diff options
| -rw-r--r-- | gnu/local.mk | 4 | ||||
| -rw-r--r-- | gnu/packages/maths.scm | 41 | ||||
| -rw-r--r-- | gnu/packages/patches/python-accupy-fix-use-of-perfplot.patch | 48 | ||||
| -rw-r--r-- | gnu/packages/patches/python-accupy-use-matplotx.patch | 113 |
4 files changed, 205 insertions, 1 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 063262eefd..5df953272c 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -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 \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 386fb30cd9..2769c4f6ec 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -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") diff --git a/gnu/packages/patches/python-accupy-fix-use-of-perfplot.patch b/gnu/packages/patches/python-accupy-fix-use-of-perfplot.patch new file mode 100644 index 0000000000..5b874e0056 --- /dev/null +++ b/gnu/packages/patches/python-accupy-fix-use-of-perfplot.patch @@ -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 + diff --git a/gnu/packages/patches/python-accupy-use-matplotx.patch b/gnu/packages/patches/python-accupy-use-matplotx.patch new file mode 100644 index 0000000000..f3dd17da22 --- /dev/null +++ b/gnu/packages/patches/python-accupy-use-matplotx.patch @@ -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 + |