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|
From: Ole Streicher <olebole@debian.org>
Date: Wed, 16 Dec 2020 11:26:58 +0100
Subject: Skip tests that need the python3-pooch package and internet
connection
python3-pooch is not available yet (RFS #968470)
---
skimage/data/tests/test_data.py | 16 ++++++++++++++++
skimage/filters/rank/tests/test_rank.py | 3 +--
skimage/measure/tests/test_blur_effect.py | 1 +
skimage/morphology/tests/test_gray.py | 4 ++++
.../tests/test_masked_phase_cross_correlation.py | 1 +
.../registration/tests/test_phase_cross_correlation.py | 1 +
skimage/restoration/tests/test_restoration.py | 1 +
skimage/restoration/tests/test_rolling_ball.py | 1 +
8 files changed, 26 insertions(+), 2 deletions(-)
diff --git a/skimage/data/tests/test_data.py b/skimage/data/tests/test_data.py
index 301306c..663bbc6 100644
--- a/skimage/data/tests/test_data.py
+++ b/skimage/data/tests/test_data.py
@@ -7,6 +7,15 @@ import os
import pytest
+@pytest.mark.skip(reason="test fails without pooch")
+def test_data_dir():
+ # data_dir should be a directory people can use as a standard directory
+ # https://github.com/scikit-image/scikit-image/pull/3945#issuecomment-498141893
+ data_dir = data.data_dir
+ assert 'astronaut.png' in os.listdir(data_dir)
+
+
+@pytest.mark.skip(reason="requires data downloaded from internet")
def test_download_all_with_pooch():
# jni first wrote this test with the intention of
# fully deleting the files in the data_dir,
@@ -62,6 +71,7 @@ def test_coffee():
data.coffee()
+@pytest.mark.skip(reason="requires data downloaded from internet")
def test_eagle():
"""Test that "eagle" image can be loaded."""
# Fetching the data through the testing module will
@@ -137,6 +147,7 @@ def test_lfw_subset():
data.lfw_subset()
+@pytest.mark.skip(reason="Needs python3-pooch and internet connection")
def test_skin():
"""Test that "skin" image can be loaded.
@@ -151,6 +162,7 @@ def test_cell():
data.cell()
+@pytest.mark.skip(reason="requires data downloaded from internet")
def test_cells3d():
"""Needs internet connection."""
path = fetch('data/cells3d.tif')
@@ -158,6 +170,7 @@ def test_cells3d():
assert image.shape == (60, 2, 256, 256)
+@pytest.mark.skip(reason="requires data downloaded from internet")
def test_brain_3d():
"""Needs internet connection."""
path = fetch('data/brain.tiff')
@@ -165,6 +178,7 @@ def test_brain_3d():
assert image.shape == (10, 256, 256)
+@pytest.mark.skip(reason="requires data downloaded from internet")
def test_kidney_3d_multichannel():
"""Test that 3D multichannel image of kidney tissue can be loaded.
@@ -175,6 +189,7 @@ def test_kidney_3d_multichannel():
assert kidney.shape == (16, 512, 512, 3)
+@pytest.mark.skip(reason="requires data downloaded from internet")
def test_lily_multichannel():
"""Test that microscopy image of lily of the valley can be loaded.
@@ -185,6 +200,7 @@ def test_lily_multichannel():
assert lily.shape == (922, 922, 4)
+@pytest.mark.skip(reason="requires data downloaded from internet")
def test_vortex():
fetch('data/pivchallenge-B-B001_1.tif')
fetch('data/pivchallenge-B-B001_2.tif')
diff --git a/skimage/filters/rank/tests/test_rank.py b/skimage/filters/rank/tests/test_rank.py
index 2f82c8b..5758bbd 100644
--- a/skimage/filters/rank/tests/test_rank.py
+++ b/skimage/filters/rank/tests/test_rank.py
@@ -58,7 +58,6 @@ def test_subtract_mean_underflow_correction(dtype):
# Note: Explicitly read all values into a dict. Otherwise, stochastic test
# failures related to I/O can occur during parallel test cases.
ref_data = dict(np.load(fetch("data/rank_filter_tests.npz")))
-ref_data_3d = dict(np.load(fetch('data/rank_filters_tests_3d.npz')))
@pytest.mark.parametrize(
@@ -104,7 +103,6 @@ class TestRank:
self.footprint = morphology.disk(1)
self.footprint_3d = morphology.ball(1)
self.refs = ref_data
- self.refs_3d = ref_data_3d
@pytest.mark.parametrize('outdt', [None, np.float32, np.float64])
@pytest.mark.parametrize('filter', all_rank_filters)
@@ -158,6 +156,7 @@ class TestRank:
@pytest.mark.parametrize('outdt', [None, np.float32, np.float64])
@pytest.mark.parametrize('filter', _3d_rank_filters)
+ @pytest.mark.skip(reason="requires data downloaded from internet")
def test_rank_filters_3D(self, filter, outdt):
@run_in_parallel(warnings_matching=['Possible precision loss'])
def check():
diff --git a/skimage/measure/tests/test_blur_effect.py b/skimage/measure/tests/test_blur_effect.py
index bfd622b..e126435 100644
--- a/skimage/measure/tests/test_blur_effect.py
+++ b/skimage/measure/tests/test_blur_effect.py
@@ -44,6 +44,7 @@ def test_blur_effect_channel_axis():
np.testing.assert_array_equal(B0_arr, B1_arr)
+@pytest.mark.skip(reason="Needs python3-pooch and internet connection")
def test_blur_effect_3d():
"""Test that the blur metric works on a 3D image."""
image_3d = ski.data.cells3d()[:, 1, :, :] # grab just the nuclei
diff --git a/skimage/morphology/tests/test_gray.py b/skimage/morphology/tests/test_gray.py
index 7073f22..e392c85 100644
--- a/skimage/morphology/tests/test_gray.py
+++ b/skimage/morphology/tests/test_gray.py
@@ -67,6 +67,8 @@ class TestMorphology:
return output
+
+ @pytest.mark.skip(reason="requires data downloaded from internet")
def test_gray_morphology(self):
expected = dict(np.load(fetch('data/gray_morph_output.npz')))
calculated = self._build_expected_output()
@@ -449,6 +451,7 @@ def test_octagon_decomposition(cam_image, function, m, n, decomposition):
assert_array_equal(expected, out)
+@pytest.mark.skip(reason="requires data downloaded from internet")
@pytest.mark.parametrize(
"function",
["erosion", "dilation", "closing", "opening", "white_tophat", "black_tophat"],
@@ -468,6 +471,7 @@ def test_cube_decomposition(cell3d_image, function, shape, decomposition):
assert_array_equal(expected, out)
+@pytest.mark.skip(reason="requires data downloaded from internet")
@pytest.mark.parametrize(
"function",
["erosion", "dilation", "closing", "opening", "white_tophat", "black_tophat"],
diff --git a/skimage/registration/tests/test_masked_phase_cross_correlation.py b/skimage/registration/tests/test_masked_phase_cross_correlation.py
index 8e0fb79..37f174d 100644
--- a/skimage/registration/tests/test_masked_phase_cross_correlation.py
+++ b/skimage/registration/tests/test_masked_phase_cross_correlation.py
@@ -59,6 +59,7 @@ def test_masked_registration_random_masks():
assert_equal(measured_shift, -np.array(shift))
+@pytest.mark.skip(reason="Needs python3-pooch and internet connection")
def test_masked_registration_3d_contiguous_mask():
"""masked_register_translation should be able to register translations
between volumes with contiguous masks."""
diff --git a/skimage/registration/tests/test_phase_cross_correlation.py b/skimage/registration/tests/test_phase_cross_correlation.py
index a43f14f..4f2181e 100644
--- a/skimage/registration/tests/test_phase_cross_correlation.py
+++ b/skimage/registration/tests/test_phase_cross_correlation.py
@@ -177,6 +177,7 @@ def test_mismatch_offsets_size():
_upsampled_dft(np.ones((4, 4)), 3, axis_offsets=[3, 2, 1, 4])
+@pytest.mark.skip(reason="requires data downloaded from internet")
@pytest.mark.parametrize(
('shift0', 'shift1'),
itertools.product((100, -100, 350, -350), (100, -100, 350, -350)),
diff --git a/skimage/restoration/tests/test_restoration.py b/skimage/restoration/tests/test_restoration.py
index 6b7de49..ef71891 100644
--- a/skimage/restoration/tests/test_restoration.py
+++ b/skimage/restoration/tests/test_restoration.py
@@ -164,6 +164,7 @@ def test_richardson_lucy(ndim):
@pytest.mark.parametrize('dtype_image', [np.float16, np.float32, np.float64])
@pytest.mark.parametrize('dtype_psf', [np.float32, np.float64])
+@pytest.mark.skip(reason="requires data downloaded from internet")
def test_richardson_lucy_filtered(dtype_image, dtype_psf):
if dtype_image == np.float64:
atol = 1e-8
diff --git a/skimage/restoration/tests/test_rolling_ball.py b/skimage/restoration/tests/test_rolling_ball.py
index 42f4e57..58a2b1f 100644
--- a/skimage/restoration/tests/test_rolling_ball.py
+++ b/skimage/restoration/tests/test_rolling_ball.py
@@ -90,6 +90,7 @@ def test_threads(num_threads):
rolling_ball(img, radius=10, nansafe=True, num_threads=num_threads)
+@pytest.mark.skip(reason="Needs python3-pooch and internet connection")
def test_ndim():
image = data.cells3d()[:5, 1, ...]
kernel = ellipsoid_kernel((3, 100, 100), 100)
|
