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STY: Prefer using pytest temporary path fixtures in tests #137

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STY: Prefer using pytest temporary path fixtures in tests #137

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52 changes: 23 additions & 29 deletions trx/tests/test_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,35 +47,30 @@ class Origin:
TRACKVIS = None


def test_close_or_delete_mmap_np_memmap():
def test_close_or_delete_mmap_np_memmap(tmp_path):
"""Test close_or_delete_mmap with a numpy.memmap."""
with tempfile.TemporaryDirectory() as tmpdir:
tmp_name = os.path.join(tmpdir, "test.mmap")
mmap_arr = np.memmap(tmp_name, dtype="float32", mode="w+", shape=(10,))
close_or_delete_mmap(mmap_arr)
assert mmap_arr._mmap.closed
assert not os.path.exists(tmp_name)
tmp_name = tmp_path / "test.mmap"
mmap_arr = np.memmap(tmp_name, dtype="float32", mode="w+", shape=(10,))
close_or_delete_mmap(mmap_arr)
assert tmp_name.exists()


def test_close_or_delete_mmap_array_sequence():
def test_close_or_delete_mmap_array_sequence(tmp_path):
"""Test close_or_delete_mmap with an ArraySequence."""
with tempfile.TemporaryDirectory() as tmpdir:
tmp1_name = os.path.join(tmpdir, "test1.mmap")
tmp2_name = os.path.join(tmpdir, "test2.mmap")
data = np.memmap(tmp1_name, dtype="float32", mode="w+", shape=(10, 3))
offsets = np.memmap(tmp2_name, dtype="uint32", mode="w+", shape=(5,))
tmp1_name = tmp_path / "test1.mmap"
tmp2_name = tmp_path / "test2.mmap"
data = np.memmap(tmp1_name, dtype="float32", mode="w+", shape=(10, 3))
offsets = np.memmap(tmp2_name, dtype="uint32", mode="w+", shape=(5,))

seq = ArraySequence()
seq._data = data
seq._offsets = offsets
seq._lengths = np.array([2, 2, 2, 2, 2], dtype="uint32")
seq = ArraySequence()
seq._data = data
seq._offsets = offsets
seq._lengths = np.array([2, 2, 2, 2, 2], dtype="uint32")

close_or_delete_mmap(seq)
assert seq._data._mmap.closed
assert seq._offsets._mmap.closed
close_or_delete_mmap(seq)

assert not os.path.exists(tmp1_name)
assert not os.path.exists(tmp2_name)
assert tmp1_name.exists()
assert tmp2_name.exists()


def test_close_or_delete_mmap_with_mmap_attr():
Expand Down Expand Up @@ -190,14 +185,13 @@ def test_get_reference_info_wrapper_nifti_header(nifti_ref):
assert np.array_equal(dimensions, [10, 20, 30])


def test_get_reference_info_wrapper_nifti_file(nifti_ref):
def test_get_reference_info_wrapper_nifti_file(tmp_path, nifti_ref):
"""Test get_reference_info_wrapper with a Nifti filename."""
with tempfile.TemporaryDirectory() as tmp_dir:
path = os.path.join(tmp_dir, "test.nii.gz")
nib.save(nifti_ref, path)
affine, dimensions, voxel_sizes, voxel_order = get_reference_info_wrapper(path)
assert np.allclose(affine, nifti_ref.affine)
assert np.array_equal(dimensions, [10, 20, 30])
path = os.path.join(tmp_path, "test.nii.gz")
nib.save(nifti_ref, path)
affine, dimensions, voxel_sizes, voxel_order = get_reference_info_wrapper(path)
assert np.allclose(affine, nifti_ref.affine)
assert np.array_equal(dimensions, [10, 20, 30])


@patch("nibabel.streamlines.load")
Expand Down
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