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.
Message #29 received at 48388 <at> debbugs.gnu.org (full text, mbox):
From: Vinicius Monego <monego <at> posteo.net> To: 48388 <at> debbugs.gnu.org Cc: Vinicius Monego <monego <at> posteo.net> Subject: [PATCH v3 3/3] gnu: Add python-xgboost. Date: Sun, 27 Jun 2021 17:30:47 +0000
* gnu/packages/machine-learning.scm (python-xgboost): New variable.
* gnu/packages/patches/python-xgboost-use-system-libxgboost.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Add it.
---
Changed source to inherit from xgboost.
Added phase after 'install to add a VERSION file and symlink libxgboost, so it can be found at runtime. This change allowed to greatly simplify the patch.
Also removed #t from phases.
If this patchset is good enough now, I will do the same changes to LightGBM: http://issues.guix.gnu.org/48785
gnu/local.mk | 1 +
gnu/packages/machine-learning.scm | 66 +++++++++++++++++++
...python-xgboost-use-system-libxgboost.patch | 18 +++++
3 files changed, 85 insertions(+)
create mode 100644 gnu/packages/patches/python-xgboost-use-system-libxgboost.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index 19db9787dc..821fd390a4 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1632,6 +1632,7 @@ dist_patch_DATA = \
%D%/packages/patches/python-unittest2-python3-compat.patch \
%D%/packages/patches/python-unittest2-remove-argparse.patch \
%D%/packages/patches/python-waitress-fix-tests.patch \
+ %D%/packages/patches/python-xgboost-use-system-libxgboost.patch \
%D%/packages/patches/pypy3-7.3.1-fix-tests.patch \
%D%/packages/patches/qemu-build-info-manual.patch \
%D%/packages/patches/qemu-CVE-2021-20203.patch \
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index bbdfba960e..69b96ffd61 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1991,6 +1991,72 @@ 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-xgboost
+ (package
+ (inherit xgboost)
+ (name "python-xgboost")
+ (source
+ (origin
+ (inherit (package-source xgboost))
+ (patches (search-patches "python-xgboost-use-system-libxgboost.patch"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'preparations
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; Move python-package content to parent directory to silence
+ ;; some warnings about files not being found if we chdir.
+ (rename-file "python-package/xgboost" "xgboost")
+ (rename-file "python-package/README.rst" "README.rst")
+ (rename-file "python-package/setup.cfg" "setup.cfg")
+ (rename-file "python-package/setup.py" "setup.py")))
+ (add-after 'install 'install-version-and-libxgboost
+ (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"))
+ (xgbdir (string-append pylib "/xgboost"))
+ (version-file (string-append xgbdir "/VERSION"))
+ (libxgboost (string-append (assoc-ref inputs "xgboost")
+ "/lib/libxgboost.so")))
+ (with-output-to-file version-file
+ (lambda ()
+ (display ,(package-version xgboost))))
+ (mkdir-p (string-append xgbdir "/lib"))
+ (symlink libxgboost (string-append xgbdir "/lib"
+ "/libxgboost.so")))))
+ (replace 'check
+ ;; Python-specific tests are located in tests/python.
+ (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+ (when tests?
+ (add-installed-pythonpath inputs outputs)
+ (invoke "pytest" "tests/python"
+ ;; FIXME: CLI tests fail with PermissionError.
+ "--ignore" "tests/python/test_cli.py" "-k"
+ (string-append
+ "not test_cli_regression_demo"
+ ;; The tests below open a network connection.
+ " and not test_model_compatibility"
+ " and not test_get_group"
+ " and not test_cv_no_shuffle"
+ " and not test_cv"
+ " and not test_training"
+ ;; "'['./runexp.sh']' returned non-zero exit status 1"
+ " and not test_cli_binary_classification"))))))))
+ (native-inputs
+ `(("python-pandas" ,python-pandas)
+ ("python-pytest" ,python-pytest)
+ ("python-scikit-learn" ,python-scikit-learn)))
+ (inputs
+ `(("xgboost" ,xgboost)))
+ (propagated-inputs
+ `(("python-numpy" ,python-numpy)
+ ("python-scipy" ,python-scipy)))
+ (synopsis "Python interface for the XGBoost library")))
+
(define-public python-iml
(package
(name "python-iml")
diff --git a/gnu/packages/patches/python-xgboost-use-system-libxgboost.patch b/gnu/packages/patches/python-xgboost-use-system-libxgboost.patch
new file mode 100644
index 0000000000..ce82309afd
--- /dev/null
+++ b/gnu/packages/patches/python-xgboost-use-system-libxgboost.patch
@@ -0,0 +1,18 @@
+This patch was imported from Debian: https://sources.debian.org/src/xgboost/1.2.1-1/debian/patches/setup.py.patch/
+
+Description: the libxgboost.so has been installed by another package already
+Forwarded: no need
+--- a/python-package/setup.py
++++ b/python-package/setup.py
+@@ -286,10 +286,8 @@
+ 'numpy',
+ 'scipy',
+ ],
+- ext_modules=[CMakeExtension('libxgboost')],
+ cmdclass={
+ 'build_ext': BuildExt,
+ 'sdist': Sdist,
+- 'install_lib': InstallLib,
+ 'install': Install
+ },
+ extras_require={
\ No newline at end of file
--
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