GNU bug report logs - #66929
[PATCH 00/10] Add python-quadpy and dependencies.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: guix-patches <at> gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 00/10] Add python-quadpy and dependencies.
Date: Sat,  4 Nov 2023 15:00:34 +0000

This patchset adds the quadpy Python library which collects a large
number of different numerical integration algorithms.

I've packaged a fork of the last GPL-licensed version of quadpy. Newer
versions are distributed under a proprietary license and the history of
the original git repository on https://github.com/nschloe/quadpy had
been removed (hence I'm referring to a fork in the source and home-page
fields). The same holds for the python-orthopy, python-ndim,
python-accupy and python-meshzoo packages.
Also, quadpy stores some required data files via git-lfs. I couldn't
figure out how to download those git-lfs stored files in the source of
the python-quadpy package. In the end, I resorted to instead point the
source field to a zip file that contained the source code including
those data files.

Felix Gruber (10):
  gnu: Add python-meshzoo.
  gnu: Add python-matplotx.
  gnu: Add python-npx.
  gnu: Add python-cplot.
  gnu: Add python-perfplot.
  gnu: Add python-pyfma.
  gnu: Add python-accupy.
  gnu: Add python-ndim.
  gnu: Add python-orthopy.
  gnu: Add python-quadpy.

 gnu/local.mk                                  |   4 +-
 gnu/packages/maths.scm                        | 145 ++++++++++++++++++
 .../python-accupy-fix-use-of-perfplot.patch   |  48 ++++++
 .../patches/python-accupy-use-matplotx.patch  | 113 ++++++++++++++
 gnu/packages/python-science.scm               |  52 ++++++-
 gnu/packages/python-xyz.scm                   | 110 ++++++++++++-
 6 files changed, 469 insertions(+), 3 deletions(-)
 create mode 100644 gnu/packages/patches/python-accupy-fix-use-of-perfplot.patch
 create mode 100644 gnu/packages/patches/python-accupy-use-matplotx.patch


base-commit: 9dcd8802f5bc472579f23a38dcf437f8a9ac976c
-- 
2.42.0

Message #8 received at 66929 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 66929 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 01/10] gnu: Add python-meshzoo.
Date: Sat,  4 Nov 2023 15:02:30 +0000

* gnu/packages/python-science.scm (python-meshzoo): New variable.

Change-Id: Ia41d62ebd6c4cb3c22ebe0668c36279a9ca191ac
---
 gnu/packages/python-science.scm | 27 ++++++++++++++++++++++++++-
 1 file changed, 26 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 4063797a30..275f9a27c1 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -14,7 +14,7 @@
 ;;; Copyright © 2021 Roel Janssen <roel <at> gnu.org>
 ;;; Copyright © 2021 Paul Garlick <pgarlick <at> tourbillion-technology.com>
 ;;; Copyright © 2021 Arun Isaac <arunisaac <at> systemreboot.net>
-;;; Copyright © 2021 Felix Gruber <felgru <at> posteo.net>
+;;; Copyright © 2021, 2023 Felix Gruber <felgru <at> posteo.net>
 ;;; Copyright © 2022 Malte Frank Gerdes <malte.f.gerdes <at> gmail.com>
 ;;; Copyright © 2022 Guillaume Le Vaillant <glv <at> posteo.net>
 ;;; Copyright © 2022 Paul A. Patience <paul <at> apatience.com>
@@ -387,6 +387,31 @@ (define-public python-trimesh
 library.")
     (license license:expat)))
 
+(define-public python-meshzoo
+  (package
+    (name "python-meshzoo")
+    (version "0.9.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/diego-hayashi/meshzoo")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "107byfppbq16fqyp2hw7ydcvvahspzq0hzvlvzqg2zxi1aigbr68"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+      (list python-numpy))
+    (native-inputs (list python-flit-core python-matplotlib python-pytest))
+    (home-page "https://github.com/diego-hayashi/meshzoo")
+    (synopsis "Mesh generator for simple geometries")
+    (description
+      "@code{meshzoo} is a mesh generator for finite element or finite
+volume computations for simple domains like regular polygons, disks,
+spheres, cubes, etc.")
+    (license license:gpl3)))
+
 (define-public python-tspex
   (package
     (name "python-tspex")
-- 
2.42.0

Message #11 received at 66929 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 66929 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 02/10] gnu: Add python-matplotx.
Date: Sat,  4 Nov 2023 15:02:31 +0000

* gnu/packages/python-xyz.scm (python-matplotx): New variable.

Change-Id: I354732edeaa30cbae506e78a16f42e66edb3011b
---
 gnu/packages/python-xyz.scm | 39 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 38 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e521c1580d..33b0c401ef 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -108,7 +108,7 @@
 ;;; Copyright © 2021 Simon Streit <simon <at> netpanic.org>
 ;;; Copyright © 2021, 2022, 2023 Daniel Meißner <daniel.meissner-i4k <at> ruhr-uni-bochum.de>
 ;;; Copyright © 2021, 2022 Pradana Aumars <paumars <at> courrier.dev>
-;;; Copyright © 2021, 2022 Felix Gruber <felgru <at> posteo.net>
+;;; Copyright © 2021, 2022, 2023 Felix Gruber <felgru <at> posteo.net>
 ;;; Copyright © 2021 Sébastien Lerique <sl <at> eauchat.org>
 ;;; Copyright © 2021 Raphaël Mélotte <raphael.melotte <at> mind.be>
 ;;; Copyright © 2021 ZmnSCPxj <ZmnSCPxj <at> protonmail.com>
@@ -8262,6 +8262,43 @@ (define-public python-matplotlib-venn
 three-way Venn diagrams in @code{matplotlib}.")
     (license license:expat)))
 
+(define-public python-matplotx
+  (package
+    (name "python-matplotx")
+    (version "0.3.10")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/nschloe/matplotx")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1j301mr7ai2jmbm5mkva0jd99fzxhyq585pqzqfmrf5pil8j4q8i"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+      (list python-matplotlib
+            python-numpy
+            ;; optional dependencies
+            python-networkx
+            python-pypng
+            python-scipy))
+    (native-inputs (list python-imageio
+                         python-meshzoo
+                         python-pytest
+                         python-scikit-fem))
+    (arguments
+     (list
+      #:test-flags
+      ;; This test fails with ValueError: not enough values to unpack.
+      #~(list "--deselect" "tests/test_spy.py::test_cli")))
+    (home-page "https://github.com/nschloe/matplotx")
+    (synopsis "Minimal matplotlib styles")
+    (description
+      "This package includes some extensions for Matplotlib to create
+clean plots with a minimalistic style.")
+    (license license:expat)))
+
 (define-public python-pysnptools
   (package
     (name "python-pysnptools")
-- 
2.42.0

Message #14 received at 66929 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 66929 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 03/10] gnu: Add python-npx.
Date: Sat,  4 Nov 2023 15:02:32 +0000

* gnu/packages/python-xyz.scm (python-npx): New variable.

Change-Id: I9520ce12a936c68d38f2ac706165eff816d8b1ad
---
 gnu/packages/python-xyz.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 33b0c401ef..54e1086af8 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7431,6 +7431,28 @@ (define-public python-numpy-documentation
     (description "This package provides the complete NumPy documentation in
 the Texinfo, HTML, and PDF formats.")))
 
+(define-public python-npx
+  (package
+    (name "python-npx")
+    (version "0.1.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "npx" version))
+              (sha256
+               (base32
+                "1m0v2p5mh3aqrypl4ipgzvr5nhx7bk5vv9ah2xr9l1xgj6nnmqnc"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-numpy))
+    (native-inputs (list python-flit-core python-networkx python-pytest))
+    (home-page "https://github.com/nschloe/npx")
+    (synopsis "Extensions for NumPy")
+    (description "NumPy is a large library used everywhere in scientific
+computing.  That's why breaking backwards-compatibility comes at a
+significant cost and is almost always avoided, even if the API of some
+methods is arguably lacking.  This package provides drop-in wrappers
+\"fixing\" those.")
+    (license license:bsd-3)))
+
 (define-public python-munch
   (package
     (name "python-munch")
-- 
2.42.0

Message #17 received at 66929 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 66929 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 04/10] gnu: Add python-cplot.
Date: Sat,  4 Nov 2023 15:02:33 +0000

* gnu/packages/python-xyz.scm (python-cplot): New variable.

Change-Id: I8e634799954b120e00d900ae26b16af1717d4474
---
 gnu/packages/python-xyz.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 54e1086af8..f2e55e2788 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -8321,6 +8321,31 @@ (define-public python-matplotx
 clean plots with a minimalistic style.")
     (license license:expat)))
 
+(define-public python-cplot
+  (package
+    (name "python-cplot")
+    (version "0.9.3")
+    (source
+     (origin
+       (method git-fetch)   ;for tests
+       (uri (git-reference
+             (url "https://github.com/nschloe/cplot")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0zk7hpq358sbympmkms7w2wjs7nw8mdfvkvdasblg2nhqayv42qz"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-matplotlib
+                             python-matplotx
+                             python-npx
+                             python-numpy))
+    (native-inputs (list python-pytest))
+    (home-page "https://github.com/nschloe/cplot")
+    (synopsis "Plot complex-valued functions")
+    (description "@code{cplot} is a Python library for plotting
+complex-valued functions.")
+    (license license:gpl3)))
+
 (define-public python-pysnptools
   (package
     (name "python-pysnptools")
-- 
2.42.0

Message #20 received at 66929 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 66929 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 05/10] gnu: Add python-perfplot.
Date: Sat,  4 Nov 2023 15:02:34 +0000

* gnu/packages/python-xyz.scm (python-perfplot): New variable.

Change-Id: I04266dfd7081bd3f917a48b2667137b829680498
---
 gnu/packages/python-xyz.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f2e55e2788..b69cd19f45 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -8346,6 +8346,30 @@ (define-public python-cplot
 complex-valued functions.")
     (license license:gpl3)))
 
+(define-public python-perfplot
+  (package
+    (name "python-perfplot")
+    (version "0.10.2")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "perfplot" version))
+              (sha256
+               (base32
+                "0hbyv17f9ra6l6albcrqx4rylmfv2m6z4qsnhb4bar256dralvfp"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-matplotlib
+                             python-matplotx
+                             python-numpy
+                             python-rich))
+    (native-inputs (list python-flit-core
+                         python-pytest))
+    (home-page "https://github.com/nschloe/perfplot")
+    (synopsis "Performance plots for Python code snippets")
+    (description "@code{perfplot} extends Python's timeit by testing
+snippets with input parameters (e.g., the size of an array) and plotting
+the results.")
+    (license license:gpl3)))
+
 (define-public python-pysnptools
   (package
     (name "python-pysnptools")
-- 
2.42.0

Message #23 received at 66929 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 66929 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 06/10] gnu: Add python-pyfma.
Date: Sat,  4 Nov 2023 15:02:35 +0000

* gnu/packages/python-science.scm (python-pyfma): New variable.

Change-Id: I354d3d56f2799c8c9ac9b868fcacbf88dcc5c25d
---
 gnu/packages/python-science.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 275f9a27c1..83255fff90 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1858,6 +1858,31 @@ (define-public python-gpy
 machine learning algorithms based on GPs.")
     (license license:bsd-3)))
 
+(define-public python-pyfma
+  (package
+    (name "python-pyfma")
+    (version "0.1.6")
+    (source (origin
+              (method git-fetch)   ;for tests
+              (uri (git-reference
+                    (url "https://github.com/nschloe/pyfma")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "12i68jj9n1qj9phjnj6f0kmfhlsd3fqjlk9p6d4gs008azw5m8yn"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-numpy))
+    (native-inputs (list pybind11 python-pytest))
+    (home-page "https://github.com/nschloe/pyfma")
+    (synopsis "Fused multiply-add for Python")
+    (description "@code{pyfma} provides an implementation of fused
+multiply-add which computes @code{(x*y) + z} with a single rounding.
+This is useful for dot products, matrix multiplications, polynomial
+evaluations (e.g., with Horner's rule), Newton's method for evaluating
+functions, convolutions, artificial neural networks etc.")
+    (license license:expat)))
+
 (define-public python-pydicom
   (package
     (name "python-pydicom")
-- 
2.42.0

Message #26 received at 66929 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 66929 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 07/10] gnu: Add python-accupy.
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 <vkor <at> vkten.in>
 # Copyright © 2020 Nicolò Balzarotti <nicolo <at> nixo.xyz>
 # Copyright © 2020 Michael Rohleder <mike <at> rohleder.de>
-# Copyright © 2020, 2021, 2022 Felix Gruber <felgru <at> posteo.net>
+# Copyright © 2020, 2021, 2022, 2023 Felix Gruber <felgru <at> posteo.net>
 # Copyright © 2020 Ryan Prior <rprior <at> protonmail.com>
 # Copyright © 2020 Jan Wielkiewicz <tona_kosmicznego_smiecia <at> interia.pl>
 # Copyright © 2020, 2021 Brice Waegeneire <brice <at> waegenei.re>
@@ -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 <felgru <at> 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 <at> 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
+
-- 
2.42.0

Message #29 received at 66929 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 66929 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 08/10] gnu: Add python-ndim.
Date: Sat,  4 Nov 2023 15:02:37 +0000

* gnu/packages/maths.scm (python-ndim): New variable.

Change-Id: I543f1f5e195f4f2fd5bd70f9ce29ec750a24439b
---
 gnu/packages/maths.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 28e023190f..3c12cf7622 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -162,6 +162,7 @@ (define-module (gnu packages maths)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages qt)
@@ -3689,6 +3690,30 @@ (define-public python-accupy
 algorithm and summation in K-fold precision.")
     (license license:gpl3)))
 
+(define-public python-ndim
+  (package
+    (name "python-ndim")
+    (version "0.1.6")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/diego-hayashi/ndim")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1hri82k7pcpw9dns8l1f2asa3dm7hjv71wnxi3752258ia2qa44v"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-sympy))
+    (native-inputs (list python-flit-core python-pytest))
+    (home-page "https://github.com/diego-hayashi/ndim")
+    (synopsis "Multidimensional volumes and monomial integrals")
+    (description
+      "@code{ndim} computes all kinds of volumes and integrals of
+monomials over such volumes in a fast, numerically stable way, using
+recurrence relations.")
+    (license license:gpl3)))
+
 (define-public slepc
   (package
     (name "slepc")
-- 
2.42.0

Message #32 received at 66929 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 66929 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 09/10] gnu: Add python-orthopy.
Date: Sat,  4 Nov 2023 15:02:38 +0000

* gnu/packages/maths.scm (python-orthopy): New variable.

Change-Id: I75e528f30d285666b8012a9cbc5cbb7e28aaf764
---
 gnu/packages/maths.scm | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 3c12cf7622..2474e463c5 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -172,6 +172,7 @@ (define-module (gnu packages maths)
   #:use-module (gnu packages scheme)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages shells)
+  #:use-module (gnu packages simulation)
   #:use-module (gnu packages sphinx)
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages swig)
@@ -3714,6 +3715,47 @@ (define-public python-ndim
 recurrence relations.")
     (license license:gpl3)))
 
+(define-public python-orthopy
+  (package
+    (name "python-orthopy")
+    (version "0.9.5")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/diego-hayashi/orthopy")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "00s2rwjdlq38zkf7wl1gvm2aw057r30266lkzfxkrfzr4i705xnq"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+      (list python-importlib-metadata
+            python-ndim
+            python-numpy
+            python-sympy))
+    (native-inputs (list ;python-cplot  ;only used in deselected tests
+                         python-matplotx
+                         python-meshio
+                         python-meshzoo
+                         python-pytest
+                         python-scipy))
+    (arguments
+     (list
+      #:test-flags
+      ;; These tests fails with unexpected keyword arguments
+      ;; in calls to cplot.
+      #~(list "--deselect" "tests/test_u3.py::test_write_single"
+              "--deselect" "tests/test_u3.py::test_write_tree")))
+    (home-page "https://github.com/diego-hayashi/orthopy")
+    (synopsis "Tools for orthogonal polynomials, Gaussian quadrature")
+    (description "@code{orthopy} provides various orthogonal polynomial
+classes for lines, triangles, quadrilaterals, disks, spheres, hexahedra,
+and n-cubes.  All computations are done using numerically stable
+recurrence schemes.  Furthermore, all functions are fully vectorized and
+can return results in exact arithmetic.")
+    (license license:gpl3)))
+
 (define-public slepc
   (package
     (name "slepc")
-- 
2.42.0

Message #35 received at 66929 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 66929 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 10/10] gnu: Add python-quadpy.
Date: Sat,  4 Nov 2023 15:02:39 +0000

* gnu/packages/maths.scm (python-quadpy): New variable.

Change-Id: Icb5a60920465bc5861cf32ffe5dc44a9088af890
---
 gnu/packages/maths.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 2474e463c5..d73546d4c2 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -135,6 +135,7 @@ (define-module (gnu packages maths)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages image)
+  #:use-module (gnu packages image-processing)
   #:use-module (gnu packages java)
   #:use-module (gnu packages less)
   #:use-module (gnu packages lisp)
@@ -163,6 +164,7 @@ (define-module (gnu packages maths)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-build)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages qt)
@@ -3756,6 +3758,41 @@ (define-public python-orthopy
 can return results in exact arithmetic.")
     (license license:gpl3)))
 
+(define-public python-quadpy
+  (package
+    (name "python-quadpy")
+    (version "0.16.10")
+    (source
+      (origin
+        (method url-fetch)
+        ; Download zipfile from zenodo, because git checkout is missing
+        ; some data files that are stored via git-lfs.
+        (uri (string-append
+               "https://zenodo.org/records/5541216/files/nschloe/quadpy-v"
+               version
+               ".zip"))
+        (sha256
+          (base32
+            "1f989dipv7lqxvalfrvvlmhlxyl67a87lavyyqrr1mh88glhl592"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+      (list python-importlib-metadata
+            python-numpy
+            python-orthopy
+            python-scipy
+            python-sympy))
+    (native-inputs (list python-accupy python-pytest unzip vtk))
+    (home-page "https://github.com/diego-hayashi/quadpy")
+    (synopsis
+      "Numerical integration, quadrature for various domains")
+    (description
+      "More than 1500 numerical integration schemes for line segments, circles,
+  disks, triangles, quadrilaterals, spheres, balls, tetrahedra, hexahedra,
+  wedges, pyramids, n-spheres, n-balls, n-cubes, n-simplices, and the
+  1D/2D/3D/nD spaces with weight functions exp(-r) and exp(-r2) for fast
+  integration of real-, complex-, and vector-valued functions.")
+    (license license:gpl3)))
+
 (define-public slepc
   (package
     (name "slepc")
-- 
2.42.0

Message #40 received at 66929-done <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Felix Gruber <felgru <at> posteo.net>
Cc: 66929-done <at> debbugs.gnu.org
Subject: Re: [bug#66929] [PATCH 00/10] Add python-quadpy and dependencies.
Date: Mon, 04 Dec 2023 22:23:08 +0100

Hi Felix,

Felix Gruber <felgru <at> posteo.net> skribis:

> This patchset adds the quadpy Python library which collects a large
> number of different numerical integration algorithms.
>
> I've packaged a fork of the last GPL-licensed version of quadpy. Newer
> versions are distributed under a proprietary license and the history of
> the original git repository on https://github.com/nschloe/quadpy had
> been removed (hence I'm referring to a fork in the source and home-page
> fields). The same holds for the python-orthopy, python-ndim,
> python-accupy and python-meshzoo packages.
> Also, quadpy stores some required data files via git-lfs. I couldn't
> figure out how to download those git-lfs stored files in the source of
> the python-quadpy package. In the end, I resorted to instead point the
> source field to a zip file that contained the source code including
> those data files.
>
> Felix Gruber (10):
>   gnu: Add python-meshzoo.
>   gnu: Add python-matplotx.
>   gnu: Add python-npx.
>   gnu: Add python-cplot.
>   gnu: Add python-perfplot.
>   gnu: Add python-pyfma.
>   gnu: Add python-accupy.
>   gnu: Add python-ndim.
>   gnu: Add python-orthopy.
>   gnu: Add python-quadpy.

I applied the whole series with one change: replaced ‘gpl3’ with ‘gpl3+’
because these packages were all explicitly or implicitly “version 3 or
any later version”.

Thanks, and sorry for the delay!

Ludo’.

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