diff --git a/setup.cfg b/setup.cfg
index 989b6fc378d37625ab788c27b6e5b6613bf880a1..591cd65648df855238f8e4ee50a08c20888b1fd7 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -5,8 +5,17 @@ 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
+# - longtest: Takes a long time
+#
+
testpaths = tests
-addopts = -v --niters=50 --cov=fsl
+addopts = -v --niters=50 --cov=fsl -m "not longtest"
[flake8]
ignore = E127,E201,E203,E221,E222,E241,E271,E272,E301,E302,E303,E701
\ No newline at end of file
diff --git a/tests/test_atlases.py b/tests/test_atlases.py
index b20b06602878c0467326cf54d8e450a6f3cf6afb..9853c5a73a2b6d73cede0606638906f9f817a40d 100644
--- a/tests/test_atlases.py
+++ b/tests/test_atlases.py
@@ -11,7 +11,6 @@
import os
import os.path as op
-import itertools as it
import numpy as np
import mock
@@ -26,6 +25,9 @@ import fsl.data.image as fslimage
datadir = op.join(op.dirname(__file__), 'testdata')
+pytestmark = pytest.mark.fsltest
+
+
def setup_module():
if os.environ.get('FSLDIR', None) is None:
raise Exception('FSLDIR is not set - atlas tests cannot be run')
diff --git a/tests/test_atlases_query.py b/tests/test_atlases_query.py
index 1bdb28a7ada825558f03a218bbf041402010e763..d512f400f92aad64a750f3c90ddcb9992bb0e184 100644
--- a/tests/test_atlases_query.py
+++ b/tests/test_atlases_query.py
@@ -7,7 +7,6 @@
import os
import itertools as it
-from collections import defaultdict
import numpy as np
import pytest
@@ -20,6 +19,9 @@ import fsl.utils.cache as cache
from . import (testdir, make_random_mask)
+pytestmark = pytest.mark.fsltest
+
+
def setup_module():
if os.environ.get('FSLDIR', None) is None:
raise Exception('FSLDIR is not set - atlas tests cannot be run')
diff --git a/tests/test_atlasq_list_summary.py b/tests/test_atlasq_list_summary.py
index 7eba70fe1d8fa4f03d1fb1e44539230f5e4a10f9..310ef9212af987dd96f81b6340a9c8307d7031fa 100644
--- a/tests/test_atlasq_list_summary.py
+++ b/tests/test_atlasq_list_summary.py
@@ -8,12 +8,17 @@
import os
import itertools as it
+import pytest
+
import fsl.data.atlases as fslatlases
import fsl.scripts.atlasq as fslatlasq
from . import CaptureStdout
+pytestmark = pytest.mark.fsltest
+
+
def setup_module():
if os.environ.get('FSLDIR', None) is None:
raise Exception('FSLDIR is not set - atlas tests cannot be run')
diff --git a/tests/test_atlasq_ohi.py b/tests/test_atlasq_ohi.py
index 2204b08f5e525470d65f4c167bdcff1d91ec03fe..0f36eb20c9567d0ff4215b65a5e8f1e67e68e02a 100644
--- a/tests/test_atlasq_ohi.py
+++ b/tests/test_atlasq_ohi.py
@@ -11,6 +11,8 @@ import os.path as op
import os
import shlex
+import pytest
+
import numpy as np
import fsl.scripts.atlasq as fslatlasq
@@ -21,6 +23,9 @@ from . import (tempdir,
CaptureStdout)
+pytestmark = pytest.mark.fsltest
+
+
def setup_module():
if os.environ.get('FSLDIR', None) is None:
raise Exception('FSLDIR is not set - atlas tests cannot be run')
diff --git a/tests/test_atlasq_query.py b/tests/test_atlasq_query.py
index 1fb887a1a32e69a093f8d6d0c1f97aede29b69cc..427815405e810f9ba04d9250f1e72410574794c7 100644
--- a/tests/test_atlasq_query.py
+++ b/tests/test_atlasq_query.py
@@ -10,10 +10,11 @@ import os
import os.path as op
import re
import itertools as it
-import six
import numpy as np
import scipy.ndimage as ndi
+import pytest
+
import fsl.utils.transform as transform
import fsl.data.atlases as fslatlases
import fsl.data.image as fslimage
@@ -24,6 +25,9 @@ from . import (tempdir,
CaptureStdout)
+pytestmark = pytest.mark.fsltest
+
+
def setup_module():
if os.environ.get('FSLDIR', None) is None:
raise Exception('FSLDIR is not set - atlas tests cannot be run')
diff --git a/tests/test_callfsl.py b/tests/test_callfsl.py
index 85176b2124e565a0ad13df3131ce75cd535eb55f..25c156f8783aa8e5dca554af7d0454a3d58a0ca7 100644
--- a/tests/test_callfsl.py
+++ b/tests/test_callfsl.py
@@ -20,6 +20,10 @@ from fsl.utils.platform import platform as fslplatform
import tests
+
+pytestmark = pytest.mark.fsltest
+
+
def setup_module():
fsldir = os.environ.get('FSLDIR', None)
if fsldir is None or not op.exists(fsldir):
diff --git a/tests/test_dicom.py b/tests/test_dicom.py
index a728c0b46db32ec39f2cb9bada40dc5fd8a05cac..325a15b4a8cc94b172998e8712a4d87318a8b100 100644
--- a/tests/test_dicom.py
+++ b/tests/test_dicom.py
@@ -18,6 +18,9 @@ import fsl.utils.tempdir as tempdir
datadir = op.join(op.dirname(__file__), 'testdata')
+pytestmark = pytest.mark.dicomtest
+
+
def setup_module():
if not fsldcm.enabled():
diff --git a/tests/test_idle.py b/tests/test_idle.py
index 96bc3c022178db32fa3ef1459ef952735b7444d1..18b2c4420efb5d9780fb87295dbcb452be1da456 100644
--- a/tests/test_idle.py
+++ b/tests/test_idle.py
@@ -18,6 +18,7 @@ import mock
import fsl.utils.idle as idle
from fsl.utils.platform import platform as fslplatform
+
def _run_with_wx(func, *args, **kwargs):
gc.collect()
@@ -91,6 +92,7 @@ def _wait_for_idle_loop_to_clear():
wx.Yield()
+@pytest.mark.wxtest
def test_run_with_gui(): _run_with_wx( _test_run)
def test_run_without_gui(): _run_without_wx(_test_run)
def _test_run():
@@ -143,7 +145,7 @@ def _test_run():
assert onErrorCalled[ 0]
-
+@pytest.mark.wxtest
def test_idleTimeout_with_gui(): _run_with_wx( _test_idleTimeout)
def test_idleTimeout_without_gui(): _run_without_wx(_test_idleTimeout)
def _test_idleTimeout():
@@ -155,6 +157,7 @@ def _test_idleTimeout():
assert idle.getIdleTimeout() == default
+@pytest.mark.wxtest
def test_idle():
called = [False]
@@ -185,6 +188,7 @@ def test_idle():
_run_with_wx(idle.idle, errtask, 1, kwarg1=2)
+@pytest.mark.wxtest
def test_inidle():
called = [False]
@@ -203,6 +207,7 @@ def test_inidle():
assert called[0]
+@pytest.mark.wxtest
def test_cancelidle():
called = [False]
@@ -221,6 +226,7 @@ def test_cancelidle():
assert not called[0]
+@pytest.mark.wxtest
def test_idle_skipIfQueued():
task1called = [False]
@@ -244,6 +250,7 @@ def test_idle_skipIfQueued():
assert not task2called[0]
+@pytest.mark.wxtest
def test_idle_dropIfQueued():
task1called = [False]
@@ -278,6 +285,7 @@ def test_idle_dropIfQueued():
assert task2called[0]
+@pytest.mark.wxtest
def test_idle_alwaysQueue1():
# Test scheduling the task before
@@ -304,6 +312,7 @@ def test_idle_alwaysQueue1():
assert called[0]
+@pytest.mark.wxtest
def test_idle_alwaysQueue2():
# Test scheduling the task
@@ -323,6 +332,7 @@ def test_idle_alwaysQueue2():
assert called[0]
+@pytest.mark.wxtest
def test_idle_alwaysQueue3():
# Test scheduling the task
@@ -343,6 +353,7 @@ def test_idle_alwaysQueue3():
assert called[0]
+@pytest.mark.wxtest
def test_idle_alwaysQueue4():
# Test scheduling the task when
@@ -370,6 +381,7 @@ def test_idle_alwaysQueue4():
assert called[0]
+@pytest.mark.wxtest
def test_idle_timeout():
called = [False]
@@ -382,7 +394,7 @@ def test_idle_timeout():
assert not called[0]
-
+@pytest.mark.wxtest
def test_idleWhen():
called = [False]
@@ -403,6 +415,7 @@ def test_idleWhen():
assert timesPolled[0] == 50
+@pytest.mark.wxtest
def test_wait_with_gui(): _run_with_wx(_test_wait, finishingDelay=1100)
def test_wait_without_gui(): _test_wait()
def _test_wait():
diff --git a/tests/test_image_advanced.py b/tests/test_image_advanced.py
index a05f5d521995363df77012ed85cdc02c5f217198..69756278781902081f2b8c3250d7eb6d40319a96 100644
--- a/tests/test_image_advanced.py
+++ b/tests/test_image_advanced.py
@@ -9,6 +9,7 @@ import os.path as op
import time
import mock
+import pytest
import numpy as np
import nibabel as nib
@@ -22,15 +23,22 @@ from . import make_random_image
# make sure Image(indexed=True) works
# even if indexed_gzip is not present
+@pytest.mark.longtest
def test_image_indexed_no_igzip_threaded():
with mock.patch.dict('sys.modules', indexed_gzip=None):
_test_image_indexed(True)
+@pytest.mark.longtest
def test_image_indexed_no_igzip_unthreaded():
with mock.patch.dict('sys.modules', indexed_gzip=None):
_test_image_indexed(False)
+
+@pytest.mark.longtest
+@pytest.mark.igziptest
def test_image_indexed_threaded( ): _test_image_indexed(True)
+@pytest.mark.longtest
+@pytest.mark.igziptest
def test_image_indexed_unthreaded(): _test_image_indexed(False)
def _test_image_indexed(threaded):
@@ -74,8 +82,12 @@ def _test_image_indexed(threaded):
assert (end1 - start1) > (end2 - start2)
+@pytest.mark.longtest
+@pytest.mark.igziptest
def test_image_indexed_read4D_threaded(seed):
_test_image_indexed_read4D(True)
+@pytest.mark.longtest
+@pytest.mark.igziptest
def test_image_indexed_read4D_unthreaded(seed):
_test_image_indexed_read4D(False)
def _test_image_indexed_read4D(threaded):
@@ -115,7 +127,11 @@ def _test_image_indexed_read4D(threaded):
assert np.all(data == np.arange(nvols))
+@pytest.mark.igziptest
+@pytest.mark.longtest
def test_image_indexed_save_threaded( ): _test_image_indexed_save(True)
+@pytest.mark.longtest
+@pytest.mark.igziptest
def test_image_indexed_save_unthreaded(): _test_image_indexed_save(False)
def _test_image_indexed_save(threaded):
@@ -186,7 +202,11 @@ def _test_image_indexed_save(threaded):
assert np.all(img[..., 40] == 45)
+@pytest.mark.longtest
+@pytest.mark.igziptest
def test_image_no_calcRange_threaded(): _test_image_no_calcRange(True)
+@pytest.mark.longtest
+@pytest.mark.igziptest
def test_image_no_calcRange_unthreaded(): _test_image_no_calcRange(False)
def _test_image_no_calcRange(threaded):
@@ -217,7 +237,11 @@ def _test_image_no_calcRange(threaded):
assert img.dataRange == (0, i)
+@pytest.mark.longtest
+@pytest.mark.igziptest
def test_image_calcRange_threaded(): _test_image_calcRange(True)
+@pytest.mark.longtest
+@pytest.mark.igziptest
def test_image_calcRange_unthreaded(): _test_image_calcRange(False)
def _test_image_calcRange(threaded):
diff --git a/tests/test_imagewrapper.py b/tests/test_imagewrapper.py
index 3c89d435042896527d603ff1f1714bb42ecd68c2..c481ada3158b475846ba7bd17d57a4f91abf2297 100644
--- a/tests/test_imagewrapper.py
+++ b/tests/test_imagewrapper.py
@@ -13,6 +13,7 @@ import time
import itertools as it
import numpy as np
import nibabel as nib
+import pytest
import fsl.data.image as image
@@ -566,12 +567,16 @@ def _ImageWraper_busy_wait(wrapper, v=0):
if tt is not None:
tt.waitUntilIdle()
+@pytest.mark.longtest
def test_ImageWrapper_read_threaded(niters, seed):
_test_ImageWrapper_read(niters, seed, True)
+@pytest.mark.longtest
def test_ImageWrapper_read_unthreaded(niters, seed):
_test_ImageWrapper_read(niters, seed, False)
+@pytest.mark.longtest
def test_ImageWrapper_read_nans_threaded(niters, seed):
_test_ImageWrapper_read(niters, seed, True, True)
+@pytest.mark.longtest
def test_ImageWrapper_read_nans_unthreaded(niters, seed):
_test_ImageWrapper_read(niters, seed, False, True)
@@ -658,9 +663,10 @@ def _test_ImageWrapper_read(niters, seed, threaded, addnans=False):
else: assert wrapper.covered
-
+@pytest.mark.longtest
def test_ImageWrapper_write_out_threaded(niters, seed):
_test_ImageWrapper_write_out(niters, seed, True)
+@pytest.mark.longtest
def test_ImageWrapper_write_out_unthreaded(niters, seed):
_test_ImageWrapper_write_out(niters, seed, False)
def _test_ImageWrapper_write_out(niters, seed, threaded):
@@ -799,8 +805,10 @@ def _test_ImageWrapper_write_out(niters, seed, threaded):
# print('--------------')
+@pytest.mark.longtest
def test_ImageWrapper_write_in_overlap_threaded(niters, seed):
_test_ImageWrapper_write_in_overlap(niters, seed, True)
+@pytest.mark.longtest
def test_ImageWrapper_write_in_overlap_unthreaded(niters, seed):
_test_ImageWrapper_write_in_overlap(niters, seed, False)
def _test_ImageWrapper_write_in_overlap(niters, seed, threaded):
@@ -910,8 +918,10 @@ def _test_ImageWrapper_write_in_overlap(niters, seed, threaded):
assert np.isclose(newHi, expHi)
+@pytest.mark.longtest
def test_ImageWrapper_write_different_volume_threaded(niters, seed):
_test_ImageWrapper_write_different_volume(niters, seed, True)
+@pytest.mark.longtest
def test_ImageWrapper_write_different_volume_unthreaded(niters, seed):
_test_ImageWrapper_write_different_volume(niters, seed, False)
def _test_ImageWrapper_write_different_volume(niters, seed, threaded):
diff --git a/tests/test_mesh.py b/tests/test_mesh.py
index 5dca80f2140c6f48540caa09a3e529cccf4d119a..97f2c9b2f3eb63b02a2c06fec81c508e53f5e713 100644
--- a/tests/test_mesh.py
+++ b/tests/test_mesh.py
@@ -279,6 +279,7 @@ def test_trimesh_no_trimesh():
assert faces.size == 0
+@pytest.mark.meshtest
def test_trimesh():
import trimesh
@@ -290,6 +291,7 @@ def test_trimesh():
assert isinstance(mesh.trimesh, trimesh.Trimesh)
+@pytest.mark.meshtest
def test_rayIntersection():
verts = np.array(CUBE_VERTICES)
@@ -318,6 +320,7 @@ def test_rayIntersection():
assert tri.size == 0
+@pytest.mark.meshtest
def test_nearestVertex():
verts = np.array(CUBE_VERTICES)
@@ -331,6 +334,7 @@ def test_nearestVertex():
assert np.all(np.isclose(ndists, np.sqrt(3)))
+@pytest.mark.meshtest
def test_planeIntersection():
verts = np.array(CUBE_VERTICES)
diff --git a/tests/test_platform.py b/tests/test_platform.py
index addddbc24cffce0df8a6ca566fa2420dfd7e0347..6088009ef09628523e62157e05f47806517ea807 100644
--- a/tests/test_platform.py
+++ b/tests/test_platform.py
@@ -11,6 +11,7 @@ import os.path as op
import sys
import shutil
import tempfile
+import pytest
import mock
@@ -35,6 +36,7 @@ def test_atts():
p.glIsSoftwareRenderer
+@pytest.mark.wxtest
def test_haveGui():
import wx
@@ -207,6 +209,7 @@ def test_detect_ssh():
assert not p.inVNCSession
+@pytest.mark.wxtest
def test_IsWidgetAlive():
import wx