[PATCH 0/3] Update LightGBM and split frontends.

+++ b/gnu/packages/cpp.scm

+;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>

+(define-public fast-double-parser

+  (package

+    (name "fast-double-parser")

+    (version "0.5.0")

+    (source

+     (origin

+       (method git-fetch)

+       (uri (git-reference

+             (url "https://github.com/lemire/fast_double_parser")

+             (commit (string-append "v" version))))

+       (file-name (git-file-name name version))

+       (sha256

+        (base32 "10mfpy4i7lpavghb15s4d0920nlwsac1ri2sxkcqbrj9iq94qj71"))))

+    (build-system cmake-build-system)

+    (arguments

+     `(#:phases

+       (modify-phases %standard-phases

+         (replace 'install ;no install target, have to do it manually

+           (lambda* (#:key outputs #:allow-other-keys)

+             (let ((out-include (string-append (assoc-ref outputs "out")

+                                               "/include")))

+               (mkdir-p out-include)

+               (copy-file "../source/include/fast_double_parser.h"

+                          (string-append out-include

+                                         "/fast_double_parser.h"))))))))

+    (home-page "https://github.com/lemire/fast_double_parser")

+    (synopsis "Parse strings into double (binary64) floating-point values")

+    (description "Fast function to parse strings containing decimal numbers

+into double-precision (binary64) floating-point values.  That is, given the

+string \"1.0e10\", it should return a 64-bit floating-point value equal to

+10000000000.  The function will match exactly (down the smallest bit) the

+result of a standard function like @code{strtod}.")

+    ;; Dual-licensed, either license applies.

+    (license (list license:asl2.0

+                   license:boost1.0))))

+

+++ b/gnu/local.mk

+  %D%/packages/patches/lightgbm-python-use-system-lib-lightgbm.patch \

+  %D%/packages/patches/lightgbm-use-system-libraries.patch	\

+++ b/gnu/packages/machine-learning.scm

+  #:use-module (gnu packages cpp)

+  #:use-module (gnu packages opencl)

+  #:use-module (gnu packages pretty-print)

+    (version "3.2.1")

+    (source

+     (origin

+       (method git-fetch)

+       (uri (git-reference

+             (url "https://github.com/Microsoft/LightGBM")

+             (commit (string-append "v" version))))

+       (patches

+        (search-patches "lightgbm-use-system-libraries.patch"

+                        "lightgbm-python-use-system-lib-lightgbm.patch"))

+       (sha256

+        (base32 "1fchiiwl3pz1kpi0kbfanif6c6b688wmmjjbqz4ff4djc6g2sg7z"))

+       (file-name (git-file-name name version))))

+     `(("googletest" ,googletest)

+       ("opencl-headers" ,opencl-headers)))

+     `(("boost" ,boost)

+       ("eigen" ,eigen)

+       ("fast-double-parser" ,fast-double-parser)

+       ("fmt" ,fmt)

+       ("ocl-icd" ,ocl-icd)

+       ("openmpi" ,openmpi)))

+     `(;; FIXME: With 'find_package(GTest CONFIG)' (default), googletest

+       ;; is not found by CMake.  If we replace CONFIG with REQUIRED, the

+       ;; test files fail to link with googletest in the build phase.

+       #:tests? #f

+       #:test-target "testlightgbm"

+       #:configure-flags

+       (list "-DBUILD_CPP_TEST=OFF"

+             "-DUSE_GPU=ON" ;using OpenCL

+             "-DUSE_MPI=ON")))

+++ b/gnu/packages/patches/lightgbm-python-use-system-lib-lightgbm.patch

+From c73be84d8ec6ac71dfdaa71b7943ae344f5d7cde Mon Sep 17 00:00:00 2001

+From: Vinicius Monego <monego@posteo.net>

+Date: Tue, 1 Jun 2021 00:24:38 -0300

+Subject: [PATCH] Use system lib_lightgbm.

+

+---

+ python-package/lightgbm/libpath.py |  4 ++++

+ python-package/setup.py            | 12 ++++++++----

+ 2 files changed, 12 insertions(+), 4 deletions(-)

+

+diff --git a/python-package/lightgbm/libpath.py b/python-package/lightgbm/libpath.py

+index 6533792..27af2b9 100644

+--- a/python-package/lightgbm/libpath.py

++++ b/python-package/lightgbm/libpath.py

+@@ -17,8 +17,12 @@ def find_lib_path() -> List[str]:

+         # we don't need lib_lightgbm while building docs

+         return []

+ 

++    # This variable will be set during substitution.

++    lib_lightgbm_path = ''

++

+     curr_path = os.path.dirname(os.path.abspath(os.path.expanduser(__file__)))

+     dll_path = [curr_path,

++                lib_lightgbm_path,

+                 os.path.join(curr_path, '../../'),

+                 os.path.join(curr_path, 'compile'),

+                 os.path.join(curr_path, '../compile'),

+diff --git a/python-package/setup.py b/python-package/setup.py

+index ee98b1a..2f7ce38 100644

+--- a/python-package/setup.py

++++ b/python-package/setup.py

+@@ -231,7 +231,7 @@ class CustomInstall(install):

+         self.opencl_library = None

+         self.mpi = 0

+         self.hdfs = 0

+-        self.precompile = 0

++        self.precompile = 1

+         self.nomp = 0

+         self.bit32 = 0

+ 

+@@ -274,7 +274,7 @@ class CustomBdistWheel(bdist_wheel):

+         self.opencl_library = None

+         self.mpi = 0

+         self.hdfs = 0

+-        self.precompile = 0

++        self.precompile = 1

+         self.nomp = 0

+         self.bit32 = 0

+ 

+@@ -324,7 +324,10 @@ if __name__ == "__main__":

+         copy_file(os.path.join(CURRENT_DIR, os.path.pardir, 'VERSION.txt'),

+                   os.path.join(CURRENT_DIR, 'lightgbm', 'VERSION.txt'),

+                   verbose=0)  # type:ignore

+-    version = open(os.path.join(CURRENT_DIR, 'lightgbm', 'VERSION.txt'), encoding='utf-8').read().strip()

++

++    # This variable will be set during substitution.

++    version = ''

++

+     readme = open(os.path.join(CURRENT_DIR, 'README.rst'), encoding='utf-8').read()

+ 

+     sys.path.insert(0, CURRENT_DIR)

+@@ -355,7 +358,8 @@ if __name__ == "__main__":

+           zip_safe=False,

+           cmdclass={

+               'install': CustomInstall,

+-              'install_lib': CustomInstallLib,

++              # Lib will be loaded from the lightgbm package.

++              # 'install_lib': CustomInstallLib,

+               'bdist_wheel': CustomBdistWheel,

+               'sdist': CustomSdist,

+           },

+-- 

+2.31.1

+

+++ b/gnu/packages/patches/lightgbm-use-system-libraries.patch

+From 894648291b9629d51785e4fd1cae820d2858e039 Mon Sep 17 00:00:00 2001

+From: Vinicius Monego <monego@posteo.net>

+Date: Mon, 31 May 2021 21:23:52 -0300

+Subject: [PATCH] Use system libraries.

+

+---

+ CMakeLists.txt                  | 11 ++++++++---

+ include/LightGBM/utils/common.h |  4 ++--

+ 2 files changed, 10 insertions(+), 5 deletions(-)

+

+diff --git a/CMakeLists.txt b/CMakeLists.txt

+index b845f36..560e477 100644

+--- a/CMakeLists.txt

++++ b/CMakeLists.txt

+@@ -93,9 +93,6 @@ if(USE_SWIG)

+   endif()

+ endif(USE_SWIG)

+ 

+-SET(EIGEN_DIR "${PROJECT_SOURCE_DIR}/external_libs/eigen")

+-include_directories(${EIGEN_DIR})

+-

+ # See https://gitlab.com/libeigen/eigen/-/blob/master/COPYING.README

+ ADD_DEFINITIONS(-DEIGEN_MPL2_ONLY)

+ 

+@@ -399,6 +396,14 @@ if(USE_SWIG)

+   endif()

+ endif(USE_SWIG)

+ 

++find_package (Eigen3 3.3 REQUIRED NO_MODULE)

++TARGET_LINK_LIBRARIES (lightgbm Eigen3::Eigen)

++TARGET_LINK_LIBRARIES (_lightgbm Eigen3::Eigen)

++

++find_package(fmt)

++TARGET_LINK_LIBRARIES(lightgbm fmt::fmt)

++TARGET_LINK_LIBRARIES(_lightgbm fmt::fmt)

++

+ if(USE_MPI)

+   TARGET_LINK_LIBRARIES(lightgbm ${MPI_CXX_LIBRARIES})

+   TARGET_LINK_LIBRARIES(_lightgbm ${MPI_CXX_LIBRARIES})

+diff --git a/include/LightGBM/utils/common.h b/include/LightGBM/utils/common.h

+index 4357357..00101a5 100644

+--- a/include/LightGBM/utils/common.h

++++ b/include/LightGBM/utils/common.h

+@@ -32,9 +32,9 @@

+ 

+ #if (!((defined(sun) || defined(__sun)) && (defined(__SVR4) || defined(__svr4__))))

+ #define FMT_HEADER_ONLY

+-#include "../../../external_libs/fmt/include/fmt/format.h"

++#include "fmt/format.h"

+ #endif

+-#include "../../../external_libs/fast_double_parser/include/fast_double_parser.h"

++#include "fast_double_parser.h"

+ 

+ #ifdef _MSC_VER

+ #include <intrin.h>

+-- 

+2.31.1

+

+++ b/gnu/packages/machine-learning.scm

+(define-public python-lightgbm

+  (package

+    (inherit lightgbm)

+    (name "python-lightgbm")

+    (build-system python-build-system)

+    (arguments

+     `(#:phases

+       (modify-phases %standard-phases

+         (add-after 'unpack 'preparations

+           (lambda* (#:key inputs #:allow-other-keys)

+             (setenv "HOME" "/tmp") ;to write a log file

+             ;; Move Python files to source root to silence some warnings.

+             (rename-file "python-package/setup.py" "setup.py")

+             (rename-file "python-package/README.rst" "README.rst")

+             (rename-file "python-package/lightgbm" "lightgbm")

+             (substitute* "setup.py"

+               (("version = ''")

+                (string-append "version = " "'"

+                               ,(package-version lightgbm) "'")))

+             (substitute* "lightgbm/libpath.py"

+               (("lib_lightgbm_path = ''")

+                (string-append "lib_lightgbm_path = " "'"

+                               (assoc-ref inputs "lightgbm")

+                               "/lib" "'")))))

+         (replace 'check

+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)

+             (when tests?

+               (add-installed-pythonpath inputs outputs)

+               (invoke "python" "-m" "pytest"

+                       "tests/python_package_test")))))))

+    (native-inputs

+     `(("python-psutil" ,python-psutil)

+       ("python-pytest" ,python-pytest)

+       ("python-wheel" ,python-wheel)))

+    (inputs

+     `(("lightgbm" ,lightgbm)))

+    (propagated-inputs

+     `(("python-numpy" ,python-numpy)

+       ("python-pandas" ,python-pandas)

+       ("python-scipy" ,python-scipy)

+       ("python-scikit-learn" ,python-scikit-learn)))

+    (synopsis "Python frontend for LightGBM")))

+

+++ b/gnu/local.mk

+  %D%/packages/patches/lightgbm-use-system-libraries.patch	\

+++ b/gnu/packages/machine-learning.scm

+  #:use-module (gnu packages cpp)

+  #:use-module (gnu packages opencl)

+  #:use-module (gnu packages pretty-print)

+    (version "3.2.1")

+    (source

+     (origin

+       (method git-fetch)

+       (uri (git-reference

+             (url "https://github.com/Microsoft/LightGBM")

+             (commit (string-append "v" version))))

+       (patches

+        (search-patches "lightgbm-use-system-libraries.patch"))

+       (sha256

+        (base32 "1fchiiwl3pz1kpi0kbfanif6c6b688wmmjjbqz4ff4djc6g2sg7z"))

+       (file-name (git-file-name name version))))

+     `(("googletest" ,googletest)

+       ("opencl-headers" ,opencl-headers)))

+     `(("boost" ,boost)

+       ("eigen" ,eigen)

+       ("fast-double-parser" ,fast-double-parser)

+       ("fmt" ,fmt)

+       ("ocl-icd" ,ocl-icd)

+       ("openmpi" ,openmpi)))

+     `(;; FIXME: With 'find_package(GTest CONFIG)' (default), googletest

+       ;; is not found by CMake.  If we replace CONFIG with REQUIRED, the

+       ;; test files fail to link with googletest in the build phase.

+       #:tests? #f

+       #:test-target "testlightgbm"

+       #:configure-flags

+       (list "-DBUILD_CPP_TEST=OFF"

+             "-DUSE_GPU=ON" ;using OpenCL

+             "-DUSE_MPI=ON")))

+++ b/gnu/packages/patches/lightgbm-use-system-libraries.patch

+From 894648291b9629d51785e4fd1cae820d2858e039 Mon Sep 17 00:00:00 2001

+From: Vinicius Monego <monego@posteo.net>

+Date: Mon, 31 May 2021 21:23:52 -0300

+Subject: [PATCH] Use system libraries.

+

+---

+ CMakeLists.txt                  | 11 ++++++++---

+ include/LightGBM/utils/common.h |  4 ++--

+ 2 files changed, 10 insertions(+), 5 deletions(-)

+

+diff --git a/CMakeLists.txt b/CMakeLists.txt

+index b845f36..560e477 100644

+--- a/CMakeLists.txt

++++ b/CMakeLists.txt

+@@ -93,9 +93,6 @@ if(USE_SWIG)

+   endif()

+ endif(USE_SWIG)

+ 

+-SET(EIGEN_DIR "${PROJECT_SOURCE_DIR}/external_libs/eigen")

+-include_directories(${EIGEN_DIR})

+-

+ # See https://gitlab.com/libeigen/eigen/-/blob/master/COPYING.README

+ ADD_DEFINITIONS(-DEIGEN_MPL2_ONLY)

+ 

+@@ -399,6 +396,14 @@ if(USE_SWIG)

+   endif()

+ endif(USE_SWIG)

+ 

++find_package (Eigen3 3.3 REQUIRED NO_MODULE)

++TARGET_LINK_LIBRARIES (lightgbm Eigen3::Eigen)

++TARGET_LINK_LIBRARIES (_lightgbm Eigen3::Eigen)

++

++find_package(fmt)

++TARGET_LINK_LIBRARIES(lightgbm fmt::fmt)

++TARGET_LINK_LIBRARIES(_lightgbm fmt::fmt)

++

+ if(USE_MPI)

+   TARGET_LINK_LIBRARIES(lightgbm ${MPI_CXX_LIBRARIES})

+   TARGET_LINK_LIBRARIES(_lightgbm ${MPI_CXX_LIBRARIES})

+diff --git a/include/LightGBM/utils/common.h b/include/LightGBM/utils/common.h

+index 4357357..00101a5 100644

+--- a/include/LightGBM/utils/common.h

++++ b/include/LightGBM/utils/common.h

+@@ -32,9 +32,9 @@

+ 

+ #if (!((defined(sun) || defined(__sun)) && (defined(__SVR4) || defined(__svr4__))))

+ #define FMT_HEADER_ONLY

+-#include "../../../external_libs/fmt/include/fmt/format.h"

++#include "fmt/format.h"

+ #endif

+-#include "../../../external_libs/fast_double_parser/include/fast_double_parser.h"

++#include "fast_double_parser.h"

+ 

+ #ifdef _MSC_VER

+ #include <intrin.h>

+-- 

+2.31.1

+

+++ b/gnu/packages/cpp.scm

+;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>

+(define-public fast-double-parser

+  (package

+    (name "fast-double-parser")

+    (version "0.5.0")

+    (source

+     (origin

+       (method git-fetch)

+       (uri (git-reference

+             (url "https://github.com/lemire/fast_double_parser")

+             (commit (string-append "v" version))))

+       (file-name (git-file-name name version))

+       (sha256

+        (base32 "10mfpy4i7lpavghb15s4d0920nlwsac1ri2sxkcqbrj9iq94qj71"))))

+    (build-system cmake-build-system)

+    (arguments

+     `(#:phases

+       (modify-phases %standard-phases

+         (replace 'install ;no install target, have to do it manually

+           (lambda* (#:key outputs #:allow-other-keys)

+             (let ((out-include (string-append (assoc-ref outputs "out")

+                                               "/include")))

+               (mkdir-p out-include)

+               (copy-file "../source/include/fast_double_parser.h"

+                          (string-append out-include

+                                         "/fast_double_parser.h"))))))))

+    (home-page "https://github.com/lemire/fast_double_parser")

+    (synopsis "Parse strings into double (binary64) floating-point values")

+    (description "Fast function to parse strings containing decimal numbers

+into double-precision (binary64) floating-point values.  That is, given the

+string \"1.0e10\", it should return a 64-bit floating-point value equal to

+10000000000.  The function will match exactly (down the smallest bit) the

+result of a standard function like @code{strtod}.")

+    ;; Dual-licensed, either license applies.

+    (license (list license:asl2.0

+                   license:boost1.0))))

+

+++ b/gnu/packages/machine-learning.scm

+(define-public python-lightgbm

+  (package

+    (inherit lightgbm)

+    (name "python-lightgbm")

+    (source (package-source lightgbm))

+    (build-system python-build-system)

+    (arguments

+     `(#:configure-flags (list "--precompile")

+       #:phases

+       (modify-phases %standard-phases

+         (add-after 'unpack 'preparations

+           (lambda _

+             (setenv "HOME" "/tmp") ;to write a log file

+             ;; Move Python files to source root to silence some warnings.

+             (rename-file "python-package/setup.py" "setup.py")

+             (rename-file "python-package/README.rst" "README.rst")

+             (rename-file "python-package/lightgbm" "lightgbm")

+             ;; Install version file to read the library's version.

+             (with-output-to-file "lightgbm/VERSION.txt"

+               (lambda ()

+                 (display ,(package-version lightgbm))))

+             ;; Skip building the shared library.

+             (substitute* "setup.py"

+               (("'install_lib': CustomInstallLib,") ""))))

+         (add-after 'install 'install-liblightgbm

+           (lambda* (#:key inputs outputs #:allow-other-keys)

+             (let* ((out (assoc-ref outputs "out"))

+                    (pylib (string-append out "/lib/python"

+                                          ,(version-major+minor

+                                            (package-version python))

+                                          "/site-packages"))

+                    (lgbdir (string-append pylib "/lightgbm"))

+                    (lib-lightgbm (string-append (assoc-ref inputs "lightgbm")

+                                                 "/lib/lib_lightgbm.so")))

+               ;; This symlink is necessary for tests.

+               (symlink lib-lightgbm "lightgbm/lib_lightgbm.so")

+               ;; And this one for runtime.

+               (mkdir-p (string-append lgbdir "/lib"))

+               (symlink lib-lightgbm (string-append lgbdir

+                                                    "/lib_lightgbm.so")))))

+         (replace 'check

+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)

+             (when tests?

+               (add-installed-pythonpath inputs outputs)

+               (invoke "python" "-m" "pytest"

+                       "tests/python_package_test")))))))

+    (native-inputs

+     `(("python-psutil" ,python-psutil)

+       ("python-pytest" ,python-pytest)

+       ("python-wheel" ,python-wheel)))

+    (inputs

+     `(("lightgbm" ,lightgbm)))

+    (propagated-inputs

+     `(("python-numpy" ,python-numpy)

+       ("python-pandas" ,python-pandas)

+       ("python-scipy" ,python-scipy)

+       ("python-scikit-learn" ,python-scikit-learn)))

+    (synopsis "Python frontend for LightGBM")))

+

+++ b/gnu/packages/cpp.scm

+;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>

+(define-public fast-double-parser

+  (package

+    (name "fast-double-parser")

+    (version "0.5.0")

+    (source

+     (origin

+       (method git-fetch)

+       (uri (git-reference

+             (url "https://github.com/lemire/fast_double_parser")

+             (commit (string-append "v" version))))

+       (file-name (git-file-name name version))

+       (sha256

+        (base32 "10mfpy4i7lpavghb15s4d0920nlwsac1ri2sxkcqbrj9iq94qj71"))))

+    (build-system cmake-build-system)

+    (arguments

+     `(#:phases

+       (modify-phases %standard-phases

+         (replace 'install ;no install target, have to do it manually

+           (lambda* (#:key outputs #:allow-other-keys)

+             (let ((out-include (string-append (assoc-ref outputs "out")

+                                               "/include")))

+               (mkdir-p out-include)

+               (copy-file "../source/include/fast_double_parser.h"

+                          (string-append out-include

+                                         "/fast_double_parser.h"))))))))

+    (home-page "https://github.com/lemire/fast_double_parser")

+    (synopsis "Parse strings into double (binary64) floating-point values")

+    (description "Fast function to parse strings containing decimal numbers

+into double-precision (binary64) floating-point values.  That is, given the

+string @code{1.0e10}, it should return a 64-bit floating-point value equal to

+10000000000.  The function will match exactly (down the smallest bit) the

+result of a standard function like @code{strtod}.")

+    ;; Dual-licensed, either license applies.

+    (license (list license:asl2.0

+                   license:boost1.0))))

+

+++ b/gnu/local.mk

+  %D%/packages/patches/lightgbm-use-system-libraries.patch	\

+++ b/gnu/packages/machine-learning.scm

+  #:use-module (gnu packages opencl)

+  #:use-module (gnu packages pretty-print)

+    (version "3.2.1")

+    (source

+     (origin

+       (method git-fetch)

+       (uri (git-reference

+             (url "https://github.com/Microsoft/LightGBM")

+             (commit (string-append "v" version))))

+       (patches

+        (search-patches "lightgbm-use-system-libraries.patch"))

+       (sha256

+        (base32 "1fchiiwl3pz1kpi0kbfanif6c6b688wmmjjbqz4ff4djc6g2sg7z"))

+       (file-name (git-file-name name version))))

+     `(("googletest" ,googletest)

+       ("opencl-headers" ,opencl-headers)))

+     `(("boost" ,boost)

+       ("eigen" ,eigen)

+       ("fast-double-parser" ,fast-double-parser)

+       ("fmt" ,fmt)

+       ("ocl-icd" ,ocl-icd)

+       ("openmpi" ,openmpi)))

+     `(;; FIXME: With 'find_package(GTest CONFIG)' (default), googletest

+       ;; is not found by CMake.  If we replace CONFIG with REQUIRED, the

+       ;; test files fail to link with googletest in the build phase.

+       #:tests? #f

+       #:test-target "testlightgbm"

+       #:configure-flags

+       (list "-DBUILD_CPP_TEST=OFF"

+             "-DUSE_GPU=ON" ;using OpenCL

+             "-DUSE_MPI=ON")))

+++ b/gnu/packages/patches/lightgbm-use-system-libraries.patch

+From 894648291b9629d51785e4fd1cae820d2858e039 Mon Sep 17 00:00:00 2001

+From: Vinicius Monego <monego@posteo.net>

+Date: Mon, 31 May 2021 21:23:52 -0300

+Subject: [PATCH] Use system libraries.

+

+---

+ CMakeLists.txt                  | 11 ++++++++---

+ include/LightGBM/utils/common.h |  4 ++--

+ 2 files changed, 10 insertions(+), 5 deletions(-)

+

+diff --git a/CMakeLists.txt b/CMakeLists.txt

+index b845f36..560e477 100644

+--- a/CMakeLists.txt

++++ b/CMakeLists.txt

+@@ -93,9 +93,6 @@ if(USE_SWIG)

+   endif()

+ endif(USE_SWIG)

+ 

+-SET(EIGEN_DIR "${PROJECT_SOURCE_DIR}/external_libs/eigen")

+-include_directories(${EIGEN_DIR})

+-

+ # See https://gitlab.com/libeigen/eigen/-/blob/master/COPYING.README

+ ADD_DEFINITIONS(-DEIGEN_MPL2_ONLY)

+ 

+@@ -399,6 +396,14 @@ if(USE_SWIG)

+   endif()

+ endif(USE_SWIG)

+ 

++find_package (Eigen3 3.3 REQUIRED NO_MODULE)

++TARGET_LINK_LIBRARIES (lightgbm Eigen3::Eigen)

++TARGET_LINK_LIBRARIES (_lightgbm Eigen3::Eigen)

++

++find_package(fmt)

++TARGET_LINK_LIBRARIES(lightgbm fmt::fmt)

++TARGET_LINK_LIBRARIES(_lightgbm fmt::fmt)

++

+ if(USE_MPI)

+   TARGET_LINK_LIBRARIES(lightgbm ${MPI_CXX_LIBRARIES})

+   TARGET_LINK_LIBRARIES(_lightgbm ${MPI_CXX_LIBRARIES})

+diff --git a/include/LightGBM/utils/common.h b/include/LightGBM/utils/common.h

+index 4357357..00101a5 100644

+--- a/include/LightGBM/utils/common.h

++++ b/include/LightGBM/utils/common.h

+@@ -32,9 +32,9 @@

+ 

+ #if (!((defined(sun) || defined(__sun)) && (defined(__SVR4) || defined(__svr4__))))

+ #define FMT_HEADER_ONLY

+-#include "../../../external_libs/fmt/include/fmt/format.h"

++#include "fmt/format.h"

+ #endif

+-#include "../../../external_libs/fast_double_parser/include/fast_double_parser.h"

++#include "fast_double_parser.h"

+ 

+ #ifdef _MSC_VER

+ #include <intrin.h>

+-- 

+2.31.1

+

+++ b/gnu/packages/machine-learning.scm

+(define-public python-lightgbm

+  (package

+    (inherit lightgbm)

+    (name "python-lightgbm")

+    (source (package-source lightgbm))

+    (build-system python-build-system)

+    (arguments

+     `(#:configure-flags (list "--precompile")

+       #:phases

+       (modify-phases %standard-phases

+         (add-after 'unpack 'preparations

+           (lambda _

+             (setenv "HOME" "/tmp") ;to write a log file

+             ;; Move Python files to source root to silence some warnings.

+             (rename-file "python-package/setup.py" "setup.py")

+             (rename-file "python-package/README.rst" "README.rst")

+             (rename-file "python-package/lightgbm" "lightgbm")

+             ;; Install version file to read the library's version.

+             (with-output-to-file "lightgbm/VERSION.txt"

+               (lambda ()

+                 (display ,(package-version lightgbm))))

+             ;; Skip building the shared library.

+             (substitute* "setup.py"

+               (("'install_lib': CustomInstallLib,") ""))))

+         (add-after 'install 'install-liblightgbm

+           (lambda* (#:key inputs outputs #:allow-other-keys)

+             (let* ((out (assoc-ref outputs "out"))

+                    (pylib (string-append out "/lib/python"

+                                          ,(version-major+minor

+                                            (package-version python))

+                                          "/site-packages"))

+                    (lgbdir (string-append pylib "/lightgbm"))

+                    (lib-lightgbm (string-append (assoc-ref inputs "lightgbm")

+                                                 "/lib/lib_lightgbm.so")))

+               ;; This symlink is necessary for tests.

+               (symlink lib-lightgbm "lightgbm/lib_lightgbm.so")

+               ;; And this one for runtime.

+               (mkdir-p (string-append lgbdir "/lib"))

+               (symlink lib-lightgbm (string-append lgbdir

+                                                    "/lib_lightgbm.so")))))

+         (replace 'check

+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)

+             (when tests?

+               (add-installed-pythonpath inputs outputs)

+               (invoke "python" "-m" "pytest"

+                       "tests/python_package_test")))))))

+    (native-inputs

+     `(("python-psutil" ,python-psutil)

+       ("python-pytest" ,python-pytest)

+       ("python-wheel" ,python-wheel)))

+    (inputs

+     `(("lightgbm" ,lightgbm)))

+    (propagated-inputs

+     `(("python-numpy" ,python-numpy)

+       ("python-pandas" ,python-pandas)

+       ("python-scikit-learn" ,python-scikit-learn)

+       ("python-scipy" ,python-scipy)))

+    (synopsis "Python frontend for LightGBM")))

+

+++ b/gnu/packages/cpp.scm

+;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>

+(define-public fast-double-parser

+  (package

+    (name "fast-double-parser")

+    (version "0.5.0")

+    (source

+     (origin

+       (method git-fetch)

+       (uri (git-reference

+             (url "https://github.com/lemire/fast_double_parser")

+             (commit (string-append "v" version))))

+       (file-name (git-file-name name version))

+       (sha256

+        (base32 "10mfpy4i7lpavghb15s4d0920nlwsac1ri2sxkcqbrj9iq94qj71"))))

+    (build-system cmake-build-system)

+    (arguments

+     `(#:phases

+       (modify-phases %standard-phases

+         (replace 'install ;no install target, have to do it manually

+           (lambda* (#:key outputs #:allow-other-keys)

+             (let ((out-include (string-append (assoc-ref outputs "out")

+                                               "/include")))

+               (mkdir-p out-include)

+               (copy-file "../source/include/fast_double_parser.h"

+                          (string-append out-include

+                                         "/fast_double_parser.h"))))))))

+    (home-page "https://github.com/lemire/fast_double_parser")

+    (synopsis "Parse strings into double (binary64) floating-point values")

+    (description "Fast function to parse strings containing decimal numbers

+into double-precision (binary64) floating-point values.  That is, given the

+string @code{1.0e10}, it should return a 64-bit floating-point value equal to

+10000000000.  The function will match exactly (down the smallest bit) the

+result of a standard function like @code{strtod}.")

+    ;; Dual-licensed, either license applies.

+    (license (list license:asl2.0

+                   license:boost1.0))))

+

+++ b/gnu/local.mk

+  %D%/packages/patches/lightgbm-use-system-libraries.patch	\

+++ b/gnu/packages/machine-learning.scm

+  #:use-module (gnu packages opencl)

+  #:use-module (gnu packages pretty-print)

+    (version "3.3.1")

+    (source

+     (origin

+       (method git-fetch)

+       (uri (git-reference

+             (url "https://github.com/Microsoft/LightGBM")

+             (commit (string-append "v" version))))

+       (patches

+        (search-patches "lightgbm-use-system-libraries.patch"))

+       (sha256

+        (base32 "0cwyb371xra5qnwkhpn223z3yqrppisgvx173an8i3f6m83zwb38"))

+       (file-name (git-file-name name version))))

+     `(;; ("googletest" ,googletest)

+       ("opencl-headers" ,opencl-headers)))

+     `(("boost" ,boost)

+       ("eigen" ,eigen)

+       ("fast-double-parser" ,fast-double-parser)

+       ("fmt" ,fmt)

+       ("ocl-icd" ,ocl-icd)

+       ("openmpi" ,openmpi)))

+     `(#:tests? #f ;; FIXME: googletest is not found by CMake

+       #:test-target "testlightgbm"

+       #:configure-flags

+       (list "-DBUILD_CPP_TEST=OFF"

+             "-DUSE_GPU=ON" ;using OpenCL

+             "-DUSE_MPI=ON")))

+++ b/gnu/packages/patches/lightgbm-use-system-libraries.patch

+From 894648291b9629d51785e4fd1cae820d2858e039 Mon Sep 17 00:00:00 2001

+From: Vinicius Monego <monego@posteo.net>

+Date: Mon, 31 May 2021 21:23:52 -0300

+Subject: [PATCH] Use system libraries.

+

+---

+ CMakeLists.txt                  | 11 ++++++++---

+ include/LightGBM/utils/common.h |  4 ++--

+ 2 files changed, 10 insertions(+), 5 deletions(-)

+

+diff --git a/CMakeLists.txt b/CMakeLists.txt

+index b845f36..560e477 100644

+--- a/CMakeLists.txt

++++ b/CMakeLists.txt

+@@ -93,9 +93,6 @@ if(USE_SWIG)

+   endif()

+ endif(USE_SWIG)

+ 

+-SET(EIGEN_DIR "${PROJECT_SOURCE_DIR}/external_libs/eigen")

+-include_directories(${EIGEN_DIR})

+-

+ # See https://gitlab.com/libeigen/eigen/-/blob/master/COPYING.README

+ ADD_DEFINITIONS(-DEIGEN_MPL2_ONLY)

+ 

+@@ -399,6 +396,14 @@ if(USE_SWIG)

+   endif()

+ endif(USE_SWIG)

+ 

++find_package (Eigen3 3.3 REQUIRED NO_MODULE)

++TARGET_LINK_LIBRARIES (lightgbm Eigen3::Eigen)

++TARGET_LINK_LIBRARIES (_lightgbm Eigen3::Eigen)

++

++find_package(fmt)

++TARGET_LINK_LIBRARIES(lightgbm fmt::fmt)

++TARGET_LINK_LIBRARIES(_lightgbm fmt::fmt)

++

+ if(USE_MPI)

+   TARGET_LINK_LIBRARIES(lightgbm ${MPI_CXX_LIBRARIES})

+   TARGET_LINK_LIBRARIES(_lightgbm ${MPI_CXX_LIBRARIES})

+diff --git a/include/LightGBM/utils/common.h b/include/LightGBM/utils/common.h

+index 4357357..00101a5 100644

+--- a/include/LightGBM/utils/common.h

++++ b/include/LightGBM/utils/common.h

+@@ -32,9 +32,9 @@

+ 

+ #if (!((defined(sun) || defined(__sun)) && (defined(__SVR4) || defined(__svr4__))))

+ #define FMT_HEADER_ONLY

+-#include "../../../external_libs/fmt/include/fmt/format.h"

++#include "fmt/format.h"

+ #endif

+-#include "../../../external_libs/fast_double_parser/include/fast_double_parser.h"

++#include "fast_double_parser.h"

+ 

+ #ifdef _MSC_VER

+ #include <intrin.h>

+-- 

+2.31.1

+

+++ b/gnu/packages/machine-learning.scm

+(define-public python-lightgbm

+  (package

+    (inherit lightgbm)

+    (name "python-lightgbm")

+    (source (package-source lightgbm))

+    (build-system python-build-system)

+    (arguments

+     `(#:configure-flags (list "--precompile") ; use precompiled library

+       #:phases

+       (modify-phases %standard-phases

+         (add-after 'unpack 'preparations

+           (lambda _

+             (setenv "HOME" "/tmp")     ;to write a log file

+             ;; Move Python files to source root to silence some warnings.

+             (rename-file "python-package/setup.py" "setup.py")

+             (rename-file "python-package/README.rst" "README.rst")

+             (rename-file "python-package/lightgbm" "lightgbm")

+             ;; Install version file to read the library's version.

+             (with-output-to-file "lightgbm/VERSION.txt"

+               (lambda ()

+                 (display ,(package-version lightgbm))))

+             ;; Skip building the shared library.

+             (substitute* "setup.py"

+               (("'install_lib': CustomInstallLib,") ""))))

+         (add-after 'install 'install-liblightgbm

+           (lambda* (#:key inputs outputs #:allow-other-keys)

+             (let* ((out (assoc-ref outputs "out"))

+                    (pylib (string-append out "/lib/python"

+                                          ,(version-major+minor

+                                            (package-version python))

+                                          "/site-packages"))

+                    (lgbdir (string-append pylib "/lightgbm"))

+                    (lib-lightgbm (string-append (assoc-ref inputs "lightgbm")

+                                                 "/lib/lib_lightgbm.so")))

+               ;; This symlink is necessary for tests.

+               (symlink lib-lightgbm "lightgbm/lib_lightgbm.so")

+               ;; And this one for runtime.

+               (mkdir-p (string-append lgbdir "/lib"))

+               (symlink lib-lightgbm (string-append lgbdir

+                                                    "/lib_lightgbm.so")))))

+         (replace 'check

+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)

+             (when tests?

+               (add-installed-pythonpath inputs outputs)

+               (invoke "python" "-m" "pytest"

+                       "tests/python_package_test")))))))

+    (native-inputs

+     `(("python-psutil" ,python-psutil)

+       ("python-pytest" ,python-pytest)

+       ("python-wheel" ,python-wheel)))

+    (inputs

+     `(("lightgbm" ,lightgbm)))

+    (propagated-inputs

+     `(("python-numpy" ,python-numpy)

+       ("python-pandas" ,python-pandas)

+       ("python-scikit-learn" ,python-scikit-learn)

+       ("python-scipy" ,python-scipy)))

+    (synopsis "Python frontend for LightGBM")))

+