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AttributeError: module 'zarr.storage' has no attribute 'DirectoryStore' #8298

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KumoLiu opened this issue Jan 14, 2025 · 5 comments · Fixed by #8299, #8313 or #8319
Closed

AttributeError: module 'zarr.storage' has no attribute 'DirectoryStore' #8298

KumoLiu opened this issue Jan 14, 2025 · 5 comments · Fixed by #8299, #8313 or #8319
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bug Something isn't working

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@KumoLiu
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KumoLiu commented Jan 14, 2025 

Traceback (most recent call last):
  File "/home/runner/work/MONAI/MONAI/tests/runner.py", line 135, in <module>
    tests = unittest.TestLoader().loadTestsFromNames(cases)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/unittest/loader.py", line 232, in loadTestsFromNames
    suites = [self.loadTestsFromName(name, module) for name in names]
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/unittest/loader.py", line 232, in <listcomp>
    suites = [self.loadTestsFromName(name, module) for name in names]
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/unittest/loader.py", line 162, in loadTestsFromName
    module = __import__(module_name)
             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 157, in <module>
    dict(merged_shape=TENSOR_4x4.shape, store=zarr.storage.DirectoryStore("test.zarr")),
                                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'DirectoryStore'
@KumoLiu
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KumoLiu commented Jan 14, 2025 •
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May related to the new release: https://pypi.org/project/zarr/3.0.0/

zarr-developers/zarr-python#2699

@KumoLiu KumoLiu added the bug Something isn't working label Jan 14, 2025
KumoLiu added a commit to KumoLiu/MONAI that referenced this issue Jan 14, 2025
@KumoLiu
fix Project-MONAI#8298
b49ce64 
Signed-off-by: YunLiu <[email protected]>
@KumoLiu KumoLiu mentioned this issue Jan 14, 2025
Merged
7 tasks
KumoLiu added a commit to KumoLiu/MONAI that referenced this issue Jan 14, 2025
@KumoLiu
fix Project-MONAI#8298
a777268 
Signed-off-by: YunLiu <[email protected]>
@KumoLiu
Copy link
Contributor Author

KumoLiu commented Jan 20, 2025

More deprecated usage found here: https://github.com/Project-MONAI/MONAI/actions/runs/12862267071/job/35856920175

Error Logs 

======================================================================
ERROR: test_zarr_avg_merger_finalized_error (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_finalized_error)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 314, in test_zarr_avg_merger_finalized_error
    merger = ZarrAvgMerger(merged_shape=(1, 3, 2, 3))
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
    return call_obj(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 249, in __init__
    self.value_store = zarr.storage.TempStore() if value_store is None else value_store
                       ^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'TempStore'

======================================================================
ERROR: test_zarr_avg_merger_patches_00 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_00)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 299, in test_zarr_avg_merger_patches
    merger = ZarrAvgMerger(**arguments)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
    return call_obj(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 249, in __init__
    self.value_store = zarr.storage.TempStore() if value_store is None else value_store
                       ^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'TempStore'

======================================================================
ERROR: test_zarr_avg_merger_patches_01 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_01)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 299, in test_zarr_avg_merger_patches
    merger = ZarrAvgMerger(**arguments)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
    return call_obj(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 249, in __init__
    self.value_store = zarr.storage.TempStore() if value_store is None else value_store
                       ^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'TempStore'

======================================================================
ERROR: test_zarr_avg_merger_patches_02 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_02)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 299, in test_zarr_avg_merger_patches
    merger = ZarrAvgMerger(**arguments)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
    return call_obj(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 249, in __init__
    self.value_store = zarr.storage.TempStore() if value_store is None else value_store
                       ^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'TempStore'

======================================================================
ERROR: test_zarr_avg_merger_patches_03 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_03)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 299, in test_zarr_avg_merger_patches
    merger = ZarrAvgMerger(**arguments)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
    return call_obj(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 249, in __init__
    self.value_store = zarr.storage.TempStore() if value_store is None else value_store
                       ^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'TempStore'

======================================================================
ERROR: test_zarr_avg_merger_patches_04 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_04)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 299, in test_zarr_avg_merger_patches
    merger = ZarrAvgMerger(**arguments)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
    return call_obj(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 249, in __init__
    self.value_store = zarr.storage.TempStore() if value_store is None else value_store
                       ^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'TempStore'

======================================================================
ERROR: test_zarr_avg_merger_patches_05 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_05)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 299, in test_zarr_avg_merger_patches
    merger = ZarrAvgMerger(**arguments)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
    return call_obj(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 249, in __init__
    self.value_store = zarr.storage.TempStore() if value_store is None else value_store
                       ^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'TempStore'

======================================================================
ERROR: test_zarr_avg_merger_patches_06 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_06)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 299, in test_zarr_avg_merger_patches
    merger = ZarrAvgMerger(**arguments)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
    return call_obj(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 249, in __init__
    self.value_store = zarr.storage.TempStore() if value_store is None else value_store
                       ^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'TempStore'

======================================================================
ERROR: test_zarr_avg_merger_patches_07 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_07)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 299, in test_zarr_avg_merger_patches
    merger = ZarrAvgMerger(**arguments)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
    return call_obj(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 249, in __init__
    self.value_store = zarr.storage.TempStore() if value_store is None else value_store
                       ^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'TempStore'

======================================================================
ERROR: test_zarr_avg_merger_patches_08 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_08)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 299, in test_zarr_avg_merger_patches
    merger = ZarrAvgMerger(**arguments)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
    return call_obj(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 249, in __init__
    self.value_store = zarr.storage.TempStore() if value_store is None else value_store
                       ^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'TempStore'

======================================================================
ERROR: test_zarr_avg_merger_patches_09 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_09)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 299, in test_zarr_avg_merger_patches
    merger = ZarrAvgMerger(**arguments)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
    return call_obj(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 249, in __init__
    self.value_store = zarr.storage.TempStore() if value_store is None else value_store
                       ^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'TempStore'

======================================================================
ERROR: test_zarr_avg_merger_patches_10 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_10)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 299, in test_zarr_avg_merger_patches
    merger = ZarrAvgMerger(**arguments)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
    return call_obj(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 249, in __init__
    self.value_store = zarr.storage.TempStore() if value_store is None else value_store
                       ^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'TempStore'

======================================================================
ERROR: test_zarr_avg_merger_patches_11 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_11)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 299, in test_zarr_avg_merger_patches
    merger = ZarrAvgMerger(**arguments)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
    return call_obj(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 255, in __init__
    self.output = zarr.empty(
                  ^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/zarr/api/synchronous.py", line 918, in empty
    return Array(sync(async_api.empty(shape, **kwargs)))
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/zarr/core/sync.py", line 142, in sync
    raise return_result
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/zarr/core/sync.py", line 98, in _runner
    return await coro
           ^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/zarr/api/asynchronous.py", line 1084, in empty
    return await create(shape=shape, fill_value=None, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/zarr/api/asynchronous.py", line 1044, in create
    return await AsyncArray._create(
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/zarr/core/array.py", line 603, in _create
    raise ValueError(
ValueError: compressor cannot be used for arrays with zarr_format 3. Use bytes-to-bytes codecs instead.

======================================================================
ERROR: test_zarr_avg_merger_patches_12 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_12)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 299, in test_zarr_avg_merger_patches
    merger = ZarrAvgMerger(**arguments)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
    return call_obj(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 249, in __init__
    self.value_store = zarr.storage.TempStore() if value_store is None else value_store
                       ^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'TempStore'

======================================================================
ERROR: test_zarr_avg_merger_patches_13 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_13)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 292, in test_zarr_avg_merger_patches
    arguments["compressor"] = zarr.codec_registry[arguments["compressor"].lower()]()
                              ^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr' has no attribute 'codec_registry'

======================================================================
ERROR: test_zarr_avg_merger_patches_14 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_14)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 292, in test_zarr_avg_merger_patches
    arguments["compressor"] = zarr.codec_registry[arguments["compressor"].lower()]()
                              ^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr' has no attribute 'codec_registry'

======================================================================
ERROR: test_zarr_avg_merger_patches_15 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_15)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 292, in test_zarr_avg_merger_patches
    arguments["compressor"] = zarr.codec_registry[arguments["compressor"].lower()]()
                              ^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr' has no attribute 'codec_registry'

======================================================================
ERROR: test_zarr_avg_merger_patches_16 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_16)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 299, in test_zarr_avg_merger_patches
    merger = ZarrAvgMerger(**arguments)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
    return call_obj(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 249, in __init__
    self.value_store = zarr.storage.TempStore() if value_store is None else value_store
                       ^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'TempStore'

======================================================================
ERROR: test_zarr_avg_merger_patches_17 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_17)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 299, in test_zarr_avg_merger_patches
    merger = ZarrAvgMerger(**arguments)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
    return call_obj(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 249, in __init__
    self.value_store = zarr.storage.TempStore() if value_store is None else value_store
                       ^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'TempStore'

----------------------------------------------------------------------

@KumoLiu KumoLiu reopened this Jan 20, 2025
KumoLiu added a commit to KumoLiu/MONAI that referenced this issue Jan 24, 2025
@KumoLiu
fix Project-MONAI#8298
4c877dc 
Signed-off-by: YunLiu <[email protected]>
@KumoLiu KumoLiu mentioned this issue Jan 24, 2025
Merged
7 tasks
garciadias pushed a commit to garciadias/MONAI that referenced this issue Jan 27, 2025
@KumoLiu @ericspod @garciadias
Fix deprecated usage in zarr (Project-MONAI#8313)
cfd497b 
Fixes Project-MONAI#8298

### 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: YunLiu <[email protected]>
Co-authored-by: Eric Kerfoot <[email protected]>
@KumoLiu KumoLiu reopened this Jan 27, 2025
@KumoLiu
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KumoLiu commented Jan 27, 2025

Hi @ericspod and @virginiafdez, please help take a look at this issue.

There are still several places have deprecated usage. For details, please see: https://github.com/Project-MONAI/MONAI/actions/runs/12952100697/job/36128672442

Thanks!

@ericspod
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There are 3 errors all saying the same thing:

======================================================================
ERROR: test_zarr_avg_merger_patches_13 (tests.test_zarr_avg_merger.ZarrAvgMergerTests.test_zarr_avg_merger_patches_13)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/tests/test_zarr_avg_merger.py", line 300, in test_zarr_avg_merger_patches
    merger = ZarrAvgMerger(**arguments)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/utils/module.py", line 477, in _wrapper
    return call_obj(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/MONAI/MONAI/monai/inferers/merger.py", line 270, in __init__
    self.output = zarr.empty(
                  ^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/zarr/api/synchronous.py", line 918, in empty
    return Array(sync(async_api.empty(shape, **kwargs)))
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/zarr/core/sync.py", line 142, in sync
    raise return_result
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/zarr/core/sync.py", line 98, in _runner
    return await coro
           ^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/zarr/api/asynchronous.py", line 1084, in empty
    return await create(shape=shape, fill_value=None, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/zarr/api/asynchronous.py", line 1044, in create
    return await AsyncArray._create(
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/zarr/core/array.py", line 603, in _create
    raise ValueError(
ValueError: compressor cannot be used for arrays with zarr_format 3. Use bytes-to-bytes codecs instead.

@ericspod
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The underlying cause is that the compressor argument doesn't work for Zarr version 3 and instead codecs should be used. If we wanted to use codecs we'd have to work out what would be worth testing. Honestly, since these arguments are just being passed to zarr calls, I don't think we really need to test them. I can do a quick PR to remove these tests or only run them if zarr<3 is used.

@ericspod ericspod mentioned this issue Jan 29, 2025
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7 tasks
KumoLiu pushed a commit that referenced this issue Feb 3, 2025
@ericspod
Zarr compression tests only with versions before 3.0 (#8319)
8dcb9dc 
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 <[email protected]>
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