Merge branch 'rf/wsl-popen' into 'master'

Adjust fsl.utils.run.run to workaround Windows issue

See merge request fsl/fslpy!272

.gitlab-ci.yml

@@ -173,6 +173,12 @@ test:3.8:
   <<: *test_template
 
 
+test:3.9:
+  stage: test
+  image: pauldmccarthy/fsleyes-py39-wxpy4-gtk3
+  <<: *test_template
+
+
 test:build-pypi-dist:
   stage: test
   image: pauldmccarthy/fsleyes-py36-wxpy4-gtk3

CHANGELOG.rst

@@ -2,6 +2,29 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
+3.5.0 (Tuesday 19th January 2021)
+---------------------------------
+
+
+Added
+^^^^^
+
+
+* New ``fsl_anat.tree``, for use with the :mod:`.filetree` package (!264).
+* New :func:`.fsl_prepare_fieldmap` wrapper function (!265).
+* The :class:`.fslmaths` wrapper now supports the ``fslmaths -s`` option
+  via the :meth:`.fslmaths.smooth` method (!271).
+
+
+Fixed
+^^^^^
+
+
+* Windows/WSL-specific workaround to the :func:`fsl.utils.run.run` function to
+  avoid console windows from popping up, when used from a graphical program
+  (!272).
+
+
 3.4.0 (Tuesday 20th October 2020)
 ---------------------------------
 

COPYRIGHT

-Copyright 2016-2020 University of Oxford, Oxford, UK
+Copyright 2016-2021 University of Oxford, Oxford, UK

LICENSE

 The fslpy library
 
-Copyright 2016-2020 University of Oxford, Oxford, UK.
+Copyright 2016-2021 University of Oxford, Oxford, UK.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

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 3.5, 3.6 and 3.7.
+``fslpy`` is tested against Python versions 3.6, 3.7, 3.8 and 3.9.
 
 
 Installation

fsl/utils/run.py

@@ -286,6 +286,12 @@ def _realrun(tee, logStdout, logStderr, logCmd, *args, **kwargs):
                       - the command's standard error as a string.
                       - the command's exit code.
     """
+    if fslplatform.fslwsl:
+        # On Windows this prevents opening of a popup window
+        startupinfo = sp.STARTUPINFO()
+        startupinfo.dwFlags |= sp.STARTF_USESHOWWINDOW
+        kwargs["startupinfo"] = startupinfo
+
     proc = sp.Popen(args, stdout=sp.PIPE, stderr=sp.PIPE, **kwargs)
     with tempdir.tempdir(changeto=False) as td:
 
@@ -403,7 +409,7 @@ def wslcmd(cmdpath, *args):
     # Check if command exists in WSL (remembering that the command path may include FSLDIR which
     # is a Windows path)
     cmdpath = fslpath.wslpath(cmdpath)
-    retcode = sp.call(["wsl", "test", "-x", cmdpath])
+    _stdout, _stderr, retcode = _realrun(False, None, None, None, "wsl", "test", "-x", cmdpath)
     if retcode == 0:
         # Form a new argument list and convert any Windows paths in it into WSL paths
         wslargs = [fslpath.wslpath(arg) for arg in args]

fsl/version.py

@@ -47,7 +47,7 @@ import            re
 import            string
 
 
-__version__ = '3.5.0.dev0'
+__version__ = '3.6.0.dev0'
 """Current version number, as a string. """
 
 

tests/test_dicom.py

@@ -29,10 +29,10 @@ pytestmark = pytest.mark.dicomtest
 
 
 @contextlib.contextmanager
-def install_dcm2niix(version='1.0.20190902'):
+def install_dcm2niix(version='1.0.20201102'):
     filenames = {
+        '1.0.20201102' : 'v1.0.20201102/dcm2niix_lnx.zip',
         '1.0.20190902' : 'v1.0.20190902/dcm2niix_lnx.zip',
-        '1.0.20190410' : 'v1.0.20190410/dcm2niix_11-Apr-2019_lnx.zip',
         '1.0.20181125' : 'v1.0.20181125/dcm2niix_25-Nov-2018_lnx.zip',
         '1.0.20171017' : 'v1.0.20171017/dcm2niix_18-Oct-2017_lnx.zip',
     }
@@ -128,8 +128,9 @@ def test_scanDir():
         assert len(series) == 2
 
         for s in series:
-            assert (s['PatientName'] == 'MCCARTHY_PAUL' or
-                    s['PatientName'] == 'MCCARTHY_PAUL_2')
+            assert s['PatientName'] in ('MCCARTHY_PAUL',
+                                        'MCCARTHY^PAUL',
+                                        'MCCARTHY_PAUL_2')
 
 
 def test_sersiesCRC():
@@ -158,7 +159,7 @@ def test_sersiesCRC():
 def test_loadSeries():
 
     # test a pre-CRC and a post-CRC version
-    for version in ('1.0.20190410', '1.0.20190902'):
+    for version in ('1.0.20181125', '1.0.20201102'):
 
         with install_dcm2niix(version):
 
@@ -170,23 +171,23 @@ def test_loadSeries():
             dcmdir   = os.getcwd()
             series   = fsldcm.scanDir(dcmdir)
             expShape = (512, 512, 1)
-            explens  = [1, 1]
 
-            for s, explen in zip(series, explens):
+            for s in series:
 
                 imgs = fsldcm.loadSeries(s)
 
-                assert len(imgs) == explen
-
                 for img in imgs:
 
                     assert img.dicomDir               == dcmdir
                     assert img.shape                  == expShape
                     assert img[:].shape               == expShape
-                    assert img.getMeta('PatientName') == 'MCCARTHY_PAUL' or \
-                           img.getMeta('PatientName') == 'MCCARTHY_PAUL_2'
+                    assert img.getMeta('PatientName') in ('MCCARTHY_PAUL',
+                                                          'MCCARTHY^PAUL',
+                                                          'MCCARTHY_PAUL_2')
                     assert 'PatientName'                      in img.metaKeys()
                     assert 'MCCARTHY_PAUL'                    in img.metaValues() or \
+                           'MCCARTHY^PAUL'                    in img.metaValues() or \
                            'MCCARTHY_PAUL_2'                  in img.metaValues()
                     assert ('PatientName', 'MCCARTHY_PAUL')   in img.metaItems() or \
+                           ('PatientName', 'MCCARTHY^PAUL')   in img.metaItems() or \
                            ('PatientName', 'MCCARTHY_PAUL_2') in img.metaItems()