From 52d7ab7851a5ced97c0c8f1a602a103b5ca0b046 Mon Sep 17 00:00:00 2001
From: Ghislain Vaillant <ghislain.vaillant@inria.fr>
Date: Fri, 21 Aug 2026 11:28:54 +0200
Subject: physics: silx: Update to 3.1.1.

* guix-science/packages/physics.scm (silx)
  [source]: Swith to git-fetch, update to 3.1.1.
  [propagated-inputs]: Add python-{filelock,pydantic}.
Remove python-{hdf5plugin, pint}.
  [native-inputs]: Add python-{h5pyd,meson,pytest-httpserver,qtawesome}.
Remove python-setuptools.
---
 guix-science/packages/physics.scm | 32 +++++++++++++++++++++-----------
 1 file changed, 21 insertions(+), 11 deletions(-)

diff --git a/guix-science/packages/physics.scm b/guix-science/packages/physics.scm
index 860d7c8..f6c6b5e 100644
--- a/guix-science/packages/physics.scm
+++ b/guix-science/packages/physics.scm
@@ -57,6 +57,7 @@
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages swig)
   #:use-module (gnu packages tbb)
+  #:use-module (gnu packages time)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
@@ -1213,38 +1214,47 @@ processing analysis of X-Ray Fluorescence Spectra.")
 (define-public python-silx
   (package
     (name "python-silx")
-    (version "2.2.2")
+    (version "3.1.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "silx" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/silx-kit/silx")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "07sp5hs0ldfi5yai1jbnfvmpn390f4yqyf0ij35w8p3inmks76sx"))))
+        (base32 "1r78q7f61qpm663h7gk7rh5ymrx7knnz0gnp9k750dyip8bygjs2"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:phases
       #~(modify-phases %standard-phases
+          ;; Requires install first.
           (delete 'check)
-          (add-after 'install 'check
-            (lambda* (#:key tests? inputs outputs #:allow-other-keys)
+
+          (add-after 'add-install-to-pythonpath 'check
+            (lambda* (#:key tests? #:allow-other-keys)
               (when tests?
-                (add-installed-pythonpath inputs outputs)
                 (invoke "python3" "-c"
                  "import silx.test, sys; sys.exit(silx.test.run_tests(verbosity=2, args=['--no-gui', '--no-opengl', '--no-opencl', '-k', 'not TestHistogramnd']))")))))))
     (propagated-inputs (list python-fabio
+                             python-filelock
                              python-h5py
-                             python-hdf5plugin
                              python-numpy
                              python-packaging
-                             python-pint))
+                             python-pydantic))
     (native-inputs (list python-cython
+                         python-dateutil
+                         python-h5pyd
+                         python-matplotlib
+                         python-meson
                          python-pyopengl
-                         python-pyqt
+                         python-pyside-6
                          python-pytest
+                         python-pytest-httpserver
                          python-pytest-mock
                          python-pytest-xvfb
-                         python-setuptools))
+                         python-qtawesome))
     (home-page "https://www.silx.org")
     (synopsis "Software library for X-ray data analysis")
     (description
-- 
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