fix + tests: AF3 fold without ranked samples; cover the scenarios the suites missed

alphapulldown/folding_backend/alphafold3_outputs.py

@@ -135,11 +135,16 @@ def write_seed_outputs(
 
 def write_fold_outputs(output_dir: os.PathLike[str] | str, job_name: str) -> None:
     """Copy the best ranked sample under the job name, with the terms of use: the same
-    bytes AlphaFold 3 writes there, also for samples of an interrupted earlier run."""
+    bytes AlphaFold 3 writes there, also for samples of an interrupted earlier run.
+
+    Without ranked samples this raises rather than returns: the fold has no model, and
+    post-processing it to the end would record it complete for ``--allow_resume`` to skip.
+    """
     best = af3_best_sample_dir(output_dir)
     if best is None:
-        logging.warning(f'No ranked samples in {output_dir}; writing no best model.')
-        return
+        raise FileNotFoundError(
+            f'No ranked samples in {output_dir}: no model to write under {job_name}.'
+        )
     for name in _SAMPLE_OUTPUTS:
         with open(os.path.join(output_dir, best, name), 'rb') as source, open_atomic(
             os.path.join(output_dir, f'{job_name}_{name}'), 'wb'

test/unit/test_alphafold2_backend_helpers.py

@@ -2105,3 +2105,14 @@ def test_af2_predict_reports_an_option_no_backend_takes(af2_backend_module):
     assert list(predict(**common, num_diffusion_samples=5, crosslinks=None)) == []
     with pytest.raises(ValueError, match="debug_msa"):
         list(predict(**common, debug_msa=True))
+
+
+def test_an_unreadable_json_left_by_an_older_version_is_ignored(
+    af2_backend_module, tmp_path, caplog
+):
+    # Truncated by a run killed while writing it, before writes were atomic.
+    path = tmp_path / "timings.json"
+    path.write_text('{"predict_and_compile_model_1": 12.', encoding="utf-8")
+
+    assert af2_backend_module._read_from_json_if_exists(str(path)) == {}
+    assert "Ignoring unreadable" in caplog.text