[ENH] Add change suffix workflow

[Remi-Gau]

@marcobarilari

Was turning out to be too annoying to incorporate a change suffix only into bidsRename (that will have to happen later) so in the meantime I am adding a small workflow to change suffixes only.

[codecov]

Codecov Report

Merging #516 (891b08d) into dev (c76e644) will decrease coverage by 0.74%.
The diff coverage is 0.00%.

@@            Coverage Diff             @@
##              dev     #516      +/-   ##
==========================================
- Coverage   72.99%   72.24%   -0.75%     
==========================================
  Files         192      193       +1     
  Lines        4058     4104      +46     
==========================================
+ Hits         2962     2965       +3     
- Misses       1096     1139      +43     

Flag	Coverage Δ
unittests	72.24% <0.00%> (-0.75%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/workflows/bidsChangeSuffix.m	0.00% <0.00%> (ø)
src/IO/saveSpmScript.m	88.46% <0.00%> (+0.96%)	⬆️
src/infra/getEnvInfo.m	79.54% <0.00%> (+2.27%)	⬆️

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[marcobarilari]

reporting the behavior here when setting derivatives as input:

FOR TASK(s): visualLocalizerFingerTapping
Getting data from:
 /Users/barilari/data/temp_to_delete/ses-007_2delete/derivatives
Error using errorHandling (line 52)
This file does not exist: /Users/barilari/data/temp_to_delete/ses-007_2delete/derivatives/dataset_description.json[.gz]

Error in validationInputFile (line 77)
    errorHandling(mfilename(), 'nonExistentFile', msg, false, true);

Error in getData (line 39)
  validationInputFile(bidsDir, 'dataset_description.json');

Error in setUpWorkflow (line 39)
  [BIDS, opt] = getData(opt, bidsDir);

Error in bidsChangeSuffix (line 52)
  [BIDS, opt] = setUpWorkflow(opt, 'changing suffix', opt.dir.input);

Error in SpatialPrepro (line 50)
  bidsChangeSuffix(opt, newSuffix, ...

so the file it is looking for is in /Users/barilari/data/temp_to_delete/ses-007_2delete/derivatives/cpp_spm-preproc/dataset_description.json

[Remi-Gau]

reporting the behavior here when setting derivatives as input:

FOR TASK(s): visualLocalizerFingerTapping
Getting data from:
 /Users/barilari/data/temp_to_delete/ses-007_2delete/derivatives
Error using errorHandling (line 52)
This file does not exist: /Users/barilari/data/temp_to_delete/ses-007_2delete/derivatives/dataset_description.json[.gz]

Error in validationInputFile (line 77)
    errorHandling(mfilename(), 'nonExistentFile', msg, false, true);

Error in getData (line 39)
  validationInputFile(bidsDir, 'dataset_description.json');

Error in setUpWorkflow (line 39)
  [BIDS, opt] = getData(opt, bidsDir);

Error in bidsChangeSuffix (line 52)
  [BIDS, opt] = setUpWorkflow(opt, 'changing suffix', opt.dir.input);

Error in SpatialPrepro (line 50)
  bidsChangeSuffix(opt, newSuffix, ...

so the file it is looking for is in /Users/barilari/data/temp_to_delete/ses-007_2delete/derivatives/cpp_spm-preproc/dataset_description.json

yup we at least expect the input dataset to have data_description.json file

add a dummy one in there : even with just {} should already help

[Remi-Gau]

that or you forgot one folder in your path ?

It says it is reading the data from

/Users/barilari/data/temp_to_delete/ses-007_2delete/derivatives

When it should be reading them from

/Users/barilari/data/temp_to_delete/ses-007_2delete/derivatives/cpp_spm-preproc/