Merge branch 'no_cluster' into 'main'

Allowing the code to be run without a cluster

See merge request !4

pydr/__init__.py

 #!/usr/bin/env python
 
-__version__ = '0.1.2'
+__version__ = '0.1.3'

pydr/dr.py

@@ -140,13 +140,13 @@ def calc_spec(timeseries, TR=0.392, nfft=1024):
 
 
 def dr_single_subject(
-    func:                  str,
-    map:                   str,
-    timecourse:            str,
-    grp_map:               str,
-    amplitude:             str = None,
-    spectra:               str = None,
-    func_smooth:           str = None
+    func:              str,
+    map:               str,
+    timecourse:        str,
+    grp_map:           str,
+    amplitude:         str = None,
+    spectra:           str = None,
+    func_smooth:       str = None
 ):
 
     assert_env('FSLDIR')
@@ -245,7 +245,7 @@ def dr_single_subject(
         np.savetxt(spectra, spec, delimiter='\t', fmt='%.6f')
 
 
-def dr(files, grp_maps, workdir):
+def dr(files, grp_maps, workdir, submit_to_cluster=True):
 
     assert_env('FSLDIR')
     assert_env('FSLOUTPUTTYPE')
@@ -308,14 +308,24 @@ def dr(files, grp_maps, workdir):
             logger.info(cmd)
             fpr.write(cmd + '\n')
 
-    fsl_sub = [
-        'fsl_sub',
-        '-T', '1400',
-        '-l', f'{workdir}/logs',
-        '--export', f'FSLDIR={os.environ["FSLDIR"]}',
-        '--export', f'FSLOUTPUTTYPE={os.environ["FSLOUTPUTTYPE"]}',
-        '-t', f'{workdir}/logs/dr_commands.txt',
-    ]
+    # Run all commands sequentially in case user does not want to run them in the cluster 
+    if not submit_to_cluster:
+        with open(f'{workdir}/logs/dr_commands.txt', 'r') as fpr:
+            for command in fpr.readlines():
+                logger.info(' '.join(command))
+                output=run(command)
+                print(output)
 
-    logger.info(' '.join(fsl_sub))
-    run(fsl_sub)
+    # Run all commands in the cluster with fsl_sub
+    else:
+        command =[
+            'fsl_sub',
+            '-T', '1400',
+            '-l', f'{workdir}/logs',
+            '--export', f'FSLDIR={os.environ["FSLDIR"]}',
+            '--export', f'FSLOUTPUTTYPE={os.environ["FSLOUTPUTTYPE"]}',
+            '-t', f'{workdir}/logs/dr_commands.txt',
+         ]
+
+        logger.info(' '.join(command))
+        run(command)