Replaces deepcopy with a smarter copy implementation, which only copies the instance attributes.

This is a speedup of about 20x (and yes, the deepcopy was getting annoyingly slow in some of my code).

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

The problem here is not that it can't find the folder but that FSLDIR
suggests a WSL installation but does not match the format required to
identify the distro folder.

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)

Still using `partial_fill` when creating FileTreeQuery

Added test for I/O to both JSON and pickle files

Also added test for add_to_parser

env option

double-barrelled filename support (but not HCP files :( )

This is now the new default behaviour when loading a new file

This change is not backwards compatible!

There were some subtle bugs in the use of get_all, which should now be fixed. They were caused by having multiple optional variables and the result not being deterministic if these were iterated in different orders.

affine.rescale function, for reuse.

directory check to be skipped

auto-load any JSON files that sre found. Fix to bids.isBIDSFile

flag.