Merge remote-tracking branch 'upstream/master' into doc_improvements

.github/stale.yml

@@ -0,0 +1,16 @@
+# Number of days of inactivity before an issue becomes stale
+daysUntilStale: 90
+# Number of days of inactivity before a stale issue is closed
+daysUntilClose: 7
+# Issues with these labels will never be considered stale
+exemptLabels:
+  - community
+# Label to use when marking an issue as stale
+staleLabel: stale
+# Comment to post when marking an issue as stale. Set to `false` to disable
+markComment: >
+  This issue has been automatically marked as stale because it has not had
+  recent activity. It will be closed if no further activity occurs. Thank you
+  for your contributions to tedana:tada: !
+# Comment to post when closing a stale issue. Set to `false` to disable
+closeComment: false

tedana/tests/test_integration.py

@@ -81,8 +81,11 @@ def test_integration_five_echo(skip_integration):
     # download data and run the test
     download_test_data('https://osf.io/9c42e/download',
                        os.path.dirname(out_dir))
+    prepend = '/tmp/data/five-echo/p06.SBJ01_S09_Task11_e'
+    suffix = '.sm.nii.gz'
+    datalist = [prepend + str(i+1) + suffix for i in range(5)]
     tedana_workflow(
-        data='/tmp/data/five-echo/p06.SBJ01_S09_Task11_e[1,2,3,4,5].sm.nii.gz',
+        data=datalist,
         tes=[15.4, 29.7, 44.0, 58.3, 72.6],
         out_dir=out_dir,
         debug=True, verbose=True)

tedana/workflows/tedana.py

@@ -366,6 +366,8 @@ def tedana_workflow(data, tes, mask=None, mixm=None, ctab=None, manacc=None,
 
     # coerce data to samples x echos x time array
     if isinstance(data, str):
+        if not op.exists(data):
+            raise ValueError('Zcat file {} does not exist'.format(data))
         data = [data]
 
     LGR.info('Loading input data: {}'.format([f for f in data]))