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Better defaults for chunks parameters #704

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Better defaults for chunks parameters #704

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94f7fb4
First prototype
jonbrenas Jan 8, 2025
e938ae1
Merge branch 'master' into 629-better-default-chunks
jonbrenas May 21, 2025
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9 changes: 9 additions & 0 deletions malariagen_data/anoph/base_params.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,8 @@
single_contig_param_type,
single_region_param_type,
chunks_param_type,
zarr_chunks_type,
dask_chunks_type,
)

contig: TypeAlias = Annotated[
Expand Down Expand Up @@ -256,6 +258,13 @@ def validate_sample_selection_params(
# amounts of data.
native_chunks: chunks = "native"


def call_chunks_func(zarr_chunks: zarr_chunks_type) -> dask_chunks_type:
return tuple([10 * i for i in zarr_chunks])


call_chunks: chunks = call_chunks_func

gff_attributes: TypeAlias = Annotated[
Optional[Union[Sequence[str], str]],
"""
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2 changes: 1 addition & 1 deletion malariagen_data/anoph/pca.py
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Expand Up @@ -76,7 +76,7 @@ def pca(
fit_exclude_samples: Optional[base_params.samples] = None,
random_seed: base_params.random_seed = 42,
inline_array: base_params.inline_array = base_params.inline_array_default,
chunks: base_params.chunks = base_params.native_chunks,
chunks: base_params.chunks = base_params.call_chunks,
) -> Tuple[pca_params.df_pca, pca_params.evr]:
# Change this name if you ever change the behaviour of this function, to
# invalidate any previously cached data.
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