diff --git a/gnu/local.mk b/gnu/local.mk index 34b082ea8a..0a6c3fad00 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -2085,8 +2085,6 @@ dist_patch_DATA = \ %D%/packages/patches/pthreadpool-system-libraries.patch \ %D%/packages/patches/python-3.11-fix-tests.patch \ %D%/packages/patches/python-3.12-fix-tests.patch \ - %D%/packages/patches/python-accupy-use-matplotx.patch \ - %D%/packages/patches/python-accupy-fix-use-of-perfplot.patch \ %D%/packages/patches/python-anyio-unuse-exceptiongroup-in-test.patch \ %D%/packages/patches/python-bed-reader-use-store-samples.patch \ %D%/packages/patches/python-chai-drop-python2.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 1c066ec941..72b383fffa 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4352,54 +4352,6 @@ primes and prime k-tuplets up to 264.") (home-page "https://github.com/kimwalisch/primesieve") (license license:bsd-2))) -(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 - ;; tests: 30 passed, 10 warnings - #: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/") - "\"],")))))))) - (native-inputs - (list pybind11-2 - python-matplotx - python-perfplot - python-pytest - python-setuptools)) - (propagated-inputs - (list eigen - python-mpmath - python-numpy-1 - python-pyfma)) - (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+))) - ;; It is unfortunate that we cannot just link with the existing blis package. (define-public python-blis (package diff --git a/gnu/packages/patches/python-accupy-fix-use-of-perfplot.patch b/gnu/packages/patches/python-accupy-fix-use-of-perfplot.patch deleted file mode 100644 index 5b874e0056..0000000000 --- a/gnu/packages/patches/python-accupy-fix-use-of-perfplot.patch +++ /dev/null @@ -1,48 +0,0 @@ -From 567558a4eb9b73ab30f9e469b36091eccf445f80 Mon Sep 17 00:00:00 2001 -From: Felix Gruber -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 deleted file mode 100644 index f3dd17da22..0000000000 --- a/gnu/packages/patches/python-accupy-use-matplotx.patch +++ /dev/null @@ -1,113 +0,0 @@ -From 1da1ed24cfba8a051b6c2f452a67ebfee77ca040 Mon Sep 17 00:00:00 2001 -From: Felix Gruber -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 -