From c04c7442f658982702e92a78c296ee8e22d46f5f Mon Sep 17 00:00:00 2001 From: Cayetano Santos Date: Fri, 1 Aug 2025 18:16:57 +0200 Subject: [PATCH 01/13] gnu: adaptivecpp: Update to 25.02.0. * gnu/packages/sycl.scm (adaptivecpp): Update to 25.02.0. [arguments]<#:phases>{create-symlinks}: New phase. [inputs]: Add spirv-tools, numactl and libffi. [native-inputs]: Add python-minimal, clang-19, llvm-19; remove python, clang-15, llvm-15, spirv-tools. [synopsys]: Fix max column. Change-Id: I175287b08a409d4c5a495cd71f81ae11e23950a2 Signed-off-by: Andreas Enge --- gnu/packages/sycl.scm | 52 ++++++++++++++++++++++++++++++++++++++----- 1 file changed, 46 insertions(+), 6 deletions(-) diff --git a/gnu/packages/sycl.scm b/gnu/packages/sycl.scm index aede061ecba..de33de8a71d 100644 --- a/gnu/packages/sycl.scm +++ b/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 From 35892a7a59744d1c32c8c03eabe57d377cc38051 Mon Sep 17 00:00:00 2001 From: Gabriel Santos Date: Sun, 21 Sep 2025 07:38:56 -0300 Subject: [PATCH 02/13] gnu: Add font-alcarin-tengwar. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fonts.scm (font-alcarin-tengwar): New variable. Closes: #2850 Change-Id: I803c012dff56f24470db8cd356afca8b0275fee1 Signed-off-by: 宋文武 --- gnu/packages/fonts.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index 7f1494c45d8..2d433e8f03e 100644 --- a/gnu/packages/fonts.scm +++ b/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")) From 9a59e74beef4867699a10b6af82244c1c80389c6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= Date: Fri, 26 Sep 2025 17:06:29 +0800 Subject: [PATCH 03/13] gnu: uxn: Update to 1.0-1.f2e8582. * gnu/packages/emulators.scm (uxn): Update to 1.0-1.f2e8582. [arguments]: Adjust install phase. Change-Id: I24c076aa5eddafd30cc09f4f97c445c4c0994ce9 --- gnu/packages/emulators.scm | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index 7fa39385096..807026e60e7 100644 --- a/gnu/packages/emulators.scm +++ b/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") From 3c96d9fb1e1ee8fe4efd44ba6e8f3886b43668be Mon Sep 17 00:00:00 2001 From: Hugo Buddelmeijer Date: Fri, 26 Sep 2025 11:04:23 +0200 Subject: [PATCH 04/13] gnu: reducelcs: Fix build with gcc-14. * gnu/packages/maths.scm (reducelcs): Fix build with gcc14. [origin]: Use git-version and git-file-name. [arguments]<#:phases>: Add patch-source phase. Change-Id: I906d899700ec9805c2c4a080cb303c6e9e90a271 Signed-off-by: Andreas Enge --- gnu/packages/maths.scm | 43 ++++++++++++++++++++++++++---------------- 1 file changed, 27 insertions(+), 16 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 2e46a6050d0..234b0927967 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -8210,33 +8210,44 @@ instruction sets. Thus, an application written with Vc can be compiled for: (revision "1")) (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")))) (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. + (add-after 'unpack 'patch-source + ;; See: + (lambda _ + (substitute* "Approximation.c" + (("char min_alphabet,max_alphabet;\n$" all) + (string-append all " +int ExactLcs2(char lcs[MAXLEN], char *seq1, char *seq2);"))) + (substitute* "GenerateInstances.c" + (("#include " all) + (string-append all " +#include +#include "))))) + (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 From d2d02faf1845d6a1d12ec46d7e0d9b43d77a8c6b Mon Sep 17 00:00:00 2001 From: Hugo Buddelmeijer Date: Fri, 26 Sep 2025 12:22:13 +0200 Subject: [PATCH 05/13] gnu: reducelcs: Update to latest commit. * gnu/packages/maths.scm (reducelcs): Update to latest commit. [source]: Update to latest commit, increase revision to 2. [arguments]<#:phases>{patch-source}: Remove upstreamed phase. Change-Id: I3a49a03b8093961d166e2d2350638a0e652de3df Signed-off-by: Andreas Enge --- gnu/packages/maths.scm | 18 +++--------------- 1 file changed, 3 insertions(+), 15 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 234b0927967..1cd0865263a 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -8206,8 +8206,8 @@ 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 (git-version "1.0" revision commit)) @@ -8220,7 +8220,7 @@ instruction sets. Thus, an application written with Vc can be compiled for: (file-name (git-file-name name version)) (sha256 (base32 - "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm")))) + "03chvd9wb2z08r7ka2npr49dbimjvzn2gfm7cnp5l079vbw1dfny")))) (build-system gnu-build-system) (inputs (list openlibm)) (arguments @@ -8229,18 +8229,6 @@ instruction sets. Thus, an application written with Vc can be compiled for: #:phases #~(modify-phases %standard-phases (delete 'configure) ; No configure script exists. - (add-after 'unpack 'patch-source - ;; See: - (lambda _ - (substitute* "Approximation.c" - (("char min_alphabet,max_alphabet;\n$" all) - (string-append all " -int ExactLcs2(char lcs[MAXLEN], char *seq1, char *seq2);"))) - (substitute* "GenerateInstances.c" - (("#include " all) - (string-append all " -#include -#include "))))) (replace 'install ; No install phase exists. (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) From 593cd7f73f4079beb4ac2e0641891e69c659a36a Mon Sep 17 00:00:00 2001 From: Gabriel Santos Date: Mon, 25 Aug 2025 15:56:24 -0300 Subject: [PATCH 06/13] gnu: Add xiphos. * gnu/packages/books.scm (xiphos): New variable. * gnu/packages/patches/xiphos-glib.patch: New file. * gnu/local.mk (dist_PATCH_DATA): Add it. Change-Id: I17f3e14c7721887fcb1852e7f07e80fc48d48a79 Signed-off-by: Andreas Enge --- gnu/local.mk | 1 + gnu/packages/books.scm | 59 +++++++++++++++++++++++++- gnu/packages/patches/xiphos-glib.patch | 43 +++++++++++++++++++ 3 files changed, 102 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/xiphos-glib.patch diff --git a/gnu/local.mk b/gnu/local.mk index f02a5277bcb..43de2994f45 100644 --- a/gnu/local.mk +++ b/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 \ diff --git a/gnu/packages/books.scm b/gnu/packages/books.scm index 5257d33a040..ada2cfe0603 100644 --- a/gnu/packages/books.scm +++ b/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+))) diff --git a/gnu/packages/patches/xiphos-glib.patch b/gnu/packages/patches/xiphos-glib.patch new file mode 100644 index 00000000000..4fdb09fa638 --- /dev/null +++ b/gnu/packages/patches/xiphos-glib.patch @@ -0,0 +1,43 @@ +This patch has already been upstreamed, see: . +It should be removed once Xiphos updates. + +From 0e9e686c902935c0f00afdf9d0d45f9635995988 Mon Sep 17 00:00:00 2001 +From: Jan Tojnar +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 + | ^~~~~~~~~~~~~~~~~~ + 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 \ No newline at end of file From 56e892e100b8b29bc57213aa286f164487ada4db Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Fri, 26 Sep 2025 12:54:19 +0100 Subject: [PATCH 07/13] gnu: gemma: Refresh package style. * gnu/packages/bioinformatics.scm (gemma): Apply G-Expressions, remove trailing #t from procedures and lambdas, fix indentation. [version]: Remove "v" to improve format, seen in . [source] : Add "v" to {commit} field. [native-inputs]: Remove labels. Change-Id: I9c2113dbdc265e3726b548670d450d0cdcbf1bea --- gnu/packages/bioinformatics.scm | 60 +++++++++++++++------------------ 1 file changed, 28 insertions(+), 32 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 16f6941946d..d3d50d30826 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8691,52 +8691,48 @@ 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 From 1c22d2938897029dc1017cbfb101df6c357427e5 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Fri, 26 Sep 2025 13:49:50 +0100 Subject: [PATCH 08/13] gnu: efitools: Fix build with gcc-14. * gnu/packages/efi.scm (efitools):[arguments] : Add options relaxing GCC 14 strictness. Fixes: guix/guix#3012 Change-Id: I1466b6ded8039ec222e905554b23e9bf99dba486 --- gnu/packages/efi.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/efi.scm b/gnu/packages/efi.scm index 99b41e91693..9a80ca954cd 100644 --- a/gnu/packages/efi.scm +++ b/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 From d59508b9b4e4a58a3e591ecd9b4bf7a6009cbc8b Mon Sep 17 00:00:00 2001 From: Hugo Buddelmeijer Date: Fri, 26 Sep 2025 11:46:13 +0200 Subject: [PATCH 09/13] gnu: python-bcbio-gff: Update to 0.7.1. * gnu/packages/bioinformatics.scm (python-bcbio-gff): Update to 0.7.1. [source]: Switch to git-fetch. [arguments] <#:phases>: Enter correct directory. [propagated-inputs]: Remove python-setuptools and python-wheel. [native-inputs]: Add python-setuptools. Change-Id: Ie961c40e9335f31d512e23658cbc3269a61126d0 Signed-off-by: Sharlatan Hellseher --- gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++-------- 1 file changed, 20 insertions(+), 8 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d3d50d30826..5d218e6a690 100644 --- a/gnu/packages/bioinformatics.scm +++ b/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 From cb2c75aa929525bf7612ae27f0ab648c1ed07cba Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Fri, 26 Sep 2025 15:10:14 +0100 Subject: [PATCH 10/13] gnu: instantmusic: Update to 1.0-2.0477dd3, fix build. * gnu/packages/music.scm (instantmusic): Update to 1.0-2.0477dd3. [arguments] : No tests provided. [native-inputs]: Remove python-wheel. Change-Id: I928c4cc909b6d57738eb6bd8b0cae7debb53f085 --- gnu/packages/music.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 5e7b7015a05..c789ae54fa2 100644 --- a/gnu/packages/music.scm +++ b/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") From 6851e548a337c976e0e6e575bfb318b0719e2751 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Fri, 26 Sep 2025 15:15:45 +0100 Subject: [PATCH 11/13] gnu: epour: Fix bulid. * gnu/packages/enlightenment.scm (epour)[native-inputs]: Remove python-setuptools and python-wheel; add python-setuptools-67 and python-wheel-0.40. Change-Id: Ia3863aa7f0af1d9e20ae78a875b6108d973ee410 --- gnu/packages/enlightenment.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm index 8a08262e22d..f0229489570 100644 --- a/gnu/packages/enlightenment.scm +++ b/gnu/packages/enlightenment.scm @@ -561,6 +561,7 @@ directories. @dfn{Enlightenment Foundation Libraries} (EFL).") (license license:bsd-2))) +;; XXX: See: . (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") From 04f3f640a2963a34f00dde54da7c26a702d4738e Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Fri, 26 Sep 2025 15:23:39 +0100 Subject: [PATCH 12/13] gnu: nerd-dictation: Fix tests. * gnu/packages/machine-learning.scm (nerd-dictation)[arguments] : Use 'custom. : Provide the path to test file. [native-inputs]: Remove python-wheel. Change-Id: Ia6e2c497ffe9315a87dc20b4d845fea111a144c9 --- gnu/packages/machine-learning.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index e04525b3d6d..8e8b4c9d088 100644 --- a/gnu/packages/machine-learning.scm +++ b/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") From 771659666dbccbe9d24e561d8ad7b5badf771f98 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Fri, 26 Sep 2025 15:35:20 +0100 Subject: [PATCH 13/13] 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/packages/python-web.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index fe7f39333f1..3fe87747bfc 100644 --- a/gnu/packages/python-web.scm +++ b/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")