feat: accept --allow_resume for AlphaFold 3

README.md

@@ -693,8 +693,8 @@ batch_max_tokens: 0    # optional cap on summed residues per batch (0 = no cap)
   share a shape, whereas for AlphaFold3 the point is queueing once instead of once
   per fold.
 - For AlphaFold2 batches, `--allow_resume` is enabled automatically, so if a job is
-  interrupted a rerun skips folds whose outputs already exist (AlphaFold3 does not accept
-  that flag, so its batches recompute the unfinished folds on rerun).
+  interrupted a rerun skips folds whose outputs already exist (AlphaFold3 images from
+  2.11.0 resume by default as well, keeping finished folds and seeds).
 - Analysis and reports are unaffected — `alphajudge` still runs per fold (one
   `interfaces.csv` + `report.pdf` each) and the recursive summary still aggregates them.
 - **Trade-off:** a batch is one SLURM job, so a failure reruns the whole batch (minus the
@@ -861,7 +861,7 @@ You can pass backend CLI switches through `structure_inference_arguments`. Commo
 > against the selected `--fold_backend` and aborts the job with
 > `ValueError: The following flags are not supported by backend '<name>'` if you pass one the
 > backend does not accept. Only use flags from **your** backend's list below — e.g.
-> `--allow_resume` is AlphaFold2-only. A single wrong flag fails the job immediately
+> `--models_to_relax` is AlphaFold2-only. A single wrong flag fails the job immediately
 > (before any prediction runs).
 >
 > When **batching** (`batch_size > 1`) the workflow adds what each backend needs —

config/config.yaml

@@ -52,6 +52,9 @@ structure_inference_arguments:
   # 1.1-2x AlphaFold 3. Keep the quotes: YAML reads bare on/off as booleans.
   # README: "AlphaFold2 flags", "AlphaFold3 flags"
   # --fast_kernels: "auto"
+  # A rerun skips finished folds and resumes interrupted ones (AlphaFold3: images from
+  # 2.11.0). Set false to predict everything again.
+  # --allow_resume: false
 
 # SLURM only: replace "gpu" with your cluster's GPU partition. Several names can
 # be comma-separated. Desktop runs ignore these scheduler settings.

test/test_batch_inference_args.py

@@ -2,7 +2,8 @@
 
 Regression guard: ``run_structure_prediction.py`` hard-errors on a flag its backend does
 not accept (``ValueError: not supported by backend '<name>'``). Adding the wrong flag once
-broke ALL batched AlphaFold2 inference. ``--allow_resume`` is AlphaFold2-only;
+broke ALL batched AlphaFold2 inference. ``--allow_resume`` is added for AlphaFold2 only
+(AlphaFold3 resumes by default where it accepts the flag, from AlphaPulldown 2.11.0);
 ``--jax_compilation_cache_dir`` is accepted by both JAX backends (AlphaFold2 since
 AlphaPulldown 2.8.0). These tests pin each flag to the backends that accept it.
 
@@ -44,7 +45,8 @@ def test_af3_batch_gets_jax_cache_not_allow_resume():
         jax_cache_dir=_CACHE,
     )
     assert args["--jax_compilation_cache_dir"] == _CACHE
-    # the AF2-only flag must NOT be present for AF3 (it would ValueError at runtime)
+    # Not added for AF3: it resumes by default, and images up to AlphaPulldown 2.10.0
+    # reject the flag (ValueError at runtime).
     assert "--allow_resume" not in args
 
 

test/test_inference_command_line.py

@@ -145,7 +145,8 @@ def test_fast_kernels_and_cache_reach_every_inference_call(tmp_path, backend):
         assert flags["fast_kernels"] == "True", script
         assert flags["jax_compilation_cache_dir"] == str(cache), script
         assert flags["fold_backend"] == backend, script
-        # --allow_resume is added to AlphaFold 2 batches only; AlphaFold 3 rejects it.
+        # --allow_resume is added to AlphaFold 2 batches only: AlphaFold 3 resumes by
+        # default, and its images up to AlphaPulldown 2.10.0 reject the flag.
         assert ("allow_resume" in flags) == (backend == "alphafold2"), script
     assert job.index(_XLA_CACHES_EXPORT) < job.index("run_structure_prediction")
 

test/test_inference_flag_tables.py

@@ -24,8 +24,8 @@
 
 _COMMON = SourceFileLoader("common_flag_tables", str(COMMON_SMK)).load_module()
 
-# The AlphaPulldown the shipped default containers run (2.10.0).
-SHIPPED_ALPHAPULLDOWN_COMMIT = "6e7f98695f576cf7ec087dbaef39b1f39652054e"
+# The AlphaPulldown the tables come from: main after 2.10.0, where AF3 accepts --allow_resume.
+SHIPPED_ALPHAPULLDOWN_COMMIT = "228c5eed6c7066467e46b87fb3054cc2c2e73ae1"
 
 # Shaped like AlphaPulldown's inference_flags.py: named sets, unions, an annotated dict.
 _SOURCE = '''
@@ -197,6 +197,12 @@ def test_fast_kernels_is_valid_on_both_backends():
     assert _COMMON.unknown_inference_flags(args, "alphalink") == ["fast_kernels"]
 
 
+def test_allow_resume_is_valid_on_both_backends():
+    for backend in ("alphafold2", "alphafold3"):
+        args = {"--fold_backend": backend, "--allow_resume": False}
+        assert _COMMON.unknown_inference_flags(args, backend) == []
+
+
 def test_jax_compile_cache_is_valid_on_both_backends():
     for backend in ("alphafold2", "alphafold3"):
         args = {"--fold_backend": backend, "--jax_compilation_cache_dir": "/cache"}

test/test_unknown_inference_flags.py

@@ -26,8 +26,8 @@ def test_af2_flags_all_accepted():
 
 
 def test_af2_only_flag_flagged_on_af3():
-    args = {"--fold_backend": "alphafold3", "--allow_resume": "true"}
-    assert unknown_inference_flags(args, "alphafold3") == ["allow_resume"]
+    args = {"--fold_backend": "alphafold3", "--models_to_relax": "best"}
+    assert unknown_inference_flags(args, "alphafold3") == ["models_to_relax"]
 
 
 def test_af3_flags_all_accepted():
@@ -45,7 +45,7 @@ def test_alphalink_accepts_crosslinks_and_af2_flags():
 
 def test_leading_dashes_and_equals_are_stripped():
     # keys may arrive with or without dashes, or with an inline value
-    assert unknown_inference_flags({"allow_resume": "true"}, "alphafold3") == ["allow_resume"]
+    assert unknown_inference_flags({"num_cycle": 3}, "alphafold3") == ["num_cycle"]
     assert unknown_inference_flags({"--bogus=1": "x"}, "alphafold3") == ["bogus"]
 
 
@@ -55,14 +55,14 @@ def test_unknown_backend_stays_silent():
 
 
 def test_backend_name_case_insensitive():
-    assert unknown_inference_flags({"--allow_resume": "t"}, "AlphaFold3") == ["allow_resume"]
+    assert unknown_inference_flags({"--num_cycle": 3}, "AlphaFold3") == ["num_cycle"]
 
 
 def test_order_preserved_and_deduped():
-    args = {"--allow_resume": "t", "--models_to_relax": "best", "--allow_resume2": "t"}
+    args = {"--num_cycle": 3, "--models_to_relax": "best", "--num_cycle2": "t"}
     # only genuinely-unknown AF3 flags, in order
     out = unknown_inference_flags(args, "alphafold3")
-    assert out == ["allow_resume", "models_to_relax", "allow_resume2"]
+    assert out == ["num_cycle", "models_to_relax", "num_cycle2"]
 
 
 if __name__ == "__main__":

workflow/Snakefile

@@ -353,7 +353,7 @@ _structure_inference_args = batch_inference_args(
     jax_cache_dir=JAX_CACHE_DIR,
 )
 # Parse-time guard: run_structure_prediction.py aborts the inference job on the first
-# flag its backend does not accept (e.g. --allow_resume on AF3). Warn here -- on the
+# flag its backend does not accept (e.g. --models_to_relax on AF3). Warn here -- on the
 # head node, in seconds -- instead of failing deep in a Slurm job. Uses the RAW
 # --fold_backend (so alphalink's --crosslinks is not mis-flagged); a warning only,
 # since the container is the source of truth (see unknown_inference_flags).

workflow/rules/common.smk

@@ -818,8 +818,9 @@ def batch_inference_args(
     any it does not recognise (``ValueError: not supported by backend '<name>'``), so a
     flag must ONLY be added for the backend(s) that accept it:
 
-    * ``--allow_resume`` (AlphaFold2 only, ``batch_size > 1``): a crashed batch re-runs
-      all its folds, so resume the ones already done. AlphaFold3 rejects it.
+    * ``--allow_resume`` (AlphaFold2, ``batch_size > 1``): a crashed batch re-runs all
+      its folds, so resume the ones already done. Not added for AlphaFold3: its images
+      from AlphaPulldown 2.11.0 resume by default, and 2.10.0 and older reject the flag.
     * ``--jax_compilation_cache_dir`` (AlphaFold2 and AlphaFold3, every batch size): one
       on-disk JAX compile cache shared by every inference process. Without it every
       process compiles its models from scratch (AlphaFold3: once per token bucket, and
@@ -913,7 +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@6e7f98695f576cf7ec087dbaef39b1f39652054e
+# Source: KosinskiLab/AlphaPulldown@228c5eed6c7066467e46b87fb3054cc2c2e73ae1
 #         alphapulldown/prediction/inference_flags.py, FLAGS_BY_BACKEND
 ALLOWED_INFERENCE_FLAGS = {
     "alphafold2": frozenset({
@@ -957,6 +958,7 @@ ALLOWED_INFERENCE_FLAGS = {
         "use_gpu_relax",
     }),
     "alphafold3": frozenset({
+        "allow_resume",
         "buckets",
         "convert_to_modelcif",
         "data_directory",