diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 10c1c88da120f620f30ad21ea131693453c51544..ebbb4a14792901da84824e7c12480a8cb3ee9cec 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -11,18 +11,21 @@ Changed
^^^^^^^
* The ``fslpy`` API ocumentation is now hosted at
- https://open.win.ox.ac.uk/fsl/fslpy
+ https://open.win.ox.ac.uk/fsl/fslpy (!290).
* The :mod:`fsl` and :mod:`fsl.scripts` packages have been changed from being
`pkgutil-style
<https://packaging.python.org/guides/packaging-namespace-packages/#pkgutil-style-namespace-packages>`_
namespace packages to now being `native
<https://packaging.python.org/guides/packaging-namespace-packages/#native-namespace-packages>`_
- namespace packages.
+ namespace packages (!290).
* The :class:`.TaskThread` now allows an error handler function to be
- specified, which is run on the :mod:`.idle` loop.
+ specified, which is run on the :mod:`.idle` loop (!283).
* The :func:`.bids.loadMetadata` function no long resolves sym-links when
- determining whether a file is contained within a BIDS data set.
-
+ determining whether a file is contained within a BIDS data set (!287).
+* The :class:`.Image` class can now be created from a ``pathlib.Path`` object
+ (!292).
+* Some functions in the :mod:`.path` module can now be used with
+ ``pathlib.Path`` objects (!293).
Deprecated
^^^^^^^^^^
@@ -32,17 +35,20 @@ Deprecated
:mod:`fsl.utils.platform` module, including ``frozen``, ``haveGui``,
``canHaveGui``, ``inSSHSession``, ``inVNCSession``, ``wxPlatform``,
``wxFlavour``, ``glVersion``, ``glRenderer``, and ``glIsSoftwareRenderer``.
- Equivalent functions are being added to the ``fsleyes-widgets`` library.
+ Equivalent functions are being added to the ``fsleyes-widgets`` library
+ (!285).
* The :mod:`fsl.utils.filetree` package has been deprecated, and will be
removed in a future version of ``fslpy`` - it is now published as a separate
- library on [PyPI](https://pypi.org/project/file-tree/).
+ library on [PyPI](https://pypi.org/project/file-tree/) (!286).
Fixed
^^^^^
* Fixed an edge-case in the :mod:`.gifti` module, where a surface with a
- single triangle was being loaded incorrectly.
+ single triangle was being loaded incorrectly (!288).
+* Fixed an issue in the :func:`.func_to_cmd` function, where it was
+ unintentionally leaving flie handles open (!291).
diff --git a/README.rst b/README.rst
index f8b8fd8a118d8b0ee4e3070735c2d56b6d3e7b56..06df04918be7c407e33517f1466553048e2c5edc 100644
--- a/README.rst
+++ b/README.rst
@@ -19,7 +19,7 @@ programming library written in Python. It is used by `FSLeyes
<https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/>`_.
-``fslpy`` is tested against Python versions 3.6, 3.7, 3.8 and 3.9.
+``fslpy`` is tested against Python versions 3.7, 3.8 and 3.9.
Installation
diff --git a/fsl/data/bitmap.py b/fsl/data/bitmap.py
index 51b354f7ddfcef93cb44a2d2a83231b518d89fe2..4562300a794357d6382a3317a34b277f62d2b816 100644
--- a/fsl/data/bitmap.py
+++ b/fsl/data/bitmap.py
@@ -9,13 +9,13 @@ files. Pillow is required to use the ``Bitmap`` class.
"""
-import os.path as op
-import logging
-import six
+import os.path as op
+import pathlib
+import logging
-import numpy as np
+import numpy as np
-from . import image as fslimage
+import fsl.data.image as fslimage
log = logging.getLogger(__name__)
@@ -51,7 +51,7 @@ class Bitmap(object):
data.
"""
- if isinstance(bmp, six.string_types):
+ if isinstance(bmp, (pathlib.Path, str)):
try:
# Allow big images
@@ -61,7 +61,7 @@ class Bitmap(object):
except ImportError:
raise RuntimeError('Install Pillow to use the Bitmap class')
- src = bmp
+ src = str(bmp)
img = Image.open(src)
# If this is a palette/LUT
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 3dfe8a818286126c98939d83a3979f2f363cb375..b5d0cad72d12850aecbeeab7ac072aca9f9d3485 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -32,22 +32,21 @@ and file names:
"""
-import os
-import os.path as op
-import itertools as it
-import json
-import string
-import logging
-import tempfile
-
-import six
-import numpy as np
+import os
+import os.path as op
+import itertools as it
+import json
+import string
+import logging
+import tempfile
+
+from pathlib import Path
+from typing import Union
+import numpy as np
import nibabel as nib
import nibabel.fileslice as fileslice
-from pathlib import Path
-
import fsl.utils.meta as meta
import fsl.transform.affine as affine
import fsl.utils.notifier as notifier
@@ -58,6 +57,10 @@ import fsl.data.constants as constants
import fsl.data.imagewrapper as imagewrapper
+PathLike = Union[str, Path]
+ImageSource = Union[PathLike, nib.Nifti1Image, np.ndarray, 'Image']
+
+
log = logging.getLogger(__name__)
@@ -993,21 +996,21 @@ class Image(Nifti):
def __init__(self,
- image,
- name=None,
- header=None,
- xform=None,
- loadData=True,
- calcRange=True,
- threaded=False,
- dataSource=None,
- loadMeta=False,
+ image : ImageSource,
+ name : str = None,
+ header : nib.Nifti1Header = None,
+ xform : np.ndarray = None,
+ loadData : bool = True,
+ calcRange : bool = True,
+ threaded : bool = False,
+ dataSource : PathLike = None,
+ loadMeta : bool = False,
**kwargs):
"""Create an ``Image`` object with the given image data or file name.
:arg image: A string containing the name of an image file to load,
- or a Path object pointing to an image file, or a
- :mod:`numpy` array, or a :mod:`nibabel` image object,
+ or a Path object pointing to an image file, or a
+ :mod:`numpy` array, or a :mod:`nibabel` image object,
or an ``Image`` object.
:arg name: A name for the image.
@@ -1086,16 +1089,11 @@ class Image(Nifti):
header.set_qform(xform, code=qform)
# The image parameter may be the name of an image file
- if isinstance(image, six.string_types):
+ if isinstance(image, (str, Path)):
image = op.abspath(addExt(image))
nibImage = nib.load(image, **kwargs)
dataSource = image
saved = True
- # The image parameter may be a Path object pointing to an image file
- elif isinstance(image, Path):
- nibImage = nib.load(image, **kwargs)
- dataSource = str(image)
- saved = True
# Or a numpy array - we wrap it in a nibabel image,
# with an identity transformation (each voxel maps
@@ -1141,15 +1139,13 @@ class Image(Nifti):
nibImage = image
# Figure out the name of this image, if
- # it has not beenbeen explicitly passed in
+ # it has not been explicitly passed in
if name is None:
# If this image was loaded
# from disk, use the file name.
- if isinstance(image, six.string_types):
+ if isinstance(image, (str, Path)):
name = removeExt(op.basename(image))
- elif isinstance(image, Path):
- name = image.name
# Or the image was created from a numpy array
elif isinstance(image, np.ndarray):
diff --git a/fsl/data/mghimage.py b/fsl/data/mghimage.py
index 38f854446d3333cd7f150bd082d80d76df6cc236..8464d3d2ce674e7c07fc7d7b03b3c5b2f4cdd898 100644
--- a/fsl/data/mghimage.py
+++ b/fsl/data/mghimage.py
@@ -10,8 +10,8 @@ Freesurfer ``mgh``/``mgz`` image files.
import os.path as op
+import pathlib
-import six
import numpy as np
import nibabel as nib
@@ -47,7 +47,7 @@ class MGHImage(fslimage.Image):
All other arguments are passed through to :meth:`Image.__init__`
"""
- if isinstance(image, six.string_types):
+ if isinstance(image, (str, pathlib.Path)):
filename = op.abspath(image)
name = op.basename(filename)
image = nib.load(image)
diff --git a/fsl/utils/ensure.py b/fsl/utils/ensure.py
index a2fd8d4913dc921f541a1e8430933b72bec43b12..3e3ea8e92e1a2ce570a53c3898521af38c1af0ef 100644
--- a/fsl/utils/ensure.py
+++ b/fsl/utils/ensure.py
@@ -14,8 +14,6 @@ that some condition is met.
"""
-import six
-
import nibabel as nib
import fsl.data.image as fslimage
@@ -24,7 +22,7 @@ import fsl.data.image as fslimage
def ensureIsImage(img):
"""Ensures that the given ``img`` is an in-memory ``nibabel`` object.
"""
- if isinstance(img, six.string_types):
+ if isinstance(img, str):
img = fslimage.addExt(img)
img = nib.load(img)
return img
diff --git a/fsl/utils/fslsub.py b/fsl/utils/fslsub.py
index 4a09f0828cb0bea65305c1e4272437fc4094b57f..22e9de1ece00c4d7a62238f6da0c4193274dac88 100644
--- a/fsl/utils/fslsub.py
+++ b/fsl/utils/fslsub.py
@@ -37,7 +37,7 @@ Example usage, building a short pipeline::
"""
-from six import BytesIO
+from io import BytesIO
import os.path as op
import glob
import time
@@ -439,9 +439,9 @@ _external_job = ("""#!{}
# This is a temporary file designed to run the python function {},
# so that it can be submitted to the cluster
import pickle
-from six import BytesIO
+from io import BytesIO
from importlib import import_module
-{}
+{}
pickle_bytes = BytesIO({})
name_type, name, func_name, args, kwargs = pickle.load(pickle_bytes)
@@ -455,7 +455,7 @@ elif name_type == 'script':
func = local_execute[func_name]
else:
raise ValueError('Unknown name_type: %r' % name_type)
-
+
{}
""")
diff --git a/fsl/utils/memoize.py b/fsl/utils/memoize.py
index b777eed0c945a048858806107487bf214d710984..b7ee159c2d891db915e92d0bf37929ff3b5a7870 100644
--- a/fsl/utils/memoize.py
+++ b/fsl/utils/memoize.py
@@ -21,7 +21,6 @@ a function:
import logging
import hashlib
import functools
-import six
log = logging.getLogger(__name__)
@@ -171,7 +170,7 @@ def memoizeMD5(func):
# compatible) bytes , and take
# the hash of those bytes.
for arg in args:
- if not isinstance(arg, six.string_types):
+ if not isinstance(arg, str):
arg = str(arg)
arg = arg.encode('utf-8')
hashobj.update(arg)
diff --git a/fsl/utils/notifier.py b/fsl/utils/notifier.py
index cd07204e4907175c8f8a5bf3bfa21ebd7a5d2fd9..b294f6192ce01261275aed1f07213d3d0cb7a01d 100644
--- a/fsl/utils/notifier.py
+++ b/fsl/utils/notifier.py
@@ -14,9 +14,6 @@ import inspect
import contextlib
import collections
-import six
-
-
import fsl.utils.idle as idle
import fsl.utils.weakfuncref as weakfuncref
@@ -297,7 +294,7 @@ class Notifier(object):
:arg topic: Topic or topics that the listener is registered on.
"""
- if topic is None or isinstance(topic, six.string_types):
+ if topic is None or isinstance(topic, str):
topic = [topic]
topics = topic
diff --git a/fsl/utils/path.py b/fsl/utils/path.py
index 0a0859528945a7b944482442b0ffc658d0dc05f9..09546f4b2cdf2660e234e49a7b09814232fac83e 100644
--- a/fsl/utils/path.py
+++ b/fsl/utils/path.py
@@ -32,16 +32,21 @@ import os.path as op
import os
import glob
import operator
+import pathlib
import re
+from typing import Sequence, Tuple, Union
+
from fsl.utils.platform import platform
+PathLike = Union[str, pathlib.Path]
+
+
class PathError(Exception):
"""``Exception`` class raised by the functions defined in this module
when something goes wrong.
"""
- pass
def deepest(path, suffixes):
@@ -52,12 +57,12 @@ def deepest(path, suffixes):
path = path.strip()
- if path == op.sep or path == '':
+ if path in (op.sep, ''):
return None
path = path.rstrip(op.sep)
- if any([path.endswith(s) for s in suffixes]):
+ if any(path.endswith(s) for s in suffixes):
return path
return deepest(op.dirname(path), suffixes)
@@ -81,7 +86,7 @@ def shallowest(path, suffixes):
if parent is not None:
return parent
- if any([path.endswith(s) for s in suffixes]):
+ if any(path.endswith(s) for s in suffixes):
return path
return None
@@ -101,19 +106,23 @@ def allFiles(root):
return files
-def hasExt(path, allowedExts):
+def hasExt(path : PathLike,
+ allowedExts : Sequence[str]) -> bool:
"""Convenience function which returns ``True`` if the given ``path``
ends with any of the given ``allowedExts``, ``False`` otherwise.
"""
- return any([path.endswith(e) for e in allowedExts])
-
-
-def addExt(prefix,
- allowedExts=None,
- mustExist=True,
- defaultExt=None,
- fileGroups=None,
- unambiguous=True):
+ path = str(path)
+ return any(path.endswith(e) for e in allowedExts)
+
+
+def addExt(
+ prefix : PathLike,
+ allowedExts : Sequence[str] = None,
+ mustExist : bool = True,
+ defaultExt : str = None,
+ fileGroups : Sequence[Sequence[str]] = None,
+ unambiguous : bool = True
+) -> Union[Sequence[str], str]:
"""Adds a file extension to the given file ``prefix``.
If ``mustExist`` is False, and the file does not already have a
@@ -148,6 +157,8 @@ def addExt(prefix,
containing *all* matching files is returned.
"""
+ prefix = str(prefix)
+
if allowedExts is None: allowedExts = []
if fileGroups is None: fileGroups = {}
@@ -189,7 +200,8 @@ def addExt(prefix,
# If ambiguity is ok, return
# all matching paths
- elif not unambiguous:
+ if not unambiguous:
+
return allPaths
# Ambiguity is not ok! More than
@@ -223,19 +235,29 @@ def addExt(prefix,
return allPaths[0]
-def removeExt(filename, allowedExts=None, firstDot=False):
+def removeExt(
+ filename : PathLike,
+ allowedExts : Sequence[str] = None,
+ firstDot : bool = False
+) -> str:
"""Returns the base name of the given file name. See :func:`splitExt`. """
-
return splitExt(filename, allowedExts, firstDot)[0]
-def getExt(filename, allowedExts=None, firstDot=False):
+def getExt(
+ filename : PathLike,
+ allowedExts : Sequence[str] = None,
+ firstDot : bool = False
+) -> str:
"""Returns the extension of the given file name. See :func:`splitExt`. """
-
return splitExt(filename, allowedExts, firstDot)[1]
-def splitExt(filename, allowedExts=None, firstDot=False):
+def splitExt(
+ filename : PathLike,
+ allowedExts : Sequence[str] = None,
+ firstDot : bool = False
+) -> Tuple[str, str]:
"""Returns the base name and the extension from the given file name.
If ``allowedExts`` is ``None`` and ``firstDot`` is ``False``, this
@@ -262,6 +284,8 @@ def splitExt(filename, allowedExts=None, firstDot=False):
last period. Ignored if ``allowedExts`` is specified.
"""
+ filename = str(filename)
+
# If allowedExts is not specified
# we split on a period character
if allowedExts is None:
@@ -465,7 +489,7 @@ def removeDuplicates(paths, allowedExts=None, fileGroups=None):
groupFiles = getFileGroup(path, allowedExts, fileGroups)
- if not any([p in unique for p in groupFiles]):
+ if not any(p in unique for p in groupFiles):
unique.append(groupFiles[0])
return unique
@@ -492,14 +516,13 @@ def uniquePrefix(path):
break
# Should never happen if path is valid
- elif len(hits) == 0 or idx >= len(filename) - 1:
+ if len(hits) == 0 or idx >= len(filename) - 1:
raise PathError('No unique prefix for {}'.format(filename))
# Not unique - continue looping
- else:
- idx += 1
- prefix = prefix + filename[idx]
- hits = [h for h in hits if h.startswith(prefix)]
+ idx += 1
+ prefix = prefix + filename[idx]
+ hits = [h for h in hits if h.startswith(prefix)]
return prefix
@@ -525,54 +548,56 @@ def commonBase(paths):
last = base
- if all([p.startswith(base) for p in paths]):
+ if all(p.startswith(base) for p in paths):
return base
raise PathError('No common base')
-def wslpath(winpath):
- """
- Convert Windows path (or a command line argument containing a Windows path)
- to the equivalent WSL path (e.g. ``c:\\Users`` -> ``/mnt/c/Users``). Also supports
- paths in the form ``\\wsl$\\(distro)\\users\\...``
-
- :param winpath: Command line argument which may (or may not) contain a Windows path. It is assumed to be
- either of the form <windows path> or --<arg>=<windows path>. Note that we don't need to
- handle --arg <windows path> or -a <windows path> since in these cases the argument
- and the path will be parsed as separate entities.
- :return: If ``winpath`` matches a Windows path, the converted argument (including the --<arg>= portion).
- Otherwise returns ``winpath`` unchanged.
+def wslpath(path):
+ """Convert Windows path (or a command line argument containing a Windows
+ path) to the equivalent WSL path (e.g. ``c:\\Users`` -> ``/mnt/c/Users``).
+ Also supports paths in the form ``\\wsl$\\(distro)\\users\\...``
+
+ :param winpath: Command line argument which may (or may not) contain a
+ Windows path. It is assumed to be either of the form
+ <windows path> or --<arg>=<windows path>. Note that we
+ don't need to handle --arg <windows path> or -a <windows
+ path> since in these cases the argument and the path will
+ be parsed as separate entities.
+ :return: If ``winpath`` matches a Windows path, the converted
+ argument (including the --<arg>= portion). Otherwise
+ returns ``winpath`` unchanged.
+
"""
- match = re.match(r"^(--[\w-]+=)?\\\\wsl\$[\\\/][^\\^\/]+(.*)$", winpath)
+ match = re.match(r"^(--[\w-]+=)?\\\\wsl\$[\\\/][^\\^\/]+(.*)$", path)
if match:
arg, path = match.group(1, 2)
if arg is None:
arg = ""
return arg + path.replace("\\", "/")
- match = re.match(r"^(--[\w-]+=)?([a-zA-z]):(.+)$", winpath)
+ match = re.match(r"^(--[\w-]+=)?([a-zA-z]):(.+)$", path)
if match:
arg, drive, path = match.group(1, 2, 3)
if arg is None:
arg = ""
return arg + "/mnt/" + drive.lower() + path.replace("\\", "/")
- return winpath
+ return path
-def winpath(wslpath):
- """
- Convert a WSL-local filepath (for example ``/usr/local/fsl/``) into a path that can be used from
- Windows.
+def winpath(path):
+ """Convert a WSL-local filepath (for example ``/usr/local/fsl/``) into a
+ path that can be used from Windows.
If ``self.fslwsl`` is ``False``, simply returns ``wslpath`` unmodified
Otherwise, uses ``FSLDIR`` to deduce the WSL distro in use for FSL.
- This requires WSL2 which supports the ``\\wsl$\`` network path.
+ This requires WSL2 which supports the ``\\wsl$\\`` network path.
wslpath is assumed to be an absolute path.
"""
if not platform.fslwsl:
- return wslpath
+ return path
else:
match = re.match(r"^\\\\wsl\$\\([^\\]+).*$", platform.fsldir)
if match:
@@ -581,6 +606,7 @@ def winpath(wslpath):
distro = None
if not distro:
- raise RuntimeError("Could not identify WSL installation from FSLDIR (%s)" % platform.fsldir)
+ raise RuntimeError('Could not identify WSL installation from '
+ 'FSLDIR (%s)' % platform.fsldir)
- return "\\\\wsl$\\" + distro + wslpath.replace("/", "\\")
+ return "\\\\wsl$\\" + distro + path.replace("/", "\\")
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index 1e535c8a336de44f3a7d819f067417075eaa16d3..a7e4971baea5125e9723ce184d6a65dc5a58c0ce 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -30,8 +30,6 @@ import subprocess as sp
import os.path as op
import os
-import six
-
from fsl.utils.platform import platform as fslplatform
import fsl.utils.fslsub as fslsub
import fsl.utils.tempdir as tempdir
@@ -83,7 +81,7 @@ def prepareArgs(args):
if len(args) == 1:
# Argument was a command string
- if isinstance(args[0], six.string_types):
+ if isinstance(args[0], str):
args = shlex.split(args[0])
# Argument was an unpacked sequence
diff --git a/fsl/utils/weakfuncref.py b/fsl/utils/weakfuncref.py
index 37e118566e814da3c5421037377ae02496483ab0..6216c2dd5f3ed267c6cdf2643707db7865634c69 100644
--- a/fsl/utils/weakfuncref.py
+++ b/fsl/utils/weakfuncref.py
@@ -7,13 +7,12 @@
"""This module provides the :class:`WeakFunctionRef` class. """
-import six
import types
import weakref
import inspect
-class WeakFunctionRef(object):
+class WeakFunctionRef:
"""Class which encapsulates a :mod:`weakref` to a function or method.
This class is used by :class:`.Notifier` instances to reference
@@ -28,10 +27,10 @@ class WeakFunctionRef(object):
"""
# Bound method
- if self.__isMethod(func):
+ if inspect.ismethod(func):
- boundMeth = six.get_method_function(func)
- boundSelf = six.get_method_self( func)
+ boundMeth = func.__func__
+ boundSelf = func.__self__
# We can't take a weakref of the method
# object, so we have to weakref the object
@@ -73,35 +72,6 @@ class WeakFunctionRef(object):
return self.__str__()
- def __isMethod(self, func):
- """Returns ``True`` if the given function is a bound method,
- ``False`` otherwise.
-
- This seems to be one of the few areas where python 2 and 3 are
- irreconcilably incompatible (or just where :mod:`six` does not have a
- function to help us).
-
- In Python 3 there is no difference between an unbound method and a
- function. But in Python 2, an unbound method is still a method (and
- inspect.ismethod returns True).
- """
-
- ismethod = False
-
- # Therefore, in python2 we need to test
- # whether the function is a method, and
- # also test whether it is bound.
- if six.PY2:
- ismethod = (inspect.ismethod(func) and
- six.get_method_self(func) is not None)
-
- # But in python3, if the function is a
- # method it is, by definition, bound.
- elif six.PY3:
- ismethod = inspect.ismethod(func)
-
- return ismethod
-
def __findPrivateMethod(self):
"""Finds and returns the bound method associated with the encapsulated
@@ -125,8 +95,7 @@ class WeakFunctionRef(object):
att = getattr(obj, name)
- if isinstance(att, types.MethodType) and \
- six.get_method_function(att) is func:
+ if isinstance(att, types.MethodType) and att.__func__ is func:
return att
return None
diff --git a/fsl/wrappers/fast.py b/fsl/wrappers/fast.py
index e18ec69effd6be4b6ef7cac023f7b1ae77a2414e..c51c9f245ad153018d1a76a81dd2d743f3b437c5 100644
--- a/fsl/wrappers/fast.py
+++ b/fsl/wrappers/fast.py
@@ -10,8 +10,6 @@
"""
-import six
-
import fsl.utils.assertions as asrt
from . import wrapperutils as wutils
@@ -28,7 +26,7 @@ def fast(imgs, out='fast', **kwargs):
command line option)
"""
- if isinstance(imgs, six.string_types):
+ if isinstance(imgs, str):
imgs = [imgs]
asrt.assertIsNifti(*imgs)
diff --git a/fsl/wrappers/fsl_anat.py b/fsl/wrappers/fsl_anat.py
index 868dacb70d206fe5a9b53907668cc7641513bf52..0b5e5e163ceb7b885bebf95e2bc714b13c12ebc0 100644
--- a/fsl/wrappers/fsl_anat.py
+++ b/fsl/wrappers/fsl_anat.py
@@ -8,8 +8,6 @@
`FSL_ANAT <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/fsl_anat>`_ command.
"""
-import six
-
import fsl.utils.assertions as asrt
from . import wrapperutils as wutils
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index 8739a1a34fea38b025a956326e23d11471f343e5..60413b866bee6100c3e9be198ac14abb42e221fd 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -103,8 +103,6 @@ import tempfile
import warnings
import functools
-
-import six
import nibabel as nib
import numpy as np
@@ -346,8 +344,7 @@ def applyArgStyle(style,
# always returns a sequence
def fmtval(val):
- if isinstance(val, abc.Sequence) and \
- not isinstance(val, six.string_types):
+ if isinstance(val, abc.Sequence) and (not isinstance(val, str)):
val = [str(v) for v in val]
if valsep == ' ': return val
@@ -711,8 +708,7 @@ class FileOrThing(object):
kwargs.get('cmdonly', False):
allargs = {**dict(zip(argnames, args)), **kwargs}
for name, val in allargs.items():
- if (name in self.__things) and \
- (not isinstance(val, six.string_types)):
+ if (name in self.__things) and (not isinstance(val, str)):
raise ValueError('Cannot use in-memory objects '
'or LOAD with submit=True!')
return func(*args, **kwargs)
diff --git a/requirements.txt b/requirements.txt
index 23dc58fde626c364d58edc0b6ac7d76f077412b7..faf34174fc2bb63d9c44706feb097f8f2b619dee 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,5 +2,4 @@ h5py>=2.9
nibabel>=2.4
numpy>=1
scipy>=0.18
-six>=1
dataclasses
diff --git a/setup.py b/setup.py
index ebfa3afea50ef5e16cb9ccdeda8022dac84d3876..60c5d46c22b80ed27ad076a5e4ffe4c4b41c057e 100644
--- a/setup.py
+++ b/setup.py
@@ -8,8 +8,9 @@
from __future__ import print_function
-import os.path as op
-import shutil
+import os.path as op
+import shutil
+import unittest.mock as mock
from setuptools import setup
from setuptools import find_namespace_packages
@@ -68,11 +69,6 @@ class doc(Command):
import sphinx.cmd.build as sphinx_build
- try:
- import unittest.mock as mock
- except:
- import mock
-
mockobj = mock.MagicMock()
mockobj.__version__ = '2.2.0'
mockedModules = open(op.join(docdir, 'mock_modules.txt')).readlines()
@@ -104,6 +100,7 @@ setup(
'License :: OSI Approved :: Apache Software License',
'Programming Language :: Python :: 3.7',
'Programming Language :: Python :: 3.8',
+ 'Programming Language :: Python :: 3.9',
'Topic :: Software Development :: Libraries :: Python Modules'],
packages=packages,
diff --git a/tests/__init__.py b/tests/__init__.py
index 24587392fc29de81bea199cb8e991b6012cba22e..58e6d23beda36a3c4cf2ce61046c54310173d5e8 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -20,11 +20,9 @@ import os.path as op
import numpy as np
import nibabel as nib
-from six import StringIO
+from io import StringIO
-
-try: from unittest import mock
-except ImportError: import mock
+from unittest import mock
import fsl.data.image as fslimage
from fsl.utils.tempdir import tempdir
diff --git a/tests/test_fsl_utils_path.py b/tests/test_fsl_utils_path.py
index 0361ced5ee2843f4c6827e4bbcabd705251d6cdf..fbf95953682951961db2078bdc26f04b98d310c5 100644
--- a/tests/test_fsl_utils_path.py
+++ b/tests/test_fsl_utils_path.py
@@ -5,15 +5,15 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-from __future__ import print_function
-
import os
import os.path as op
import shutil
+import pathlib
import tempfile
+from unittest import mock
+
import pytest
-import mock
import fsl.utils.path as fslpath
import fsl.data.image as fslimage
@@ -150,7 +150,8 @@ def test_hasExt():
]
for path, aexts, expected in tests:
- assert fslpath.hasExt(path, aexts) == expected
+ assert fslpath.hasExt(path, aexts) == expected
+ assert fslpath.hasExt(pathlib.Path(path), aexts) == expected
def test_addExt_imageFiles_mustExist_shouldPass():
@@ -248,18 +249,15 @@ def test_addExt_imageFiles_mustExist_shouldPass():
for f in files_to_create:
make_dummy_image_file(op.join(workdir, f))
- print('files_to_create: ', files_to_create)
- print('workdir: ', os.listdir(workdir))
- print('prefix: ', prefix)
- print('expected: ', expected)
-
- result = fslpath.addExt(op.join(workdir, prefix),
- allowedExts,
- mustExist=True,
- fileGroups=groups)
-
- print('result: ', result)
-
+ result = fslpath.addExt(op.join(workdir, prefix),
+ allowedExts,
+ mustExist=True,
+ fileGroups=groups)
+ assert result == op.join(workdir, expected)
+ result = fslpath.addExt(pathlib.Path(op.join(workdir, prefix)),
+ allowedExts,
+ mustExist=True,
+ fileGroups=groups)
assert result == op.join(workdir, expected)
cleardir(workdir)
@@ -336,20 +334,15 @@ def test_addExt_otherFiles_mustExist_shouldPass():
for f in files_to_create:
make_dummy_file(op.join(workdir, f))
- print('files_to_create: ', files_to_create)
- print('prefix: ', prefix)
- print('allowedExts: ', allowedExts)
- print('fileGroups: ', fileGroups)
- print('workdir: ', os.listdir(workdir))
- print('expected: ', expected)
-
- result = fslpath.addExt(op.join(workdir, prefix),
- allowedExts=allowedExts,
- mustExist=True,
- fileGroups=fileGroups)
-
- print('result: ', result)
-
+ result = fslpath.addExt(op.join(workdir, prefix),
+ allowedExts=allowedExts,
+ mustExist=True,
+ fileGroups=fileGroups)
+ assert result == op.join(workdir, expected)
+ result = fslpath.addExt(pathlib.Path(op.join(workdir, prefix)),
+ allowedExts=allowedExts,
+ mustExist=True,
+ fileGroups=fileGroups)
assert result == op.join(workdir, expected)
cleardir(workdir)
@@ -422,18 +415,16 @@ def test_addExt_imageFiles_mustExist_shouldFail():
for f in files_to_create:
make_dummy_file(op.join(workdir, f))
- print('files_to_create: ', files_to_create)
- print('prefix: ', prefix)
- print('workdir: ', os.listdir(workdir))
-
with pytest.raises(fslpath.PathError):
-
- result = fslpath.addExt(op.join(workdir, prefix),
- allowedExts=allowedExts,
- mustExist=True,
- fileGroups=fileGroups)
-
- print('result: ', result)
+ fslpath.addExt(op.join(workdir, prefix),
+ allowedExts=allowedExts,
+ mustExist=True,
+ fileGroups=fileGroups)
+ with pytest.raises(fslpath.PathError):
+ fslpath.addExt(pathlib.Path(op.join(workdir, prefix)),
+ allowedExts=allowedExts,
+ mustExist=True,
+ fileGroups=fileGroups)
finally:
shutil.rmtree(workdir)
@@ -481,23 +472,19 @@ def test_addExt_otherFiles_mustExist_shouldFail():
for f in files_to_create:
make_dummy_file(op.join(workdir, f))
- print('files_to_create: ', files_to_create)
- print('prefix: ', prefix)
- print('workdir: ', os.listdir(workdir))
-
with pytest.raises(fslpath.PathError):
-
- result = fslpath.addExt(op.join(workdir, prefix),
- allowedExts=allowedExts,
- mustExist=True,
- fileGroups=fileGroups)
-
- print('result: ', result)
-
+ fslpath.addExt(op.join(workdir, prefix),
+ allowedExts=allowedExts,
+ mustExist=True,
+ fileGroups=fileGroups)
+ with pytest.raises(fslpath.PathError):
+ fslpath.addExt(pathlib.Path(op.join(workdir, prefix)),
+ allowedExts=allowedExts,
+ mustExist=True,
+ fileGroups=fileGroups)
finally:
shutil.rmtree(workdir)
- pass
def test_addExt_noExist():
@@ -544,11 +531,14 @@ def test_addExt_noExist():
]
for prefix, defaultExt, allowedExts, expected in tests:
-
assert fslpath.addExt(prefix,
allowedExts,
defaultExt=defaultExt,
mustExist=False) == expected
+ assert fslpath.addExt(pathlib.Path(prefix),
+ allowedExts,
+ defaultExt=defaultExt,
+ mustExist=False) == expected
def test_addExt_unambiguous():
@@ -582,15 +572,20 @@ def test_addExt_unambiguous():
expected = expected.split()
with testdir(create) as td:
-
result = fslpath.addExt(prefix,
allowedExts=exts,
fileGroups=groups,
defaultExt=defaultExt,
unambiguous=False)
-
+ assert sorted(expected) == sorted(result)
+ result = fslpath.addExt(pathlib.Path(prefix),
+ allowedExts=exts,
+ fileGroups=groups,
+ defaultExt=defaultExt,
+ unambiguous=False)
assert sorted(expected) == sorted(result)
+
def test_removeExt():
allowedExts = fslimage.ALLOWED_EXTENSIONS
@@ -622,7 +617,8 @@ def test_removeExt():
if len(test) == 2: allowed = allowedExts
else: allowed = test[2]
- assert fslpath.removeExt(path, allowed) == output
+ assert fslpath.removeExt(path, allowed) == output
+ assert fslpath.removeExt(pathlib.Path(path), allowed) == output
def test_getExt():
@@ -658,8 +654,8 @@ def test_getExt():
if len(test) == 2: allowed = allowedExts
else: allowed = test[2]
- print(filename, '==', output)
- assert fslpath.getExt(filename, allowed) == output
+ assert fslpath.getExt(filename, allowed) == output
+ assert fslpath.getExt(pathlib.Path(filename), allowed) == output
def test_splitExt():
@@ -704,13 +700,14 @@ def test_splitExt():
for test in tests:
filename = test[0]
+ pfilename = pathlib.Path(filename)
outbase, outext = test[1]
if len(test) == 2: allowed = allowedExts
else: allowed = test[2]
- print(filename, '==', (outbase, outext))
- assert fslpath.splitExt(filename, allowed) == (outbase, outext)
+ assert fslpath.splitExt(filename, allowed) == (outbase, outext)
+ assert fslpath.splitExt(pfilename, allowed) == (outbase, outext)
# firstDot=True
tests = [
@@ -721,7 +718,9 @@ def test_splitExt():
]
for f, exp in tests:
- assert fslpath.splitExt(f, firstDot=True) == exp
+ pf = pathlib.Path(f)
+ assert fslpath.splitExt(f, firstDot=True) == exp
+ assert fslpath.splitExt(pf, firstDot=True) == exp
def test_getFileGroup_imageFiles_shouldPass():
@@ -798,11 +797,6 @@ def test_getFileGroup_imageFiles_shouldPass():
with open(op.join(workdir, fn), 'wt') as f:
f.write('{}\n'.format(fn))
- print()
- print('files_to_create: ', files_to_create)
- print('path: ', path)
- print('files_to_expect: ', files_to_expect)
-
fullPaths = fslpath.getFileGroup(
op.join(workdir, path),
allowedExts=allowedExts,
@@ -918,13 +912,6 @@ def test_getFileGroup_otherFiles_shouldPass():
with open(op.join(workdir, fn), 'wt') as f:
f.write('{}\n'.format(fn))
- print()
- print('files_to_create: ', files_to_create)
- print('path: ', path)
- print('allowedExts: ', allowedExts)
- print('fileGroups: ', fileGroups)
- print('files_to_expect: ', files_to_expect)
-
fullPaths = fslpath.getFileGroup(
op.join(workdir, path),
allowedExts=allowedExts,
@@ -1006,32 +993,22 @@ def test_getFileGroup_shouldFail():
with open(op.join(workdir, fn), 'wt') as f:
f.write('{}\n'.format(fn))
- print()
- print('files_to_create: ', files_to_create)
- print('path: ', path)
- print('allowedExts: ', allowedExts)
- print('fileGroups: ', fileGroups)
-
with pytest.raises(fslpath.PathError):
- fullPaths = fslpath.getFileGroup(
+ fslpath.getFileGroup(
op.join(workdir, path),
allowedExts=allowedExts,
fileGroups=fileGroups,
fullPaths=True,
unambiguous=unambiguous)
- print('fullPaths: ', fullPaths)
-
with pytest.raises(fslpath.PathError):
- exts = fslpath.getFileGroup(
+ fslpath.getFileGroup(
op.join(workdir, path),
allowedExts=allowedExts,
fileGroups=fileGroups,
fullPaths=False,
unambiguous=unambiguous)
- print('exts: ', exts)
-
cleardir(workdir)
finally:
@@ -1117,16 +1094,9 @@ def test_removeDuplicates_imageFiles_shouldPass():
paths = paths.split()
expected = expected.split()
- print()
- print('files_to_create: ', files_to_create)
- print('paths: ', paths)
- print('expected: ', expected)
-
paths = [op.join(workdir, p) for p in paths]
result = fslpath.removeDuplicates(paths, allowedExts, groups)
- print('result: ', result)
-
assert result == [op.join(workdir, e) for e in expected]
cleardir(workdir)
@@ -1196,20 +1166,10 @@ def test_removeDuplicates_otherFiles_shouldPass():
for f in files_to_create:
make_dummy_file(op.join(workdir, f))
-
- print('files_to_create: {}'.format(files_to_create))
- print('paths: {}'.format(paths))
- print('allowedExts: {}'.format(allowedExts))
- print('fileGroups: {}'.format(fileGroups))
- print('workdir: {}'.format(os.listdir(workdir)))
- print('expected: {}'.format(expected))
-
result = fslpath.removeDuplicates([op.join(workdir, p) for p in paths],
allowedExts=allowedExts,
fileGroups=fileGroups)
- print('result: {}'.format(result))
-
assert result == [op.join(workdir, e) for e in expected]
cleardir(workdir)
@@ -1256,17 +1216,10 @@ def test_removeDuplicates_shouldFail():
with open(op.join(workdir, fn), 'wt') as f:
f.write('{}\n'.format(fn))
- print()
- print('files_to_create: ', files_to_create)
- print('path: ', path)
- print('allowedExts: ', allowedExts)
- print('fileGroups: ', fileGroups)
-
with pytest.raises(fslpath.PathError):
- result = fslpath.removeDuplicates(path,
- allowedExts=allowedExts,
- fileGroups=fileGroups)
- print('result: ', result)
+ fslpath.removeDuplicates(path,
+ allowedExts=allowedExts,
+ fileGroups=fileGroups)
finally:
shutil.rmtree(workdir)
diff --git a/tests/test_idle.py b/tests/test_idle.py
index edf0ecb171b54fe382d233c5c69a49ae77b57f1c..6ceb010bb91aa36ce642d1b3034f5655d7bc58c8 100644
--- a/tests/test_idle.py
+++ b/tests/test_idle.py
@@ -9,11 +9,10 @@ import gc
import time
import threading
import random
-
-from six.moves import reload_module
+import importlib
import pytest
-import mock
+from unittest import mock
import fsl.utils.idle as idle
from fsl.utils.platform import platform as fslplatform
@@ -428,7 +427,7 @@ def test_idle_alwaysQueue4():
with pytest.raises(ImportError):
import wx
- reload_module(fsl.utils.platform)
+ importlib.reload(fsl.utils.platform)
assert called[0]
diff --git a/tests/test_image.py b/tests/test_image.py
index e2e7f213f0d7c791737c62ceb9eaa57a75f42344..34a5482ce8f63a7d66ed83d881f9a575680a55ab 100644
--- a/tests/test_image.py
+++ b/tests/test_image.py
@@ -32,11 +32,7 @@ from fsl.utils.tempdir import tempdir
from . import make_random_image
from . import make_dummy_file
-try:
- from unittest import mock
-except ImportError:
- import mock
-
+from unittest import mock
try:
import indexed_gzip as igzip
@@ -208,6 +204,23 @@ def test_create():
assert np.all(np.isclose(img.pixdim, (2, 3, 4)))
+def test_name_dataSource():
+ with tempdir():
+
+ expName = 'image'
+ expDataSource = op.abspath('image.nii.gz')
+ make_image('image.nii.gz')
+
+ tests = ['image', 'image.nii.gz', op.abspath('image'),
+ op.abspath('image.nii.gz')]
+ tests = tests + [Path(t) for t in tests]
+
+ for t in tests:
+ i = fslimage.Image(t)
+ assert i.name == expName
+ assert i.dataSource == expDataSource
+
+
def test_bad_create():
class BadThing(object):
diff --git a/tests/test_image_advanced.py b/tests/test_image_advanced.py
index fd7f64359d9bc071b33689ff95a8697170c247d0..1f1aed8a2ba827836314f61709e3a0316e41616f 100644
--- a/tests/test_image_advanced.py
+++ b/tests/test_image_advanced.py
@@ -7,8 +7,8 @@
import os.path as op
import time
+from unittest import mock
-import mock
import pytest
import numpy as np
diff --git a/tests/test_memoize.py b/tests/test_memoize.py
index 386674659b4a9af2648dadf445efd1a84a170f37..30844884d4695c040e82c11af2db7295118d1a17 100644
--- a/tests/test_memoize.py
+++ b/tests/test_memoize.py
@@ -6,7 +6,6 @@
#
import collections
-import six
import numpy as np
@@ -44,7 +43,7 @@ def test_memoize():
assert timesCalled[0] == 6
# Unicode arg
- s = six.u('\u25B2')
+ s = '\u25B2'
assert memoized(s) == s * 5
assert timesCalled[0] == 7
assert memoized(s) == s * 5
@@ -146,7 +145,7 @@ def test_memoizeMD5():
assert timesCalled[0] == 6
# Unicode arg (and return value)
- s = six.u('\u25B2')
+ s = '\u25B2'
assert memoized(s) == s * 5
assert timesCalled[0] == 7
assert memoized(s) == s * 5
diff --git a/tests/test_platform.py b/tests/test_platform.py
index 9024bec8262658dd419c48ef288f2d4af2a75c8c..a38408175e438447570a75b9c0115e9da3f1d927 100644
--- a/tests/test_platform.py
+++ b/tests/test_platform.py
@@ -6,15 +6,14 @@
#
-import os
-import gc
-import os.path as op
-import sys
-import shutil
-import tempfile
-import pytest
-
-import mock
+import os
+import gc
+import os.path as op
+import sys
+import shutil
+import tempfile
+import pytest
+from unittest import mock
import fsl.utils.platform as fslplatform
@@ -216,7 +215,7 @@ def test_detect_ssh():
def test_fslwsl():
"""
Note that ``Platform.fsldir`` requires the directory in ``FSLDIR`` to exist and
- sets ``FSLDIR`` to ``None`` if it doesn't. So we create a ``Platform`` first
+ sets ``FSLDIR`` to ``None`` if it doesn't. So we create a ``Platform`` first
and then overwrite ``FSLDIR``. This is a bit of a hack but the logic we are testing
here is whether ``Platform.fslwsl`` recognizes a WSL ``FSLDIR`` string
"""
diff --git a/tests/test_run.py b/tests/test_run.py
index 7308b849c72f6f82afd00eb417c4d479b58d0f30..287ccd6432c4d98223f23712dda1da2c1bf668c2 100644
--- a/tests/test_run.py
+++ b/tests/test_run.py
@@ -11,12 +11,8 @@ import os
import shutil
import textwrap
-# python 3
-try: from unittest import mock
-# python 2
-except ImportError: import mock
+from unittest import mock
-import six
import pytest
import fsl.utils.tempdir as tempdir
@@ -273,7 +269,7 @@ def test_runfsl():
def mock_submit(cmd, **kwargs):
- if isinstance(cmd, six.string_types):
+ if isinstance(cmd, str):
name = cmd.split()[0]
else:
name = cmd[0]
diff --git a/tests/test_settings.py b/tests/test_settings.py
index b17b1b87ab8e7ed747d2c2d0dd56d4e13053737a..fc0ca9edf7f90c0f5051d09c8e30a59319aae6c4 100644
--- a/tests/test_settings.py
+++ b/tests/test_settings.py
@@ -12,12 +12,7 @@ import pickle
import textwrap
import tempfile
-# python 3
-try:
- import unittest.mock as mock
-# python 2
-except:
- import mock
+import unittest.mock as mock
import pytest
diff --git a/tests/test_transform/test_affine.py b/tests/test_transform/test_affine.py
index f1dceb61312c7f05f97c9d871dc8a4a0ae95f492..e686080fc7040983b61047ce207f8d0fcb1966b2 100644
--- a/tests/test_transform/test_affine.py
+++ b/tests/test_transform/test_affine.py
@@ -6,8 +6,6 @@
#
-from __future__ import division
-
import random
import glob
import os.path as op
@@ -15,8 +13,6 @@ import itertools as it
import numpy as np
import numpy.linalg as npla
-import six
-
import pytest
import fsl.transform.affine as affine
@@ -39,8 +35,7 @@ def readlines(filename):
#
# Pass it [bytes, bytes, ...], and it works
# fine.
- if six.PY3:
- lines = [l.encode('ascii') for l in lines]
+ lines = [l.encode('ascii') for l in lines]
return lines
diff --git a/tests/test_wrappers/test_wrapperutils.py b/tests/test_wrappers/test_wrapperutils.py
index 9bddb5c6b97e7ba6b9b78690c579fc3011aada81..f8a9d0dd4baa98f47003bf1846a92652f8e270bd 100644
--- a/tests/test_wrappers/test_wrapperutils.py
+++ b/tests/test_wrappers/test_wrapperutils.py
@@ -11,10 +11,8 @@ import shlex
import pathlib
import textwrap
-try: from unittest import mock
-except ImportError: import mock
+from unittest import mock
-import six
import pytest
import numpy as np
@@ -317,7 +315,7 @@ def test_fileOrThing_sequence():
@wutils.fileOrArray('arrs', 'out')
def func(arrs, out):
- if isinstance(arrs, six.string_types):
+ if isinstance(arrs, str):
arrs = [arrs]
arrs = [np.loadtxt(a) for a in arrs]