zarr v2.10.2

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Dependency Analysis

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Analysis of the source code shows a discrepancy between the library's imports and the package's stated requirements in the meta.yaml.

Packages found by inspection but not in the meta.yaml:

• line_profiler

[conda-forge-linter]

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

[joshmoore]

Hmmm..... unexpected test failure:

   def test_nested(dataset):
        """
        Use NestedDirectoryStore to open the dataset fixture. This is the only
        method that is expected to successfully open legacy nested datasets
        without the dimension_separator metadata. However, for none-Nested
        datasets without any metadata, NestedDirectoryStore will fail.
        """
        failure = (
            "flat_legacy" in dataset or
            "directory_default" in dataset or
            "fs_default" in dataset
        )
>       verify(Array(store=NestedDirectoryStore(dataset)), failure)

../_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.9/site-packages/zarr/tests/test_dim_separator.py:129: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

array = <zarr.core.Array (2, 2) int64>, expect_failure = False

    def verify(array, expect_failure=False):
        try:
>           assert_array_equal(array[:], [[1, 2], [3, 4]])
E           AssertionError: 
E           Arrays are not equal
E           
E           Mismatched elements: 4 / 4 (100%)
E           Max absolute difference: 4
E           Max relative difference: 1.
E            x: array([[0, 0],
E                  [0, 0]])
E            y: array([[1, 2],
E                  [3, 4]])

[jakirkham]

Have a question about what we are doing in CI there ( zarr-developers/zarr-python#850 (comment) ). Wondering if it might be relevant

[joshmoore]

I don't think so. Those builds failed on install of zarr.

[joshmoore]

@jakirkham, similar to zarr-developers/zarr-python#858, can you help me reproduce this failure locally preferably in Docker?

[jakirkham]

Would try running python build-locally.py and that should spin up a container and do a build for the specific Python and OS requested

[joshmoore]

Have definitely reproduced locally. Interesting...

[joshmoore]

Well that's at least something. The fixtures for the tests themselves are somehow "corrupted":

[root@da80464b860e fixture]# pwd
/home/conda/feedstock_root/build_artifacts/zarr_1636989511725/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.9/site-packages/fixture
[root@da80464b860e fixture]# diff flat*/.zarray
[root@da80464b860e fixture]#

whereas in the mainline:

(base) /opt/zarr-python/fixture $diff flat*/.zarray
13d12
<     "dimension_separator": ".",
23c22
< }
---
> }
\ No newline at end of file

[jakirkham]

Looked at the sdist that gets downloaded and the fixture seems ok there

Is it possible that one of the tests makes a change to fixture's contents, which then causes a later test (that assumes what the contents are) to break? IOW is this an issue that shows up in-between tests where something is missed?

[joshmoore]

So it looks like this is another result of their not being packaged:

            if not static.exists():  # pragma: no cover
>               raise Exception(f"{static} does not exist")
E               Exception: $PREFIX/lib/python3.9/site-packages/fixture/flat_legacy does not exist

commit d3f421e2abe8c05d9dc8185f0fee001b94ae1c7d (HEAD -> issue-858, josh/issue-858)
Author: jmoore <[email protected]>
Date:   Tue Nov 16 12:33:18 2021 +0100

    See if the fixtures are being re-written

diff --git a/zarr/tests/test_dim_separator.py b/zarr/tests/test_dim_separator.py
index 85138800..93c947c6 100644
--- a/zarr/tests/test_dim_separator.py
+++ b/zarr/tests/test_dim_separator.py
@@ -41,6 +41,7 @@ def dataset(tmpdir, request):
         static = project_root / "fixture" / suffix

         if not static.exists():  # pragma: no cover
+            raise Exception(f"{static} does not exist")

i.e. we're back to the discussion in #50 (comment)

[joshmoore]

zarr-developers/zarr-python@053cbde explicitly passes dimension_separator="." which lets tests pass.

[joshmoore]

Hopefully zarr-developers/zarr-python#871 will fix the situation, but 2.10.2 will remain undeployable unless we skip that particular test. Alternatively, I can try to release a 2.10.3 with just this test fix.