Merge 8a84e28 into 1d090b9

.github/workflows/tests.yml

@@ -9,8 +9,7 @@ jobs:
   unit:
     strategy:
       matrix:
-        # TODO: add windows-latest
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest, macos-latest, windows-latest]
         python: ['3.6', '3.7', '3.8', '3.9']
 
     runs-on: ${{ matrix.os }}

tests/data/test_image.py

@@ -2,9 +2,11 @@
 
 """Tests for Image."""
 
+import sys
 import copy
 import tempfile
 
+import pytest
 import torch
 import numpy as np
 import nibabel as nib
@@ -20,6 +22,7 @@ def test_image_not_found(self):
         with self.assertRaises(FileNotFoundError):
             tio.ScalarImage('nopath')
 
+    @pytest.mark.skipif(sys.platform == 'win32', reason='Path not valid')
     def test_wrong_path_value(self):
         with self.assertRaises(RuntimeError):
             tio.ScalarImage('~&./@#"!?X7=+')
@@ -157,7 +160,7 @@ def test_load_uint(self):
         for dtype in np.uint16, np.uint32:
             data = np.ones((3, 3, 3), dtype=dtype)
             img = nib.Nifti1Image(data, affine)
-            with tempfile.NamedTemporaryFile(suffix='.nii') as f:
+            with tempfile.NamedTemporaryFile(suffix='.nii', delete=False) as f:
                 nib.save(img, f.name)
                 tio.ScalarImage(f.name).load()
 
@@ -204,9 +207,9 @@ def assert_shape(shape_in, shape_out):
 
     def test_fast_gif(self):
         with self.assertWarns(UserWarning):
-            with tempfile.NamedTemporaryFile(suffix='.gif') as f:
+            with tempfile.NamedTemporaryFile(suffix='.gif', delete=False) as f:
                 self.sample_subject.t1.to_gif(0, 0.0001, f.name)
 
     def test_gif_rgb(self):
-        with tempfile.NamedTemporaryFile(suffix='.gif') as f:
+        with tempfile.NamedTemporaryFile(suffix='.gif', delete=False) as f:
             tio.ScalarImage(tensor=torch.rand(3, 4, 5, 6)).to_gif(0, 1, f.name)

tests/data/test_subject.py

@@ -10,17 +10,16 @@ class TestSubject(TorchioTestCase):
     """Tests for `Subject`."""
     def test_positional_args(self):
         with self.assertRaises(ValueError):
-            with tempfile.NamedTemporaryFile() as f:
-                tio.Subject(tio.ScalarImage(f.name))
+            tio.Subject(0)
 
     def test_input_dict(self):
-        with tempfile.NamedTemporaryFile() as f:
+        with tempfile.NamedTemporaryFile(delete=False) as f:
             input_dict = {'image': tio.ScalarImage(f.name)}
             tio.Subject(input_dict)
             tio.Subject(**input_dict)
 
     def test_no_sample(self):
-        with tempfile.NamedTemporaryFile() as f:
+        with tempfile.NamedTemporaryFile(delete=False) as f:
             input_dict = {'image': tio.ScalarImage(f.name)}
             subject = tio.Subject(input_dict)
             with self.assertRaises(RuntimeError):

tests/utils.py

@@ -1,3 +1,4 @@
+import os
 import copy
 import shutil
 import random
@@ -16,7 +17,7 @@ class TorchioTestCase(unittest.TestCase):
 
     def setUp(self):
         """Set up test fixtures, if any."""
-        self.dir = Path(tempfile.gettempdir()) / '.torchio_tests'
+        self.dir = Path(tempfile.gettempdir()) / os.urandom(24).hex()
         self.dir.mkdir(exist_ok=True)
         random.seed(42)
         np.random.seed(42)

torchio/datasets/ixi.py

@@ -153,7 +153,7 @@ def _download(self, root, modalities):
             url = self.base_url.format(modality=modality)
             md5 = self.md5_dict[modality]
 
-            with NamedTemporaryFile(suffix='.tar') as f:
+            with NamedTemporaryFile(suffix='.tar', delete=False) as f:
                 download_and_extract_archive(
                     url,
                     download_root=modality_dir,
@@ -229,7 +229,7 @@ def _download(self, root):
             return
         print('Root directory for IXITiny not found:', root)  # noqa: T001
         print('Downloading...')  # noqa: T001
-        with NamedTemporaryFile(suffix='.zip') as f:
+        with NamedTemporaryFile(suffix='.zip', delete=False) as f:
             download_and_extract_archive(
                 self.url,
                 download_root=root,