Merge pull request #197 from mwaskom/nipype_fixes

Adapt to changes in nipype
mwaskom · Apr 9, 2020 · d75749a · d75749a
2 parents 6701801 + 7efb189
commit d75749a
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Showing 2 changed files with 14 additions and 11 deletions.
diff --git a/lyman/frontend.py b/lyman/frontend.py
@@ -447,7 +447,10 @@ def execute(wf, args, info):
     else:
 
         # TODO expose other nipype plugins as a command-line parameter
-        plugin, plugin_args = "MultiProc", {"n_procs": args.n_procs}
+        if args.n_procs == 1:
+            plugin, plugin_args = "Linear", {}
+        else:
+            plugin, plugin_args = "MultiProc", {"n_procs": args.n_procs}
         res = wf.run(plugin, plugin_args)
 
     # After successful completion of the workflow, optionally delete the

diff --git a/lyman/workflows/preproc.py b/lyman/workflows/preproc.py
@@ -503,14 +503,14 @@ def write_time_series_gif(self, runtime, img, fname, title=None):
 class SessionInput(LymanInterface):
 
     class input_spec(TraitedSpec):
-        session = traits.Tuple()
+        session = traits.Tuple(traits.Str(), traits.Str())
         data_dir = traits.Directory(exists=True)
         proc_dir = traits.Directory(exists=True)
         fm_template = traits.Str()
         phase_encoding = traits.Either("ap", "pa")
 
     class output_spec(TraitedSpec):
-        session_tuple = traits.Tuple()
+        session_tuple = traits.Tuple(traits.Str(), traits.Str())
         subject = traits.Str()
         session = traits.Str()
         fm_file = traits.File(exists=True)
@@ -596,7 +596,7 @@ def _run_interface(self, runtime):
 class RunInput(LymanInterface, TimeSeriesGIF):
 
     class input_spec(TraitedSpec):
-        run = traits.Tuple()
+        run = traits.Tuple(traits.Str(), traits.Str(), traits.Str())
         data_dir = traits.Directory(exists=True)
         proc_dir = traits.Directory(exists=True)
         experiment = traits.Str()
@@ -605,7 +605,7 @@ class input_spec(TraitedSpec):
         crop_frames = traits.Int(0, usedefault=True)
 
     class output_spec(TraitedSpec):
-        run_tuple = traits.Tuple()
+        run_tuple = traits.Tuple(traits.Str(), traits.Str(), traits.Str())
         subject = traits.Str()
         session = traits.Str()
         run = traits.Str()
@@ -725,7 +725,7 @@ class input_spec(TraitedSpec):
         warp_files = traits.List(traits.File(exists=True))
         jacobian_files = traits.List(traits.File(Exists=True))
         phase_encoding = traits.List(traits.Str)
-        session_tuple = traits.Tuple()
+        session_tuple = traits.Tuple(traits.Str(), traits.Str())
 
     class output_spec(TraitedSpec):
         raw_file = traits.File(exists=True)
@@ -896,7 +896,7 @@ class FinalizeTimeseries(LymanInterface, TimeSeriesGIF):
 
     class input_spec(TraitedSpec):
         experiment = traits.Str()
-        run_tuple = traits.Tuple()
+        run_tuple = traits.Tuple(traits.Str(), traits.Str(), traits.Str())
         anat_file = traits.File(exists=True)
         in_files = traits.List(traits.File(exists=True))
         seg_file = traits.File(exists=True)
@@ -1038,7 +1038,7 @@ class FinalizeTemplate(LymanInterface):
 
     class input_spec(TraitedSpec):
         experiment = traits.Str()
-        session_tuple = traits.Tuple()
+        session_tuple = traits.Tuple(traits.Str(), traits.Str())
         in_files = traits.List(traits.File(exists=True))
         seg_file = traits.File(exists=True)
         anat_file = traits.File(exists=True)
@@ -1170,7 +1170,7 @@ class RealignmentReport(LymanInterface):
     class input_spec(TraitedSpec):
         target_file = traits.File(exists=True)
         realign_params = traits.File(exists=True)
-        run_tuple = traits.Tuple()
+        run_tuple = traits.Tuple(traits.Str(), traits.Str(), traits.Str())
 
     class output_spec(TraitedSpec):
         params_plot = traits.File(exists=True)
@@ -1237,7 +1237,7 @@ class AnatRegReport(LymanInterface):
 
     class input_spec(TraitedSpec):
         subject_id = traits.Str()
-        session_tuple = traits.Tuple()
+        session_tuple = traits.Tuple(traits.Str(), traits.Str())
         data_dir = traits.Directory(exists=True)
         in_file = traits.File(exists=True)
         cost_file = traits.File(exists=True)
@@ -1279,7 +1279,7 @@ def _run_interface(self, runtime):
 class CoregGIF(LymanInterface):
 
     class input_spec(TraitedSpec):
-        run_tuple = traits.Tuple()
+        run_tuple = traits.Tuple(traits.Str(), traits.Str(), traits.Str())
         in_file = traits.File(exists=True)
         ref_file = traits.File(exists=True)
         out_file = traits.File()