Merge branch 'master' into msc

.conda/post-link.sh

-if [ -e ${FSLDIR}/etc/fslconf/requestFSLpythonLink.sh ]; then 
-    $FSLDIR/etc/fslconf/requestFSLpythonLink.sh atlasquery atlasq imcp immv imglob
+if [ -e ${FSLDIR}/etc/fslconf/requestFSLpythonLink.sh ]; then
+    $FSLDIR/etc/fslconf/requestFSLpythonLink.sh atlasquery atlasq imcp immv imglob extract_noise
 fi
-

CHANGELOG.rst

@@ -2,9 +2,8 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
-
-1.10.0 (Under development)
---------------------------
+1.10.0 (Wednesday July 18th 2018)
+---------------------------------
 
 
 Added
@@ -15,8 +14,9 @@ Added
   component time courses from a MELODIC ICA analysis.
 * New :func:`.path.allFiles` function which returns all files underneath a
   directory.
-* The :func:`.fileOrImage`   and :func:`.fileOrArray` decorators now support
+* The :func:`.fileOrImage` and :func:`.fileOrArray` decorators now support
   loading of files which are specified with an output basename.
+* New :mod:`.fast` wrapper function for the FSL FAST tool.
 
 
 Changed
@@ -28,7 +28,6 @@ Changed
 * Removed dependency on ``pytest-runner``.
 
 
-
 1.9.0 (Monday June 4th 2018)
 ----------------------------
 

doc/fsl.utils.fslsub.rst

+``fsl.utils.fslsub``
+====================
+
+.. automodule:: fsl.utils.fslsub
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.utils.rst

@@ -7,6 +7,7 @@
    fsl.utils.assertions
    fsl.utils.cache
    fsl.utils.ensure
+   fsl.utils.fslsub
    fsl.utils.idle
    fsl.utils.imcp
    fsl.utils.memoize

doc/fsl.wrappers.fast.rst

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

doc/fsl.wrappers.rst

@@ -6,6 +6,7 @@
 
    fsl.wrappers.bet
    fsl.wrappers.eddy
+   fsl.wrappers.fast
    fsl.wrappers.flirt
    fsl.wrappers.fnirt
    fsl.wrappers.fslmaths

fsl/data/fixlabels.py

@@ -62,8 +62,10 @@ def loadLabelFile(filename,
     separated by commas:
 
       - The component index (starting from 1).
+
       - One or more labels for the component (multiple labels must be
         comma-separated).
+
       - ``'True'`` if the component has been classified as *bad*,
         ``'False'`` otherwise. This field is optional - if the last
         comma-separated token on a line is not equal (case-insensitive)
@@ -91,12 +93,15 @@ def loadLabelFile(filename,
                         file is returned.
 
     :returns: A tuple containing:
-                - The path to the melodic directory as specified in the label
-                  file
-                - A list of lists, one list per component, with each list
-                  containing the labels for the corresponding component.
-                - If ``returnIndices is True``, a list of the noisy component
-                  indices (starting from 1) that were specified in the file.
+
+               - The path to the melodic directory as specified in the label
+                 file
+
+               - A list of lists, one list per component, with each list
+                 containing the labels for the corresponding component.
+
+               - If ``returnIndices is True``, a list of the noisy component
+                 indices (starting from 1) that were specified in the file.
     """
 
     signalLabels = None

fsl/utils/fslsub.py

@@ -90,8 +90,11 @@ def submit(command,
                          queuing options
     :arg multi_threaded: Submit a multi-threaded task - Set to a tuple
                          containing two elements:
+
                           - <pename>: a PE configures for the requested queues
+
                           - <threads>: number of threads to run
+
     :arg verbose:        If True, use verbose mode
 
     :return:             tuple of submitted job ids

fsl/version.py

@@ -41,7 +41,7 @@ import            re
 import            string
 
 
-__version__ = '1.10.0.dev0'
+__version__ = '1.11.0.dev0'
 """Current version number, as a string. """
 
 

tests/test_image.py

@@ -39,8 +39,12 @@ except ImportError:
 try:
     import indexed_gzip as igzip
 except ImportError:
+
+    class MockError(Exception):
+        pass
+
     igzip           = mock.MagicMock()
-    igzip.ZranError = mock.MagicMock()
+    igzip.ZranError = MockError
 
 
 def make_image(filename=None,