debugging singularity tests

Author: tclose

pydra/engine/tests/test_environments.py

@@ -144,10 +144,10 @@ def newcache(x):
 
     with Submitter(cache_dir=newcache("shelly_sub"), environment=sing) as sub:
         results = sub(shelly)
-    assert outputs_dict == attrs_values(results.outputs)
+    assert drop_stderr(outputs_dict) == drop_stderr(attrs_values(results.outputs))
 
     outputs = shelly(environment=sing, cache_dir=newcache("shelly_call"))
-    assert outputs_dict == attrs_values(outputs)
+    assert drop_stderr(outputs_dict) == drop_stderr(attrs_values(outputs))
 
 
 @no_win
@@ -170,7 +170,9 @@ def newcache(x):
     assert shelly.cmdline == cmd
     outputs_dict = sing.execute(shelly_job)
 
-    with Submitter(worker=plugin, cache_dir=newcache("shelly_sub")) as sub:
+    with Submitter(
+        worker=plugin, environment=sing, cache_dir=newcache("shelly_sub")
+    ) as sub:
         results = sub(shelly)
 
     outputs = shelly(environment=sing, cache_dir=newcache("shelly_call"))

pydra/engine/tests/test_singularity.py

@@ -46,7 +46,8 @@ def test_singularity_2_nosubm(tmp_path):
     assert singu.cmdline == " ".join(cmd)
 
     outputs = singu(
-        Singularity(image=image),
+        environment=Singularity(image=image),
+        cache_dir=tmp_path,
     )
     assert outputs.stdout.strip() == " ".join(cmd[1:])
     assert outputs.return_code == 0
@@ -379,7 +380,7 @@ def test_singularity_cmd_inputspec_copyfile_1(plugin, tmp_path):
                 position=1,
                 argstr="",
                 help="orig file",
-                copyfile=True,
+                copy_mode=File.CopyMode.copy,
             ),
         ],
         outputs=[