01/01: gnu: python-scikit-learn: Update to 0.20.1.

[guix-commits]

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