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Adjust codebase to allow building as FSL conda package

Paul McCarthy requested to merge paulmc/profumo:mnt/conda into master

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 file has been added to the Python 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 (formerly
    • pfm_postprocess_results (formerly
    • pfm_visualise_convergence (formerly
    • visualise_pfms (formerly
  • The Makefile has been simplified to make it to conform to FSL conventions. The custom install target, which versions and timestamps the PROFUMO binary, has been removed
  • Dependence on a $PROFUMODIR environment variable has been removed - this was only used to find the Default.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 that PROFUMO is being run from an in-source installation)

The conda recipe for building PROFUMO is hosted at

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.

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