Subject: [bug#66929] [PATCH 07/10] gnu: Add python-accupy.

From: Felix Gruber <[email-masked]>
Date: Sat, 4 Nov 2023 15:02:36 +0000

* 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
---
 gnu/local.mk                                  |   4 +-
 gnu/packages/maths.scm                        |  41 +++++++
 .../python-accupy-fix-use-of-perfplot.patch   |  48 ++++++++
 .../patches/python-accupy-use-matplotx.patch  | 113 ++++++++++++++++++
 4 files changed, 205 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/python-accupy-fix-use-of-perfplot.patch
 create mode 100644 gnu/packages/patches/python-accupy-use-matplotx.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 8d817379a7..3fbdc3ee9d 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -31,7 +31,7 @@
 # Copyright © 2020 R Veera Kumar <[email-masked]>
 # Copyright © 2020 Nicolò Balzarotti <[email-masked]>
 # Copyright © 2020 Michael Rohleder <[email-masked]>
-# Copyright © 2020, 2021, 2022 Felix Gruber <[email-masked]>
+# Copyright © 2020, 2021, 2022, 2023 Felix Gruber <[email-masked]>
 # Copyright © 2020 Ryan Prior <[email-masked]>
 # Copyright © 2020 Jan Wielkiewicz <[email-masked]>
 # Copyright © 2020, 2021 Brice Waegeneire <[email-masked]>
@@ -1753,6 +1753,8 @@ 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 ed1708c77b..28e023190f 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -3648,6 +3648,47 @@ (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")
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 <[email-masked]>
+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 <[email-masked]>
+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
+
-- 
2.42.0