chore!: remove "rapids" flavor for louvain, umap, and neighbors (#4052)

Author: flying-sheep

docs/release-notes/4052.breaking.md

@@ -0,0 +1 @@
+Remove `'rapids'` flavor for {func}`scanpy.pp.neighbors`, {func}`scanpy.tl.louvain`, {func}`scanpy.tl.umap` {smaller}`P Angerer`

pyproject.toml

@@ -93,8 +93,6 @@ louvain = [ "igraph", "louvain>=0.8.2", "setuptools" ]
 magic = [ "magic-impute>=2.0.4" ]
 paga = [ "igraph" ]
 plotting = [ "colour-science" ]
-# Neighbors acceleration
-rapids = [ "cudf>=0.9", "cugraph>=0.9", "cuml>=0.9" ]
 scanorama = [ "scanorama" ]
 scrublet = [ "scikit-image>=0.23.1" ]
 # highly_variable_genes method 'seurat_v3'

src/scanpy/neighbors/__init__.py

@@ -149,11 +149,6 @@ def neighbors(  # noqa: PLR0913
             :class:`~pynndescent.pynndescent_.PyNNDescentTransformer`
         `'pynndescent'`
             :class:`~pynndescent.pynndescent_.PyNNDescentTransformer`
-        `'rapids'`
-            A transformer based on :class:`cuml.neighbors.NearestNeighbors`.
-
-            .. deprecated:: 1.10.0
-               Use :func:`rapids_singlecell.pp.neighbors` instead.
     metric
         A known metric’s name or a callable that returns a distance.
         If `distances` is given, this parameter is simply stored in `.uns` (see below),
@@ -749,15 +744,7 @@ def _handle_transformer(
         )
 
         # Coerce `method` to 'gauss', 'umap', or 'jaccard'
-        if method == "rapids":
-            if transformer is not None:
-                msg = "Can’t specify both `method = 'rapids'` and `transformer`."
-                raise ValueError(msg)
-            method = "umap"
-            transformer = "rapids"
-        elif (
-            method not in (methods := get_literal_vals(_Method)) and method is not None
-        ):
+        if method not in (methods := get_literal_vals(_Method)) and method is not None:
             msg = f"`method` needs to be one of {methods}."
             raise ValueError(msg)
 
@@ -797,15 +784,6 @@ def _handle_transformer(
                     n_iters=max(5, round(np.log2(self._adata.n_obs))),
                 )
             transformer = PyNNDescentTransformer(**kwds)
-        elif transformer == "rapids":
-            msg = (
-                "`transformer='rapids'` is deprecated. "
-                "Use `rapids_singlecell.tl.neighbors` instead."
-            )
-            warn(msg, FutureWarning)
-            from scanpy.neighbors._backends.rapids import RapidsKNNTransformer
-
-            transformer = RapidsKNNTransformer(**kwds)
         elif isinstance(transformer, str):
             msg = (
                 f"Unknown transformer: {transformer}. "

src/scanpy/neighbors/_types.py

@@ -21,7 +21,7 @@
 ]
 
 type _Method = Literal["umap", "gauss", "jaccard"]
-type _KnownTransformer = Literal["pynndescent", "sklearn", "rapids"]
+type _KnownTransformer = Literal["pynndescent", "sklearn"]
 
 type _MetricFn = Callable[[np.ndarray, np.ndarray], float]
 # from sklearn.metrics.pairwise_distances.__doc__:

src/scanpy/tools/_louvain.py

@@ -10,8 +10,8 @@
 
 from .. import _utils
 from .. import logging as logg
-from .._compat import deprecated, pkg_version, warn
-from .._utils import _choose_graph, _doc_params, dematrix
+from .._compat import deprecated, pkg_version
+from .._utils import _choose_graph, _doc_params
 from ._docs import (
     doc_adata,
     doc_adjacency,
@@ -54,7 +54,7 @@ def louvain(  # noqa: PLR0912, PLR0913, PLR0915
     restrict_to: tuple[str, Sequence[str]] | None = None,
     key_added: str = "louvain",
     adjacency: CSBase | None = None,
-    flavor: Literal["vtraag", "igraph", "rapids"] = "vtraag",
+    flavor: Literal["vtraag", "igraph"] = "vtraag",
     directed: bool = True,
     use_weights: bool = False,
     partition_type: type[MutableVertexPartition] | None = None,
@@ -99,11 +99,6 @@ def louvain(  # noqa: PLR0912, PLR0913, PLR0915
             Much more powerful than ``'igraph'``, and the default.
         ``'igraph'``
             Built in ``igraph`` method.
-        ``'rapids'``
-            GPU accelerated implementation.
-
-            .. deprecated:: 1.10.0
-                Use :func:`rapids_singlecell.tl.louvain` instead.
     directed
         Interpret the ``adjacency`` matrix as directed graph?
     use_weights
@@ -180,44 +175,6 @@ def louvain(  # noqa: PLR0912, PLR0913, PLR0915
         else:
             part = g.community_multilevel(weights=weights)
         groups = np.array(part.membership)
-    elif flavor == "rapids":
-        msg = (
-            "`flavor='rapids'` is deprecated. "
-            "Use `rapids_singlecell.tl.louvain` instead."
-        )
-        warn(msg, FutureWarning)
-        # nvLouvain only works with undirected graphs,
-        # and `adjacency` must have a directed edge in both directions
-        import cudf
-        import cugraph
-
-        offsets = cudf.Series(adjacency.indptr)
-        indices = cudf.Series(adjacency.indices)
-        if use_weights:
-            sources, targets = adjacency.nonzero()
-            weights = dematrix(adjacency[sources, targets]).ravel()
-            weights = cudf.Series(weights)
-        else:
-            weights = None
-        g = cugraph.Graph()
-
-        if hasattr(g, "add_adj_list"):
-            g.add_adj_list(offsets, indices, weights)
-        else:
-            g.from_cudf_adjlist(offsets, indices, weights)
-
-        logg.info('    using the "louvain" package of rapids')
-        if resolution is not None:
-            louvain_parts, _ = cugraph.louvain(g, resolution=resolution)
-        else:
-            louvain_parts, _ = cugraph.louvain(g)
-        groups = (
-            louvain_parts
-            .to_pandas()
-            .sort_values("vertex")[["partition"]]
-            .to_numpy()
-            .ravel()
-        )
     elif flavor == "taynaud":
         # this is deprecated
         import community

src/scanpy/tools/_umap.py

@@ -6,7 +6,6 @@
 from sklearn.utils import check_array
 
 from .. import logging as logg
-from .._compat import warn
 from .._docs import doc_rng
 from .._settings import settings
 from .._utils import NeighborsView, _doc_params
@@ -44,7 +43,7 @@ def umap(  # noqa: PLR0913
     rng: SeedLike | RNGLike | None = None,
     a: float | None = None,
     b: float | None = None,
-    method: Literal["umap", "rapids"] = "umap",
+    method: Literal["umap"] = "umap",
     key_added: str | None = None,
     neighbors_key: str = "neighbors",
     copy: bool = False,
@@ -117,11 +116,6 @@ def umap(  # noqa: PLR0913
 
         ``'umap'``
             Umap’s simplical set embedding.
-        ``'rapids'``
-            GPU accelerated implementation.
-
-            .. deprecated:: 1.10.0
-                Use :func:`rapids_singlecell.tl.umap` instead.
     key_added
         If not specified, the embedding is stored as
         :attr:`~anndata.AnnData.obsm`\ `['X_umap']` and the the parameters in
@@ -218,40 +212,9 @@ def umap(  # noqa: PLR0913
             output_dens=False,
             verbose=settings.verbosity > 3,
         )
-    elif method == "rapids":
-        msg = (
-            "`method='rapids'` is deprecated. Use `rapids_singlecell.tl.umap` instead."
-        )
-        warn(msg, FutureWarning)
-        metric = neigh_params.get("metric", "euclidean")
-        if metric != "euclidean":
-            msg = (
-                f"`sc.pp.neighbors` was called with `metric` {metric!r}, "
-                "but umap `method` 'rapids' only supports the 'euclidean' metric."
-            )
-            raise ValueError(msg)
-        from cuml import UMAP
-
-        n_neighbors = neighbors["params"]["n_neighbors"]
-        n_epochs = (
-            500 if maxiter is None else maxiter
-        )  # 0 is not a valid value for rapids, unlike original umap
-        x_contiguous = np.ascontiguousarray(x, dtype=np.float32)
-        umap = UMAP(
-            n_neighbors=n_neighbors,
-            n_components=n_components,
-            n_epochs=n_epochs,
-            learning_rate=alpha,
-            init=init_pos,
-            min_dist=min_dist,
-            spread=spread,
-            negative_sample_rate=negative_sample_rate,
-            a=a,
-            b=b,
-            verbose=settings.verbosity > 3,
-            random_state=_legacy_random_state(rng),
-        )
-        x_umap = umap.fit_transform(x_contiguous)
+    else:
+        msg = f"Unknown method {method}"
+        raise ValueError(msg)
     adata.obsm[key_obsm] = x_umap  # annotate samples with UMAP coordinates
     logg.info(
         "    finished",