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make random state argument handling more consistent #166

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make random state argument handling more consistent #166

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2 changes: 1 addition & 1 deletion muon/_atac/tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -900,7 +900,7 @@ def tss_enrichment(
extend_downstream: int = 1000,
n_tss: int = 2000,
return_tss: bool = True,
random_state=None,
random_state: int | None = 0,
barcodes: Optional[str] = None,
):
"""
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10 changes: 5 additions & 5 deletions muon/_core/tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -930,7 +930,7 @@ def _cluster(
data: Union[MuData, AnnData],
resolution: Optional[Union[float, Sequence[float], Mapping[str, float]]] = None,
mod_weights: Optional[Union[Sequence[float], Mapping[str, float]]] = None,
random_state: int = 0,
random_state: int | None = 0,
key_added: str = "louvain",
neighbors_key: str = None,
directed: bool = True,
Expand Down Expand Up @@ -1003,7 +1003,7 @@ def _cluster(
partition_type = alg.RBConfigurationVertexPartition

optimiser = alg.Optimiser()
if random_state:
if random_state is not None:
optimiser.set_rng_seed(random_state)

# The same as leiden.find_partition_multiplex() (louvain.find_partition_multiplex())
Expand Down Expand Up @@ -1059,7 +1059,7 @@ def leiden(
data: Union[MuData, AnnData],
resolution: Optional[Union[float, Sequence[float], Mapping[str, float]]] = None,
mod_weights: Optional[Union[Sequence[float], Mapping[str, float]]] = None,
random_state: int = 0,
random_state: int | None = 0,
key_added: str = "leiden",
neighbors_key: str = None,
directed: bool = True,
Expand Down Expand Up @@ -1135,7 +1135,7 @@ def louvain(
data: Union[MuData, AnnData],
resolution: Optional[Union[float, Sequence[float], Mapping[str, float]]] = None,
mod_weights: Optional[Union[Sequence[float], Mapping[str, float]]] = None,
random_state: int = 0,
random_state: int | None = 0,
key_added: str = "louvain",
neighbors_key: str = None,
directed: bool = True,
Expand Down Expand Up @@ -1368,7 +1368,7 @@ def ica(
basis="X_pca",
n_components=None,
*,
random_state=None,
random_state: int | None = 0,
scale=False,
copy=False,
**kwargs,
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2 changes: 1 addition & 1 deletion muon/_prot/preproc.py
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Expand Up @@ -22,7 +22,7 @@ def dsb(
empty_counts_range: Optional[Tuple[Real, Real]] = None,
cell_counts_range: Optional[Tuple[Real, Real]] = None,
add_layer: bool = False,
random_state: Optional[Union[int, np.random.RandomState, None]] = None,
random_state: Optional[Union[int, np.random.RandomState, None]] = 0,
) -> Union[None, MuData]:
"""
Normalize protein expression with DSB (Denoised and Scaled by Background)
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