Merge branch 'mnt/py38' into 'master'

Mnt/py38

See merge request fsl/fslpy!165

.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"

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)
 -----------------------------------
 

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
 

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::
 

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
 

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

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

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))

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):