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01/01: gnu: python-scikit-learn: Update to 0.20.1.
From: |
guix-commits |
Subject: |
01/01: gnu: python-scikit-learn: Update to 0.20.1. |
Date: |
Thu, 22 Nov 2018 11:03:58 -0500 (EST) |
mbakke pushed a commit to branch core-updates
in repository guix.
commit 7ff3f3d22caaf03948a60ae691313db28f4fab06
Author: Marius Bakke <address@hidden>
Date: Thu Nov 22 01:47:36 2018 +0100
gnu: python-scikit-learn: Update to 0.20.1.
* gnu/packages/patches/python-scikit-learn-fix-test-non-determinism.patch:
Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 0.20.1.
[source](patches): Remove.
[arguments]: Skip network tests with pytest instead of deleting files. Make
sure $HOME is writable.
(python2-scikit-learn): Rewrite in terms of PACKAGE-WITH-PYTHON2.
---
gnu/local.mk | 1 -
gnu/packages/machine-learning.scm | 35 +++++-----------------
...hon-scikit-learn-fix-test-non-determinism.patch | 25 ----------------
3 files changed, 8 insertions(+), 53 deletions(-)
diff --git a/gnu/local.mk b/gnu/local.mk
index e56f8a2..b67958d 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1090,7 +1090,6 @@ dist_patch_DATA =
\
%D%/packages/patches/python-fix-tests.patch \
%D%/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch \
%D%/packages/patches/python2-rdflib-drop-sparqlwrapper.patch \
- %D%/packages/patches/python-scikit-learn-fix-test-non-determinism.patch
\
%D%/packages/patches/python-configobj-setuptools.patch \
%D%/packages/patches/python-faker-fix-build-32bit.patch \
%D%/packages/patches/python-mox3-python3.6-compat.patch \
diff --git a/gnu/packages/machine-learning.scm
b/gnu/packages/machine-learning.scm
index 09c525f..4b2447e 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -706,7 +706,7 @@ computing environments.")
(define-public python-scikit-learn
(package
(name "python-scikit-learn")
- (version "0.19.2")
+ (version "0.20.1")
(source
(origin
(method git-fetch)
@@ -716,9 +716,7 @@ computing environments.")
(file-name (git-file-name name version))
(sha256
(base32
- "1dk9hdj01c0bny4ps78b7869fjw9gr6qklxf6wyql8h6nh4k19xm"))
- (patches (search-patches
- "python-scikit-learn-fix-test-non-determinism.patch"))))
+ "0qv7ir1fy9vjar3llc72yxmfja3gxm5icdf0y3q57vsn3wcdglkz"))))
(build-system python-build-system)
(arguments
`(#:phases
@@ -729,11 +727,11 @@ computing environments.")
(lambda _
;; Restrict OpenBLAS threads to prevent segfaults while testing!
(setenv "OPENBLAS_NUM_THREADS" "1")
- ;; Disable tests that require network access
- (delete-file "sklearn/datasets/tests/test_mldata.py")
- (delete-file "sklearn/datasets/tests/test_rcv1.py")
- (invoke "pytest" "sklearn")
- #t))
+
+ ;; Some tests require write access to $HOME.
+ (setenv "HOME" "/tmp")
+
+ (invoke "pytest" "sklearn" "-m" "not network")))
;; FIXME: This fails with permission denied
(delete 'reset-gzip-timestamps))))
(inputs
@@ -753,24 +751,7 @@ data analysis.")
(license license:bsd-3)))
(define-public python2-scikit-learn
- (let ((parent (package-with-python2 python-scikit-learn)))
- (package (inherit parent)
- (arguments
- (substitute-keyword-arguments (package-arguments parent)
- ((#:phases phases)
- `(modify-phases ,phases
- (replace 'check
- (lambda _
- ;; Restrict OpenBLAS threads to prevent segfaults while
testing!
- (setenv "OPENBLAS_NUM_THREADS" "1")
- ;; Some tests expect to be able to write to HOME.
- (setenv "HOME" "/tmp")
- ;; Disable tests that require network access
- (delete-file "sklearn/datasets/tests/test_kddcup99.py")
- (delete-file "sklearn/datasets/tests/test_mldata.py")
- (delete-file "sklearn/datasets/tests/test_rcv1.py")
- (invoke "pytest" "sklearn")
- #t)))))))))
+ (package-with-python2 python-scikit-learn))
(define-public python-autograd
(let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
diff --git
a/gnu/packages/patches/python-scikit-learn-fix-test-non-determinism.patch
b/gnu/packages/patches/python-scikit-learn-fix-test-non-determinism.patch
deleted file mode 100644
index 90328cc..0000000
--- a/gnu/packages/patches/python-scikit-learn-fix-test-non-determinism.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-This patch stops a test sometimes failing because of non-determinism. See
-https://github.com/scikit-learn/scikit-learn/pull/9542
-
-From ff9f6db6e8b59c2b3528c8137ed4054f57c1d7c4 Mon Sep 17 00:00:00 2001
-From: Hanmin Qin <address@hidden>
-Date: Sun, 13 Aug 2017 22:13:49 +0800
-Subject: [PATCH] add random_state
-
----
- sklearn/tests/test_kernel_ridge.py | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/sklearn/tests/test_kernel_ridge.py
b/sklearn/tests/test_kernel_ridge.py
-index 4750a096ac6..979875870b6 100644
---- a/sklearn/tests/test_kernel_ridge.py
-+++ b/sklearn/tests/test_kernel_ridge.py
-@@ -10,7 +10,7 @@
- from sklearn.utils.testing import assert_array_almost_equal
-
-
--X, y = make_regression(n_features=10)
-+X, y = make_regression(n_features=10, random_state=0)
- Xcsr = sp.csr_matrix(X)
- Xcsc = sp.csc_matrix(X)
- Y = np.array([y, y]).T