[rfc]changing Task initialization syntax closes #295

pydra/engine/core.py

@@ -125,7 +125,6 @@ def __init__(
 
         if TaskBase._etelemetry_version_data is None:
             TaskBase._etelemetry_version_data = check_latest_version()
-
         # raise error if name is same as of attributes
         if name in dir(self):
             raise ValueError("Cannot use names of attributes or methods as task name")
@@ -166,7 +165,6 @@ def __init__(
             self.inputs = attr.evolve(self.inputs, **inputs)
             self.inputs.check_metadata()
             self.state_inputs = inputs
-
         self.audit = Audit(
             audit_flags=audit_flags,
             messengers=messengers,
@@ -664,6 +662,7 @@ class Workflow(TaskBase):
     def __init__(
         self,
         name,
+        inputs: ty.Optional[ty.Union[ty.Text, File, ty.Dict]] = None,
         audit_flags: AuditFlag = AuditFlag.NONE,
         cache_dir=None,
         cache_locations=None,
@@ -730,7 +729,7 @@ def __init__(
 
         super(Workflow, self).__init__(
             name=name,
-            inputs=kwargs,
+            inputs=inputs,
             cache_dir=cache_dir,
             cache_locations=cache_locations,
             audit_flags=audit_flags,

pydra/engine/specs.py

@@ -432,7 +432,7 @@ def _file_check(self, field):
             pass
         # if this is a local path, checking if the path exists
         elif file.exists():
-            if self.bindings is None:
+            if self.bindings in [None, attr.NOTHING]:
                 self.bindings = []
             self.bindings.append((file.parent, f"/pydra_inp_{field.name}", "ro"))
         else:

pydra/engine/task.py

@@ -67,6 +67,7 @@ class FunctionTask(TaskBase):
     def __init__(
         self,
         func: ty.Callable,
+        inputs: ty.Optional[ty.Union[ty.Text, File, ty.Dict]] = None,
         audit_flags: AuditFlag = AuditFlag.NONE,
         cache_dir=None,
         cache_locations=None,
@@ -138,7 +139,7 @@ def __init__(
             name = func.__name__
         super(FunctionTask, self).__init__(
             name,
-            inputs=kwargs,
+            inputs=inputs,
             audit_flags=audit_flags,
             messengers=messengers,
             messenger_args=messenger_args,
@@ -244,6 +245,9 @@ def __new__(cls, container_info=None, *args, **kwargs):
 
     def __init__(
         self,
+        inputs: ty.Optional[ty.Union[ty.Text, File, ty.Dict]] = None,
+        executable: ty.Optional[ty.Union[ty.List, str]] = None,
+        args: ty.Optional[ty.Union[ty.List, str, File]] = None,
         audit_flags: AuditFlag = AuditFlag.NONE,
         cache_dir=None,
         input_spec: ty.Optional[SpecInfo] = None,
@@ -283,12 +287,21 @@ def __init__(
         self.input_spec = input_spec
         if output_spec is None:
             output_spec = SpecInfo(name="Output", fields=[], bases=(ShellOutSpec,))
+        if inputs is None:
+            inputs = {}
+        # adding executable and args to inputs
+        inputs["executable"] = executable
+        inputs["args"] = args
+        if isinstance(self, ContainerTask):
+            # adding image and bindings when ContainerTask
+            inputs["image"] = kwargs["image"]
+            inputs["bindings"] = kwargs["bindings"]
 
         self.output_spec = output_spec
 
         super(ShellCommandTask, self).__init__(
             name=name,
-            inputs=kwargs,
+            inputs=inputs,
             audit_flags=audit_flags,
             messengers=messengers,
             messenger_args=messenger_args,
@@ -350,6 +363,8 @@ def _command_args_single(self, state_ind, ind=None):
             if f.type is bool:
                 if value is not True:
                     break
+            elif value in [None, attr.NOTHING]:
+                continue
             else:
                 cmd_add += ensure_list(value, tuple2list=True)
             if cmd_add is not None:
@@ -419,6 +434,8 @@ class ContainerTask(ShellCommandTask):
     def __init__(
         self,
         name,
+        image: ty.Optional[str] = None,
+        bindings: ty.Optional[ty.List] = None,
         audit_flags: AuditFlag = AuditFlag.NONE,
         cache_dir=None,
         input_spec: ty.Optional[SpecInfo] = None,
@@ -468,6 +485,8 @@ def __init__(
             cache_dir=cache_dir,
             strip=strip,
             rerun=rerun,
+            image=image,
+            bindings=bindings,
             **kwargs,
         )
 
@@ -479,14 +498,14 @@ def container_check(self, container_type):
             raise AttributeError(
                 f"Container type should be {container_type}, but {self.inputs.container} given"
             )
-        if self.inputs.image is attr.NOTHING:
+        if self.inputs.image in [None, attr.NOTHING]:
             raise AttributeError("Container image is not specified")
 
     def bind_paths(self, ind=None):
         """Return bound mount points: ``dict(lpath: (cpath, mode))``."""
         bind_paths = {}
         output_dir_cpath = None
-        if self.inputs.bindings is None:
+        if self.inputs.bindings in [None, attr.NOTHING]:
             self.inputs.bindings = []
         if ind is None:
             output_dir = self.output_dir

pydra/engine/tests/test_boutiques.py

@@ -51,8 +51,7 @@ def test_boutiques_spec_1():
     btask = BoshTask(
         name="NA",
         zenodo_id="1482743",
-        infile=Infile,
-        maskfile="test_brain.nii.gz",
+        inputs={"infile": Infile, "maskfile": "test_brain.nii.gz"},
         input_spec_names=["infile", "maskfile"],
         output_spec_names=["outfile", "out_outskin_off"],
     )
@@ -76,8 +75,7 @@ def test_boutiques_spec_2():
     btask = BoshTask(
         name="NA",
         zenodo_id="1482743",
-        infile=Infile,
-        maskfile="test_brain.nii.gz",
+        inputs={"infile": Infile, "maskfile": "test_brain.nii.gz"},
         input_spec_names=["infile"],
         output_spec_names=[],
     )
@@ -107,8 +105,7 @@ def test_boutiques_wf_1(maskfile, plugin):
         BoshTask(
             name="bet",
             zenodo_id="1482743",
-            infile=wf.lzin.infile,
-            maskfile=wf.lzin.maskfile,
+            inputs={"infile": wf.lzin.infile, "maskfile": wf.lzin.maskfile},
         )
     )
 
@@ -138,13 +135,14 @@ def test_boutiques_wf_2(maskfile, plugin):
         BoshTask(
             name="bet",
             zenodo_id="1482743",
-            infile=wf.lzin.infile,
-            maskfile=wf.lzin.maskfile,
+            inputs={"infile": wf.lzin.infile, "maskfile": wf.lzin.maskfile},
         )
     )
     wf.add(
         BoshTask(
-            name="stat", zenodo_id="3240521", input_file=wf.bet.lzout.outfile, v=True
+            name="stat",
+            zenodo_id="3240521",
+            inputs={"input_file": wf.bet.lzout.outfile, "v": True},
         )
     )
     wf.add(ShellCommandTask(name="cat", executable="cat", args=wf.stat.lzout.output))

pydra/engine/tests/test_dockertask.py

@@ -689,7 +689,7 @@ def test_docker_inputspec_1(plugin, tmpdir):
         name="docky",
         image="busybox",
         executable=cmd,
-        file=filename,
+        inputs={"file": filename},
         input_spec=my_input_spec,
         strip=True,
     )
@@ -776,7 +776,7 @@ def test_docker_inputspec_2(plugin, tmpdir):
         name="docky",
         image="busybox",
         executable=cmd,
-        file1=filename_1,
+        inputs={"file1": filename_1},
         input_spec=my_input_spec,
         strip=True,
     )
@@ -826,7 +826,7 @@ def test_docker_inputspec_2a_except(plugin, tmpdir):
         name="docky",
         image="busybox",
         executable=cmd,
-        file2=filename_2,
+        inputs={"file2": filename_2},
         input_spec=my_input_spec,
         strip=True,
     )
@@ -878,7 +878,7 @@ def test_docker_inputspec_2a(plugin, tmpdir):
         name="docky",
         image="busybox",
         executable=cmd,
-        file2=filename_2,
+        inputs={"file2": filename_2},
         input_spec=my_input_spec,
         strip=True,
     )
@@ -919,7 +919,7 @@ def test_docker_inputspec_3(plugin, tmpdir):
         name="docky",
         image="busybox",
         executable=cmd,
-        file=filename,
+        inputs={"file": filename},
         input_spec=my_input_spec,
         strip=True,
     )
@@ -963,7 +963,7 @@ def test_docker_inputspec_3a(plugin, tmpdir):
         name="docky",
         image="busybox",
         executable=cmd,
-        file=filename,
+        inputs={"file": filename},
         input_spec=my_input_spec,
         strip=True,
     )
@@ -1020,7 +1020,7 @@ def test_docker_cmd_inputspec_copyfile_1(plugin, tmpdir):
         image="busybox",
         executable=cmd,
         input_spec=my_input_spec,
-        orig_file=str(file),
+        inputs={"orig_file": str(file)},
     )
 
     res = docky()
@@ -1073,7 +1073,7 @@ def test_docker_inputspec_state_1(plugin, tmpdir):
         name="docky",
         image="busybox",
         executable=cmd,
-        file=filename,
+        inputs={"file": filename},
         input_spec=my_input_spec,
         strip=True,
     ).split("file")
@@ -1122,7 +1122,7 @@ def test_docker_inputspec_state_1b(plugin, tmpdir):
         name="docky",
         image="busybox",
         executable=cmd,
-        file=filename,
+        inputs={"file": filename},
         input_spec=my_input_spec,
         strip=True,
     ).split("file")
@@ -1168,7 +1168,7 @@ def test_docker_wf_inputspec_1(plugin, tmpdir):
         name="docky",
         image="busybox",
         executable=wf.lzin.cmd,
-        file=wf.lzin.file,
+        inputs={"file": wf.lzin.file},
         input_spec=my_input_spec,
         strip=True,
     )
@@ -1223,7 +1223,7 @@ def test_docker_wf_state_inputspec_1(plugin, tmpdir):
         name="docky",
         image="busybox",
         executable=wf.lzin.cmd,
-        file=wf.lzin.file,
+        inputs={"file": wf.lzin.file},
         input_spec=my_input_spec,
         strip=True,
     )
@@ -1280,7 +1280,7 @@ def test_docker_wf_ndst_inputspec_1(plugin, tmpdir):
         name="docky",
         image="busybox",
         executable=wf.lzin.cmd,
-        file=wf.lzin.file,
+        inputs={"file": wf.lzin.file},
         input_spec=my_input_spec,
         strip=True,
     ).split("file")

pydra/engine/tests/test_helpers.py

@@ -18,7 +18,7 @@ def test_save(tmpdir):
     outdir = Path(tmpdir)
     with pytest.raises(ValueError):
         save(tmpdir)
-    foo = multiply(name="mult", x=1, y=2)
+    foo = multiply(name="mult", inputs={"x": 1, "y": 2})
     # save task
     save(outdir, task=foo)
     del foo
@@ -203,7 +203,7 @@ def test_load_and_run(tmpdir):
     """ testing load_and_run for pickled task"""
     task_pkl = Path(tmpdir.join("task_main.pkl"))
 
-    task = multiply(name="mult", x=[1, 2], y=10).split("x")
+    task = multiply(name="mult", inputs={"x": [1, 2], "y": 10}).split("x")
     task.state.prepare_states(inputs=task.inputs)
     task.state.prepare_inputs()
     with task_pkl.open("wb") as fp:
@@ -221,7 +221,7 @@ def test_load_and_run(tmpdir):
 def test_load_and_run_exception_load(tmpdir):
     """ testing raising exception and saving info in crashfile when when load_and_run"""
     task_pkl = Path(tmpdir.join("task_main.pkl"))
-    task = raise_xeq1(name="raise", x=[1, 2]).split("x")
+    task = raise_xeq1(name="raise", inputs={"x": [1, 2]}).split("x")
     with pytest.raises(FileNotFoundError) as excinfo:
         task_0 = load_and_run(task_pkl=task_pkl, ind=0)
 
@@ -230,7 +230,7 @@ def test_load_and_run_exception_run(tmpdir):
     """ testing raising exception and saving info in crashfile when when load_and_run"""
     task_pkl = Path(tmpdir.join("task_main.pkl"))
 
-    task = raise_xeq1(name="raise", x=[1, 2]).split("x")
+    task = raise_xeq1(name="raise", inputs={"x": [1, 2]}).split("x")
     task.state.prepare_states(inputs=task.inputs)
     task.state.prepare_inputs()
 
@@ -262,7 +262,7 @@ def test_load_and_run_wf(tmpdir):
     wf_pkl = Path(tmpdir.join("wf_main.pkl"))
 
     wf = Workflow(name="wf", input_spec=["x", "y"])
-    wf.add(multiply(name="mult", x=wf.lzin.x, y=wf.lzin.y))
+    wf.add(multiply(name="mult", inputs={"x": wf.lzin.x, "y": wf.lzin.y}))
     wf.split(("x"))
     wf.inputs.x = [1, 2]
     wf.inputs.y = 10