Bf/startup

This fixes two issues

1. Using the system activate may fail as it can start using the conda libraries in FSLDIR which may not be compatible, e.g.:

  File "/opt/fmrib/conda/python3/bin/conda", line 12, in <module>
    from conda.cli import main
  File "/vols/Scratch/mwebster/fsl_dafc4c0c/lib/python3.12/site-packages/conda/cli/__init__.py", line 3, in <modul
e>
    from .main import main  # NOQA
  File "/vols/Scratch/mwebster/fsl_dafc4c0c/lib/python3.12/site-packages/conda/cli/main.py", line 6, in <module>
    from ..deprecations import deprecated
  File "/vols/Scratch/mwebster/fsl_dafc4c0c/lib/python3.12/site-packages/conda/deprecations.py", line 60
    if version_tuple := self._get_version_tuple(version):

2. The current script will try to build in the test directory and not the output directory. This fix simply copies the Makefile and source files to the output directory.

unit_tests/utils/feedsRun.fslStartup

@@ -4,10 +4,13 @@
 
 import os
 import shlex
+import sys
 import tempfile
 
 import subprocess as sp
 
+from pathlib import Path
+
 def run(cmd, ompthreads=None, blasthreads=None, fslskipglobal=None):
 
     env = os.environ.copy()
@@ -33,12 +36,22 @@ def run(cmd, ompthreads=None, blasthreads=None, fslskipglobal=None):
 
 
 def main():
+    env = os.environ.copy()
+    activatePath = Path(f'''{env['FSLDIR']}/bin/activate''')
+    if not activatePath.is_file():
+       activatePath='activate'
 
-    buildcmds = ['source activate $FSLDIR',
+    outdir        = Path(sys.argv[1])
+
+    buildcmds = [f'''source {activatePath} $FSLDIR''',
                  'source $FSLDIR/etc/fslconf/fsl-devel.sh',
+		 f'''cp Makefile test_fslStartup.cc {outdir}''',
+		 f'''cd {outdir}''',
                  'make']
     sp.run('; '.join(buildcmds), check=True, shell=True)
 
+    os.chdir(outdir)    
+
     # Default behaviour should be: OMP multi-threaded, BLAS single threaded.
     assert run('./test_fslStartup', 8, 8) == '8 1 8'
     assert run('./test_fslStartup', 4, 4) == '4 1 4'