Small but important pre-release fixes #652
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… white spaces are not dropped
…s to a bug in recon-surf, where this output is used to read the voxel size. Using the logger meant that the file and line are prepended, which did not used to be prepended. That changes the line and the extraction command became invalid. Now fixed by using grep in recon-surf and adding setup_logging in conform.py. Also added extra optional --log flag to write the log to a file and adding a make_parser function for future integration into documentation.
….log and scripts/BUILD.log
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In #649, the output format of
conform.pyis changed. This leads to a bug in recon-surf, where this output is used to read the voxel size. Using the logger meant that the file and line are prepended, which did not used to be prepended. That changes the line and the extraction command became invalid.Now fixed by using grep in
recon-surfand addingsetup_logginginconform.py. Also added extra optional--logflag to write the log to a file and adding a make_parser function for future integration into documentation.Make sure all bash read statements are started with IFS="" so initial white spaces are not dropped
Removed the extra warning of expected-to-exist files
scripts/deep-seg.logandscripts/BUILD.log