release: 2.11.0

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

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.

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 <valentin.maurer@embl-hamburg.de>
 

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"

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 = '''

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 <alphapulldown@embl-hamburg.de>
 """

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 <valentin.maurer@embl-hamburg.de>
 """
@@ -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({