From 9ab143dc6c6bc3c409bc720abf930b1556e0e283 Mon Sep 17 00:00:00 2001 From: Dima Molodenskiy Date: Wed, 14 Oct 2026 12:15:44 +0200 Subject: [PATCH] release: 2.11.0 - Default prediction images alphafold3:2.11.0 / alphafold2:2.11.0, the first whose AlphaFold 3 accepts --allow_resume (and resumes by default). - Inference flag tables regenerated from AlphaPulldown 2.11.0 (50b508dd), the release the default images run; only the recorded source changes. - Installer and README pinned to workflow 2.11.0. - Copyright headers say 2026. Co-Authored-By: Claude Opus 5.5 --- README.md | 10 +++++----- config/config.yaml | 4 ++-- config/split_fasta.py | 2 +- install.sh | 4 ++-- test/test_inference_flag_tables.py | 4 ++-- workflow/Snakefile | 2 +- workflow/rules/common.smk | 4 ++-- 7 files changed, 15 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index a2c81a9..b4e9230 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ AlphaPulldownSnakemake provides a convenient way to run AlphaPulldown using a Sn ### Quick install (recommended) ```bash -curl -O https://raw.githubusercontent.com/KosinskiLab/AlphaPulldownSnakemake/2.10.0/install.sh +curl -O https://raw.githubusercontent.com/KosinskiLab/AlphaPulldownSnakemake/2.11.0/install.sh bash install.sh conda activate snake cd AlphaPulldownSnakemake @@ -25,7 +25,7 @@ Useful options: | Option | Meaning | | --- | --- | | `-d, --dest DIR` | working directory to deploy into (default `AlphaPulldownSnakemake`) | -| `-v, --version TAG` | workflow version to deploy (default `2.10.0`) | +| `-v, --version TAG` | workflow version to deploy (default `2.11.0`) | | `-i, --image-dir DIR` | shared container image directory | | `-n, --env-name NAME` | conda environment name (default `snake`) | | `--no-pull` | skip container pre-fetch (Snakemake will fetch on first run) | @@ -43,7 +43,7 @@ Create and activate the conda environment: ```bash conda env create \ -n snake \ - -f https://raw.githubusercontent.com/KosinskiLab/AlphaPulldownSnakemake/2.10.0/workflow/envs/alphapulldown.yaml + -f https://raw.githubusercontent.com/KosinskiLab/AlphaPulldownSnakemake/2.11.0/workflow/envs/alphapulldown.yaml conda activate snake ``` @@ -55,7 +55,7 @@ Then deploy the workflow into a new processing directory for your project: snakedeploy deploy-workflow \ https://github.com/KosinskiLab/AlphaPulldownSnakemake \ AlphaPulldownSnakemake \ - --tag 2.10.0 + --tag 2.11.0 cd AlphaPulldownSnakemake ``` @@ -809,7 +809,7 @@ require `pdb_seqres`, and every search requires `mmcif`. Update the relevant ID rebuilding a database, even at the same path; this invalidates finalized features. The native MSA arguments do not reach finalization because this stage replaces that search. Use a matching prediction image, such as -`docker://kosinskilab/alphafold2:2.10.0`, for AlphaFold 2. AlphaFold 2 finalization is +`docker://kosinskilab/alphafold2:2.11.0`, for AlphaFold 2. AlphaFold 2 finalization is heavier than AlphaFold 3's because template featurization dominates it — median ~1 GB and 2 min, but up to 19 GB and 90 min, set by which structures the templates come from rather than by length — so its defaults request 16 GB (times the safety factor) and 60 min. Against native diff --git a/config/config.yaml b/config/config.yaml index 3f7780e..92fa550 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -26,9 +26,9 @@ databases_directory: /path/to/alphafold/databases backend_weights_directory: /path/to/alphafold3/weights/ # These defaults run AlphaFold 3. To use AlphaFold 2, change the image to -# alphafold2:2.10.0, both backend flags below to alphafold2, and the paths above. +# alphafold2:2.11.0, both backend flags below to alphafold2, and the paths above. # A local .sif image also works. README: "Changing folding backends" -prediction_container: "docker://kosinskilab/alphafold3:2.10.0" +prediction_container: "docker://kosinskilab/alphafold3:2.11.0" # Features are the sequence alignments and templates used for prediction. # Keep any additional feature flags inside this block. diff --git a/config/split_fasta.py b/config/split_fasta.py index e8ef3b9..fb0bce7 100755 --- a/config/split_fasta.py +++ b/config/split_fasta.py @@ -1,7 +1,7 @@ #!python3 """ Utility to split multi-line fasta into individual files for use in pulldowns. - Copyright (c) 2025 European Molecular Biology Laboratory + Copyright (c) 2026 European Molecular Biology Laboratory Author: Valentin Maurer diff --git a/install.sh b/install.sh index fca5599..a0f0f1d 100755 --- a/install.sh +++ b/install.sh @@ -8,13 +8,13 @@ # # ./install.sh # deploy into ./AlphaPulldownSnakemake # ./install.sh -d my_project # deploy into ./my_project -# ./install.sh -v 2.10.0 # pin a workflow version +# ./install.sh -v 2.11.0 # pin a workflow version # ./install.sh -i /path/to/shared/images # shared image directory # ./install.sh --no-pull # skip container pre-fetch # set -euo pipefail -VERSION="2.10.0" +VERSION="2.11.0" DEST="AlphaPulldownSnakemake" ENV_NAME="snake" IMAGE_DIR_DEFAULT="$HOME/.apptainer/snakemake-images" diff --git a/test/test_inference_flag_tables.py b/test/test_inference_flag_tables.py index e1aac59..7bec36d 100644 --- a/test/test_inference_flag_tables.py +++ b/test/test_inference_flag_tables.py @@ -24,8 +24,8 @@ _COMMON = SourceFileLoader("common_flag_tables", str(COMMON_SMK)).load_module() -# The AlphaPulldown the tables come from: main after 2.10.0, where AF3 accepts --allow_resume. -SHIPPED_ALPHAPULLDOWN_COMMIT = "228c5eed6c7066467e46b87fb3054cc2c2e73ae1" +# The AlphaPulldown the shipped default containers run (2.11.0). +SHIPPED_ALPHAPULLDOWN_COMMIT = "50b508dd235e8c551c45de0c17a90607ea8a0c5b" # Shaped like AlphaPulldown's inference_flags.py: named sets, unions, an annotated dict. _SOURCE = ''' diff --git a/workflow/Snakefile b/workflow/Snakefile index 0a74a3b..43e8930 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -1,6 +1,6 @@ """ Snakemake pipeline for automated structure prediction using various backends. - Copyright (c) 2025 European Molecular Biology Laboratory + Copyright (c) 2026 European Molecular Biology Laboratory Authors: Kosinski Lab """ diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index 1da795f..d20821e 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -1,6 +1,6 @@ """ Snakemake I/O and utility functions - Copyright (c) 2024 European Molecular Biology Laboratory + Copyright (c) 2026 European Molecular Biology Laboratory Authors: Valentin Maurer """ @@ -914,7 +914,7 @@ def prediction_batch_id(folds: Iterable[str]) -> str: # to update for a new release; CI regenerates from the recorded commit and fails on any # difference. # BEGIN GENERATED: inference flags (tools/generate_inference_flag_tables.py; do not edit by hand) -# Source: KosinskiLab/AlphaPulldown@228c5eed6c7066467e46b87fb3054cc2c2e73ae1 +# Source: KosinskiLab/AlphaPulldown@50b508dd235e8c551c45de0c17a90607ea8a0c5b # alphapulldown/prediction/inference_flags.py, FLAGS_BY_BACKEND ALLOWED_INFERENCE_FLAGS = { "alphafold2": frozenset({