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

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Package: guix-patches; Reported by: Lars Bilke <lars.bilke@HIDDEN>; Keywords: patch; dated Thu, 13 Feb 2025 09:36:02 UTC; Maintainer for guix-patches is guix-patches@HIDDEN.

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From: Sharlatan Hellseher <sharlatanus@HIDDEN>
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
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--=-=-=
Content-Type: text/plain


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@HIDDEN
openfoam-com@2212 openfoam-org@HIDDEN
--8<---------------cut here---------------end--------------->8---

Waiting for v2!

--
Oleg

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Information forwarded to guix-patches@HIDDEN:
bug#76259; Package guix-patches. Full text available.

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Date: Thu, 13 Feb 2025 10:38:43 +0100
From: Lars Bilke <lars.bilke@HIDDEN>
Subject: [PATCH 3/3] gnu: Add python-pandamesh.
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* 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
Information forwarded to andreas@HIDDEN, bavier@HIDDEN, sharlatanus@HIDDEN, guix-patches@HIDDEN:
bug#76259; Package guix-patches. Full text available.

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Date: Thu, 13 Feb 2025 10:38:42 +0100
From: Lars Bilke <lars.bilke@HIDDEN>
Subject: [PATCH 2/3] gnu: Add python-triangle.
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* 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@HIDDEN>
 ;;; Copyright © 2025 Dariqq <dariqq@HIDDEN>
 ;;; Copyright © 2025 Nguyễn Gia Phong <mcsinyx@HIDDEN>
+;;; Copyright © 2025 Lars Bilke <lars.bilke@HIDDEN>
 ;;;
 ;;; 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
Information forwarded to lars@HIDDEN, marius@HIDDEN, me@HIDDEN, sharlatanus@HIDDEN, tanguy@HIDDEN, jgart@HIDDEN, guix-patches@HIDDEN:
bug#76259; Package guix-patches. Full text available.

Message received at 76259 <at> debbugs.gnu.org:


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Date: Thu, 13 Feb 2025 10:38:41 +0100
From: Lars Bilke <lars.bilke@HIDDEN>
Subject: [PATCH 1/3] gnu: gmsh: Update to 4.13.1.
In-reply-to: <cover.1739439090.git.lars.bilke@HIDDEN>
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* 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
Information forwarded to andreas@HIDDEN, bavier@HIDDEN, sharlatanus@HIDDEN, guix-patches@HIDDEN:
bug#76259; Package guix-patches. Full text available.

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Date: Thu, 13 Feb 2025 10:34:32 +0100
From: Lars Bilke <lars.bilke@HIDDEN>
Subject: [PATCH 0/3] Add python-triangle,
 python-pandamesh and update gmsh to 4.13.1.
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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
Acknowledgement sent to Lars Bilke <lars.bilke@HIDDEN>:
New bug report received and forwarded. Copy sent to andreas@HIDDEN, bavier@HIDDEN, sharlatanus@HIDDEN, guix-patches@HIDDEN. Full text available.
Report forwarded to andreas@HIDDEN, bavier@HIDDEN, sharlatanus@HIDDEN, guix-patches@HIDDEN:
bug#76259; Package guix-patches. Full text available.
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