[WIP] FIX - AFNI Zeropad sets out_file

[zachlindsey]

Summary

Fixes #3640 .

List of changes proposed in this PR (pull-request)

• Remove name_template from ZeropadInputSpec, since it is useless if it is not a format string and the underlying command doesn't form outputs from the input name.
• Implement a custom _list_outputs method to set the correct out file.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 0.00%. Comparing base (edf7a4a) to head (bc4af2b).
Report is 12 commits behind head on master.

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Additional details and impacted files

@@            Coverage Diff             @@
##           master   #3641       +/-   ##
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- Coverage   63.44%       0   -63.45%     
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  Files         308       0      -308     
  Lines       40887       0    -40887     
  Branches     5655       0     -5655     
==========================================
- Hits        25942       0    -25942     
+ Misses      13909       0    -13909     
+ Partials     1036       0     -1036     

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[zachlindsey]

After trying out this fix for my workflow, I've realized that out_file needs to be an absolute path! Will fix.

[effigies]

Suggested change

	from pathlib import Path
	from nipype import Node
	from nipype.interfaces.afni import Zeropad
	from nipype.testing.fixtures import create_files_in_directory
	def test_zeropad_handles_outfile_default(create_files_in_directory):
	filelist, outdir = create_files_in_directory
	zp = Zeropad(I=1)
	zp.inputs.in_files = filelist[0]
	result = zp.run()
	assert (Path(outdir) / "zeropad+tlrc.BRIK").exists()
	assert Path(result.outputs.out_file).name == "zeropad+tlrc.BRIK"
	def test_zeropad_handles_outfile_specified_nii_gz(create_files_in_directory):
	filelist, outdir = create_files_in_directory
	zp = Zeropad(I=1, out_file="padded.nii.gz")
	zp.inputs.in_files = filelist[0]
	result = zp.run()
	assert (Path(outdir) / "padded.nii.gz").exists()
	assert Path(result.outputs.out_file).name == "padded.nii.gz"
	def test_zeropad_keeps_file_after_node_run(create_files_in_directory):
	from pathlib import Path
	from shutil import which
	import pytest
	from nipype import Node
	from nipype.interfaces.afni import Zeropad
	from nipype.testing.fixtures import create_files_in_directory
	needs_3dZeropad = pytest.mark.skipif(
	not which('3dZeropad'),
	reason='Needs AFNI 3dZeropad installed'
	)
	@needs_3dZeropad
	def test_zeropad_handles_outfile_default(create_files_in_directory):
	filelist, outdir = create_files_in_directory
	zp = Zeropad(I=1)
	zp.inputs.in_files = filelist[0]
	result = zp.run()
	assert (Path(outdir) / "zeropad+tlrc.BRIK").exists()
	assert Path(result.outputs.out_file).name == "zeropad+tlrc.BRIK"
	@needs_3dZeropad
	def test_zeropad_handles_outfile_specified_nii_gz(create_files_in_directory):
	filelist, outdir = create_files_in_directory
	zp = Zeropad(I=1, out_file="padded.nii.gz")
	zp.inputs.in_files = filelist[0]
	result = zp.run()
	assert (Path(outdir) / "padded.nii.gz").exists()
	assert Path(result.outputs.out_file).name == "padded.nii.gz"
	@needs_3dZeropad
	def test_zeropad_keeps_file_after_node_run(create_files_in_directory):

[effigies]

Made a suggestion. Haven't tested it, but if you commit and run locally, those tests should pass. They'll skip on CI.