Merge pull request #160 from djarecka/list_inp

list as a single element of an input

Author: djarecka

pydra/engine/helpers.py

@@ -11,11 +11,13 @@
 from .specs import Runtime, File
 
 
-def ensure_list(obj):
+def ensure_list(obj, tuple2list=False):
     if obj is None:
         return []
     if isinstance(obj, list):
         return obj
+    elif tuple2list and isinstance(obj, tuple):
+        return list(obj)
     return [obj]
 
 

pydra/engine/task.py

@@ -240,7 +240,7 @@ def command_args(self):
                 if value is not True:
                     break
             else:
-                cmd_add += ensure_list(value)
+                cmd_add += ensure_list(value, tuple2list=True)
             if cmd_add is not None:
                 pos_args.append((pos, cmd_add))
         # sorting all elements of the command

pydra/engine/tests/test_node_task.py

@@ -642,6 +642,91 @@ def test_task_state_2(plugin):
     assert nn.output_dir == []
 
 
+@pytest.mark.parametrize("plugin", Plugins)
+def test_task_state_3(plugin):
+    """ task with a tuple as an input, and a simple splitter """
+    nn = moment(name="NA", n=3, lst=[(2, 3, 4), (1, 2, 3)]).split(splitter="lst")
+    assert np.allclose(nn.inputs.n, 3)
+    assert np.allclose(nn.inputs.lst, [[2, 3, 4], [1, 2, 3]])
+    assert nn.state.splitter == "NA.lst"
+
+    with Submitter(plugin=plugin) as sub:
+        sub(nn)
+
+    # checking the results
+    results = nn.result()
+    for i, expected in enumerate([33, 12]):
+        assert results[i].output.out == expected
+    # checking the output_dir
+    assert nn.output_dir
+    for odir in nn.output_dir:
+        assert odir.exists()
+
+
+@pytest.mark.parametrize("plugin", Plugins)
+def test_task_state_4(plugin):
+    """ task with a tuple as an input, and the variable is part of the scalar splitter"""
+    nn = moment(name="NA", n=[1, 3], lst=[(2, 3, 4), (1, 2, 3)]).split(
+        splitter=("n", "lst")
+    )
+    assert np.allclose(nn.inputs.n, [1, 3])
+    assert np.allclose(nn.inputs.lst, [[2, 3, 4], [1, 2, 3]])
+    assert nn.state.splitter == ("NA.n", "NA.lst")
+
+    with Submitter(plugin=plugin) as sub:
+        sub(nn)
+
+    # checking the results
+    results = nn.result()
+    for i, expected in enumerate([3, 12]):
+        assert results[i].output.out == expected
+    # checking the output_dir
+    assert nn.output_dir
+    for odir in nn.output_dir:
+        assert odir.exists()
+
+
+@pytest.mark.parametrize("plugin", Plugins)
+def test_task_state_4_exception(plugin):
+    """ task with a tuple as an input, and the variable is part of the scalar splitter
+        the shapes are not matching, so exception should be raised
+    """
+    nn = moment(name="NA", n=[1, 3, 3], lst=[(2, 3, 4), (1, 2, 3)]).split(
+        splitter=("n", "lst")
+    )
+    assert np.allclose(nn.inputs.n, [1, 3, 3])
+    assert np.allclose(nn.inputs.lst, [[2, 3, 4], [1, 2, 3]])
+    assert nn.state.splitter == ("NA.n", "NA.lst")
+
+    with pytest.raises(Exception) as excinfo:
+        with Submitter(plugin=plugin) as sub:
+            sub(nn)
+    assert "shape" in str(excinfo.value)
+
+
+@pytest.mark.parametrize("plugin", Plugins)
+def test_task_state_5(plugin):
+    """ ask with a tuple as an input, and the variable is part of the outer splitter """
+    nn = moment(name="NA", n=[1, 3], lst=[(2, 3, 4), (1, 2, 3)]).split(
+        splitter=["n", "lst"]
+    )
+    assert np.allclose(nn.inputs.n, [1, 3])
+    assert np.allclose(nn.inputs.lst, [[2, 3, 4], [1, 2, 3]])
+    assert nn.state.splitter == ["NA.n", "NA.lst"]
+
+    with Submitter(plugin=plugin) as sub:
+        sub(nn)
+
+    # checking the results
+    results = nn.result()
+    for i, expected in enumerate([3, 2, 33, 12]):
+        assert results[i].output.out == expected
+    # checking the output_dir
+    assert nn.output_dir
+    for odir in nn.output_dir:
+        assert odir.exists()
+
+
 @pytest.mark.parametrize("plugin", Plugins)
 def test_task_state_comb_1(plugin):
     """ task with the simplest splitter and combiner"""