[bug#55502] [PATCH 0/3] Add python-gpy

[bug#55502] [PATCH 0/3] Add python-gpy

[Wiktor Zelazny]

guix import originally put python-cython in propagated-inputs of
python-gpy, but I followed the linter advice and moved it to
native-inputs. I could not figure out the role of this input.

Wiktor Żelazny (3):
  gnu: Add python-climin.
  gnu: Add python-paramz.
  gnu: Add python-gpy.

 gnu/packages/python-science.scm | 85 +++++++++++++++++++++++++++++++++
 1 file changed, 85 insertions(+)


base-commit: a028eafcc2c6beffcb370296a4c5a90fe34fbcca
-- 
2.36.0

-- 
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[bug#55502] [PATCH 1/3] gnu: Add python-climin.

[Wiktor Zelazny]

* gnu/packages/python-science.scm (python-climin): New variable.
---
 gnu/packages/python-science.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index bf7c7ce45f..ad17401a61 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -18,6 +18,7 @@
 ;;; Copyright © 2022 Malte Frank Gerdes <malte.f.gerdes@gmail.com>
 ;;; Copyright © 2022 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2022 Paul A. Patience <paul@apatience.com>
+;;; Copyright © 2022 Wiktor Żelazny <wzelazny@vurv.cz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1222,3 +1223,25 @@ (define-public python-traittypes
 out of the scope of the main traitlets project but are a common requirement to
 build applications with traitlets in combination with the scipy stack.")
     (license license:bsd-3)))
+
+(define-public python-climin
+  (package
+    (name "python-climin")
+    (version "0.1a1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "climin" version))
+              (sha256
+               (base32
+                "1wpjisd5zzi5yvjff02hnxn84822k8sdxvvd33lil2x79wdb36rv"))))
+    (build-system python-build-system)
+    (native-inputs (list python-nose))
+    (propagated-inputs (list python-numpydoc python-numpy python-scipy))
+    (home-page "https://github.com/BRML/climin")
+    (synopsis "Optimization for machine learning")
+    (description
+     "@command{climin} is a Python package for optimization,
+heavily biased to machine learning scenarios distributed under the BSD 3-clause
+license.  It works on top of @command{numpy} and (partially)
+@command{gnumpy}.")
+    (license license:bsd-3)))
-- 
2.36.0

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[bug#55502] [PATCH 2/3] gnu: Add python-paramz.

[Wiktor Zelazny]

* gnu/packages/python-science.scm (python-paramz): New variable.
---
 gnu/packages/python-science.scm | 34 +++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index ad17401a61..a871bcf89e 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1245,3 +1245,37 @@ (define-public python-climin
 license.  It works on top of @command{numpy} and (partially)
 @command{gnumpy}.")
     (license license:bsd-3)))
+
+(define-public python-paramz
+  (package
+    (name "python-paramz")
+    (version "0.9.5")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "paramz" version))
+              (sha256
+               (base32
+                "16hbh97kj6b1c2gw22rqnr3w3nqkszh9gj8vgx738gq81wf225q9"))))
+    (build-system python-build-system)
+    (propagated-inputs (list python-decorator python-numpy python-scipy
+                             python-six))
+    (home-page "https://github.com/sods/paramz")
+    (synopsis "The Parameterization Framework")
+    (description
+     "@command{paramz} is a lightweight parameterization framework
+for parameterized model creation and handling.  Its features include:
+
+@itemize
+ @item Easy model creation with parameters.
+ @item Fast optimized access of parameters for optimization routines.
+ @item Memory efficient storage of parameters (only one copy in memory).
+ @item Renaming of parameters.
+ @item Intuitive printing of models and parameters.
+ @item Gradient saving directly inside parameters.
+ @item Gradient checking of parameters.
+ @item Optimization of parameters.
+ @item Jupyter notebook integration.
+ @item Efficient storage of models, for reloading.
+ @item Efficient caching.
+@end itemize")
+    (license license:bsd-3)))
-- 
2.36.0

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[bug#55502] [PATCH 3/3] gnu: Add python-gpy.

[Wiktor Zelazny]

* gnu/packages/python-science.scm (python-gpy): New variable.
---
 gnu/packages/python-science.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index a871bcf89e..fcc17a0b26 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1279,3 +1279,31 @@ (define-public python-paramz
  @item Efficient caching.
 @end itemize")
     (license license:bsd-3)))
+
+(define-public python-gpy
+  (package
+    (name "python-gpy")
+    (version "1.10.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "GPy" version))
+              (sha256
+               (base32
+                "1yx65ajrmqp02ykclhlb0n8s3bx5r0xj075swwwigiqaippr7dx2"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (add-before 'check 'remove-plotting-tests
+                    ;; These fail
+                    (lambda _
+                      (delete-file "GPy/testing/plotting_tests.py"))))))
+    (native-inputs (list python-cython python-nose python-climin))
+    (propagated-inputs (list python-numpy python-paramz python-scipy
+                             python-six))
+    (home-page "https://sheffieldml.github.io/GPy/")
+    (synopsis "The Gaussian Process Toolbox")
+    (description
+     "@command{GPy} is a Gaussian Process (GP) framework written in
+Python, from the Sheffield machine learning group.  GPy implements a range of
+machine learning algorithms based on GPs.")
+    (license license:bsd-3)))
-- 
2.36.0

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bug#55502: [PATCH 0/3] Add python-gpy

[Ludovic Courtès]

Hi,

Wiktor Zelazny <wzelazny@vurv.cz> skribis:

>   gnu: Add python-climin.
>   gnu: Add python-paramz.
>   gnu: Add python-gpy.

Applied, thanks!

Ludo’.