perf: speed up igraph RNG adapter for rng Generators (#4518)

Author: flying-sheep

docs/release-notes/4518.perf.md

@@ -0,0 +1 @@
+Speed up igraph-based functions ({func}`~scanpy.tl.leiden` with `flavor="igraph"`, {func}`~scanpy.tl.draw_graph`, {func}`~scanpy.pl.paga`) when `rng` is a {class}`numpy.random.Generator` {smaller}`P. Angerer`

src/scanpy/_utils/random.py

@@ -53,14 +53,16 @@ class _RNGIgraph:
 
     def __init__(self, rng: SeedLike | RNGLike | None) -> None:
         self._rng = np.random.default_rng(rng)
+        # igraph calls `getrandbits` a lot, so bind the fastest source once.
+        # (`random_raw` is ~10× faster than `.integers(…)`)
+        self._raw: Callable[[], int] = (
+            self._rng.state.tomaxint
+            if isinstance(self._rng, _LegacyRng)
+            else self._rng.bit_generator.random_raw
+        )
 
     def getrandbits(self, k: int) -> int:
-        if isinstance(self._rng, _LegacyRng):
-            i = self._rng.state.tomaxint()
-        else:
-            lims = np.iinfo(np.uint64)
-            i = int(self._rng.integers(0, lims.max, dtype=np.uint64, endpoint=True))
-        return i & ((1 << k) - 1)
+        return self._raw() & ((1 << k) - 1)
 
     def randint(self, a: int, b: int) -> np.int64:
         """Can’t use `endpoint` here as _LegacyRng doesn’t support it."""
@@ -75,6 +77,9 @@ def _set_igraph_rng(rng: SeedLike | RNGLike | None) -> Generator[None]:
     ensure_igraph()
     import igraph
 
+    if rng is None:  # unseeded, so igraph’s native (and fastest) RNG is fine
+        yield None
+        return
     ig_rng = _RNGIgraph(rng)
     try:
         igraph.set_random_number_generator(ig_rng)

src/scanpy/tools/_leiden.py

@@ -190,6 +190,7 @@ def leiden(  # noqa: PLR0913
     if n_jobs is None:
         # unseeded runs needn’t be reproducible, so they can be parallel
         n_jobs = settings.n_jobs if rng is None else 1
+    seeded = rng is not None
     rng = np.random.default_rng(rng)
     meta_random_state = (
         dict(random_state=rng.arg) if isinstance(rng, _LegacyRng) else {}
@@ -250,7 +251,7 @@ def leiden(  # noqa: PLR0913
     else:
         part = _leiden_igraph(
             adjacency,
-            rng=rng,
+            rng=rng if seeded else None,
             directed=directed,
             use_weights=use_weights,
             resolution=resolution,
@@ -339,7 +340,7 @@ def _leiden_networkit(
 def _leiden_igraph(
     adjacency: CSBase,
     *,
-    rng: np.random.Generator,
+    rng: np.random.Generator | None,
     directed: bool,
     use_weights: bool,
     resolution: float | None,