RF + BF: pmu2bids returns the PhysioData, saved to file in main

It modifies `physio2bidsphysio` accordingly.
Addresses second part of #5

bidsphysio.physio2bids/bidsphysio/physio2bids/physio2bidsphysio.py

@@ -73,7 +73,7 @@ def main():
     # make sure input files exist:
     for infile in args.infiles:
         if not os.path.exists(infile):
-            raise FileNotFoundError( '{i} file not found'.format(i=infile))
+            raise FileNotFoundError('{i} file not found'.format(i=infile))
 
     # check that the input file is recognized (check extension):
     knownExtensions = ['dcm', 'puls', 'resp', 'acq', 'log']
@@ -97,17 +97,20 @@ def main():
             os.makedirs(odir)
 
     # depending on the allowedExtension, call the XXX2bids method of corresponding module:
+    physio_data = None
     if allowedExtensions == 'dcm':
         if len(args.infiles) > 1:
             raise Exception('Only one input file is allowed for DICOM physio files')
-        d2bp.dcm2bids( args.infiles, args.bidsprefix, verbose=args.verbose )
+        physio_data = d2bp.dcm2bids(args.infiles, verbose=args.verbose)
     elif allowedExtensions == 'log':
-        d2bp.dcm2bids(args.infiles, args.bidsprefix, verbose=args.verbose)
+        physio_data = d2bp.dcm2bids(args.infiles, verbose=args.verbose)
     elif allowedExtensions == 'acq':
-        a2bp.acq2bids( args.infiles, args.bidsprefix )
-    elif allowedExtensions == ['puls','resp']:
-        p2bp.pmu2bids( args.infiles, args.bidsprefix, verbose=args.verbose )
+        physio_data = a2bp.acq2bids(args.infiles)
+    elif allowedExtensions == ['puls', 'resp']:
+        physio_data = p2bp.pmu2bids(args.infiles, verbose=args.verbose)
 
+    if physio_data.labels():
+        physio_data.save_to_bids_with_trigger(args.bidsprefix)
 
 
 # This is the standard boilerplate that calls the main() function.

bidsphysio.physio2bids/tests/test_physio2bidsphysio.py

@@ -5,6 +5,7 @@
 import pytest
 
 from bidsphysio.physio2bids import physio2bidsphysio
+from bidsphysio.base.bidsphysio import PhysioData
 from bidsphysio.acq2bids import acq2bidsphysio as a2bp
 from bidsphysio.dcm2bids import dcm2bidsphysio as d2bp
 from bidsphysio.pmu2bids import pmu2bidsphysio as p2bp
@@ -31,16 +32,19 @@ def mock_acq2bids(*args, **kwargs):
         print('mock_acq2bids called')
         for a in args:
             print(a)
+        return PhysioData()
 
     def mock_dcm2bids(*args, **kwargs):
         print('mock_dcm2bids called')
         for a in args:
             print(a)
+        return PhysioData()
 
     def mock_pmu2bids(*args, **kwargs):
         print('mock_pmu2bids called')
         for a in args:
             print(a)
+        return PhysioData()
 
     monkeypatch.setattr(a2bp, "acq2bids", mock_acq2bids)
     monkeypatch.setattr(d2bp, "dcm2bids", mock_dcm2bids)
@@ -95,10 +99,9 @@ def test_main(
         monkeypatch.setattr(sys, 'argv', args)
         physio2bidsphysio.main()
         out = capfd.readouterr().out
-        printout, inarg, bidsarg, _ = out.split('\n')
+        printout, inarg, _ = out.split('\n')
         assert 'mock_' in printout and '2bids called' in printout
         assert infile in inarg
-        assert bidsarg == bidsPrefix
 
     # also, check that the output folder is created:
     assert (tmpdir / 'mydir').exists()
@@ -124,7 +127,6 @@ def test_main(
         monkeypatch.setattr(sys, 'argv', args)
         physio2bidsphysio.main()
         out = capfd.readouterr().out
-        printout, inarg, bidsarg, _ = out.split('\n')
+        printout, inarg, _ = out.split('\n')
         assert 'mock_' in printout and '2bids called' in printout
         assert inarg == str(multifile)
-        assert bidsarg == bidsPrefix