 2001 From: FranCDoc Date: Wed, 10 Jun 2026 23:12:59 -0300 Subject: [PATCH 2/2] chore: rerun checks