Package: guix-patches;
Reported by: Vinicius Monego <monego <at> posteo.net>
Date: Wed, 12 May 2021 23:58:01 UTC
Severity: normal
Tags: patch
Done: Leo Famulari <leo <at> famulari.name>
Bug is archived. No further changes may be made.
View this message in rfc822 format
From: Vinicius Monego <monego <at> posteo.net> To: 48388 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [bug#48388] [PATCH 2/3] gnu: Add xgboost. Date: Wed, 12 May 2021 23:58:43 +0000
* gnu/packages/machine-learning.scm (xgboost): New variable.
---
gnu/local.mk | 2 +
gnu/packages/machine-learning.scm | 33 +++++++++
...xgboost-python-use-system-libxgboost.patch | 69 +++++++++++++++++++
.../xgboost-use-system-dmlc-core.patch | 35 ++++++++++
4 files changed, 139 insertions(+)
create mode 100644 gnu/packages/patches/xgboost-python-use-system-libxgboost.patch
create mode 100644 gnu/packages/patches/xgboost-use-system-dmlc-core.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index 37166bb2fc..e1d382c543 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1823,6 +1823,8 @@ dist_patch_DATA = \
%D%/packages/patches/xf86-video-voodoo-pcitag.patch \
%D%/packages/patches/xfce4-panel-plugins.patch \
%D%/packages/patches/xfce4-settings-defaults.patch \
+ %D%/packages/patches/xgboost-python-use-system-libxgboost.patch \
+ %D%/packages/patches/xgboost-use-system-dmlc-core.patch \
%D%/packages/patches/xmonad-dynamic-linking.patch \
%D%/packages/patches/xplanet-1.3.1-cxx11-eof.patch \
%D%/packages/patches/xplanet-1.3.1-libdisplay_DisplayOutput.cpp.patch \
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 9d6c5505f7..fd10de427f 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1959,6 +1959,39 @@ offers the bricks to build efficient and scalable distributed machine
learning libraries.")
(license license:asl2.0))))
+(define-public xgboost
+ (package
+ (name "xgboost")
+ (version "1.4.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dmlc/xgboost")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (patches (search-patches "xgboost-python-use-system-libxgboost.patch"
+ "xgboost-use-system-dmlc-core.patch"))
+ (sha256
+ (base32 "0ixacmpcj844c09xigi1vd4rrckld84k32iarvhnvvm6yjih756y"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:configure-flags (list "-DGOOGLE_TEST=ON")))
+ (native-inputs
+ `(("googletest" ,googletest)
+ ("python" ,python-wrapper)))
+ (inputs
+ `(("dmlc-core" ,dmlc-core)))
+ (home-page "https://xgboost.ai/")
+ (synopsis "Gradient boosting (GBDT, GBRT or GBM) library in C++")
+ (description
+ "XGBoost is an optimized distributed gradient boosting library designed
+to be highly efficient, flexible and portable. It implements machine learning
+algorithms under the Gradient Boosting framework. XGBoost provides a parallel
+tree boosting (also known as GBDT, GBM) that solve many data science problems
+in a fast and accurate way.")
+ (license license:asl2.0)))
+
(define-public python-iml
(package
(name "python-iml")
diff --git a/gnu/packages/patches/xgboost-python-use-system-libxgboost.patch b/gnu/packages/patches/xgboost-python-use-system-libxgboost.patch
new file mode 100644
index 0000000000..992e6bb3fd
--- /dev/null
+++ b/gnu/packages/patches/xgboost-python-use-system-libxgboost.patch
@@ -0,0 +1,69 @@
+From 768192b9c6700f0ae6b750c56b114d7022692a0b Mon Sep 17 00:00:00 2001
+From: Vinicius Monego <monego <at> posteo.net>
+Date: Tue, 11 May 2021 19:30:55 -0300
+Subject: [PATCH] Python wrapper: use system libxgboost.
+
+---
+This patch was extended from the following Debian patch: https://sources.debian.org/src/xgboost/1.2.1-1/debian/patches/setup.py.patch/
+
+ python-package/setup.py | 4 ++--
+ python-package/xgboost/__init__.py | 5 ++---
+ python-package/xgboost/libpath.py | 5 +++++
+ 3 files changed, 9 insertions(+), 5 deletions(-)
+
+diff --git a/python-package/setup.py b/python-package/setup.py
+index a2feb766..b8b78429 100644
+--- a/python-package/setup.py
++++ b/python-package/setup.py
+@@ -312,11 +312,11 @@ if __name__ == '__main__':
+ 'numpy',
+ 'scipy',
+ ],
+- ext_modules=[CMakeExtension('libxgboost')],
++ # ext_modules=[CMakeExtension('libxgboost')],
+ cmdclass={
+ 'build_ext': BuildExt,
+ 'sdist': Sdist,
+- 'install_lib': InstallLib,
++ # 'install_lib': InstallLib,
+ 'install': Install
+ },
+ extras_require={
+diff --git a/python-package/xgboost/__init__.py b/python-package/xgboost/__init__.py
+index e0ff434d..658e84e6 100644
+--- a/python-package/xgboost/__init__.py
++++ b/python-package/xgboost/__init__.py
+@@ -21,9 +21,8 @@ try:
+ except ImportError:
+ pass
+
+-VERSION_FILE = os.path.join(os.path.dirname(__file__), 'VERSION')
+-with open(VERSION_FILE) as f:
+- __version__ = f.read().strip()
++# This variable will be set during substitution.
++__version__ = ''
+
+ __all__ = ['DMatrix', 'DeviceQuantileDMatrix', 'Booster',
+ 'train', 'cv',
+diff --git a/python-package/xgboost/libpath.py b/python-package/xgboost/libpath.py
+index f7a7d9cd..88d9d986 100644
+--- a/python-package/xgboost/libpath.py
++++ b/python-package/xgboost/libpath.py
+@@ -19,9 +19,14 @@ def find_lib_path() -> List[str]:
+ lib_path
+ List of all found library path to xgboost
+ """
++
++ # This variable will be set during substitution.
++ XGBOOST_PATH = ''
++
+ curr_path = os.path.dirname(os.path.abspath(os.path.expanduser(__file__)))
+ dll_path = [
+ # normal, after installation `lib` is copied into Python package tree.
++ os.path.join(XGBOOST_PATH, 'lib'),
+ os.path.join(curr_path, 'lib'),
+ # editable installation, no copying is performed.
+ os.path.join(curr_path, os.path.pardir, os.path.pardir, 'lib'),
+--
+2.31.1
+
diff --git a/gnu/packages/patches/xgboost-use-system-dmlc-core.patch b/gnu/packages/patches/xgboost-use-system-dmlc-core.patch
new file mode 100644
index 0000000000..6209ae1f10
--- /dev/null
+++ b/gnu/packages/patches/xgboost-use-system-dmlc-core.patch
@@ -0,0 +1,35 @@
+From 34167cc105e47589b86b6f62da76e0ab744002dd Mon Sep 17 00:00:00 2001
+From: Vinicius Monego <monego <at> posteo.net>
+Date: Tue, 11 May 2021 19:35:30 -0300
+Subject: [PATCH] Use dmlc-core from Guix.
+
+---
+This patch is a subset from the following Debian patch: https://sources.debian.org/src/xgboost/1.2.1-1/debian/patches/cmake.patch/
+
+Rabit is now developed as part of xgboost, so we don't build it separately.
+
+ CMakeLists.txt | 8 +++-----
+ 1 file changed, 3 insertions(+), 5 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 6cc19fbd..3b42bc17 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -150,11 +150,9 @@ endif (USE_OPENMP)
+
+ # dmlc-core
+ msvc_use_static_runtime()
+-add_subdirectory(${xgboost_SOURCE_DIR}/dmlc-core)
+-set_target_properties(dmlc PROPERTIES
+- CXX_STANDARD 14
+- CXX_STANDARD_REQUIRED ON
+- POSITION_INDEPENDENT_CODE ON)
++add_library(dmlc SHARED IMPORTED)
++find_library(DMLC_LIBRARY dmlc)
++set_property(TARGET dmlc PROPERTY IMPORTED_LOCATION "${DMLC_LIBRARY}")
+ if (MSVC)
+ target_compile_options(dmlc PRIVATE
+ -D_CRT_SECURE_NO_WARNINGS -D_CRT_SECURE_NO_DEPRECATE)
+--
+2.31.1
+
--
2.31.1
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.