Merge branch 'master' into gnome-team.

1 files changed, 18 insertions, 9 deletions

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index e3f3b05ccd..0e099989c8 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -3,7 +3,7 @@
 ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
-;;; Copyright © 2016, 2022 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2022, 2023 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016-2020, 2022 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
@@ -290,11 +290,19 @@ logic, also known as grey logic.")
     (name "python-scikit-optimize")
     (version "0.9.0")
     (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "scikit-optimize" version))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/scikit-optimize/scikit-optimize")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0230ya8bwrzxjwcy2vz23a3hg6caggnnmg2vq1f9zz2797kckn3p"))))
+                "0hsq6pmryimxc275yrcy4bv217bx7ma6rz0q6m4138bv4zgq18d1"))
+              (patches
+               ;; These are for compatibility with more recent versions of
+               ;; numpy and scikit-learn.
+               (search-patches "python-scikit-optimize-1148.patch"
+                               "python-scikit-optimize-1150.patch"))))
     (build-system pyproject-build-system)
     (propagated-inputs
      (list python-joblib
@@ -568,20 +576,21 @@ Python module with the same interface, but (hopefully) faster.")
 (define-public python-bottleneck
   (package
     (name "python-bottleneck")
-    (version "1.3.2")
+    (version "1.3.7")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Bottleneck" version))
        (sha256
-        (base32 "0wz5320jx3n4q2nsvwvc7cpi66b46qbals9v53m955rmcq5ry5r0"))))
+        (base32 "1y410r3scfhs6s1j1jpxig01qlyn2hr2izyh1qsdlsfl78vpwip1"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
-           (lambda _
-             (invoke "python" "setup.py" "pytest"))))))
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "python" "setup.py" "pytest")))))))
     (native-inputs
      (list python-hypothesis python-pytest python-pytest-runner))
     (propagated-inputs
@@ -1762,7 +1771,7 @@ NeuroML2 models.")
      "This package provides a Python library for working with NeuroML descriptions of
 neuronal models")
     (license license:bsd-3)))
-    
+
 ;;;
 ;;; Avoid adding new packages to the end of this file. To reduce the chances
 ;;; of a merge conflict, place them above by existing packages with similar