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| author | Liliana Marie Prikler <liliana.prikler@gmail.com> | 2023-06-08 15:33:29 +0200 |
|---|---|---|
| committer | Liliana Marie Prikler <liliana.prikler@gmail.com> | 2023-06-08 15:33:29 +0200 |
| commit | 909788c0aebd8098084c009afa98d1209c9ec869 (patch) | |
| tree | ffe6735a2db3b0ac595b90a52825fe82eca9b803 /gnu | |
| parent | 16a5ce3bb7fbd14fb17a6ba6a62fb079d2379fcc (diff) | |
| parent | 872b2487451c39020a78ed3227992fb02a7ed5e5 (diff) | |
| download | guix-909788c0aebd8098084c009afa98d1209c9ec869.tar guix-909788c0aebd8098084c009afa98d1209c9ec869.tar.gz | |
Merge branch 'master' into gnome-team
Diffstat (limited to 'gnu')
62 files changed, 2238 insertions, 625 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 9f9fba0c4a..4d0e34cf09 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -885,6 +885,10 @@ dist_patch_DATA = \ %D%/packages/patches/aegisub-icu59-include-unistr.patch \ %D%/packages/patches/aegisub-boost68.patch \ %D%/packages/patches/aegisub-make43.patch \ + %D%/packages/patches/agda-categories-remove-incompatible-flags.patch \ + %D%/packages/patches/agda-categories-use-find.patch \ + %D%/packages/patches/agda-libdirs-env-variable.patch \ + %D%/packages/patches/agda-stdlib-use-runhaskell.patch \ %D%/packages/patches/agg-am_c_prototype.patch \ %D%/packages/patches/agg-2.5-gcc8.patch \ %D%/packages/patches/akonadi-paths.patch \ @@ -1033,6 +1037,7 @@ dist_patch_DATA = \ %D%/packages/patches/curl-use-ssl-cert-env.patch \ %D%/packages/patches/cursynth-wave-rand.patch \ %D%/packages/patches/cvs-CVE-2017-12836.patch \ + %D%/packages/patches/d-feet-drop-unused-meson-argument.patch \ %D%/packages/patches/date-output-pkg-config-files.patch \ %D%/packages/patches/datefudge-gettimeofday.patch \ %D%/packages/patches/dbacl-include-locale.h.patch \ @@ -1750,6 +1755,8 @@ dist_patch_DATA = \ %D%/packages/patches/procmail-ambiguous-getline-debian.patch \ %D%/packages/patches/procmail-CVE-2014-3618.patch \ %D%/packages/patches/procmail-CVE-2017-16844.patch \ + %D%/packages/patches/proj-7-initialize-memory.patch \ + %D%/packages/patches/proot-add-clone3.patch \ %D%/packages/patches/protobuf-fix-build-on-32bit.patch \ %D%/packages/patches/psm-arch.patch \ %D%/packages/patches/psm-disable-memory-stats.patch \ @@ -1889,6 +1896,7 @@ dist_patch_DATA = \ %D%/packages/patches/sbcl-clml-fix-types.patch \ %D%/packages/patches/sbcl-eazy-gnuplot-skip-path-check.patch \ %D%/packages/patches/sbcl-png-fix-sbcl-compatibility.patch \ + %D%/packages/patches/sbcl-riscv-Make-contribs-build-again.patch \ %D%/packages/patches/scalapack-gcc-10-compilation.patch \ %D%/packages/patches/scheme48-tests.patch \ %D%/packages/patches/scons-test-environment.patch \ diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index f0eed185dd..3193aa1456 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -9,7 +9,7 @@ ;;; Copyright © 2016, 2017, 2020 Leo Famulari <leo@famulari.name> ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net> -;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2016-2023 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 Peter Feigl <peter.feigl@nexoid.at> ;;; Copyright © 2016 John J. Foerch <jjfoerch@earthlink.net> ;;; Copyright © 2016, 2017 Nikita <nikita@n0.is> @@ -2603,24 +2603,20 @@ characters can be replaced as well, as can UTF-8 characters.") (define-public tree (package (name "tree") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (string-append "https://mama.indstate.edu/users/ice/tree/src/tree-" version ".tgz")) (sha256 - (base32 "1xmbxgx72w7ddjlqsx1yys076hp3h7ll968bhdmdrc7jpwswaq01")))) + (base32 "1mchmdkq77d4c2mx7xmarccbk46a3sm2aqslarjwgxrs81gxbhyk")))) (build-system gnu-build-system) (arguments (list #:phases #~(modify-phases %standard-phases - (delete 'configure) ; No configure script. - (add-after 'unpack 'fix-manpage-version - (lambda _ - (substitute* "doc/tree.1" - (("Tree 2\\.0\\.0") (string-append "Tree " #$version)))))) + (delete 'configure)) ; No configure script. #:tests? #f ; No check target. #:make-flags #~(list (string-append "PREFIX=" #$output) diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm index 7128a3f108..88626b823c 100644 --- a/gnu/packages/agda.scm +++ b/gnu/packages/agda.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2018, 2022 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2018 John Soo <jsoo1@asu.edu> ;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2023 Josselin Poiret <dev@jpoiret.xyz> ;;; ;;; This file is part of GNU Guix. ;;; @@ -22,9 +23,15 @@ ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. (define-module (gnu packages agda) + #:use-module (gnu packages) #:use-module (gnu packages haskell-check) #:use-module (gnu packages haskell-web) #:use-module (gnu packages haskell-xyz) + #:use-module (gnu packages imagemagick) + #:use-module (gnu packages python) + #:use-module (gnu packages sphinx) + #:use-module (gnu packages texinfo) + #:use-module (guix build-system agda) #:use-module (guix build-system emacs) #:use-module (guix build-system gnu) #:use-module (guix build-system haskell) @@ -37,15 +44,18 @@ (define-public agda (package (name "agda") - (version "2.6.2.2") + (version "2.6.3") (source (origin - (method url-fetch) - (uri (hackage-uri "Agda" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/agda/agda.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "0yjjbhc593ylrm4mq4j01nkdvh7xqsg5in30wxj4y53vf5hkggp5")))) + (base32 "1s7zd01i8pmvi90ywx497kc07z50nah7h0fc2dn6jzb132k5sh1q")) + (patches (search-patches "agda-libdirs-env-variable.patch")))) (build-system haskell-build-system) - (properties '((upstream-name . "Agda"))) (inputs (list ghc-aeson ghc-alex @@ -68,7 +78,14 @@ ghc-strict ghc-unordered-containers ghc-uri-encode + ghc-vector-hashtables ghc-zlib)) + (native-inputs + (list python + python-sphinx + python-sphinx-rtd-theme + texinfo + imagemagick)) (arguments (list #:modules `((guix build haskell-build-system) (guix build utils) @@ -85,7 +102,22 @@ (let ((agda-compiler (string-append #$output "/bin/agda"))) (for-each (cut invoke agda-compiler <>) (find-files (string-append #$output "/share") - "\\.agda$")))))))) + "\\.agda$"))))) + (add-after 'agda-compile 'install-info + (lambda _ + (with-directory-excursion "doc/user-manual" + (invoke "sphinx-build" "-b" "texinfo" + "." "_build_texinfo") + (with-directory-excursion "_build_texinfo" + (setenv "infodir" (string-append #$output + "/share/info")) + (invoke "make" "install-info")))))))) + (search-paths + (list (search-path-specification + (variable "AGDA_LIBDIRS") + (files (list "lib/agda"))))) + (native-search-paths + search-paths) (home-page "https://wiki.portal.chalmers.se/agda/") (synopsis "Dependently typed functional programming language and proof assistant") @@ -106,58 +138,184 @@ such as Coq, Epigram and NuPRL.") (define-public emacs-agda2-mode (package - (inherit agda) (name "emacs-agda2-mode") + (version (package-version agda)) + (source (package-source agda)) (build-system emacs-build-system) - (inputs '()) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'enter-elisp-dir - (lambda _ (chdir "src/data/emacs-mode") #t))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'enter-elisp-dir + (lambda _ (chdir "src/data/emacs-mode")))))) (home-page "https://agda.readthedocs.io/en/latest/tools/emacs-mode.html") (synopsis "Emacs mode for Agda") (description "This Emacs mode enables interactive development with -Agda. It also aids the input of Unicode characters."))) +Agda. It also aids the input of Unicode characters.") + (license (package-license agda)))) (define-public agda-ial + (let ((revision "1") + ;; There hasn't been a release in a long time, and the last one + ;; doesn't build with Agda 2.6. + (commit "ded30c410d5d40142249686572aa1acd1b2f8cc7")) + (package + (name "agda-ial") + (version (git-version "1.5.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference (url "https://github.com/cedille/ial") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0xn6zvp1wnm0i84pz1rfbzfmayd15ch4i5s11ycd88d22pxd55dc")))) + (build-system agda-build-system) + (arguments + (list + #:gnu-and-haskell? #t + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'patch-dependencies + (lambda _ (patch-shebang "find-deps.sh"))) + (replace 'build + (lambda _ + (invoke "make")))))) + (home-page "https://github.com/cedille/ial") + (synopsis "The Iowa Agda Library") + (description + "The goal is to provide a concrete library focused on verification +examples, as opposed to mathematics. The library has a good number +of theorems for booleans, natural numbers, and lists. It also has +trees, tries, vectors, and rudimentary IO. A number of good ideas +come from Agda's standard library.") + (license license:expat)))) + +(define-public agda-stdlib (package - (name "agda-ial") - (version "1.5.0") - (home-page "https://github.com/cedille/ial") + (name "agda-stdlib") + (version "1.7.2") (source (origin (method git-fetch) - (uri (git-reference (url home-page) - (commit (string-append "v" version)))) + (uri (git-reference + (url "https://github.com/agda/agda-stdlib") + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 - "0dlis6v6nzbscf713cmwlx8h9n2gxghci8y21qak3hp18gkxdp0g")))) - (build-system gnu-build-system) - (inputs - (list agda)) + "065hf24xjpciwdrvk4isslgcgi01q0k93ql0y1sjqqvy5ryg5xmy")))) + (build-system agda-build-system) (arguments - `(#:parallel-build? #f - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-before 'build 'patch-dependencies - (lambda _ (patch-shebang "find-deps.sh") #t)) - (delete 'check) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (include (string-append out "/include/agda/ial"))) - (for-each (lambda (file) - (make-file-writable file) - (install-file file include)) - (find-files "." "\\.agdai?(-lib)?$")) - #t)))))) - (synopsis "The Iowa Agda Library") + (list + #:plan '(("^\\./README.agda$" "-i.")) + #:gnu-and-haskell? #t + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'generate-everything + (lambda* (#:key inputs native-inputs #:allow-other-keys) + (invoke + (search-input-file (or native-inputs inputs) "/bin/runhaskell") + "GenerateEverything.hs")))))) + (native-inputs (list ghc-filemanip)) + (synopsis "The Agda Standard Library") (description - "The goal is to provide a concrete library focused on verification -examples, as opposed to mathematics. The library has a good number -of theorems for booleans, natural numbers, and lists. It also has -trees, tries, vectors, and rudimentary IO. A number of good ideas -come from Agda's standard library.") + "The standard library aims to contain all the tools needed to write +both programs and proofs easily. While we always try and write efficient +code, we prioritize ease of proof over type-checking and normalization +performance. If computational performance is important to you, then perhaps +try agda-prelude instead.") + (home-page "https://wiki.portal.chalmers.se/agda/pmwiki.php") + (license license:expat))) + +(define-public agda-categories + (package + (name "agda-categories") + (version "0.1.7.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/agda/agda-categories.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0xwgm2mfl2pxipsv31bin8p14y1yhd9n27lv3clvsxd4z9yc034m")) + (patches (search-patches "agda-categories-remove-incompatible-flags.patch" + "agda-categories-use-find.patch")))) + (build-system agda-build-system) + (arguments + (list + #:gnu-and-haskell? #t + #:phases + #~(modify-phases %standard-phases + (replace 'build + (lambda _ + (invoke "make")))))) + (propagated-inputs + (list agda-stdlib)) + (synopsis "New Categories library for Agda") + (description "A new Categories library for Agda") + (home-page "https://github.com/agda/agda-categories") (license license:expat))) + +(define-public agda-cubical + ;; Upstream's HEAD follows the latest Agda release, but they don't release + ;; until a newer Agda release comes up, so their releases are always one + ;; version late. + (let* ((revision "1") + (commit "814d54b08b360b8e80828065f54b80e3a98a0092")) + (package + (name "agda-cubical") + (version (git-version "0.4" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/agda/cubical.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0d25gb1qzpx539k62qjsjq4xmzp34qk7n3hmd9y6v8slhrrxw312")))) + (build-system agda-build-system) + (arguments + (list + #:gnu-and-haskell? #t + #:phases + #~(modify-phases %standard-phases + (replace 'build + (lambda _ + (invoke "make")))))) + (synopsis "Standard library for Cubical Agda") + (description "A standard library for Cubical Agda, comparable to +agda-stdlib but using cubical methods.") + (home-page "https://github.com/agda/cubical") + (license license:expat)))) + +(define-public agda-1lab + ;; Upstream doesn't do releases (yet). Use a commit that builds with 2.6.3, + ;; since they use Agda HEAD. + (let* ((revision "1") + (commit "47ca1d23640a6f49a3abe3c2fe27738bcc10c9c6")) + (package + (name "agda-1lab") + (version (git-version "0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/plt-amy/1lab.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0j7mp6c0xd0849skdxzncklkxynxnyfrbpcjv4qp5p1xfn0dnfqx")))) + (build-system agda-build-system) + (arguments + (list #:plan '(("src/index\\.lagda\\.md$")))) + (synopsis "Reference resource for mathematics done in Homotopy Type Theory") + (description "A formalised, cross-linked reference resource for +mathematics done in Homotopy Type Theory. Unlike the HoTT book, the 1lab is +not a “linear” resource: Concepts are presented as a directed graph, with +links indicating dependencies.") + (home-page "https://1lab.dev") + (license license:agpl3)))) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ec52cd6e2d..00701c4463 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10313,17 +10313,18 @@ fitting of some classes of graphical Markov models.") (define-public r-ggpicrust2 (package (name "r-ggpicrust2") - (version "1.6.5") + (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "ggpicrust2" version)) (sha256 (base32 - "02ais1y3z85vykxd9975gz33s80d1nhivly6a07y98dbmlzjyr6a")))) + "0rw2nrmnniff5hb56r21rk0mphba74fppxsa5ps2xamg1a63qfyw")))) (properties `((upstream-name . "ggpicrust2"))) (build-system r-build-system) (propagated-inputs (list r-aldex2 r-aplot + r-circlize r-deseq2 r-dplyr r-edger @@ -10341,6 +10342,7 @@ fitting of some classes of graphical Markov models.") r-summarizedexperiment r-tibble r-tidyr)) + (native-inputs (list r-knitr)) (home-page "https://github.com/cafferychen777/ggpicrust2") (synopsis "Make PICRUSt2 output analysis and visualization easier") (description diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0b67d8fbe6..9ce28596c2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1337,6 +1337,75 @@ pretty, publication-quality figures for next-generation sequencing experiments.") (license license:expat))) +(define-public python-bulkvis + (let ((commit "00a82a90c7e748a34af896e779d27e78a2c82b5e") + (revision "2")) + (package + (name "python-bulkvis") + (version (git-version "2.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/LooseLab/bulkVis") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02blai158xyyqcg0ljzkmfa6ci05m4awrl4njvp9nwfp717xq8n0")) + (modules '((guix build utils))) + (snippet + '(substitute* '("requirements.txt" + "setup.py") + (("tqdm~=4.46.1") "tqdm") + (("tornado~=6.0.4") "tornado") + (("pandas~=1.0.5") "pandas") + (("h5py~=2.10.0") "h5py") + ;; See below for com + (("bokeh~=2.1.0") "bokeh"))))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f ;There are no tests + #:phases + '(modify-phases %standard-phases + ;; See https://github.com/LooseLab/bulkvis/issues/58 + (add-after 'unpack 'bokeh-compatibility + (lambda _ + (substitute* "bulkvis/bulkvis.py" + (("import importlib" m) + (string-append m " +from bokeh.command.subcommand import Argument +from bokeh.util.dataclasses import entries\n")) + (("( *)_parser.add_argument" m indent) + (string-append + (string-join (list "if isinstance(opts, Argument):\n" + " opts = dict(entries(opts))\n") + indent 'prefix) + m)))))))) + (propagated-inputs (list python-bokeh + python-dill + python-h5py + python-joblib + python-matplotlib + python-numpy + python-pandas + python-plotly + python-readpaf + python-scikit-learn + python-scikit-image + python-scipy + python-seaborn + python-tornado-6 + python-tqdm + python-umap-learn)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/LooseLab/bulkVis") + (synopsis "Interactive visualization of bulk RNA-seq data") + (description + "This is a Python package for the interactive visualization of bulk +RNA-seq data. It provides a range of plotting functions and interactive tools +to explore and analyze bulk RNA-seq data.") + (license license:expat)))) + (define-public python-cell2cell (package (name "python-cell2cell") @@ -1480,6 +1549,69 @@ from high-throughput single-cell RNA sequencing (scRNA-seq) data.") and sequence consensus.") (license license:expat))) +(define-public python-decoupler-py + ;; This latest commit fixes a bug in test_omnip.py. + (let ((commit "b84c524ec4a9280a56c0db963e2c7b010316ce8f") + (revision "1")) + (package + (name "python-decoupler-py") + (version (git-version "1.3.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/saezlab/decoupler-py") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0d74yr5jqc52vcxaca84kxqw7m5rbazpmvnrcp2y4xxrj6yr1sfc")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + '(list "-k" + ;; These tests require internet access + (string-append "not test_get_resource" + " and not test_show_resources" + " and not test_get_dorothea" + " and not test_get_progeny" + ;; XXX This one fails because the "texts" list + ;; is empty, so there are no texts to adjust. + ;; It is not clear whether this a compatibility + ;; problem with our adjusttext package. + " and not test_plot_volcano")) + #:phases + '(modify-phases %standard-phases + (add-before 'check 'set-home + ;; Some tests require a home directory to be set. + (lambda _ (setenv "HOME" "/tmp"))) + ;; Numba needs a writable dir to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (propagated-inputs (list python-adjusttext + python-anndata + python-ipython + python-matplotlib + python-nbsphinx + python-numba + python-numpy + python-numpydoc + python-omnipath + python-scanpy + python-scikit-learn + python-scipy + python-skranger + python-tqdm + python-typing-extensions)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/saezlab/decoupler-py") + (synopsis + "Framework for modeling, analyzing and interpreting single-cell RNA-seq data") + (description + "This package provides different statistical methods to extract +biological activities from omics data within a unified framework.") + (license license:gpl3+)))) + (define-public python-demuxem (package (name "python-demuxem") @@ -1998,6 +2130,25 @@ alignments and perform the following operations: ") (license license:expat))) +(define-public python-readpaf + (package + (name "python-readpaf") + (version "0.0.10") + (source (origin + (method url-fetch) + (uri (pypi-uri "readpaf" version)) + (sha256 + (base32 + "15m6ffks4zwpp1ycwk6n02py6mw2yh7qr0vhpc178b91gldr97ia")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-pandas)) + (home-page "https://github.com/alexomics/read-paf") + (synopsis "Minimap2 PAF file reader") + (description + "This is a fast parser for minimap2 PAF (Pairwise mApping Format) +files.") + (license license:expat))) + (define-public bioperl-minimal (package (name "bioperl-minimal") diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 8a8b94c07b..bedc6ecca9 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2015, 2016, 2017, 2018, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015, 2017, 2018 Leo Famulari <leo@famulari.name> ;;; Copyright © 2015 Jeff Mickey <j@codemac.net> -;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2015-2023 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2016 Danny Milosavljevic <dannym@scratchpost.org> ;;; Copyright © 2016–2022 Tobias Geerinckx-Rice <me@tobias.gr> @@ -2687,12 +2687,8 @@ to their original, binary CD format.") (build-system cmake-build-system) (arguments (list #:configure-flags - #~(list "-DLIBDEFLATE_BUILD_STATIC_LIB=NO") - #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda _ - (invoke "../source/scripts/run_tests.sh")))))) + #~(list "-DLIBDEFLATE_BUILD_STATIC_LIB=NO" + "-DLIBDEFLATE_BUILD_TESTS=YES"))) (inputs (list zlib)) (home-page "https://github.com/ebiggers/libdeflate") diff --git a/gnu/packages/conky.scm b/gnu/packages/conky.scm index 9843cbe3c0..afc6374554 100644 --- a/gnu/packages/conky.scm +++ b/gnu/packages/conky.scm @@ -40,7 +40,7 @@ (package (name "conky") (home-page "https://github.com/brndnmtthws/conky") - (version "1.12.2") + (version "1.19.2") (source (origin (method git-fetch) @@ -49,7 +49,7 @@ (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1grxapl4q37fzk2rsijwz2rrl0aj520y8daki6bg48jb9vjd39n7")))) + (base32 "196wqr477fch1152cqmf11ckwrgkk2wmhl56ms6jk19hfs83d980")))) (build-system cmake-build-system) (arguments `(#:configure-flags diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm index 9983213f7f..365b15a3b9 100644 --- a/gnu/packages/cpp.scm +++ b/gnu/packages/cpp.scm @@ -25,7 +25,7 @@ ;;; Copyright © 2021 jgart <jgart@dismail.de> ;;; Copyright © 2021 Julien Lepiller <julien@lepiller.eu> ;;; Copyright © 2021 Disseminate Dissent <disseminatedissent@protonmail.com> -;;; Copyright © 2022 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2022, 2023 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2022 muradm <mail@muradm.net> ;;; Copyright © 2022 Attila Lendvai <attila@lendvai.name> ;;; Copyright © 2022 Arun Isaac <arunisaac@systemreboot.net> @@ -821,7 +821,7 @@ tools: ;; header (package (name "cpp-httplib") - (version "0.8.8") + (version "0.12.5") (source (origin (method git-fetch) @@ -829,16 +829,19 @@ tools: (url "https://github.com/yhirose/cpp-httplib") (commit (string-append "v" version)))) (sha256 - (base32 "0c0gyfbvm34bgrqy9fhfxw1f8nb9zhf063j7xq91k892flb7qm1c")) + (base32 "1m1p6h1dsxg4kg5zziffb6xl8zgjbkw7gmgmmlnrhpl3bswam87n")) (file-name (git-file-name name version)))) (build-system cmake-build-system) (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON" + "-DHTTPLIB_TEST=ON" "-DHTTPLIB_COMPILE=ON" "-DHTTPLIB_REQUIRE_BROTLI=ON" "-DHTTPLIB_REQUIRE_OPENSSL=ON" "-DHTTPLIB_REQUIRE_ZLIB=ON") + #:make-flags + '(,(string-append "CXX=" (cxx-for-target))) #:phases (modify-phases %standard-phases (add-after 'unpack 'disable-network-tests @@ -850,21 +853,19 @@ tools: (string-append "(DISABLED_" test)))) ;; There are tests requiring network access, disable them '("AbsoluteRedirectTest" "BaseAuthTest" "CancelTest" + "ConnectionErrorTest" "ChunkedEncodingTest" "ChunkedEncodingTest" + "ClientDefaultHeadersTest" "DecodeWithChunkedEncoding" "DefaultHeadersTest" "DigestAuthTest" "HttpsToHttpRedirectTest" + "HostnameToIPConversionTest" "RangeTest" "RedirectTest" "RelativeRedirectTest" - "SSLClientTest" "SendAPI" "TooManyRedirectTest" "UrlWithSpace" - "YahooRedirectTest" "YahooRedirectTest")))) - (replace 'check - (lambda* (#:key source tests? #:allow-other-keys) - ;; openssl genrsa wants to write a file in the git checkout - (when tests? - (with-directory-excursion "../source/test" - (invoke "make")))))))) + "SSLClientTest" "SendAPI" + "SpecifyServerIPAddressTest" + "TooManyRedirectTest" "UrlWithSpace" + "YahooRedirectTest" "YahooRedirectTest"))))))) (native-inputs - ;; required to build shared lib - (list python)) + (list googletest python)) (inputs (list brotli openssl zlib)) (home-page "https://github.com/yhirose/cpp-httplib") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 688621343e..53c49e3ac7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1927,13 +1927,13 @@ Prism-look is achieved with @code{theme_prism()} and (define-public r-ggrastr (package (name "r-ggrastr") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "ggrastr" version)) (sha256 (base32 - "07sx5wlawfyb0zy5am2q1ajhkdym5r9ih47p57l8bv4dlc7ykml2")))) + "1l90mlb6bqq98ifmlbs5481vch9inmzdnvnz192adklrr9nl09yb")))) (properties `((upstream-name . "ggrastr"))) (build-system r-build-system) (propagated-inputs (list r-cairo r-ggbeeswarm r-ggplot2 r-png r-ragg)) @@ -6203,13 +6203,13 @@ most popular ones.") (define-public r-sp (package (name "r-sp") - (version "1.6-0") + (version "1.6-1") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 - (base32 "1npwz49qmlqz46jrwlmv4929hb3wv3whxzj1bplyipp7h2z7z5zm")))) + (base32 "09d3jhk7iwjfhzyq0cwws1p5gspj9nxww5x7xvngh8hr9gan5wkn")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) @@ -7784,14 +7784,14 @@ or between integer vectors representing generic sequences.") (define-public r-ucminf (package (name "r-ucminf") - (version "1.1-4.3") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "ucminf" version)) (sha256 (base32 - "1vjrbavj909wlsyb82dq3rybk0nqay6vl81f2qiqrm12ks9pw3js")))) + "1x3d3l500kyqamzfjpz4qc38d6d3sha9av3rpxz0m4dhms28zpas")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ucminf/") @@ -10804,15 +10804,17 @@ methods.") (define-public r-catdap (package (name "r-catdap") - (version "1.3.5") + (version "1.3.7") (source (origin (method url-fetch) (uri (cran-uri "catdap" version)) (sha256 (base32 - "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5")))) + "0z84bx808hy70bkzdda9l42ljh9i9pz07isxq756axi7nr0ky6p9")))) (build-system r-build-system) + (propagated-inputs + (list r-rcolorbrewer)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/catdap/") @@ -11023,14 +11025,14 @@ simple method for converting between file types.") (define-public r-maptools (package (name "r-maptools") - (version "1.1-6") + (version "1.1-7") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 - "024kyq81gwpl7shil63nng1z6pgqcwy6j6wj44gj7ch3vd9dz9fn")))) + "0m576fzaaqbz1pqjv585841k93xnmx844kpsjzivmpfyvhbmw81v")))) (build-system r-build-system) (propagated-inputs (list r-foreign r-lattice r-sp)) @@ -12769,14 +12771,14 @@ contains or can be specified by the user.") (define-public r-biasedurn (package (name "r-biasedurn") - (version "2.0.9") + (version "2.0.10") (source (origin (method url-fetch) (uri (cran-uri "BiasedUrn" version)) (sha256 (base32 - "02bb81x1hfvhm6qlcvp88bdpm1fhqak9cjbqz1r7fhg2qfxjpims")))) + "0jv0zvz1zs34h12zdgn3lqmn7hfkk2z6fkwbd9mlyddf34rkvfqv")))) (properties `((upstream-name . "BiasedUrn"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/BiasedUrn/") @@ -15318,14 +15320,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.10.3") + (version "0.10.4") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "1l4sr6cgg8rkgs5w98a36n79b1lbg241p60grsnz12hskppa1a6q")))) + "0ddwfkrzwbj1bykvifzrb11hs5kh2a6ykr3ac1hi7cqpqikymfna")))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight)) @@ -18188,14 +18190,14 @@ library.") (define-public r-ontologyindex (package (name "r-ontologyindex") - (version "2.10") + (version "2.11") (source (origin (method url-fetch) (uri (cran-uri "ontologyIndex" version)) (sha256 (base32 - "0hisb9scxyyqkxhxhvgsgwix54pkq0zma3xq3ywczyazvzcxd5f9")))) + "17ndvqvb74b980gpb3hpg9bd68bb5f52k9s1i2kd1f9cdrdjvw97")))) (properties `((upstream-name . "ontologyIndex"))) (build-system r-build-system) (native-inputs @@ -18576,14 +18578,14 @@ packages.") (define-public r-assertive-code (package (name "r-assertive-code") - (version "0.0-3") + (version "0.0-4") (source (origin (method url-fetch) (uri (cran-uri "assertive.code" version)) (sha256 (base32 - "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g")))) + "11qkhbjyxw0njzhcszyc2452518yrn3jr5l4n9jnzq10xms090ig")))) (properties `((upstream-name . "assertive.code"))) (build-system r-build-system) @@ -25192,14 +25194,18 @@ effect size.") (define-public r-rgdal (package (name "r-rgdal") - (version "1.6-6") + (version "1.6-7") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 - (base32 "16irhw858771bc8ikshxk3ddpd7ymwgqmhnac4g7f160vymdfhnp")))) - (properties `((upstream-name . "rgdal"))) + (base32 "0cxfmm7niixw3dnbqm7a00603dyqjrphajqx0q5vjpdhmpyysp2m")))) + (properties + `((upstream-name . "rgdal") + (updater-extra-inputs . ("gdal" "proj")) + ;; These are only needed for Windows + (updater-ignored-inputs . ("curl" "openssl" "openssh" "pcre2")))) (build-system r-build-system) (inputs (list gdal proj zlib)) @@ -27915,21 +27921,58 @@ it may be seen by an animal with less acute vision.") classification and regression models.") (license license:gpl2+))) +(define-public r-caretensemble + (package + (name "r-caretensemble") + (version "2.0.2") + (source (origin + (method url-fetch) + (uri (cran-uri "caretEnsemble" version)) + (sha256 + (base32 + "0kagw1ilfz1yy1q0ysmkp3f13k08hiq84xk7d0xp5p7d5dsg7z6q")))) + (properties `((upstream-name . "caretEnsemble"))) + (build-system r-build-system) + (propagated-inputs (list r-caret + r-data-table + r-digest + r-ggplot2 + r-gridextra + r-lattice + r-pbapply + r-plyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/zachmayer/caretEnsemble") + (synopsis "Ensembles of caret models") + (description + "This is a framework for fitting multiple caret models. It uses the same +re-sampling strategy as well as creating ensembles of such models. Use +@code{caretList} to fit multiple models and then use @code{caretEnsemble} to +combine them greedily or @code{caretStack} to combine them using a caret +model.") + (license license:expat))) + (define-public r-adabag (package (name "r-adabag") - (version "4.3") + (version "5.0") (source (origin (method url-fetch) (uri (cran-uri "adabag" version)) (sha256 (base32 - "1v4cl50wbv834cpbwkkhaq5wf8s746fp8xkjrwvyw912x6b2zmik")))) + "03nnqgia61pavic9l6av0hh81wilxlkrx3g244ypar1fv9ppan7c")))) (properties `((upstream-name . "adabag"))) (build-system r-build-system) (propagated-inputs - (list r-caret r-doparallel r-foreach r-rpart)) + (list r-caret + r-consrank + r-doparallel + r-dplyr + r-foreach + r-rpart + r-tidyr)) (home-page "https://cran.r-project.org/web/packages/adabag/") (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging") (description @@ -29527,14 +29570,14 @@ least squares.") (define-public r-regsem (package (name "r-regsem") - (version "1.9.3") + (version "1.9.5") (source (origin (method url-fetch) (uri (cran-uri "regsem" version)) (sha256 (base32 - "0vpizmdml55naxmhy9nfcm9ylhy15p9na7l0c6z3rvk29ck3g3sw")))) + "0lvsy7byrhiizyhwnwr22v8g36735nb0liyzl1nzk0py9rjbv4kk")))) (properties `((upstream-name . "regsem"))) (build-system r-build-system) (propagated-inputs @@ -29554,14 +29597,14 @@ perform @dfn{exploratory mediation} (XMed).") (define-public r-stanheaders (package (name "r-stanheaders") - (version "2.26.25") + (version "2.26.26") (source (origin (method url-fetch) (uri (cran-uri "StanHeaders" version)) (sha256 (base32 - "1xds719xga7144mxirjnqxmcv1ncj5fb5z247blm4dkbn9q2vg4k")))) + "1jr5sflqhg70jkgz3x0q9nrk2xjzm1l4zmyc7j89m755b209sq4k")))) (properties `((upstream-name . "StanHeaders"))) (build-system r-build-system) (inputs (list pandoc)) @@ -31265,14 +31308,14 @@ here.") (define-public r-projpred (package (name "r-projpred") - (version "2.5.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (cran-uri "projpred" version)) (sha256 (base32 - "0faf0hq5kvibqyzgqqz2sdqms8g3vvxy6calpm6d2wzmbczi5v5n")))) + "1nkil537n43sz0ajkcyr0i38hb852qgcdxlgnirqkl0w98ax2hac")))) (properties `((upstream-name . "projpred"))) (build-system r-build-system) (propagated-inputs @@ -31290,7 +31333,7 @@ here.") r-rcpp r-rcpparmadillo r-rstantools - r-ucminf)) + r-scales)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://mc-stan.org/projpred/") (synopsis "Projection predictive feature selection") @@ -31702,14 +31745,14 @@ designed to be distributed and efficient with the following goals: (define-public r-shapforxgboost (package (name "r-shapforxgboost") - (version "0.1.1") + (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "SHAPforxgboost" version)) (sha256 (base32 - "106nsf02b1w3yshb55lwnyw1rl1a60162v2wk8znjz3b4ln3mqj5")))) + "0b3h6py80a0dmb8f8j4h7a7d0k6ld8l0qr24r8pxxy7dbqbyxh5x")))) (properties `((upstream-name . "SHAPforxgboost"))) (build-system r-build-system) @@ -31900,6 +31943,33 @@ a Huber regression warm start. Confidence intervals for regression coefficients are constructed using multiplier bootstrap.") (license license:gpl3))) +(define-public r-consrank + (package + (name "r-consrank") + (version "2.1.3") + (source (origin + (method url-fetch) + (uri (cran-uri "ConsRank" version)) + (sha256 + (base32 + "0v1dr7zj2fpgncymakv5qszdrlqzvc5zxfyc3yrsj09gbm0gvyby")))) + (properties `((upstream-name . "ConsRank"))) + (build-system r-build-system) + (propagated-inputs (list r-gtools r-proxy r-rgl r-rlist r-tidyr)) + (home-page "https://www.r-project.org/") + (synopsis + "Compute median rankings according to Kemeny's axiomatic approach") + (description + "This package lets you compute the median ranking according to Kemeny's +axiomatic approach. Rankings can or cannot contain ties, rankings can be both +complete or incomplete. The package contains both branch-and-bound algorithms +and heuristic solutions recently proposed. The searching space of the +solution can either be restricted to the universe of the permutations or +unrestricted to all possible ties. The package also provides some useful +utilities for deal with preference rankings, including both element-weight +Kemeny distance and correlation coefficient.") + (license license:gpl3))) + (define-public r-fastshap (package (name "r-fastshap") @@ -33395,13 +33465,13 @@ observations.") (define-public r-scico (package (name "r-scico") - (version "1.3.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "scico" version)) (sha256 - (base32 "1f2czfhzdpi5dqjbxvbrrcnxjpylc5zzghj70ihlh2agq3n9hw5g")))) + (base32 "1zcsqmsr9vjs4krz8vmq4z59wh6x25g9ca6yxb0wlq58nmws77k6")))) (properties `((upstream-name . "scico"))) (build-system r-build-system) (propagated-inputs (list r-scales)) @@ -36953,14 +37023,14 @@ the @code{raster} package that is suitable for extracting raster values using (define-public r-stringfish (package (name "r-stringfish") - (version "0.15.7") + (version "0.15.8") (source (origin (method url-fetch) (uri (cran-uri "stringfish" version)) (sha256 (base32 - "0ddpsi7z0kzqgbq9y646pk9afclq0r7ak22zsdh0i93ni0x71c9l")))) + "16w3i3d7jw2s1hzxr3mngrh7yjxvhswqdlpjw5g4z25i84lixcnz")))) (properties `((upstream-name . "stringfish"))) (build-system r-build-system) (propagated-inputs diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 43f5f9c072..74483d27f7 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -4677,13 +4677,11 @@ algorithm implementations.") (delete 'build) ; XXX the build is performed again during the install phase (add-after 'unpack 'enter-source-directory (lambda _ (chdir "python"))) - (add-after 'unpack 'make-git-checkout-writable - (lambda _ - (for-each make-file-writable (find-files ".")))) - (add-before 'install 'set-PYARROW_WITH_PARQUET + (add-before 'install 'set-pyarrow-build-options (lambda _ (setenv "PYARROW_BUNDLE_ARROW_CPP_HEADERS" "0") - (setenv "PYARROW_WITH_PARQUET" "1")))))) + (setenv "PYARROW_WITH_PARQUET" "1") + (setenv "PYARROW_WITH_DATASET" "1")))))) (propagated-inputs (list (list apache-arrow "lib") (list apache-arrow "include") diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index 406c1c1a35..4118c84bbf 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2016 Danny Milosavljevic <dannym@scratchpost.org> ;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com> -;;; Copyright © 2017, 2018, 2019, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2017-2023 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2018–2021 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2018-2023 Nicolas Goaziou <mail@nicolasgoaziou.fr> ;;; Copyright © 2020 Robert Smith <robertsmith@posteo.net> @@ -150,7 +150,7 @@ of categories with some of the activities available in that category. (define-public gcompris-qt (package (name "gcompris-qt") - (version "2.3") + (version "3.2") (source (origin (method url-fetch) @@ -158,7 +158,7 @@ of categories with some of the activities available in that category. "mirror://kde/stable/gcompris/qt/src/gcompris-qt-" version ".tar.xz")) (sha256 - (base32 "0qncknaaf168anh4cjp7dqz6qzgx948kvgr32j2vga8mjakqn1aj")))) + (base32 "06yisr5qd2ri8qgpmlri0yic45fdfcdjn12anp17f6kvv83lk2js")))) (build-system qt-build-system) (arguments `(#:phases @@ -183,13 +183,13 @@ of categories with some of the activities available in that category. (list openssl python-wrapper qtbase-5 + qtcharts qtdeclarative-5 qtgraphicaleffects qtmultimedia-5 - qtquickcontrols-5 + qtquickcontrols2-5 qtsensors - qtsvg-5 - qtxmlpatterns)) + qtsvg-5)) (home-page "https://gcompris.net/index-en.html") (synopsis "Educational games for small children") (description diff --git a/gnu/packages/efi.scm b/gnu/packages/efi.scm index 75eb24bf86..499745eba1 100644 --- a/gnu/packages/efi.scm +++ b/gnu/packages/efi.scm @@ -30,6 +30,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix build-system gnu) #:use-module (guix download) + #:use-module (guix gexp) #:use-module (guix git-download) #:use-module (guix packages) #:use-module (guix utils) @@ -99,7 +100,7 @@ information.") (define-public sbsigntools (package (name "sbsigntools") - (version "0.9.4") + (version "0.9.5") (source (origin (method git-fetch) @@ -110,34 +111,32 @@ information.") (recursive? #t))) (file-name (git-file-name name version)) (sha256 - (base32 "1y76wy65y6k10mjl2dm5hb5ms475alr4s080xzj8y833x01xvf3m")))) + (base32 "060n6w0dx1mrilhdv482ncckanqz6pdv53piimiki0bm15d2fcp4")))) (build-system gnu-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-more-shebangs - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "lib/ccan.git/tools/create-ccan-tree" - (("#!/bin/bash") - (string-append "#!" - (assoc-ref inputs "bash") - "/bin/bash"))) - #t)) - (add-after 'unpack 'patch - (lambda* (#:key inputs outputs #:allow-other-keys) - (substitute* '("configure.ac" - "tests/Makefile.am") - (("/usr/include/efi") - (string-append (assoc-ref inputs "gnu-efi") - "/include/efi")) - (("/usr/lib/gnuefi") - (string-append (assoc-ref inputs "gnu-efi") - "/lib"))) - #t)) - (add-after 'unpack 'setenv - (lambda _ - (setenv "CC" "gcc") - #t))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-more-shebangs + (lambda* (#:key inputs native-inputs #:allow-other-keys) + (substitute* "lib/ccan.git/tools/create-ccan-tree" + (("#!/bin/bash") + (string-append "#!" + (search-input-file (or native-inputs inputs) + "/bin/bash")))))) + (add-after 'unpack 'patch + (lambda _ + (substitute* '("configure.ac" + "tests/Makefile.am") + (("/usr/include/efi") + (string-append #$(this-package-input "gnu-efi") + "/include/efi")) + (("/usr/lib/gnuefi") + (string-append #$(this-package-input "gnu-efi") + "/lib"))))) + (add-after 'unpack 'setenv + (lambda _ + (setenv "CC" #$(cc-for-target))))))) (native-inputs (list autoconf automake @@ -146,9 +145,9 @@ information.") pkg-config util-linux)) ; getopt (inputs - `(("gnu-efi" ,gnu-efi) - ("libuuid" ,util-linux "lib") - ("openssl" ,openssl))) + (list gnu-efi + `(,util-linux "lib") ; libuuid + openssl)) (synopsis "EFI signing tools") (description "This package provides tools for signing EFI binaries.") (home-page "https://git.kernel.org/pub/scm/linux/kernel/git/jejb/sbsigntools.git/") diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 7575049ea3..b77bd0aa83 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -36463,8 +36463,8 @@ headlines, keywords, tables and source blocks.") (license license:gpl3+)))) ; License is in pyimport.el (define-public emacs-straight-el - (let ((commit "f21103d97d180fba0b6e2e86ebb0b6269219ef2c") - (revision "1")) + (let ((commit "039e5c9a9b5c00749602afb41341e9e77ba09429") + (revision "2")) (package (name "emacs-straight-el") (version (git-version "0" revision commit)) @@ -36477,7 +36477,7 @@ headlines, keywords, tables and source blocks.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "1dqhb7kx4hr3cm4gj6qdk9aav05vc016y4nks2dj1sy88wia6wsv")))) + (base32 "05avzakgkwzrj1pxa1pkcv96knqq4mnkv2cszn4cs4kmvr2mchxm")))) (build-system emacs-build-system) (arguments (list diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm index 50a3abd1fd..215007dd31 100644 --- a/gnu/packages/embedded.scm +++ b/gnu/packages/embedded.scm @@ -69,6 +69,7 @@ #:use-module (gnu packages readline) #:use-module (gnu packages swig) #:use-module (gnu packages texinfo) + #:use-module (gnu packages tls) #:use-module (gnu packages version-control) #:use-module (gnu packages xorg) #:use-module (srfi srfi-1)) @@ -511,7 +512,7 @@ languages are C and C++.") (define-public libjaylink (package (name "libjaylink") - (version "0.2.0") + (version "0.3.1") (source (origin (method git-fetch) (uri (git-reference @@ -520,7 +521,7 @@ languages are C and C++.") (file-name (git-file-name name version)) (sha256 (base32 - "0ndyfh51hiqyv2yscpj6qd091w7myxxjid3a6rx8f6k233vy826q")))) + "1wps72ir2kwdr7dphx4vp6cy0d46dm3nkwbk0mpryn9la09l7lm1")))) (build-system gnu-build-system) (native-inputs (list autoconf automake libtool pkg-config)) @@ -535,7 +536,7 @@ SEGGER J-Link and compatible devices.") (define-public jimtcl (package (name "jimtcl") - (version "0.80") + (version "0.82") (source (origin (method git-fetch) (uri (git-reference @@ -544,23 +545,22 @@ SEGGER J-Link and compatible devices.") (file-name (git-file-name name version)) (sha256 (base32 - "06rn60cx9sapc175vxvan87b8j5rkhh5gvvz7343xznzwlr0wcgk")))) + "01nxqzn41797ypph1vpwjfh3zqgks0l8ihh6932b4kb83apy6f08")))) (build-system gnu-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'configure - ;; This package doesn't use autoconf. - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (invoke "./configure" - (string-append "--prefix=" out))))) - (add-before 'check 'delete-failing-tests - (lambda _ - ;; XXX All but 1 TTY tests fail (Inappropriate ioctl for device). - (delete-file "tests/tty.test") - #t)) - ))) + (list #:phases + #~(modify-phases %standard-phases + (replace 'configure + ;; This package doesn't use autoconf. + (lambda _ + (invoke "./configure" + (string-append "--prefix=" #$output)))) + (add-before 'check 'delete-failing-tests + (lambda _ + ;; XXX All but 1 SSL tests fail (tries connecting to Google + ;; servers). + (delete-file "tests/ssl.test")))))) + (inputs (list openssl)) (native-inputs ;; For tests. (list inetutils)) ; for hostname @@ -573,7 +573,7 @@ language.") (define-public openocd (package (name "openocd") - (version "0.11.0") + (version "0.12.0") (source (origin (method git-fetch) (uri (git-reference @@ -582,7 +582,7 @@ language.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0qi4sixwvw1i7c64sy221fsjs82qf3asmdk86g74ds2jjm3f8pzp")))) + "09wb11zlmrw6rx1bql3kafgi3ilzp9mhvb6j6rql216by06csing")))) (build-system gnu-build-system) (native-inputs (list autoconf @@ -592,10 +592,10 @@ language.") pkg-config texinfo)) (inputs - (list hidapi jimtcl libftdi libjaylink libusb-compat)) + (list hidapi jimtcl libftdi libjaylink openssl)) (arguments '(#:configure-flags - (append (list "LIBS=-lutil" + (append (list "LIBS=-lutil -lcrypto -lssl" "--disable-werror" "--enable-sysfsgpio" "--disable-internal-jimtcl" diff --git a/gnu/packages/fltk.scm b/gnu/packages/fltk.scm index 5a1582b1bc..4518a1e30a 100644 --- a/gnu/packages/fltk.scm +++ b/gnu/packages/fltk.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2015, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net> ;;; Copyright © 2018 Mark H Weaver <mhw@netris.org> -;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2018, 2023 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2021 Tobias Geerinckx-Rice <me@tobias.gr> ;;; ;;; This file is part of GNU Guix. @@ -43,15 +43,15 @@ (define-public fltk (package (name "fltk") - (version "1.3.6") + (version "1.3.8") (source (origin (method url-fetch) - (uri (string-append "http://fltk.org/pub/fltk/" + (uri (string-append "https://www.fltk.org/pub/fltk/" (first (string-split version #\-)) "/fltk-" version "-source.tar.gz")) (sha256 - (base32 "1arp1niiz3qxm8iacpmilwpc5rinsm6hsk4a6fsxfywvkvppbb4s")))) + (base32 "1gyisjwjbdsax4kbdm3hpijp2f0qgh1wk7wgad87l3pb0wmi1hgk")))) (build-system gnu-build-system) (native-inputs (list pkg-config)) diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index 0a897fcf0b..91e7ccc49f 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -19,7 +19,7 @@ ;;; Copyright © 2017 Alex Griffin <a@ajgrf.com> ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org> ;;; Copyright © 2017 Brendan Tildesley <mail@brendan.scot> -;;; Copyright © 2017, 2018, 2019, 2020, 2022 Arun Isaac <arunisaac@systemreboot.net> +;;; Copyright © 2017–2023 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2017 Mohammed Sadiq <sadiq@sadiqpk.org> ;;; Copyright © 2018 Charlie Ritter <chewzerita@posteo.net> ;;; Copyright © 2018 Gabriel Hondet <gabrielhondet@gmail.com> @@ -2845,18 +2845,7 @@ optimized for using musical symbols inline with regular text.") (file-name (string-append name "-" version ".zip")) (sha256 (base32 "1j8iv2dl695zrabs2knb7jsky8mjis29a2ddpna4by8mlvqrf0ml")))) - (outputs '("out" "woff2")) (build-system font-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'install 'install-woff2 - (lambda* (#:key outputs #:allow-other-keys) - (let ((dest (string-append (assoc-ref outputs "woff2") - "/share/fonts/woff2"))) - (for-each (lambda (file) - (install-file file dest)) - (find-files "." "\\.woff2$")))))))) (home-page "https://practicaltypography.com/charter.html") (synopsis "Charter fonts in OpenType and TrueType formats") (description "Charter was designed by Matthew Carter in 1987 and was diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 25805fe2e5..6ad3c87ff1 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -738,7 +738,9 @@ lets developers use the functionality of Proj in their own software.") version ".tar.gz")) (sha256 (base32 - "050apzdn0isxpsblys1shrl9ccli5vd32kgswlgx1imrbwpg915k")))) + "050apzdn0isxpsblys1shrl9ccli5vd32kgswlgx1imrbwpg915k")) + (patches + (search-patches "proj-7-initialize-memory.patch")))) (arguments `(#:configure-flags '("-DUSE_EXTERNAL_GTEST=ON") #:phases diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index de6de1f3f0..9400abe79a 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -524,7 +524,10 @@ be used when cross-compiling." "/_giscanner")))) #~())))) (native-inputs - `(("glib" ,glib "bin") + `(,@(if (%current-target-system) + `(("python" ,python)) + '()) + ("glib" ,glib "bin") ("pkg-config" ,pkg-config) ("bison" ,bison) ("flex" ,flex))) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 39d7dc5954..6db2d6569e 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -76,6 +76,7 @@ ;;; Copyright © 2023 Kaelyn Takata <kaelyn.alexi@protonmail.com> ;;; Copyright © 2023 Juliana Sims <juli@incana.org> ;;; Copyright © 2023 Dominik Delgado Steuter <d@delgado.nrw> +;;; Copyright © 2023 Zhu Zihao <all_but_last@163.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -2701,7 +2702,7 @@ on the GNOME Desktop with a single simple application.") "/share/backgrounds/gnome")) ;; Do not reference fonts, that may not exist. (("'Source Code Pro 10'") "'Monospace 11'"))))))) - (inputs (list glib gnome-backgrounds)) + (inputs (list glib gnome-backgrounds gobject-introspection)) (native-inputs (list gettext-minimal `(,glib "bin") ;glib-compile-schemas, etc. gobject-introspection @@ -7199,7 +7200,9 @@ principles are simplicity and standards compliance.") name "-" version ".tar.xz")) (sha256 (base32 - "1jqw5ndpgyb0zxh0g21ai1911lfrm56vz18xbccfqm4sk95wwcw7")))) + "1jqw5ndpgyb0zxh0g21ai1911lfrm56vz18xbccfqm4sk95wwcw7")) + (patches + (search-patches "d-feet-drop-unused-meson-argument.patch")))) (build-system meson-build-system) (arguments (list diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index fd7f4565f9..e40d2b8922 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -518,9 +518,9 @@ variable defined below. It requires guile-json to be installed." ;; XXXX: Workaround 'snippet' limitations. (define computed-origin-method (@@ (guix packages) computed-origin-method)) -(define %icecat-base-version "102.11.0") +(define %icecat-base-version "102.12.0") (define %icecat-version (string-append %icecat-base-version "-guix0-preview1")) -(define %icecat-build-id "20230509000000") ;must be of the form YYYYMMDDhhmmss +(define %icecat-build-id "20230606000000") ;must be of the form YYYYMMDDhhmmss ;; 'icecat-source' is a "computed" origin that generates an IceCat tarball ;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat' @@ -540,12 +540,12 @@ variable defined below. It requires guile-json to be installed." "firefox-" upstream-firefox-version ".source.tar.xz")) (sha256 (base32 - "0cyfij00i9m1pwwyfhiq2qasbfr2ykdwziqykj8878kyjvkj1wg7")))) + "189irpd8xkwh3qixbbcmn5jblx7jz80rilcq8ihaawpmdh76safp")))) ;; The upstream-icecat-base-version may be older than the ;; %icecat-base-version. - (upstream-icecat-base-version "102.11.0") - (gnuzilla-commit "5a1894fc966840dc242110ec0459471c637a4675") + (upstream-icecat-base-version "102.12.0") + (gnuzilla-commit "b2d463b0e331795eebe3ee62f2c58c1bd05b9899") (gnuzilla-source (origin (method git-fetch) @@ -557,7 +557,7 @@ variable defined below. It requires guile-json to be installed." (string-take gnuzilla-commit 8))) (sha256 (base32 - "1816lm4cl45l1zbc043827rfnzzzxckhxk16gvj3a8kyg7fxvv3v")))) + "0db03i3xmapdr0xyb9yg6cl66kyxavnl22hhhnf85ffnlfrcdx2r")))) ;; 'search-patch' returns either a valid file name or #f, so wrap it ;; in 'assume-valid-file-name' to avoid 'local-file' warnings. diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index a7b226091c..750e11d687 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -3843,7 +3843,7 @@ debugging code.") (define-public guile-png (package (name "guile-png") - (version "0.4.1") + (version "0.5.0") (source (origin (method git-fetch) (uri (git-reference @@ -3852,7 +3852,7 @@ debugging code.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1vkhv0dip0na6d9g478i587n5y6046vn5rsjmfnbibi9yx4rkrf8")))) + "0dnahq05mwxzbsqb0qjkyysylc54qr8l5839zyc4sanl2syzhvwk")))) (build-system gnu-build-system) (arguments `(#:make-flags '("GUILE_AUTO_COMPILE=0"))) ;to prevent guild warnings diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm index 929ee08387..a819698710 100644 --- a/gnu/packages/haskell-xyz.scm +++ b/gnu/packages/haskell-xyz.scm @@ -31,6 +31,7 @@ ;;; Copyright © 2021–2023 Alice BRENON <alice.brenon@ens-lyon.fr> ;;; Copyright © 2021 John Kehayias <john.kehayias@protonmail.com> ;;; Copyright © 2022 jgart <jgart@dismail.de> +;;; Copyright © 2023 Josselin Poiret <dev@jpoiret.xyz> ;;; ;;; This file is part of GNU Guix. ;;; @@ -8602,6 +8603,26 @@ of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.") (license license:bsd-3))) +(define-public ghc-peano + (package + (name "ghc-peano") + (version "0.1.0.1") + (source (origin + (method url-fetch) + (uri (hackage-uri "peano" version)) + (sha256 + (base32 + "0yzcxrl41dacvx2wkyxjj7hgvz56l4qb59r4h9rmaqd7jcwx5z9i")))) + (build-system haskell-build-system) + (arguments + `(#:cabal-revision ("3" + "0wl22dnz6ld300cg6id3lw991bp8kdfi8h0nbv37vn79i1zdcj5n"))) + (home-page "http://hackage.haskell.org/package/peano") + (synopsis "Peano numbers") + (description "Provides an efficient Haskell implementation of Peano +numbers") + (license license:bsd-3))) + (define-public ghc-persistent (package (name "ghc-persistent") @@ -13308,6 +13329,27 @@ the vector; then you can execute the builder to actually produce the vector.") (license license:expat))) +(define-public ghc-vector-hashtables + (package + (name "ghc-vector-hashtables") + (version "0.1.1.2") + (source (origin + (method url-fetch) + (uri (hackage-uri "vector-hashtables" version)) + (sha256 + (base32 + "0hrjvy9qg1m5g3w91zxy4syqmp8jk7ajjbxbzkhy282dwfigkyd2")))) + (build-system haskell-build-system) + (inputs (list ghc-primitive ghc-vector ghc-hashable)) + (native-inputs (list ghc-hspec ghc-quickcheck ghc-quickcheck-instances + hspec-discover)) + (home-page "https://github.com/klapaucius/vector-hashtables#readme") + (synopsis "Efficient vector-based mutable hashtables implementation") + (description + "This package provides efficient vector-based hashtable implementation +similar to .NET Generic Dictionary implementation (at the time of 2015).") + (license license:bsd-3))) + (define-public ghc-vector-th-unbox (package (name "ghc-vector-th-unbox") diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index d1330d17f7..069a214b8c 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -571,9 +571,27 @@ official designation is ISO/IEC 29199-2). This library is an implementation of t (sha256 (base32 "06f6d08xvmsiki4mc1qs985gsjqmsxx793a93b72y25q84wbg9x9")))) (build-system gnu-build-system) - (inputs (list libjpeg-turbo)) (arguments - '(#:tests? #f)) ; no tests + `(#:tests? #f ; no tests + ,@(if (and (target-riscv64?) + (%current-target-system)) + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'update-config-scripts + (lambda* (#:key native-inputs inputs #:allow-other-keys) + (for-each (lambda (file) + (install-file + (search-input-file + (or native-inputs inputs) + (string-append "/bin/" file)) "./tools")) + '("config.guess" "config.sub")))))) + '()))) + (inputs (list libjpeg-turbo)) + (native-inputs + (if (and (target-riscv64?) + (%current-target-system)) + (list config) + '())) (synopsis "Optimize JPEG images") (description "jpegoptim provides lossless optimization (based on optimizing @@ -595,6 +613,25 @@ maximum quality factor.") (base32 "1hjm8lwap7bjyyxsyi94fh5817xzqhk4kb5y0b7mb6675xw10prk")))) (build-system gnu-build-system) + (arguments + (if (and (target-riscv64?) + (%current-target-system)) + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'update-config-scripts + (lambda* (#:key native-inputs inputs #:allow-other-keys) + (for-each (lambda (file) + (install-file + (search-input-file + (or native-inputs inputs) + (string-append "/bin/" file)) ".")) + '("config.guess" "config.sub"))))) ) + '())) + (native-inputs + (if (and (target-riscv64?) + (%current-target-system)) + (list config) + '())) (inputs (list libpng jasper)) (home-page "https://icns.sourceforge.io/") @@ -2105,7 +2142,7 @@ losslessly translates between SNG and PNG.") (define-public blurhash (package (name "blurhash") - (version "0.0.1") + (version "0.2.0") (source (origin (method git-fetch) @@ -2114,10 +2151,10 @@ losslessly translates between SNG and PNG.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0jy2iigarskwfhskyladbb6l92x1fb3i3vz4bvcks0za4w5hfxk5")))) + (base32 "0hx15fspava43z47kv17ivxv56g03fb2zf45dl07v3shickqxw0x")))) (build-system meson-build-system) (native-inputs - (list cmake doctest)) + (list doctest pkg-config)) (home-page "https://github.com/Nheko-Reborn/blurhash") (synopsis "C++ blurhash encoder/decoder") (description "Simple encoder and decoder for blurhashes. Contains a diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 058f64187d..1b802922a8 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -40,6 +40,7 @@ #:use-module (gnu packages acl) #:use-module (gnu packages admin) #:use-module (gnu packages aidc) + #:use-module (gnu packages aspell) #:use-module (gnu packages attr) #:use-module (gnu packages avahi) #:use-module (gnu packages base) @@ -1450,7 +1451,8 @@ system.") (native-inputs (list extra-cmake-modules pkg-config qttools-5)) (inputs - (list hunspell + (list aspell + hunspell ;; TODO: hspell (for Hebrew), Voikko (for Finish) qtdeclarative-5 qtbase-5)) diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index f9c0a260f0..28b4ce1ee0 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2016, 2017, 2019-2021, 2023 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 David Craven <david@craven.ch> ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be> ;;; Copyright © 2017, 2018 Mark Meyer <mark@ofosos.org> @@ -516,15 +516,16 @@ the functionality of the KDE resource and network access abstractions.") (define-public kirigami-addons (package (name "kirigami-addons") - (version "0.3") + (version "0.8.0") (source (origin - (method url-fetch) - (uri (string-append - "https://invent.kde.org/libraries/kirigami-addons/-/archive/v" - version "/kirigami-addons-v" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/libraries/kirigami-addons") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1zr8dpc7bzw6g3y0jaxsr2lqlxqwlcphchpk8iah6g1f3n9fq73r")))) + "1bi6sc1fpycxj1ydd08gkbw1x1pi2ab6p9bk4175hm0mb0rykdir")))) (build-system qt-build-system) (arguments (list #:tests? #f)) ; failing test diff --git a/gnu/packages/kerberos.scm b/gnu/packages/kerberos.scm index c553f8180a..241881ea47 100644 --- a/gnu/packages/kerberos.scm +++ b/gnu/packages/kerberos.scm @@ -183,14 +183,7 @@ After installation, the system administrator should generate keys using (base32 "0f4dblav859p5hn7b2jdj1akw6d8p32as6bj6zym19kghh3s51zx")) (patches - (search-patches "heimdal-CVE-2022-45142.patch")) - (modules '((guix build utils))) - (snippet - '(begin - (substitute* "configure" - (("User=.*$") "User=Guix\n") - (("Host=.*$") "Host=GNU") - (("Date=.*$") "Date=2022\n")))))) + (search-patches "heimdal-CVE-2022-45142.patch")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -221,9 +214,20 @@ After installation, the system administrator should generate keys using "/libexec/heimdal"))) #~())) #:phases (modify-phases %standard-phases + ;; Skip the appl folder as obsolete per message from Brian May <brian@linuxpenguins.xyz> + ;; <MDAEMON-F202305111940.AA401569md5001000003030@sequoia-grove.ad.secure-endpoints.com> + (add-after 'unpack 'drop-obsolete-executables + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("Makefile.am") + (("appl") "")))) (add-before 'configure 'pre-configure (lambda* (#:key inputs #:allow-other-keys) + (invoke (search-input-file inputs "bin/autoreconf") "--install" "--force") (substitute* "configure" + ;; Reproducible build date, etc. + (("User=.*$") "User=Guix\n") + (("Host=.*$") "Host=GNU\n") + (("Date=.*$") "Date=2022\n") ;; The e2fsprogs input is included for libcom_err, ;; let's use it even if cross-compiling. (("test \"\\$\\{krb_cv_com_err\\}\" = \"yes\"") @@ -232,15 +236,6 @@ After installation, the system administrator should generate keys using ;; which confuses heimdal. (("ac_cv_prog_COMPILE_ET=\\$\\{with_cross_tools\\}compile_et") "ac_cv_PROG_COMPILE_ET=compile_et")) - (substitute* '("appl/afsutil/pagsh.c" "appl/su/su.c") - (("/bin/sh") - (search-input-file inputs "bin/sh")) - ;; Use the cross-compiled bash instead of the - ;; native bash (XXX shouldn't _PATH_BSHELL point - ;; to a cross-compiled bash?). - (("_PATH_BSHELL") - (string-append - "\"" (search-input-file inputs "bin/sh") "\""))) (substitute* '("tools/Makefile.in") (("/bin/sh") (which "sh"))))) (add-before 'check 'pre-check @@ -255,12 +250,17 @@ After installation, the system administrator should generate keys using (format #t "#!~a~%exit 1~%" (which "sh"))))))) ;; Tests fail when run in parallel. #:parallel-tests? #f)) - (native-inputs (list bison + (native-inputs (list autoconf + automake + bison e2fsprogs ;for 'compile_et' flex + libtool texinfo unzip ;for tests pkg-config + perl + perl-json python)) (inputs (list readline bash-minimal diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index fc6f3cbda5..3bcc34374c 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -485,7 +485,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernels. That is, the most recently released major ;; versions that are still supported upstream. -(define-public linux-libre-6.3-version "6.3.5") +(define-public linux-libre-6.3-version "6.3.6") (define-public linux-libre-6.3-gnu-revision "gnu") (define deblob-scripts-6.3 (linux-libre-deblob-scripts @@ -495,7 +495,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0la20slh52jm4cg4v2liphhqqx4808gm6pfqcxiawj13a4ps9ygk"))) (define-public linux-libre-6.3-pristine-source (let ((version linux-libre-6.3-version) - (hash (base32 "0pl2zypsmrnna69850jadccffxwg9xdfkldg0sv8m44b7n64gkgm"))) + (hash (base32 "1vr418rf0zd16fq4vaxda1w2ccng2n9l0ysakmgz9xqbz86iysks"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-6.3))) @@ -503,7 +503,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; <https://www.kernel.org/category/releases.html> -(define-public linux-libre-6.1-version "6.1.31") +(define-public linux-libre-6.1-version "6.1.32") (define-public linux-libre-6.1-gnu-revision "gnu") (define deblob-scripts-6.1 (linux-libre-deblob-scripts @@ -513,12 +513,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1yv15mb278wlrn8gb2yjm0mczirzixy668h221vcpbz416ibxx1m"))) (define-public linux-libre-6.1-pristine-source (let ((version linux-libre-6.1-version) - (hash (base32 "1hbkw290kmf1dj8a255ik1gk5fk458c88m348dwrc3lrl6xifsg8"))) + (hash (base32 "0v0saai735jzaj3dbpgp6sbdi95n3lmv78pbg1xy9fd2kfhbg23w"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-6.1))) -(define-public linux-libre-5.15-version "5.15.114") +(define-public linux-libre-5.15-version "5.15.115") (define-public linux-libre-5.15-gnu-revision "gnu") (define deblob-scripts-5.15 (linux-libre-deblob-scripts @@ -528,12 +528,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "00n8c7ghfs36bvz0yjw6w9daf5zcgj94kxxn27bfyfm274rkddmz"))) (define-public linux-libre-5.15-pristine-source (let ((version linux-libre-5.15-version) - (hash (base32 "1lkpa9wv1qj90qdzzi71qf5dyy7mi95fixx3ymdp6xwz45fym0g9"))) + (hash (base32 "050j9z0wg5glgxwbmzfq4l8lv8y7g3nc2rz8342yjdcjfxh6h1qv"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.15))) -(define-public linux-libre-5.10-version "5.10.181") +(define-public linux-libre-5.10-version "5.10.182") (define-public linux-libre-5.10-gnu-revision "gnu1") (define deblob-scripts-5.10 (linux-libre-deblob-scripts @@ -543,12 +543,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "12jhak2bw1jy2jk70vrm66kjvh0cd6c8f2qiy2bk40rq7bf62mr6"))) (define-public linux-libre-5.10-pristine-source (let ((version linux-libre-5.10-version) - (hash (base32 "1rx43dkxspris9529vl11blzhvsxnpaqr6yb3fy089az7yvwxrmc"))) + (hash (base32 "1xp9bxk2vyw29bq3z854ly4cj94z8i52yl5hq4a3l3j6564wb3ny"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.10))) -(define-public linux-libre-5.4-version "5.4.244") +(define-public linux-libre-5.4-version "5.4.245") (define-public linux-libre-5.4-gnu-revision "gnu1") (define deblob-scripts-5.4 (linux-libre-deblob-scripts @@ -558,7 +558,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "070j069sj6spy2wkzfzm1d5jd7pffm0s1m917wblc8d3x8pbgvf8"))) (define-public linux-libre-5.4-pristine-source (let ((version linux-libre-5.4-version) - (hash (base32 "06x20aq7bv86ghv2sdsz3q2rmqh8h389x5zksr53fyzdjl72ixch"))) + (hash (base32 "195ixy9l18mhwvzj7v63fkyifb9mysq950afxh6ixlpvg0c8h1wn"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.4))) @@ -8159,7 +8159,7 @@ Text-based output formats: CSV, XML, Netfilter's LOG, Netfilter's conntrack (define-public proot (package (name "proot") - (version "5.3.0") + (version "5.4.0") (source (origin (method git-fetch) @@ -8168,7 +8168,10 @@ Text-based output formats: CSV, XML, Netfilter's LOG, Netfilter's conntrack (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1r1ga3xbwq5kx4i8ihj1p6nmgaa14lfkwxzpsbdcmfh1jimpbmzk")))) + (base32 "186qsg4yvisqjgf8w5jxhnlig7x341vpqwcgp8as3r59qmqkpmk7")) + ;; Waiting for upstream inclusion at + ;; https://github.com/proot-me/proot/pull/355 + (patches (search-patches "proot-add-clone3.patch")))) (build-system gnu-build-system) ;; Many architectures are not supported (see: ;; https://github.com/proot-me/proot/blob/master/src/arch.h#L51). diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index fd09b4f52c..16deb85e5e 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -4978,7 +4978,7 @@ is a library for creating graphical user interfaces.") (define-public sbcl-cl-webkit (package (name "sbcl-cl-webkit") - (version "3.5.7") + (version "3.5.9") (source (origin (method git-fetch) @@ -4988,7 +4988,7 @@ is a library for creating graphical user interfaces.") (file-name (git-file-name "cl-webkit" version)) (sha256 (base32 - "0aqkqcs0n5wkgjx3lb513fvm7f2jw3d5daisc9mw1bmbbcqh2sba")))) + "00h61p5mrvvbycp703isy0wvgqlfb7k0cidw4vg75y7s29m3k6k0")))) (build-system asdf-build-system/sbcl) (inputs `(("cffi" ,sbcl-cffi) @@ -21176,9 +21176,10 @@ window it creates as just another output for your graphics, analogous to how (sbcl-package->cl-source-package sbcl-cepl)) (define-public sbcl-stmx - ;; No release for years and recent commits contain fixes for revent SBCL versions. - (let ((commit "a7bb44082cd53ee968965adff03d4351750711a1") - (revision "1")) + ;; No release for years and recent commits contain fixes for recent SBCL + ;; versions. + (let ((commit "f71e742a50b85e3abc0af9bb5f02802f218a1705") + (revision "2")) (package (name "sbcl-stmx") (version (git-version "2.0.5" revision commit)) @@ -21190,11 +21191,22 @@ window it creates as just another output for your graphics, analogous to how (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "1hfmh4vj271jdilir97qs6nqbi5nmn5alyls0w3d3xxqwi6ffqjs")))) + (base32 "0q739mlw3s3z5kclzccz4r64ag38ks11fmd38109qwjv5knn69jv")))) (build-system asdf-build-system/sbcl) (inputs (list sbcl-alexandria sbcl-bordeaux-threads sbcl-log4cl sbcl-closer-mop sbcl-trivial-garbage)) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-build + (lambda _ + (substitute* "asm/transaction.lisp" + (("\\(ftype \\(function \\(\\) fixnum\\) transaction-begin\\)") + "(ftype (function () (unsigned-byte 32)) transaction-begin)") + (("\\(values fixnum &optional\\)") + "(unsigned-byte 32)"))))))) (home-page "https://stmx.org/") (synopsis "High performance Transactional Memory for Common Lisp") (description diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index 000c8e8e66..a7e06dd34c 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -23,6 +23,7 @@ ;;; Copyright © 2022 Joeke de Graaf <joeke@posteo.net> ;;; Copyright © 2021, 2022 jgart <jgart@dismail.de> ;;; Copyright © 2022 ( <paren@disroot.org> +;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -57,6 +58,7 @@ #:use-module (guix build-system haskell) #:use-module (guix build-system trivial) #:use-module (gnu packages admin) + #:use-module (gnu packages algebra) #:use-module (gnu packages base) #:use-module (gnu packages bash) #:use-module (gnu packages bdw-gc) @@ -83,6 +85,7 @@ #:use-module (gnu packages maths) #:use-module (gnu packages multiprecision) #:use-module (gnu packages ncurses) + #:use-module (gnu packages notcurses) #:use-module (gnu packages onc-rpc) #:use-module (gnu packages perl) #:use-module (gnu packages readline) @@ -93,7 +96,8 @@ #:use-module (gnu packages tls) #:use-module (gnu packages version-control) #:use-module (gnu packages xorg) - #:use-module (ice-9 match)) + #:use-module (ice-9 match) + #:use-module (srfi srfi-1)) (define-public cl-asdf (package @@ -428,20 +432,22 @@ an interpreter, a compiler, a debugger, and much more.") (define-public sbcl (package (name "sbcl") - (version "2.3.2") + (version "2.3.5") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/sbcl/sbcl/" version "/sbcl-" version "-source.tar.bz2")) (sha256 - (base32 "1ahyrc3p9cf7y5zbgzvb9yxa8a480ccis4ksijlajck3z8n1dk24")) + (base32 "11ji5n65l31249r0v7hm0wc0yk2ila0y746nj36xn1cxrwh0gjc9")) (modules '((guix build utils))) + ;; backport from upstream. + (patches (search-patches "sbcl-riscv-Make-contribs-build-again.patch")) (snippet '(begin ;; Don't force ARMv5. (substitute* "src/runtime/Config.arm-linux" - (("-march=armv5") "")))))) + (("-march=armv5t") "")))))) (build-system gnu-build-system) (outputs '("out" "doc")) (native-inputs @@ -987,7 +993,7 @@ the HTML documentation of TXR.") (define-public txr (package (name "txr") - (version "286") + (version "287") (source (origin (method git-fetch) @@ -996,7 +1002,7 @@ the HTML documentation of TXR.") (commit (string-append "txr-" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0c5prq9ans4qv8dgfn85555by9rb22p276g21w4mns0rqhjd0ij8")))) + (base32 "0bwa40l5c0dnpcpfbysqbv8ch58sycbb31dnskmhr387jlv938dl")))) (build-system gnu-build-system) (arguments (list #:configure-flags @@ -1478,3 +1484,129 @@ includes a compiler as well as an interpreter.") license:expat ;; cii/LICENSE license:gpl2+ ;; nana/gdb/test.c and others under nana/ license:bsd-3)))) ;; bench/* + +(define-public s7-bootstrap + ;; Need s7-bootstrap to build libc_s7.so (for the REPL) and run tests + (let ((commit "a5b4bb49f8bcd7c33ae2366065fc8c254b734460") ;no releases + (revision "0")) + (hidden-package + (package + (name "s7-bootstrap") + (version (git-version "23.3" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://cm-gitlab.stanford.edu/bil/s7.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03n1axdlypzmbgzrhlwfqwa1xiw36hi25j2hwc7vw77mz90cd9f8")))) + (build-system gnu-build-system) + (arguments + (list #:tests? #f ;no tests in bootstrap + #:phases #~(modify-phases %standard-phases + (delete 'configure) ;no configure + (replace 'build + (lambda _ + ;; using build commands from s7 home page + (display "[BUILD] repl\n") + (invoke #$(cc-for-target) "s7.c" "-o" "repl" + "-I." "-O2" "-g" + "-DWITH_MAIN" + (string-append + "-DS7_LOAD_PATH=\"" + #$output "/share/s7/scm\"") + "-ldl" "-lm" + "-Wl,-export-dynamic") + (display "[BUILD] nrepl\n") + (invoke #$(cc-for-target) "s7.c" "-o" "nrepl" + "-I." "-O2" "-g" + "-DWITH_MAIN" "-DWITH_NOTCURSES" + (string-append + "-DS7_LOAD_PATH=\"" + #$output "/share/s7/scm\"") + "-ldl" "-lm" "-lnotcurses-core" + "-Wl,-export-dynamic") + (display "[BUILD] libarb_s7.so\n") + (invoke #$(cc-for-target) "libarb_s7.c" + "-I." "-O2" "-g" + "-shared" "-o" "libarb_s7.so" + "-larb" "-lflint" "-lmpc" "-fPIC") + (display "[BUILD] libnotcurses_s7.so\n") + (invoke #$(cc-for-target) "notcurses_s7.c" + "-I." "-O2" "-g" + "-shared" "-o" "libnotcurses_s7.so" + "-lnotcurses-core" "-fPIC") + ;; Need s7.o and ffitest for tests + (display "[BUILD] s7.o\n") + (invoke #$(cc-for-target) "-c" "s7.c" "-o" + "s7.o" "-I." "-O2" "-ldl" "-lm") + (display "[BUILD] ffitest\n") + (invoke #$(cc-for-target) "-o" "ffitest" + "ffitest.c" "-g2" "s7.o" "-lm" "-I." + "-ldl" "-Wl,-export-dynamic"))) + (add-before 'check 'install-scm + ;; scm files need to be installed before testing + (lambda _ + (for-each (lambda (x) + (install-file + x (string-append + #$output "/share/s7/scm/"))) + (find-files "." "\\.scm")))) + (replace 'install + (lambda _ + (let ((bin (string-append #$output "/bin")) + (share (string-append #$output + "/share/s7/")) + (doc (string-append #$output + "/share/doc/s7/")) + (lib (string-append #$output "/lib")) + (inc (string-append #$output "/include/"))) + (install-file "repl" bin) + (install-file "nrepl" bin) + (install-file "ffitest" bin) + (install-file "libarb_s7.so" lib) + (install-file "libnotcurses_s7.so" lib) + (install-file "s7.c" share) + (install-file "s7.h" inc) + (install-file "s7.html" doc))))))) + (inputs (list arb flint mpc notcurses)) + (home-page "https://ccrma.stanford.edu/software/snd/snd/s7.html") + (synopsis "Scheme interpreter intended as an extension language") + (description + "s7 is a Scheme interpreter intended as an extension language for +other applications. It exists as just two files, @code{s7.c} and @code{s7.h}, +that may be copied into the source tree of another application. There are no +libraries, no run-time init files, and no configuration scripts. It can also +be built as a stand-alone REPL interpreter.") + (license license:bsd-0))))) + +(define-public s7 + (package + (inherit s7-bootstrap) + (name "s7") + (arguments + (substitute-keyword-arguments (package-arguments s7-bootstrap) + ((#:tests? _) #t) + ((#:phases phases) + #~(modify-phases #$phases + (add-after 'unpack 'patch + (lambda _ + (substitute* "s7.c" + (("libc_s7.so") + (string-append #$output "/lib/libc_s7.so"))))) + (add-after 'build 'build-full + (lambda _ + (invoke "repl" "./libc.scm"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "repl" "./s7test.scm")))) + (add-after 'install 'install-full + (lambda _ + (install-file "libc_s7.so" + (string-append #$output "/lib/")) + (delete-file (string-append #$output "/bin/ffitest")))))))) + (native-inputs (list s7-bootstrap)) + (properties (alist-delete 'hidden? (package-properties s7-bootstrap))))) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index c9bc5e8b68..827bcd597b 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -727,6 +727,112 @@ depend on language-specific pre- or post-processing.") unsupervised text tokenizer.") (license license:asl2.0))) +(define-public python-spacy-legacy + (package + (name "python-spacy-legacy") + (version "3.0.12") + (source (origin + (method url-fetch) + (uri (pypi-uri "spacy-legacy" version)) + (sha256 + (base32 + "0x57aw1qgjrzgapsv1cwymqlck2anqm1bisvryhpq7bfkc66wzdk")))) + (build-system pyproject-build-system) + ;; This package depends on spacy, which depends on this package. + (arguments (list #:tests? #false)) + (native-inputs (list python-pytest)) + (home-page "https://spacy.io") + (synopsis "Legacy registered functions for spaCy backwards compatibility") + (description + "This package contains legacy registered functions for spaCy backwards +compatibility.") + (license license:expat))) + +(define-public python-spacy-loggers + (package + (name "python-spacy-loggers") + (version "1.0.4") + (source (origin + (method url-fetch) + (uri (pypi-uri "spacy-loggers" version)) + (sha256 + (base32 + "0a5zjfxd0mci7pwda24ihg55whalpmjby4bvpgar2013f6zq7yg6")))) + (build-system pyproject-build-system) + ;; This package depends on spacy, which depends on this package. + (arguments (list #:tests? #false)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/explosion/spacy-loggers") + (synopsis "Logging utilities for SpaCy") + (description "This package provides logging utilities for the SpaCy +natural language processing framework.") + (license license:expat))) + +(define-public python-spacy + (package + (name "python-spacy") + (version "3.5.3") + (source (origin + (method url-fetch) + (uri (pypi-uri "spacy" version)) + (sha256 + (base32 + "13141hc966d8nxbnlwj01vhndgq0rq4nmii3qkb3hrap45kiv5rm")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + '(list "-k" + (string-append + ;; We don't do that around here. + "not test_download_compatibility" + ;; This needs to download a model. + " and not test_validate_compatibility_table" + ;; This tries to run the application with typer, which fails + ;; with an unspecified error, possibly because the build + ;; container doesn't have /bin/sh. + " and not test_project_assets")) + #:phases + '(modify-phases %standard-phases + (add-after 'build 'build-ext + (lambda _ + (invoke "python" "setup.py" "build_ext" "--inplace" + "-j" (number->string (parallel-job-count)))))))) + (propagated-inputs (list python-catalogue + python-cymem + python-jinja2 + python-langcodes + python-murmurhash + python-numpy + python-packaging + python-pathy + python-preshed + python-pydantic + python-requests + python-setuptools + python-smart-open + python-spacy-legacy + python-spacy-loggers + python-srsly + python-thinc + python-tqdm + python-typer + python-typing-extensions + python-wasabi)) + (native-inputs + (list python-cython python-pytest python-mock)) + (home-page "https://spacy.io") + (synopsis "Natural Language Processing (NLP) in Python") + (description + "SpaCy is a library for advanced Natural Language Processing in Python +and Cython. It comes with pretrained pipelines and currently supports +tokenization and training for 70+ languages. It features state-of-the-art +speed and neural network models for tagging, parsing, named entity +recognition, text classification and more, multi-task learning with pretrained +transformers like BERT, as well as a production-ready training system and easy +model packaging, deployment and workflow management.") + (license license:expat))) + (define-public shogun (package (name "shogun") @@ -1276,6 +1382,46 @@ computing environments.") data analysis.") (license license:bsd-3))) +(define-public python-thinc + (package + (name "python-thinc") + (version "8.1.10") + (source (origin + (method url-fetch) + (uri (pypi-uri "thinc" version)) + (sha256 + (base32 + "14drmwa2sh8fqszv1fm2jl4lky1j5yrbkjv89bl49q07vbblhjkc")))) + (build-system pyproject-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'build 'build-ext + (lambda _ + (invoke "python" "setup.py" "build_ext" "--inplace" + "-j" (number->string (parallel-job-count)))))))) + (propagated-inputs (list python-blis-for-thinc + python-catalogue + python-confection + python-contextvars + python-cymem + python-dataclasses + python-murmurhash + python-numpy + python-packaging + python-preshed + python-pydantic + python-srsly + python-typing-extensions + python-wasabi)) + (native-inputs (list python-cython python-mock python-pytest)) + (home-page "https://github.com/explosion/thinc") + (synopsis "Functional take on deep learning") + (description + "This package provides a functional take on deep learning, compatible +with your favorite libraries.") + (license license:expat))) + (define-public python-threadpoolctl (package (name "python-threadpoolctl") diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 02e0da2ec8..ee6e19fcfe 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -188,6 +188,7 @@ #:use-module (guix build-system meson) #:use-module (guix build-system perl) #:use-module (guix build-system python) + #:use-module (guix build-system pyproject) #:use-module (guix build-system trivial) #:use-module (srfi srfi-1) #:use-module (ice-9 match)) @@ -4039,16 +4040,20 @@ servers. The 4rev1 and 4 versions of IMAP are supported.") (define-public urlscan (package (name "urlscan") - (version "0.9.10") + (version "1.0.0") (source (origin (method url-fetch) (uri (pypi-uri "urlscan" version)) (sha256 - (base32 "1ir6dxifkd8hv048p65jyz4wyg6ll002fzvbmajpdnvs6mvkj1md")))) - (build-system python-build-system) + (base32 "0rxqdrss34rgnfmbn8ab976dchjbz72wp4ywqrdib119a5xnhqzh")))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f)) ; No tests. (propagated-inputs (list python-urwid)) + (native-inputs + (list python-hatch-vcs python-hatchling)) (home-page "https://github.com/firecat53/urlscan") (synopsis "View/select the URLs in an email message or file") (description diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 4e34124469..f89e70c0bb 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -96,6 +96,7 @@ #:use-module (guix build-system meson) #:use-module (guix build-system ocaml) #:use-module (guix build-system perl) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (guix build-system ruby) #:use-module (gnu packages algebra) @@ -1314,13 +1315,12 @@ computations.") #:phases (modify-phases %standard-phases ;; This is inspired by two of Debian's patches. - (add-before 'configure 'add-more-aarch64-support + (add-before 'configure 'add-more-architecture-support (lambda _ (substitute* '("mfhdf/ncgen/ncgen.l" "mfhdf/ncgen/ncgenyy.c" "mfhdf/libsrc/netcdf.h.in") - (("AIX5L64") "__aarch64__")) - #t)) + (("AIX5L64") "__aarch64__ || ( __riscv && __riscv_xlen == 64)")))) (add-before 'configure 'patchbuild (lambda _ (substitute* @@ -4682,90 +4682,85 @@ library.") (define-public blis (package (name "blis") - (version "0.8.1") + (version "0.9.0") (home-page "https://github.com/flame/blis") (source (origin (method git-fetch) (uri (git-reference (url home-page) (commit version))) (sha256 (base32 - "05ifil6jj9424sr8kmircl8k4bmxnl3y12a79vwj1kxxva5gz50g")) + "14v2awhxma6nzas42hq97702672f2njrskqhsv9kl23hvrvci8fm")) (file-name (git-file-name "blis" version)))) (native-inputs (list python perl)) (build-system gnu-build-system) (arguments - `(#:modules - ((guix build gnu-build-system) + (list + #:modules + '((guix build gnu-build-system) (guix build utils) (srfi srfi-1)) - #:test-target "test" - #:phases - (modify-phases %standard-phases - (replace 'configure - (lambda* (#:key outputs - target - system - (configure-flags '()) - #:allow-other-keys) - ;; This is a home-made 'configure' script. - (let* ((out (assoc-ref outputs "out")) - ;; Guix-specific support for choosing the configuration + #:test-target "test" + #:phases + #~(modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs target system (configure-flags '()) + #:allow-other-keys) + ;; This is a home-made 'configure' script. + (let* (;; Guix-specific support for choosing the configuration ;; via #:configure-flags: see below for details. - (config-flag-prefix "--blis-config=") - (maybe-config-flag (find - (lambda (s) - (string-prefix? config-flag-prefix s)) - configure-flags)) - (configure-flags (if maybe-config-flag - (delete maybe-config-flag - configure-flags) + (config-flag-prefix "--blis-config=") + (maybe-config-flag (find + (lambda (s) + (string-prefix? config-flag-prefix s)) configure-flags)) - ;; Select the "configuration" to build. - ;; The "generic" configuration is non-optimized but - ;; portable (no assembly). - ;; The "x86_64" configuration family includes - ;; sub-configurations for all supported - ;; x86_64 microarchitectures. - ;; BLIS currently lacks runtime hardware detection - ;; for other architectures: see - ;; <https://github.com/flame/blis/commit/c534da6>. - ;; Conservatively, we stick to "generic" on armhf, - ;; aarch64, and ppc64le for now. (But perhaps - ;; "power9", "cortexa9", and "cortexa57" might be - ;; general enough to use?) - ;; Another approach would be to use the "auto" - ;; configuration and make this package - ;; non-substitutable. - ;; The build is fairly intensive, though. - (blis-config - (cond - (maybe-config-flag - (substring maybe-config-flag - (string-length config-flag-prefix))) - ((string-prefix? "x86_64" (or target system)) - "x86_64") - (else - "generic"))) - (configure-args - `("-p" ,out - "-d" "opt" - "--disable-static" - "--enable-shared" - "--enable-threading=openmp" - "--enable-verbose-make" - ,@configure-flags - ,blis-config))) - (format #t "configure args: ~s~%" configure-args) - (apply invoke - "./configure" - configure-args) - #t))) - (add-before 'check 'show-test-output - (lambda _ - ;; By default "make check" is silent. Make it verbose. - (system "tail -F output.testsuite &") - #t))))) + (configure-flags (if maybe-config-flag + (delete maybe-config-flag + configure-flags) + configure-flags)) + ;; Select the "configuration" to build. + ;; The "generic" configuration is non-optimized but + ;; portable (no assembly). + ;; The "x86_64" configuration family includes + ;; sub-configurations for all supported + ;; x86_64 microarchitectures. + ;; BLIS currently lacks runtime hardware detection + ;; for other architectures: see + ;; <https://github.com/flame/blis/commit/c534da6>. + ;; Conservatively, we stick to "generic" on armhf, + ;; aarch64, and ppc64le for now. (But perhaps + ;; "power9", "cortexa9", and "cortexa57" might be + ;; general enough to use?) + ;; Another approach would be to use the "auto" + ;; configuration and make this package + ;; non-substitutable. + ;; The build is fairly intensive, though. + (blis-config + (cond + (maybe-config-flag + (substring maybe-config-flag + (string-length config-flag-prefix))) + ((string-prefix? "x86_64" (or target system)) + "x86_64") + (else + "generic"))) + (configure-args + `("-p" ,#$output + "-d" "opt" + "--disable-static" + "--enable-shared" + "--enable-threading=openmp" + "--enable-verbose-make" + ,@configure-flags + ,blis-config))) + (format #t "configure args: ~s~%" configure-args) + (apply invoke + "./configure" + configure-args)))) + (add-before 'check 'show-test-output + (lambda _ + ;; By default "make check" is silent. Make it verbose. + (system "tail -F output.testsuite &")))))) (synopsis "High-performance basic linear algebra (BLAS) routines") (description "BLIS is a portable software framework for instantiating high-performance @@ -4779,6 +4774,47 @@ access to BLIS implementations via traditional BLAS routine calls.") (define ignorance blis) +;; It is unfortunate that we cannot just link with the existing blis package. +(define-public python-blis + (package + (name "python-blis") + (version "0.9.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "blis" version)) + (sha256 + (base32 + "0vrnzk9jx7fcl56q6zpa4w4mxkr4iknxs42fngn9g78zh1kc9skw")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'build 'build-ext + (lambda _ + (invoke "python" "setup.py" "build_ext" "--inplace" + "-j" (number->string (parallel-job-count)))))))) + (propagated-inputs (list python-numpy)) + (native-inputs (list python-cython python-pytest)) + (home-page "https://github.com/explosion/cython-blis") + (synopsis "Blis as a self-contained C-extension for Python") + (description + "This package provides the Blis BLAS-like linear algebra library, as a +self-contained C-extension for Python.") + (license license:bsd-3))) + +(define-public python-blis-for-thinc + (package + (inherit python-blis) + (name "python-blis") + (version "0.7.8") + (source (origin + (method url-fetch) + (uri (pypi-uri "blis" version)) + (sha256 + (base32 + "0mvcif9g69424bk8xiflacxzpvz802ns791v2r8a6fij0sxl3mgp")))))) + (define-public openlibm (package (name "openlibm") diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 46170ff31e..00897ea451 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -39,6 +39,7 @@ ;;; Copyright © 2022 Giovanni Biscuolo <g@xelera.eu> ;;; Copyright © 2023 Giacomo Leidi <goodoldpaul@autistici.org> ;;; Copyright © 2023 Yovan Naumovski <yovan@gorski.stream> +;;; Copyright © 2023 gemmaro <gemmaro.dev@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -3085,7 +3086,13 @@ designed for experienced users.") (file-name (git-file-name name version)) (sha256 (base32 - "0da1ki1v252avy27j6d7snnc0gyq0xa9fypm3qdmxhw2w79d6q36")))) + "0da1ki1v252avy27j6d7snnc0gyq0xa9fypm3qdmxhw2w79d6q36")) + (modules '((guix build utils))) + (snippet + '(begin + ;; TODO: This is fixed upstream in later versions + (substitute* "zulip/tests/test_default_arguments.py" + (("optional arguments:") "options:")))))) (build-system python-build-system) (arguments `(#:phases diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index 5005da4e87..9884bc0487 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -118,7 +118,7 @@ interfacing MPD in the C, C++ & Objective C languages.") (define-public mpd (package (name "mpd") - (version "0.23.12") + (version "0.23.13") (source (origin (method url-fetch) (uri @@ -127,12 +127,13 @@ interfacing MPD in the C, C++ & Objective C languages.") "/mpd-" version ".tar.xz")) (sha256 (base32 - "1rq2hyfvwwri3sivab747csza2i096y7m8563rl5mhpchhiadz5p")))) + "06fmy68lfrsi5y03l53dnwcynqhwh5f5vhdpbsr8lzmvzgk02sx9")))) (build-system meson-build-system) (arguments (list #:configure-flags #~(list "-Ddocumentation=enabled" - "-Dsystemd=enabled") + "-Dsystemd=enabled" + "-Dtest=true") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'enable-elogind @@ -145,7 +146,15 @@ interfacing MPD in the C, C++ & Objective C languages.") (("systemd_dep = declare_dependency" all) (string-append "_" all))) (substitute* "meson.build" - (("systemd_dep,") "systemd_dep, _systemd_dep,"))))))) + (("systemd_dep,") "systemd_dep, _systemd_dep,")))) + (add-after 'install 'split-package + (lambda _ + ;; The HTML manual accounts for over 40% of the disk + ;; space used by the package. + (let* ((old (string-append #$output "/share/doc")) + (new (string-append #$output:doc "/share/doc"))) + (mkdir-p (dirname new)) + (rename-file old new))))))) (inputs (append (if (target-linux?) (list liburing) '()) (list ao @@ -182,7 +191,13 @@ interfacing MPD in the C, C++ & Objective C languages.") yajl zlib zziplib))) - (native-inputs (list cmake pkg-config python-sphinx)) + (native-inputs (list pkg-config python-sphinx googletest + ;; See test/meson.build for information about these + ;; additional dependencies. + ;; + ;; Used when zziplib feature is enabled. + zip)) + (outputs (list "out" "doc")) ;; Missing optional inputs: ;; libcdio_paranoia ;; libmms diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 7e4a7d1169..b7369391db 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -3215,7 +3215,7 @@ capabilities, custom envelopes, effects, etc.") (define-public yoshimi (package (name "yoshimi") - (version "2.2.2.1") + (version "2.3.0") (source (origin (method url-fetch) @@ -3223,7 +3223,7 @@ capabilities, custom envelopes, effects, etc.") (version-major+minor version) "/yoshimi-" version ".tar.bz2")) (sha256 - (base32 "1axrbk1qwsiq77g5957db744481zb2v158psnk2w530wxhls2442")))) + (base32 "0rkwz545bipanyl8kcp6rgdqppiad7s0j409a4n8dd97maislsa0")))) (build-system cmake-build-system) (arguments (list diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 9dfc785f04..2055ed93c7 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -59,6 +59,7 @@ ;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com> ;;; Copyright © 2023 Bruno Victal <mirai@makinata.eu> ;;; Copyright © 2023 Yovan Naumovski <yovan@gorski.stream> +;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -3097,7 +3098,10 @@ The filters can be aggregated and exported in the most common formats.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "07kwika1zdq62s5p5z94xznm77dxjxdg8k0hrg7wygz50151nzmx")))) + (base32 "07kwika1zdq62s5p5z94xznm77dxjxdg8k0hrg7wygz50151nzmx")) + (modules '((guix build utils))) + (snippet '(begin (substitute* '("Makefile") + (("-march=native") "")))))) (build-system gnu-build-system) (arguments (list @@ -3126,6 +3130,7 @@ The filters can be aggregated and exported in the most common formats.") libpcap openssl perl)) + (properties '((tunable? . #t))) (home-page "https://github.com/vanhauser-thc/thc-ipv6") (synopsis "IPv6 security research toolkit") (description "The THC IPv6 Toolkit provides command-line tools and a library diff --git a/gnu/packages/nim.scm b/gnu/packages/nim.scm index 6da382119f..ebcff26c7b 100644 --- a/gnu/packages/nim.scm +++ b/gnu/packages/nim.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2020 Tanguy Le Carrour <tanguy@bioneland.org> ;;; Copyright © 2022 (unmatched parenthesis <paren@disroot.org> ;;; Copyright © 2022 Trevor Richards <trev@trevdev.ca> +;;; Copyright © 2023 Gruruya <greytest@disroot.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -36,14 +37,14 @@ (define-public nim (package (name "nim") - (version "1.6.6") + (version "1.6.12") (source (origin (method url-fetch) (uri (string-append "https://nim-lang.org/download/" name "-" version ".tar.xz")) (sha256 - (base32 "0lm4450ig8k4l3rzxv6kcqji5l1lzicsw76ckwxm0q9qdz713cb7")))) + (base32 "1hjd9dxhqzn2ifr988li8q7v6kxpxlcqbdllfd6lsq3knw50pvxc")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; TODO: Investigate tests failures. @@ -55,6 +56,7 @@ (let ((out (assoc-ref outputs "out"))) (substitute* "install.sh" (("/usr/local") out) + (("/lib/nim") "/lib") (("/opt/nimble") (string-append out "/share/nimble")) (("configdir=/etc/nim") (string-append "configdir=" out "/etc/nim")))))) @@ -102,7 +104,7 @@ "lib/pure/osproc.nim" "lib/pure/strscans.nim") (("/bin/sh") sh)) - (substitute* (find-files "c_code" "stdlib_osproc\\.nim\\.c") + (substitute* (find-files "c_code" "@m\\.\\.@slib@spure@sosproc\\.nim\\.c") (("\"/bin/sh\", 7") (format #f "~s, ~s" sh (string-length sh))))))) (replace 'build (lambda* (#:key (parallel-build? #t) #:allow-other-keys) diff --git a/gnu/packages/notcurses.scm b/gnu/packages/notcurses.scm index bb0086d4b3..20b2cbb225 100644 --- a/gnu/packages/notcurses.scm +++ b/gnu/packages/notcurses.scm @@ -1,5 +1,6 @@ ;;; Copyright © 2021 Blake Shaw <blake@nonconstructivism.com> ;;; Copyright © 2022 Marius Bakke <marius@gnu.org> +;;; Copyright © 2023 Efraim Flashner <efraim@flashner.co.il> ;;; ;;; This file is part of GNU Guix. ;;; @@ -35,7 +36,7 @@ (define-public notcurses (package (name "notcurses") - (version "3.0.8") + (version "3.0.9") (source (origin (method url-fetch) @@ -48,7 +49,7 @@ "+dfsg.1.orig.tar.xz")) (file-name (string-append name "-" version ".tar.xz")) (sha256 - (base32 "1nz32nqh7fn4i06hvl8ndkm0z4g08a6wzhilvv8ggx2hc5axsz89")))) + (base32 "1sj2m7sil2i3yw73z15947kypsp0rnapwpwanwzam15lbicc8c3y")))) (build-system cmake-build-system) (arguments `(#:make-flags @@ -59,6 +60,10 @@ "-DUSE_COVERAGE=off" ;; Do not build HTML documentation "-DUSE_DOXYGEN=off" + ;; Unfortunately this disables the manpages. + ,@(if (supported-package? pandoc) + '() + '("-DUSE_PANDOC=off")) ;; Don't include mouse support "-DUSE_GPM=off" ;; Use FFmpeg for multimedia support @@ -66,9 +71,12 @@ ;; Follow the Debian Free Software Guidelines, omitting nonfree content. "-DDFSG_BUILD=ON"))) (native-inputs - (list pkg-config - pandoc - doctest)) + (append + (list pkg-config) + (if (supported-package? pandoc) + (list pandoc) + '()) + (list doctest))) (inputs (list ffmpeg libdeflate diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 3006631b66..9532fd7187 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013-2023 Ludovic Courtès <ludo@gnu.org> -;;; Copyright © 2015, 2017, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2017, 2020, 2021, 2022, 2023 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2017 Muriithi Frederick Muriuki <fredmanglis@gmail.com> ;;; Copyright © 2017, 2018 Oleg Pykhalov <go.wigust@gmail.com> ;;; Copyright © 2017 Roel Janssen <roel@gnu.org> @@ -120,6 +120,7 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system guile) #:use-module (guix build-system meson) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (guix build-system ruby) #:use-module (guix build-system trivial) @@ -917,7 +918,34 @@ transactions from C or Python.") (sha256 (base32 "1vyk0g0gci4z9psisb8h50zi3j1nwfdg1jw3j76cxv0brln0v3fw")))) - (build-system python-build-system) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; These tests require a network connection + '(append (map (lambda (file) + (string-append "--ignore=binstar_client/" file)) + (list "tests/test_upload.py" + "tests/test_authorizations.py" + "tests/test_login.py" + "tests/test_whoami.py" + "utils/notebook/tests/test_data_uri.py" + "utils/notebook/tests/test_base.py" + "utils/notebook/tests/test_downloader.py" + "inspect_package/tests/test_conda.py")) + ;; get_conda_root returns None + (list "-k" + "not test_conda_root \ +and not test_conda_root_outside_root_environment")) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'python3.10-compatibility + (lambda _ + (substitute* "binstar_client/utils/config.py" + (("collections.Mapping") "collections.abc.Mapping")))) + ;; This is needed for some tests. + (add-before 'check 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list python-clyent python-nbformat python-pyyaml python-requests)) (native-inputs @@ -926,27 +954,8 @@ transactions from C or Python.") python-freezegun python-mock python-pillow + python-pytest python-pytz)) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; This is needed for some tests. - (add-before 'check 'set-up-home - (lambda* _ (setenv "HOME" "/tmp") #t)) - (add-before 'check 'remove-network-tests - (lambda* _ - ;; Remove tests requiring a network connection - (let ((network-tests '("tests/test_upload.py" - "tests/test_authorizations.py" - "tests/test_login.py" - "tests/test_whoami.py" - "utils/notebook/tests/test_data_uri.py" - "utils/notebook/tests/test_base.py" - "utils/notebook/tests/test_downloader.py" - "inspect_package/tests/test_conda.py"))) - (with-directory-excursion "binstar_client" - (for-each delete-file network-tests))) - #t))))) (home-page "https://github.com/Anaconda-Platform/anaconda-client") (synopsis "Anaconda Cloud command line client library") (description @@ -1384,8 +1393,8 @@ environments.") "0k9zkdyyzir3fvlbcfcqy17k28b51i20rpbjwlx2i1mwd2pw9cxc"))))))) (define-public guix-build-coordinator - (let ((commit "99981dc3270d79ae0b83f94386e26cc75a7162b3") - (revision "84")) + (let ((commit "c44d485bba42034804beb47afc23005c4e73ea96") + (revision "85")) (package (name "guix-build-coordinator") (version (git-version "0" revision commit)) @@ -1396,7 +1405,7 @@ environments.") (commit commit))) (sha256 (base32 - "047qqqhpcg5rrzgpp2qlijn6rhlm2ipqhqr1yj1lrnx12dld2kqk")) + "1y69yrmmifdp55l5c5b8iiq0llwpggxmq6a4233cdll3bhfxaicl")) (file-name (string-append name "-" version "-checkout")))) (build-system gnu-build-system) (arguments diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index f5f301308a..74e465d21e 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Steve Sprang <scs@stevesprang.com> -;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2015-2023 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2015 Aljosha Papsch <misc@rpapsch.de> ;;; Copyright © 2016 Christine Lemmer-Webber <cwebber@dustycloud.org> ;;; Copyright © 2016 Jessica Tallon <tsyesika@tsyesika.se> @@ -142,7 +142,7 @@ human.") (define-public keepassxc (package (name "keepassxc") - (version "2.7.4") + (version "2.7.5") (source (origin (method url-fetch) @@ -150,7 +150,7 @@ human.") "/releases/download/" version "/keepassxc-" version "-src.tar.xz")) (sha256 - (base32 "1knywp38byq0jq9vdyp1ykha9prh09k1y5srwwkr6f503nb5402n")))) + (base32 "03002fncllr658mgl5s6an5wnh0a333qnkxad6aw85hqj004iqpd")))) (build-system cmake-build-system) (arguments (list diff --git a/gnu/packages/patches/agda-categories-remove-incompatible-flags.patch b/gnu/packages/patches/agda-categories-remove-incompatible-flags.patch new file mode 100644 index 0000000000..dc33af7cf9 --- /dev/null +++ b/gnu/packages/patches/agda-categories-remove-incompatible-flags.patch @@ -0,0 +1,31 @@ +From 3d73d59617281c6ae9c19032eae381ff77fd2e65 Mon Sep 17 00:00:00 2001 +Message-Id: <3d73d59617281c6ae9c19032eae381ff77fd2e65.1682841188.git.dev@jpoiret.xyz> +From: Josselin Poiret <dev@jpoiret.xyz> +Date: Sun, 30 Apr 2023 09:51:12 +0200 +Subject: [PATCH] Remove stdlib-incompatible flags + +From: Josselin Poiret <dev@jpoiret.xyz> + +--- + Makefile | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/Makefile b/Makefile +index 68846579..ba5923a2 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,6 +1,6 @@ + .PHONY: test Everything.agda clean + +-OTHEROPTS = --auto-inline -Werror ++OTHEROPTS = + + RTSARGS = +RTS -M6G -A128M -RTS ${OTHEROPTS} + + +base-commit: 20397e93a60ed1439ed57ee76ae377c66a5eb8d9 +prerequisite-patch-id: da10df58fa86d08b31174a01db7b9a02377aba55 +prerequisite-patch-id: 508dabd923ba9ac1ee4d8dab6697432b4bd8ba18 +-- +2.39.2 + diff --git a/gnu/packages/patches/agda-categories-use-find.patch b/gnu/packages/patches/agda-categories-use-find.patch new file mode 100644 index 0000000000..772352a0cb --- /dev/null +++ b/gnu/packages/patches/agda-categories-use-find.patch @@ -0,0 +1,31 @@ +From 53922aedd81d5111d9007b41235aa12eaa2a863d Mon Sep 17 00:00:00 2001 +Message-Id: <53922aedd81d5111d9007b41235aa12eaa2a863d.1682840933.git.dev@jpoiret.xyz> +From: Josselin Poiret <dev@jpoiret.xyz> +Date: Sun, 30 Apr 2023 09:48:21 +0200 +Subject: [PATCH] Use find instead of git ls-tree in Makefile + +From: Josselin Poiret <dev@jpoiret.xyz> + +--- + Makefile | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/Makefile b/Makefile +index 158802d1..68846579 100644 +--- a/Makefile ++++ b/Makefile +@@ -11,7 +11,7 @@ html: Everything.agda + agda ${RTSARGS} --html -i. Everything.agda + + Everything.agda: +- git ls-tree --full-tree -r --name-only HEAD | grep '^src/[^\.]*.agda' | sed -e 's|^src/[/]*|import |' -e 's|/|.|g' -e 's/.agda//' -e '/import Everything/d' | LC_COLLATE='C' sort > Everything.agda ++ find src -iname '*.agda' | sed -e 's|^src/[/]*|import |' -e 's|/|.|g' -e 's/.agda//' -e '/import Everything/d' | LC_COLLATE='C' sort > Everything.agda + + clean: + find . -name '*.agdai' -exec rm \{\} \; + +base-commit: 20397e93a60ed1439ed57ee76ae377c66a5eb8d9 +prerequisite-patch-id: da10df58fa86d08b31174a01db7b9a02377aba55 +-- +2.39.2 + diff --git a/gnu/packages/patches/agda-libdirs-env-variable.patch b/gnu/packages/patches/agda-libdirs-env-variable.patch new file mode 100644 index 0000000000..3b291358a6 --- /dev/null +++ b/gnu/packages/patches/agda-libdirs-env-variable.patch @@ -0,0 +1,49 @@ +From 457bc7438a4f0801dbf332fa2369248bddf5da0c Mon Sep 17 00:00:00 2001 +Message-Id: <457bc7438a4f0801dbf332fa2369248bddf5da0c.1678309546.git.dev@jpoiret.xyz> +From: Josselin Poiret <dev@jpoiret.xyz> +Date: Wed, 8 Mar 2023 18:31:52 +0100 +Subject: [PATCH] Add environment variable for library directories + +AGDA_LIBDIRS is a new environment colon-separated variable for site libraries. +Agda will look for .agda-lib files directly inside direct descendants of these. +--- + src/full/Agda/Interaction/Library.hs | 16 ++++++++++++++-- + 1 file changed, 14 insertions(+), 2 deletions(-) + +diff --git a/src/full/Agda/Interaction/Library.hs b/src/full/Agda/Interaction/Library.hs +index 09c1f2a82..774cc3e74 100644 +--- a/src/full/Agda/Interaction/Library.hs ++++ b/src/full/Agda/Interaction/Library.hs +@@ -323,13 +323,25 @@ getInstalledLibraries overrideLibFile = mkLibM [] $ do + raiseErrors' [ LibrariesFileNotFound theOverrideLibFile ] + return [] + Right file -> do +- if not (lfExists file) then return [] else do ++ siteLibDirs <- liftIO $ fromMaybe [] . fmap splitAtColon . lookup "AGDA_LIBDIRS" <$> getEnvironment ++ siteLibs <- liftIO $ concat <$> mapM findSiteLibs siteLibDirs ++ if not (lfExists file) then parseLibFiles Nothing $ nubOn snd ((0,) <$> siteLibs) else do + ls <- liftIO $ stripCommentLines <$> UTF8.readFile (lfPath file) + files <- liftIO $ sequence [ (i, ) <$> expandEnvironmentVariables s | (i, s) <- ls ] +- parseLibFiles (Just file) $ nubOn snd files ++ parseLibFiles (Just file) $ nubOn snd (files ++ fmap (0,) siteLibs) + `catchIO` \ e -> do + raiseErrors' [ ReadError e "Failed to read installed libraries." ] + return [] ++ where splitAtColon :: String -> [String] ++ splitAtColon "" = [] ++ splitAtColon str = case break (==':') str of ++ (a, _:b) -> a : splitAtColon b ++ (a, "") -> [a] ++ findSiteLibs :: String -> IO [String] ++ findSiteLibs dir = do ++ subDirs <- filterM doesDirectoryExist =<< map (dir </>) <$> listDirectory dir ++ subFiles <- mapM (\dir -> map (dir </>) <$> listDirectory dir) subDirs ++ return $ concatMap (filter (List.isSuffixOf ".agda-lib")) subFiles + + -- | Parse the given library files. + -- + +base-commit: 183534bc41af5a53daf685122997dc98883f2be2 +-- +2.39.1 + diff --git a/gnu/packages/patches/agda-stdlib-use-runhaskell.patch b/gnu/packages/patches/agda-stdlib-use-runhaskell.patch new file mode 100644 index 0000000000..21ce16689f --- /dev/null +++ b/gnu/packages/patches/agda-stdlib-use-runhaskell.patch @@ -0,0 +1,28 @@ +From 3dc3c0856906d25bb697a4480a8457a69637cd51 Mon Sep 17 00:00:00 2001 +Message-Id: <3dc3c0856906d25bb697a4480a8457a69637cd51.1682798848.git.dev@jpoiret.xyz> +From: Josselin Poiret <dev@jpoiret.xyz> +Date: Sat, 29 Apr 2023 22:06:55 +0200 +Subject: [PATCH] Makefile: use runhaskell instead of cabal + +From: Josselin Poiret <dev@jpoiret.xyz> + +--- + GNUmakefile | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/GNUmakefile b/GNUmakefile +index c5d886e03..f3cb2a1e7 100644 +--- a/GNUmakefile ++++ b/GNUmakefile +@@ -21,7 +21,7 @@ Everything.agda: + # command `cabal install` is needed by cabal-install <= 2.4.*. I did + # not found any problem running both commands with different versions + # of cabal-install. See Issue #1001. +- cabal run GenerateEverything ++ runhaskell GenerateEverything + + .PHONY: listings + listings: Everything.agda +-- +2.39.2 + diff --git a/gnu/packages/patches/d-feet-drop-unused-meson-argument.patch b/gnu/packages/patches/d-feet-drop-unused-meson-argument.patch new file mode 100644 index 0000000000..5d728d7d60 --- /dev/null +++ b/gnu/packages/patches/d-feet-drop-unused-meson-argument.patch @@ -0,0 +1,36 @@ +From 05465d486afdba116dbc22fc22c1e6573aea4f22 Mon Sep 17 00:00:00 2001 +From: Jan Beich <jbeich@FreeBSD.org> +Date: Mon, 24 Jan 2022 12:11:57 +0000 +Subject: [PATCH] meson: drop unused argument for i18n.merge_file() + +Ignored in Meson < 0.60.0, deprecated since 0.60.1 and fatal since 0.61.0. + +data/meson.build:15:0: ERROR: Function does not take positional arguments. +data/meson.build:27:0: ERROR: Function does not take positional arguments. +--- + data/meson.build | 2 -- + 1 file changed, 2 deletions(-) + +diff --git a/data/meson.build b/data/meson.build +index 026bd80..3b03b94 100644 +--- a/data/meson.build ++++ b/data/meson.build +@@ -13,7 +13,6 @@ desktop_in = configure_file( + ) + + i18n.merge_file( +- desktop, + type: 'desktop', + input: desktop_in, + output: '@BASENAME@', +@@ -25,7 +24,6 @@ i18n.merge_file( + appdata = df_namespace + '.appdata.xml' + + i18n.merge_file( +- appdata, + input: appdata + '.in', + output: '@BASENAME@', + po_dir: po_dir, +-- +GitLab + diff --git a/gnu/packages/patches/hdf4-architectures.patch b/gnu/packages/patches/hdf4-architectures.patch index 5549f11277..aa71d5a383 100644 --- a/gnu/packages/patches/hdf4-architectures.patch +++ b/gnu/packages/patches/hdf4-architectures.patch @@ -21,7 +21,7 @@ Author: Francesco Paolo Lovergine <frankie@debian.org> #define DFMT_PC 0x4441 #define DFMT_APPLE 0x1111 #define DFMT_APPLE_INTEL 0x4441 -@@ -75,6 +77,12 @@ +@@ -75,6 +77,13 @@ #define DFMT_IA64 0x4441 #define DFMT_LINUX64 0x4441 #define DFMT_POWERPC64 0x1111 @@ -29,12 +29,13 @@ Author: Francesco Paolo Lovergine <frankie@debian.org> +#define DFMT_ARMV4L 0x4441 +#define DFMT_AARCH64 0x4441 +#define DFMT_X86_64 0x4441 -+#define DFMT_SH 0x4441 -+#define DFMT_SHEB 0x1111 ++#define DFMT_SH 0x4441 ++#define DFMT_SHEB 0x1111 ++#define DFMT_RISCV64 0x4441 /* I/O library constants */ #define UNIXUNBUFIO 1 -@@ -288,7 +296,7 @@ typedef int hdf_pint_t; +@@ -288,7 +297,7 @@ typedef int hdf_pint_t; #endif /* IBM6000 */ @@ -43,7 +44,7 @@ Author: Francesco Paolo Lovergine <frankie@debian.org> #ifndef HP9000 #define HP9000 -@@ -347,6 +355,10 @@ typedef int hdf_pint_t; +@@ -347,6 +356,10 @@ typedef int hdf_pint_t; /* what each does */ #define JMEMSYS MEM_ANSI @@ -54,7 +55,7 @@ Author: Francesco Paolo Lovergine <frankie@debian.org> #endif /* HP9000 */ -@@ -666,6 +678,410 @@ typedef int hdf_pint_t; +@@ -670,6 +683,462 @@ typedef int hdf_pint_t; #endif /* !(defined(__APPLE__)) */ /*-----------------------------------------------------*/ @@ -462,10 +463,62 @@ Author: Francesco Paolo Lovergine <frankie@debian.org> + +#endif /* Linux/aarch64 */ + ++#if defined (__linux__) && defined (__riscv) && (__riscv_xlen == 64) ++ ++#ifdef GOT_MACHINE ++If you get an error on this line more than one machine type has been defined. ++Please check your Makefile. ++#endif ++#define GOT_MACHINE 1 ++ ++#include <fcntl.h> ++#include <sys/types.h> /* for unbuffered file I/O */ ++#include <sys/stat.h> ++#include <unistd.h> ++#include <ctype.h> /* for character macros */ ++ ++#define DF_MT DFMT_RISCV64 ++ ++typedef void VOID; ++typedef void * VOIDP; ++typedef char * _fcd; ++typedef char char8; ++typedef unsigned char uchar8; ++typedef signed char int8; ++typedef unsigned char uint8; ++typedef short int int16; ++typedef unsigned short int uint16; ++typedef int int32; ++typedef unsigned int uint32; ++typedef int intn; ++typedef unsigned int uintn; ++typedef float float32; ++typedef double float64; ++typedef int intf; /* size of INTEGERs in Fortran compiler */ ++typedef long hdf_pint_t; /* an integer the same size as a pointer */ ++#define FNAME_POST_UNDERSCORE ++#define _fcdtocp(desc) (desc) ++#define FILELIB UNIXBUFIO ++ ++#ifndef BIG_LONGS ++#define BIG_LONGS ++#endif ++ ++/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ ++ ++/* Determine the memory manager we are going to use. Valid values are: */ ++/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ ++/* what each does */ ++#define JMEMSYS MEM_ANSI ++#define HAVE_STDC ++#define INCLUDES_ARE_ANSI ++ ++#endif /* Linux/riscv64 */ ++ #if defined(NEXT) || defined(NeXT) #ifndef NEXT -@@ -928,7 +1344,11 @@ Please check your Makefile. +@@ -932,7 +1401,11 @@ Please check your Makefile. #include <sys/file.h> /* for unbuffered i/o stuff */ #include <sys/stat.h> @@ -478,7 +531,7 @@ Author: Francesco Paolo Lovergine <frankie@debian.org> typedef void VOID; typedef void *VOIDP; typedef char *_fcd; -@@ -952,6 +1372,11 @@ typedef long hdf_pint_t; +@@ -956,6 +1429,11 @@ typedef long hdf_pint_t; #define _fcdtocp(desc) (desc) #define FILELIB UNIXBUFIO @@ -490,7 +543,7 @@ Author: Francesco Paolo Lovergine <frankie@debian.org> /* JPEG #define's - Look in the JPEG docs before changing - (Q) */ /* Determine the memory manager we are going to use. Valid values are: */ -@@ -1097,6 +1522,8 @@ typedef long hdf_pint_t; +@@ -1101,6 +1579,8 @@ typedef long hdf_pint_t; #define _fcdtocp(desc) (desc) #define FILELIB UNIXBUFIO @@ -499,7 +552,7 @@ Author: Francesco Paolo Lovergine <frankie@debian.org> /* JPEG #define's - Look in the JPEG docs before changing - (Q) */ /* Determine the memory manager we are going to use. Valid values are: */ -@@ -1111,6 +1538,66 @@ typedef long hdf_pint_t; +@@ -1115,6 +1595,66 @@ typedef long hdf_pint_t; #endif /* IA64 */ @@ -573,7 +626,7 @@ Author: Francesco Paolo Lovergine <frankie@debian.org> /*****************************************************************************/ /* Generally Big-Endian machines */ -#if !defined(INTEL86) && !defined(MIPSEL) && !defined(DEC_ALPHA) && !defined(I860) && !defined(SUN386) && !(defined(__ia64) && !(defined(hpux) || defined(__hpux))) && !defined(__x86_64__) -+#if !defined(INTEL86) && !defined(MIPSEL) && !defined(DEC_ALPHA) && !defined(I860) && !defined(SUN386) && !(defined(__ia64) && !(defined(hpux) || defined(__hpux))) && !defined(__x86_64__) && !(defined(__powerpc__) && defined(__LITTLE_ENDIAN__)) && !defined(__aarch64__) && !defined(__ARM_EABI__) ++#if !defined(INTEL86) && !defined(MIPSEL) && !defined(DEC_ALPHA) && !defined(I860) && !defined(SUN386) && !(defined(__ia64) && !(defined(hpux) || defined(__hpux))) && !defined(__x86_64__) && !(defined(__powerpc__) && defined(__LITTLE_ENDIAN__)) && !defined(__aarch64__) && !defined(__ARM_EABI__) && !defined(__riscv) # define UI8_IN DFKnb1b /* Unsigned Integer, 8 bits */ # define UI8_OUT DFKnb1b # define SI16_IN DFKnb2b /* S = Signed */ diff --git a/gnu/packages/patches/proj-7-initialize-memory.patch b/gnu/packages/patches/proj-7-initialize-memory.patch new file mode 100644 index 0000000000..81481f9a46 --- /dev/null +++ b/gnu/packages/patches/proj-7-initialize-memory.patch @@ -0,0 +1,98 @@ +From 6f1a3c4648bf06862dca0b3725cbb3b7ee0284e3 Mon Sep 17 00:00:00 2001 +From: Even Rouault <even.rouault@spatialys.com> +Date: Sat, 6 Mar 2021 22:12:27 +0100 +Subject: [PATCH] =?UTF-8?q?gie=5Fself=5Ftests:=20fix=20use=20of=20uninitia?= + =?UTF-8?q?lized=20memory=20(fixes=C2=A0#2557)?= +MIME-Version: 1.0 +Content-Type: text/plain; charset=UTF-8 +Content-Transfer-Encoding: 8bit + +--- + test/unit/gie_self_tests.cpp | 39 ++++++++++++++++++++++-------------- + 1 file changed, 24 insertions(+), 15 deletions(-) + +diff --git a/test/unit/gie_self_tests.cpp b/test/unit/gie_self_tests.cpp +index 4244766ebf..92f1c758dc 100644 +--- a/test/unit/gie_self_tests.cpp ++++ b/test/unit/gie_self_tests.cpp +@@ -268,8 +268,10 @@ TEST_F(gieTest, proj_create_crs_to_crs) { + ASSERT_TRUE(P != nullptr); + PJ_COORD a, b; + +- a.xy.x = 700000.0; +- a.xy.y = 6000000.0; ++ a.xyzt.x = 700000.0; ++ a.xyzt.y = 6000000.0; ++ a.xyzt.z = 0; ++ a.xyzt.t = HUGE_VAL; + b.xy.x = 307788.8761171057; + b.xy.y = 5999669.3036037628; + +@@ -306,8 +308,10 @@ TEST_F(gieTest, proj_create_crs_to_crs_EPSG_4326) { + PJ_COORD a, b; + + // Lat, long degrees +- a.xy.x = 0.0; +- a.xy.y = 3.0; ++ a.xyzt.x = 0.0; ++ a.xyzt.y = 3.0; ++ a.xyzt.z = 0; ++ a.xyzt.t = HUGE_VAL; + + b.xy.x = 500000.0; + b.xy.y = 0.0; +@@ -328,8 +332,10 @@ TEST_F(gieTest, proj_create_crs_to_crs_proj_longlat) { + PJ_COORD a, b; + + // Long, lat degrees +- a.xy.x = 3.0; +- a.xy.y = 0; ++ a.xyzt.x = 3.0; ++ a.xyzt.y = 0; ++ a.xyzt.z = 0; ++ a.xyzt.t = HUGE_VAL; + + b.xy.x = 500000.0; + b.xy.y = 0.0; +@@ -718,9 +724,10 @@ TEST(gie, proj_create_crs_to_crs_PULKOVO42_ETRS89) { + proj_destroy(target_crs); + + // Romania +- c.xyz.x = 45; // Lat +- c.xyz.y = 25; // Long +- c.xyz.z = 0; ++ c.xyzt.x = 45; // Lat ++ c.xyzt.y = 25; // Long ++ c.xyzt.z = 0; ++ c.xyzt.t = HUGE_VAL; + c = proj_trans(P, PJ_FWD, c); + EXPECT_NEAR(c.xy.x, 44.999701238, 1e-9); + EXPECT_NEAR(c.xy.y, 24.998474948, 1e-9); +@@ -740,9 +747,10 @@ TEST(gie, proj_create_crs_to_crs_PULKOVO42_ETRS89) { + EXPECT_NEAR(c.xy.x, 45, 1e-8); + EXPECT_NEAR(c.xy.y, 25, 1e-8); + +- c.xyz.x = 45; // Lat +- c.xyz.y = 25; // Long +- c.xyz.z = 0; ++ c.xyzt.x = 45; // Lat ++ c.xyzt.y = 25; // Long ++ c.xyzt.z = 0; ++ c.xyzt.t = HUGE_VAL; + proj_trans_generic(P, PJ_FWD, &(c.xyz.x), sizeof(double), 1, &(c.xyz.y), + sizeof(double), 1, &(c.xyz.z), sizeof(double), 1, + nullptr, 0, 0); +@@ -783,9 +791,10 @@ TEST(gie, proj_create_crs_to_crs_outside_area_of_use) { + EXPECT_EQ(P->fwd, nullptr); + + // Test point outside area of use of both candidate coordinate operations +- c.xyz.x = 58; // Lat in deg +- c.xyz.y = 5; // Long in deg +- c.xyz.z = 0; ++ c.xyzt.x = 58; // Lat in deg ++ c.xyzt.y = 5; // Long in deg ++ c.xyzt.z = 0; ++ c.xyzt.t = HUGE_VAL; + c = proj_trans(P, PJ_FWD, c); + EXPECT_NEAR(c.xy.x, 64.44444444444444, 1e-9); // Lat in grad + EXPECT_NEAR(c.xy.y, 2.958634259259258, 1e-9); // Long in grad diff --git a/gnu/packages/patches/proot-add-clone3.patch b/gnu/packages/patches/proot-add-clone3.patch new file mode 100644 index 0000000000..c09d99a743 --- /dev/null +++ b/gnu/packages/patches/proot-add-clone3.patch @@ -0,0 +1,114 @@ +From 4699a580ca1aeecd35742494eb0259ee962e89a8 Mon Sep 17 00:00:00 2001 +Message-Id: <4699a580ca1aeecd35742494eb0259ee962e89a8.1685735399.git.dev@jpoiret.xyz> +From: Josselin Poiret <dev@jpoiret.xyz> +Date: Fri, 2 Jun 2023 21:42:31 +0200 +Subject: [PATCH] Add clone3. + +From: Josselin Poiret <dev@jpoiret.xyz> + +--- + src/syscall/sysnums-arm.h | 1 + + src/syscall/sysnums-arm64.h | 1 + + src/syscall/sysnums-i386.h | 1 + + src/syscall/sysnums-sh4.h | 1 + + src/syscall/sysnums-x32.h | 1 + + src/syscall/sysnums-x86_64.h | 1 + + src/syscall/sysnums.list | 1 + + src/tracee/tracee.c | 4 ++++ + 8 files changed, 11 insertions(+) + +diff --git a/src/syscall/sysnums-arm.h b/src/syscall/sysnums-arm.h +index dfd512f..306e2b1 100644 +--- a/src/syscall/sysnums-arm.h ++++ b/src/syscall/sysnums-arm.h +@@ -341,4 +341,5 @@ static const Sysnum sysnums_arm[] = { + [ 382 ] = PR_renameat2, + [ 397 ] = PR_statx, + [ 412 ] = PR_utimensat_time64, ++ [ 435 ] = PR_clone3, + }; +diff --git a/src/syscall/sysnums-arm64.h b/src/syscall/sysnums-arm64.h +index dfb9889..65ccc4e 100644 +--- a/src/syscall/sysnums-arm64.h ++++ b/src/syscall/sysnums-arm64.h +@@ -264,4 +264,5 @@ static const Sysnum sysnums_arm64[] = { + [ 275 ] = PR_sched_getattr, + [ 276 ] = PR_renameat2, + [ 291 ] = PR_statx, ++ [ 435 ] = PR_clone3, + }; +diff --git a/src/syscall/sysnums-i386.h b/src/syscall/sysnums-i386.h +index 3bbb70e..0f3daf2 100644 +--- a/src/syscall/sysnums-i386.h ++++ b/src/syscall/sysnums-i386.h +@@ -353,4 +353,5 @@ static const Sysnum sysnums_i386[] = { + [ 353 ] = PR_renameat2, + [ 383 ] = PR_statx, + [ 412 ] = PR_utimensat_time64, ++ [ 435 ] = PR_clone3, + }; +diff --git a/src/syscall/sysnums-sh4.h b/src/syscall/sysnums-sh4.h +index 1d3758c..09acca6 100644 +--- a/src/syscall/sysnums-sh4.h ++++ b/src/syscall/sysnums-sh4.h +@@ -344,4 +344,5 @@ static const Sysnum sysnums_sh4[] = { + [ 369 ] = PR_sched_setattr, + [ 370 ] = PR_sched_getattr, + [ 371 ] = PR_renameat2, ++ [ 435 ] = PR_clone3, + }; +diff --git a/src/syscall/sysnums-x32.h b/src/syscall/sysnums-x32.h +index 448c699..a9fdb48 100644 +--- a/src/syscall/sysnums-x32.h ++++ b/src/syscall/sysnums-x32.h +@@ -277,6 +277,7 @@ static const Sysnum sysnums_x32[] = { + [ 315 ] = PR_sched_getattr, + [ 316 ] = PR_renameat2, + [ 332 ] = PR_statx, ++ [ 435 ] = PR_clone3, + [ 439 ] = PR_faccessat2, + [ 512 ] = PR_rt_sigaction, + [ 513 ] = PR_rt_sigreturn, +diff --git a/src/syscall/sysnums-x86_64.h b/src/syscall/sysnums-x86_64.h +index 92229f8..9840b4a 100644 +--- a/src/syscall/sysnums-x86_64.h ++++ b/src/syscall/sysnums-x86_64.h +@@ -319,5 +319,6 @@ static const Sysnum sysnums_x86_64[] = { + [ 315 ] = PR_sched_getattr, + [ 316 ] = PR_renameat2, + [ 332 ] = PR_statx, ++ [ 435 ] = PR_clone3, + [ 439 ] = PR_faccessat2, + }; +diff --git a/src/syscall/sysnums.list b/src/syscall/sysnums.list +index 1d6e666..2b6c9b2 100644 +--- a/src/syscall/sysnums.list ++++ b/src/syscall/sysnums.list +@@ -38,6 +38,7 @@ SYSNUM(clock_gettime) + SYSNUM(clock_nanosleep) + SYSNUM(clock_settime) + SYSNUM(clone) ++SYSNUM(clone3) + SYSNUM(close) + SYSNUM(connect) + SYSNUM(creat) +diff --git a/src/tracee/tracee.c b/src/tracee/tracee.c +index 58ab7df..9b16f6a 100644 +--- a/src/tracee/tracee.c ++++ b/src/tracee/tracee.c +@@ -403,6 +403,10 @@ int new_child(Tracee *parent, word_t clone_flags) + status = fetch_regs(parent); + if (status >= 0 && get_sysnum(parent, CURRENT) == PR_clone) + clone_flags = peek_reg(parent, CURRENT, SYSARG_1); ++ else if (status >= 0 && get_sysnum(parent, CURRENT) == PR_clone3) ++ // Look at the first word of the clone_args structure, which ++ // contains the usual clone flags. ++ clone_flags = peek_word(parent, peek_reg(parent, CURRENT, SYSARG_1)); + + /* Get the pid of the parent's new child. */ + status = ptrace(PTRACE_GETEVENTMSG, parent->pid, NULL, &pid); + +base-commit: bd5a5f63d72f8210d8cee76195eb9f0749e5bd70 +-- +2.40.1 + diff --git a/gnu/packages/patches/sbcl-riscv-Make-contribs-build-again.patch b/gnu/packages/patches/sbcl-riscv-Make-contribs-build-again.patch new file mode 100644 index 0000000000..85b96e1b20 --- /dev/null +++ b/gnu/packages/patches/sbcl-riscv-Make-contribs-build-again.patch @@ -0,0 +1,71 @@ +From 8704f528f227f587d0e06dfd2f807aeca7a69a71 Mon Sep 17 00:00:00 2001 +From: Charles Zhang <charleszhang99@yahoo.com> +Date: Thu, 1 Jun 2023 16:39:26 +0200 +Subject: [PATCH] riscv: Make contribs build again. + +The issue was that the LINKAGE_TEMP_REG being NL3 was a C argument +register, so of course that caused clashing on C call-out, causing +problems with run-program. Going back to NL7 didn't work either +because it wasn't getting saved before entry into the trampoline. The +code here used to have NL7 before the trampoline code was gutted and +then restored, so I'm wondering how this ever worked before, because +it definitely did. Pick LIP as the TEMP_REG now because not only does +it get saved, it's also the least likely thing to get disturbed by +clobbering. + +Fixes #lp2002930. + +Also remove assembly routine printing because it doesn't need to be +part of the build script (unlike the other files in output/ which +can't trivially be recovered from a built image), and because not all +disassembler printers have been written on riscv yet. +--- + NEWS | 3 +++ + make-target-2-load.lisp | 4 ---- + src/runtime/riscv-arch.c | 2 +- + 3 files changed, 4 insertions(+), 5 deletions(-) + +diff --git a/NEWS b/NEWS +index 17537ff92..5c0f7777b 100644 +--- a/NEWS ++++ b/NEWS +@@ -1,5 +1,8 @@ + ;;;; -*- coding: utf-8; fill-column: 78 -*- + ++changes relative to sbcl-2.3.5: ++ * bug fix: riscv can build contribs again. ++ + changes in sbcl-2.3.5 relative to sbcl-2.3.4: + * enhancement: Unicode support has been updated to support version 15.0.0 of + the Unicode standard, including addition of characters and their collation +diff --git a/make-target-2-load.lisp b/make-target-2-load.lisp +index 885ebda74..b9a1a1e36 100644 +--- a/make-target-2-load.lisp ++++ b/make-target-2-load.lisp +@@ -6,10 +6,6 @@ + (defvar *compile-files-p* nil) + (load (merge-pathnames "src/cold/warm.lisp" *load-pathname*)) + +-(with-open-file (stream "output/asm-routines.txt" :direction :output +- :if-does-not-exist :create :if-exists :supersede) +- (sb-c:dis sb-fasl:*assembler-routines* stream)) +- + ;; sb-xref-for-internals is actively harmful to tree-shaking. + ;; Remove some symbols to make the hide-packages test pass. + #+sb-xref-for-internals +diff --git a/src/runtime/riscv-arch.c b/src/runtime/riscv-arch.c +index 6c1994829..062623899 100644 +--- a/src/runtime/riscv-arch.c ++++ b/src/runtime/riscv-arch.c +@@ -159,7 +159,7 @@ arch_install_interrupt_handlers(void) + * Linkage entry size is 8 or 20, because we need 2 instructions for the 32-bit case and we need 3 instructions and an 8 byte address in the 64-bit case. + */ + +-#define LINKAGE_TEMP_REG reg_NL3 ++#define LINKAGE_TEMP_REG reg_LIP // Lisp needs to save before entry. + + void arch_write_linkage_table_entry(int index, void *target_addr, int datap) + { +-- +2.40.1 + diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index ec4e4620f8..1f3cc4ba46 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -824,14 +824,14 @@ and based on PDF specification 1.7.") (define-public mupdf (package (name "mupdf") - (version "1.22.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (string-append "https://mupdf.com/downloads/archive/" "mupdf-" version "-source.tar.lz")) (sha256 - (base32 "0ghwam1c1izks1n2zq2pr8z67nvrx4njk5rla86b75l4pw58mmxy")) + (base32 "1px73qnazjvmbwf1fab8ad8j1dmiddg1mjb7zg7h9i1vp4bh7c1k")) (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1))) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 50a586d773..98abf038a5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -156,12 +156,14 @@ (define-module (gnu packages python-xyz) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) - #:use-module (gnu packages algebra) #:use-module (gnu packages adns) #:use-module (gnu packages aidc) + #:use-module (gnu packages algebra) #:use-module (gnu packages attr) #:use-module (gnu packages backup) + #:use-module (gnu packages base) #:use-module (gnu packages bash) + #:use-module (gnu packages bdw-gc) #:use-module (gnu packages check) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) @@ -177,28 +179,28 @@ #:use-module (gnu packages documentation) #:use-module (gnu packages enchant) #:use-module (gnu packages file) - #:use-module (gnu packages fontutils) #:use-module (gnu packages fonts) + #:use-module (gnu packages fontutils) #:use-module (gnu packages freedesktop) - #:use-module (gnu packages gdb) #:use-module (gnu packages gcc) + #:use-module (gnu packages gdb) #:use-module (gnu packages geo) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) #:use-module (gnu packages gnupg) - #:use-module (gnu packages graphviz) #:use-module (gnu packages graphics) + #:use-module (gnu packages graphviz) #:use-module (gnu packages gsasl) #:use-module (gnu packages gstreamer) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages icu4c) - #:use-module (gnu packages inkscape) #:use-module (gnu packages image) #:use-module (gnu packages image-processing) #:use-module (gnu packages imagemagick) + #:use-module (gnu packages inkscape) #:use-module (gnu packages java) #:use-module (gnu packages jupyter) #:use-module (gnu packages kerberos) @@ -214,10 +216,10 @@ #:use-module (gnu packages maths) #:use-module (gnu packages monitoring) #:use-module (gnu packages multiprecision) - #:use-module (gnu packages networking) #:use-module (gnu packages ncurses) - #:use-module (gnu packages node) + #:use-module (gnu packages networking) #:use-module (gnu packages ninja) + #:use-module (gnu packages node) #:use-module (gnu packages openstack) #:use-module (gnu packages pcre) #:use-module (gnu packages pdf) @@ -236,14 +238,15 @@ #:use-module (gnu packages rdf) #:use-module (gnu packages readline) #:use-module (gnu packages regex) - #:use-module (gnu packages sdl) #:use-module (gnu packages scanner) + #:use-module (gnu packages sdl) #:use-module (gnu packages search) #:use-module (gnu packages serialization) #:use-module (gnu packages shells) #:use-module (gnu packages sphinx) #:use-module (gnu packages ssh) #:use-module (gnu packages swig) + #:use-module (gnu packages tcl) #:use-module (gnu packages terminals) #:use-module (gnu packages tex) #:use-module (gnu packages texinfo) @@ -254,24 +257,20 @@ #:use-module (gnu packages video) #:use-module (gnu packages web) #:use-module (gnu packages wxwidgets) - #:use-module (gnu packages base) #:use-module (gnu packages xml) - #:use-module (gnu packages xorg) #:use-module (gnu packages xdisorg) - #:use-module (gnu packages tcl) - #:use-module (gnu packages bdw-gc) - #:use-module (gnu packages serialization) + #:use-module (gnu packages xorg) #:use-module (guix packages) - #:use-module (guix download) - #:use-module (guix git-download) - #:use-module (guix hg-download) - #:use-module (guix gexp) - #:use-module (guix utils) - #:use-module (guix build-system gnu) #:use-module (guix build-system cargo) #:use-module (guix build-system cmake) + #:use-module (guix build-system gnu) #:use-module (guix build-system pyproject) #:use-module (guix build-system python) + #:use-module (guix download) + #:use-module (guix hg-download) + #:use-module (guix git-download) + #:use-module (guix gexp) + #:use-module (guix utils) #:use-module (srfi srfi-1) #:use-module (srfi srfi-26)) @@ -1342,15 +1341,10 @@ threads.") (sha256 (base32 "0bwkvjpjfyi9dgszzad9aww2vc00w3bczjnbifi92cp7wch2l923")))) - (build-system python-build-system) + (build-system pyproject-build-system) (native-inputs - (list python-setuptools-scm python-tornado python-typeguard + (list python-setuptools-scm python-tornado-6 python-typeguard python-pytest)) - (arguments - (list #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda _ (invoke "pytest" "-vv")))))) (home-page "https://github.com/jd/tenacity") (synopsis "Retrying library for python") (description "Tenacity is a general-purpose python library to simplify the @@ -2693,48 +2687,32 @@ class.") (define-public python-can (package (name "python-can") - (version "4.0.0") + (version "4.2.0") (source (origin (method url-fetch) (uri (pypi-uri "python-can" version)) (sha256 (base32 - "0pcbdgdw94lc2sxd56w6wdsshrs9dd5d3wp0x4sfd0drzx32inar")))) - (build-system python-build-system) + "1w5sdzxivpd3pw4pypwnjlksvfimdb93qnlddbrh5f13flhsgg8g")))) + (build-system pyproject-build-system) (arguments - `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'relax-version-requirements - (lambda _ - (substitute* "setup.py" - (("mock~=2\\.0") "mock") - (("coverage<5") "coverage") - (("pytest~=4\\.6") "pytest") - (("pytest-timeout~=1\\.3") "pytest-timeout") - (("pytest-cov.*") "pytest-cov\n") - (("hypothesis~=4\\.56") "hypothesis")))) - (add-after 'unpack 'fix-broken-tests - ;; The tests try to run two scripts it expects should be - ;; in PATH, but they aren't at this time (see: - ;; https://github.com/hardbyte/python-can/issues/805). - (lambda _ - (substitute* "test/test_scripts.py" - (("\"can_logger\\.py --help\"") "") - (("\"can_player\\.py --help\"") "")))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-vv" "test" - ;; Disable tests which require specific CAN - ;; drivers we have no package for in Guix. - "--ignore" "test/test_interface_canalystii.py" - ;; These tests fail with "OSError: [Errno 19] - ;; No such device". - "-k" "not BasicTestUdpMulticastBusIPv"))))))) + (list + #:test-flags + #~(list + ;; TODO: Check if it could be packed: + ;; https://github.com/projectgus/python-canalystii + ;; + ;; Disable tests which require specific CAN drivers we have no + ;; package for in Guix. + "--ignore" "test/test_interface_canalystii.py" + ;; These tests fail with "OSError: [Errno 19] No such device". + "-k" "not BasicTestUdpMulticastBusIPv"))) (propagated-inputs (list python-msgpack python-typing-extensions python-wrapt)) (native-inputs - (list python-codecov + (list ;; python-canalystii ; Not packed yet + python-codecov python-coverage python-future python-hypothesis @@ -4419,6 +4397,58 @@ with sensible defaults out of the box.") clickgen is using @code{anicursorgen} and @code{xcursorgen} under the hood.") (license license:expat))) +(define-public python-clickhouse-connect + (package + (name "python-clickhouse-connect") + (version "0.6.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ClickHouse/clickhouse-connect") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1s0lk7xdq8f351cmpbp6jidqi5zdazrdba7w7fxph0w8sd74amry")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; All these tests require docker-compose + '(list "--ignore-glob=tests/integration_tests/*") + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'patch-pyproject + (lambda _ + ;; Our version of pytest is confused by this field. + (substitute* "pyproject.toml" + (("^env_files.*") "")))) + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python" "setup.py" "build_ext" "--inplace")))))) + (propagated-inputs + (list python-arrow + python-certifi + python-lz4 + python-numpy + python-orjson + python-pandas + python-pytz + python-sqlalchemy + python-urllib3 + python-zstandard)) + (native-inputs + (list python-cython + python-pytest)) + (home-page "https://github.com/ClickHouse/clickhouse-connect") + (synopsis + "ClickHouse database core driver for Python, Pandas, and Superset") + (description + "This package provides a high performance core database driver for +connecting ClickHouse to Python, Pandas, and Superset.") + (license license:asl2.0))) + (define-public python-cligj (package (name "python-cligj") @@ -9411,6 +9441,28 @@ all the newest features of the standard @code{pathlib} can be used also on older Python versions.") (license license:expat))) +(define-public python-pathy + (package + (name "python-pathy") + (version "0.10.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "pathy" version)) + (sha256 + (base32 + "12v196q3rai33cfzrmb9pqfqv7ailngssjdrzdf8gzym9hdygmjc")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-dataclasses python-smart-open python-typer)) + (native-inputs (list python-mock python-pytest)) + (home-page "https://github.com/justindujardin/pathy") + (synopsis "Path interface for local and cloud bucket storage") + (description "Pathy is a python package (with type annotations) for +working with Cloud Bucket storage providers using a @code{pathlib} interface. +It provides @code{pathlib.Path} subclasses for local and cloud bucket +storage.") + (license license:asl2.0))) + (define-public python-importlib-resources (package (name "python-importlib-resources") @@ -10305,6 +10357,36 @@ you're careful. The @code{backcall} package provides a way of specifying the callback signature using a prototype function.") (license license:bsd-3))) +(define-public python-pubmed-parser + (package + (name "python-pubmed-parser") + (version "0.3.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/titipata/pubmed_parser") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "195cmjjg7xdwjj5455h78q7jnxnccia07a19xwndhlkxv7vk9v60")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-lxml + python-numpy + python-requests + python-six + python-unidecode)) + (native-inputs + (list python-pytest + python-pytest-cov)) + (home-page "https://github.com/titipata/pubmed_parser") + (synopsis "Parser for Pubmed Open-Access Subset and MEDLINE XML repository") + (description + "This package provides a Python parser for Pubmed Open-Access Subset and +MEDLINE XML repository.") + (license license:expat))) + (define-public python-pure-eval (package (name "python-pure-eval") @@ -15351,6 +15433,27 @@ provide an easy to use, pythonic and comprehensive Python interface to dialog. This allows one to make simple text-mode user interfaces on Unix-like systems") (license license:lgpl2.1))) +(define-public python-confection + (package + (name "python-confection") + (version "0.0.4") + (source (origin + (method url-fetch) + (uri (pypi-uri "confection" version)) + (sha256 + (base32 + "1ksfn10zhnpkcj3y0c3xs4dznvc062bk62x4c3ig0dd6bn4gbpdi")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-pydantic python-srsly + python-typing-extensions)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/explosion/confection") + (synopsis "Config system for Python") + (description "Confection is a lightweight library that offers a +configuration system letting you conveniently describe arbitrary trees of +objects.") + (license license:expat))) + (define-public python-configobj (package (name "python-configobj") @@ -16408,7 +16511,7 @@ enhancements to optimization and data fitting problems.") python-packaging python-pillow python-pyyaml - python-tornado + python-tornado-6 python-typing-extensions)) (native-inputs (list python-beautifulsoup4 @@ -17235,19 +17338,23 @@ checking library.") (define-public python-codespell (package (name "python-codespell") - (version "2.1.0") + (version "2.2.4") (source (origin (method url-fetch) (uri (pypi-uri "codespell" version)) (sha256 - (base32 "1r9y714cz8m894rxp7pyvicr1lw2iid24vz6fxbl5wzy8ibgxlqr")))) - (build-system python-build-system) + (base32 "0fp8ihlj8q23qdfryj5pq8srl85vn8k8p6gq3zg9qz957i3j0ihb")))) + (build-system pyproject-build-system) (inputs (list python-chardet)) (native-inputs - (list python-check-manifest python-flake8 python-pytest - python-pytest-cov python-pytest-dependency)) + (list python-flake8 + python-pygments + python-pytest + python-pytest-cov + python-pytest-dependency + python-tomli)) (arguments `(#:phases (modify-phases %standard-phases @@ -20481,6 +20588,59 @@ from the header, as well as section details and data available.") Mustache templating language renderer.") (license license:expat))) +(define-public python-duckdb + (package + (name "python-duckdb") + (version "0.8.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "duckdb" version)) + (sha256 + (base32 + "13y1gs565q51li5fi9m7fpf0sqns8frsaii6v95acwjhmdds73f6")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + '(list "--ignore=tests/slow/test_h2oai_arrow.py" + ;; Don't install anything, thank you. + "-k" "not test_install_non_existent_extension") + #:phases + #~(modify-phases %standard-phases + ;; Tests need this + (add-before 'check 'set-HOME + (lambda _ (setenv "HOME" "/tmp"))) + (add-before 'build 'set-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version) + (substitute* "setup.py" + (("\"setuptools_scm<7.0.0\",") "")))) + ;; Later versions of pybind replace "_" with "const_name". + (add-after 'unpack 'pybind-compatibility + (lambda _ + (with-directory-excursion "src/include/duckdb_python" + (substitute* '("python_objects.hpp" + "pyfilesystem.hpp" + "pybind11/conversions/pyconnection_default.hpp") + (("const_name") "_")))))))) + (native-inputs + (list pybind11 + python-fsspec + python-google-cloud-storage + python-mypy + python-numpy + python-pandas + python-psutil + python-pyarrow + python-pytest + python-pytest-runner + python-setuptools-scm)) + (home-page "https://www.duckdb.org") + (synopsis "DuckDB embedded database") + (description "DuckDB is an in-process SQL OLAP database management +system.") + (license license:expat))) + (define-public python-dulwich (package (name "python-dulwich") @@ -26647,32 +26807,29 @@ the syntactic logic to configure and launch jobs in an execution environment.") (define-public python-flit (package (name "python-flit") - (version "3.5.1") + (version "3.8.0") ;same as python-flit-core (source (origin (method url-fetch) (uri (pypi-uri "flit" version)) (sha256 - (base32 "04152qj46sqbnlrj7ch9p7svjrrlpzbk0qr39g2yr0s4f5vp6frf")))) - (build-system python-build-system) + (base32 "0dz9sp2zlhkmk6sm5gapbbb30f7xq3n3jn5zxx5pkp25ppsaiwnh")))) + (build-system pyproject-build-system) (arguments (list + #:test-flags + ;; These tests fail when FLIT_NO_NETWORK is set + '(list "-k" "not test_invalid_classifier \ +and not test_install_requires \ +and not test_install_requires_extra \ +and not test_validate_classifiers_private") #:phases #~(modify-phases %standard-phases - ;; XXX: PEP 517 manual build copied from python-isort. - (replace 'build - (lambda _ - (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) - (replace 'check + (add-before 'check 'pre-check (lambda* (#:key tests? inputs outputs #:allow-other-keys) (when tests? (setenv "HOME" "/tmp") - (setenv "FLIT_NO_NETWORK" "1")))) - (replace 'install - (lambda _ - (let ((whl (car (find-files "dist" "\\.whl$")))) - (invoke "pip" "--no-cache-dir" "--no-input" - "install" "--no-deps" "--prefix" #$output whl))))))) + (setenv "FLIT_NO_NETWORK" "1"))))))) (propagated-inputs (list python-pypa-build python-tomli-w @@ -31767,6 +31924,40 @@ uses the parsed regular expression, so you get a much more accurate result than trying to just split strings.") (license license:asl2.0))) +(define-public python-srsly + (package + (name "python-srsly") + (version "2.4.6") + (source (origin + (method url-fetch) + (uri (pypi-uri "srsly" version)) + (sha256 + (base32 + "0vsafkvk4g0p5m0dqrczqvlyza837i20xxmb24rrqk5s78r1zd27")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python" "setup.py" "build_ext" "--inplace")))))) + (propagated-inputs (list python-catalogue)) + (native-inputs + (list python-cython + python-pytest + python-pytest-timeout + python-mock + python-numpy + python-psutil)) + (home-page "https://github.com/explosion/srsly") + (synopsis "Serialization utilities for Python") + (description "This package bundles some of the best Python serialization +libraries into one standalone package, with a high-level API that makes it +easy to write code that's correct across platforms and Pythons.") + (license license:expat))) + (define-public python-pyperf (package (name "python-pyperf") diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 450bf933db..e025653338 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2866,14 +2866,16 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "2.21") + (version "2.22") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 - (base32 "0a5czn18clfnw0a9nd5v98ah4h47i32423s6jdf126ni4aj20ny2")))) - (properties `((upstream-name . "rmarkdown"))) + (base32 "1f47ccph09ilqlr0bnyrxkadja4ddp4klvb933aws3rya0cmaqy6")))) + (properties + `((upstream-name . "rmarkdown") + (updater-extra-propagated-inputs . ("pandoc")))) (build-system r-build-system) (propagated-inputs (list r-bslib @@ -4172,13 +4174,13 @@ vignettes.") (define-public r-mvtnorm (package (name "r-mvtnorm") - (version "1.1-3") + (version "1.2-0") (source (origin (method url-fetch) (uri (cran-uri "mvtnorm" version)) (sha256 (base32 - "0j14q2bkc14v35s5k03sw44zsssrd2qjljlwzj014qxs74hk0kpz")))) + "1q1bmsvd10iz003xlsd40dj5bhmy2069p88ydf9f4gj56mysnlpm")))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -4191,13 +4193,13 @@ t-probabilities, quantiles, random deviates and densities.") (define-public r-matrixstats (package (name "r-matrixstats") - (version "0.63.0") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "matrixStats" version)) (sha256 (base32 - "0pqz6mn5l7inh464yj45i6rf8ycab0zdvvjczwsv0bkl442bc060")))) + "0vxd7g1fm4x0f72bs1xfik1d4yklvpjdyg1hpx86pl8fwr86i1wl")))) (properties `((upstream-name . "matrixStats"))) (build-system r-build-system) (arguments @@ -4505,14 +4507,14 @@ data behind them) can be viewed and modified in a web browser.") (define-public r-biased-urn (package (name "r-biased-urn") - (version "2.0.9") + (version "2.0.10") (source (origin (method url-fetch) (uri (cran-uri "BiasedUrn" version)) (sha256 (base32 - "02bb81x1hfvhm6qlcvp88bdpm1fhqak9cjbqz1r7fhg2qfxjpims")))) + "0jv0zvz1zs34h12zdgn3lqmn7hfkk2z6fkwbd9mlyddf34rkvfqv")))) (properties `((upstream-name . "BiasedUrn"))) (build-system r-build-system) (home-page "https://www.agner.org/random/") diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index ab19c2dd8c..3b6af31b76 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -3475,37 +3475,6 @@ and JACK.") (home-page "https://obsproject.com") (license license:gpl2+))) -(define-public obs-spectralizer - (package - (name "obs-spectralizer") - (version "1.3.3") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/univrsal/spectralizer") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - - ;; Remove bundled Windows DLLs. - (snippet '(delete-file-recursively "fftw3")) - (modules '((guix build utils))) - - (sha256 - (base32 - "0q75cnyqydpvfda51zm9gxqj3wqr99ad0lxzjhw0ld67qvj1ag6i")))) - (build-system cmake-build-system) - (arguments - `(#:tests? #f - #:configure-flags - (list "-DGLOBAL_INSTALLATION=ON" "-DUSE_CMAKE_LIBDIR=ON"))) - (inputs (list obs fftw)) - (home-page "https://github.com/univrsal/spectralizer") - (synopsis "OBS plugin for audio visualization") - (description "This OBS plugins allows you to vizualize MPD and internal -OBS audio sources.") - (license license:gpl2))) - (define-public obs-websocket (package (name "obs-websocket") diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm index 500461fecf..af070526ec 100644 --- a/gnu/packages/vpn.scm +++ b/gnu/packages/vpn.scm @@ -20,7 +20,7 @@ ;;; Copyright © 2021 jgart <jgart@dismail.de> ;;; Copyright © 2022 Josselin Poiret <josselin.poiret@protonmail.ch> ;;; Copyright © 2022 Lu hui <luhux76@gmail.com> -;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2022 Jean-Pierre De Jesus DIAZ <me@jeandudey.tech> ;;; Copyright © 2022 Arun Isaac <arunisaac@systemreboot.net> ;;; @@ -677,35 +677,31 @@ the user specifically asks to proxy, so the @dfn{VPN} interface no longer (define-public openconnect (package - (name "openconnect") - (version "9.01") - (source (origin - (method url-fetch) - (uri (string-append "ftp://ftp.infradead.org/pub/openconnect/" - "openconnect-" version ".tar.gz")) - (sha256 - (base32 "1iz4j00031a5ircrx30lkiwf58yl9kc827m4ssck4yg963wgmmxk")))) - (build-system gnu-build-system) - (propagated-inputs - (list libxml2 gnutls zlib)) - (inputs - (list lz4 vpnc-scripts)) - (native-inputs - `(("gettext" ,gettext-minimal) - ("pkg-config" ,pkg-config))) - (arguments - `(#:configure-flags - `(,(string-append "--with-vpnc-script=" - (assoc-ref %build-inputs "vpnc-scripts") - "/etc/vpnc/vpnc-script")))) - (synopsis "Client for Cisco VPN") - (description - "OpenConnect is a client for Cisco's AnyConnect SSL VPN, which is -supported by the ASA5500 Series, by IOS 12.4(9)T or later on Cisco SR500, -870, 880, 1800, 2800, 3800, 7200 Series and Cisco 7301 Routers, -and probably others.") - (license license:lgpl2.1) - (home-page "https://www.infradead.org/openconnect/"))) + (name "openconnect") + (version "9.12") + (source (origin + (method url-fetch) + (uri (string-append "ftp://ftp.infradead.org/pub/openconnect/" + "openconnect-" version ".tar.gz")) + (sha256 + (base32 "0gj1nba1pygvcjasqdakxxnx94dwx3l4hzj0dvipbzjdmbixrgm2")))) + (build-system gnu-build-system) + (arguments + (list #:configure-flags + #~(list (string-append "--with-vpnc-script=" + (search-input-file %build-inputs + "etc/vpnc/vpnc-script"))))) + (native-inputs (list gettext-minimal pkg-config)) + (inputs (list lz4 vpnc-scripts)) + (propagated-inputs (list libxml2 gnutls zlib)) + (synopsis "Client for Cisco VPN") + (description + "OpenConnect is a client for Cisco's AnyConnect SSL VPN, which is +supported by the ASA5500 Series, by IOS 12.4(9)T or later on Cisco SR500, 870, +880, 1800, 2800, 3800, 7200 Series and Cisco 7301 Routers, and probably +others.") + (license license:lgpl2.1) + (home-page "https://www.infradead.org/openconnect/"))) (define-public openconnect-sso (package diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index 1fe5ef5c82..7d1f61be53 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -724,7 +724,7 @@ is fully configurable and extensible in Common Lisp.") (define-public lagrange (package (name "lagrange") - (version "1.15.9") + (version "1.16.3") (source (origin (method url-fetch) @@ -732,7 +732,7 @@ is fully configurable and extensible in Common Lisp.") (string-append "https://git.skyjake.fi/skyjake/lagrange/releases/" "download/v" version "/lagrange-" version ".tar.gz")) (sha256 - (base32 "19pn5nnlskyj7w61s9vg5c0vb0hpdyalj3m8znvs4lgw3463ijs3")) + (base32 "1kmhxacka0rixxv1r5vqjhxmdxll73b5w5ja18m1qpbk2sk00bg8")) (modules '((guix build utils))) (snippet '(begin diff --git a/gnu/packages/wxwidgets.scm b/gnu/packages/wxwidgets.scm index e6194e6f50..d0c323e30c 100644 --- a/gnu/packages/wxwidgets.scm +++ b/gnu/packages/wxwidgets.scm @@ -112,6 +112,7 @@ libsecret libsm libtiff + libxtst ;for wxUIActionSimulator mesa pcre2 sdl2 diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 462ac082f5..b8671d1cf6 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -41,7 +41,7 @@ ;;; Copyright © 2020 Gabriel Arazas <foo.dogsquared@gmail.com> ;;; Copyright © 2020 James Smith <jsubuntuxp@disroot.org> ;;; Copyright © 2020 B. Wilson <elaexuotee@wilsonb.com> -;;; Copyright © 2020, 2021 Zheng Junjie <873216071@qq.com> +;;; Copyright © 2020, 2021, 2023 Zheng Junjie <873216071@qq.com> ;;; Copyright © 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2021, 2022 Nicolas Goaziou <mail@nicolasgoaziou.fr> ;;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz> @@ -768,7 +768,28 @@ and Matrox.") (base32 "1q700h9dqcm3zl6c3gj0qxxjcx6ibw2c51wjijydhwdcm26v5mqm")))) (build-system gnu-build-system) - (arguments '(#:configure-flags '("--disable-static"))) + (arguments + `(#:configure-flags + '("--disable-static") + ,@(if (and (target-riscv64?) + (%current-target-system)) + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'update-config-scripts + (lambda* (#:key inputs native-inputs #:allow-other-keys) + ;; Replace outdated config.guess and config.sub. + (for-each (lambda (file) + (install-file + (search-input-file + (or native-inputs inputs) + (string-append "/bin/" file)) "./config-aux")) + '("config.guess" "config.sub")))))) + '()))) + (native-inputs + (if (and (target-riscv64?) + (%current-target-system)) + (list config) + '())) (home-page "https://bitmath.org/code/mtdev/") (synopsis "Multitouch protocol translation library") (description "Mtdev is a stand-alone library which transforms all diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index 2eb90ed4b2..31dc750101 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -185,7 +185,7 @@ storage system.") (define-public libxfce4ui (package (name "libxfce4ui") - (version "4.18.3") + (version "4.18.4") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/xfce/" @@ -193,7 +193,7 @@ storage system.") name "-" version ".tar.bz2")) (sha256 (base32 - "1g8a067xbazgh0qc25nc7k1zc6aqmznhh4vy5wnn3aykxrpa98xg")))) + "0k6b8al8cy2w5zi8iywkzjsz2cgiz9r8ir2dflzxw9kdgiwzxvl7")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -398,7 +398,7 @@ management D-Bus specification.") (define-public xfce4-panel (package (name "xfce4-panel") - (version "4.18.3") + (version "4.18.4") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/xfce/" @@ -406,7 +406,7 @@ management D-Bus specification.") name "-" version ".tar.bz2")) (sha256 (base32 - "06sy6vjydx1p8rx8z94ya6szvmvyarijl5x0pm5ij4cqbihviq2a")) + "0m7vmk7rc2sjfqba0flgnw77kn1j222xqs7r86bpg8sf1614yc1j")) (patches (search-patches "xfce4-panel-plugins.patch")))) (build-system gnu-build-system) (arguments @@ -498,7 +498,7 @@ matching them against regular expressions.") (define-public xfce4-pulseaudio-plugin (package (name "xfce4-pulseaudio-plugin") - (version "0.4.6") + (version "0.4.7") (source (origin (method url-fetch) @@ -507,7 +507,7 @@ matching them against regular expressions.") (version-major+minor version) "/" "xfce4-pulseaudio-plugin-" version ".tar.bz2")) (sha256 - (base32 "05k02ilvffddgbp6in9wpjvg6vzlcxxw09nmj29hzba44klc04bf")))) + (base32 "0b4fjvrrah0b97cbv8ds7r6cwnj392ya2r7703ixf724f43hkpah")))) (build-system gnu-build-system) (native-inputs (list intltool pkg-config dbus-glib dbus)) @@ -630,7 +630,7 @@ your system in categories, so you can quickly find and launch them.") (define-public xfce4-session (package (name "xfce4-session") - (version "4.18.2") + (version "4.18.3") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/xfce/" @@ -638,7 +638,7 @@ your system in categories, so you can quickly find and launch them.") "xfce4-session-" version ".tar.bz2")) (sha256 (base32 - "12pbppyhg0jdwswwk59fffh2n5ckpfvwc999zkg1l2f2skl7zzq1")) + "1v4lfgz7az8iqp01a1ww8sxxjfmr676bijhrhw4r6r7cjvh96brq")) (modules '((guix build utils))) (snippet '(begin @@ -1222,7 +1222,7 @@ system resources, while still being visually appealing and user friendly.") (define-public xfce4-power-manager (package (name "xfce4-power-manager") - (version "4.18.1") + (version "4.18.2") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/xfce/" @@ -1230,7 +1230,7 @@ system resources, while still being visually appealing and user friendly.") "xfce4-power-manager-" version ".tar.bz2")) (sha256 (base32 - "00zz9bhzsf2vww8mym9c093sz7va5716qb6kvdvn6ldp9h6b223b")))) + "0kfzvhb1hnr16fcplm7bdpp4fcxr3irzq3w4q0lpbc5n6kaqyq71")))) (build-system gnu-build-system) (native-inputs (list pkg-config intltool)) @@ -1453,7 +1453,7 @@ of data to either CD/DVD/BD.") (define-public xfce4-screenshooter (package (name "xfce4-screenshooter") - (version "1.10.3") + (version "1.10.4") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/apps/" @@ -1463,7 +1463,7 @@ of data to either CD/DVD/BD.") version ".tar.bz2")) (sha256 (base32 - "061qixpz8krvpixs6ickl9ha5m0pb078rdd5fjifrkxy8yc1am54")))) + "1534h1a3a8b9pl20zpccaifrlsrbsihdcdjndn9nmqalgrl9kwd2")))) (build-system gnu-build-system) (native-inputs (list pkg-config intltool @@ -1482,7 +1482,7 @@ A plugin for the Xfce panel is also available.") (define-public xfce4-screensaver (package (name "xfce4-screensaver") - (version "4.18.1") + (version "4.18.2") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/apps/" @@ -1492,7 +1492,7 @@ A plugin for the Xfce panel is also available.") version ".tar.bz2")) (sha256 (base32 - "0p2an3g5jlhmr60if319cfgkqacziym52csj7dfwq64assmyhcdp")))) + "161bdsvkbknaf9fpz4b1r4amnm72hzfmx9c6krg2396k2k2d5z74")))) (build-system gnu-build-system) (arguments `(#:phases diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index d6c388739f..e1a7cf96f9 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -34,6 +34,7 @@ ;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be> ;;; Copyright © 2021 qblade <qblade@protonmail.com> ;;; Copyright © 2021 Lu Hui <luhux76@gmail.com> +;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -4493,13 +4494,30 @@ cannot be adequately worked around on the client side of the wire.") "012jpyj7xfm653a9jcfqbzxyywdmwb2b5wr1dwylx14f3f54jma6")))) (build-system gnu-build-system) (arguments - '(#:configure-flags '("--disable-static"))) + `(#:configure-flags '("--disable-static") + ,@(if (and (target-riscv64?) + (%current-target-system)) + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'update-config + (lambda* (#:key native-inputs inputs #:allow-other-keys) + (for-each (lambda (file) + (install-file + (search-input-file + (or native-inputs inputs) + (string-append "/bin/" file)) ".")) + '("config.guess" "config.sub")))))) + '()))) (propagated-inputs (list libxi xorgproto)) (inputs - (list libx11)) + (list libx11)) (native-inputs - (list pkg-config)) + (append (if (and (target-riscv64?) + (%current-target-system)) + (list config) + '()) + (list pkg-config))) (home-page "https://www.x.org/wiki/") (synopsis "Xorg library for Xtest and Record extensions") (description @@ -5620,11 +5638,29 @@ The XCB util-renderutil module provides the following library: "0gra7hfyxajic4mjd63cpqvd20si53j1q3rbdlkqkahfciwq3gr8")))) (build-system gnu-build-system) (arguments - '(#:configure-flags '("--disable-static"))) + `(#:configure-flags '("--disable-static") + ,@(if (and (target-riscv64?) + (%current-target-system)) + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'update-config-scripts + (lambda* (#:key inputs native-inputs #:allow-other-keys) + ;; Replace outdated config.guess and config.sub. + (for-each (lambda (file) + (install-file + (search-input-file + (or native-inputs inputs) + (string-append "/bin/" file)) ".")) + '("config.guess" "config.sub")))))) + '()))) (propagated-inputs (list libxcb)) (native-inputs - (list m4 pkg-config)) + (append (if (and (target-riscv64?) + (%current-target-system)) + (list config) + '()) + (list m4 pkg-config))) (home-page "https://cgit.freedesktop.org/xcb/util-wm/") (synopsis "Client and window-manager helpers for ICCCM and EWMH") (description diff --git a/gnu/services.scm b/gnu/services.scm index a990d297c9..109e050a23 100644 --- a/gnu/services.scm +++ b/gnu/services.scm @@ -51,6 +51,7 @@ #:use-module (srfi srfi-26) #:use-module (srfi srfi-34) #:use-module (srfi srfi-35) + #:use-module (srfi srfi-71) #:use-module (ice-9 vlist) #:use-module (ice-9 match) #:autoload (ice-9 pretty-print) (pretty-print) @@ -297,35 +298,67 @@ singleton service type NAME, of which the returned service is an instance." (description "This is a simple service.")))) (service type value))) -(define (%delete-service kind services) - (let loop ((found #f) - (return '()) - (services services)) +(define-syntax clause-alist + (syntax-rules (=> delete) + "Build an alist of clauses. Each element has the form (KIND PROC LOC) +where PROC is the service transformation procedure to apply for KIND, and LOC +is the source location information." + ((_ (delete kind) rest ...) + (cons (list kind + (lambda (service) + #f) + (current-source-location)) + (clause-alist rest ...))) + ((_ (kind param => exp ...) rest ...) + (cons (list kind + (lambda (svc) + (let ((param (service-value svc))) + (service (service-kind svc) + (begin exp ...)))) + (current-source-location)) + (clause-alist rest ...))) + ((_) + '()))) + +(define (apply-clauses clauses services) + "Apply CLAUSES, an alist as returned by 'clause-alist', to SERVICES, a list +of services. Use each clause at most once; raise an error if a clause was not +used." + (let loop ((services services) + (clauses clauses) + (result '())) (match services - ('() - (if found - (values return found) - (raise (formatted-message + (() + (match clauses + (() ;all clauses fired, good + (reverse result)) + (((kind _ properties) _ ...) ;one or more clauses didn't match + (raise (make-compound-condition + (condition + (&error-location + (location (source-properties->location properties)))) + (formatted-message (G_ "modify-services: service '~a' not found in service list") - (service-type-name kind))))) - ((service . rest) - (if (eq? (service-kind service) kind) - (loop service return rest) - (loop found (cons service return) rest)))))) - -(define-syntax %apply-clauses - (syntax-rules (=> delete) - ((_ ((delete kind) . rest) services) - (%apply-clauses rest (%delete-service kind services))) - ((_ ((kind param => exp ...) . rest) services) - (call-with-values (lambda () (%delete-service kind services)) - (lambda (svcs found) - (let ((param (service-value found))) - (cons (service (service-kind found) - (begin exp ...)) - (%apply-clauses rest svcs)))))) - ((_ () services) - services))) + (service-type-name kind))))))) + ((head . tail) + (let ((service clauses + (fold2 (lambda (clause service remainder) + (if service + (match clause + ((kind proc properties) + (if (eq? kind (service-kind service)) + (values (proc service) remainder) + (values service + (cons clause remainder))))) + (values #f (cons clause remainder)))) + head + '() + clauses))) + (loop tail + (reverse clauses) + (if service + (cons service result) + result))))))) (define-syntax modify-services (syntax-rules () @@ -358,11 +391,9 @@ Consider this example: It changes the configuration of the GUIX-SERVICE-TYPE instance, and that of all the MINGETTY-SERVICE-TYPE instances, and it deletes instances of the -UDEV-SERVICE-TYPE. - -This is a shorthand for (filter-map (lambda (svc) ...) %base-services)." - ((_ services . clauses) - (%apply-clauses clauses services)))) +UDEV-SERVICE-TYPE." + ((_ services clauses ...) + (apply-clauses (clause-alist clauses ...) services)))) ;;; diff --git a/gnu/services/desktop.scm b/gnu/services/desktop.scm index 64eac1117d..a63748b652 100644 --- a/gnu/services/desktop.scm +++ b/gnu/services/desktop.scm @@ -1839,10 +1839,12 @@ applications needing access to be root.") ;; Screen lockers are a pretty useful thing and these are small. (service screen-locker-service-type (screen-locker-configuration - "slock" (file-append slock "/bin/slock") #f)) + (name "slock") + (program (file-append slock "/bin/slock")))) (service screen-locker-service-type (screen-locker-configuration - "xlock" (file-append xlockmore "/bin/xlock") #f)) + (name "xlock") + (program (file-append xlockmore "/bin/xlock")))) ;; Add udev rules for MTP devices so that non-root users can access ;; them. diff --git a/gnu/services/xorg.scm b/gnu/services/xorg.scm index 8b6080fd26..f8cf9f25b6 100644 --- a/gnu/services/xorg.scm +++ b/gnu/services/xorg.scm @@ -13,6 +13,7 @@ ;;; Copyright © 2021 Josselin Poiret <josselin.poiret@protonmail.ch> ;;; Copyright © 2022 Chris Marusich <cmmarusich@gmail.com> ;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2023 muradm <mail@muradm.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -112,6 +113,8 @@ screen-locker-configuration-name screen-locker-configuration-program screen-locker-configuration-allow-empty-password? + screen-locker-configuration-using-pam? + screen-locker-configuration-using-setuid? screen-locker-service-type screen-locker-service ; deprecated @@ -703,30 +706,38 @@ reboot_cmd " shepherd "/sbin/reboot\n" ;;; Screen lockers & co. ;;; -(define-record-type <screen-locker-configuration> - (screen-locker-configuration name program allow-empty-password?) - screen-locker-configuration? - (name screen-locker-configuration-name) ;string - (program screen-locker-configuration-program) ;gexp +(define-configuration/no-serialization screen-locker-configuration + (name + string + "Name of the screen locker.") + (program + file-like + "Path to the executable for the screen locker as a G-Expression.") (allow-empty-password? - screen-locker-configuration-allow-empty-password?)) ;Boolean - -(define-deprecated/public-alias - screen-locker - screen-locker-configuration) - -(define-deprecated/public-alias - screen-locker? - screen-locker-configuration?) - -(define screen-locker-pam-services - (match-lambda - (($ <screen-locker-configuration> name _ empty?) - (list (unix-pam-service name - #:allow-empty-passwords? empty?))))) + (boolean #f) + "Whether to allow empty passwords.") + (using-pam? + (boolean #t) + "Whether to setup PAM entry.") + (using-setuid? + (boolean #t) + "Whether to setup program as setuid binary.")) + +(define (screen-locker-pam-services config) + (match-record config <screen-locker-configuration> + (name allow-empty-password? using-pam?) + (if using-pam? + (list (unix-pam-service name + #:allow-empty-passwords? + allow-empty-password?)) + '()))) -(define screen-locker-setuid-programs - (compose list file-like->setuid-program screen-locker-configuration-program)) +(define (screen-locker-setuid-programs config) + (match-record config <screen-locker-configuration> + (name program using-setuid?) + (if using-setuid? + (list (file-like->setuid-program program)) + '()))) (define screen-locker-service-type (service-type (name 'screen-locker) @@ -740,6 +751,9 @@ reboot_cmd " shepherd "/sbin/reboot\n" the graphical server by making it setuid-root, so it can authenticate users, and by creating a PAM service for it."))) +(define (screen-locker-generate-doc) + (configuration->documentation 'screen-locker-configuration)) + (define-deprecated (screen-locker-service package #:optional (program (package-name package)) @@ -755,9 +769,10 @@ for it. For example: makes the good ol' XlockMore usable." (service screen-locker-service-type - (screen-locker-configuration program - (file-append package "/bin/" program) - allow-empty-passwords?))) + (screen-locker-configuration + (name program) + (program (file-append package "/bin/" program)) + (allow-empty-password? allow-empty-passwords?)))) ;;; |