[FIX] Add quiet and debug options to t2smap

[emdupre]

Changes proposed in this pull request:

• HOTFIX ! Adds missing arguments to t2smap.
• This was previously unnoticed since the t2smap workflow was only called in the context of the tedana workflow

[codecov]

Codecov Report

Merging #123 into master will decrease coverage by 0.04%.
The diff coverage is 33.33%.

@@            Coverage Diff             @@
##           master     #123      +/-   ##
==========================================
- Coverage   49.72%   49.68%   -0.05%     
==========================================
  Files          32       32              
  Lines        2035     2037       +2     
==========================================
  Hits         1012     1012              
- Misses       1023     1025       +2

Impacted Files	Coverage Δ
tedana/workflows/t2smap.py	70.83% <33.33%> (-2.03%)	⬇️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update e7f04ff...1a9cac3. Read the comment docs.

[emdupre]

Merging for nipreps/fmriprep#1263, unless @tsalo has any objections !

[tsalo]

Do debug and quiet need to be popped out of options before they're fed into t2smap_workflow or will it work as is?

[emdupre]

Sorry, could you confirm what you mean by "popped out" ? I'm not sure I'm following..

[tsalo]

I just meant that they might need to be removed from the options dictionary somehow before being fed into t2smap_workflow. Or maybe they could be added as arguments to t2smap_workflow?

[tsalo]

To clarify, I get this error if I try running t2smap from the command line with the changes:

Traceback (most recent call last):
  File "/Users/tsalo/anaconda/envs/python3/bin/t2smap", line 11, in <module>
    load_entry_point('tedana', 'console_scripts', 't2smap')()
  File "/Users/tsalo/Documents/tsalo/tedana/tedana/workflows/t2smap.py", line 214, in _main
    t2smap_workflow(**vars(options))
TypeError: t2smap_workflow() got an unexpected keyword argument 'debug'

[emdupre]

Oh I see, thanks ! Yes, you're right, I'll change this.

[emdupre]

OK, I think this is fixed. I'll merge and try moving forward with the fmriprep PR pinned to this commit !

[emdupre]

@all-contributors add @tsalo for reviewing and tests, please !

[allcontributors]

@emdupre

We had trouble processing your request. Please try again later.

[allcontributors]

@emdupre

I've put up a pull request to add @tsalo! 🎉

[emdupre]

@all-contributors add @tsalo for reviewing pull requests, please ?

[allcontributors]

@emdupre

I couldn't determine any contributions to add, did you specify any contributions?
Please make sure to use valid contribution names.

[emdupre]

@all-contributors add @tsalo for pull requests review, please ?

[allcontributors]

@emdupre

I've updated the pull request to add @tsalo! 🎉