fix: do not use nipype.utils.filemanip.ensure_list

Because that function utilizes ``is_container``, which is imported at
global context, nipype could not evaluate ``ensure_list`` calls inlined
inside ``connect``. This would end up failing with:

```
fMRIPrep failed: name 'is_container' is not defined
```

A new module for nipype connections is created to provide this kind of
commodity functions for all NiPreps.

Author: oesteban

niworkflows/anat/ants.py

@@ -15,7 +15,8 @@
 from nipype.interfaces.fsl.maths import ApplyMask
 from nipype.interfaces.ants import N4BiasFieldCorrection, Atropos, MultiplyImages
 
-from ..utils.misc import get_template_specs, select_first as _pop
+from ..utils.misc import get_template_specs
+from ..utils.connections import pop_file as _pop
 
 # niworkflows
 from ..interfaces.ants import (

niworkflows/func/tests/test_util.py

@@ -5,9 +5,10 @@
 
 import numpy as np
 from nipype.pipeline import engine as pe
-from nipype.utils.filemanip import fname_presuffix, copyfile, ensure_list
+from nipype.utils.filemanip import fname_presuffix, copyfile
 from nilearn.image import load_img
 
+from ...utils.connections import listify
 from niworkflows.interfaces.masks import ROIsPlot
 
 from ..util import init_bold_reference_wf
@@ -40,7 +41,7 @@
 ds001240/sub-26_task-rest_bold.nii.gz
 ds001362/sub-01_task-taskname_run-01_bold.nii.gz""".splitlines()
 
-bold_datasets = [ensure_list(d) for d in bold_datasets]
+bold_datasets = [listify(d) for d in bold_datasets]
 
 
 def symmetric_overlap(img1, img2):

niworkflows/func/util.py

@@ -6,7 +6,6 @@
 
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu, fsl, afni
-from nipype.utils.filemanip import ensure_list
 
 from templateflow.api import get as get_template
 
@@ -21,6 +20,7 @@
 from ..interfaces.masks import SimpleShowMaskRPT
 from ..interfaces.registration import EstimateReferenceImage
 from ..interfaces.utils import CopyXForm
+from ..utils.connections import listify
 from ..utils.misc import pass_dummy_scans as _pass_dummy_scans
 
 
@@ -176,7 +176,7 @@ def init_bold_reference_wf(
 
     # fmt: off
     workflow.connect([
-        (inputnode, val_bold, [(("bold_file", ensure_list), "in_file")]),
+        (inputnode, val_bold, [(("bold_file", listify), "in_file")]),
         (inputnode, enhance_and_skullstrip_bold_wf, [
             ("bold_mask", "inputnode.pre_mask"),
         ]),
@@ -185,7 +185,7 @@ def init_bold_reference_wf(
         (gen_ref, enhance_and_skullstrip_bold_wf, [
             ("ref_image", "inputnode.in_file"),
         ]),
-        (val_bold, bold_1st, [(("out_file", ensure_list), "inlist")]),
+        (val_bold, bold_1st, [(("out_file", listify), "inlist")]),
         (gen_ref, calc_dummy_scans, [("n_volumes_to_discard", "algo_dummy_scans")]),
         (calc_dummy_scans, outputnode, [("skip_vols_num", "skip_vols")]),
         (gen_ref, outputnode, [
@@ -197,7 +197,7 @@ def init_bold_reference_wf(
             ("outputnode.mask_file", "bold_mask"),
             ("outputnode.skull_stripped_file", "ref_image_brain"),
         ]),
-        (val_bold, validate_1st, [(("out_report", ensure_list), "inlist")]),
+        (val_bold, validate_1st, [(("out_report", listify), "inlist")]),
         (bold_1st, outputnode, [("out", "bold_file")]),
         (validate_1st, outputnode, [("out", "validation_report")]),
     ])
@@ -218,7 +218,7 @@ def init_bold_reference_wf(
         )
         # fmt: off
         workflow.connect([
-            (inputnode, val_sbref, [(("sbref_file", ensure_list), "in_file")]),
+            (inputnode, val_sbref, [(("sbref_file", listify), "in_file")]),
             (val_sbref, gen_ref, [("out_file", "sbref_file")]),
         ])
         # fmt: on

niworkflows/interfaces/registration.py

@@ -8,7 +8,7 @@
 import numpy as np
 from nilearn import image as nli
 from nilearn.image import index_img
-from nipype.utils.filemanip import fname_presuffix, ensure_list
+from nipype.utils.filemanip import fname_presuffix
 from nipype.interfaces.base import (
     traits,
     isdefined,
@@ -467,9 +467,7 @@ class EstimateReferenceImage(SimpleInterface):
 
     def _run_interface(self, runtime):
         is_sbref = isdefined(self.inputs.sbref_file)
-        ref_input = ensure_list(
-            self.inputs.sbref_file if is_sbref else self.inputs.in_file
-        )
+        ref_input = self.inputs.sbref_file if is_sbref else self.inputs.in_file
 
         if self.inputs.multiecho:
             if len(ref_input) < 2:

niworkflows/utils/connections.py

@@ -0,0 +1,58 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""
+Utilities for the creation of nipype workflows.
+
+Because these functions are meant to be inlined in nipype's ``connect`` invocations,
+all the imports MUST be done in each function's context.
+
+"""
+
+__all__ = [
+    "listify",
+    "pop_file",
+]
+
+
+def pop_file(in_files):
+    """
+    Select the first file from a list of filenames.
+
+    Used to grab the first echo's file when processing
+    multi-echo data through workflows that only accept
+    a single file.
+
+    Examples
+    --------
+    >>> pop_file('some/file.nii.gz')
+    'some/file.nii.gz'
+    >>> pop_file(['some/file1.nii.gz', 'some/file2.nii.gz'])
+    'some/file1.nii.gz'
+
+    """
+    if isinstance(in_files, (list, tuple)):
+        return in_files[0]
+    return in_files
+
+
+def listify(value):
+    """
+    Convert to a list (inspired by bids.utils.listify).
+
+    Examples
+    --------
+    >>> listify('some/file.nii.gz')
+    ['some/file.nii.gz']
+    >>> listify((0.1, 0.2))
+    [0.1, 0.2]
+    >>> listify(None) is None
+    True
+
+    """
+    from pathlib import Path
+    from nipype.interfaces.base import isdefined
+    if not isdefined(value) or isinstance(value, type(None)):
+        return value
+    if isinstance(value, (str, bytes, Path)):
+        return [str(value)]
+    return list(value)

niworkflows/utils/misc.py

@@ -212,27 +212,6 @@ def splitext(fname):
     return stem, basename[len(stem):]
 
 
-def select_first(in_files):
-    """
-    Select the first file from a list of filenames.
-
-    Used to grab the first echo's file when processing
-    multi-echo data through workflows that only accept
-    a single file.
-
-    Examples
-    --------
-    >>> select_first('some/file.nii.gz')
-    'some/file.nii.gz'
-    >>> select_first(['some/file1.nii.gz', 'some/file2.nii.gz'])
-    'some/file1.nii.gz'
-
-    """
-    if isinstance(in_files, (list, tuple)):
-        return in_files[0]
-    return in_files
-
-
 def _copy_any(src, dst):
     import os
     import gzip