ingest _{{test_,}eager_iter,fast_csr}.py from SOMA core

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ repos:
         # for more info.
         - "pandas-stubs>=2"
         # Temporary, for PR: see https://github.com/single-cell-data/SOMA/pull/244
-        - "git+https://github.com/single-cell-data/soma@9e81f07"
+        - "git+https://github.com/single-cell-data/soma@rw/abcs"
         - types-setuptools
       args: ["--config-file=apis/python/pyproject.toml", "apis/python/src", "apis/python/devtools"]
       pass_filenames: false

apis/python/src/tiledbsoma/_eager_iter.py

@@ -0,0 +1,51 @@
+from concurrent import futures
+from typing import Iterator, Optional, TypeVar
+
+_T = TypeVar("_T")
+
+
+class EagerIterator(Iterator[_T]):
+    def __init__(
+        self,
+        iterator: Iterator[_T],
+        pool: Optional[futures.Executor] = None,
+    ):
+        super().__init__()
+        self.iterator = iterator
+        self._pool = pool or futures.ThreadPoolExecutor()
+        self._own_pool = pool is None
+        self._preload_future = self._pool.submit(self.iterator.__next__)
+
+    def __next__(self) -> _T:
+        stopped = False
+        try:
+            if self._preload_future.cancel():
+                # If `.cancel` returns True, cancellation was successful.
+                # The self.iterator.__next__ call has not yet been started,
+                # and will never be started, so we can compute next ourselves.
+                # This prevents deadlocks if the thread pool is too small
+                # and we can never create a preload thread.
+                return next(self.iterator)
+            # `.cancel` returned false, so the preload is already running.
+            # Just wait for it.
+            return self._preload_future.result()
+        except StopIteration:
+            self._cleanup()
+            stopped = True
+            raise
+        finally:
+            if not stopped:
+                # If we have more to do, go for the next thing.
+                self._preload_future = self._pool.submit(self.iterator.__next__)
+
+    def _cleanup(self) -> None:
+        if self._own_pool:
+            self._pool.shutdown()
+
+    def __del__(self) -> None:
+        # Ensure the threadpool is cleaned up in the case where the
+        # iterator is not exhausted. For more information on __del__:
+        # https://docs.python.org/3/reference/datamodel.html#object.__del__
+        self._cleanup()
+        super_del = getattr(super(), "__del__", lambda: None)
+        super_del()

apis/python/src/tiledbsoma/_fast_csr.py

@@ -0,0 +1,281 @@
+import os
+from concurrent.futures import Executor, ThreadPoolExecutor, wait
+from typing import List, NamedTuple, Tuple, Type, Union, cast
+
+import numba
+import numba.typed
+import numpy as np
+import numpy.typing as npt
+import pyarrow as pa
+import scipy.sparse as sp
+from somacore.query.types import IndexFactory, IndexLike
+
+from ._eager_iter import EagerIterator
+from ._funcs import typeguard_ignore
+from ._sparse_nd_array import SparseNDArray
+from ._types import NPIntArray, NPNDArray
+
+
+def read_csr(
+    matrix: SparseNDArray,
+    obs_joinids: pa.IntegerArray,
+    var_joinids: pa.IntegerArray,
+    index_factory: IndexFactory,
+) -> "AccumulatedCSR":
+    if not isinstance(matrix, SparseNDArray) or matrix.ndim != 2:
+        raise TypeError("Can only read from a 2D SparseNDArray")
+
+    max_workers = (os.cpu_count() or 4) + 2
+    with ThreadPoolExecutor(max_workers=max_workers) as pool:
+        acc = _CSRAccumulator(
+            obs_joinids=obs_joinids,
+            var_joinids=var_joinids,
+            pool=pool,
+            index_factory=index_factory,
+        )
+        for tbl in EagerIterator(
+            matrix.read((obs_joinids, var_joinids)).tables(),
+            pool=pool,
+        ):
+            acc.append(tbl["soma_dim_0"], tbl["soma_dim_1"], tbl["soma_data"])
+
+        return acc.finalize()
+
+
+class AccumulatedCSR(NamedTuple):
+    """
+    Private.
+
+    Return type for the _CSRAccumulator.finalize method.
+    Contains a sparse CSR's constituent elements.
+    """
+
+    data: NPNDArray
+    indptr: NPIntArray
+    indices: NPIntArray
+    shape: Tuple[int, int]
+
+    def to_scipy(self) -> sp.csr_matrix:
+        """Create a Scipy ``sparse.csr_matrix`` from component elements.
+
+        Conceptually, this is identical to::
+
+            sparse.csr_matrix((data, indices, indptr), shape=shape)
+
+        This ugliness is to bypass the O(N) scan that
+        :meth:`sparse._cs_matrix.__init__`
+        does when a new compressed matrix is created.
+
+        See `SciPy bug 11496 <https://github.com/scipy/scipy/issues/11496>`
+        for details.
+        """
+        matrix = sp.csr_matrix.__new__(sp.csr_matrix)
+        matrix.data = self.data
+        matrix.indptr = self.indptr
+        matrix.indices = self.indices
+        matrix._shape = self.shape
+        return matrix
+
+
+class _CSRAccumulator:
+    """
+    Fast accumulator of a CSR, based upon COO input.
+    """
+
+    def __init__(
+        self,
+        obs_joinids: pa.IntegerArray,
+        var_joinids: pa.IntegerArray,
+        pool: Executor,
+        index_factory: IndexFactory,
+    ):
+        self.obs_joinids = obs_joinids
+        self.var_joinids = var_joinids
+        self.pool = pool
+
+        self.shape: Tuple[int, int] = (len(self.obs_joinids), len(self.var_joinids))
+        self.obs_indexer = index_factory(self.obs_joinids)
+        self.var_indexer = index_factory(self.var_joinids)
+        self.row_length: NPIntArray = np.zeros(
+            (self.shape[0],), dtype=_select_dtype(self.shape[1])
+        )
+
+        # COO accumulated chunks, stored as list of triples (row_ind, col_ind, data)
+        self.coo_chunks: List[
+            Tuple[
+                NPIntArray,  # row_ind
+                NPIntArray,  # col_ind
+                NPNDArray,  # data
+            ]
+        ] = []
+
+    def append(
+        self,
+        row_joinids: Union[pa.Array, pa.ChunkedArray],
+        col_joinids: Union[pa.Array, pa.ChunkedArray],
+        data: Union[pa.Array, pa.ChunkedArray],
+    ) -> None:
+        """
+        At accumulation time, do several things:
+
+        * re-index to positional indices, and if possible, cast to smaller dtype
+          to minimize memory footprint (at cost of some amount of time)
+        * accumulate column counts by row, i.e., build the basis of the indptr
+        * cache the tuple of data, row, col
+        """
+        rows_future = self.pool.submit(
+            _reindex_and_cast,
+            self.obs_indexer,
+            row_joinids.to_numpy(),
+            _select_dtype(self.shape[0]),
+        )
+        cols_future = self.pool.submit(
+            _reindex_and_cast,
+            self.var_indexer,
+            col_joinids.to_numpy(),
+            _select_dtype(self.shape[1]),
+        )
+        row_ind = rows_future.result()
+        col_ind = cols_future.result()
+        self.coo_chunks.append((row_ind, col_ind, data.to_numpy()))  # type: ignore[arg-type]
+        _accum_row_length(self.row_length, row_ind)
+
+    def finalize(self) -> AccumulatedCSR:
+        nnz = sum(len(chunk[2]) for chunk in self.coo_chunks)
+        index_dtype = _select_dtype(nnz)
+        if nnz == 0:
+            # There is no way to infer matrix dtype, so use a default and return
+            # an empty matrix. Float32 is used as a default type, as it is most
+            # compatible with AnnData expectations.
+            empty = sp.csr_matrix((0, 0), dtype=np.float32)
+            return AccumulatedCSR(
+                data=empty.data,
+                indptr=empty.indptr,
+                indices=empty.indices,
+                shape=self.shape,
+            )
+
+        # cumsum row lengths to get indptr
+        indptr: NPIntArray = np.empty((self.shape[0] + 1,), dtype=index_dtype)
+        indptr[0:1] = 0
+        np.cumsum(self.row_length, out=indptr[1:])
+
+        # Parallel copy of data and column indices
+        indices: NPIntArray = np.empty((nnz,), dtype=index_dtype)
+        data: NPNDArray = np.empty((nnz,), dtype=self.coo_chunks[0][2].dtype)
+
+        # Empirically determined value. Needs to be large enough for reasonable
+        # concurrency, without excessive write cache conflict. Controls the
+        # number of rows that are processed in a single thread, and therefore
+        # is the primary tuning parameter related to concurrency.
+        row_rng_mask_bits = 18
+
+        n_jobs = (self.shape[0] >> row_rng_mask_bits) + 1
+        chunk_list = numba.typed.List(self.coo_chunks)
+        wait(
+            [
+                self.pool.submit(
+                    _copy_chunklist_range,
+                    chunk_list,
+                    data,
+                    indices,
+                    indptr,
+                    row_rng_mask_bits,
+                    job,
+                )
+                for job in range(n_jobs)
+            ]
+        )
+        _finalize_indptr(indptr)
+        return AccumulatedCSR(
+            data=data, indptr=indptr, indices=indices, shape=self.shape
+        )
+
+
+@typeguard_ignore
+@numba.jit(nopython=True, nogil=True)  # type: ignore[attr-defined,misc]
+def _accum_row_length(
+    row_length: npt.NDArray[np.int64], row_ind: npt.NDArray[np.int64]
+) -> None:
+    for rind in row_ind:
+        row_length[rind] += 1
+
+
+@typeguard_ignore
+@numba.jit(nopython=True, nogil=True)  # type: ignore[attr-defined,misc]
+def _copy_chunk_range(
+    row_ind_chunk: npt.NDArray[np.signedinteger[npt.NBitBase]],
+    col_ind_chunk: npt.NDArray[np.signedinteger[npt.NBitBase]],
+    data_chunk: NPNDArray,
+    data: NPNDArray,
+    indices: npt.NDArray[np.signedinteger[npt.NBitBase]],
+    indptr: npt.NDArray[np.signedinteger[npt.NBitBase]],
+    row_rng_mask: int,
+    row_rng_val: int,
+) -> None:
+    for n in range(len(data_chunk)):
+        row = row_ind_chunk[n]
+        if (row & row_rng_mask) != row_rng_val:
+            continue
+        ptr = indptr[row]
+        indices[ptr] = col_ind_chunk[n]
+        data[ptr] = data_chunk[n]
+        indptr[row] += 1
+
+
+@typeguard_ignore
+@numba.jit(nopython=True, nogil=True)  # type: ignore[attr-defined,misc]
+def _copy_chunklist_range(
+    chunk_list: numba.typed.List,
+    data: NPNDArray,
+    indices: npt.NDArray[np.signedinteger[npt.NBitBase]],
+    indptr: npt.NDArray[np.signedinteger[npt.NBitBase]],
+    row_rng_mask_bits: int,
+    job: int,
+) -> None:
+    assert row_rng_mask_bits >= 1 and row_rng_mask_bits < 64
+    row_rng_mask = (2**64 - 1) >> row_rng_mask_bits << row_rng_mask_bits
+    row_rng_val = job << row_rng_mask_bits
+    for row_ind_chunk, col_ind_chunk, data_chunk in chunk_list:
+        _copy_chunk_range(
+            row_ind_chunk,
+            col_ind_chunk,
+            data_chunk,
+            data,
+            indices,
+            indptr,
+            row_rng_mask,
+            row_rng_val,
+        )
+
+
+@typeguard_ignore
+@numba.jit(nopython=True, nogil=True)  # type: ignore[attr-defined,misc]
+def _finalize_indptr(indptr: npt.NDArray[np.signedinteger[npt.NBitBase]]) -> None:
+    prev = 0
+    for r in range(len(indptr)):
+        t = indptr[r]
+        indptr[r] = prev
+        prev = t
+
+
+def _select_dtype(
+    maxval: int,
+) -> Union[Type[np.int32], Type[np.int64]]:
+    """
+    Ascertain the "best" dtype for a zero-based index. Given our
+    goal of minimizing memory use, "best" is currently defined as
+    smallest.
+    """
+    if maxval > np.iinfo(np.int32).max:
+        return np.int64
+    else:
+        return np.int32
+
+
+def _reindex_and_cast(
+    index: IndexLike, ids: npt.NDArray[np.int64], target_dtype: npt.DTypeLike
+) -> npt.NDArray[np.int64]:
+    return cast(
+        npt.NDArray[np.int64], index.get_indexer(ids).astype(target_dtype, copy=False)
+    )

apis/python/src/tiledbsoma/_query.py

@@ -46,7 +46,6 @@
     ResultOrder,
     ResultOrderStr,
 )
-from somacore.query import _fast_csr
 from somacore.query.query import (
     AxisColumnNames,
     Numpyable,
@@ -56,6 +55,7 @@
 
 if TYPE_CHECKING:
     from ._experiment import Experiment
+from ._fast_csr import read_csr
 from ._measurement import Measurement
 from ._sparse_nd_array import SparseNDArray
 
@@ -579,7 +579,7 @@ def _read_axis_mappings(
 
         x_matrices = {
             _xname: (
-                _fast_csr.read_csr(
+                read_csr(
                     layer,
                     obs_joinids,
                     var_joinids,

apis/python/src/tiledbsoma/_read_iters.py

@@ -29,12 +29,12 @@
 import somacore
 from scipy import sparse
 from somacore import options
-from somacore.query._eager_iter import EagerIterator
 
 # This package's pybind11 code
 import tiledbsoma.pytiledbsoma as clib
 
 from . import _util
+from ._eager_iter import EagerIterator
 from ._exception import SOMAError
 from ._indexer import IntIndexer
 from ._types import NTuple

apis/python/src/tiledbsoma/_types.py

@@ -27,6 +27,7 @@
     NPInteger = np.integer[npt.NBitBase]
     NPFloating = np.floating[npt.NBitBase]
     NPNDArray = npt.NDArray[np.number[npt.NBitBase]]
+    NPIntArray = npt.NDArray[np.integer[npt.NBitBase]]
 else:
     # When not-type-checking, but running with `pandas>=2`, the "missing" type-params don't affect anything.
     PDSeries = pd.Series
@@ -38,6 +39,7 @@
     NPInteger = np.integer
     NPFloating = np.floating
     NPNDArray = np.ndarray
+    NPIntArray = np.ndarray
 
 
 Path = Union[str, pathlib.Path]