Zarr compression tests only with versions before 3.0 (#8319)

Fixes #8298.

### Description

This includes the tests for the `compressor` argument when testing with
Zarr before version 3.0 when this argument was deprecated. A fix to
upgrade the version of `pycln` used is also included. The version of
PyTorch is also fixed to below 2.6 to avoid issues with misuse of
`torch.load` which must be addressed later.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

Author: ericspod

.pre-commit-config.yaml

@@ -66,7 +66,7 @@ repos:
           )$
 
   - repo: https://github.com/hadialqattan/pycln
-    rev: v2.4.0
+    rev: v2.5.0
     hooks:
       - id: pycln
         args: [--config=pyproject.toml]

monai/data/meta_tensor.py

@@ -607,3 +607,8 @@ def print_verbose(self) -> None:
         print(self)
         if self.meta is not None:
             print(self.meta.__repr__())
+
+
+# needed in later versions of Pytorch to indicate the class is safe for serialisation
+if hasattr(torch.serialization, "add_safe_globals"):
+    torch.serialization.add_safe_globals([MetaTensor])

monai/utils/jupyter_utils.py

@@ -234,7 +234,7 @@ def plot_engine_status(
 
 
 def _get_loss_from_output(
-    output: list[torch.Tensor | dict[str, torch.Tensor]] | dict[str, torch.Tensor] | torch.Tensor
+    output: list[torch.Tensor | dict[str, torch.Tensor]] | dict[str, torch.Tensor] | torch.Tensor,
 ) -> torch.Tensor:
     """Returns a single value from the network output, which is a dict or tensor."""
 

monai/visualize/img2tensorboard.py

@@ -65,11 +65,11 @@ def _image3_animated_gif(
     img_str = b""
     for b_data in PIL.GifImagePlugin.getheader(ims[0])[0]:
         img_str += b_data
-    img_str += b"\x21\xFF\x0B\x4E\x45\x54\x53\x43\x41\x50" b"\x45\x32\x2E\x30\x03\x01\x00\x00\x00"
+    img_str += b"\x21\xff\x0b\x4e\x45\x54\x53\x43\x41\x50" b"\x45\x32\x2e\x30\x03\x01\x00\x00\x00"
     for i in ims:
         for b_data in PIL.GifImagePlugin.getdata(i):
             img_str += b_data
-    img_str += b"\x3B"
+    img_str += b"\x3b"
 
     summary = SummaryX if has_tensorboardx and isinstance(writer, SummaryWriterX) else Summary
     summary_image_str = summary.Image(height=10, width=10, colorspace=1, encoded_image_string=img_str)

requirements-dev.txt

@@ -18,7 +18,7 @@ pep8-naming
 pycodestyle
 pyflakes
 black>=22.12
-isort>=5.1
+isort>=5.1, <6.0
 ruff
 pytype>=2020.6.1; platform_system != "Windows"
 types-setuptools

requirements.txt

@@ -1,2 +1,2 @@
-torch>=1.9
+torch>=1.9,<2.6
 numpy>=1.24,<2.0

tests/test_zarr_avg_merger.py

@@ -260,32 +260,33 @@
     TENSOR_4x4,
 ]
 
+ALL_TESTS = [
+    TEST_CASE_0_DEFAULT_DTYPE,
+    TEST_CASE_1_DEFAULT_DTYPE,
+    TEST_CASE_2_DEFAULT_DTYPE,
+    TEST_CASE_3_DEFAULT_DTYPE,
+    TEST_CASE_4_DEFAULT_DTYPE,
+    TEST_CASE_5_VALUE_DTYPE,
+    TEST_CASE_6_COUNT_DTYPE,
+    TEST_CASE_7_COUNT_VALUE_DTYPE,
+    TEST_CASE_8_DTYPE,
+    TEST_CASE_9_LARGER_SHAPE,
+    TEST_CASE_10_DIRECTORY_STORE,
+    TEST_CASE_11_MEMORY_STORE,
+    TEST_CASE_12_CHUNKS,
+    TEST_CASE_16_WITH_LOCK,
+    TEST_CASE_17_WITHOUT_LOCK,
+]
+
+# add compression tests only when using Zarr version before 3.0
+if not version_geq(get_package_version("zarr"), "3.0.0"):
+    ALL_TESTS += [TEST_CASE_13_COMPRESSOR_LZ4, TEST_CASE_14_COMPRESSOR_PICKLE, TEST_CASE_15_COMPRESSOR_LZMA]
+
 
 @unittest.skipUnless(has_zarr and has_numcodecs, "Requires zarr (and numcodecs) packages.)")
 class ZarrAvgMergerTests(unittest.TestCase):
 
-    @parameterized.expand(
-        [
-            TEST_CASE_0_DEFAULT_DTYPE,
-            TEST_CASE_1_DEFAULT_DTYPE,
-            TEST_CASE_2_DEFAULT_DTYPE,
-            TEST_CASE_3_DEFAULT_DTYPE,
-            TEST_CASE_4_DEFAULT_DTYPE,
-            TEST_CASE_5_VALUE_DTYPE,
-            TEST_CASE_6_COUNT_DTYPE,
-            TEST_CASE_7_COUNT_VALUE_DTYPE,
-            TEST_CASE_8_DTYPE,
-            TEST_CASE_9_LARGER_SHAPE,
-            TEST_CASE_10_DIRECTORY_STORE,
-            TEST_CASE_11_MEMORY_STORE,
-            TEST_CASE_12_CHUNKS,
-            TEST_CASE_13_COMPRESSOR_LZ4,
-            TEST_CASE_14_COMPRESSOR_PICKLE,
-            TEST_CASE_15_COMPRESSOR_LZMA,
-            TEST_CASE_16_WITH_LOCK,
-            TEST_CASE_17_WITHOUT_LOCK,
-        ]
-    )
+    @parameterized.expand(ALL_TESTS)
     def test_zarr_avg_merger_patches(self, arguments, patch_locations, expected):
         codec_reg = numcodecs.registry.codec_registry
         if "compressor" in arguments: