Merge branch 'bf/fileorimage-fsloutputtype' into 'main'

BF: Fix issue with `fsl.wrappers` functions ignoring  `$FSLOUTPUTTYPE` when searching for output files

See merge request fsl/fslpy!452

CHANGELOG.rst

@@ -2,6 +2,17 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
+3.18.3 (Saturday 4th May 2024)
+------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed an issue with :mod:``fsl.wrappers`` functions not finding output files
+  when ``$FSLOUTPUTTYPE`` is set to something other than ``NIFTI_GZ`` (!452).
+
 
 3.18.2 (Wednesday 3rd April 2024)
 ---------------------------------

fsl/tests/test_assertions.py

@@ -14,8 +14,8 @@ import pytest
 import fsl.utils.assertions as assertions
 import fsl.utils.tempdir    as tempdir
 
-from . import make_random_image
-from . import testdir
+from fsl.tests import make_random_image
+from fsl.tests import testdir
 
 
 def test_assertFileExists():

fsl/tests/test_atlases_query.py

@@ -17,7 +17,7 @@ import fsl.transform.affine     as affine
 import fsl.utils.image.resample as resample
 import fsl.utils.cache          as cache
 
-from . import (testdir, make_random_mask)
+from fsl.tests import (testdir, make_random_mask)
 
 
 pytestmark = pytest.mark.fsltest

fsl/tests/test_dicom.py

@@ -22,7 +22,7 @@ import fsl.data.dicom    as fsldcm
 import fsl.utils.tempdir as tempdir
 
 
-from . import mockFSLDIR, touch
+from fsl.tests import mockFSLDIR, touch
 
 
 datadir = op.join(op.dirname(__file__), 'testdata')

fsl/tests/test_ensure.py

@@ -13,7 +13,7 @@ import nibabel as nib
 import fsl.utils.tempdir as tempdir
 import fsl.utils.ensure  as ensure
 
-from . import make_random_image
+from fsl.tests import make_random_image
 
 
 def test_ensureIsImage():

fsl/tests/test_filetree/test_query.py

@@ -13,7 +13,7 @@ import contextlib
 import textwrap as tw
 import itertools as it
 
-from .. import testdir
+from fsl.tests import testdir
 
 import fsl.utils.filetree       as filetree
 import fsl.utils.filetree.query as ftquery

fsl/tests/test_freesurfer.py

@@ -19,9 +19,9 @@ import pytest
 import fsl.version         as fslver
 import fsl.data.freesurfer as fslfs
 
-from .test_mesh import (CUBE_VERTICES, CUBE_TRIANGLES_CCW)
+from fsl.tests.test_mesh import (CUBE_VERTICES, CUBE_TRIANGLES_CCW)
 
-from . import tempdir, touch
+from fsl.tests import tempdir, touch
 
 
 def gen_freesurfer_geometry(fname, verts, tris):

fsl/tests/test_fsl_data_utils.py

@@ -26,10 +26,10 @@ import fsl.data.dtifit          as dtifit
 import fsl.data.melodicanalysis as melanalysis
 import fsl.data.featanalysis    as featanalysis
 
-from . import (touch,
-               make_mock_feat_analysis,
-               make_mock_melodic_analysis,
-               make_mock_dtifit_analysis)
+from fsl.tests import (touch,
+                       make_mock_feat_analysis,
+                       make_mock_melodic_analysis,
+                       make_mock_dtifit_analysis)
 
 
 def test_guessType():

fsl/tests/test_fsl_utils_path.py

@@ -18,7 +18,7 @@ import pytest
 import fsl.utils.path as fslpath
 import fsl.data.image as fslimage
 
-from . import testdir
+from fsl.tests import testdir
 
 
 def make_dummy_file(path):

fsl/tests/test_fslsub.py

@@ -19,7 +19,7 @@ import fsl.version as fv
 from fsl.utils         import fslsub, run
 from fsl.utils.tempdir import tempdir
 
-from . import mockFSLDIR
+from fsl.tests import mockFSLDIR
 
 
 mock_fsl_sub = """
@@ -239,4 +239,4 @@ def test_info():
     assert res2['1'] is None
 
     with pytest.raises(ValueError):
-        fslsub._parse_qstat(valid_job_ids[0], example_qstat_reply)
\ No newline at end of file
+        fslsub._parse_qstat(valid_job_ids[0], example_qstat_reply)

fsl/tests/test_gifti.py

@@ -16,7 +16,8 @@ import pytest
 
 import fsl.data.gifti as gifti
 
-from . import tempdir
+from fsl.tests import tempdir
+from fsl.tests import test_mesh
 
 
 def test_GiftiMesh_create():
@@ -364,7 +365,6 @@ def test_GiftiMesh_multiple_vertices():
 
 
 def test_GiftiMesh_needsFixing():
-    from . import test_mesh
 
     verts      = test_mesh.CUBE_VERTICES
     idxs       = test_mesh.CUBE_TRIANGLES_CW

fsl/tests/test_image.py

@@ -29,8 +29,8 @@ import fsl.transform.affine as affine
 
 from fsl.utils.tempdir import tempdir
 
-from . import make_random_image
-from . import make_dummy_file
+from fsl.tests import make_random_image
+from fsl.tests import make_dummy_file
 
 from unittest import mock
 

fsl/tests/test_image_resample.py

@@ -12,7 +12,7 @@ import fsl.data.image           as     fslimage
 import fsl.transform.affine     as     affine
 import fsl.utils.image.resample as     resample
 
-from . import make_random_image
+from fsl.tests import make_random_image
 
 def random_affine():
     return affine.compose(

fsl/tests/test_immv_imcp.py

@@ -20,9 +20,9 @@ import nibabel as nib
 import fsl.utils.imcp        as imcp
 import fsl.data.image        as fslimage
 
-from . import make_random_image
-from . import make_dummy_file
-from . import looks_like_image
+from fsl.tests import make_random_image
+from fsl.tests import make_dummy_file
+from fsl.tests import looks_like_image
 
 
 real_print = print

fsl/tests/test_mesh.py

@@ -14,7 +14,7 @@ import                 pytest
 import fsl.transform.affine as affine
 import fsl.data.mesh        as fslmesh
 
-from . import tempdir
+from fsl.tests import tempdir
 
 
 # vertices of a cube

fsl/tests/test_parse_data.py

@@ -13,7 +13,7 @@ from fsl.data.gifti import GiftiMesh
 from fsl.data.image import Image
 from fsl.data.atlases import Atlas
 from pytest import raises
-from .test_image import make_image
+from fsl.tests.test_image import make_image
 import os
 import pytest
 

fsl/tests/test_run.py

@@ -22,7 +22,7 @@ from   fsl.utils.platform import platform as fslplatform
 import fsl.utils.run                      as run
 import fsl.wrappers                       as wrappers
 
-from . import make_random_image, mockFSLDIR, CaptureStdout, touch
+from fsl.tests import make_random_image, mockFSLDIR, CaptureStdout, touch
 
 
 pytestmark = pytest.mark.unixtest

fsl/tests/test_scripts/test_atlasq_list_summary.py

@@ -13,7 +13,7 @@ import              pytest
 import fsl.data.atlases   as fslatlases
 import fsl.scripts.atlasq as fslatlasq
 
-from .. import CaptureStdout
+from fsl.tests import CaptureStdout
 
 
 pytestmark = pytest.mark.fsltest

fsl/tests/test_scripts/test_atlasq_ohi.py

@@ -18,9 +18,9 @@ import numpy as np
 import fsl.scripts.atlasq as fslatlasq
 import fsl.data.atlases   as fslatlases
 
-from .. import (tempdir,
-                make_random_mask,
-                CaptureStdout)
+from fsl.tests import (tempdir,
+                       make_random_mask,
+                       CaptureStdout)
 
 
 pytestmark = pytest.mark.fsltest

fsl/tests/test_scripts/test_atlasq_query.py

@@ -21,9 +21,9 @@ import fsl.utils.image.resample as resample
 import fsl.data.image           as fslimage
 import fsl.scripts.atlasq       as fslatlasq
 
-from .. import (tempdir,
-                make_random_mask,
-                CaptureStdout)
+from fsl.tests import (tempdir,
+                       make_random_mask,
+                       CaptureStdout)
 
 
 pytestmark = pytest.mark.fsltest