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Fix view behavior for AwkwardArrays #1070

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Fix view behavior for AwkwardArrays #1070

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b23eda3
Use __record__ instead of __list__ to store behavior
grst Jul 24, 2023
b640617
Fix views of views
grst Jul 25, 2023
843833f
Update anndata/_core/views.py
grst Jul 25, 2023
8aa09cc
Remove all custom code for views
grst Aug 30, 2023
86c5ff8
WIP add test cases
grst Sep 1, 2023
a01b80e
Merge remote-tracking branch 'origin/main' into ak-array-views
grst Sep 1, 2023
dfe7008
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 1, 2023
8b14e57
More test cases
grst Sep 1, 2023
4870553
Add comment about view behavior
grst Sep 1, 2023
257c063
Merge branch 'main' into ak-array-views
grst Sep 7, 2023
4b34598
Fix akward array view test
grst Sep 8, 2023
fdeff90
Fix that awkward arrays in an awyward array view could not be modified.
grst Sep 8, 2023
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16 changes: 10 additions & 6 deletions anndata/_core/views.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
from copy import deepcopy
from collections.abc import Sequence, KeysView, Callable, Iterable, Mapping
from functools import reduce, singledispatch, wraps
from typing import Any, Literal
from typing import Any, Literal, Dict, cast
import warnings

import numpy as np
Expand Down Expand Up @@ -295,8 +295,8 @@ def __copy__(self) -> AwkArray:
"""
array = self
# makes a shallow copy and removes the reference to the original AnnData object
array = ak.with_parameter(self, _PARAM_NAME, None)
array = ak.with_parameter(array, "__list__", None)
array = ak.with_parameter(array, _PARAM_NAME, None)
array = ak.with_parameter(array, "__record__", None)
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This should use with_name, so that we can traverse into the layout to find the record-node

Suggested change
array = ak.with_parameter(array, "__record__", None)
array = ak.with_name(array, None)

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I imagine that after our dicsussion @grst could not get that working (see #1040 (comment))

Is there a reason traversing is better than what we have (assuming @grst could not get the with_name working)? We only ever deal with this at a "top level."

return array

@as_view.register(AwkArray)
Expand All @@ -308,15 +308,19 @@ def as_view_awkarray(array, view_args):
# possible strategies to stack behaviors.
# A better solution might be based on xarray-style "attrs", once this is implemented
# https://github.com/scikit-hep/awkward/issues/1391#issuecomment-1412297114
if type(array).__name__ != "Array":
#
# Allow only Arrays that have no record behavior attached, or with __record__ explicitly
# set to None
if array.layout.purelist_parameter("__record__") is not None:
raise NotImplementedError(
"Cannot create a view of an awkward array with __array__ parameter. "
"Cannot create a view of an awkward array with __record__ parameter. "
"Please open an issue in the AnnData repo and describe your use-case."
)
array = ak.with_parameter(array, _PARAM_NAME, (parent_key, attrname, keys))
array = ak.with_parameter(array, "__list__", "AwkwardArrayView")
array = ak.with_parameter(array, "__record__", "AwkwardArrayView")
return array

ak.behavior["*", "AwkwardArrayView"] = AwkwardArrayView
ak.behavior["AwkwardArrayView"] = AwkwardArrayView

except ImportError:
Expand Down
2 changes: 1 addition & 1 deletion anndata/tests/test_awkward.py
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Expand Up @@ -159,7 +159,7 @@ def reversed(self):
ak.behavior[BEHAVIOUR_ID] = ReversibleArray
adata = gen_adata((3, 3), varm_types=(), obsm_types=(), layers_types=())
adata.obsm["awk_string"] = ak.with_parameter(
ak.Array(["AAA", "BBB", "CCC"]), "__list__", BEHAVIOUR_ID
ak.Array(["AAA", "BBB", "CCC"]), "__record__", BEHAVIOUR_ID
)
adata_view = adata[:2]

Expand Down
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