debugged singularity tests

Author: tclose

pydra/engine/environments.py

@@ -147,6 +147,10 @@ def get_bindings(
                     if isinstance(fileset, os.PathLike)
                     else tuple(env_path / rel for rel in fileset.relative_fspaths)
                 )
+
+        # Add the cache directory to the list of mounts
+        bindings[task.cache_dir] = (f"{self.root}/{task.cache_dir}", "rw")
+
         return bindings, input_updates
 
 
@@ -158,9 +162,6 @@ def execute(self, task: "Task[ShellDef]") -> dict[str, ty.Any]:
         # mounting all input locations
         mounts, input_updates = self.get_bindings(task=task, root=self.root)
 
-        # add the cache directory to the list of mounts
-        mounts[task.cache_dir] = (f"{self.root}{task.cache_dir}", "rw")
-
         docker_args = [
             "docker",
             "run",
@@ -202,8 +203,6 @@ def execute(self, task: "Task[ShellDef]") -> dict[str, ty.Any]:
         singularity_args = [
             "singularity",
             "exec",
-            "-B",
-            self.bind(task.cache_dir, "rw"),
             *self.xargs,
         ]
         singularity_args.extend(

pydra/engine/helpers_file.py

@@ -269,7 +269,7 @@ def _single_template_formatting(
     # inp_fields = set(re.findall(r"{(\w+)(?:\.\w+)?(?::[0-9.]+f)?}", template))
 
     if len(inp_fields) == 0:
-        return template
+        return Path(template)
 
     val_dict = {}
     file_template = None

pydra/engine/tests/test_environments.py

@@ -131,7 +131,7 @@ def newcache(x):
         makedir(tmp_path, x)
 
     cmd = "whoami"
-    sing = Singularity(image="docker://alpine")
+    sing = Singularity(image="docker://alpine", xargs=["--fakeroot"])
     Shelly = shell.define(cmd)
     shelly = Shelly()
     shelly_job = Task(
@@ -159,7 +159,7 @@ def newcache(x):
         makedir(tmp_path, x)
 
     cmd = "whoami"
-    sing = Singularity(image="docker://alpine")
+    sing = Singularity(image="docker://alpine", xargs=["--fakeroot"])
     Shelly = shell.define(cmd)
     shelly = Shelly()
     shelly_job = Task(

pydra/engine/tests/test_singularity.py

@@ -70,6 +70,7 @@ def test_singularity_2(plugin, tmp_path):
         worker=plugin, environment=Singularity(image=image), cache_dir=tmp_path
     ) as sub:
         res = sub(singu)
+    assert not res.errored, "\n".join(res.errors["error message"])
     assert res.outputs.stdout.strip() == " ".join(cmd[1:])
     assert res.outputs.return_code == 0
 
@@ -110,11 +111,13 @@ def test_singularity_st_1(plugin, tmp_path):
     singu = Singu().split("executable", executable=cmd)
 
     outputs = singu(
-        plugin=plugin, environment=Singularity(image=image), cache_dir=tmp_path
+        plugin=plugin,
+        environment=Singularity(image=image, xargs=["--fakeroot"]),
+        cache_dir=tmp_path,
     )
-    assert outputs.stdout[0] == "root"
-    assert outputs.stdout[1] == "/mnt/pydra"
-    assert outputs.stdout[2] == ""
+    assert outputs.stdout[0].strip() == "root"
+    assert "/mnt/pydra" in outputs.stdout[1]
+    assert outputs.stdout[2].strip() == "_task.pklz"
     assert outputs.return_code == [0, 0, 0]
 
 
@@ -161,11 +164,10 @@ def test_singularity_outputspec_1(plugin, tmp_path):
     )
     singu = Singu()
 
-    with Submitter(
-        worker=plugin, environment=Singularity(image=image), cache_dir=tmp_path
-    ) as sub:
+    with Submitter(environment=Singularity(image=image), cache_dir=tmp_path) as sub:
         res = sub(singu)
 
+    assert not res.errored, "\n".join(res.errors["error message"])
     assert res.outputs.stdout == ""
     assert res.outputs.newfile.fspath.exists()
 
@@ -386,7 +388,7 @@ class Singu(ShellDef["Singu.Outputs"]):
 
         class Outputs(ShellOutputs):
             out_file: File = shell.outarg(
-                path_template="{orig_file}",
+                path_template="{orig_file}.txt",  # FIXME: Shouldn't have to specify the extension
                 help="output file",
             )
 
@@ -396,7 +398,7 @@ class Outputs(ShellOutputs):
     assert outputs.stdout == ""
     assert outputs.out_file.fspath.exists()
     # the file is  copied, and than it is changed in place
-    assert outputs.out_file.fspath.parent == singu.output_dir
+    assert outputs.out_file.fspath.parent.parent == tmp_path
     with open(outputs.out_file) as f:
         assert "hi from pydra\n" == f.read()
     # the original file is unchanged