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gnu: Add python-accupy.

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* 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>
This commit is contained in:
Felix Gruber 2023-11-04 15:02:36 +00:00 committed by Ludovic Courtès
parent 8803100072
commit be73e08ba2
No known key found for this signature in database
GPG key ID: 090B11993D9AEBB5
4 changed files with 205 additions and 1 deletions
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4
gnu/local.mk
View file

@ -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 \

41
gnu/packages/maths.scm
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@ -3650,6 +3650,47 @@ (define-public python-kiwisolver
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")

48
gnu/packages/patches/python-accupy-fix-use-of-perfplot.patch Normal file
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@ -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

113
gnu/packages/patches/python-accupy-use-matplotx.patch Normal file
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@ -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