(feat): xarray with experimental backed reading
#1247
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1247 +/- ##
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- Coverage 86.87% 84.56% -2.31%
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Files 39 44 +5
Lines 6033 6303 +270
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+ Hits 5241 5330 +89
- Misses 792 973 +181
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src/anndata/_core/storage.py
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| """Coerce arrays stored in layers/X, and aligned arrays ({obs,var}{m,p}).""" | ||
| # If value is a scalar and we allow that, return it | ||
| if allow_array_like and np.isscalar(value): | ||
| return value | ||
| # If value is one of the allowed types, return it | ||
| if isinstance(value, StorageType.classes()): | ||
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| if isinstance(value, (*StorageType.classes(), Dataset2D)): |
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so that we don’t forget: let’s get rid of the circular import hack
| elem_name = get_elem_name(elem) | ||
| index_label = f'{elem_name.replace("/", "")}_names' | ||
| index_key = elem.attrs["_index"] | ||
| index = elem_dict[index_key] # no sense in reading this in multiple times |
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this line can move into the helper
| needs_xarray = pytest.mark.skipif( | ||
| not find_spec("xarray"), reason="Xarray is not installed" | ||
| ) |
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you could just set pytestmark once at the top, then the whole file is skipped and you don’t have to annotate each individual function.
pytestmark = pytest.mark.skipif(
not find_spec("xarray"), reason="Xarray is not installed"
)| assert store.get_access_count("obs/int64") == 1, store.get_subkeys_accessed( | ||
| "obs/int64" | ||
| ) | ||
| # one for 0, .zmetadata handles .zarray |
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I don’t understand either part of this comment, maybe expand a bit
| assert store.get_access_count("obs/.zgroup") == 1, store.get_subkeys_accessed( | ||
| "obs/.zgroup" | ||
| ) |
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you know, reading this pattern again and again, maybe we should make this a helper.
It could go directly into the AccessTrackingStore.
That way it’s not possible to ever use two different strings on the left and right side of this statement, which would probably cause hours of debugging.
Co-authored-by: Philipp A. <[email protected]>
Co-authored-by: Philipp A. <[email protected]>
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This PR is a ligther weight version of #947 that involves using the original
AnnDataobject as the class to holdobsandvarxr.Dataset..obsand.varwithbacked="r"mode #981