~ruther/guix-local

be73e08ba2fd8e9280840f8fa962e9821ba5b71e — Felix Gruber 2 years ago 8803100
gnu: Add python-accupy.

* gnu/packages/maths.scm (python-accupy): New variable.
* gnu/packages/patches/python-accupy-fix-use-of-perfplot.patch: New
  file.
* gnu/packages/patches/python-accupy-use-matplotx.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add new patch files.

Change-Id: I0222665d54a36830844b3b33e3dcb546741cfaa1
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
M gnu/local.mk => gnu/local.mk +3 -1
@@ 31,7 31,7 @@
# Copyright © 2020 R Veera Kumar <vkor@vkten.in>
# Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
# Copyright © 2020 Michael Rohleder <mike@rohleder.de>
# Copyright © 2020, 2021, 2022 Felix Gruber <felgru@posteo.net>
# Copyright © 2020, 2021, 2022, 2023 Felix Gruber <felgru@posteo.net>
# Copyright © 2020 Ryan Prior <rprior@protonmail.com>
# Copyright © 2020 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
# Copyright © 2020, 2021 Brice Waegeneire <brice@waegenei.re>


@@ 1761,6 1761,8 @@ dist_patch_DATA =						\
  %D%/packages/patches/prusa-slicer-fix-tests.patch		\
  %D%/packages/patches/prusa-slicer-with-cereal-1.3.1.patch	\
  %D%/packages/patches/pthreadpool-system-libraries.patch	\
  %D%/packages/patches/python-accupy-use-matplotx.patch		\
  %D%/packages/patches/python-accupy-fix-use-of-perfplot.patch	\
  %D%/packages/patches/python-chai-drop-python2.patch		\
  %D%/packages/patches/python-docrepr-fix-tests.patch		\
  %D%/packages/patches/python-feedparser-missing-import.patch	\

M gnu/packages/maths.scm => gnu/packages/maths.scm +41 -0
@@ 3650,6 3650,47 @@ Cassowary solver with typical use cases gaining a 40x improvement.  Memory
savings are consistently > 5x.")
    (license license:bsd-3)))

(define-public python-accupy
  (package
    (name "python-accupy")
    (version "0.3.6")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/diego-hayashi/accupy")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0sxkwpp2xy2jgakhdxr4nh1cspqv8l89kz6s832h05pbpyc0n767"))
       (patches (search-patches "python-accupy-use-matplotx.patch"
                                "python-accupy-fix-use-of-perfplot.patch"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'set-eigen-include-dir
            (lambda _
              (substitute* "setup.py"
                (("include_dirs=\\[\"\\/usr\\/include\\/eigen3\\/\"\\]," _)
                 (string-append "include_dirs=[\""
                                #$(file-append (this-package-input "eigen")
                                             "/include/eigen3/")
                                "\"],"))))))))
    (propagated-inputs (list eigen python-mpmath python-pyfma))
    (native-inputs (list pybind11
                         python-matplotx
                         python-perfplot
                         python-pytest))
    (home-page "https://github.com/diego-hayashi/accupy")
    (synopsis "Accurate calculation of sums and dot products")
    (description
      "@code{accupy} is a Python library for accurately computing sums
and (dot) products.  It implements Kahan summation, Shewchuck's
algorithm and summation in K-fold precision.")
    (license license:gpl3+)))

(define-public slepc
  (package
    (name "slepc")

A gnu/packages/patches/python-accupy-fix-use-of-perfplot.patch => gnu/packages/patches/python-accupy-fix-use-of-perfplot.patch +48 -0
@@ 0,0 1,48 @@
From 567558a4eb9b73ab30f9e469b36091eccf445f80 Mon Sep 17 00:00:00 2001
From: Felix Gruber <felgru@posteo.net>
Date: Sun, 23 Apr 2023 16:48:59 +0200
Subject: [PATCH] Fix use of perfplot.

data tuples are unpacked by perfplot before it calls the kernel
functions.
---
 tests/test_dot.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/tests/test_dot.py b/tests/test_dot.py
index a8160fe..51307ad 100644
--- a/tests/test_dot.py
+++ b/tests/test_dot.py
@@ -76,10 +76,10 @@ def test_speed_comparison1(n_range=None):
     perfplot.plot(
         setup=lambda n: (np.random.rand(n, 100), np.random.rand(100, n)),
         kernels=[
-            lambda xy: np.dot(*xy),
-            lambda xy: accupy.kdot(*xy, K=2),
-            lambda xy: accupy.kdot(*xy, K=3),
-            lambda xy: accupy.fdot(*xy),
+            lambda x, y: np.dot(x, y),
+            lambda x, y: accupy.kdot(x, y, K=2),
+            lambda x, y: accupy.kdot(x, y, K=3),
+            lambda x, y: accupy.fdot(x, y),
         ],
         labels=["np.dot", "accupy.kdot[2]", "accupy.kdot[3]", "accupy.fdot"],
         n_range=n_range,
@@ -96,10 +96,10 @@ def test_speed_comparison2(n_range=None):
     perfplot.plot(
         setup=lambda n: (np.random.rand(100, n), np.random.rand(n, 100)),
         kernels=[
-            lambda xy: np.dot(*xy),
-            lambda xy: accupy.kdot(*xy, K=2),
-            lambda xy: accupy.kdot(*xy, K=3),
-            lambda xy: accupy.fdot(*xy),
+            lambda x, y: np.dot(x, y),
+            lambda x, y: accupy.kdot(x, y, K=2),
+            lambda x, y: accupy.kdot(x, y, K=3),
+            lambda x, y: accupy.fdot(x, y),
         ],
         labels=["np.dot", "accupy.kdot[2]", "accupy.kdot[3]", "accupy.fdot"],
         n_range=n_range,
-- 
2.39.2


A gnu/packages/patches/python-accupy-use-matplotx.patch => gnu/packages/patches/python-accupy-use-matplotx.patch +113 -0
@@ 0,0 1,113 @@
From 1da1ed24cfba8a051b6c2f452a67ebfee77ca040 Mon Sep 17 00:00:00 2001
From: Felix Gruber <felgru@posteo.net>
Date: Sun, 23 Apr 2023 15:42:19 +0200
Subject: [PATCH] Use dufte style from matplotx.

The stand-alone dufte package has been deprecated in favor of the dufte
style that has been integrated into matplotx.
---
 tests/test_dot.py  | 10 +++++-----
 tests/test_sums.py | 12 ++++++------
 tox.ini            |  2 +-
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/tests/test_dot.py b/tests/test_dot.py
index 0a40a0c..a8160fe 100644
--- a/tests/test_dot.py
+++ b/tests/test_dot.py
@@ -1,5 +1,5 @@
-import dufte
 import matplotlib.pyplot as plt
+import matplotx
 import numpy as np
 import perfplot
 import pytest
@@ -33,7 +33,7 @@ def test_fdot(cond):
 
 
 def test_accuracy_comparison_illcond(target_cond=None):
-    plt.style.use(dufte.style)
+    plt.style.use(matplotx.styles.dufte)
 
     if target_cond is None:
         target_cond = [10 ** k for k in range(2)]
@@ -61,13 +61,13 @@ def test_accuracy_comparison_illcond(target_cond=None):
     for label, d in zip(labels, data.T):
         plt.loglog(condition_numbers, d, label=label)
 
-    dufte.legend()
+    matplotx.line_labels()
     plt.xlabel("condition number")
-    dufte.ylabel("relative error")
+    matplotx.ylabel_top("relative error")
 
 
 def test_speed_comparison1(n_range=None):
-    plt.style.use(dufte.style)
+    plt.style.use(matplotx.styles.dufte)
 
     if n_range is None:
         n_range = [2 ** k for k in range(2)]
diff --git a/tests/test_sums.py b/tests/test_sums.py
index 1c0f6b0..8cd9ddb 100644
--- a/tests/test_sums.py
+++ b/tests/test_sums.py
@@ -1,5 +1,5 @@
-import dufte
 import matplotlib.pyplot as plt
+import matplotx
 import numpy as np
 import perfplot
 import pytest
@@ -32,7 +32,7 @@ def test_fsum(cond):
 
 
 def test_accuracy_comparison_illcond(target_conds=None):
-    plt.style.use(dufte.style)
+    plt.style.use(matplotx.styles.dufte)
 
     if target_conds is None:
         target_conds = [10 ** k for k in range(1, 2)]
@@ -71,14 +71,14 @@ def test_accuracy_comparison_illcond(target_conds=None):
     for label, color, d in zip(labels, colors, data.T):
         plt.loglog(condition_numbers, d, label=label, color=color)
 
-    dufte.legend()
+    matplotx.line_labels()
     plt.xlabel("condition number")
-    dufte.ylabel("relative error")
+    matplotx.ylabel_top("relative error")
     # plt.gca().set_aspect(1.3)
 
 
 def test_speed_comparison1(n_range=None):
-    plt.style.use(dufte.style)
+    plt.style.use(matplotx.styles.dufte)
 
     if n_range is None:
         n_range = [2 ** k for k in range(2)]
@@ -109,7 +109,7 @@ def test_speed_comparison1(n_range=None):
 
 
 def test_speed_comparison2(n_range=None):
-    plt.style.use(dufte.style)
+    plt.style.use(matplotx.styles.dufte)
 
     if n_range is None:
         n_range = [2 ** k for k in range(2)]
diff --git a/tox.ini b/tox.ini
index 79a53ec..524b3bc 100644
--- a/tox.ini
+++ b/tox.ini
@@ -4,7 +4,7 @@ isolated_build = True
 
 [testenv]
 deps =
-    dufte
+    matplotx
     perfplot
     pytest
     pytest-cov
-- 
2.39.2