fix: undeprecate dcm2niix source_names option #2550
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mgxd
approved these changes
Apr 25, 2018
| mandatory=True, | ||
| desc=('A set of filenames to be converted. Note that the current ' |
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We should probably specify the latest as being 1.0.20180328 in case this behavior changes down the line
| @@ -399,7 +414,7 @@ def _format_arg(self, opt, spec, val): | |||
| spec.argstr += ' n' | |||
| val = True | |||
| if opt == 'source_names': | |||
| return spec.argstr % val[0] | |||
| return spec.argstr % (os.path.dirname(val[0]) or '.') | |||
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since the dicoms are copied to the node, couldn't this just be '.'
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not when used as an interface.
Codecov Report
@@ Coverage Diff @@
## master #2550 +/- ##
==========================================
- Coverage 67.12% 67.12% -0.01%
==========================================
Files 333 333
Lines 42538 42538
Branches 5264 5264
==========================================
- Hits 28555 28553 -2
- Misses 13281 13284 +3
+ Partials 702 701 -1
Continue to review full report at Codecov.
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* upstream/master: (42 commits) removing default value from out_intensity_fusion_name_format removing gen_file and using a default value in ICA_AROMA fix test [skip ci] improve description forgot make specs make threshold mandatory without default TEST: Test xor, requires constraints on name_source traits FIX: Remove -mcmap argument in absence of -nodv FIX: Only find paths for created files FIX: Do not generate filename when required fields are missing fixing the test changinf freesurfer test_preprocess (default number of iterat) changinf freesurfer test_preprocess (default number of iterat) removing usedefault=False from traits (for traits were default was set i also remove this value) warnings for usedefault=False suggestions from chris increasing atol in the test adding tests that checks pos/neg for normal distribution changing hash in test_core correcting traits to remove warnings ...
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Fixes dcm2niix issue in heudiconv: nipy/heudiconv#189
Changes proposed in this pull request
rationale:
with node, these files get copied to the current working directory and dcm2niix will only need to convert the local files
as an interface, this allows users to point at a set of files. it's possible in this case that all files in the directory get converted, not just the files pointed to. i have tried to include documentation to guide in this scenario.