Add replace option to subsample and rename function to sample (scverse#943)

Author: gokceneraslan

docs/api/deprecated.md

@@ -11,4 +11,5 @@
 
    pp.filter_genes_dispersion
    pp.normalize_per_cell
+   pp.subsample
 ```

docs/api/preprocessing.md

@@ -31,7 +31,7 @@ For visual quality control, see {func}`~scanpy.pl.highest_expr_genes` and
    pp.normalize_total
    pp.regress_out
    pp.scale
-   pp.subsample
+   pp.sample
    pp.downsample_counts
 ```
 

docs/release-notes/943.feature.md

@@ -0,0 +1 @@
+{func}`~scanpy.pp.sample` supports both upsampling and downsampling of observations and variables. {func}`~scanpy.pp.subsample` is now deprecated. {smaller}`G Eraslan` & {smaller}`P Angerer`

pyproject.toml

@@ -47,7 +47,7 @@ classifiers = [
 ]
 dependencies = [
     "anndata>=0.8",
-    "numpy>=1.23",
+    "numpy>=1.24",
     "matplotlib>=3.6",
     "pandas >=1.5",
     "scipy>=1.8",
@@ -60,7 +60,7 @@ dependencies = [
     "networkx>=2.7",
     "natsort",
     "joblib",
-    "numba>=0.56",
+    "numba>=0.57",
     "umap-learn>=0.5,!=0.5.0",
     "pynndescent>=0.5",
     "packaging>=21.3",

src/scanpy/_compat.py

@@ -4,7 +4,7 @@
 import sys
 import warnings
 from dataclasses import dataclass, field
-from functools import cache, partial, wraps
+from functools import WRAPPER_ASSIGNMENTS, cache, partial, wraps
 from importlib.util import find_spec
 from pathlib import Path
 from typing import TYPE_CHECKING, Literal, ParamSpec, TypeVar, cast, overload
@@ -224,3 +224,42 @@ def _numba_threading_layer() -> Layer:
         f" ({available=}, {numba.config.THREADING_LAYER_PRIORITY=})"
     )
     raise ValueError(msg)
+
+
+def _legacy_numpy_gen(
+    random_state: _LegacyRandom | None = None,
+) -> np.random.Generator:
+    """Return a random generator that behaves like the legacy one."""
+
+    if random_state is not None:
+        if isinstance(random_state, np.random.RandomState):
+            np.random.set_state(random_state.get_state(legacy=False))
+            return _FakeRandomGen(random_state)
+        np.random.seed(random_state)
+    return _FakeRandomGen(np.random.RandomState(np.random.get_bit_generator()))
+
+
+class _FakeRandomGen(np.random.Generator):
+    _state: np.random.RandomState
+
+    def __init__(self, random_state: np.random.RandomState) -> None:
+        self._state = random_state
+
+    @classmethod
+    def _delegate(cls) -> None:
+        for name, meth in np.random.Generator.__dict__.items():
+            if name.startswith("_") or not callable(meth):
+                continue
+
+            def mk_wrapper(name: str):
+                # Old pytest versions try to run the doctests
+                @wraps(meth, assigned=set(WRAPPER_ASSIGNMENTS) - {"__doc__"})
+                def wrapper(self: _FakeRandomGen, *args, **kwargs):
+                    return getattr(self._state, name)(*args, **kwargs)
+
+                return wrapper
+
+            setattr(cls, name, mk_wrapper(name))
+
+
+_FakeRandomGen._delegate()

src/scanpy/preprocessing/__init__.py

@@ -3,6 +3,7 @@
 from ..neighbors import neighbors
 from ._combat import combat
 from ._deprecated.highly_variable_genes import filter_genes_dispersion
+from ._deprecated.sampling import subsample
 from ._highly_variable_genes import highly_variable_genes
 from ._normalization import normalize_total
 from ._pca import pca
@@ -17,8 +18,8 @@
     log1p,
     normalize_per_cell,
     regress_out,
+    sample,
     sqrt,
-    subsample,
 )
 
 __all__ = [
@@ -40,6 +41,7 @@
     "log1p",
     "normalize_per_cell",
     "regress_out",
+    "sample",
     "scale",
     "sqrt",
     "subsample",

src/scanpy/preprocessing/_deprecated/sampling.py

@@ -0,0 +1,60 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+from ..._compat import _legacy_numpy_gen, old_positionals
+from .._simple import sample
+
+if TYPE_CHECKING:
+    import numpy as np
+    from anndata import AnnData
+    from numpy.typing import NDArray
+    from scipy.sparse import csc_matrix, csr_matrix
+
+    from ..._compat import _LegacyRandom
+
+    CSMatrix = csr_matrix | csc_matrix
+
+
+@old_positionals("n_obs", "random_state", "copy")
+def subsample(
+    data: AnnData | np.ndarray | CSMatrix,
+    fraction: float | None = None,
+    *,
+    n_obs: int | None = None,
+    random_state: _LegacyRandom = 0,
+    copy: bool = False,
+) -> AnnData | tuple[np.ndarray | CSMatrix, NDArray[np.int64]] | None:
+    """\
+    Subsample to a fraction of the number of observations.
+
+    .. deprecated:: 1.11.0
+
+       Use :func:`~scanpy.pp.sample` instead.
+
+    Parameters
+    ----------
+    data
+        The (annotated) data matrix of shape `n_obs` × `n_vars`.
+        Rows correspond to cells and columns to genes.
+    fraction
+        Subsample to this `fraction` of the number of observations.
+    n_obs
+        Subsample to this number of observations.
+    random_state
+        Random seed to change subsampling.
+    copy
+        If an :class:`~anndata.AnnData` is passed,
+        determines whether a copy is returned.
+
+    Returns
+    -------
+    Returns `X[obs_indices], obs_indices` if data is array-like, otherwise
+    subsamples the passed :class:`~anndata.AnnData` (`copy == False`) or
+    returns a subsampled copy of it (`copy == True`).
+    """
+
+    rng = _legacy_numpy_gen(random_state)
+    return sample(
+        data=data, fraction=fraction, n=n_obs, rng=rng, copy=copy, replace=False, axis=0
+    )