gnu: python-aiorpcx: Fix tests.

* gnu/packages/python-web.scm (python-aiorpcx)[native-inputs]: Remove
python-pytest-asyncio and python-wheel; add python-pytest-asyncio-0.26.

Change-Id: I8acf3eb36a0ab1a41038471456aa15d0fef92cbc

gnu/local.mk

@@ -2460,6 +2460,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/xfce4-settings-defaults.patch		\
   %D%/packages/patches/xgboost-use-system-dmlc-core.patch	\
   %D%/packages/patches/xinit-startx-mcookie-path.patch		\
+  %D%/packages/patches/xiphos-glib.patch                        \
   %D%/packages/patches/xmonad-dynamic-linking.patch		\
   %D%/packages/patches/xplanet-1.3.1-cxx11-eof.patch		\
   %D%/packages/patches/xplanet-1.3.1-libdisplay_DisplayOutput.cpp.patch	\

gnu/packages/bioinformatics.scm

@@ -2204,26 +2204,38 @@ intended to behave exactly the same as the original BWK awk.")
 (define-public python-bcbio-gff
   (package
     (name "python-bcbio-gff")
-    (version "0.6.9")
+    ;; python-bcbio-gff can only be refreshed manually, because guix refresh
+    ;; does not understand the tags on the github repository.
+    (version "0.7.1")
     (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "bcbio-gff" version))
+              ;; No tests in PyPI package.
+              (method git-fetch)
+              (uri (git-reference
+               (url "https://github.com/chapmanb/bcbb")
+               (commit (string-append "bcbio-gff-v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1pm1szyxabhn8jismrj9cjhf88ajgcmm39f0cgf36iagw5qakprl"))))
+                "0144xxzibq4mrg8a1w2scs120rd9svq07hm5ccs91n3a4nvwjfsd"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'enter-directory
+            (lambda _ (chdir "gff"))))))
     (native-inputs
-     (list python-pytest))
+     (list python-setuptools python-pytest))
     (propagated-inputs
      (list python-biopython
-           python-setuptools
-           python-six
-           python-wheel))
+           python-six))
     (home-page "https://github.com/chapmanb/bcbb/tree/master/gff")
     (synopsis "Read and write GFF files with Biopython integration")
     (description
      "This package lets you read and write files in Generic Feature
 Format (GFF) with Biopython integration.")
+    (properties
+     '((upstream-name . "bcbio-gff")))
     (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))))
 
 (define-public python-bcbio-gff/biopython-1.73
@@ -8691,52 +8703,48 @@ comment or quality sections.")
 (define-public gemma
   (package
     (name "gemma")
-    (version "v0.98.5")
+    (version "0.98.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                    (url "https://github.com/genetics-statistics/GEMMA")
-                    (commit version)))
+                     (url "https://github.com/genetics-statistics/GEMMA")
+                     (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
                 "1dm8pf1fbdmv2yiz5aybcvk3050m5350gq8xlr4j6swzm3wwhydn"))
               (modules '((guix build utils)))
               (snippet
-               '(begin
-                  (delete-file-recursively "contrib")
-                  #t))))
+               #~(begin
+                   (delete-file-recursively "contrib")))))
     (build-system gnu-build-system)
     (inputs
      (list gsl openblas zlib))
     (native-inputs
-     `(("catch" ,catch2-1)
-       ("perl" ,perl)
-       ("shunit2" ,shunit2)
-       ("which" ,which)))
+     (list catch2-1
+           perl
+           shunit2
+           which))
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (delete 'configure)
-         (add-after 'unpack 'prepare-build
-           (lambda* (#:key inputs #:allow-other-keys)
-             (mkdir-p "bin")
-             (substitute* "Makefile"
-               (("/usr/local/opt/openblas")
-                (assoc-ref inputs "openblas")))
-             #t))
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               ;; 'make slow-check' expects shunit2-2.0.3.
-               (with-directory-excursion "test"
-                 (invoke "./test_suite.sh"))
-               #t)))
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (install-file "bin/gemma"
-                           (string-append (assoc-ref outputs "out") "/bin"))
-             #t)))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure)
+          (add-after 'unpack 'prepare-build
+            (lambda _
+              (mkdir-p "bin")
+              (substitute* "Makefile"
+                (("/usr/local/opt/openblas")
+                 #$(this-package-input "openblas")))))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                ;; 'make slow-check' expects shunit2-2.0.3.
+                (with-directory-excursion "test"
+                  (invoke "./test_suite.sh")))))
+          (replace 'install
+            (lambda _
+              (install-file "bin/gemma" (string-append #$output "/bin")))))))
     (home-page "https://github.com/genetics-statistics/GEMMA")
     (synopsis "Tool for genome-wide efficient mixed model association")
     (description

gnu/packages/books.scm

@@ -31,18 +31,29 @@
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
+  #:use-module (gnu packages cpp)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)
+  #:use-module (gnu packages freedesktop)
+  #:use-module (gnu packages gettext)
+  #:use-module (gnu packages glib)
+  #:use-module (gnu packages gtk)
+  #:use-module (gnu packages gnome)
   #:use-module (gnu packages inkscape)
   #:use-module (gnu packages icu4c)
+  #:use-module (gnu packages linux)
   #:use-module (gnu packages music)
   #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages tex)
   #:use-module (gnu packages texlive)
-  #:use-module (gnu packages version-control))
+  #:use-module (gnu packages version-control)
+  #:use-module (gnu packages webkit)
+  #:use-module (gnu packages xml))
 
 (define-public book-sparc
   (package
@@ -170,3 +181,49 @@ is available in Russian and English.")
      "The SWORD Project is a free Bible software project used to create Bible
 software, with support for multiple texts and languages.")
     (license license:gpl2+)))
+
+(define-public xiphos
+  (package
+    (name "xiphos")
+    (version "4.3.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/crosswire/xiphos")
+             (commit version)))
+       (sha256
+        (base32 "15p8ahbcd8vjm1ch0wahjfj20agd06va8rvgw1awnyzkcw2xsf8x"))
+       (patches (search-patches "xiphos-glib.patch"))
+       (file-name (git-file-name name version))))
+    (build-system cmake-build-system)
+    (native-inputs (list appstream
+                         appstream-glib
+                         atk
+                         biblesync
+                         desktop-file-utils ;for 'desktop-file-validate'
+                         (list glib "bin")
+                         gettext-minimal
+                         gsettings-desktop-schemas
+                         gtk+
+                         libgsf
+                         minizip
+                         pkg-config
+                         sword
+                         util-linux ;for 'uuidgen'
+                         (list util-linux "lib") ;for 'libuuid'
+                         webkitgtk-with-libsoup2
+                         yelp-tools
+                         zip))
+    (inputs (list dbus dbus-glib libxml2 python python-lxml))
+    (arguments
+     (list
+      #:tests? #f)) ;No tests
+    (home-page "https://xiphos.org/")
+    (synopsis "Open Source Bible Study Software")
+    (description
+     "Xiphos is a Bible study tool using GTK.  It uses Sword to
+display bibles, commentaries, dictionaries, and other texts and images.
+Xiphos includes features such as searching, biblesync, bookmarks,
+parallel study, and original language study.")
+    (license license:gpl2+)))

gnu/packages/efi.scm

@@ -172,7 +172,7 @@ information.")
     (arguments
      `(#:tests? #f  ; No tests exist.
        #:make-flags
-       '("CC=gcc")
+       '("CC=gcc -g -O2 -Wno-error=implicit-function-declaration")
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'patch

gnu/packages/emulators.scm

@@ -4555,11 +4555,11 @@ cache visualization.  Developed at FEE CTU for computer architecture classes.")
     (license license:zlib)))
 
 (define-public uxn
-  (let ((commit "83237c9641490d303a42c81ca247314d11055dea")
+  (let ((commit "f2e858273890abcffe7451b0566669e610036f49")
         (revision "1"))
     (package
       (name "uxn")
-      (version (git-version "0.1.0" revision commit))
+      (version (git-version "1.0" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -4568,7 +4568,7 @@ cache visualization.  Developed at FEE CTU for computer architecture classes.")
                 (file-name (string-append name "-" version))
                 (sha256
                  (base32
-                  "159qfz66k1jc43jhyl8by3yiphsr2dyiyclw1x7mkr3zciwc29z3"))))
+                  "1li0ly8di2vpzvi3wzlcm355dg38m6sfp0i6mryp9x4ibq7kqmy0"))))
       (build-system gnu-build-system)
       (arguments
        (list #:tests? #f ;no tests
@@ -4584,12 +4584,10 @@ cache visualization.  Developed at FEE CTU for computer architecture classes.")
                                     (share (string-append #$output
                                                           "/share/uxn")))
                                 (with-directory-excursion "bin"
-                                  (for-each (lambda (x)
-                                              (install-file x bin))
-                                            '("uxnasm" "uxncli" "uxnemu"))
-                                  (for-each (lambda (x)
-                                              (install-file x share))
-                                            '("asma.rom" "launcher.rom")))))))))
+                                  (for-each
+                                   (lambda (x)
+                                     (install-file x bin))
+                                   '("uxnasm" "uxncli" "uxnemu")))))))))
       (inputs (list sdl2))
       (home-page "https://100r.co/site/uxn.html")
       (synopsis "Assembler and emulator for the Uxn stack-machine")

gnu/packages/enlightenment.scm

@@ -561,6 +561,7 @@ directories.
 @dfn{Enlightenment Foundation Libraries} (EFL).")
     (license license:bsd-2)))
 
+;; XXX: See: <https://codeberg.org/guix/guix/issues/3014>.
 (define-public epour
   (package
     (name "epour")
@@ -583,8 +584,8 @@ directories.
               (substitute* "epour/gui/__init__.py"
                 (("join\\(data_path")
                  (string-append "join(\"" #$output "/share/epour\""))))))))
-    (native-inputs (list intltool python-distutils-extra python-setuptools
-                         python-wheel))
+    (native-inputs (list intltool python-distutils-extra python-setuptools-67
+                         python-wheel-0.40))
     (inputs (list libtorrent-rasterbar-1.2 python-dbus python-efl python-pyxdg))
     (home-page "https://www.enlightenment.org")
     (synopsis "EFL Bittorrent client")

gnu/packages/fonts.scm

@@ -176,6 +176,29 @@ source code legibility.")
  Mono, Iosevka customized to match Inter.")
     (license license:silofl1.1)))
 
+(define-public font-alcarin-tengwar
+  (let ((commit "a4530d430ea01871b0b0a54d1de218d2ffde0ea5")
+        (revision "1"))
+    (package
+      (name "font-alcarin-tengwar")
+      (version "0.83")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/Tosche/Alcarin-Tengwar")
+                       (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "190g43y7b8kiswnc3d1mdyw7p336p950b5wyb8hnbd3303ccjlsv"))))
+      (build-system font-build-system)
+      (home-page "https://tosche.net/fonts/alcarin-tengwar")
+      (synopsis "Tengwar font")
+      (description
+       "Alcarin Tengwar is a Tengwar (script invented by J. R. R. Tolkien)
+typeface.  It is designed with an academic context in mind.")
+      (license license:silofl1.1))))
+
 (define-public font-arapey
   (let ((commit  "28fa45c7f31afe62f577b0b857570ab0326b9113")
         (revision "1"))

gnu/packages/machine-learning.scm

@@ -6121,12 +6121,14 @@ simple speech recognition.")
       (build-system pyproject-build-system)
       (arguments
        (list
+        #:test-backend #~'custom
+        #:test-flags #~(list "../../tests/from_words_to_digits.py")
         #:phases
         #~(modify-phases %standard-phases
             (add-after 'unpack 'chdir
               (lambda _
                 (chdir "package/python"))))))
-      (native-inputs (list python-setuptools python-wheel))
+      (native-inputs (list python-setuptools))
       (propagated-inputs (list python-vosk))
       (home-page "https://github.com/ideasman42/nerd-dictation")
       (synopsis "Offline speech-to-text for desktop Linux")

gnu/packages/maths.scm

@@ -8206,37 +8206,36 @@ instruction sets.  Thus, an application written with Vc can be compiled for:
 (define-public reducelcs
   ;; This is the last commit which is available upstream, no
   ;; release happened since 2010.
-  (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
-        (revision "1"))
+  (let ((commit "963f74f7279ba6fc0ea7d8ddfd361ea190c80313")
+        (revision "2"))
     (package
       (name "reducelcs")
-      (version (string-append "1.0-" revision "." (string-take commit 7)))
+      (version (git-version "1.0" revision commit))
       (source
        (origin
          (method git-fetch)
          (uri (git-reference
                (url "https://github.com/gdv/Reduce-Expand-for-LCS")
                (commit commit)))
-         (file-name (string-append name "-" version "-checkout"))
+         (file-name (git-file-name name version))
          (sha256
           (base32
-           "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
+           "03chvd9wb2z08r7ka2npr49dbimjvzn2gfm7cnp5l079vbw1dfny"))))
       (build-system gnu-build-system)
-      (inputs
-       (list openlibm))
+      (inputs (list openlibm))
       (arguments
-       `(#:tests? #f ; no tests
-         #:phases
-         (modify-phases %standard-phases
-           (delete 'configure) ; No configure script exists.
-           (replace 'install ; No install phase exists.
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let* ((out (assoc-ref outputs "out"))
-                      (bin (string-append out "/bin")))
-                 (install-file "Approximation" bin)
-                 (install-file "CollectResults" bin)
-                 (install-file "GenerateInstances" bin)
-                 #t))))))
+       (list
+        #:tests? #f ; no tests
+        #:phases
+        #~(modify-phases %standard-phases
+            (delete 'configure) ; No configure script exists.
+            (replace 'install ; No install phase exists.
+              (lambda* (#:key outputs #:allow-other-keys)
+                (let* ((out (assoc-ref outputs "out"))
+                       (bin (string-append out "/bin")))
+                  (install-file "Approximation" bin)
+                  (install-file "CollectResults" bin)
+                  (install-file "GenerateInstances" bin)))))))
       (synopsis "Approximate Longest Commons Subsequence computation tool")
       (description
        "@code{reduceLCS} is an implementation of the Reduce-Expand

gnu/packages/music.scm

@@ -4206,8 +4206,8 @@ websites such as Libre.fm.")
     (license license:asl2.0)))
 
 (define-public instantmusic
-  (let ((commit "300891d09c703525215fa5a116b9294af1c923c8")
-        (revision "1"))
+  (let ((commit "0477dd310e0aeb11d4d113bb96baa40d824cc330")
+        (revision "2"))
     (package
       (name "instantmusic")
       (version (git-version "1.0" revision commit))
@@ -4219,10 +4219,11 @@ websites such as Libre.fm.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0j7qivaa04bpdz3anmgci5833dgiyfqqwq9fdrpl9m68b34gl773"))))
+                  "0pxp1h0q4j7bidgdh4wgrvnm4ckdr4bvgk1wccr02mynfsjq8x5c"))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:tests? #f ;no tests
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'build 'change-directory
@@ -4243,7 +4244,7 @@ websites such as Libre.fm.")
                           (chmod file #o644))
                         (find-files "instantmusic.egg-info"
                                     "PKG-INFO|.*\\.txt")))))))
-    (native-inputs (list python-setuptools python-wheel))
+    (native-inputs (list python-setuptools))
     (inputs (list yt-dlp))
     (propagated-inputs (list python-requests eyed3 python-beautifulsoup4))
     (home-page "https://github.com/yask123/Instant-Music-Downloader")

gnu/packages/patches/xiphos-glib.patch

@@ -0,0 +1,43 @@
+This patch has already been upstreamed, see: <https://github.com/crosswire/xiphos/pull/1103>.
+It should be removed once Xiphos updates.
+
+From 0e9e686c902935c0f00afdf9d0d45f9635995988 Mon Sep 17 00:00:00 2001
+From: Jan Tojnar <jtojnar@gmail.com>
+Date: Sat, 15 Jan 2022 05:00:37 +0100
+Subject: [PATCH] Add dbus-glib dependency to main
+
+It is required through the ipc header and the build will fail without it on Nix:
+
+	In file included from /build/source/src/main/search_sidebar.cc:48:
+	/build/source/src/gui/ipc.h:26:10: fatal error: dbus/dbus-glib.h: No such file or directory
+	   26 | #include <dbus/dbus-glib.h>
+	      |          ^~~~~~~~~~~~~~~~~~
+	compilation terminated.
+---
+ src/main/CMakeLists.txt | 11 +++++++++++
+ 1 file changed, 11 insertions(+)
+
+diff --git a/src/main/CMakeLists.txt b/src/main/CMakeLists.txt
+index 49b86371..bb8e4bb6 100644
+--- a/src/main/CMakeLists.txt
++++ b/src/main/CMakeLists.txt
+@@ -75,7 +75,18 @@ target_link_libraries(main
+   PkgConfig::Soup
+   PkgConfig::Sword
+   PkgConfig::Biblesync
+-  )
++)
++
++IF (DBUS)
++  target_include_directories (main
++    PRIVATE ${CMAKE_CURRENT_BINARY_DIR}
++    PkgConfig::DBus
++    )
++  target_link_libraries(main
++    PRIVATE
++    PkgConfig::DBus
++    )
++ENDIF (DBUS)
+ 
+ if(WK_FOUND)
+   target_compile_definitions(main

gnu/packages/python-web.scm

@@ -1699,9 +1699,8 @@ It features a minimal TLS 1.3 implementation, a QUIC stack and an HTTP/3 stack."
       ;; This test opens a remote connection.
       #~(list "-k" "not test_create_connection_resolve_good")))
     (native-inputs (list python-pytest
-                         python-pytest-asyncio
-                         python-setuptools
-                         python-wheel))
+                         python-pytest-asyncio-0.26
+                         python-setuptools))
     (propagated-inputs
      (list python-attrs python-websockets))
     (home-page "https://github.com/kyuupichan/aiorpcX")

gnu/packages/sycl.scm

@@ -18,12 +18,15 @@
 
 (define-module (gnu packages sycl)
   #:use-module (guix build-system cmake)
+  #:use-module (guix gexp)
   #:use-module (guix git-download)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (gnu packages)
   #:use-module (gnu packages boost)
+  #:use-module (gnu packages linux)
   #:use-module (gnu packages llvm)
+  #:use-module (gnu packages libffi)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages rocm)
@@ -37,7 +40,7 @@
 (define-public adaptivecpp
   (package
     (name "adaptivecpp")
-    (version "24.10.0")
+    (version "25.02.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -46,13 +49,50 @@
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1gha90zkvg6nabyj1y55rflxzygdkznkjqj8v6zb1jgm1f5w60b7"))))
+                "01wajw1vvbic1hiyz4rj7in09js3kl0xvaa2qpcg1pv7xkrz0xxx"))))
     (build-system cmake-build-system)
-    (native-inputs (list clang-15 llvm-15 python spirv-tools))
-    (inputs (list boost rocm-opencl-runtime spirv-headers))
-    (arguments `(#:tests? #f)) ; no tests
+    ;; Sync with llvm-for-rocm llvm release.
+    (native-inputs (list clang-19 llvm-19 python-minimal))
+    (inputs
+     (list boost
+           libffi
+           numactl
+           rocm-opencl-runtime
+           spirv-headers
+           spirv-tools))
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; FIXME: There is probably a much better way.
+          ;; This file: bin/hipSYCL/llvm-to-backend/llvm-to-host-tool
+          ;; requires libacpp-common.so and libllvm-to-{backend,host}.so
+          ;; in RUNPATH
+          (add-before 'validate-runpath 'create-symlinks
+            (lambda _
+              (symlink
+               (string-append #$output "/lib/libacpp-common.so")
+               (string-append
+                #$output
+                "/bin/hipSYCL/llvm-to-backend/libacpp-common.so"))
+              (symlink
+               (string-append
+                #$output
+                "/lib/hipSYCL/llvm-to-backend/libllvm-to-backend.so")
+               (string-append
+                #$output
+                "/bin/hipSYCL/llvm-to-backend/libllvm-to-backend.so"))
+              (symlink
+               (string-append
+                #$output
+                "/lib/hipSYCL/llvm-to-backend/libllvm-to-host.so")
+               (string-append
+                #$output
+                "/bin/hipSYCL/llvm-to-backend/libllvm-to-host.so")))))
+      #:tests? #f)) ; no tests
     (home-page "https://adaptivecpp.github.io/")
-    (synopsis "Implementation of the SYCL programming language for accelerators")
+    (synopsis
+     "Implementation of the SYCL programming language for accelerators")
     (description
      "AdaptiveCpp is aImplementation of SYCL and C++ standard parallelism
 for CPUs and GPUs from all vendors, with independent, community-driven