Commit a81c4b89 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

Merge branch 'rel/2.0.1' into 'v2.0'

Rel/2.0.1

See merge request fsl/fslpy!112
parents 160e2226 4c6d8ff2
Pipeline #3527 passed with stages
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...@@ -2,6 +2,18 @@ This document contains the ``fslpy`` release history in reverse chronological ...@@ -2,6 +2,18 @@ This document contains the ``fslpy`` release history in reverse chronological
order. 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) 2.0.0 (Friday March 20th 2019)
------------------------------ ------------------------------
......
``fsl.utils.temdir`` ``fsl.utils.tempdir``
==================== =====================
.. automodule:: fsl.utils.tempdir .. automodule:: fsl.utils.tempdir
:members: :members:
......
``fsl.wrappers.fsl_anat``
=========================
.. automodule:: fsl.wrappers.fsl_anat
:members:
:undoc-members:
:show-inheritance:
...@@ -10,6 +10,7 @@ ...@@ -10,6 +10,7 @@
fsl.wrappers.flirt fsl.wrappers.flirt
fsl.wrappers.fnirt fsl.wrappers.fnirt
fsl.wrappers.fslmaths fsl.wrappers.fslmaths
fsl.wrappers.fsl_anat
fsl.wrappers.fugue fsl.wrappers.fugue
fsl.wrappers.melodic fsl.wrappers.melodic
fsl.wrappers.misc fsl.wrappers.misc
......
...@@ -333,7 +333,7 @@ def relatedFiles(fname, ftypes=None): ...@@ -333,7 +333,7 @@ def relatedFiles(fname, ftypes=None):
related = [] related = []
for ftype in ftypes: for ftype in ftypes:
related.extend( hits = glob.glob(op.join(dirname, '{}*{}'.format(prefix, ftype)))
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] return [r for r in related if r != path]
...@@ -47,7 +47,7 @@ import re ...@@ -47,7 +47,7 @@ import re
import string import string
__version__ = '2.0.0' __version__ = '2.0.1'
"""Current version number, as a string. """ """Current version number, as a string. """
......
...@@ -10,7 +10,7 @@ ...@@ -10,7 +10,7 @@
functions. 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 decorators which allow you to write your wrapper function such that it simply
generates the command-line needed to respectively run a standard shell generates the command-line needed to respectively run a standard shell
command or a FSL command. For example:: command or a FSL command. For example::
...@@ -39,7 +39,7 @@ patterns. For example:: ...@@ -39,7 +39,7 @@ patterns. For example::
The :func:`fileOrImage` and :func:`fileOrArray` functions can be used to The :func:`fileOrImage` and :func:`fileOrArray` functions can be used to
decorate a wrapper function such that in-memory ``nibabel`` images or Numpy 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 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') @fileOrImage('src', 'ref')
...@@ -225,18 +225,18 @@ def applyArgStyle(style, ...@@ -225,18 +225,18 @@ def applyArgStyle(style,
========= ========== =========================== ========= ========== ===========================
``style`` ``valsep`` Result ``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``
``'--'`` ' ' ``--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 ``'-='`` ``' '`` Not supported
``'-='`` '"' ``-name="val1 val2 val3"`` ``'-='`` ``'"'`` ``-name="val1 val2 val3"``
``'-='`` ',' ``-name=val1,val2,val3`` ``'-='`` ``','`` ``-name=val1,val2,val3``
``'--='`` ' ' Not supported ``'--='`` ``' '`` Not supported
``'--='`` '"' ``--name="val1 val2 val3"`` ``'--='`` ``'"'`` ``--name="val1 val2 val3"``
``'--='`` ',' ``--name=val1,val2,val3`` ``'--='`` ``','`` ``--name=val1,val2,val3``
========= ========== =========================== ========= ========== ===========================
......
...@@ -224,6 +224,7 @@ def test_relatedFiles(): ...@@ -224,6 +224,7 @@ def test_relatedFiles():
assert len(gifti.relatedFiles(badname)) == 0 assert len(gifti.relatedFiles(badname)) == 0
assert len(gifti.relatedFiles('nonexistent')) == 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] lsurfaces = [op.join(td, f) for f in lsurfaces]
rsurfaces = [op.join(td, f) for f in rsurfaces] rsurfaces = [op.join(td, f) for f in rsurfaces]
lrelated = [op.join(td, f) for f in lrelated] lrelated = [op.join(td, f) for f in lrelated]
...@@ -236,6 +237,12 @@ def test_relatedFiles(): ...@@ -236,6 +237,12 @@ def test_relatedFiles():
result = gifti.relatedFiles(s) result = gifti.relatedFiles(s)
assert sorted(rrelated) == sorted(result) 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([ TEST_VERTS = np.array([
[0, 0, 0], [0, 0, 0],
[1, 0, 0], [1, 0, 0],
......
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