make random state argument handling more consistent

- always default to non-None random_state (consistent within muon and
  with scanpy)
- fix condition before setting random state in .tl.leiden (closes #154)

Author: ilia-kats

muon/_atac/tools.py

@@ -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,
 ):
     """

muon/_core/tools.py

@@ -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,
@@ -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())
@@ -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,
@@ -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,
@@ -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,

muon/_prot/preproc.py

@@ -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)