Martin Craig authored 4 years ago and Paul McCarthy committed 4 years ago

Also minor bugfix - allow forward or backslash after \\wsl$ when
specifying FSLDIR as a WSL network share

Martin Craig authored 4 years ago and Paul McCarthy committed 4 years ago

This requires  WSL 2.0 but enables FSLDIR to be a genuine
WIndows path so that atlases and standard data can be loaded
transparently. It also means we no longer need FSLWSL environment
variable, just to be a bit careful with path mapping

Martin Craig authored 5 years ago and Paul McCarthy committed 4 years ago

This means that users who have FSL installed in Windows Subsystem
for Linux can call the wrappers directly from a Windows python
program (after setting the environment variable FSLWSL=1)

env option

This enables a common use case - logging the command but not the standard output

Previously this would assume $FSLDEVDIR/bin whenever $FSLDEVDIR was set
even if there was no matching command there, but there was one in $FSLDIR

stdout/stderr streams go.

gives $FSLDEVDIR precedence, and also allows a global override.

stdout/stderr, and also redirects it to real stdout/stderr.

testing. Tweaks to various wrapper functions. fslmaths returns results dict,
rather than file name (for testing).

be standardised. Subsequent refactorings to _FileOrThing class, to make
sure that wrapper functions can be updated correctly. runfsl function
passes kwargs through to run.