XGBoost: Fix type mismatch for CSR conversion in c_api (#3194)

docs/project/changelog.md

@@ -98,6 +98,9 @@ substitutions:
 - {{ Fix }} Shared libraries with version suffix are now handled correctly.
   {pr}`3154`
 
+- {{ Fix }} Scipy CSR data is now handled correctly in XGBoost.
+  {pr}`3194`
+
 - Added a new CLI command `pyodide sekeleton` which creates a package build recipe.
   `pyodide-build mkpkg` will be replaced by `pyodide sekeleton pypi`.
   {pr}`3175`

packages/xgboost/meta.yaml

@@ -9,6 +9,7 @@ source:
   patches:
     - patches/0001-Add-missing-template-type.patch
     - patches/0002-Add-library-loading-path.patch
+    - patches/0003-Fix-type-mismatch-for-CSR-conversion-in-c_api.patch
 build:
   cflags: |
     -DDMLC_USE_FOPEN64=0

packages/xgboost/patches/0001-Add-missing-template-type.patch

@@ -1,7 +1,7 @@
 From 4ac9a00d9e16b0879b4e734a4b604c7ce672894e Mon Sep 17 00:00:00 2001
 From: Gyeongjae Choi <def6488@gmail.com>
 Date: Mon, 9 May 2022 06:42:07 +0000
-Subject: [PATCH 1/2] Add missing template type
+Subject: [PATCH 1/3] Add missing template type
 
 TODO: Remove this patch when XGBoost version is updated.
 (Upstream PR: https://github.com/dmlc/xgboost/pull/7954)

packages/xgboost/patches/0002-Add-library-loading-path.patch

@@ -1,7 +1,7 @@
 From 54c2a9faeb0b0169172c5ab53367e6092f132c5a Mon Sep 17 00:00:00 2001
 From: Gyeongjae Choi <def6488@gmail.com>
 Date: Mon, 9 May 2022 12:07:44 +0000
-Subject: [PATCH 2/2] Add library loading path
+Subject: [PATCH 2/3] Add library loading path
 
 TODO: Remove this patch when XGBoost version is updated.
 (Upstream PR: https://github.com/dmlc/xgboost/pull/7954)

packages/xgboost/patches/0003-Fix-type-mismatch-for-CSR-conversion-in-c_api.patch

@@ -0,0 +1,42 @@
+From 4ec1b506b424dd9e81fd7127f5712522800a5596 Mon Sep 17 00:00:00 2001
+From: Yizhi Liu <liuyizhi@apache.org>
+Date: Mon, 17 Oct 2022 15:16:45 -0700
+Subject: [PATCH 3/3] Fix type mismatch for CSR conversion in c_api
+
+TODO: Remove this patch when XGBoost version is updated.
+(Upstream PR: https://github.com/dmlc/xgboost/pull/8369)
+
+---
+ xgboost/core.py | 2 +-
+ xgboost/data.py | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/xgboost/core.py b/xgboost/core.py
+index 36548d8..0246779 100644
+--- a/xgboost/core.py
++++ b/xgboost/core.py
+@@ -2119,7 +2119,7 @@ class Booster:
+                     _array_interface(csr.indptr),
+                     _array_interface(csr.indices),
+                     _array_interface(csr.data),
+-                    ctypes.c_size_t(csr.shape[1]),
++                    c_bst_ulong(csr.shape[1]),
+                     from_pystr_to_cstr(json.dumps(args)),
+                     p_handle,
+                     ctypes.byref(shape),
+diff --git a/xgboost/data.py b/xgboost/data.py
+index 119b354..b958436 100644
+--- a/xgboost/data.py
++++ b/xgboost/data.py
+@@ -88,7 +88,7 @@ def _from_scipy_csr(
+             _array_interface(data.indptr),
+             _array_interface(data.indices),
+             _array_interface(data.data),
+-            ctypes.c_size_t(data.shape[1]),
++            c_bst_ulong(data.shape[1]),
+             config,
+             ctypes.byref(handle),
+         )
+-- 
+2.35.1
+

packages/xgboost/test_xgboost.py

@@ -319,3 +319,21 @@ def test_pandas_weight(selenium):
     assert data.num_col() == kCols
 
     np.testing.assert_array_equal(data.get_weight(), w)
+
+
+@pytest.mark.driver_timeout(60)
+@run_in_pyodide(packages=["xgboost", "numpy", "scipy"])
+def test_scipy_sparse(selenium):
+    import numpy as np
+    import scipy
+    import xgboost as xgb
+
+    n_rows = 100
+    n_cols = 10
+    X = scipy.sparse.random(n_rows, n_cols, format="csr")
+    y = np.random.randn(n_rows)
+    dtrain = xgb.DMatrix(X, y)
+    booster = xgb.train({}, dtrain, num_boost_round=1)
+    copied_predt = booster.predict(xgb.DMatrix(X))
+    predt = booster.inplace_predict(X)
+    np.testing.assert_allclose(copied_predt, predt)