switch command if singularity >= 3.10 or apptainer >=1.1

Author: sameeul

cwltool/singularity.py

@@ -74,6 +74,14 @@ def is_apptainer_1_or_newer() -> bool:
         return False
     return v[0][0] >= 1
 
+def is_apptainer_1_1_or_newer() -> bool:
+    """
+    Check if apptainer singularity distribution is version 1.1 or higher.
+    """
+    v = get_version()
+    if v[1] != "apptainer":
+        return False
+    return v[0][0] >= 1 and v[0][1] >= 1
 
 def is_version_2_6() -> bool:
     """
@@ -118,6 +126,10 @@ def is_version_3_9_or_newer() -> bool:
     v = get_version()
     return v[0][0] >= 4 or (v[0][0] == 3 and v[0][1] >= 9)
 
+def is_version_3_10_or_newer() -> bool:
+    """Detect if Singularity v3.10+ is available."""
+    v = get_version()
+    return v[0][0] >= 4 or (v[0][0] == 3 and v[0][1] >= 10)
 
 def _normalize_image_id(string: str) -> str:
     return string.replace("/", "_") + ".img"
@@ -467,11 +479,17 @@ def create_runtime(
         runtime = [
             "singularity",
             "--quiet",
-            "run",
             "--contain",
             "--ipc",
             "--cleanenv",
         ]
+
+        if is_apptainer_1_1_or_newer() or is_version_3_10_or_newer():
+            runtime.append("run")
+            runtime.append("--no-eval")
+        else:
+            runtime.append("exec")
+            
         if singularity_supports_userns():
             runtime.append("--userns")
         else:

tests/test_environment.py

@@ -149,7 +149,7 @@ def PWD(v: str, env: Env) -> bool:
         if vminor == 5:
             sing_vars["SINGULARITY_INIT"] = "1"
         elif vminor > 5:
-            sing_vars["SINGULARITY_COMMAND"] = "run"
+            sing_vars["SINGULARITY_COMMAND"] = "exec"
             if vminor >= 7:
                 if vminor > 9:
                     sing_vars["SINGULARITY_BIND"] = ""
@@ -159,6 +159,8 @@ def BIND(v: str, env: Env) -> bool:
                         return v.startswith(tmp_prefix) and v.endswith(":/tmp")
 
                     sing_vars["SINGULARITY_BIND"] = BIND
+        if vminor >= 10:
+            sing_vars["SINGULARITY_COMMAND"] = "run"
 
         result.update(sing_vars)