Add travis wait command

.travis.yml

@@ -35,7 +35,7 @@ before_install:
       pip install flake8;
     fi
   - if [ "${CHECK_TYPE}" == "test" ]; then
-      pip install "pytest>=4.6" pytest-cov coverage coveralls codecov;
+      pip install "pytest>=5.3" pytest-cov coverage coveralls codecov;
     fi
   - if [ "${CHECK_TYPE}" == "docdoctest" ]; then
       pip install "sphinx>2.0" sphinx_rtd_theme pandas sphinx-argparse;

phys2bids/cli/run.py

@@ -76,9 +76,9 @@ def _get_parser():
                           dest='chtrig',
                           type=int,
                           help='The column number of the trigger channel. '
-                               'Channel numbering starts with 0. '
-                               'Default is 0.',
-                          default=0)
+                               'Channel numbering starts with 1. '
+                               'Default is 1.',
+                          default=1)
     optional.add_argument('-chsel', '--channel-selection',
                           dest='chsel',
                           nargs='*',

phys2bids/interfaces/acq.py

@@ -21,23 +21,29 @@ def populate_phys_input(filename, chtrig):
     filename: str
         path to the txt labchart file
     chtrig : int
-        index of trigger channel
+        index of trigger channel.
+        !!! ATTENTION: IT'S MEANT TO REPRESENT AN INDEX STARTING FROM 1 !!!
 
     Returns
     -------
     BlueprintInput
 
+    Note
+    ----
+    chtrig is not a 0-based Python index - instead, it's human readable (i.e., 1-based).
+    This is handy because, when initialising the class, a new channel corresponding
+    to time is added at the beginning - that is already taken into account!
+
     See Also
     --------
     physio_obj.BlueprintInput
     """
-
     with warnings.catch_warnings():
         warnings.filterwarnings('ignore', category=DeprecationWarning)
         data = read_file(filename).channels
 
-    freq = [data[chtrig].samples_per_second, ]
-    timeseries = [data[chtrig].time_index, ]
+    freq = [data[chtrig - 1].samples_per_second, ]
+    timeseries = [data[chtrig - 1].time_index, ]
     units = ['s', ]
     names = ['time', ]
 

phys2bids/phys2bids.py

@@ -127,7 +127,7 @@ def print_json(outfile, samp_freq, time_offset, ch_name):
     description='The BIDS specification',
     cite_module=True)
 def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
-              sub=None, ses=None, chtrig=0, chsel=None, num_timepoints_expected=None,
+              sub=None, ses=None, chtrig=1, chsel=None, num_timepoints_expected=None,
               tr=None, thr=None, pad=9, ch_name=[], yml='', debug=False, quiet=False):
     """
     Run main workflow of phys2bids.
@@ -191,6 +191,9 @@ def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
     # Check options to make them internally coherent pt. II
     # #!# This can probably be done while parsing?
     indir = utils.check_input_dir(indir)
+    if chtrig < 1:
+        raise Exception('Wrong trigger channel. Channel indexing starts with 1!')
+
     filename, ftype = utils.check_input_type(filename,
                                              indir)
 

phys2bids/tests/conftest.py

@@ -72,3 +72,9 @@ def multifreq_lab_file(testpath):
 def notime_lab_file(testpath):
     return fetch_file('cv5zr', testpath,
                       'Test2_samefreq_onescan_notime.txt')
+
+
+@pytest.fixture
+def multi_run_file(testpath):
+    return fetch_file('gvy84', testpath,
+                      'Test2_samefreq_TWOscans.txt')

phys2bids/tests/test_integration.py

@@ -221,4 +221,4 @@ def test_integration_multirun(multi_run_file):
     base_filename = 'Test2_samefreq_TWOscans_'
     for run in ['1', '2']:
         assert isfile(join(conversion_path, f'Test2_samefreq_TWOscans_{run}_trigger_time.png'))
-    assert isfile(join(conversion_path, 'Test2_samefreq_TWOscans.png'))
+    assert isfile(join(conversion_path, 'Test2_samefreq_TWOscans.png'))

setup.cfg

@@ -26,7 +26,7 @@ install_requires =
     matplotlib >=3.1.1, !=3.3.0rc1
     PyYAML !=*rc*
 tests_require =
-    pytest >=3.6
+    pytest >=5.3
 test_suite = pytest
 zip_safe = False
 packages = find: