Merge branch 'rel/3.0.1' into 'v3.0'

Rel/3.0.1

See merge request fsl/fslpy!225

.gitlab-ci.yml

@@ -206,7 +206,7 @@ build-doc:
    - docker
 
   stage: doc
-  image: python:3.6
+  image: python:3.7
 
   script:
     - bash ./.ci/build_doc.sh
@@ -227,7 +227,7 @@ build-pypi-dist:
   <<: *check_version
 
   stage: build
-  image: python:3.6
+  image: python:3.7
 
   tags:
     - docker
@@ -251,7 +251,7 @@ deploy-doc:
   <<: *setup_ssh
   stage: deploy
   when:  manual
-  image: python:3.6
+  image: python:3.7
 
   tags:
     - docker
@@ -268,7 +268,7 @@ deploy-pypi:
   <<: *setup_ssh
   stage: deploy
   when:  manual
-  image: python:3.6
+  image: python:3.7
 
   tags:
     - docker
@@ -285,7 +285,7 @@ deploy-zenodo:
   <<: *setup_ssh
   stage: deploy
   when:  manual
-  image: python:3.6
+  image: python:3.7
 
   tags:
     - docker

CHANGELOG.rst

@@ -2,6 +2,17 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
+3.0.1 (Wednesday 15th April 2020)
+---------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* The :func:`.isMelodicDir` function now accepts directories that do not end
+  with ``.ica``, as long as all required files are present.
+
 
 3.0.0 (Sunday 29th March 2020)
 ------------------------------
@@ -52,7 +63,7 @@ Changed
   :attr:`.LOAD` symbol, can now be accessed as attributes of the returned
   results object, in addition to being accessed as dict items.
 * Wrapper functions decorated with the :func:`.fileOrImage`,
- :func:`.fileOrArray`, or :func:`.fileOrText` decorators will now pass all
+  :func:`.fileOrArray`, or :func:`.fileOrText` decorators will now pass all
   arguments and return values through unchanged if an argument called ``submit``
   is passed in, and is set to ``True`` (or any non-``False``
   value). Furthermore, in such a scenario a :exc:`ValueError` will be raised if

fsl/data/image.py

@@ -622,8 +622,9 @@ class Nifti(notifier.Notifier, meta.Meta):
 
         if from_ not in ('voxel', 'fsl', 'world') or \
            to    not in ('voxel', 'fsl', 'world'):
-            raise ValueError('Invalid source/reference spaces: '
-                             '{} -> {}'.format(from_, to))
+            raise ValueError('Invalid source/reference spaces: "{}" -> "{}".'
+                             'Recognised spaces are "voxel", "fsl", and '
+                             '"world"'.format(from_, to))
 
         return np.copy(self.__affines[from_, to])
 

fsl/data/melodicanalysis.py

@@ -33,7 +33,6 @@ import logging
 import os.path as op
 import numpy   as np
 
-import fsl.utils.path        as fslpath
 import fsl.data.image        as fslimage
 import fsl.data.featanalysis as featanalysis
 
@@ -63,10 +62,9 @@ def isMelodicImage(path):
 
 
 def isMelodicDir(path):
-    """Returns ``True`` if the given path looks like it is contained within
-    a MELODIC directory, ``False`` otherwise. A melodic directory:
+    """Returns ``True`` if the given path looks like it is a MELODIC directory,
+    ``False`` otherwise. A MELODIC directory:
 
-      - Must be named ``*.ica``.
       - Must contain a file called ``melodic_IC.nii.gz`` or
         ``melodic_oIC.nii.gz``.
       - Must contain a file called ``melodic_mix``.
@@ -75,12 +73,7 @@ def isMelodicDir(path):
 
     path = op.abspath(path)
 
-    if op.isdir(path): dirname = path
-    else:              dirname = op.dirname(path)
-
-    sufs = ['.ica']
-
-    if not any([dirname.endswith(suf) for suf in sufs]):
+    if not op.isdir(path):
         return False
 
     # Must contain an image file called
@@ -88,7 +81,7 @@ def isMelodicDir(path):
     prefixes = ['melodic_IC', 'melodic_oIC']
     for p in prefixes:
         try:
-            fslimage.addExt(op.join(dirname, p))
+            fslimage.addExt(op.join(path, p))
             break
         except fslimage.PathError:
             pass
@@ -97,8 +90,8 @@ def isMelodicDir(path):
 
     # Must contain files called
     # melodic_mix and melodic_FTmix
-    if not op.exists(op.join(dirname, 'melodic_mix')):   return False
-    if not op.exists(op.join(dirname, 'melodic_FTmix')): return False
+    if not op.exists(op.join(path, 'melodic_mix')):   return False
+    if not op.exists(op.join(path, 'melodic_FTmix')): return False
 
     return True
 
@@ -108,10 +101,13 @@ def getAnalysisDir(path):
     to that MELODIC directory is returned. Otherwise, ``None`` is returned.
     """
 
-    meldir = fslpath.deepest(path, ['.ica'])
+    if not op.isdir(path):
+        path = op.dirname(path)
 
-    if meldir is not None and isMelodicDir(meldir):
-        return meldir
+    while path not in (op.sep, ''):
+        if isMelodicDir(path):
+            return path
+        path = op.dirname(path)
 
     return None
 

fsl/version.py

@@ -47,7 +47,7 @@ import            re
 import            string
 
 
-__version__ = '3.0.0'
+__version__ = '3.0.1'
 """Current version number, as a string. """
 
 

fsl/wrappers/flirt.py

@@ -98,19 +98,26 @@ def invxfm(inmat, omat):
     return ['convert_xfm', '-omat', omat, '-inverse', inmat]
 
 
-@wutils.fileOrArray('inmat1', 'inmat2', 'outmat')
+@wutils.fileOrArray('atob', 'atoc', 'btoc')
 @wutils.fslwrapper
-def concatxfm(inmat1, inmat2, outmat):
-    """Use ``convert_xfm`` to concatenate two affines."""
+def concatxfm(atob, btoc, atoc):
+    """Use ``convert_xfm`` to concatenate two affines. Note that the
+    order of the input matrices is the opposite of the order expected
+    by ``convert_xfm``.
+
+    :arg atob: Input matrix, transforming from "A" to "B".
+    :arg btoc: Input matrix, transforming from "B" to "C".
+    :arg atoc: Output matrix, transforming from "A" to "C".
+    """
 
-    asrt.assertFileExists(inmat1, inmat2)
+    asrt.assertFileExists(atob, btoc)
 
     cmd = ['convert_xfm',
            '-omat',
-           outmat,
+           atoc,
            '-concat',
-           inmat2,
-           inmat1]
+           btoc,
+           atob]
 
     return cmd
 

tests/test_assertions.py

@@ -160,14 +160,14 @@ def test_assertIsMelodicDir():
         ('analysis.ica', [                      'melodic_mix', 'melodic_FTmix'], False),
         ('analysis.ica', ['melodic_IC.nii.gz',                 'melodic_FTmix'], False),
         ('analysis.ica', ['melodic_IC.nii.gz',  'melodic_mix'],                  False),
-        ('analysis',     ['melodic_IC.nii.gz',  'melodic_mix', 'melodic_FTmix'], False),
-        ('analysis',     ['melodic_oIC.nii.gz', 'melodic_mix', 'melodic_FTmix'], False),
+        ('analysis',     ['melodic_IC.nii.gz',  'melodic_mix', 'melodic_FTmix'], True),
+        ('analysis',     [                      'melodic_mix', 'melodic_FTmix'], False),
     ]
 
     for dirname, paths, expected in tests:
         with testdir(paths, dirname):
             if expected:
-                assertions.assertIsMelodicDir(dirname)
+                assertions.assertIsMelodicDir('.')
             else:
                 with pytest.raises(AssertionError):
                     assertions.assertIsMelodicDir(dirname)

tests/test_atlases.py

@@ -13,7 +13,8 @@ import              os
 import os.path   as op
 import numpy     as np
 
-import mock
+
+from unittest import mock
 import pytest
 
 import tests

tests/test_fslsub.py

@@ -22,7 +22,7 @@ from . import mockFSLDIR
 
 
 mock_fsl_sub = """
-#!{}
+#!/usr/bin/env python3
 
 import random
 import os
@@ -62,8 +62,7 @@ with open('{{}}.o{{}}'.format(cmd, jobid), 'w') as stdout, \
 
 print(str(jobid))
 sys.exit(0)
-""".format(sys.executable, op.dirname(fsl.__file__)).strip()
-
+""".format(op.dirname(fsl.__file__)).strip()
 
 @contextlib.contextmanager
 def fslsub_mockFSLDIR():

tests/test_melodicanalysis.py

@@ -55,10 +55,10 @@ def test_isMelodicDir():
         meldir = op.join(testdir, 'analysis.ica')
         assert mela.isMelodicDir(meldir)
 
-    # Directory must end in .ica
+    # non-.ica prefix is ok
     with tests.testdir([p.replace('.ica', '.blob') for p in paths]) as testdir:
         meldir = op.join(testdir, 'analysis.blob')
-        assert not mela.isMelodicDir(meldir)
+        assert mela.isMelodicDir(meldir)
 
     # Directory must exist!
     assert not mela.isMelodicDir('non-existent.ica')

tests/test_wrappers/test_fslstats.py

@@ -18,9 +18,9 @@ from .. import mockFSLDIR as mockFSLDIR_base, make_random_image
 
 
 mock_fslstats = """
-#!{}
+#!/usr/bin/env python3
 
-shape = {{outshape}}
+shape = {outshape}
 
 import sys
 import numpy as np
@@ -31,7 +31,7 @@ if len(shape) == 1:
     data = data.reshape(1, -1)
 
 np.savetxt(sys.stdout, data, fmt='%i')
-""".format(sys.executable).strip()
+""".strip()
 
 
 @contextlib.contextmanager