gnu: Add python-openspace-api.

* gnu/packages/astronomy.scm (python-openspace-api): New variable.

Change-Id: Idffd14b9600024a31adbb479c25ca498781853c1

doc/guix.texi

@@ -53,7 +53,7 @@ Copyright @copyright{} 2017, 2019--2026 Maxim Cournoyer@*
 Copyright @copyright{} 2017–2022 Tobias Geerinckx-Rice@*
 Copyright @copyright{} 2017 George Clemmer@*
 Copyright @copyright{} 2017 Andy Wingo@*
-Copyright @copyright{} 2017, 2018, 2019, 2020, 2023, 2024, 2025 Arun Isaac@*
+Copyright @copyright{} 2017, 2018, 2019, 2020, 2023, 2024, 2025, 2026 Arun Isaac@*
 Copyright @copyright{} 2017 nee@*
 Copyright @copyright{} 2018 Rutger Helling@*
 Copyright @copyright{} 2018, 2021, 2023, 2025, 2026 Oleg Pykhalov@*
@@ -124,7 +124,7 @@ Copyright @copyright{} 2023 Thomas Ieong@*
 Copyright @copyright{} 2023 Saku Laesvuori@*
 Copyright @copyright{} 2023 Graham James Addis@*
 Copyright @copyright{} 2023-2025 Tomas Volf@*
-Copyright @copyright{} 2024, 2025 Herman Rimm@*
+Copyright @copyright{} 2024-2026 Herman Rimm@*
 Copyright @copyright{} 2024 Matthew Trzcinski@*
 Copyright @copyright{} 2024 Richard Sent@*
 Copyright @copyright{} 2024 Dariqq@*
@@ -16710,6 +16710,12 @@ guix lint @var{options} @var{package}@dots{}
 @end example
 
 If no package is given on the command line, then all packages are checked.
+To check packages in particular source files, the syntax is:
+
+@example
+guix lint @var{options} --whole-file @var{file}@dots{}
+@end example
+
 The @var{options} may be zero or more of the following:
 
 @table @code
@@ -16747,9 +16753,23 @@ Only enable the checkers that do not depend on Internet access.
 Add @var{directory} to the front of the package module search path
 (@pxref{Package Modules}).
 
-This allows users to define their own packages and make them visible to
-the command-line tools.
+@item --whole-file
+@itemx -f
+Check the top-level package definitions in the given files; subsequent
+arguments are treated as file names rather than package names.  This
+option also enables a special checker which checks if a package
+alphabetically succeeds the one above it.
 
+For example, to check if the packages in @file{gnu/packages/matrix.scm}
+are sorted alphabetically, and if the package names therein follow
+established conventions, run:
+
+@example
+guix lint -c name -f gnu/packages/matrix.scm
+@end example
+
+The previous two options allow users to define their own packages and
+make them visible to the command-line tools.
 @end table
 
 @node Invoking guix size
@@ -36741,13 +36761,16 @@ The Mumi package to use.
 Data directory to store Debbugs data from upstream Debbugs instance.
 
 @item @code{rsync-remote}
-Remote rsync path from which to download Debbugs data.  The remote is
-polled every 5 minutes, unless a previous instance of rsync is already
-running.
+Remote rsync path from which to download Debbugs data.
 
 @item @code{rsync-flags} (default: @code{'()})
 Additional flags to pass to @command{rsync}.
 
+@item @code{rsync-and-index-event} (default: @code{#~(calendar-event #:minutes '#$(iota 12 0 5))})
+Shepherd calendar event to run the rsync and indexing timer at.  By
+default, this is once every 5 minutes.  The timer job is not run if an
+earlier instance of it is still running.
+
 @item @code{mailer?} (default: @code{#true})
 Whether to enable or disable the mailer component.
 

gnu/local.mk

@@ -1101,7 +1101,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/catdoc-CVE-2017-11110.patch		\
   %D%/packages/patches/chez-irregex-import-cond-expand.patch	\
   %D%/packages/patches/chez-scheme-bin-sh.patch			\
-  %D%/packages/patches/cianna-remove-error-for-missing-cuda.patch		\
   %D%/packages/patches/circos-remove-findbin.patch		\
   %D%/packages/patches/cdparanoia-fpic.patch			\
   %D%/packages/patches/cdrkit-libre-cross-compile.patch	\
@@ -2023,7 +2022,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/ocaml-4.07-dynamically-allocate-signal-stack.patch	\
   %D%/packages/patches/ocaml-4.09-dynamically-allocate-signal-stack.patch	\
   %D%/packages/patches/ocaml-4.09-multiple-definitions.patch	\
-  %D%/packages/patches/ogs-6.5.7-netcdfconverter.patch \
   %D%/packages/patches/omake-fix-non-determinism.patch	\
   %D%/packages/patches/oneko-remove-nonfree-characters.patch	\
   %D%/packages/patches/onetbb-other-arches.patch	\
@@ -2628,6 +2626,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/x265-arm-flags.patch			\
   %D%/packages/patches/x265-4-arm-flags.patch			\
   %D%/packages/patches/xdg-desktop-portal-wlr-harcoded-length.patch\
+  %D%/packages/patches/xdmf-3.0.0-hdf5.patch \
   %D%/packages/patches/xf86-video-siliconmotion-fix-ftbfs.patch \
   %D%/packages/patches/xfig-Enable-error-message-for-missing-libraries.patch		\
   %D%/packages/patches/xfig-Fix-double-free-when-requesting-MediaBox.patch		\

gnu/packages/bioinformatics.scm

@@ -18002,7 +18002,7 @@ expression report comparing samples in an easily configurable manner.")
            fastqc
            bowtie
            idr
-           snakemake-7
+           snakemake
            samtools
            bedtools
            kentutils))
@@ -18020,80 +18020,87 @@ in an easily configurable manner.")
     (license license:gpl3+)))
 
 (define-public pigx-bsseq
-  (package
-    (name "pigx-bsseq")
-    (version "0.1.10")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
-                                  "releases/download/v" version
-                                  "/pigx_bsseq-" version ".tar.gz"))
-              (sha256
-               (base32
-                "1vy3mhbrfdnjbhikwg3mgkfnwnzk96a1n27cxrr7gsffpmz9q6wa"))))
-    (build-system gnu-build-system)
-    (arguments
-     (list
-      ;; TODO: tests currently require 12+GB of RAM.  See
-      ;; https://github.com/BIMSBbioinfo/pigx_bsseq/issues/164
-      #:tests? #f
-      #:phases
-      '(modify-phases %standard-phases
-         (add-before 'configure 'set-PYTHONPATH
-           (lambda _
-             (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))
-         (add-before 'check 'set-timezone
-           ;; The readr package is picky about timezones.
-           (lambda* (#:key inputs #:allow-other-keys)
-             (setenv "TZ" "UTC+1")
-             (setenv "TZDIR"
-                     (search-input-directory inputs
-                                             "share/zoneinfo"))))
-         (add-before 'check 'pre-check
-           (lambda _
-             ;; Needed for tests
-             (setenv "HOME" "/tmp"))))))
-    (native-inputs
-     (list tzdata-for-tests))
-    (inputs
-     (list coreutils
-           sed
-           grep
-           r-minimal
-           r-annotationhub
-           r-dt
-           r-genomation
-           r-ggbio
-           r-ggrepel
-           r-matrixstats
-           r-methylkit
-           r-reshape2
-           r-rtracklayer
-           r-rmarkdown
-           r-bookdown
-           r-ggplot2
-           r-ggbio
-           pandoc
-           python-wrapper
-           python-pyyaml
-           snakemake-7
-           bismark
-           bowtie
-           bwa-meth
-           fastqc
-           methyldackel
-           multiqc
-           trim-galore
-           cutadapt
-           samblaster
-           samtools))
-    (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
-    (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")
-    (description "PiGx BSseq is a data processing pipeline for raw fastq read
+  (let ((commit "1b3a69bd5363fa882af4193215de7fb475bae066"))
+    (package
+      (name "pigx-bsseq")
+      (version (git-version "0.1.10" "0" commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/BIMSBbioinfo/pigx_bsseq/")
+                       (commit commit)
+                       (recursive? #true)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0r0gjfycgh1hqba7ma03bwxlvr2kz68yzclx5iba3wrxxqmivil6"))))
+      (build-system gnu-build-system)
+      (arguments
+       (list
+        ;; TODO: tests currently require 12+GB of RAM.  See
+        ;; https://github.com/BIMSBbioinfo/pigx_bsseq/issues/164
+        #:tests? #f
+        #:phases
+        '(modify-phases %standard-phases
+           ;; This file is meant for development, but it interferes with
+           ;; Makefile.
+           (add-after 'unpack 'delete-GNUmakefile
+             (lambda _ (delete-file "GNUmakefile")))
+           (add-before 'configure 'set-PYTHONPATH
+             (lambda _
+               (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))
+           (add-before 'check 'set-timezone
+             ;; The readr package is picky about timezones.
+             (lambda* (#:key inputs #:allow-other-keys)
+               (setenv "TZ" "UTC+1")
+               (setenv "TZDIR"
+                       (search-input-directory inputs
+                                               "share/zoneinfo"))))
+           (add-before 'check 'pre-check
+             (lambda _
+               ;; Needed for tests
+               (setenv "HOME" "/tmp"))))))
+      (native-inputs
+       (list tzdata-for-tests autoconf automake))
+      (inputs
+       (list coreutils
+             sed
+             grep
+             r-minimal
+             r-annotationhub
+             r-dt
+             r-genomation
+             r-ggbio
+             r-ggrepel
+             r-matrixstats
+             r-methylkit
+             r-reshape2
+             r-rtracklayer
+             r-rmarkdown
+             r-bookdown
+             r-ggplot2
+             r-ggbio
+             pandoc
+             python-wrapper
+             python-pyyaml
+             snakemake
+             bismark
+             bowtie
+             bwa-meth
+             fastqc
+             methyldackel
+             multiqc
+             trim-galore
+             cutadapt
+             samblaster
+             samtools))
+      (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
+      (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")
+      (description "PiGx BSseq is a data processing pipeline for raw fastq read
 data of bisulfite experiments; it produces reports on aggregate methylation
 and coverage and can be used to produce information on differential
 methylation and segmentation.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public pigx-scrnaseq
   (package
@@ -18266,7 +18273,7 @@ based methods.")
            r-tidyr
            r-viridis
            samtools
-           snakemake-7
+           snakemake
            wget))
     (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
     (synopsis "Analysis pipeline for wastewater sequencing")

gnu/packages/clojure.scm

@@ -23,19 +23,24 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages clojure)
-  #:use-module (gnu packages)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages golang-build)
+  #:use-module (gnu packages golang-check)
+  #:use-module (gnu packages golang-xyz)
+  #:use-module (gnu packages golang)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages java)
   #:use-module (gnu packages maven)
-  #:use-module (guix gexp)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages)
-  #:use-module (guix download)
-  #:use-module (guix git-download)
+  #:use-module (gnu packages)
   #:use-module (guix build-system ant)
+  #:use-module (guix build-system clojure)
   #:use-module (guix build-system copy)
-  #:use-module (guix build-system clojure))
+  #:use-module (guix build-system go)
+  #:use-module (guix download)
+  #:use-module (guix gexp)
+  #:use-module (guix git-download)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages))
 
 (define-public clojure-spec-alpha
   (package
@@ -1253,3 +1258,44 @@ an operation on the service. invoke takes a map and returns a map, and works
 the same way for every operation on every service.")
     (home-page "https://github.com/cognitect-labs/aws-api")
     (license license:asl2.0)))
+
+(define-public let-go
+  (package
+    (name "let-go")
+    (version "1.7.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/nooga/let-go")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "139a129fw3w9a4bcfgms60ll90vy2vmqinbmjn44zmgx4fr2adif"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:go go-1.26
+      #:install-source? #f
+      #:import-path "github.com/nooga/let-go"))
+    (native-inputs
+     (list go-github-com-davecgh-go-spew
+           go-github-com-alimpfard-line
+           go-github-com-hashicorp-go-uuid
+           go-github-com-kr-pretty
+           go-github-com-pmezard-go-difflib
+           go-github-com-stretchr-testify
+           go-github-com-zeebo-bencode
+           go-golang-org-x-sys
+           go-gopkg-in-check-v1
+           go-gopkg-in-yaml-v3))
+    (home-page "https://nooga.github.io/let-go")
+    (synopsis "Clojure dialect written in Go")
+    (description
+     "let-go is a Clojure dialect with a bytecode compiler and a stack virtual
+machine, written in the Go programming language.
+
+It is not a drop-in replacement for Clojure JVM.  It does not load JARs and
+does not aim to.  Most idiomatic Clojure code runs unmodified, but a real
+project with library dependencies will need adjustments.")
+    (license license:expat)))

gnu/packages/geo.scm

@@ -807,7 +807,7 @@ OpenGeoSys")
 (define-public ogs-serial
   (package
     (name "ogs-serial")
-    (version "6.5.7")
+    (version "6.5.8")
     (source
      (origin
        (method git-fetch)
@@ -816,9 +816,7 @@ OpenGeoSys")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1wflgkbcsa4sr8g63img0ld6h4jm1b7hjzsa2m4gsbzc6j7kd41w"))
-       ;; Remove patch on next release, likely 6.5.8
-       (patches (search-patches "ogs-6.5.7-netcdfconverter.patch"))))
+        (base32 "037il6jw2j1g7bvrwvbp20yf0cnz7c7f3wmszxfv5ay7l54sffqg"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -873,6 +871,7 @@ OpenGeoSys")
            tclap
            tfel
            vtk
+           xdmf
            xmlpatch
            zlib))
     (propagated-inputs
@@ -1249,21 +1248,32 @@ readily with other Python GIS packages such as pyproj, Rtree, and Shapely.")
 (define-public python-geopack
   (package
     (name "python-geopack")
-    (version "1.0.12")
+    ;; See: <https://github.com/tsssss/geopack/issues/26>.
+    (properties '((commit . "8c5f0e0f6752604c5a6f57bac752059e0f85edbb")
+                  (revision . "0")))
+    (version (git-version "1.0.13"
+                          (assoc-ref properties 'revision)
+                          (assoc-ref properties 'commit)))
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
               (url "https://github.com/tsssss/geopack")
-              (commit (string-append "v" version))))
+              (commit (assoc-ref properties 'commit))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0ap5j4359xxjkbz06y097yq5d37sxcwlnlsfwrv6dvza7ydmgcgg"))))
+        (base32 "0ywqg9j09mhpfb9dcjmnlvh26s0v4lvzfwdmlivgx9ypamafa117"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       ;; XXX Reported upstream <https://github.com/tsssss/geopack/issues/21>.
-      #:tests? #f))
+      #:tests? #f
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'set-version
+            (lambda _
+              (substitute* "setup.py"
+                (("1.0.12") "1.0.13")))))))
     (native-inputs
      (list python-setuptools))
     (propagated-inputs

gnu/packages/golang-crypto.scm

@@ -4293,7 +4293,7 @@ purpose of improving obfs4proxy's meek_lite transport.")
 (define-public go-go-mau-fi-libsignal
   (package
     (name "go-go-mau-fi-libsignal")
-    (version "0.1.2")
+    (version "0.2.1")
     (source
      (origin
        (method git-fetch)
@@ -4309,7 +4309,7 @@ purpose of improving obfs4proxy's meek_lite transport.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1pd2kijza7dr5nbgfw176ca1r3rmgpx8h22gqjp557awxqhw9lzr"))))
+        (base32 "0jwqhaaqjf5fb322karppisbg5s1la459a0cwvhbii899nzyd59k"))))
     (build-system go-build-system)
     (arguments
      (list

gnu/packages/golang-graphics.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2026 Sughosha <sughosha@disroot.org>
+;;; Copyright © 2026 orahcio <orahcio@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -249,3 +250,88 @@ multiple return values, Go's native multiple return values are used instead.
 Whenever a native GTK call could return an unexpected NULL pointer, an
 additional error is returned in the Go binding.")
     (license license:isc)))
+
+(define-public go-github-com-jackmordaunt-icns-v3
+  (package
+    (name "go-github-com-jackmordaunt-icns-v3")
+    (version "3.0.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/JackMordaunt/icns")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "04wnxv79b1xbca16kgz98zc929q60lwcgcc6q784lkz2a1clh2z2"))
+       (modules '((guix build utils)))
+       (snippet
+        #~(begin
+            ;; Submodules with their own go.mod files and packaged separately:
+            (delete-file-recursively "cmd")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/jackmordaunt/icns/v3"
+      #:test-flags #~(list "-vet=off")))
+    (propagated-inputs
+     (list go-github-com-nfnt-resize))
+    (home-page "https://github.com/jackmordaunt/icns")
+    (synopsis "Easily create .icns files")
+    (description
+     "This package provides Go library to easily convert @code{.jpg} and
+@code{.png} to @code{.icns}, or to convert from any @code{image.Image} to
+@code{.icns}.")
+    (license license:expat)))
+
+(define-public go-github-com-sergeymakinen-go-bmp
+  (package
+    (name "go-github-com-sergeymakinen-go-bmp")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/sergeymakinen/go-bmp")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0bglvxqmjvgclcfjpkznxyifj5r0bh837c2iw6x1vylc7lqcq07h"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/sergeymakinen/go-bmp"))
+    (home-page "https://github.com/sergeymakinen/go-bmp")
+    (synopsis "BMP image decoder and encoder")
+    (description "Package bmp implements a BMP image decoder and encoder.")
+    (license license:bsd-3)))
+
+(define-public go-github-com-sergeymakinen-go-ico
+  (package
+    (name "go-github-com-sergeymakinen-go-ico")
+    (version "1.0.0-beta.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/sergeymakinen/go-ico")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "115fgnhn1j91zvkigl1x03jkc2dn6vx7qvfmm6l59d24qkfv6cwn"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/sergeymakinen/go-ico"))
+    (propagated-inputs
+     (list go-github-com-sergeymakinen-go-bmp))
+    (home-page "https://github.com/sergeymakinen/go-ico")
+    (synopsis "ICO and CUR file decoders and encoders")
+    (description "Package ico implements an ICO file decoder and encoder.")
+    (license license:bsd-3)))
+
+;;;
+;;; Avoid adding new packages to the end of this file. To reduce the chances
+;;; of a merge conflict, place them above in alphabetic order:
+;;; guix import --insert=gnu/packages/golang-graphics.scm pypi <package-name>.
+;;;

gnu/packages/golang-web.scm

@@ -3724,6 +3724,51 @@ lookups.  It implements looking up the following records:
 Storage}.")
     (license license:asl2.0)))
 
+(define-public go-github-com-beeper-argo-go
+  (package
+    (name "go-github-com-beeper-argo-go")
+    (version "1.1.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/beeper/argo-go")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1c11aqbap9yxpnc8bvzjiy5cg53brhc47hw2q24xjvbw5d90r2ff"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/beeper/argo-go"
+      #:embed-files #~(list "prelude.graphql")
+      #:test-flags
+      #~(list "-vet=off"
+              "-skip" (string-join
+                       ;; These test groups fail with panic by similar error:
+                       ;; UnsignedDecode failed for 10000000000000000000000:
+                       ;; varint: varint too large for 64-bit. Encoded:
+                       ;; 80808092abb7b2f099bc08.
+                       (list "TestUnsignedRoundTrip"
+                             "TestQueriesEquivalence"
+                             "TestStarWarsEquivalence"
+                             "TestZigZagRoundTrip"
+                             ;; UnsignedDecode error mismatch for too long
+                             ;; varint.
+                             "TestUnsignedDecodeTooLong")
+                       "|"))))
+    (native-inputs
+     (list go-github-com-stretchr-testify))
+    (propagated-inputs
+     (list go-github-com-elliotchance-orderedmap-v3
+           go-github-com-vektah-gqlparser-v2))
+    (home-page "https://github.com/beeper/argo-go")
+    (synopsis "Go implementation of Argo for GraphQL")
+    (description
+     "Go implementation of Argo, a compact and compressible binary
+serialization format for GraphQL.")
+    (license license:expat)))
+
 (define-public go-github-com-beevik-ntp
   (package
     (name "go-github-com-beevik-ntp")
@@ -20872,28 +20917,30 @@ state machine.  See @url{https://raft.github.io/raft.pdf} for more info.")
 (define-public go-go-mau-fi-whatsmeow
   (package
     (name "go-go-mau-fi-whatsmeow")
-    (version "0.0.0-20241215104421-68b0856cce22")
+    (version "0.0.0-20260529101937-a7ea56383ec4")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
-             (url "https://github.com/tulir/whatsmeow")
-             (commit (go-version->git-ref version))))
+              (url "https://github.com/tulir/whatsmeow")
+              (commit (go-version->git-ref version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1y3h132g3w6ihc8jn587wvyha9xm3sinjlr0znqq7krvynz3z8id"))))
+        (base32 "0i6vcn6l5sf0wsyr3k856xiz5pq3ivl9a7xd1bzqzlq74jmivivc"))))
     (build-system go-build-system)
     (arguments
      (list
       #:import-path "go.mau.fi/whatsmeow"))
     (propagated-inputs
-     (list go-github-com-google-uuid
-           go-github-com-gorilla-websocket
+     (list go-github-com-beeper-argo-go
+           go-github-com-coder-websocket
+           go-github-com-google-uuid
            go-github-com-rs-zerolog
            go-go-mau-fi-libsignal
            go-go-mau-fi-util
            go-golang-org-x-crypto
            go-golang-org-x-net
+           go-golang-org-x-sync
            go-google-golang-org-protobuf))
     (home-page "https://go.mau.fi/whatsmeow")
     (synopsis "Go library for the WhatsApp web multidevice API")
@@ -23343,16 +23390,16 @@ the code or routes.")
 (define-public go-maunium-net-go-mautrix
   (package
     (name "go-maunium-net-go-mautrix")
-    (version "0.22.1")
+    (version "0.28.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
-             (url "https://github.com/mautrix/go")
-             (commit (string-append "v" version))))
+              (url "https://github.com/mautrix/go")
+              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0msqbs3qc9ljckj41hgvp16p0sbfzm25wzldb68av9svimscwnmm"))))
+        (base32 "09isb4q876mkcwm2yk7vgzwhd3yw1n0s78qvdb7wpmab6vvxjnlf"))))
     (build-system go-build-system)
     (arguments
      (list
@@ -23368,27 +23415,32 @@ the code or routes.")
          ;; golang.org/x/net/publicsuffix/table.go:33:12: pattern data/text:
          ;; cannot embed irregular file data/text
          "text")
-    #:test-flags
-    #~(list "-skip" (string-join
-                     ;; Network access is required for the tets.
-                     (list "TestClient_Version"
-                           "TestResolveServerName/RM_Step_3B"
-                           "TestResolveServerName/RM_Step_3C"
-                           "TestResolveServerName/RM_Step_3C_MSC4040"
-                           "TestResolveServerName/RM_Step_3D"
-                           "TestResolveServerName/RM_Step_4"
-                           "TestResolveServerName/RM_Step_4_MSC4040"
-                           "TestResolveServerName/maunium")
-                     "|")
-            "-vet=off")))
-    ;; XXX: The final application needs a "libolm" package.
-    (native-inputs
-     (list olm))
+      #:test-flags
+      #~(list "-skip" (string-join
+                       ;; Network access is required for the tets.
+                       (list "TestCrossSignVerification_ScanQRAndConfirmScan"
+                             "TestSelfVerification_Accept_QRContents"
+                             "TestSelfVerification_ScanQRAndConfirmScan"
+                             "TestSelfVerification_ScanQRTransactionIDCorrup"
+                             "TestSelfVerification_ScanQRKeyCorrupted"
+                             "TestVerification_SAS"
+                             "TestVerification_SAS_BothCallStart"
+                             "TestVerification_Start"
+                             "TestVerification_StartThenCancel"
+                             "TestVerification_Accept_NoSupportedMethods"
+                             "TestVerification_Accept_CorrectMethodsPresented"
+                             "TestVerification_Accept_CancelOnNonParticipati"
+                             "TestVerification_ErrorOnDoubleAccept"
+                             "TestVerification_CancelOnDoubleStart"
+                             "TestClient_Version"
+                             "TestResolveServerName"
+                             "TestServerKeyResponse_VerifySelfSignature"
+                             "TestServerKeyResponse_FailWithFilter")
+                       "|"))))
     (propagated-inputs
      (list go-filippo-io-edwards25519
            go-github-com-chzyer-readline
-           go-github-com-gorilla-mux
-           go-github-com-gorilla-websocket
+           go-github-com-coder-websocket
            go-github-com-lib-pq
            go-github-com-mattn-go-sqlite3
            go-github-com-rs-xid
@@ -23405,7 +23457,9 @@ the code or routes.")
            go-golang-org-x-net
            go-golang-org-x-sync
            go-gopkg-in-yaml-v3
-           go-maunium-net-go-mauflag))
+           go-maunium-net-go-mauflag
+           ;; XXX: The final application needs a "libolm" package.
+           olm))
     (home-page "https://maunium.net/go/mautrix")
     (synopsis "Golang Matrix framework")
     (description

gnu/packages/golang-xyz.scm

@@ -78,6 +78,7 @@
 ;;; Copyright © 2026 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2026 Daniel Littlewood <dan@danielittlewood.xyz>
 ;;; Copyright © 2026 Sughosha <sughosha@disroot.org>
+;;; Copyright © 2026 orahcio <orahcio@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -113,6 +114,7 @@
   #:use-module (gnu packages golang-check)
   #:use-module (gnu packages golang-compression)
   #:use-module (gnu packages golang-crypto)
+  #:use-module (gnu packages golang-graphics)
   #:use-module (gnu packages golang-maths)
   #:use-module (gnu packages golang-vcs)
   #:use-module (gnu packages golang-web)
@@ -443,6 +445,33 @@ a human-readable byte format.")
 time dependencies in tests.")
     (license license:asl2.0)))
 
+(define-public go-code-rocketnine-space-tslocum-cbind
+  (package
+    (name "go-code-rocketnine-space-tslocum-cbind")
+    (version "0.1.5")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://codeberg.org/tslocum/cbind.git")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0a0gpzapm3jsivdf5h6lvlxhzngrmyj7xp5fdk20l8r4yba7yqsy"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "code.rocketnine.space/tslocum/cbind"
+      #:test-flags #~(list "--skip" "TestConfiguration")))
+    (propagated-inputs
+     (list go-github-com-gdamore-tcell-v2))
+    (home-page "https://codeberg.org/tslocum/cbind")
+    (synopsis "Key event handling library for tcell")
+    (description
+     "Package cbind provides a tcell key event encoding, decoding and handling
+as human-readable strings.")
+    (license license:expat)))
+
 (define-public go-codeberg-org-anaseto-gruid
   (package
     (name "go-codeberg-org-anaseto-gruid")
@@ -1840,6 +1869,33 @@ software (based on Python's
 @uref{https://github.com/pycontribs/tendo, tendo}).")
     (license license:expat)))
 
+(define-public go-github-com-alimpfard-line
+  (package
+    (name "go-github-com-alimpfard-line")
+    (version "0.0.0-20230131232016-03b4e7dee324")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/alimpfard/line")
+              (commit (go-version->git-ref version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0swjy1z7hqy4xgq2hfa457rs7p9d7fw5lmdh0zaf3n25rqv10ds1"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/alimpfard/line"))
+    (propagated-inputs
+     (list go-golang-org-x-sys))
+    (home-page "https://github.com/alimpfard/line")
+    (synopsis "Terminal line editor")
+    (description
+     "This package provides a full reimplementation of SerenityOS's LibLine in
+Go language.  It supports flexible autocompletion, live prompt, buffer update
+and stylisation, multiline editing and more.")
+    (license license:bsd-2)))
+
 (define-public go-github-com-alsm-ioprogress
   (package
     (name "go-github-com-alsm-ioprogress")
@@ -9770,6 +9826,37 @@ O(1) for @code{Set}, @code{Get}, @code{Delete} and @code{Len}.")
         #~(modify-phases %standard-phases
             (delete 'remove-submodule)))))))
 
+(define-public go-github-com-elliotchance-orderedmap-v3
+  (package
+    (name "go-github-com-elliotchance-orderedmap-v3")
+    (version "3.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/elliotchance/orderedmap")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1w681qsybcf34g0wn9hm6nnzc9jcdv59ahjiqdq9hs22xq0qgnjj"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      ;; Projects includes v1, v2 and v3 in the same source tree.
+      #:import-path "github.com/elliotchance/orderedmap/v3"
+      #:unpack-path "github.com/elliotchance/orderedmap"))
+    (native-inputs
+     (list go-github-com-stretchr-testify))
+    (home-page "https://github.com/elliotchance/orderedmap")
+    (synopsis "Ordered map in with amortized O(1) for Set, Get, Delete and Len")
+    (description
+     "An @code{*OrderedMap} is a high performance ordered map that maintains
+amortized O(1) for @code{Set}, @code{Get}, @code{Delete} and @code{Len}.
+Internally an @code{*OrderedMap} uses the composite type
+@url{https://go.dev/blog/maps, map} combined with a trimmed down linked list
+to maintain the order.")
+    (license license:expat)))
+
 (define-public go-github-com-elliotwutingfeng-asciiset
   (package
     (name "go-github-com-elliotwutingfeng-asciiset")
@@ -10102,6 +10189,36 @@ and @code{io.ReadCloser}) with overwrites
                     "  This package is a fork of dlclark/regexp2 providing a
 more similar API to regexp."))))
 
+(define-public go-github-com-esiqveland-notify
+  (package
+    (name "go-github-com-esiqveland-notify")
+    (version "0.13.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/esiqveland/notify")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "03d27a8rl55j6dqclg3233dj3j7v0i0p9cda06f9c4a21djamrfb"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/esiqveland/notify"))
+    (native-inputs
+     (list go-github-com-stretchr-testify))
+    (propagated-inputs
+     (list go-github-com-godbus-dbus-v5))
+    (home-page "https://github.com/esiqveland/notify")
+    (synopsis "Delivering desktop notifications over DBus")
+    (description
+     "Notify is a Go library for interacting with the DBus notification
+service defined by freedesktop.org at
+@url{https://developer.gnome.org/notification-spec/}.  Notify can deliver
+desktop notifications over DBus, ala how @code{libnotify} does it.")
+    (license license:bsd-3)))
+
 (define-public go-github-com-ettle-strcase
   (package
     (name "go-github-com-ettle-strcase")
@@ -10893,6 +11010,37 @@ library in go standard library.")
      "Go library that pluralizes and singularizes English nouns.")
     (license license:bsd-2)))
 
+(define-public go-github-com-gen2brain-beeep
+  (package
+    (name "go-github-com-gen2brain-beeep")
+    (version "0.11.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/gen2brain/beeep")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0jvfspz941r93djf83gsjqw8w9v34fa9dys1465iwbq769ayizmw"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/gen2brain/beeep"
+      #:test-flags #~(list "--skip" "TestAlert|TestNotify")))
+    (propagated-inputs
+     (list go-github-com-esiqveland-notify
+           go-github-com-godbus-dbus-v5
+           go-github-com-jackmordaunt-icns-v3
+           go-github-com-sergeymakinen-go-ico
+           go-golang-org-x-sys))
+    (home-page "https://github.com/gen2brain/beeep")
+    (synopsis "Sending desktop notifications, alerts and beeps")
+    (description
+     "Package beeep provides a cross-platform library for sending desktop
+notifications and beeps.")
+    (license license:bsd-2)))
+
 (define-public go-github-com-ghemawat-stream
   (package
     (name "go-github-com-ghemawat-stream")
@@ -29765,6 +29913,31 @@ utilities for cty Golang module.")
      "Package yaml can marshal and unmarshal cty values in YAML format.")
     (license license:asl2.0)))
 
+(define-public go-github-com-zeebo-bencode
+  (package
+    (name "go-github-com-zeebo-bencode")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/zeebo/bencode")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0c6bw1if1vbcr9l4684a4jdri8z31m8msjpp7z6y2p9s1jqjhkrp"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/zeebo/bencode"))
+    (home-page "https://github.com/zeebo/bencode")
+    (synopsis "Bencode marshal and unmarshal library")
+    (description
+     "This library implements encoding and decoding of
+@url{https://wiki.theory.org/BitTorrentSpecification#Bencoding, bencoded}
+objects.")
+    (license license:expat)))
+
 (define-public go-github-com-zeebo-errs
   (package
     (name "go-github-com-zeebo-errs")
@@ -30078,6 +30251,31 @@ connections.")
       "This package provides a pretty printing library for Golang values.")
     (license license:expat)))
 
+(define-public go-github-com-zyedidia-clipboard
+  (package
+    (name "go-github-com-zyedidia-clipboard")
+    (version "1.0.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/zyedidia/clipboard")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1nrs2ll6dh31wyzxh2zbykwvpavhlpzysfk6qgfj5s4rz6ck8glz"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:tests? #f      ;requires clipboard (xclip or xsel)
+      #:import-path "github.com/zyedidia/clipboard"))
+    (home-page "https://github.com/zyedidia/clipboard")
+    (synopsis "Clipboard for Golang")
+    (description
+     "Package clipboard read/write on clipboard.  It's an alternative fork of
+@url{https://github.com/atotto/clipboard}.")
+    (license license:bsd-3)))
+
 (define-public go-github-com-zyedidia-clipper
   (package
     (name "go-github-com-zyedidia-clipper")
@@ -30586,7 +30784,7 @@ Identifier (RFC3986) specification in Go.")
 (define-public go-go-mau-fi-util
   (package
     (name "go-go-mau-fi-util")
-    (version "0.8.4")
+    (version "0.9.9")
     (source
      (origin
        (method git-fetch)
@@ -30595,7 +30793,7 @@ Identifier (RFC3986) specification in Go.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0zzkrbwgbxfppsxjck8qgj4xxzpiq25sx4p3zwjh6s1yz3kfb97p"))))
+        (base32 "1d6365n4j5hx172mi5f9rk49l7cgcbf8qvi721b0l34j2m036rsy"))))
     (build-system go-build-system)
     (arguments
      (list

gnu/packages/guile-xyz.scm

@@ -4019,6 +4019,38 @@ with documentation.
     ;; details.
     (license license:gpl3+)))
 
+(define-public guile-scriba
+  (package
+    (name "guile-scriba")
+    (version "0.1.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://codeberg.org/jjba23/scriba.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1chhbhy21g6zghc3alpqhvb6nizylmzzapjariykv41f47ynhljs"))))
+    (build-system guile-build-system)
+    (arguments
+     (list
+      #:source-directory "src"))
+    (propagated-inputs (list guile-json-4))
+    (inputs (list guile-3.0))
+    (synopsis "Structured logging framework for Guile Scheme")
+    (description
+     "Scriba is a structured logging library for GNU Guile that prioritizes
+flexibility and observability.  It provides modular log routing, formatting,
+and filtering, allowing developers to generate human-readable console logs
+during development and machine-readable JSON logs for production environments.
+Key features include an auto-logger configured via environment variables,
+dynamically scoped log contexts using Scheme parameters, ahead-of-time log
+level filtering, and minimal runtime overhead achieved through memoization
+and compile-time macros.")
+    (home-page "https://codeberg.org/jjba23/scriba")
+    (license license:lgpl3+)))
+
 (define-public guile-simple-iterators
   (let ((commit "50f16a2b2aa57e657e52e19fb3c35bdc182cfa36")
         (revision "0"))
@@ -7526,7 +7558,7 @@ in a large number of randomly generated test cases.")
 (define-public guile-veritas
   (package
     (name "guile-veritas")
-    (version "0.1.6")
+    (version "0.3.0")
     (source
      (origin
        (method git-fetch)
@@ -7535,13 +7567,13 @@ in a large number of randomly generated test cases.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1h4si2p8gj4wfhvn4cshga2kjxf59vd4nwvxkc2i3g5gv3kxhm3k"))))
+        (base32 "1i64pd5pcx37i25hnks7zj8pbwf1fdy0s5y9ic2sgn800zqq1dxy"))))
     (build-system guile-build-system)
     (arguments
      (list
       #:source-directory "src"))
     (native-inputs (list guile-3.0))
-    (propagated-inputs (list guile-fibers))
+    (propagated-inputs (list guile-fibers guile-json-4))
     (home-page "https://codeberg.org/jjba23/veritas")
     (synopsis "Testing framework for Guile")
     (description

gnu/packages/maths.scm

@@ -11732,3 +11732,35 @@ use the library and researchers to make new capabilities available under a
 common interface.
 ")
     (license license:bsd-3)))
+
+(define-public xdmf
+  (package
+    (name "xdmf")
+    ;; Project does not publish releases / tags
+    (properties '((commit . "04a84bab0eb1568e0f1a27c8fb60c6931efda003")
+                  (revision . "0")))
+    (version (git-version "3.0.0"
+                          (assoc-ref properties 'revision)
+                          (assoc-ref properties 'commit)))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://gitlab.kitware.com/xdmf/xdmf")
+              (commit (assoc-ref properties 'commit))))
+       (file-name (git-file-name name version))
+       (patches
+        (search-patches "xdmf-3.0.0-hdf5.patch"))
+       (sha256
+        (base32 "06k4vibkvgxlzkn06x470aq5q18p7yhql8awrpdz3czys3z8i288"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list #:tests? #f)) ;has no tests
+    (inputs
+     (list boost hdf5 libxml2))
+    (home-page "https://www.xdmf.org/index.html")
+    (synopsis "XDMF library")
+    (description
+     "This package provides the eXtensible Data Model and Format (XDMF) C++
+library.")
+    (license license:bsd-4)))

gnu/packages/matrix.scm

@@ -11,6 +11,7 @@
 ;;; Copyright © 2025 Arjan Adriaanse <arjan@adriaan.se>
 ;;; Copyright © 2025 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2026 Zheng Junjie <z572@z572.online>
+;;; Copyright © 2026 orahcio <orahcio@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -59,7 +60,7 @@
 (define-public mautrix-whatsapp
   (package
     (name "mautrix-whatsapp")
-    (version "0.11.2")
+    (version "0.2605.0")
     (source
      (origin
        (method git-fetch)
@@ -68,7 +69,7 @@
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0wn9kldhh865w5mbg3cl61m0db9nr7zl1j8lqs2dixsaihv1lbnx"))))
+        (base32 "02gmzby57vn5cc23m2laqcqqkvghlabm08fzjzqfzx8g18cmymas"))))
     (build-system go-build-system)
     (arguments
      (list
@@ -105,7 +106,13 @@
          ;; go.mau.fi/webp/webp.go:14:12: pattern internal: cannot embed
          ;; directory internal: contains no embeddable files
          ".*\\.c"
-         ".*\\.h")))
+         ".*\\.h"
+         ;; go.mau.fi/whatsmeow/argo/argo.go:16:13:
+         ;; pattern argo-wire-type-store.argo: cannot embed
+         ".*\\.argo"
+         ;; go.mau.fi/whatsmeow/argo/argo.go:19:13:
+         ;; pattern name-to-queryids.json: cannot embed
+         ".*\\.json")))
     (native-inputs
      (list olm
            go-github-com-gorilla-mux

gnu/packages/messaging.scm

@@ -47,6 +47,7 @@
 ;;; Copyright © 2025 Evgeny Pisemsky <mail@pisemsky.site>
 ;;; Copyright © 2025 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2025 Adrien 'neox' Bourmault <neox@gnu.org>
+;;; Copyright © 2026 orahcio <orahcio@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -3459,6 +3460,56 @@ a persistent connection to an IRC server, acting as a proxy and buffer for
 a number of clients.")
     (license license:gpl3+)))
 
+(define-public whatscli
+  (package
+    (name "whatscli")
+    (version "1.1.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/normen/whatscli")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0ijp0783h4hivj33qi10azhq1bl512jq1wrva2alpkv7wp4qhnw6"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:install-source? #f
+      #:import-path "github.com/normen/whatscli"
+      #:embed-files #~(list ".*\\.argo" ".*\\.json" ".*\\.sql")))
+    (native-inputs
+     (list go-code-rocketnine-space-tslocum-cbind
+           go-github-com-adrg-xdg
+           go-github-com-gdamore-tcell-v2
+           go-github-com-gen2brain-beeep
+           go-github-com-mattn-go-colorable
+           go-github-com-mattn-go-sqlite3
+           go-github-com-rivo-tview
+           go-github-com-skip2-go-qrcode
+           go-github-com-skratchdot-open-golang
+           go-github-com-zyedidia-clipboard
+           go-go-mau-fi-whatsmeow
+           go-google-golang-org-protobuf
+           go-gopkg-in-ini-v1))
+    (home-page "https://github.com/normen/whatscli")
+    (synopsis "Command line interface for WhatsApp")
+    (description
+     "WhatsCLI is a command-line interface for WhatsApp that connects
+through the Web App API without requiring a browser.  It provides a
+terminal-based user interface built with tview, featuring:
+@itemize
+@item Sending and receiving WhatsApp messages in a terminal
+@item QR code setup for simple authentication
+@item Downloading and opening image, video, audio, and document attachments
+@item Sending images, video, audio, and document attachments
+@item Basic group management capabilities
+@item Desktop notifications support
+@item Color customization options
+@end itemize")
+    (license license:expat)))
+
 (define-public weechat-wee-slack
   (package
     (name "weechat-wee-slack")

gnu/packages/patches/cianna-remove-error-for-missing-cuda.patch

@@ -1,32 +0,0 @@
-From 5eed2d2ca7c13c08ca7eb92fc4a78c30ca4b6b3d Mon Sep 17 00:00:00 2001
-From: Hellseher <sharlatanus@gmail.com>
-Date: Sat, 18 Apr 2026 08:26:29 +0000
-Subject: [PATCH] Remove CUDA error handling from network.c
-
-Removed error handling for CUDA compilation check.
-
-Fixes: https://github.com/Deyht/CIANNA/issues/4
----
- src/network.c | 9 ---------
- 1 file changed, 9 deletions(-)
-
-diff --git a/src/network.c b/src/network.c
-index d454f64..5a9497c 100644
---- a/src/network.c
-+++ b/src/network.c
-@@ -155,15 +155,6 @@ CIANNA V-1.0.1.2 stable build (04/2026), by D.Cornu\n\
- 		init_cuda(networks[network_number]);
- 	#endif
- 	
--	#ifndef CUDA
--	if(comp_int == C_CUDA)
--	{
--		printf("\n ERROR: compute method set to CUDA while CIANNA was not compiled for it.\n");
--		printf(" Install Nvidia CUDA and recompile CIANNA with the appropriate option.\n\n");
--		exit(EXIT_FAILURE);
--	}
--	#endif
--	
- 	#ifndef BLAS
- 	if(comp_int == C_BLAS)
- 	{

gnu/packages/patches/ogs-6.5.7-netcdfconverter.patch

@@ -1,23 +0,0 @@
-Upstream fix
-
-https://gitlab.opengeosys.org/ogs/ogs/-/commit/9a8399b0d3cff032e70fe79a85dc35c4e7c662f2
-
-diff --git a/Applications/Utils/FileConverter/NetCdfConverter.cpp b/Applications/Utils/FileConverter/NetCdfConverter.cpp
-index c6fb9f151d..622bd2cd54 100644
---- a/Applications/Utils/FileConverter/NetCdfConverter.cpp
-+++ b/Applications/Utils/FileConverter/NetCdfConverter.cpp
-@@ -232,11 +232,12 @@ static bool dimensionSelectionLoop(NcVar const& var,
-     if (n_dims > 1)
-     {
-         std::string temp_str("");
--        cout << "Is the parameter time-dependent?\n";
-+        std::cout << "Is the parameter time-dependent?\n";
-         while (dim_idx_map[0] == std::numeric_limits<std::size_t>::max() &&
-                is_time_dep == true)
-         {
--            cout << "Enter ID for temporal dimension or \"c\" to continue: ";
-+            std::cout
-+                << "Enter ID for temporal dimension or \"c\" to continue: ";
-             std::getline(std::cin, temp_str);
-             std::stringstream str_stream(temp_str);
-             if (str_stream.str() == "c" || str_stream.str() == "continue")

gnu/packages/patches/xdmf-3.0.0-hdf5.patch

@@ -0,0 +1,45 @@
+From 92a851f1acb87ad5367eb62f9b97785bedb700bb Mon Sep 17 00:00:00 2001
+From: Dmitri Naumov <github@naumov.de>
+Date: Thu, 28 Oct 2021 22:34:00 +0200
+Subject: [PATCH] Detect if hid_t is defined in new versions of HDF5
+
+In HDF5 development the header file guards were changed,
+namely the leading underscore was removed. This lead to
+a redefinition of the hid_t type, which is int64_t.
+
+The change happened in commit
+https://github.com/HDFGroup/hdf5/commit/c17b4b93d680340af2b3f2c026f2c03c3baeb33ahttps://github.com/HDFGroup/hdf5/commit/c17b4b93d680340af2b3f2c026f2c03c3baeb33a
+and is published in HDF5 version hdf5-1_13_0-rc6.
+---
+ core/XdmfHDF5Controller.hpp | 2 +-
+ core/XdmfHDF5Writer.hpp     | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/core/XdmfHDF5Controller.hpp b/core/XdmfHDF5Controller.hpp
+index c5c15d0a..b52bab3f 100644
+--- a/core/XdmfHDF5Controller.hpp
++++ b/core/XdmfHDF5Controller.hpp
+@@ -30,7 +30,7 @@
+ 
+ // So that hdf5 does not need to be included in the header files
+ // It would add a dependancy to programs that use Xdmf
+-#ifndef _H5Ipublic_H
++#if !defined(_H5Ipublic_H) && !defined(H5Ipublic_H)
+   #ifndef XDMF_HID_T
+   #define XDMF_HID_T
+     typedef int hid_t;
+diff --git a/core/XdmfHDF5Writer.hpp b/core/XdmfHDF5Writer.hpp
+index cfbec6f4..6f8cfd4f 100644
+--- a/core/XdmfHDF5Writer.hpp
++++ b/core/XdmfHDF5Writer.hpp
+@@ -31,7 +31,7 @@
+ 
+ // So that hdf5 does not need to be included in the header files
+ // It would add a dependancy to programs that use Xdmf
+-#ifndef _H5Ipublic_H
++#if !defined(_H5Ipublic_H) && !defined(H5Ipublic_H)
+   #ifndef XDMF_HID_T
+   #define XDMF_HID_T
+     typedef int hid_t;
+-- 
+GitLab

gnu/packages/prolog.scm

@@ -237,7 +237,7 @@ it.")
 (define-public trealla
   (package
     (name "trealla")
-    (version "2.100.24")
+    (version "2.100.25")
     (source
      (origin
        (method git-fetch)
@@ -246,7 +246,7 @@ it.")
           (url "https://github.com/trealla-prolog/trealla")
           (commit (string-append "v" version))))
        (sha256
-        (base32 "09jm5hs2lv481yzf76p646jx6467zx98bbbsg24xh3glk1f9gaaq"))
+        (base32 "1si84zaihsi2zwr0qdfr6kjcrly6ih1br0r6v58xm9v9db5zpx6x"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (inputs

gnu/packages/python-web.scm

@@ -3392,6 +3392,34 @@ files.")
 code asynchronously.")
     (license license:asl2.0)))
 
+(define-public python-requests-unixsocket
+  (package
+    (name "python-requests-unixsocket")
+    (version "0.4.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/msabramo/requests-unixsocket")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1f0pi31xqzm3cdag4s4gpdj36x169jwc8ibqvcwqz6h9c0pklf3n"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-pytest
+           python-setuptools
+           python-setuptools-scm
+           python-waitress))
+    (propagated-inputs
+     (list python-requests))
+    (home-page "https://github.com/msabramo/requests-unixsocket")
+    (synopsis "Use requests to talk HTTP via a UNIX domain socket")
+    (description
+     "This package provides an extension to @code{requests} which let it talk
+HTTP via a UNIX domain socket.")
+    (license license:asl2.0)))
+
 (define-public python-s3path
   (package
     (name "python-s3path")

gnu/packages/rocm-libs.scm

@@ -297,7 +297,17 @@ configurations deterministically based on compute and memory latencies.")
                     "availableArchs = ['"
                     (string-join (current-amd-gpu-targets) "', '") "']")))
               (setenv "TENSILE_ROCM_ASSEMBLER_PATH"
-                      (string-append (which "clang"))))))))
+                      (string-append (which "clang")))))
+          ;; Packages, such as rocblas, expect to be able to run those scripts
+          ;; in their CMake builds.
+          (add-after 'install 'adjust-tensile-binaries-permissions
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (let ((site-packages (site-packages inputs outputs)))
+                (with-directory-excursion (string-append site-packages
+                                                         "/Tensile/bin")
+                  ;; Use `make-file-executable' once #7224 is merged.
+                  (chmod "Tensile" #o555)
+                  (chmod "TensileCreateLibrary" #o555))))))))
     (native-inputs
      (list python-filelock
            python-pandas

gnu/packages/sagemath.scm

@@ -365,7 +365,7 @@ database.")
 (define-public sage
   (package
     (name "sage")
-    (version "10.7")
+    (version "10.9")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -374,7 +374,7 @@ database.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0513nmym1shlj0vkb982hpj1v86f327w5kav0523wk1xljc432cx"))))
+                "1rbwhhxj6iizfcgbzd63lf1g1dh24253mmmzgfkvcbv6hx0l507h"))))
     (build-system pyproject-build-system)
     (native-inputs
       (list autoconf automake m4 pkg-config ; for ./bootstrap

gnu/packages/xfce.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2015, 2024 宋文武 <iyzsong@envs.net>
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2016, 2026 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016 Florian Paul Schmidt <mista.tapas@gmx.net>
 ;;; Copyright © 2016, 2020 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2017, 2019 Ricardo Wurmus <rekado@elephly.net>
@@ -68,6 +68,7 @@
   #:use-module (gnu packages polkit)
   #:use-module (gnu packages popt)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages search)
@@ -825,7 +826,7 @@ like appearance, display, keyboard and mouse settings.")
 (define-public thunar
   (package
     (name "thunar")
-    (version "4.20.6")                           ;stable version = even minor
+    (version "4.20.8")                           ;stable version = even minor
     (source
      (origin
        (method git-fetch)
@@ -834,7 +835,7 @@ like appearance, display, keyboard and mouse settings.")
              (commit (string-append name "-" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1ayjnnpl15v4h3rpay1a127cvrlaj6qwydk496083i9494j6cp9f"))))
+        (base32 "0605a9vxva3bplnv4pj0qf1gk1jxacqg03czhi396qs1fgs6ihw1"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      '(#:configure-flags '("--enable-maintainer-mode" ;for thunar-marshal.c
@@ -1027,7 +1028,7 @@ menu.")
         (base32 "1x39pbdx4186f7bkrc9ab5q7qs783mivm2j1msyf9m1nh09y617f"))))
     (build-system gnu-build-system)
     (native-inputs
-     (list xfce4-dev-tools))
+     (list python-setuptools xfce4-dev-tools))
     (inputs
      (list exo
            thunar

gnu/services/monitoring.scm

@@ -225,7 +225,7 @@ HTTP.")
   make-prometheus-node-exporter-configuration
   prometheus-node-exporter-configuration?
   (package prometheus-node-exporter-configuration-package
-           (default go-github-com-prometheus-node-exporter))
+           (default prometheus-node-exporter))
   (web-listen-address prometheus-node-exporter-web-listen-address
                       (default ":9100"))
   (textfile-directory prometheus-node-exporter-textfile-directory

gnu/services/web.scm

@@ -329,6 +329,7 @@
             mumi-configuration-data-directory
             mumi-configuration-rsync-remote
             mumi-configuration-rsync-flags
+            mumi-configuration-rsync-and-index-event
             mumi-configuration-mailer?
             mumi-configuration-sender
             mumi-configuration-smtp
@@ -2355,6 +2356,9 @@ WSGIPassAuthorization On
   (rsync-remote mumi-configuration-rsync-remote)
   (rsync-flags mumi-configuration-rsync-flags
                (default '()))
+  (rsync-and-index-event mumi-configuration-rsync-and-index-event
+                         ;; Run every 5 minutes by default.
+                         (default #~(calendar-event #:minutes '#$(iota 12 0 5))))
   (mailer? mumi-configuration-mailer? (default #t))
   (sender  mumi-configuration-sender (default #f))
   (smtp    mumi-configuration-smtp (default #f))
@@ -2465,7 +2469,7 @@ WSGIPassAuthorization On
                            "/lib/locale")))
 
   (match-record config <mumi-configuration>
-    (mumi mailer? sender smtp)
+    (mumi rsync-and-index-event mailer? sender smtp)
     (list (shepherd-service
             (provision '(mumi))
             (documentation "Mumi bug-tracking web interface.")
@@ -2482,9 +2486,7 @@ WSGIPassAuthorization On
             (provision '(mumi-rsync-and-index))
             (modules '((shepherd service timer)))
             (start #~(make-timer-constructor
-                      ;; Run every 5 minutes, unless an instance of
-                      ;; this job is already running.
-                      (calendar-event #:minutes '#$(iota 12 0 5))
+                      #$rsync-and-index-event
                       (command (list #$(mumi-rsync-and-index config)))
                       #:log-file #$%mumi-rsync-and-index-log
                       #:max-duration (* 2 60 60)

guix/packages.scm

@@ -120,6 +120,8 @@
             define-deprecated-package
             package-field-location
 
+            package-location<?
+
             this-package-input
             this-package-native-input
 
@@ -874,6 +876,15 @@ if FIELD could not be found."
         #f)))
     (_ #f)))
 
+(define (package-location<? p1 p2)
+  "Return true if P1's location is \"before\" P2's."
+  (let ((loc1 (package-location p1))
+        (loc2 (package-location p2)))
+    (and loc1 loc2
+         (if (string=? (location-file loc1) (location-file loc2))
+             (< (location-line loc1) (location-line loc2))
+             (string<? (location-file loc1) (location-file loc2))))))
+
 (define-syntax-rule (this-package-input name)
   "Return the input NAME of the package being defined--i.e., an input
 from the ‘inputs’ or ‘propagated-inputs’ field.  Native inputs are not

guix/scripts/lint.scm

@@ -11,6 +11,7 @@
 ;;; Copyright © 2018, 2019 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2019, 2020 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
+;;; Copyright © 2024, 2026 Herman Rimm <herman@rimm.ee>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,8 +29,10 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (guix scripts lint)
+  #:use-module (guix diagnostics)
   #:use-module (guix packages)
   #:use-module (guix lint)
+  #:use-module (guix modules)
   #:use-module (guix ui)
   #:use-module (guix store)
   #:use-module (guix scripts)
@@ -87,6 +90,28 @@
             checkers)
   (exit 0))
 
+(define* (process-whole-file file checkers #:key store)
+  "Run the given CHECKERS on packages in FILE and check that the
+packages are sorted alphabetically."
+  (load* file '())
+  (let* ((module (resolve-interface (file-name->module-name file)))
+         (packages (sort (fold-packages cons '() (list module))
+                         package-location<?)))
+    (fold (lambda (package previous)
+            (let ((line (location-line (package-location package)))
+                  (name (package-name package)))
+              (run-checkers package checkers #:store store)
+              (and (string<? name previous)
+                   (emit-warnings
+                     (list (lint-warning
+                             (package package)
+                             (location (location file line 0))
+                             (message-text
+                              (G_ "breaks from alphabetical order"))
+                             (message-data '())))))
+              name))
+          "" packages)))
+
 
 ;;;
 ;;; Command-line options.
@@ -115,6 +140,9 @@ run the checkers on all packages.\n"))
   -L, --load-path=DIR    prepend DIR to the package module search path"))
   (newline)
   (display (G_ "
+  -f, --whole-file       check the packages defined in the given file(s)"))
+  (newline)
+  (display (G_ "
   -h, --help             display this help and exit"))
   (display (G_ "
   -l, --list-checkers    display the list of available lint checkers"))
@@ -161,6 +189,9 @@ run the checkers on all packages.\n"))
                 (lambda args
                   (leave-on-EPIPE (show-help))
                   (exit 0)))
+        (option '(#\f "whole-file") #f #f
+                (lambda (opt name arg result)
+                  (alist-cons 'whole-file? #t result)))
         (option '(#\l "list-checkers") #f #f
                 (lambda (opt name arg result)
                   (alist-cons 'list? #t result)))
@@ -187,12 +218,17 @@ run the checkers on all packages.\n"))
                         #:build-options? #f))
 
   (let* ((opts (parse-options))
-         (args (filter-map (match-lambda
-                             (('argument . spec)
-                              (specification->package spec))
-                             (('expression . exp)
-                              (read/eval-package-expression exp))
-                             (_ #f))
+         (whole-file? (assoc-ref opts 'whole-file?))
+         (args (filter-map (if whole-file?
+                               (match-lambda
+                                 (('argument . file) file)
+                                 (_ #f))
+                               (match-lambda
+                                 (('argument . spec)
+                                  (specification->package spec))
+                                 (('expression . exp)
+                                  (read/eval-package-expression exp))
+                                 (_ #f)))
                            (reverse opts)))
          (no-checkers (or (assoc-ref opts 'exclude) '()))
          (the-checkers (filter (lambda (checker)
@@ -221,6 +257,13 @@ run the checkers on all packages.\n"))
         (call-maybe-with-store
          (lambda (store)
            (cond
+            (whole-file?
+             (when (null? args)
+               (warning (G_ "no files specified, nothing to do~%")))
+             (for-each
+               (lambda (file)
+                 (process-whole-file file checkers #:store store))
+               args))
             ((null? args)
              (fold-packages (lambda (p r) (run-checkers p checkers
                                                         #:store store)) '()))

guix/scripts/style.scm

@@ -603,15 +603,6 @@ bailing out~%"))
                         #:format-comment canonicalize-comment
                         #:format-vertical-space canonicalize-vertical-space)))))
 
-(define (package-location<? p1 p2)
-  "Return true if P1's location is \"before\" P2's."
-  (let ((loc1 (package-location p1))
-        (loc2 (package-location p2)))
-    (and loc1 loc2
-         (if (string=? (location-file loc1) (location-file loc2))
-             (< (location-line loc1) (location-line loc2))
-             (string<? (location-file loc1) (location-file loc2))))))
-
 
 ;;;
 ;;; Whole-file formatting.

tests/guix-lint.sh

@@ -1,5 +1,6 @@
 # GNU Guix --- Functional package management for GNU
 # Copyright © 2014 Cyril Roelandt <tipecaml@gmail.com>
+# Copyright © 2026 Herman Rimm <herman@rimm.ee>
 #
 # This file is part of GNU Guix.
 #
@@ -35,12 +36,20 @@ cat > "$module_dir/foo.scm"<<EOF
   #:use-module (guix packages)
   #:use-module (gnu packages base))
 
+;; This definition uses (the line number of) the hello package location
+;; instead of generating a new one.
+(define-public hi hello)
+
 (define-public dummy
   (package (inherit hello)
     (name "dummy")
     (version "42")
     (synopsis "dummy package")
     (description "dummy package. Only used for testing purposes.")))
+
+(define-public bar
+  (package (inherit dummy)
+    (name "bar")))
 EOF
 
 GUIX_PACKAGE_PATH="$module_dir"
@@ -52,10 +61,11 @@ grep_warning ()
     echo $res
 }
 
-# Three issues with the dummy package:
+# Issues with the dummy package:
 # 1) the synopsis starts with the package name;
 # 2) the synopsis starts with a lower-case letter;
-# 3) the description has a single space following the end-of-sentence period.
+# 3) the description has a single space following the end-of-sentence period;
+# 4) the alphabetically lesser bar package succeeds it.
 
 out=`guix lint -c synopsis,description dummy 2>&1`
 test `grep_warning "$out"` -eq 3
@@ -69,6 +79,12 @@ test `grep_warning "$out"` -eq 1
 out=`guix lint -c description,synopsis dummy 2>&1`
 test `grep_warning "$out"` -eq 3
 
+working_dir="$(pwd)"
+cd "$module_dir"
+out=`guix lint -c name -f foo.scm 2>&1`
+cd "$working_dir"
+test `echo "$out" | grep -E -c "breaks from alphabetical order"` -eq 1
+
 guix lint -c synopsis,invalid-checker dummy 2>&1 | \
    grep -q 'invalid-checker: invalid checker'