GNU bug report logs - #76259
[PATCH 0/3] Add python-triangle, python-pandamesh and update gmsh to 4.13.1.

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

From: Lars Bilke <lars.bilke <at> ufz.de>
To: guix-patches <at> gnu.org
Cc: Lars Bilke <lars.bilke <at> ufz.de>
Subject: [PATCH 0/3] Add python-triangle,
 python-pandamesh and update gmsh to 4.13.1.
Date: Thu, 13 Feb 2025 10:34:32 +0100

Added new package python-pandamesh which requires gmsh 4.13.1 and python-triangle.

Lars Bilke (3):
  gnu: gmsh: Update to 4.13.1.
  gnu: Add python-triangle.
  gnu: Add python-pandamesh.

 gnu/packages/geo.scm        | 35 +++++++++++++++++++++++++++++++++++
 gnu/packages/maths.scm      |  4 ++--
 gnu/packages/python-xyz.scm | 33 +++++++++++++++++++++++++++++++++
 3 files changed, 70 insertions(+), 2 deletions(-)


base-commit: bcce7f8fa8b821b76591b297f61d473c5972e397
-- 
2.46.1

Message #8 received at 76259 <at> debbugs.gnu.org (full text, mbox):

From: Lars Bilke <lars.bilke <at> ufz.de>
To: 76259 <at> debbugs.gnu.org
Cc: Lars Bilke <lars.bilke <at> ufz.de>
Subject: [PATCH 1/3] gnu: gmsh: Update to 4.13.1.
Date: Thu, 13 Feb 2025 10:38:41 +0100

* gnu/packages/maths.scm (gmsh): Update to 4.13.1.

Change-Id: Iee56d09055f0803c4f4bc432402dadb3d34bc107
---
 gnu/packages/maths.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 4a1637b952..8427b7f6db 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -3437,7 +3437,7 @@ (define-public fast-downward
 (define-public gmsh
   (package
     (name "gmsh")
-    (version "4.11.1")
+    (version "4.13.1")
     (source
      (origin
        (method git-fetch)
@@ -3448,7 +3448,7 @@ (define-public gmsh
                              (string-replace-substring version "." "_")))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1d6n7qqj9xpfgh7v5jif565waiqjhahkh21pi5s1vr84y61wxyx8"))
+        (base32 "16abxhadyyj7890lv6cdfxskg25w105pcpqvb5iwf6a59py8na8y"))
        (modules '((guix build utils)))
        (snippet
         '(delete-file-recursively "contrib/metis"))))
-- 
2.46.1

Message #11 received at 76259 <at> debbugs.gnu.org (full text, mbox):

From: Lars Bilke <lars.bilke <at> ufz.de>
To: 76259 <at> debbugs.gnu.org
Cc: Lars Bilke <lars.bilke <at> ufz.de>
Subject: [PATCH 2/3] gnu: Add python-triangle.
Date: Thu, 13 Feb 2025 10:38:42 +0100

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

Change-Id: I0bc8f96eaf3c2c7d45277ce2ae54ed3b526f8e15
---
 gnu/packages/python-xyz.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 5f359d9c54..dde22ebc27 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -161,6 +161,7 @@
 ;;; Copyright © 2025 Jordan Moore <lockbox <at> struct.foo>
 ;;; Copyright © 2025 Dariqq <dariqq <at> posteo.net>
 ;;; Copyright © 2025 Nguyễn Gia Phong <mcsinyx <at> disroot.org>
+;;; Copyright © 2025 Lars Bilke <lars.bilke <at> ufz.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -36144,6 +36145,38 @@ (define-public python-pyhull
 Voronoi diagram.")
     (license license:expat)))
 
+(define-public python-triangle
+  (package
+    (name "python-triangle")
+    (version "20250106")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/drufat/triangle")
+             (commit (string-append "v" version))
+             (recursive? #t)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1fj8a64k94mibdz5i6zzmlgs0bvsfsa5qns33ppv8wl306yxq1d3"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases #~(modify-phases %standard-phases
+                   (replace 'check
+                     (lambda* (#:key tests? #:allow-other-keys)
+                       (when tests?
+                         (invoke "pytest" "-v")))))))
+    (propagated-inputs (list python-numpy))
+    (native-inputs (list python-setuptools python-wheel python-pytest))
+    (home-page "https://github.com/drufat/triangle")
+    (synopsis "Python bindings to the triangle library")
+    (description
+     "Triangle is a python wrapper around Jonathan Richard
+Shewchuk's two-dimensional quality mesh generator and delaunay
+triangulator library.")
+    (license license:lgpl3)))
+
 (define-public python-opcodes
   ;; There are no tags in this repo, but 'opcodes/__init__.py' specifies a
   ;; version number, which is what we use here.
-- 
2.46.1

Message #14 received at 76259 <at> debbugs.gnu.org (full text, mbox):

From: Lars Bilke <lars.bilke <at> ufz.de>
To: 76259 <at> debbugs.gnu.org
Cc: Lars Bilke <lars.bilke <at> ufz.de>
Subject: [PATCH 3/3] gnu: Add python-pandamesh.
Date: Thu, 13 Feb 2025 10:38:43 +0100

* gnu/packages/geo.scm (python-pandamesh): New variable.

Change-Id: I084c772f859cde3be4d4b611cba6b5420067bbe8
---
 gnu/packages/geo.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index d7cef57cde..0070b8a3c1 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1091,6 +1091,41 @@ (define-public python-geopandas
 require a spatial database such as PostGIS.")
     (license license:bsd-3)))
 
+(define-public python-pandamesh
+  (package
+    (name "python-pandamesh")
+    (version "0.2.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Deltares/pandamesh")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1gnrxw8zxcdkkqzw08lrmnz946bp507r9zn1djhaxxqjs09yzmqp"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases #~(modify-phases %standard-phases
+                   (replace 'check
+                     (lambda* (#:key tests? #:allow-other-keys)
+                       (when tests?
+                         ;; tests requiring network disabled
+                         (invoke "pytest" "-v" "--ignore=tests/test_data.py")))))))
+    (propagated-inputs (list gmsh
+                             python-geopandas
+                             python-matplotlib
+                             python-pooch
+                             python-shapely
+                             python-triangle
+                             python-xarray))
+    (native-inputs (list python-hatchling python-pytest))
+    (home-page "https://deltares.github.io/pandamesh/")
+    (synopsis "From geodataframe to mesh")
+    (description "From geodataframe to mesh.")
+    (license license:expat)))
+
 (define-public python-overpass
   (package
     (name "python-overpass")
-- 
2.46.1

Message #17 received at 76259 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76259 <at> debbugs.gnu.org
Subject: [PATCH 0/3] Add python-triangle, python-pandamesh and update gmsh
 to 4.13.1.
Date: Thu, 13 Feb 2025 10:19:10 +0000

[Message part 1 (text/plain, inline)]

Hi Lars,

Thank you for the patches.

I've got some simplification review comments.

--8<---------------cut here---------------start------------->8---
+    (native-inputs (list python-setuptools python-wheel python-pytest))
--8<---------------cut here---------------end--------------->8---
Please sort alphabetically.

--8<---------------cut here---------------start------------->8---
+     (list
+      #:phases #~(modify-phases %standard-phases
+                   (replace 'check
+                     (lambda* (#:key tests? #:allow-other-keys)
+                       (when tests?
+                         (invoke "pytest" "-v")))))))
--8<---------------cut here---------------end--------------->8---
This may be removed as pyproject-build-system tries to detect available
test runner e.g. pytest in your case and does all setup within build
system flow.

--8<---------------cut here---------------start------------->8---
+    (arguments
+     (list
+      #:phases #~(modify-phases %standard-phases
+                   (replace 'check
+                     (lambda* (#:key tests? #:allow-other-keys)
+                       (when tests?
+                         ;; tests requiring network disabled
+                         (invoke "pytest" "-v" "--ignore=tests/test_data.py")))))))
--8<---------------cut here---------------end--------------->8---
Likewise, you may utiize #:test-flags instead of adding custom phase.

--8<---------------cut here---------------start------------->8---
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/drufat/triangle")
+             (commit (string-append "v" version))
+             (recursive? #t)))
--8<---------------cut here---------------end--------------->8---
I guess the project contains git submodules, may you double check if may
replace them with our own?

gmsh is save to be refreshed on master:

--8<---------------cut here---------------start------------->8---
guix refresh --list-dependent gmsh
Building the following 3 packages
would ensure 4 dependent packages are rebuilt: python-pygmsh <at> 7.1.17
openfoam-com <at> 2212 openfoam-org <at> 10.20230119
--8<---------------cut here---------------end--------------->8---

Waiting for v2!

--
Oleg

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Message #20 received at 76259 <at> debbugs.gnu.org (full text, mbox):

From: Lars Bilke <lars.bilke <at> ufz.de>
To: 76259 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 0/3] Add python-triangle,
 python-pandamesh and update gmsh to 4.13.1.
Date: Fri, 14 Feb 2025 10:04:01 +0100

Dear Oleg,

thanks a lot for your helpful review!

Unfortunately, I have to retract the patches for python-triangle and python-pandamesh:

Although python-triangle is LGPL licensed, it wraps Jonathan Richard Shewchuks triangle library, which has a proprietary non-commercial license:

--8<---------------cut here---------------start------------->8---
These programs may be freely redistributed under the condition that the
copyright notices (including the copy of this notice in the code comments
and the copyright notice printed when the `-h' switch is selected) are
not removed, and no compensation is received.  Private, research, and
institutional use is free.  You may distribute modified versions of this
code UNDER THE CONDITION THAT THIS CODE AND ANY MODIFICATIONS MADE TO IT
IN THE SAME FILE REMAIN UNDER COPYRIGHT OF THE ORIGINAL AUTHOR, BOTH
SOURCE AND OBJECT CODE ARE MADE FREELY AVAILABLE WITHOUT CHARGE, AND
CLEAR NOTICE IS GIVEN OF THE MODIFICATIONS.  Distribution of this code as
part of a commercial system is permissible ONLY BY DIRECT ARRANGEMENT
WITH THE AUTHOR.  (If you are not directly supplying this code to a
customer, and you are instead telling them how they can obtain it for
free, then you are not required to make any arrangement with me.)
--8<---------------cut here---------------end--------------->8---

So I think this is not suited for Guix.

Feel free to merge the gmsh update commit and close this issue.

Sincerely,
Lars

Message #25 received at 76259-done <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76259-done <at> debbugs.gnu.org
Subject: [PATCH 0/3] Add python-triangle, python-pandamesh and update gmsh
 to 4.13.1.
Date: Fri, 14 Feb 2025 11:08:28 +0000

[Message part 1 (text/plain, inline)]

Hi Lars,

I've pushed gmsh update after it built succefully on my machine:
--8<---------------cut here---------------start------------->8---
> ./pre-inst-env guix build  gmsh
/gnu/store/p3zgbzgv7gvzj3f2gzfv0b04g7w16dzg-gmsh-4.13.1
--8<---------------cut here---------------end--------------->8---

Pushed to master as 3a916935311568b742d734cf76be8a45737f9382.

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