Merge remote-tracking branch 'origin/master' into rust-team

Change-Id: Ic45f7071abd6a02c2ccad411500e5103c8272ffb

1 files changed, 52 insertions, 9 deletions

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 7d833005bc..c100e0be6e 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1532,6 +1532,54 @@ computing environments.")
 data analysis.")
     (license license:bsd-3)))
 
+(define-public python-scikit-learn-extra
+  (package
+    (name "python-scikit-learn-extra")
+    (version "0.3.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/scikit-learn-contrib/scikit-learn-extra")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0yy6ka94ss88f3r7b6mpjf1l8lnv7aabhsg844pigfj8lfiv0wvl"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'build 'build-ext
+                 (lambda _
+                   (invoke "python" "setup.py" "build_ext"
+                           "--inplace")))
+               (replace 'check
+                 (lambda* (#:key tests? #:allow-other-keys)
+                   (when tests?
+                     ;; Restrict OpenBLAS threads to prevent segfaults while testing!
+                     (setenv "OPENBLAS_NUM_THREADS" "1")
+
+                     ;; Some tests require write access to $HOME.
+                     (setenv "HOME" "/tmp")
+
+                     ;; Step out of the source directory to avoid interference;
+                     ;; we want to run the installed code with extensions etc.
+                     (with-directory-excursion "/tmp"
+                       (invoke "pytest" "-vv" "--pyargs"
+                               "sklearn_extra"
+                               ;; ignore tests that require network
+                               "-k" "not test_build"))))))))
+    (propagated-inputs (list python-numpy python-scikit-learn python-scipy))
+    (native-inputs (list python-pytest python-pytest-cov python-cython))
+    (home-page "https://github.com/scikit-learn-contrib/scikit-learn-extra")
+    (synopsis "Set of tools for scikit-learn")
+    (description
+     "This package provides a Python module for machine learning that extends
+scikit-learn.  It includes algorithms that are useful but do not satisfy the
+scikit-learn inclusion criteria, for instance due to their novelty or lower
+citation number.")
+    (license license:bsd-3)))
+
 (define-public python-thinc
   (package
     (name "python-thinc")
@@ -1920,9 +1968,9 @@ Covariance Matrix Adaptation Evolution Strategy (CMA-ES) for Python.")
     (license license:expat)))
 
 (define-public python-autograd
-  (let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
+  (let* ((commit "c6d81ce7eede6db801d4e9a92b27ec5d409d0eab")
          (revision "0")
-         (version (git-version "0.0.0" revision commit)))
+         (version (git-version "1.5" revision commit)))
     (package
       (name "python-autograd")
       (home-page "https://github.com/HIPS/autograd")
@@ -1933,19 +1981,14 @@ Covariance Matrix Adaptation Evolution Strategy (CMA-ES) for Python.")
                       (commit commit)))
                 (sha256
                  (base32
-                  "189sv2xb0mwnjawa9z7mrgdglc1miaq93pnck26r28fi1jdwg0z4"))
+                  "04kljgydng42xlg044h6nbzxpban1ivd6jzb8ydkngfq88ppipfk"))
                 (file-name (git-file-name name version))))
       (version version)
-      (build-system python-build-system)
+      (build-system pyproject-build-system)
       (native-inputs
        (list python-nose python-pytest))
       (propagated-inputs
        (list python-future python-numpy))
-      (arguments
-       `(#:phases (modify-phases %standard-phases
-                    (replace 'check
-                      (lambda _
-                        (invoke "py.test" "-v"))))))
       (synopsis "Efficiently computes derivatives of NumPy code")
       (description "Autograd can automatically differentiate native Python and
 NumPy code.  It can handle a large subset of Python's features, including loops,