Merge branch 'bf/gifti_related_files' into 'master'

Bf/gifti related files

See merge request fsl/fslpy!111

CHANGELOG.rst

@@ -2,6 +2,18 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
+2.0.1 (Monday April 1st 2019)
+-----------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed a bug with the :func:`.gifti.relatedFiles` function returning
+  duplicate files.
+
+
 2.0.0 (Friday March 20th 2019)
 ------------------------------
 

doc/fsl.utils.tempdir.rst

-``fsl.utils.temdir``
-====================
+``fsl.utils.tempdir``
+=====================
 
 .. automodule:: fsl.utils.tempdir
     :members:

doc/fsl.wrappers.fsl_anat.rst

+``fsl.wrappers.fsl_anat``
+=========================
+
+.. automodule:: fsl.wrappers.fsl_anat
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.wrappers.rst

@@ -10,6 +10,7 @@
    fsl.wrappers.flirt
    fsl.wrappers.fnirt
    fsl.wrappers.fslmaths
+   fsl.wrappers.fsl_anat
    fsl.wrappers.fugue
    fsl.wrappers.melodic
    fsl.wrappers.misc

fsl/data/gifti.py

@@ -333,7 +333,7 @@ def relatedFiles(fname, ftypes=None):
     related = []
 
     for ftype in ftypes:
-        related.extend(
-            glob.glob(op.join(dirname, '{}*{}'.format(prefix, ftype))))
+        hits = glob.glob(op.join(dirname, '{}*{}'.format(prefix, ftype)))
+        related.extend([h for h in hits if h not in related])
 
     return [r for r in related if r != path]

fsl/wrappers/wrapperutils.py

@@ -10,7 +10,7 @@
 functions.
 
 
-The :func:`cmdwrapper` and :func:`fslwrapper` functions are conenience
+The :func:`cmdwrapper` and :func:`fslwrapper` functions are convenience
 decorators which allow you to write your wrapper function such that it simply
 generates the command-line needed to respectively run a standard shell
 command or a FSL command. For example::
@@ -39,7 +39,7 @@ patterns. For example::
 The :func:`fileOrImage` and :func:`fileOrArray` functions can be used to
 decorate a wrapper function such that in-memory ``nibabel`` images or Numpy
 arrays can be passed in as arguments - they will be automatically saved out to
-files, and then the file names passed into the wrapper function. For exmaple::
+files, and then the file names passed into the wrapper function. For example::
 
 
     @fileOrImage('src', 'ref')
@@ -225,18 +225,18 @@ def applyArgStyle(style,
     =========  ==========  ===========================
     ``style``  ``valsep``  Result
     =========  ==========  ===========================
-    ``'-'``    ' '         ``-name val1 val2 val3``
-    ``'-'``    '"'         ``-name "val1 val2 val3"``
-    ``'-'``    ','         ``-name val1,val2,val3``
-    ``'--'``   ' '         ``--name val1 val2 val3``
-    ``'--'``   '"'         ``--name "val1 val2 val3"``
-    ``'--'``   ','         ``--name val1,val2,val3``
-    ``'-='``   ' '         Not supported
-    ``'-='``   '"'         ``-name="val1 val2 val3"``
-    ``'-='``   ','         ``-name=val1,val2,val3``
-    ``'--='``  ' '         Not supported
-    ``'--='``  '"'         ``--name="val1 val2 val3"``
-    ``'--='``  ','         ``--name=val1,val2,val3``
+    ``'-'``    ``' '``     ``-name val1 val2 val3``
+    ``'-'``    ``'"'``     ``-name "val1 val2 val3"``
+    ``'-'``    ``','``     ``-name val1,val2,val3``
+    ``'--'``   ``' '``     ``--name val1 val2 val3``
+    ``'--'``   ``'"'``     ``--name "val1 val2 val3"``
+    ``'--'``   ``','``     ``--name val1,val2,val3``
+    ``'-='``   ``' '``     Not supported
+    ``'-='``   ``'"'``     ``-name="val1 val2 val3"``
+    ``'-='``   ``','``     ``-name=val1,val2,val3``
+    ``'--='``  ``' '``     Not supported
+    ``'--='``  ``'"'``     ``--name="val1 val2 val3"``
+    ``'--='``  ``','``     ``--name=val1,val2,val3``
     =========  ==========  ===========================
 
 

tests/test_gifti.py

@@ -224,6 +224,7 @@ def test_relatedFiles():
         assert len(gifti.relatedFiles(badname))       == 0
         assert len(gifti.relatedFiles('nonexistent')) == 0
 
+        llisting  = [op.join(td, f) for f in listing]
         lsurfaces = [op.join(td, f) for f in lsurfaces]
         rsurfaces = [op.join(td, f) for f in rsurfaces]
         lrelated  = [op.join(td, f) for f in lrelated]
@@ -236,6 +237,12 @@ def test_relatedFiles():
             result = gifti.relatedFiles(s)
             assert sorted(rrelated) == sorted(result)
 
+        exp = lsurfaces + lrelated
+        exp = [f for f in exp if f != lsurfaces[0]]
+        result = gifti.relatedFiles(lsurfaces[0],
+                                    ftypes=gifti.ALLOWED_EXTENSIONS)
+        assert sorted(exp) == sorted(result)
+
 TEST_VERTS = np.array([
     [0, 0, 0],
     [1, 0, 0],