[TST] Add tests for the workflow CLIs (#538)

* Change rerun tests to use the CLI.

* Add t2smap CLI test.

* FIX

* No but fix.

* Address @rmarkello's review.

tedana/tests/test_integration.py

@@ -15,7 +15,7 @@
 import requests
 import pandas as pd
 
-from tedana.workflows import tedana_workflow
+from tedana.workflows import tedana as tedana_cli
 from tedana import io
 
 
@@ -86,9 +86,10 @@ def test_integration_five_echo(skip_integration):
     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(
+    echo_times = [15.4, 29.7, 44.0, 58.3, 72.6]
+    tedana_cli.tedana_workflow(
         data=datalist,
-        tes=[15.4, 29.7, 44.0, 58.3, 72.6],
+        tes=echo_times,
         out_dir=out_dir,
         tedpca='aic',
         fittype='curvefit',
@@ -100,19 +101,15 @@ def test_integration_five_echo(skip_integration):
     df = io.load_comptable(comptable)
     assert isinstance(df, pd.DataFrame)
 
+    # Test re-running, but use the CLI
     out_dir2 = '/tmp/data/five-echo/TED.five-echo-manual'
     acc_comps = df.loc[df['classification'] == 'accepted'].index.values
     mixing = os.path.join(out_dir, 'ica_mixing.tsv')
-    tedana_workflow(
-        data=datalist,
-        tes=[15.4, 29.7, 44.0, 58.3, 72.6],
-        out_dir=out_dir2,
-        debug=True,
-        verbose=True,
-        manacc=','.join(acc_comps.astype(str)),
-        ctab=comptable,
-        mixm=mixing,
-    )
+    args = (['-d'] + datalist + ['-e'] + [str(te) for te in echo_times] +
+            ['--out-dir', out_dir2, '--debug', '--verbose',
+             '--manacc', ','.join(acc_comps.astype(str)),
+             '--ctab', comptable, '--mix', mixing])
+    tedana_cli._main(args)
 
     # compare the generated output files
     fn = resource_filename('tedana',
@@ -137,7 +134,7 @@ def test_integration_four_echo(skip_integration):
     prepend += 'sub-PILOT_ses-01_task-localizerDetection_run-01_echo-'
     suffix = '_space-sbref_desc-preproc_bold+orig.HEAD'
     datalist = [prepend + str(i + 1) + suffix for i in range(4)]
-    tedana_workflow(
+    tedana_cli.tedana_workflow(
         data=datalist,
         tes=[11.8, 28.04, 44.28, 60.52],
         out_dir=out_dir,
@@ -166,21 +163,20 @@ def test_integration_three_echo(skip_integration):
     # download data and run the test
     download_test_data('https://osf.io/rqhfc/download',
                        os.path.dirname(out_dir))
-    tedana_workflow(
+    tedana_cli.tedana_workflow(
         data='/tmp/data/three-echo/three_echo_Cornell_zcat.nii.gz',
         tes=[14.5, 38.5, 62.5],
         out_dir=out_dir,
         low_mem=True,
         tedpca='mdl')
 
-    # test rerunning the workflow
-    tedana_workflow(
-        data='/tmp/data/three-echo/three_echo_Cornell_zcat.nii.gz',
-        tes=[14.5, 38.5, 62.5],
-        out_dir=out_dir2,
-        mixm=os.path.join(out_dir, 'ica_mixing.tsv'),
-        ctab=os.path.join(out_dir, 'ica_decomposition.json'),
-        no_png=True)
+    # Test re-running, but use the CLI
+    args = (['-d', '/tmp/data/three-echo/three_echo_Cornell_zcat.nii.gz',
+             '-e', '14.5', '38.5', '62.5',
+             '--out-dir', out_dir2, '--debug', '--verbose',
+             '--ctab', os.path.join(out_dir, 'ica_decomposition.json'),
+             '--mix', os.path.join(out_dir, 'ica_mixing.tsv')])
+    tedana_cli._main(args)
 
     # compare the generated output files
     fn = resource_filename('tedana',

tedana/tests/test_t2smap.py

@@ -94,8 +94,6 @@ def test_basic_t2smap4(self):
         """
         A very simple test, to confirm that t2smap creates output
         files when combmode is set to 'paid' and fitmode is set to 'ts'.
-
-        Not sure why this fails.
         """
         data_dir = get_test_data_path()
         data = [op.join(data_dir, 'echo1.nii.gz'),
@@ -118,6 +116,32 @@ def test_basic_t2smap4(self):
         img = nib.load(op.join(out_dir, 'ts_OC.nii.gz'))
         assert len(img.shape) == 4
 
+    def test_t2smap_cli(self):
+        """
+        Run test_basic_t2smap1, but use the CLI method.
+        """
+        data_dir = get_test_data_path()
+        data = [op.join(data_dir, 'echo1.nii.gz'),
+                op.join(data_dir, 'echo2.nii.gz'),
+                op.join(data_dir, 'echo3.nii.gz')]
+        args = (['-d'] + data +
+                ['-e', '14.5', '38.5', '62.5', '--combmode', 't2s',
+                 '--fitmode', 'all', '--label', 't2smap'])
+        workflows.t2smap._main(args)
+        out_dir = 'TED.echo1.t2smap'
+
+        # Check outputs
+        img = nib.load(op.join(out_dir, 't2sv.nii.gz'))
+        assert len(img.shape) == 3
+        img = nib.load(op.join(out_dir, 's0v.nii.gz'))
+        assert len(img.shape) == 3
+        img = nib.load(op.join(out_dir, 't2svG.nii.gz'))
+        assert len(img.shape) == 3
+        img = nib.load(op.join(out_dir, 's0vG.nii.gz'))
+        assert len(img.shape) == 3
+        img = nib.load(op.join(out_dir, 'ts_OC.nii.gz'))
+        assert len(img.shape) == 4
+
     def teardown_method(self):
         # Clean up folders
         rmtree('TED.echo1.t2smap')