From f77f44165ef59bba0685f176d03ee4b02e793967 Mon Sep 17 00:00:00 2001 From: Jack Dent Date: Fri, 6 Dec 2024 11:09:43 -0800 Subject: [PATCH] Bump version to 0.5.1 (#223) --- README.md | 4 ++-- chai_lab/__init__.py | 2 +- chai_lab/data/dataset/msas/colabfold.py | 7 +++++-- 3 files changed, 8 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 1b9f2e1..ebc388e 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ For more information on the model's performance and capabilities, see our [techn ```shell # version on pypi: -pip install chai_lab==0.5.0 +pip install chai_lab==0.5.1 # newest available version (updates daily to test features that weren't released yet): pip install git+https://github.com/chaidiscovery/chai-lab.git @@ -123,7 +123,7 @@ Devcontainers work on local Linux setup, and on remote machines over an SSH conn Since this is an initial release, we expect to make some breaking changes to the API and are not guaranteeing backwards compatibility. We recommend pinning the current version in your requirements, i.e.: ``` -chai_lab==0.5.0 +chai_lab==0.5.1 ``` ## Citations diff --git a/chai_lab/__init__.py b/chai_lab/__init__.py index 2487274..e0b8595 100644 --- a/chai_lab/__init__.py +++ b/chai_lab/__init__.py @@ -2,4 +2,4 @@ # Licensed under the Apache License, Version 2.0. # See the LICENSE file for details. -__version__ = "0.5.0" +__version__ = "0.5.1" diff --git a/chai_lab/data/dataset/msas/colabfold.py b/chai_lab/data/dataset/msas/colabfold.py index c5c3142..266b942 100644 --- a/chai_lab/data/dataset/msas/colabfold.py +++ b/chai_lab/data/dataset/msas/colabfold.py @@ -390,6 +390,9 @@ def generate_colabfold_msas( # Generate MSAs for each protein chain logger.info(f"Running MSA generation for {len(protein_seqs)} protein sequences") + # Identify ourselves to the ColabFold server + user_agent = f"chai-lab/{__version__} feedback@chaidiscovery.com" + # In paired mode, mmseqs2 returns paired a3ms where all a3ms have the same number of rows # and each row is already paired to have the same species. As such, we insert pairing key # as the i-th index of the sequence so long as it isn't a padding sequence (all -) @@ -400,7 +403,7 @@ def generate_colabfold_msas( mmseqs_paired_dir, use_pairing=True, host_url=msa_server_url, - user_agent=f"chai-lab/{__version__} feedback@chaidiscovery.com", + user_agent=user_agent, ) else: # If we only have a single protein chain, there are no paired MSAs by definition @@ -413,7 +416,7 @@ def generate_colabfold_msas( mmseqs_dir, use_pairing=False, host_url=msa_server_url, - user_agent=f"chai-lab/{__version__} feedback@chaidiscovery.com", + user_agent=user_agent, ) # Process the MSAs into our internal format