removing option to provide bindings as an input to container tasks

Author: djarecka

pydra/engine/task.py

@@ -210,25 +210,23 @@ def __new__(cls, container_info=None, *args, **kwargs):
         if not container_info:
             return super().__new__(cls)
 
-        if len(container_info) == 3:
-            type_cont, image, bind = container_info
-        elif len(container_info) == 2:
-            type_cont, image, bind = container_info + (None,)
+        if len(container_info) == 2:
+            type_cont, image = container_info
         else:
             raise Exception(
-                f"container_info has to have 2 or 3 elements, but {container_info} provided"
+                f"container_info has to have 2 elements, but {container_info} provided"
             )
 
         if type_cont == "docker":
             # changing base class of spec if user defined
             if "input_spec" in kwargs:
                 kwargs["input_spec"].bases = (DockerSpec,)
-            return DockerTask(image=image, bindings=bind, *args, **kwargs)
+            return DockerTask(image=image, *args, **kwargs)
         elif type_cont == "singularity":
             # changing base class of spec if user defined
             if "input_spec" in kwargs:
                 kwargs["input_spec"].bases = (SingularitySpec,)
-            return SingularityTask(image=image, bindings=bind, *args, **kwargs)
+            return SingularityTask(image=image, *args, **kwargs)
         else:
             raise Exception(
                 f"first element of container_info has to be "
@@ -331,7 +329,7 @@ def command_args(self):
         self._positions_provided = []
         for field in attr_fields(
             self.inputs,
-            exclude_names=("container", "image", "container_xargs", "bindings"),
+            exclude_names=("container", "image", "container_xargs"),
         ):
             name, meta = field.name, field.metadata
             if (
@@ -622,6 +620,9 @@ def bind_paths(self):
         if self.inputs.bindings is None:
             self.inputs.bindings = []
         output_dir = self.output_dir
+        # This part has to stay for now!!!
+        # I'm creating self.inputs.bindings based on the input in TaskBase._run
+        # in self.inputs.check_fields_input_spec() (see specs.py)
         for binding in self.inputs.bindings:
             binding = list(binding)
             if len(binding) == 3:
@@ -702,7 +703,6 @@ def __init__(
         if not self.init:
             if input_spec is None:
                 input_spec = SpecInfo(name="Inputs", fields=[], bases=(DockerSpec,))
-
             super().__init__(
                 name=name,
                 input_spec=input_spec,

pydra/engine/tests/test_dockertask.py

@@ -80,7 +80,7 @@ def test_docker_1_dockerflag_exception(plugin):
         shocky = ShellCommandTask(
             name="shocky", executable=cmd, container_info=("docker")
         )
-    assert "container_info has to have 2 or 3 elements" in str(excinfo.value)
+    assert "container_info has to have 2 elements" in str(excinfo.value)
 
 
 @no_win
@@ -203,6 +203,7 @@ def test_docker_2a(plugin):
 
 @no_win
 @need_docker
+@pytest.mark.skip(reason="we probably don't want to support bindings as an input")
 def test_docker_3(plugin, tmpdir):
     """a simple command in container with bindings,
     creating directory in tmp dir and checking if it is in the container
@@ -226,6 +227,7 @@ def test_docker_3(plugin, tmpdir):
 
 @no_win
 @need_docker
+@pytest.mark.skip(reason="we probably don't want to support bindings as an input")
 def test_docker_3_dockerflag(plugin, tmpdir):
     """a simple command in container with bindings,
     creating directory in tmp dir and checking if it is in the container
@@ -252,6 +254,7 @@ def test_docker_3_dockerflag(plugin, tmpdir):
 
 @no_win
 @need_docker
+@pytest.mark.skip(reason="we probably don't want to support bindings as an input")
 def test_docker_3_dockerflagbind(plugin, tmpdir):
     """a simple command in container with bindings,
     creating directory in tmp dir and checking if it is in the container
@@ -278,6 +281,7 @@ def test_docker_3_dockerflagbind(plugin, tmpdir):
 
 @no_win
 @need_docker
+@pytest.mark.skip(reason="we probably don't want to support bindings as an input")
 def test_docker_4(plugin, tmpdir):
     """task reads the file that is bounded to the container
     specifying bindings,
@@ -304,6 +308,7 @@ def test_docker_4(plugin, tmpdir):
 
 @no_win
 @need_docker
+@pytest.mark.skip(reason="we probably don't want to support bindings as an input")
 def test_docker_4_dockerflag(plugin, tmpdir):
     """task reads the file that is bounded to the container
     specifying bindings,
@@ -439,6 +444,7 @@ def test_docker_st_4(plugin):
 
 @no_win
 @need_docker
+@pytest.mark.skip(reason="we probably don't want to support bindings as an input")
 def test_wf_docker_1(plugin, tmpdir):
     """a workflow with two connected task
     the first one read the file that is bounded to the container,
@@ -483,6 +489,7 @@ def test_wf_docker_1(plugin, tmpdir):
 
 @no_win
 @need_docker
+@pytest.mark.skip(reason="we probably don't want to support bindings as an input")
 def test_wf_docker_1_dockerflag(plugin, tmpdir):
     """a workflow with two connected task
     the first one read the file that is bounded to the container,
@@ -523,6 +530,7 @@ def test_wf_docker_1_dockerflag(plugin, tmpdir):
 
 @no_win
 @need_docker
+@pytest.mark.skip(reason="we probably don't want to support bindings as an input")
 def test_wf_docker_2pre(plugin, tmpdir):
     """a workflow with two connected task that run python scripts
     the first one creates a text file and the second one reads the file
@@ -544,6 +552,7 @@ def test_wf_docker_2pre(plugin, tmpdir):
 
 @no_win
 @need_docker
+@pytest.mark.skip(reason="we probably don't want to support bindings as an input")
 def test_wf_docker_2(plugin, tmpdir):
     """a workflow with two connected task that run python scripts
     the first one creates a text file and the second one reads the file
@@ -584,6 +593,7 @@ def test_wf_docker_2(plugin, tmpdir):
 
 @no_win
 @need_docker
+@pytest.mark.skip(reason="we probably don't want to support bindings as an input")
 def test_wf_docker_3(plugin, tmpdir):
     """a workflow with two connected task
     the first one read the file that contains the name of the image,
@@ -736,6 +746,7 @@ def test_docker_inputspec_1a(tmpdir):
 
 @no_win
 @need_docker
+@pytest.mark.skip(reason="we probably don't want to support bindings as an input")
 def test_docker_inputspec_1b(tmpdir):
     """a simple customized input spec for docker task
     instead of using automatic binding I provide the bindings

pydra/engine/tests/test_singularity.py

@@ -130,6 +130,7 @@ def test_singularity_2a(plugin, tmpdir):
 
 
 @need_singularity
+@pytest.mark.skip(reason="we probably don't want to support bindings as an input")
 def test_singularity_3(plugin, tmpdir):
     """a simple command in container with bindings,
     creating directory in tmp dir and checking if it is in the container
@@ -151,6 +152,7 @@ def test_singularity_3(plugin, tmpdir):
 
 
 @need_singularity
+@pytest.mark.skip(reason="we probably don't want to support bindings as an input")
 def test_singularity_3_singuflag(plugin, tmpdir):
     """a simple command in container with bindings,
     creating directory in tmp dir and checking if it is in the container
@@ -178,6 +180,7 @@ def test_singularity_3_singuflag(plugin, tmpdir):
 
 
 @need_singularity
+@pytest.mark.skip(reason="we probably don't want to support bindings as an input")
 def test_singularity_3_singuflagbind(plugin, tmpdir):
     """a simple command in container with bindings,
     creating directory in tmp dir and checking if it is in the container
@@ -279,6 +282,7 @@ def test_singularity_st_4(tmpdir, n):
 
 
 @need_singularity
+@pytest.mark.skip(reason="we probably don't want to support bindings as an input")
 def test_wf_singularity_1(plugin, tmpdir):
     """a workflow with two connected task
     the first one read the file that is bounded to the container,
@@ -320,6 +324,7 @@ def test_wf_singularity_1(plugin, tmpdir):
 
 @need_docker
 @need_singularity
+@pytest.mark.skip(reason="we probably don't want to support bindings as an input")
 def test_wf_singularity_1a(plugin, tmpdir):
     """a workflow with two connected task - using both containers: Docker and Singul.
     the first one read the file that is bounded to the container,