Use shlex's posix=False for Windows compatibility

[kousu]

Fixes #83.

I'm a little bit worried this will cause problems on Unix. I tried it quickly and it didn't break my examples.

Maybe utils.run_shell_command() should be dropped in favour of calling subprocess.Popen() directly. It's a lot safer that way; less worries about quoting issues turning into exploits.

[codecov]

Codecov Report

Merging #84 into master will not change coverage.
The diff coverage is 0.00%.

@@           Coverage Diff           @@
##           master      #84   +/-   ##
=======================================
  Coverage   70.52%   70.52%           
=======================================
  Files           9        9           
  Lines         587      587           
  Branches       75       75           
=======================================
  Hits          414      414           
  Misses        149      149           
  Partials       24       24           

Flag	Coverage Δ
#pytest	70.52% <0.00%> (ø)

Impacted Files	Coverage Δ
dcm2bids/utils.py	68.96% <0.00%> (ø)

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[kousu]

With this patch, my reproduction in #83 now runs:

C:\Users\user\src\Dcm2bids>dcm2bids -d data_testing\data_testing\dicom_unsorted -o output -p "" -c example\config.json
INFO:dcm2bids.dcm2bids:--- dcm2bids start ---
INFO:dcm2bids.dcm2bids:OS:version: Windows-10-10.0.18362-SP0
INFO:dcm2bids.dcm2bids:python:version: 3.8.3 (tags/v3.8.3:6f8c832, May 13 2020, 22:20:19) [MSC v.1925 32 bit (Intel)]
INFO:dcm2bids.dcm2bids:dcm2bids:version: 2.1.4
INFO:dcm2bids.dcm2bids:dcm2niix:version: v1.0.20200331
INFO:dcm2bids.dcm2bids:participant: sub-
INFO:dcm2bids.dcm2bids:session:
INFO:dcm2bids.dcm2bids:config: C:\Users\user\src\Dcm2bids\example\config.json
INFO:dcm2bids.dcm2bids:BIDS directory: C:\Users\user\src\Dcm2bids\output
INFO:dcm2bids.utils:Running dcm2niix -b y -ba y -z y -f '%3s_%f_%p_%t' -o output\tmp_dcm2bids\sub- data_testing\data_testing\dicom_unsorted
INFO:dcm2bids.dcm2niix:Check log file for dcm2niix output
INFO:dcm2bids.sidecar:Sidecars pairing:
INFO:dcm2bids.sidecar:No Pairing  <-  '006_dicom_unsorted_a_gre_DYNshim_20191101153345'_e1
INFO:dcm2bids.sidecar:No Pairing  <-  '007_dicom_unsorted_a_gre_DYNshim_20191101153345'_e1_ph
INFO:dcm2bids.sidecar:No Pairing  <-  '006_dicom_unsorted_a_gre_DYNshim_20191101153345'_e2
INFO:dcm2bids.sidecar:No Pairing  <-  '007_dicom_unsorted_a_gre_DYNshim_20191101153345'_e2_ph
INFO:dcm2bids.sidecar:No Pairing  <-  '006_dicom_unsorted_a_gre_DYNshim_20191101153345'_e3
INFO:dcm2bids.sidecar:No Pairing  <-  '007_dicom_unsorted_a_gre_DYNshim_20191101153345'_e3_ph
INFO:dcm2bids.sidecar:No Pairing  <-  '006_dicom_unsorted_a_gre_DYNshim_20191101153345'_e4
INFO:dcm2bids.sidecar:No Pairing  <-  '007_dicom_unsorted_a_gre_DYNshim_20191101153345'_e4_ph
INFO:dcm2bids.sidecar:No Pairing  <-  '006_dicom_unsorted_a_gre_DYNshim_20191101153345'_e5
INFO:dcm2bids.sidecar:No Pairing  <-  '007_dicom_unsorted_a_gre_DYNshim_20191101153345'_e5_ph
INFO:dcm2bids.sidecar:No Pairing  <-  '006_dicom_unsorted_a_gre_DYNshim_20191101153345'_e6
INFO:dcm2bids.sidecar:No Pairing  <-  '007_dicom_unsorted_a_gre_DYNshim_20191101153345'_e6_ph
INFO:dcm2bids.dcm2bids:moving acquisitions into BIDS folder

[kousu]

I'm not sure what codecov is complaining about. That the patch isn't tested? But that function wasn't tested before either.

[kousu]

My solution is bad! https://stackoverflow.com/a/35900070

shlex.split(cmd, posix=0) retains backslashes in Windows paths, but it doesn't understand quoting & escaping right. Its not very clear what the posix=0 mode of shlex is good for at all - but 99% it certainly seduces Windows/cross-platform programmers ...

https://bugs.python.org/issue1724822 - last updated, 2011 :*(

[kousu]

Bad solution. I'm doing what I suggested in #83 instead.