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01/01: Merge branch 'master' into core-updates
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From: |
guix-commits |
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Subject: |
01/01: Merge branch 'master' into core-updates |
|
Date: |
Sun, 6 Jun 2021 15:36:41 -0400 (EDT) |
mbakke pushed a commit to branch core-updates
in repository guix.
commit 8d59c262ada2e2167196a8fb8cbebd9c329a79dd
Merge: e7f0835 a068ed6
Author: Marius Bakke <marius@gnu.org>
AuthorDate: Sun Jun 6 21:16:32 2021 +0200
Merge branch 'master' into core-updates
Conflicts:
gnu/local.mk
gnu/packages/algebra.scm
gnu/packages/bioinformatics.scm
gnu/packages/curl.scm
gnu/packages/docbook.scm
gnu/packages/emacs-xyz.scm
gnu/packages/maths.scm
gnu/packages/plotutils.scm
gnu/packages/python-web.scm
gnu/packages/python-xyz.scm
gnu/packages/radio.scm
gnu/packages/readline.scm
gnu/packages/tls.scm
gnu/packages/xml.scm
gnu/packages/xorg.scm
Makefile.am | 3 +
configure.ac | 6 +-
doc/contributing.texi | 36 +-
doc/guix.texi | 58 +-
etc/guix-daemon.cil.in | 7 +-
etc/news.scm | 35 +
gnu/bootloader/u-boot.scm | 7 +-
gnu/build/linux-boot.scm | 16 +-
gnu/local.mk | 13 +-
gnu/machine/ssh.scm | 41 +-
gnu/packages/admin.scm | 42 +-
gnu/packages/algebra.scm | 4 +-
gnu/packages/animation.scm | 78 +-
gnu/packages/aspell.scm | 4 +-
gnu/packages/astronomy.scm | 4 +-
gnu/packages/audio.scm | 32 +-
gnu/packages/axoloti.scm | 5 +
gnu/packages/benchmark.scm | 19 +-
gnu/packages/bioconductor.scm | 4065 +++++++++++++++-----
gnu/packages/bioinformatics.scm | 3028 +++++----------
gnu/packages/check.scm | 9 +-
gnu/packages/chromium.scm | 31 +-
gnu/packages/ci.scm | 8 +-
gnu/packages/cluster.scm | 45 +-
gnu/packages/compression.scm | 14 +-
gnu/packages/cran.scm | 904 ++++-
gnu/packages/crates-graphics.scm | 119 +-
gnu/packages/crates-io.scm | 1664 +++++++-
gnu/packages/crypto.scm | 12 +-
gnu/packages/cryptsetup.scm | 26 +-
gnu/packages/curl.scm | 15 +
gnu/packages/databases.scm | 20 +-
gnu/packages/dictionaries.scm | 5 +-
gnu/packages/diffoscope.scm | 4 +-
gnu/packages/disk.scm | 50 +-
gnu/packages/django.scm | 17 +-
gnu/packages/dns.scm | 3 +
gnu/packages/education.scm | 38 +
gnu/packages/emacs-xyz.scm | 1660 ++++----
gnu/packages/emacs.scm | 12 +-
gnu/packages/emulators.scm | 404 +-
gnu/packages/engineering.scm | 4 +-
gnu/packages/entr.scm | 5 +-
gnu/packages/file-systems.scm | 37 +-
gnu/packages/fltk.scm | 6 +-
gnu/packages/fonts.scm | 28 +-
gnu/packages/fpga.scm | 7 +-
gnu/packages/freeipmi.scm | 6 +-
gnu/packages/ftp.scm | 4 +-
gnu/packages/game-development.scm | 4 +-
gnu/packages/games.scm | 72 +-
gnu/packages/gcc.scm | 4 +-
gnu/packages/gnome.scm | 20 +-
gnu/packages/gnucash.scm | 12 +-
gnu/packages/gnuzilla.scm | 63 +-
gnu/packages/guile-xyz.scm | 39 +-
gnu/packages/guile.scm | 4 +-
gnu/packages/hardware.scm | 4 +-
gnu/packages/i2p.scm | 74 +-
gnu/packages/icu4c.scm | 16 +
gnu/packages/image-processing.scm | 5 +
gnu/packages/image.scm | 4 +-
gnu/packages/installers.scm | 3 +-
gnu/packages/jami.scm | 13 +-
gnu/packages/julia-jll.scm | 2667 +++++++++++++
gnu/packages/julia-xyz.scm | 1334 +++++--
gnu/packages/kde.scm | 4 +-
gnu/packages/libreoffice.scm | 4 +-
gnu/packages/linux.scm | 77 +-
gnu/packages/lisp-xyz.scm | 458 ++-
gnu/packages/lisp.scm | 18 +-
gnu/packages/llvm.scm | 10 +-
gnu/packages/lxqt.scm | 211 +-
gnu/packages/mail.scm | 19 +-
gnu/packages/markup.scm | 6 +-
gnu/packages/maths.scm | 179 +-
gnu/packages/mc.scm | 32 +-
gnu/packages/mes.scm | 5 +-
gnu/packages/messaging.scm | 41 +-
gnu/packages/monitoring.scm | 30 +-
gnu/packages/mpd.scm | 4 +-
gnu/packages/mtools.scm | 4 +-
gnu/packages/music.scm | 93 +-
gnu/packages/networking.scm | 190 +-
gnu/packages/ocaml.scm | 789 ++--
gnu/packages/package-management.scm | 46 +-
gnu/packages/parallel.scm | 36 +-
gnu/packages/patches/amule-crypto-6.patch | 45 -
...s-geiser-autoload-activate-implementation.patch | 26 -
.../patches/emacs-geiser-guile-auto-activate.patch | 34 -
gnu/packages/patches/freebayes-devendor-deps.patch | 152 -
.../lksctp-tools-1.0.18-fix-header-file-name.patch | 32 -
.../patches/minimap2-aarch64-support.patch | 52 -
.../patches/mosaicatcher-unbundle-htslib.patch | 49 +
gnu/packages/patches/nsis-source-date-epoch.patch | 23 +
.../patches/ppsspp-disable-upgrade-and-gold.patch | 148 +-
gnu/packages/patches/wgetpaste-update-bpaste.patch | 27 -
gnu/packages/pep.scm | 143 +-
gnu/packages/perl.scm | 156 +-
gnu/packages/php.scm | 4 +-
gnu/packages/protobuf.scm | 10 +-
gnu/packages/python-check.scm | 39 +-
gnu/packages/python-science.scm | 86 +
gnu/packages/python-web.scm | 40 +-
gnu/packages/python-xyz.scm | 391 +-
gnu/packages/python.scm | 4 +-
gnu/packages/racket.scm | 6 +-
gnu/packages/radio.scm | 434 ++-
gnu/packages/readline.scm | 28 +-
gnu/packages/rsync.scm | 41 +-
gnu/packages/rust-apps.scm | 67 +-
gnu/packages/security-token.scm | 46 +
gnu/packages/sequoia.scm | 74 -
gnu/packages/serialization.scm | 4 +-
gnu/packages/shells.scm | 4 +-
gnu/packages/smalltalk.scm | 15 +-
gnu/packages/sphinx.scm | 56 +-
gnu/packages/statistics.scm | 163 +-
gnu/packages/suckless.scm | 8 +-
gnu/packages/telephony.scm | 6 +-
gnu/packages/text-editors.scm | 11 +-
gnu/packages/tls.scm | 23 +-
gnu/packages/tryton.scm | 239 +-
gnu/packages/version-control.scm | 14 +-
gnu/packages/video.scm | 125 +-
gnu/packages/vim.scm | 2 +-
gnu/packages/virtualization.scm | 30 +
gnu/packages/vnc.scm | 4 +-
gnu/packages/web-browsers.scm | 22 +-
gnu/packages/web.scm | 28 +-
gnu/packages/wget.scm | 20 +-
gnu/packages/xdisorg.scm | 79 +-
gnu/packages/xiph.scm | 39 +-
gnu/packages/xml.scm | 21 +-
gnu/packages/xorg.scm | 31 +-
gnu/services/cuirass.scm | 12 +-
gnu/services/dns.scm | 10 +-
gnu/services/networking.scm | 3 +-
gnu/services/vpn.scm | 4 +-
gnu/tests/linux-modules.scm | 13 +-
gnu/tests/web.scm | 14 +-
guix/build-system/r.scm | 2 +-
guix/ci.scm | 25 +-
guix/download.scm | 1 +
guix/git-download.scm | 79 +-
guix/gnu-maintenance.scm | 32 +-
guix/hg-download.scm | 24 +-
guix/import/cran.scm | 4 +-
guix/import/egg.scm | 352 ++
guix/import/hackage.scm | 27 +-
guix/import/opam.scm | 4 +-
guix/licenses.scm | 8 +-
guix/lint.scm | 171 +-
guix/profiles.scm | 5 +-
guix/progress.scm | 16 +-
guix/scripts/archive.scm | 3 +
guix/scripts/build.scm | 3 +
guix/scripts/copy.scm | 9 +-
guix/scripts/deploy.scm | 12 +-
guix/scripts/edit.scm | 4 +-
guix/scripts/environment.scm | 3 +
guix/scripts/graph.scm | 5 +-
guix/scripts/import.scm | 4 +-
guix/scripts/import/egg.scm | 107 +
guix/scripts/package.scm | 8 +
guix/scripts/publish.scm | 160 +-
guix/scripts/substitute.scm | 11 +-
guix/store.scm | 16 +-
guix/swh.scm | 20 +-
guix/ui.scm | 60 +-
po/guix/POTFILES.in | 3 +
tests/egg.scm | 132 +
tests/gnu-maintenance.scm | 3 +-
tests/hackage.scm | 7 +-
tests/lint.scm | 55 +-
tests/opam.scm | 4 +-
176 files changed, 16696 insertions(+), 7094 deletions(-)
diff --cc gnu/local.mk
index fdd1227,153f6ee..890227c
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@@ -40,8 -40,8 +40,9 @@@
# Copyright © 2020 Malte Frank Gerdes <mate.f.gerdes@gmail.com>
# Copyright © 2020 Vinicius Monego <monego@posteo.net>
# Copyright © 2021 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
+# Copyright © 2021 Greg Hogan <code@greghogan.com>
# Copyright © 2021 Philip McGrath <philip@philipmcgrath.com>
+ # Copyright © 2021 Arun Isaac <arunisaac@systemreboot.net>
#
# This file is part of GNU Guix.
#
@@@ -1018,8 -1018,7 +1019,7 @@@ dist_patch_DATA =
%D%/packages/patches/fpc-reproducibility.patch \
%D%/packages/patches/fplll-std-fenv.patch \
%D%/packages/patches/freedink-engine-fix-sdl-hints.patch \
- %D%/packages/patches/freebayes-devendor-deps.patch \
+ %D%/packages/patches/freeglut-gcc-compat.patch \
%D%/packages/patches/freeimage-unbundle.patch \
%D%/packages/patches/fuse-overlapping-headers.patch
\
%D%/packages/patches/gajim-honour-GAJIM_PLUGIN_PATH.patch \
@@@ -1439,7 -1467,7 +1438,8 @@@
%D%/packages/patches/network-manager-plugin-path.patch \
%D%/packages/patches/nginx-socket-cloexec.patch \
%D%/packages/patches/nsis-env-passthru.patch \
+ %D%/packages/patches/nsis-source-date-epoch.patch \
+ %D%/packages/patches/nss-getcwd-nonnull.patch \
%D%/packages/patches/nss-increase-test-timeout.patch \
%D%/packages/patches/nss-3.56-pkgconfig.patch \
%D%/packages/patches/ntfs-3g-CVE-2019-9755.patch \
diff --cc gnu/packages/bioinformatics.scm
index fc2fc86,1e38c6e..64fc617
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@@ -12528,7 -11352,23 +11290,22 @@@ implementation differs in these ways
(delete-file "scanpy/tests/test_preprocessing.py")
(delete-file "scanpy/tests/test_read_10x.py")
+ ;; The following tests need anndata.tests, which aren't included
+ ;; in the final python-anndata package.
+ (delete-file "scanpy/tests/test_combat.py")
+ (delete-file "scanpy/tests/test_embedding_plots.py")
+ (delete-file "scanpy/tests/test_normalization.py")
+ (delete-file "scanpy/tests/test_pca.py")
+ (delete-file "scanpy/tests/external/test_scrublet.py")
+
+ ;; The following tests requires 'scanorama', which isn't
+ ;; packaged yet.
+ (delete-file "scanpy/tests/external/test_scanorama_integrate.py")
+
+ (setenv "PYTHONPATH"
+ (string-append (getcwd) ":"
+ (getenv "PYTHONPATH")))
- (invoke "pytest")
- #t)))))
+ (invoke "pytest"))))))
(propagated-inputs
`(("python-anndata" ,python-anndata)
("python-h5py" ,python-h5py)
diff --cc gnu/packages/curl.scm
index de92650,76b9b98..1075fe9
--- a/gnu/packages/curl.scm
+++ b/gnu/packages/curl.scm
@@@ -53,7 -53,8 +53,8 @@@
(define-public curl
(package
(name "curl")
+ (replacement curl-7.77.0)
- (version "7.74.0")
+ (version "7.76.1")
(source (origin
(method url-fetch)
(uri (string-append "https://curl.haxx.se/download/curl-";
@@@ -142,9 -143,29 +143,23 @@@ tunneling, and so on."
"See COPYING in the distribution."))
(home-page "https://curl.haxx.se/";)))
-;; This package exists mainly to bootstrap CMake. It must not depend on
-;; anything that uses cmake-build-system.
(define-public curl-minimal
- (hidden-package
- (package/inherit
- curl
- (name "curl-minimal")
- (inputs (alist-delete "openldap" (package-inputs curl))))))
+ (deprecated-package "curl-minimal" curl))
+ (define-public curl-7.77.0
+ (package
+ (inherit curl)
+ (version "7.77.0")
+ (source
+ (origin
+ (inherit (package-source curl))
+ (uri (string-append "https://curl.haxx.se/download/curl-";
+ version ".tar.xz"))
+ (patches (search-patches "curl-7.76-use-ssl-cert-env.patch"))
+ (sha256
+ (base32
+ "0jsrc97vbghvljic997r9nypc9qqddcil2lzvv032br8ahn5hr0g"))))))
+
(define-public kurly
(package
(name "kurly")
diff --cc gnu/packages/engineering.scm
index 180122e,981dd9e..338510d
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@@ -2752,10 -2752,12 +2752,10 @@@ GUI."
".tar.gz"))
(sha256
(base32
- "0qnz7lc681nxa16rw9n9q4spy9fas6m2adrpb49imh34bgdgh77n"))))
+ "06qgry1pal2vampmbmc1lzlhf1qnjkd8py781r5h020v981n6y5s"))))
(build-system gnu-build-system)
;; The GUI, which we elide, requires tcl and tk.
- (native-inputs `(;; Requires bison 3.6+ but we currently only have 3.5.
- ;; Bison 3.6 will be available in the next core update.
- ("bison-3.6" ,bison-3.6)
+ (native-inputs `(("bison" ,bison)
("clisp" ,clisp)
("dejagnu" ,dejagnu)
("flex" ,flex)
diff --cc gnu/packages/gnome.scm
index 2cb03a7,2f579a2..ca573d5
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@@ -1117,10 -1117,11 +1118,10 @@@ freedesktop.org desktop notification sp
"mm-common-" version ".tar.xz"))
(sha256
(base32
- "07b4s5ckcz9q5gwx8vchim19mhfgl8wysqwi30pndks3m4zrzad2"))))
+ "1x8yvjy0yg17qyhmqws8xh2k8dvzrhpwqz7j1cfwzalrb1i9c5g8"))))
(build-system meson-build-system)
(arguments
- `(#:meson ,meson-0.55
- #:phases
+ `(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch
(lambda* (#:key inputs #:allow-other-keys)
@@@ -1416,8 -1418,10 +1418,8 @@@ and implementation of UPnP A/V profiles
name "-" version ".tar.xz"))
(sha256
(base32
- "0gc10imyabk57ar54m0qzms0x9dnmkymhkzyk8w1aj3y4lby0yx5"))))
- (build-system gnu-build-system)
+ "1mlw1qgj8nkd9ll6b6h54r1gfdy3zp8a8xqz7qfyfaj85jjgbph7"))))
+ (build-system meson-build-system)
- (arguments
- `(#:meson ,meson-next))
(native-inputs
`(("glib:bin" ,glib "bin")
("pkg-config" ,pkg-config)))
diff --cc gnu/packages/gnuzilla.scm
index 212f684,c63809c..59f8a58
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@@ -1595,9 -1595,9 +1595,9 @@@ standards of the IceCat project."
(file-name (string-append "thunderbird-" version "-checkout"))
(sha256
(base32
- "18658r4b1f5p8jcz68l31z29ny73lic0br7gc827m72nfc85wqz3")))))
+ "10l042dd7b8rvla0cbiks5kjrz2b28yy7hr8sr169wlx202hxa01")))))
("autoconf" ,autoconf-2.13)
- ("cargo" ,rust-1.41 "cargo")
+ ("cargo" ,rust "cargo")
("clang" ,clang)
("llvm" ,llvm)
("nasm" ,nasm)
diff --cc gnu/packages/maths.scm
index d7ba5fc,e78c5df..4b33056
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@@ -26,9 -26,9 +26,9 @@@
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
-;;; Copyright © 2018, 2020 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018, 2020, 2021 Marius Bakke <marius@gnu.org>
;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
- ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
+ ;;; Copyright © 2018, 2021 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
;;; Copyright © 2019, 2021 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
@@@ -4719,10 -4727,12 +4753,11 @@@ set."
(with-directory-excursion "docs"
(for-each (lambda (base)
(install-file (string-append base ".pdf") docdir)
- (copy-recursively base docdir)) ; html docs
- '("HYPRE_usr_manual"
- "HYPRE_ref_manual")))
- #t))))))
+ (copy-recursively (string-append base "-html")
+ (string-append docdir "/"
base)))
+ '("usr-manual" "ref-manual")))))))))
- (home-page "http://www.llnl.gov/casc/hypre/";)
+ (home-page "https://computing.llnl.gov/projects\
+ /hypre-scalable-linear-solvers-multigrid-methods")
(synopsis "Library of solvers and preconditioners for linear equations")
(description
"HYPRE is a software library of high performance preconditioners and
diff --cc gnu/packages/readline.scm
index b4c9167,d8d333e..ced8471
--- a/gnu/packages/readline.scm
+++ b/gnu/packages/readline.scm
@@@ -2,8 -2,8 +2,8 @@@
;;; Copyright © 2012, 2013, 2014, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016, 2019 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
- ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+ ;;; Copyright © 2018, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2019 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2019, 2020 Marius Bakke <marius@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
diff --cc gnu/packages/tls.scm
index d9e62e8,55410f3..2930c61
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@@ -15,7 -15,7 +15,8 @@@
;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+ ;;; Copyright © 2021 Solene Rapenne <solene@perso.pw>
;;;
;;; This file is part of GNU Guix.
;;;
diff --cc gnu/packages/xdisorg.scm
index d339851,5573e2a..fe28585
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@@ -43,9 -43,9 +43,10 @@@
;;; Copyright © 2020 James Smith <jsubuntuxp@disroot.org>
;;; Copyright © 2020 B. Wilson <elaexuotee@wilsonb.com>
;;; Copyright © 2020, 2021 Zheng Junjie <873216071@qq.com>
+;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2021 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz>
+ ;;; Copyright © 2021 Renzo Poddighe <renzo@poddighe.nl>
;;;
;;; This file is part of GNU Guix.
;;;
diff --cc gnu/packages/xml.scm
index fb41a38,9743086..c01d9f4
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@@ -120,7 -120,8 +120,8 @@@ the entire document."
(define-public expat
(package
(name "expat")
- (version "2.2.9")
+ (replacement expat-2.4.1)
+ (version "2.3.0")
(source (let ((dot->underscore (lambda (c) (if (char=? #\. c) #\_ c))))
(origin
(method url-fetch)
diff --cc gnu/packages/xorg.scm
index 265ce81,9156fb3..488c124
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@@ -5498,7 -5483,7 +5500,8 @@@ draggable titlebars and borders."
(define-public libx11
(package
(name "libx11")
- (version "1.6.10")
++ (replacement libx11/fixed)
+ (version "1.7.0")
(source
(origin
(method url-fetch)
@@@ -5536,6 -5522,18 +5539,18 @@@
(description "Xorg Core X11 protocol client library.")
(license license:x11)))
+ (define-public libx11/fixed
+ (package
+ (inherit libx11)
- (version "1.7.1A")
++ (version "1.7.A")
+ (source
+ (origin
+ (method url-fetch)
+ (uri "mirror://xorg/individual/lib/libX11-1.7.1.tar.bz2")
+ (sha256
+ (base32
+ "0isxad59hvdwggbxqqjjjg3zmih9xiq4d9mdsnqbyb2nmbg46kp6"))))))
+
;; packages of height 5 in the propagated-inputs tree
(define-public libxcursor