diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 69c6f3d68523a2fbf36fd95709da0a6c349516d5..6a050cb81ce537763517ed9062fa6b3f48763634 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -157,27 +157,27 @@ variables:
- bash ./.ci/test_template.sh
-test:3.5:
+test:3.6:
stage: test
- image: pauldmccarthy/fsleyes-py35-wxpy4-gtk2
+ image: pauldmccarthy/fsleyes-py36-wxpy4-gtk3
<<: *test_template
-test:3.6:
+test:3.7:
stage: test
- image: pauldmccarthy/fsleyes-py36-wxpy4-gtk2
+ image: pauldmccarthy/fsleyes-py37-wxpy4-gtk3
<<: *test_template
-test:3.7:
+test:3.8:
stage: test
- image: pauldmccarthy/fsleyes-py37-wxpy4-gtk2
+ image: pauldmccarthy/fsleyes-py38-wxpy4-gtk3
<<: *test_template
test:build-pypi-dist:
stage: test
- image: pauldmccarthy/fsleyes-py35-wxpy4-gtk2
+ image: pauldmccarthy/fsleyes-py36-wxpy4-gtk3
<<: *except_releases
tags:
@@ -195,7 +195,7 @@ test:build-pypi-dist:
style:
stage: style
- image: pauldmccarthy/fsleyes-py35-wxpy4-gtk2
+ image: pauldmccarthy/fsleyes-py36-wxpy4-gtk3
<<: *test_template
variables:
TEST_STYLE: "true"
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 00de568e586038893e99e67e56a50339528f1c45..b28604e356097583239b9a91e29561b062017a2e 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,6 +2,18 @@ This document contains the ``fslpy`` release history in reverse chronological
order.
+2.6.1 (Thursday 19th September 2019)
+------------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* ``fslpy`` is no longer tested against Python 3.5, and is now tested against
+ Python 3.6, 3.7, and 3.8.
+
+
2.6.0 (Tuesday 10th September 2019)
-----------------------------------
diff --git a/fsl/utils/filetree/parse.py b/fsl/utils/filetree/parse.py
index 409a358bfdf9b9d707bc838b186742366054d51e..acfa68d17b4b3104e6de1f71d4307625bf1001f9 100644
--- a/fsl/utils/filetree/parse.py
+++ b/fsl/utils/filetree/parse.py
@@ -77,7 +77,7 @@ def read_line(line: str) -> Tuple[int, PurePath, str]:
"""
Parses line from the tree file
- :param line: input line from a \*.tree file
+ :param line: input line from a ``*.tree`` file
:return: Tuple with:
- number of spaces in front of the name
@@ -105,7 +105,7 @@ def read_subtree_line(line: str, directory: str) -> Tuple[int, "filetree.FileTre
"""
Parses the line defining a sub_tree
- :param line: input line from a \*.tree file
+ :param line: input line from a ``*.tree`` file
:param directory: containing directory
:return: Tuple with
diff --git a/fsl/utils/filetree/query.py b/fsl/utils/filetree/query.py
index ac66091cd60c9fe273b0d939cfd20c3338bbeb7c..6407b14e3a39a2c59bb12502f21f6dc0512f0eed 100644
--- a/fsl/utils/filetree/query.py
+++ b/fsl/utils/filetree/query.py
@@ -48,9 +48,8 @@ class FileTreeQuery(object):
short name that are present. The :meth:`query` method can be used to
retrieve files which match a specific template, and variable values.
- The :meth:`query` method returns a multi-dimensional ``numpy.array``
- which contains :class:`Match` objects, where each dimension one
- represents variable for the template in question.
+ The :meth:`query` method returns a collection of :class:`Match` objects,
+ each of which represents one file which matches the query.
Example usage::
diff --git a/fsl/utils/filetree/utils.py b/fsl/utils/filetree/utils.py
index 0b82929491c9a8994d252f24704f66dff87f8411..11464e93570660dd27e1fa9103a3b4ff3e731f03 100644
--- a/fsl/utils/filetree/utils.py
+++ b/fsl/utils/filetree/utils.py
@@ -98,7 +98,7 @@ def resolve_optionals(text):
else:
return ''
- res = [resolve_single_optional(text) for text in re.split('(\[.*?\])', text)]
+ res = [resolve_single_optional(text) for text in re.split(r'(\[.*?\])', text)]
return ''.join(res)
@@ -109,7 +109,7 @@ def find_variables(template):
:param template: full template
:return: sequence of variables
"""
- return tuple(var.split(':')[0] for var in re.findall("\{(.*?)\}", template))
+ return tuple(var.split(':')[0] for var in re.findall(r"\{(.*?)\}", template))
def optional_variables(template):
@@ -121,7 +121,7 @@ def optional_variables(template):
"""
include = set()
exclude = set()
- for text in re.split('(\[.*?\])', template):
+ for text in re.split(r'(\[.*?\])', template):
if len(text) == 0:
continue
variables = find_variables(text)
@@ -152,13 +152,13 @@ def extract_variables(template, filename, known_vars=None):
sub_re = resolve_optionals(fill_known(
template,
dict(
- **{var: '(\S+)' for k, var in zip(keep, optional) if k},
- **{var: '(\S+)' for var in remaining.difference(optional)}
+ **{var: r'(\S+)' for k, var in zip(keep, optional) if k},
+ **{var: r'(\S+)' for var in remaining.difference(optional)}
)
))
while '//' in sub_re:
sub_re = sub_re.replace('//', '/')
- sub_re = sub_re.replace('.', '\.')
+ sub_re = sub_re.replace('.', r'\.')
if re.match(sub_re, filename) is None:
continue
diff --git a/fsl/utils/idle.py b/fsl/utils/idle.py
index c1513708ebb401227dd1d0adb7cf9e0efd067631..f2fc9d0d2fcba36b3e0851b802d6b498ae908d67 100644
--- a/fsl/utils/idle.py
+++ b/fsl/utils/idle.py
@@ -86,7 +86,7 @@ import atexit
import logging
import functools
import threading
-import collections
+from collections import abc
try: import queue
except ImportError: import Queue as queue
@@ -610,7 +610,7 @@ def wait(threads, task, *args, **kwargs):
direct = kwargs.pop('wait_direct', False)
- if not isinstance(threads, collections.Sequence):
+ if not isinstance(threads, abc.Sequence):
threads = [threads]
haveWX = fslplatform.haveGui
diff --git a/setup.cfg b/setup.cfg
index 3f611406bec88d7cf6c581943a063647ee3b009e..9ea1ddbc4fea695ac2e0746889c32e4e510c7ce7 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -5,21 +5,21 @@ test=pytest
universal=1
[tool:pytest]
-# Available test markers:
-# - fsltest: Requires FSL
-# - wxtest: Requires wxPython
-# - dicomtest: Requires dcm2niix
-# - meshtest: Requires trimesh and rtree
-# - igziptest: Requires indexed_gzip
-# - piltest: Requires Pillow
-# - noroottest: Need to be executed as
-# non-root user (will fail
-# otherwise)
-# - longtest: Takes a long time
-#
+markers =
+ fsltest: Requires FSL
+ wxtest: Requires wxPython
+ dicomtest: Requires dcm2niix
+ meshtest: Requires trimesh and rtree
+ igziptest: Requires indexed_gzip
+ piltest: Requires Pillow
+ noroottest: Need to be executed as non-root user (will fail otherwise)
+ longtest: Takes a long time
+ unixtest: Only works on *nix systems
+
testpaths = tests
addopts = -v --niters=50 --cov=fsl -m "not longtest"
+
[flake8]
ignore = E127,E201,E203,E221,E222,E241,E271,E272,E301,E302,E303,E701,W504
\ No newline at end of file
diff --git a/tests/test_image_resample.py b/tests/test_image_resample.py
index 8fb488760ed74a14a0714c92d7815ac2a87f43f6..6961e7aa71c63a09d21f93ca5e128d8622b678a9 100644
--- a/tests/test_image_resample.py
+++ b/tests/test_image_resample.py
@@ -9,13 +9,13 @@ import pytest
import scipy.ndimage as ndimage
import fsl.data.image as fslimage
-import fsl.utils.transform as transform
+import fsl.transform.affine as affine
import fsl.utils.image.resample as resample
from . import make_random_image
def random_affine():
- return transform.compose(
+ return affine.compose(
0.25 + 4.75 * np.random.random(3),
-50 + 100 * np.random.random(3),
-np.pi + 2 * np.pi * np.random.random(3))
@@ -61,9 +61,9 @@ def test_resample(seed):
resx, resy, resz = restestcoords.T
resvals = resampled[resx, resy, resz]
- res2orig = transform.concat(img.worldToVoxMat, xf)
+ res2orig = affine.concat(img.worldToVoxMat, xf)
- origtestcoords = transform.transform(restestcoords, res2orig)
+ origtestcoords = affine.transform(restestcoords, res2orig)
# remove any coordinates which are out of
# bounds in the original image space, or
@@ -130,8 +130,8 @@ def test_resample_origin(seed):
shape = np.random.randint(5, 50, 3)
res = resample.resample(img, shape, origin='corner')
res = fslimage.Image(res[0], xform=res[1])
- imgb = transform.axisBounds(img.shape, img.voxToWorldMat)
- resb = transform.axisBounds(res.shape, res.voxToWorldMat)
+ imgb = affine.axisBounds(img.shape, img.voxToWorldMat)
+ resb = affine.axisBounds(res.shape, res.voxToWorldMat)
assert np.all(np.isclose(imgb, resb, rtol=1e-5, atol=1e-5))
# with origin='centre' image
@@ -142,8 +142,8 @@ def test_resample_origin(seed):
res = resample.resample(img, shape, origin='centre')
res = fslimage.Image(res[0], xform=res[1])
off = (np.array(img.shape) / np.array(res.shape) - 1) / 2
- imgb = np.array(transform.axisBounds(img.shape, img.voxToWorldMat))
- resb = np.array(transform.axisBounds(res.shape, res.voxToWorldMat))
+ imgb = np.array(affine.axisBounds(img.shape, img.voxToWorldMat))
+ resb = np.array(affine.axisBounds(res.shape, res.voxToWorldMat))
assert np.all(np.isclose(imgb, resb + off, rtol=1e-5, atol=1e-5))
# with origin='corner', using
@@ -165,7 +165,7 @@ def test_resample_origin(seed):
def test_resampleToPixdims():
img = fslimage.Image(make_random_image(dims=(10, 10, 10)))
- imglo, imghi = transform.axisBounds(img.shape, img.voxToWorldMat)
+ imglo, imghi = affine.axisBounds(img.shape, img.voxToWorldMat)
oldpix = np.array(img.pixdim, dtype=np.float)
oldshape = np.array(img.shape, dtype=np.float)
@@ -177,7 +177,7 @@ def test_resampleToPixdims():
res = resample.resampleToPixdims(img, newpix, origin=origin)
res = fslimage.Image(res[0], xform=res[1])
- reslo, reshi = transform.axisBounds(res.shape, res.voxToWorldMat)
+ reslo, reshi = affine.axisBounds(res.shape, res.voxToWorldMat)
resfov = reshi - reslo
expfov = newpix * res.shape
@@ -219,7 +219,7 @@ def test_resampleToReference2():
img[1, 1, 1] = 1
img = fslimage.Image(img)
- refv2w = transform.scaleOffsetXform([1, 1, 1], [-1, -1, -1])
+ refv2w = affine.scaleOffsetXform([1, 1, 1], [-1, -1, -1])
ref = np.zeros((5, 5, 5), dtype=np.float)
ref = fslimage.Image(ref, xform=refv2w)
res = resample.resampleToReference(img, ref, order=0)
@@ -235,7 +235,7 @@ def test_resampleToReference3():
# Test resampling image to ref
# with mismatched dimensions
imgdata = np.random.randint(0, 65536, (5, 5, 5))
- img = fslimage.Image(imgdata, xform=transform.scaleOffsetXform(
+ img = fslimage.Image(imgdata, xform=affine.scaleOffsetXform(
(2, 2, 2), (0.5, 0.5, 0.5)))
# reference/expected data when
@@ -270,7 +270,7 @@ def test_resampleToReference4():
# the image and ref are out of
# alignment, but this affine
# will bring them into alignment
- img2ref = transform.scaleOffsetXform([2, 2, 2], [10, 10, 10])
+ img2ref = affine.scaleOffsetXform([2, 2, 2], [10, 10, 10])
imgdata = np.random.randint(0, 65536, (5, 5, 5))
refdata = np.zeros((5, 5, 5))
diff --git a/tests/test_scripts/test_atlasq_query.py b/tests/test_scripts/test_atlasq_query.py
index 5b2ab4e9da7a634be84c3aea0fa5f8d901a1fea0..14c61b0ebbb80f723075a01eb0be50ab596b8c82 100644
--- a/tests/test_scripts/test_atlasq_query.py
+++ b/tests/test_scripts/test_atlasq_query.py
@@ -286,7 +286,7 @@ def _eval_coord_voxel_query(
else:
exp = [q_type, squery]
- _stdout = re.sub('\s+', ' ', stdout).strip()
+ _stdout = re.sub(r'\s+', ' ', stdout).strip()
assert _stdout == ' '.join(exp)
if isinstance(a_img, fslatlases.LabelAtlas):
@@ -388,7 +388,7 @@ def _eval_mask_query(
if expprop > 0:
exp.append('{} {:0.4f}'.format(explabel, expprop))
- _stdout = re.sub('\s+', ' ', stdout).strip()
+ _stdout = re.sub(r'\s+', ' ', stdout).strip()
assert _stdout == ' '.join(exp)
if isinstance(aimg, fslatlases.LabelAtlas):