Make PlotPeaks robust enough that we don't need --writable-tempfs in singularity/apptainer

[mattcieslak]

Attempt to manage xvfb outside of nipype so we can use a writable temp dir. We've had so much trouble with FURY plotting that we added the --skip-odf-reports to bypass them. But they are pretty and useful, so it would be great to get them working robustly.

There is an error that isn't captured in the logs/stdout when trying to run qsirecon with --containall in singularity/apptainer. All we typically see is that node plot_peaks failed to run and that its output was not found.

Some things we know:

• FURY Plotting always works in Docker
• If we remove _redirect_x variable from the interface, FURY plotting doesn't work. even in a container (eg c08a3f7)
• FURY plotting sometimes doesn't work in singluarity/apptainer. This is probably due to different system defaults on different clusters
• Plotting reliably works on singularity/apptainer with --writable-tempfs
• We think maybe the issue has to do with the temp directory used by xvfb. I tried changing this in [FIX] set TMPDIR before running plot_peaks #163, but @araikes tested and it causes a new error

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 0% with 25 lines in your changes missing coverage. Please review.

Project coverage is 47.73%. Comparing base (01e31d6) to head (c6e8eac).

Files with missing lines	Patch %	Lines
qsirecon/cli/recon_plot.py	0.00%	25 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #174      +/-   ##
==========================================
- Coverage   47.86%   47.73%   -0.14%     
==========================================
  Files          57       57              
  Lines        7195     7213      +18     
  Branches      983      984       +1     
==========================================
- Hits         3444     3443       -1     
- Misses       3546     3565      +19     
  Partials      205      205              

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[mattcieslak]

@araikes I wasn't able to request you as a reviewer for some reason, but could you take a look too?

The plan here is to at the bare minimum give users a more clear error message about why PlotPeaks is failing. I'm not sure we're going to be able to get around the Xvfb issues