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

PennLINC / qsirecon

Reconstruction of preprocessed q-space images (dMRI)

https://qsirecon.readthedocs.io/

BSD 3-Clause "New" or "Revised" License

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Make PlotPeaks robust enough that we don't need --writable-tempfs in singularity/apptainer #174

Closed mattcieslak closed 1 week ago

mattcieslak commented 1 week ago

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 #163, but @araikes tested and it causes a new error

codecov-commenter commented 1 week ago

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 :warning:

Additional details and impacted files

```diff @@ 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 commented 1 week ago

@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