Adjust codebase to allow building as FSL conda package
This MR makes a few structural changes to the PROFUMO code base to make it buildable as a FSL conda package:
- With the exception of the single-header-file
spline
library, all third party dependencies have been removed, as they can be provisioned through conda - A
setup.py
file has been added to thePython
directory, so that the Python scripts/modules can be installed into a Python environment. The scripts have been renamed accordingly, so that they will be installed as these commands:-
pfm_estimate_smoothness
(formerlyestimate_smoothness.py
) -
pfm_postprocess_results
(formerlypostprocess_results.py
) -
pfm_visualise_convergence
(formerlyvisualise_convergence.py
) -
visualise_pfms
(formerlyvisualise_pfms.py
)
-
- The
Makefile
has been simplified to make it to conform to FSL conventions. The custominstall
target, which versions and timestamps thePROFUMO
binary, has been removed - Dependence on a
$PROFUMODIR
environment variable has been removed - this was only used to find theDefault.phrf
file when the user does not provide a specific HRF file. Instead of using$PROFUMODIR
, the code now searches for$FSLDIR/data/PROFUMO/HRFs/Default.phrf
. If that path does not exist, the code falls back to<profumo-exe-location>/../HRFs/Default.phrf
(this assumes thatPROFUMO
is being run from an in-source installation)
The conda recipe for building PROFUMO is hosted at https://git.fmrib.ox.ac.uk/fsl/conda/fsl-profumo
This MR is intended to be merged into the master
branch, which deviates from the develop
/master
development workflow. After this MR has been merged, the develop
branch will be manually brought back into sync with master
.