Use weakref instead of id for DataIter cache. (#9445)

- Fix case where Python reuses id from freed objects.
- Small optimization to column matrix with QDM by using `realloc` instead of copying data.

demo/guide-python/external_memory.py

@@ -22,7 +22,10 @@ import xgboost
 
 
 def make_batches(
-    n_samples_per_batch: int, n_features: int, n_batches: int, tmpdir: str,
+    n_samples_per_batch: int,
+    n_features: int,
+    n_batches: int,
+    tmpdir: str,
 ) -> List[Tuple[str, str]]:
     files: List[Tuple[str, str]] = []
     rng = np.random.RandomState(1994)
@@ -38,6 +41,7 @@ def make_batches(
 
 class Iterator(xgboost.DataIter):
     """A custom iterator for loading files in batches."""
+
     def __init__(self, file_paths: List[Tuple[str, str]]):
         self._file_paths = file_paths
         self._it = 0

doc/python/python_api.rst

@@ -23,12 +23,16 @@ Core Data Structure
     :show-inheritance:
 
 .. autoclass:: xgboost.QuantileDMatrix
+    :members:
     :show-inheritance:
 
 .. autoclass:: xgboost.Booster
     :members:
     :show-inheritance:
 
+.. autoclass:: xgboost.DataIter
+    :members:
+    :show-inheritance:
 
 Learning API
 ------------

python-package/xgboost/_typing.py

@@ -8,7 +8,9 @@ from typing import (
     Callable,
     Dict,
     List,
+    Optional,
     Sequence,
+    Tuple,
     Type,
     TypeVar,
     Union,
@@ -20,8 +22,6 @@ import numpy as np
 
 DataType = Any
 
-# xgboost accepts some other possible types in practice due to historical reason, which is
-# lesser tested.  For now we encourage users to pass a simple list of string.
 FeatureInfo = Sequence[str]
 FeatureNames = FeatureInfo
 FeatureTypes = FeatureInfo
@@ -97,6 +97,13 @@ else:
         ctypes._Pointer,
     ]
 
+# The second arg is actually Optional[List[cudf.Series]], skipped for easier type check.
+# The cudf Series is the obtained cat codes, preserved in the `DataIter` to prevent it
+# being freed.
+TransformedData = Tuple[
+    Any, Optional[List], Optional[FeatureNames], Optional[FeatureTypes]
+]
+
 # template parameter
 _T = TypeVar("_T")
 _F = TypeVar("_F", bound=Callable[..., Any])

python-package/xgboost/core.py

@@ -9,6 +9,7 @@ import os
 import re
 import sys
 import warnings
+import weakref
 from abc import ABC, abstractmethod
 from collections.abc import Mapping
 from enum import IntEnum, unique
@@ -51,6 +52,7 @@ from ._typing import (
     FeatureTypes,
     ModelIn,
     NumpyOrCupy,
+    TransformedData,
     c_bst_ulong,
 )
 from .compat import PANDAS_INSTALLED, DataFrame, py_str
@@ -486,7 +488,16 @@ def _prediction_output(
 
 
 class DataIter(ABC):  # pylint: disable=too-many-instance-attributes
-    """The interface for user defined data iterator.
+    """The interface for user defined data iterator. The iterator facilitates
+    distributed training, :py:class:`QuantileDMatrix`, and external memory support using
+    :py:class:`DMatrix`. Most of time, users don't need to interact with this class
+    directly.
+
+    .. note::
+
+        The class caches some intermediate results using the `data` input (predictor
+        `X`) as key. Don't repeat the `X` for multiple batches with different meta data
+        (like `label`), make a copy if necessary.
 
     Parameters
     ----------
@@ -510,13 +521,13 @@ class DataIter(ABC):  # pylint: disable=too-many-instance-attributes
         self._allow_host = True
         self._release = release_data
         # Stage data in Python until reset or next is called to avoid data being free.
-        self._temporary_data: Optional[Tuple[Any, Any, Any, Any]] = None
-        self._input_id: int = 0
+        self._temporary_data: Optional[TransformedData] = None
+        self._data_ref: Optional[weakref.ReferenceType] = None
 
     def get_callbacks(
         self, allow_host: bool, enable_categorical: bool
     ) -> Tuple[Callable, Callable]:
-        """Get callback functions for iterating in C."""
+        """Get callback functions for iterating in C. This is an internal function."""
         assert hasattr(self, "cache_prefix"), "__init__ is not called."
         self._reset_callback = ctypes.CFUNCTYPE(None, ctypes.c_void_p)(
             self._reset_wrapper
@@ -591,7 +602,19 @@ class DataIter(ABC):  # pylint: disable=too-many-instance-attributes
             from .data import _proxy_transform, dispatch_proxy_set_data
 
             # Reduce the amount of transformation that's needed for QuantileDMatrix.
-            if self._temporary_data is not None and id(data) == self._input_id:
+            #
+            # To construct the QDM, one needs 4 iterations on CPU, or 2 iterations on
+            # GPU. If the QDM has only one batch of input (most of the cases), we can
+            # avoid transforming the data repeatly.
+            try:
+                ref = weakref.ref(data)
+            except TypeError:
+                ref = None
+            if (
+                self._temporary_data is not None
+                and ref is not None
+                and ref is self._data_ref
+            ):
                 new, cat_codes, feature_names, feature_types = self._temporary_data
             else:
                 new, cat_codes, feature_names, feature_types = _proxy_transform(
@@ -608,7 +631,7 @@ class DataIter(ABC):  # pylint: disable=too-many-instance-attributes
                 feature_types=feature_types,
                 **kwargs,
             )
-            self._input_id = id(data)
+            self._data_ref = ref
 
         # pylint: disable=not-callable
         return self._handle_exception(lambda: self.next(input_data), 0)
@@ -1134,7 +1157,7 @@ class DMatrix:  # pylint: disable=too-many-instance-attributes,too-many-public-m
         testing purposes. If this is a quantized DMatrix then quantized values are
         returned instead of input values.
 
-            .. versionadded:: 1.7.0
+        .. versionadded:: 1.7.0
 
         """
         indptr = np.empty(self.num_row() + 1, dtype=np.uint64)
@@ -1155,7 +1178,11 @@ class DMatrix:  # pylint: disable=too-many-instance-attributes,too-many-public-m
         return ret
 
     def get_quantile_cut(self) -> Tuple[np.ndarray, np.ndarray]:
-        """Get quantile cuts for quantization."""
+        """Get quantile cuts for quantization.
+
+        .. versionadded:: 2.0.0
+
+        """
         n_features = self.num_col()
 
         c_sindptr = ctypes.c_char_p()

python-package/xgboost/data.py

@@ -5,7 +5,7 @@ import ctypes
 import json
 import os
 import warnings
-from typing import Any, Callable, Iterator, List, Optional, Sequence, Tuple, Union, cast
+from typing import Any, Callable, Iterator, List, Optional, Sequence, Tuple, cast
 
 import numpy as np
 
@@ -17,6 +17,7 @@ from ._typing import (
     FloatCompatible,
     NumpyDType,
     PandasDType,
+    TransformedData,
     c_bst_ulong,
 )
 from .compat import DataFrame, lazy_isinstance
@@ -1268,12 +1269,7 @@ def _proxy_transform(
     feature_names: Optional[FeatureNames],
     feature_types: Optional[FeatureTypes],
     enable_categorical: bool,
-) -> Tuple[
-    Union[bool, ctypes.c_void_p, np.ndarray],
-    Optional[list],
-    Optional[FeatureNames],
-    Optional[FeatureTypes],
-]:
+) -> TransformedData:
     if _is_cudf_df(data) or _is_cudf_ser(data):
         return _transform_cudf_df(
             data, feature_names, feature_types, enable_categorical

python-package/xgboost/testing/__init__.py

@@ -230,7 +230,7 @@ class IteratorForTest(xgb.core.DataIter):
 
     def as_arrays(
         self,
-    ) -> Tuple[Union[np.ndarray, sparse.csr_matrix], ArrayLike, ArrayLike]:
+    ) -> Tuple[Union[np.ndarray, sparse.csr_matrix], ArrayLike, Optional[ArrayLike]]:
         if isinstance(self.X[0], sparse.csr_matrix):
             X = sparse.vstack(self.X, format="csr")
         else:
@@ -244,7 +244,12 @@ class IteratorForTest(xgb.core.DataIter):
 
 
 def make_batches(
-    n_samples_per_batch: int, n_features: int, n_batches: int, use_cupy: bool = False
+    n_samples_per_batch: int,
+    n_features: int,
+    n_batches: int,
+    use_cupy: bool = False,
+    *,
+    vary_size: bool = False,
 ) -> Tuple[List[np.ndarray], List[np.ndarray], List[np.ndarray]]:
     X = []
     y = []
@@ -255,10 +260,11 @@ def make_batches(
         rng = cupy.random.RandomState(1994)
     else:
         rng = np.random.RandomState(1994)
-    for _ in range(n_batches):
-        _X = rng.randn(n_samples_per_batch, n_features)
-        _y = rng.randn(n_samples_per_batch)
-        _w = rng.uniform(low=0, high=1, size=n_samples_per_batch)
+    for i in range(n_batches):
+        n_samples = n_samples_per_batch + i * 10 if vary_size else n_samples_per_batch
+        _X = rng.randn(n_samples, n_features)
+        _y = rng.randn(n_samples)
+        _w = rng.uniform(low=0, high=1, size=n_samples)
         X.append(_X)
         y.append(_y)
         w.append(_w)

src/common/column_matrix.h

@@ -9,12 +9,12 @@
 #define XGBOOST_COMMON_COLUMN_MATRIX_H_
 
 #include <algorithm>
-#include <cstddef>  // for size_t
+#include <cstddef>  // for size_t, byte
 #include <cstdint>  // for uint8_t
 #include <limits>
 #include <memory>
-#include <utility>  // for move
-#include <vector>
+#include <type_traits>  // for enable_if_t, is_same_v, is_signed_v
+#include <utility>      // for move
 
 #include "../data/adapter.h"
 #include "../data/gradient_index.h"
@@ -112,9 +112,6 @@ class SparseColumnIter : public Column<BinIdxT> {
  */
 template <typename BinIdxT, bool any_missing>
 class DenseColumnIter : public Column<BinIdxT> {
- public:
-  using ByteType = bool;
-
  private:
   using Base = Column<BinIdxT>;
   /* flags for missing values in dense columns */
@@ -153,8 +150,17 @@ class ColumnMatrix {
    * @brief A bit set for indicating whether an element in a dense column is missing.
    */
   struct MissingIndicator {
-    LBitField32 missing;
-    RefResourceView<std::uint32_t> storage;
+    using BitFieldT = LBitField32;
+    using T = typename BitFieldT::value_type;
+
+    BitFieldT missing;
+    RefResourceView<T> storage;
+    static_assert(std::is_same_v<T, std::uint32_t>);
+
+    template <typename U>
+    [[nodiscard]] std::enable_if_t<!std::is_signed_v<U>, U> static InitValue(bool init) {
+      return init ? ~U{0} : U{0};
+    }
 
     MissingIndicator() = default;
     /**
@@ -163,7 +169,7 @@ class ColumnMatrix {
      */
     MissingIndicator(std::size_t n_elements, bool init) {
       auto m_size = missing.ComputeStorageSize(n_elements);
-      storage = common::MakeFixedVecWithMalloc(m_size, init ? ~std::uint32_t{0} : std::uint32_t{0});
+      storage = common::MakeFixedVecWithMalloc(m_size, InitValue<T>(init));
       this->InitView();
     }
     /** @brief Set the i^th element to be a valid element (instead of missing). */
@@ -181,11 +187,12 @@ class ColumnMatrix {
       if (m_size == storage.size()) {
         return;
       }
+      // grow the storage
+      auto resource = std::dynamic_pointer_cast<common::MallocResource>(storage.Resource());
+      CHECK(resource);
+      resource->Resize(m_size * sizeof(T), InitValue<std::byte>(init));
+      storage = RefResourceView<T>{resource->DataAs<T>(), m_size, resource};
 
-      auto new_storage =
-          common::MakeFixedVecWithMalloc(m_size, init ? ~std::uint32_t{0} : std::uint32_t{0});
-      std::copy_n(storage.cbegin(), storage.size(), new_storage.begin());
-      storage = std::move(new_storage);
       this->InitView();
     }
   };
@@ -210,7 +217,6 @@ class ColumnMatrix {
   }
 
  public:
-  using ByteType = bool;
   // get number of features
   [[nodiscard]] bst_feature_t GetNumFeature() const {
     return static_cast<bst_feature_t>(type_.size());
@@ -408,6 +414,7 @@ class ColumnMatrix {
   // IO procedures for external memory.
   [[nodiscard]] bool Read(AlignedResourceReadStream* fi, uint32_t const* index_base);
   [[nodiscard]] std::size_t Write(AlignedFileWriteStream* fo) const;
+  [[nodiscard]] MissingIndicator const& Missing() const { return missing_; }
 
  private:
   RefResourceView<std::uint8_t> index_;

src/common/io.h

@@ -10,7 +10,7 @@
 #include <dmlc/io.h>
 #include <rabit/rabit.h>
 
-#include <algorithm>    // for min
+#include <algorithm>    // for min, fill_n, copy_n
 #include <array>        // for array
 #include <cstddef>      // for byte, size_t
 #include <cstdlib>      // for malloc, realloc, free
@@ -207,7 +207,7 @@ class MallocResource : public ResourceHandler {
    * @param n_bytes The new size.
    */
   template <bool force_malloc = false>
-  void Resize(std::size_t n_bytes) {
+  void Resize(std::size_t n_bytes, std::byte init = std::byte{0}) {
     // realloc(ptr, 0) works, but is deprecated.
     if (n_bytes == 0) {
       this->Clear();
@@ -236,7 +236,7 @@ class MallocResource : public ResourceHandler {
       std::copy_n(reinterpret_cast<std::byte*>(ptr_), n_, reinterpret_cast<std::byte*>(new_ptr));
     }
     // default initialize
-    std::memset(reinterpret_cast<std::byte*>(new_ptr) + n_, '\0', n_bytes - n_);
+    std::fill_n(reinterpret_cast<std::byte*>(new_ptr) + n_, n_bytes - n_, init);
     // free the old ptr if malloc is used.
     if (need_copy) {
       this->Clear();

tests/ci_build/lint_python.py

@@ -42,6 +42,7 @@ class LintersPaths:
         "demo/guide-python/feature_weights.py",
         "demo/guide-python/sklearn_parallel.py",
         "demo/guide-python/spark_estimator_examples.py",
+        "demo/guide-python/external_memory.py",
         "demo/guide-python/individual_trees.py",
         "demo/guide-python/quantile_regression.py",
         "demo/guide-python/multioutput_regression.py",

tests/cpp/common/test_column_matrix.cc

@@ -2,15 +2,26 @@
  * Copyright 2018-2023 by XGBoost Contributors
  */
 #include <gtest/gtest.h>
+#include <xgboost/base.h>     // for bst_bin_t
+#include <xgboost/context.h>  // for Context
+#include <xgboost/data.h>     // for BatchIterator, BatchSet, DMatrix, Met...
 
-#include "../../../src/common/column_matrix.h"
-#include "../helpers.h"
+#include <cstddef>      // for size_t
+#include <cstdint>      // for int32_t, uint16_t, uint8_t
+#include <limits>       // for numeric_limits
+#include <memory>       // for shared_ptr, __shared_ptr_access, allo...
+#include <type_traits>  // for remove_reference_t
 
+#include "../../../src/common/column_matrix.h"      // for ColumnMatrix, Column, DenseColumnIter
+#include "../../../src/common/hist_util.h"          // for DispatchBinType, BinTypeSize, Index
+#include "../../../src/common/ref_resource_view.h"  // for RefResourceView
+#include "../../../src/data/gradient_index.h"       // for GHistIndexMatrix
+#include "../../../src/data/iterative_dmatrix.h"    // for IterativeDMatrix
+#include "../../../src/tree/param.h"                // for TrainParam
+#include "../helpers.h"                             // for RandomDataGenerator, NumpyArrayIterFo...
 
-namespace xgboost {
-namespace common {
-
-TEST(DenseColumn, Test) {
+namespace xgboost::common {
+TEST(ColumnMatrix, Basic) {
   int32_t max_num_bins[] = {static_cast<int32_t>(std::numeric_limits<uint8_t>::max()) + 1,
                             static_cast<int32_t>(std::numeric_limits<uint16_t>::max()) + 1,
                             static_cast<int32_t>(std::numeric_limits<uint16_t>::max()) + 2};
@@ -22,7 +33,7 @@ TEST(DenseColumn, Test) {
     GHistIndexMatrix gmat{&ctx, dmat.get(), max_num_bin, sparse_thresh, false};
     ColumnMatrix column_matrix;
     for (auto const& page : dmat->GetBatches<SparsePage>()) {
-      column_matrix.InitFromSparse(page, gmat, sparse_thresh, AllThreadsForTest());
+      column_matrix.InitFromSparse(page, gmat, sparse_thresh, ctx.Threads());
     }
     ASSERT_GE(column_matrix.GetTypeSize(), last);
     ASSERT_LE(column_matrix.GetTypeSize(), kUint32BinsTypeSize);
@@ -59,7 +70,7 @@ void CheckSparseColumn(SparseColumnIter<BinIdxType>* p_col, const GHistIndexMatr
   }
 }
 
-TEST(SparseColumn, Test) {
+TEST(ColumnMatrix, SparseColumn) {
   int32_t max_num_bins[] = {static_cast<int32_t>(std::numeric_limits<uint8_t>::max()) + 1,
                             static_cast<int32_t>(std::numeric_limits<uint16_t>::max()) + 1,
                             static_cast<int32_t>(std::numeric_limits<uint16_t>::max()) + 2};
@@ -69,7 +80,7 @@ TEST(SparseColumn, Test) {
     GHistIndexMatrix gmat{&ctx, dmat.get(), max_num_bin, 0.5f, false};
     ColumnMatrix column_matrix;
     for (auto const& page : dmat->GetBatches<SparsePage>()) {
-      column_matrix.InitFromSparse(page, gmat, 1.0, AllThreadsForTest());
+      column_matrix.InitFromSparse(page, gmat, 1.0, ctx.Threads());
     }
     common::DispatchBinType(column_matrix.GetTypeSize(), [&](auto dtype) {
       using T = decltype(dtype);
@@ -90,7 +101,7 @@ void CheckColumWithMissingValue(const DenseColumnIter<BinIdxType, true>& col,
   }
 }
 
-TEST(DenseColumnWithMissing, Test) {
+TEST(ColumnMatrix, DenseColumnWithMissing) {
   int32_t max_num_bins[] = {static_cast<int32_t>(std::numeric_limits<uint8_t>::max()) + 1,
                             static_cast<int32_t>(std::numeric_limits<uint16_t>::max()) + 1,
                             static_cast<int32_t>(std::numeric_limits<uint16_t>::max()) + 2};
@@ -100,7 +111,7 @@ TEST(DenseColumnWithMissing, Test) {
     GHistIndexMatrix gmat(&ctx, dmat.get(), max_num_bin, 0.2, false);
     ColumnMatrix column_matrix;
     for (auto const& page : dmat->GetBatches<SparsePage>()) {
-      column_matrix.InitFromSparse(page, gmat, 0.2, AllThreadsForTest());
+      column_matrix.InitFromSparse(page, gmat, 0.2, ctx.Threads());
     }
     ASSERT_TRUE(column_matrix.AnyMissing());
     DispatchBinType(column_matrix.GetTypeSize(), [&](auto dtype) {
@@ -110,5 +121,29 @@ TEST(DenseColumnWithMissing, Test) {
     });
   }
 }
-}  // namespace common
-}  // namespace xgboost
+
+TEST(ColumnMatrix, GrowMissing) {
+  float sparsity = 0.5;
+  NumpyArrayIterForTest iter(sparsity);
+  auto n_threads = 0;
+  bst_bin_t n_bins = 16;
+  BatchParam batch{n_bins, tree::TrainParam::DftSparseThreshold()};
+  Context ctx;
+  auto m = std::make_shared<data::IterativeDMatrix>(&iter, iter.Proxy(), nullptr, Reset, Next,
+                                                    std::numeric_limits<float>::quiet_NaN(),
+                                                    n_threads, n_bins);
+  for (auto const& page : m->GetBatches<GHistIndexMatrix>(&ctx, batch)) {
+    auto const& column_matrix = page.Transpose();
+    auto const& missing = column_matrix.Missing();
+    auto n = NumpyArrayIterForTest::Rows() * NumpyArrayIterForTest::Cols();
+    auto expected = std::remove_reference_t<decltype(missing)>::BitFieldT::ComputeStorageSize(n);
+    auto got = missing.storage.size();
+    ASSERT_EQ(expected, got);
+    DispatchBinType(column_matrix.GetTypeSize(), [&](auto dtype) {
+      using T = decltype(dtype);
+      auto col = column_matrix.DenseColumn<T, true>(0);
+      CheckColumWithMissingValue(col, page);
+    });
+  }
+}
+}  // namespace xgboost::common

tests/cpp/common/test_io.cc

@@ -119,6 +119,20 @@ TEST(IO, Resource) {
     for (std::size_t i = n; i < 2 * n; ++i) {
       ASSERT_EQ(malloc_resource->DataAs<std::uint8_t>()[i], 0);
     }
+
+    ptr = malloc_resource->DataAs<std::uint8_t>();
+    std::fill_n(ptr, malloc_resource->Size(), 7);
+    if (force_malloc) {
+      malloc_resource->Resize<true>(n * 3, std::byte{3});
+    } else {
+      malloc_resource->Resize<false>(n * 3, std::byte{3});
+    }
+    for (std::size_t i = 0; i < n * 2; ++i) {
+      ASSERT_EQ(malloc_resource->DataAs<std::uint8_t>()[i], 7);
+    }
+    for (std::size_t i = n * 2; i < n * 3; ++i) {
+      ASSERT_EQ(malloc_resource->DataAs<std::uint8_t>()[i], 3);
+    }
   };
   test_malloc_resize(true);
   test_malloc_resize(false);

tests/cpp/data/test_iterative_dmatrix.cc

@@ -12,8 +12,7 @@
 #include "../helpers.h"
 #include "xgboost/data.h"  // DMatrix
 
-namespace xgboost {
-namespace data {
+namespace xgboost::data {
 TEST(IterativeDMatrix, Ref) {
   Context ctx;
   TestRefDMatrix<GHistIndexMatrix, NumpyArrayIterForTest>(
@@ -21,7 +20,7 @@ TEST(IterativeDMatrix, Ref) {
 }
 
 TEST(IterativeDMatrix, IsDense) {
-  int n_bins = 16;
+  bst_bin_t n_bins = 16;
   auto test = [n_bins](float sparsity) {
     NumpyArrayIterForTest iter(sparsity);
     auto n_threads = 0;
@@ -38,5 +37,4 @@ TEST(IterativeDMatrix, IsDense) {
   test(0.1);
   test(1.0);
 }
-}  // namespace data
-}  // namespace xgboost
+}  // namespace xgboost::data

tests/python/test_data_iterator.py

@@ -1,4 +1,5 @@
-from typing import Callable, Dict, List
+import weakref
+from typing import Any, Callable, Dict, List
 
 import numpy as np
 import pytest
@@ -179,5 +180,18 @@ def test_data_cache() -> None:
     data = make_batches(n_samples_per_batch, n_features, n_batches, False)
     batches = [v[0] for v in data]
     it = IterForCacheTest(*batches)
+    transform = xgb.data._proxy_transform
+
+    called = 0
+
+    def mock(*args: Any, **kwargs: Any) -> Any:
+        nonlocal called
+        called += 1
+        return transform(*args, **kwargs)
+
+    xgb.data._proxy_transform = mock
     xgb.QuantileDMatrix(it)
-    assert it._input_id == id(batches[0])
+    assert it._data_ref is weakref.ref(batches[0])
+    assert called == 1
+
+    xgb.data._proxy_transform = transform

tests/python/test_quantile_dmatrix.py

@@ -103,12 +103,29 @@ class TestQuantileDMatrix:
                 *make_batches_sparse(
                     n_samples_per_batch, n_features, n_batches, sparsity
                 ),
-                None
+                None,
             )
         Xy = xgb.QuantileDMatrix(it)
         assert Xy.num_row() == n_samples_per_batch * n_batches
         assert Xy.num_col() == n_features
 
+    def test_different_size(self) -> None:
+        n_samples_per_batch = 317
+        n_features = 8
+        n_batches = 7
+
+        it = IteratorForTest(
+            *make_batches(
+                n_samples_per_batch, n_features, n_batches, False, vary_size=True
+            ),
+            cache=None,
+        )
+        Xy = xgb.QuantileDMatrix(it)
+        assert Xy.num_row() == 2429
+        X, y, w = it.as_arrays()
+        Xy1 = xgb.QuantileDMatrix(X, y, weight=w)
+        assert predictor_equal(Xy, Xy1)
+
     @pytest.mark.parametrize("sparsity", [0.0, 0.1, 0.5, 0.8, 0.9])
     def test_training(self, sparsity: float) -> None:
         n_samples_per_batch = 317
@@ -123,7 +140,7 @@ class TestQuantileDMatrix:
                 *make_batches_sparse(
                     n_samples_per_batch, n_features, n_batches, sparsity
                 ),
-                None
+                None,
             )
 
         parameters = {"tree_method": "hist", "max_bin": 256}