Enable Installation of Python Package with System lib in a Virtual Environment (#9349)

.github/workflows/python_tests.yml

@@ -255,3 +255,44 @@ jobs:
       shell: bash -l {0}
       run: |
         pytest -s -v -rxXs --durations=0 ./tests/test_distributed/test_with_spark
+
+  python-system-installation-on-ubuntu:
+    name: Test XGBoost Python package System Installation on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: 'true'
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.8
+
+      - name: Install ninja
+        run: |
+          sudo apt-get update && sudo apt-get install -y ninja-build
+
+      - name: Build XGBoost on Ubuntu
+        run: |
+          mkdir build
+          cd build
+          cmake .. -GNinja
+          ninja
+
+      - name: Copy lib to system lib
+        run: |
+          cp lib/* "$(python -c 'import sys; print(sys.base_prefix)')/lib"
+
+      - name: Install XGBoost in Virtual Environment
+        run: |
+          cd python-package
+          pip install virtualenv
+          virtualenv venv
+          source venv/bin/activate && \
+            pip install -v . --config-settings use_system_libxgboost=True && \
+            python -c 'import xgboost'

doc/build.rst

@@ -259,7 +259,7 @@ There are several ways to build and install the package from source:
 
     import sys
     import pathlib
-    libpath = pathlib.Path(sys.prefix).joinpath("lib", "libxgboost.so")
+    libpath = pathlib.Path(sys.base_prefix).joinpath("lib", "libxgboost.so")
     assert libpath.exists()
 
   Then pass ``use_system_libxgboost=True`` option to ``pip install``:

python-package/packager/nativelib.py

@@ -132,8 +132,8 @@ def locate_or_build_libxgboost(
 
     if build_config.use_system_libxgboost:
         # Find libxgboost from system prefix
-        sys_prefix = pathlib.Path(sys.prefix).absolute().resolve()
-        libxgboost_sys = sys_prefix / "lib" / _lib_name()
+        sys_base_prefix = pathlib.Path(sys.base_prefix).absolute().resolve()
+        libxgboost_sys = sys_base_prefix / "lib" / _lib_name()
         if not libxgboost_sys.exists():
             raise RuntimeError(
                 f"use_system_libxgboost was specified but {_lib_name()} is "

python-package/xgboost/libpath.py

@@ -27,7 +27,7 @@ def find_lib_path() -> List[str]:
         os.path.join(curr_path, os.path.pardir, os.path.pardir, "lib"),
         # use libxgboost from a system prefix, if available.  This should be the last
         # option.
-        os.path.join(sys.prefix, "lib"),
+        os.path.join(sys.base_prefix, "lib"),
     ]
 
     if sys.platform == "win32":
@@ -62,8 +62,8 @@ def find_lib_path() -> List[str]:
             + ("\n- ".join(dll_path))
             + "\nXGBoost Python package path: "
             + curr_path
-            + "\nsys.prefix: "
-            + sys.prefix
+            + "\nsys.base_prefix: "
+            + sys.base_prefix
             + "\nSee: "
             + link
             + " for installing XGBoost."