Merge branch 'master' into 'master'

MNT: renamed extract_noise to fsl_ents

See merge request fsl/fslpy!72

fsl/scripts/extract_noise.py → fsl/scripts/fsl_ents.py

@@ -5,7 +5,7 @@
 #
 # Author: Paul McCarthy <pauldmccarthy@gmail.com>
 #
-"""This module defines the ``extract_noise`` script, for extracting component
+"""This module defines the ``fsl_ents`` script, for extracting component
 time series from a MELODIC ``.ica`` directory.
 """
 
@@ -28,7 +28,7 @@ with warnings.catch_warnings():
 
 
 DTYPE = np.float64
-name  = "extract_noise"
+name  = "fsl_ents"
 desc  = 'Extract component time series from a MELODIC .ica directory'
 usage = """
 {name}: {desc}
@@ -204,7 +204,7 @@ def loadConfoundFiles(conffiles, npts):
 
 
 def main(argv=None):
-    """Entry point for the ``extract_noise`` script.
+    """Entry point for the ``fsl_ents`` script.
 
     Identifies component time series to extract, extracts them, loads extra
     confound files, and saves them out to a file.

setup.py

@@ -124,7 +124,7 @@ setup(
             'imglob        = fsl.scripts.imglob:main',
             'atlasq        = fsl.scripts.atlasq:main',
             'atlasquery    = fsl.scripts.atlasq:atlasquery_emulation',
-            'extract_noise = fsl.scripts.extract_noise:main',
+            'fsl_ents = fsl.scripts.fsl_ents:main',
         ]
     }
 )

tests/test_extract_noise.py → tests/test_fsl_ents.py

 #!/usr/bin/env python
 #
-# test_extract_noise.py -
+# test_fsl_ents.py -
 #
 # Author: Paul McCarthy <pauldmccarthy@gmail.com>
 #
@@ -12,7 +12,7 @@ import numpy as np
 import pytest
 
 import fsl.utils.tempdir         as tempdir
-import fsl.scripts.extract_noise as extn
+import fsl.scripts.fsl_ents as extn
 
 
 def test_genComponentIndexList():
@@ -87,7 +87,7 @@ def test_loadConfoundFiles():
             extn.loadConfoundFiles(conffiles, npts)
 
 
-def test_extract_noise():
+def test_fsl_ents():
 
     with tempdir.tempdir() as td:
 
@@ -95,7 +95,7 @@ def test_extract_noise():
         melmix = np.random.randint(1, 100, (100, 20))
         np.savetxt('melodic_mix', melmix)
 
-        sys.argv = ['extract_noise', td] + '-o out.txt 1 2 3'.split()
+        sys.argv = ['fsl_ents', td] + '-o out.txt 1 2 3'.split()
         extn.main()
         assert np.all(np.loadtxt('out.txt') == melmix[:, :3])
 
@@ -115,13 +115,13 @@ def test_extract_noise():
         assert np.all(np.loadtxt('out.txt') == exp)
 
 
-def test_extract_noise_usage():
+def test_fsl_ents_usage():
 
     with pytest.raises(SystemExit) as e:
         extn.main([])
     assert e.value.code == 0
 
-def test_extract_noise_badargs():
+def test_fsl_ents_badargs():
 
     with pytest.raises(SystemExit) as e:
         extn.main(['non-existent.ica', '1', '2', '3'])