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expose main properties of anndata (or mudata) to base dance data #282

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Jun 23, 2023
Merged

expose main properties of anndata (or mudata) to base dance data #282

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e535898
expose main properties of anndata (or mudata) to the base dance data …
RemyLau Jun 23, 2023
84804c9
expose main properties of anndata (or mudata) to the base dance data …
RemyLau Jun 23, 2023
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2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ repos:
hooks:
- id: docformatter
name: Format docstring
args: [--config, ./pyproject.toml]
args: [--config, pyproject.toml]

- repo: https://github.com/executablebooks/mdformat
rev: 0.7.16
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9 changes: 9 additions & 0 deletions dance/data/base.py
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Expand Up @@ -55,6 +55,11 @@ class BaseData(ABC):
>>> adata = anndata.AnnData(...)
>>> ddata = dance.data.Data(adata.copy())

Note
----
You can directly access some main properties of :class:`~anndata.AnnData` (or :class:`~mudata.MuData` depending on
which type of data you passed in), such as ``X``, ``obs``, ``var``, and etc.

Parameters
----------
data
Expand All @@ -77,7 +82,11 @@ def __init__(self, data: Union[anndata.AnnData, mudata.MuData], train_size: Opti
full_split_name: Optional[str] = None):
super().__init__()

# Store data and pass through some main properties over
self._data = data
for prop in self._DATA_CHANNELS + ["X"]:
assert not hasattr(self, prop)
setattr(self, prop, getattr(data, prop))

# TODO: move _split_idx_dict into data.uns
self._split_idx_dict: Dict[str, Sequence[int]] = {}
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