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|
From: =?utf-8?q?=C3=89tienne_Mollier?= <emollier@debian.org>
Date: Fri, 3 Dec 2021 22:47:26 +0100
Subject: skip tests needing internet
Forwarded: not-needed
Last-Update: 2021-12-03
Last-Update: 2021-12-03
---
dipy/align/tests/test_api.py | 9 +++++++++
dipy/data/tests/test_fetcher.py | 3 ++-
dipy/direction/tests/test_ptt_direction_getter.py | 3 ++-
dipy/workflows/tests/test_io.py | 2 ++
4 files changed, 15 insertions(+), 2 deletions(-)
--- dipy.orig/dipy/align/tests/test_api.py
+++ dipy/dipy/align/tests/test_api.py
@@ -34,6 +34,7 @@
from dipy.tracking.utils import transform_tracking_output
+@pytest.mark.skip(reason="test needs internet")
def setup_module():
global \
subset_b0, \
@@ -61,6 +62,7 @@
subset_t2_img = nib.Nifti1Image(subset_t2, MNI_T2_affine)
+@pytest.mark.skip(reason="test needs internet")
def test_syn_registration():
with TemporaryDirectory() as tmpdir:
warped_moving, mapping = syn_registration(
@@ -97,6 +99,7 @@
)
+@pytest.mark.skip(reason="test needs internet")
def test_register_dwi_to_template():
# Default is syn registration:
warped_b0, mapping = register_dwi_to_template(
@@ -125,6 +128,7 @@
npt.assert_(affine_mat.shape == (4, 4))
+@pytest.mark.skip(reason="test needs internet")
def test_affine_registration():
moving = subset_b0
static = subset_b0
@@ -256,6 +260,7 @@
npt.assert_almost_equal(affine_mat[:3, :3], np.eye(3), decimal=1)
+@pytest.mark.skip(reason="test needs internet")
def test_single_transforms():
moving = subset_b0
static = subset_b0
@@ -284,6 +289,7 @@
npt.assert_almost_equal(affine_mat[:3, :3], np.eye(3), decimal=1)
+@pytest.mark.skip(reason="test needs internet")
def test_register_series():
fdata, fbval, fbvec = dpd.get_fnames(name="small_64D")
img = nib.load(fdata)
@@ -294,6 +300,7 @@
npt.assert_(np.all(xformed[..., ref_idx] == img.get_fdata()[..., ref_idx]))
+@pytest.mark.skip(reason="test might need internet")
def test_register_dwi_series_and_motion_correction():
fdata, fbval, fbvec = dpd.get_fnames(name="small_64D")
with TemporaryDirectory() as tmpdir:
@@ -317,6 +324,7 @@
npt.assert_array_equal(reg_affines, reg_affines_2)
+@pytest.mark.skip(reason="test needs internet")
@set_random_number_generator()
def test_streamline_registration(rng):
sl1 = [
@@ -372,6 +380,7 @@
npt.assert_almost_equal(aligned[1], sl1[1], decimal=5)
+@pytest.mark.skip(reason="test needs internet")
def test_register_dwi_series_multi_b0():
# Test if register_dwi_series works with multiple b0 images
dwi_fname, dwi_bval_fname, dwi_bvec_fname = dpd.get_fnames(name="sherbrooke_3shell")
--- dipy.orig/dipy/data/tests/test_fetcher.py
+++ dipy/dipy/data/tests/test_fetcher.py
@@ -2,6 +2,7 @@
import importlib
import os
import os.path as op
+import pytest
import tempfile
from threading import Thread
from urllib.request import pathname2url
@@ -87,7 +88,7 @@
# change to original working directory
os.chdir(current_dir)
-
+@pytest.mark.skip(reason="test skewed by dummy proxy setup")
def test_fetch_data():
symmetric362 = SPHERE_FILES["symmetric362"]
with tempfile.TemporaryDirectory() as tmpdir:
--- dipy.orig/dipy/direction/tests/test_ptt_direction_getter.py
+++ dipy/dipy/direction/tests/test_ptt_direction_getter.py
@@ -19,8 +19,9 @@
from dipy.tracking.local_tracking import LocalTracking
from dipy.tracking.stopping_criterion import BinaryStoppingCriterion
from dipy.tracking.streamline import Streamlines
+import pytest
-
+@pytest.mark.skip(reason="test needs internet")
def test_ptt_tracking():
# Test PTT direction getter generate 100 streamlines with more than 1 pts.
fod_fname, seed_coordinates_fname, _ = get_fnames(name="ptt_minimal_dataset")
--- dipy.orig/dipy/workflows/tests/test_io.py
+++ dipy/dipy/workflows/tests/test_io.py
@@ -6,6 +6,7 @@
import shutil
import sys
from tempfile import TemporaryDirectory, mkstemp
+import pytest
import numpy as np
import numpy.testing as npt
@@ -89,6 +90,7 @@
pass
+@pytest.mark.skip(reason="test needs internet")
def test_io_fetch():
fetch_flow = FetchFlow()
with TemporaryDirectory() as out_dir:
--- dipy.orig/dipy/tracking/tests/test_propspeed.pyx
+++ dipy/dipy/tracking/tests/test_propspeed.pyx
@@ -22,6 +22,8 @@
from dipy.tracking.tests.test_tractogen import get_fast_tracking_performances
from dipy.utils.fast_numpy cimport RNGState, seed_rng
+import pytest
+
def test_tracker_deterministic():
# Test the probabilistic tracker function
@@ -84,6 +86,7 @@
def test_deterministic_performances():
# Test deterministic tracker on the DiSCo dataset
+ pytest.skip(reason="test needs internet")
params = generate_tracking_parameters("det",
max_len=500,
step_size=0.2,
@@ -156,6 +159,7 @@
def test_probabilistic_performances():
# Test probabilistic tracker on the DiSCo dataset
+ pytest.skip(reason="test needs internet")
params = generate_tracking_parameters("prob",
max_len=500,
step_size=0.2,
@@ -229,6 +233,7 @@
def test_ptt_performances():
# Test ptt tracker on the DiSCo dataset
+ pytest.skip(reason="test needs internet")
params = generate_tracking_parameters("ptt",
max_len=500,
--- dipy.orig/dipy/tracking/tests/test_tracker.py
+++ dipy/dipy/tracking/tests/test_tracker.py
@@ -12,6 +12,8 @@
from dipy.tracking.streamline import Streamlines
from dipy.tracking.utils import random_seeds_from_mask
+import pytest
+
def track(method, **kwargs):
"""This tests that the number of streamlines equals the number of seeds
@@ -80,6 +82,7 @@
npt.assert_array_less(len(streamlines), len(seeds))
+@pytest.mark.skip(reason="test needs internet")
def test_deterministic_tracking():
with warnings.catch_warnings():
warnings.filterwarnings(
@@ -91,6 +94,7 @@
track(tracker.deterministic_tracking, use_sf=True, use_dirs=True)
+@pytest.mark.skip(reason="test needs internet")
def test_probabilistic_tracking():
with warnings.catch_warnings():
warnings.filterwarnings(
@@ -102,6 +106,7 @@
track(tracker.probabilistic_tracking, use_sf=True, use_dirs=True)
+@pytest.mark.skip(reason="test needs internet")
def test_ptt_tracking():
with warnings.catch_warnings():
warnings.filterwarnings(
--- dipy.orig/dipy/tracking/tests/test_tractogen.pyx
+++ dipy/dipy/tracking/tests/test_tractogen.pyx
@@ -16,6 +16,7 @@
from dipy.tracking.utils import (connectivity_matrix, random_seeds_from_mask,
seeds_from_mask, seeds_directions_pairs)
+import pytest
def get_fast_tracking_performances(params, *, nbr_seeds=1000, nbr_threads=0):
@@ -88,6 +89,7 @@
def test_tractogram_reproducibility():
# Test tractogram reproducibility
+ pytest.skip(reason="test needs internet")
params0 = generate_tracking_parameters("prob",
max_len=500,
step_size=0.2,
@@ -129,6 +131,8 @@
"""This tests that the angle between streamline points is always smaller
then the input `max_angle` parameter.
"""
+ pytest.skip(reason="test needs internet")
+ pytest.skip(reason="test needs internet")
def get_min_cos_similarity(streamlines):
min_cos_sim = 1
@@ -163,6 +167,7 @@
"""This tests that the distance between streamline
points is equal to the input `step_size` parameter.
"""
+ pytest.skip(reason="test needs internet")
def get_points_distance(streamlines):
dists = []
@@ -189,7 +194,7 @@
"""This tests that the number of streamlines equals the number of seeds
when return_all=True.
"""
-
+ pytest.skip(reason="test needs internet")
fnames = get_fnames(name="disco1", include_optional=True)
sphere = HemiSphere.from_sphere(get_sphere(name="repulsion724"))
@@ -248,6 +253,7 @@
def test_max_min_length():
"""This tests that the returned streamlines respect the length criterion.
"""
+ pytest.skip(reason="test needs internet")
fnames = get_fnames(name="disco1", include_optional=True)
sphere = HemiSphere.from_sphere(get_sphere(name="repulsion724"))
sh = nib.load(fnames[20]).get_fdata()
@@ -293,6 +299,7 @@
def test_buffer_frac():
"""This tests that the buffer fraction for generate tractogram plays well.
"""
+ pytest.skip(reason="test needs internet")
fnames = get_fnames(name="disco1", include_optional=True)
sphere = HemiSphere.from_sphere(get_sphere(name="repulsion724"))
sh = nib.load(fnames[20]).get_fdata()
|
