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01/01: Merge branch 'master' into core-updates-frozen
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From: |
guix-commits |
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Subject: |
01/01: Merge branch 'master' into core-updates-frozen |
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Date: |
Thu, 29 Jul 2021 20:23:41 -0400 (EDT) |
mbakke pushed a commit to branch core-updates-frozen
in repository guix.
commit b029be2ee0f81cdcbc14240ff426408085ab0a40
Merge: bc55f30 ffb3818
Author: Marius Bakke <marius@gnu.org>
AuthorDate: Thu Jul 29 22:34:57 2021 +0200
Merge branch 'master' into core-updates-frozen
Conflicts:
gnu/packages/bioinformatics.scm
gnu/packages/cmake.scm
gnu/packages/curl.scm
gnu/packages/emacs-xyz.scm
gnu/packages/gpodder.scm
gnu/packages/music.scm
gnu/packages/patches/glibc-bootstrap-system.patch
gnu/packages/python-xyz.scm
gnu/packages/shells.scm
gnu/packages/statistics.scm
Makefile.am | 4 -
doc/guix.texi | 45 +-
gnu/build/activation.scm | 38 +-
gnu/local.mk | 5 +
gnu/packages/admin.scm | 36 +-
gnu/packages/algebra.scm | 20 +-
gnu/packages/audio.scm | 8 +-
gnu/packages/aux-files/linux-libre/5.12-arm.conf | 9984 -----------------
gnu/packages/aux-files/linux-libre/5.12-arm64.conf | 10249 -----------------
gnu/packages/aux-files/linux-libre/5.12-i686.conf | 10829 ------------------
.../aux-files/linux-libre/5.12-x86_64.conf | 10877 -------------------
gnu/packages/bioconductor.scm | 46 +-
gnu/packages/bioinformatics.scm | 359 +-
gnu/packages/cmake.scm | 10 +
gnu/packages/code.scm | 10 +-
gnu/packages/cran.scm | 441 +-
gnu/packages/crates-io.scm | 749 +-
gnu/packages/curl.scm | 13 +
gnu/packages/databases.scm | 91 +-
gnu/packages/ebook.scm | 4 +-
gnu/packages/education.scm | 7 +-
gnu/packages/emacs-xyz.scm | 365 +-
gnu/packages/emulators.scm | 58 +-
gnu/packages/enlightenment.scm | 11 +-
gnu/packages/freedesktop.scm | 45 +-
gnu/packages/geo.scm | 55 +-
gnu/packages/gl.scm | 25 +-
gnu/packages/gnome.scm | 70 +-
gnu/packages/gnuzilla.scm | 8 +-
gnu/packages/gpodder.scm | 11 +-
gnu/packages/graph.scm | 24 +-
gnu/packages/graphviz.scm | 2 +-
gnu/packages/guile.scm | 4 +-
gnu/packages/haskell-apps.scm | 4 +-
gnu/packages/haskell.scm | 12 +-
gnu/packages/java.scm | 18 +-
gnu/packages/julia-jll.scm | 3 +
gnu/packages/julia-xyz.scm | 302 +-
gnu/packages/julia.scm | 431 +-
gnu/packages/jupyter.scm | 88 +
gnu/packages/linux.scm | 156 +-
gnu/packages/lisp-xyz.scm | 132 +-
gnu/packages/lisp.scm | 118 +-
gnu/packages/machine-learning.scm | 51 +
gnu/packages/mail.scm | 19 +-
gnu/packages/maths.scm | 280 +-
gnu/packages/messaging.scm | 40 +
gnu/packages/music.scm | 213 +-
gnu/packages/networking.scm | 11 +-
gnu/packages/node-xyz.scm | 27 +
gnu/packages/package-management.scm | 121 +-
gnu/packages/patches/esmtp-add-lesmtp.patch | 37 +
.../extempore-unbundle-external-dependencies.patch | 316 +-
gnu/packages/patches/glibc-bootstrap-system.patch | 28 +-
gnu/packages/patches/julia-tracker-16-compat.patch | 40 +
.../patches/marble-qt-add-qt-headers.patch | 189 +
gnu/packages/pcre.scm | 15 +
gnu/packages/pdf.scm | 19 +-
gnu/packages/php.scm | 16 +-
gnu/packages/plan9.scm | 66 +
gnu/packages/python-science.scm | 210 +-
gnu/packages/python-web.scm | 25 +
gnu/packages/python-xyz.scm | 218 +-
gnu/packages/rdesktop.scm | 7 +-
gnu/packages/rdf.scm | 27 +
gnu/packages/ruby.scm | 27 +-
gnu/packages/rust-apps.scm | 7 +-
gnu/packages/search.scm | 53 +-
gnu/packages/shells.scm | 805 +-
gnu/packages/simulation.scm | 81 +
gnu/packages/statistics.scm | 138 +-
gnu/packages/text-editors.scm | 21 +-
gnu/packages/textutils.scm | 43 +
gnu/packages/tls.scm | 6 +-
gnu/packages/tmux.scm | 63 +-
gnu/packages/tor.scm | 10 +-
gnu/packages/uglifyjs.scm | 50 +
gnu/packages/video.scm | 6 +-
gnu/packages/vim.scm | 6 +-
gnu/packages/visidata.scm | 4 +-
gnu/packages/web-browsers.scm | 13 +-
gnu/packages/web.scm | 184 +-
gnu/packages/webkit.scm | 4 +-
gnu/packages/xfce.scm | 5 +-
gnu/packages/xml.scm | 8 +-
gnu/packages/xorg.scm | 18 +-
gnu/services.scm | 45 +-
gnu/services/dbus.scm | 13 +-
gnu/services/desktop.scm | 26 +-
gnu/services/docker.scm | 9 +-
gnu/services/networking.scm | 6 +-
gnu/services/web.scm | 4 +-
gnu/services/xorg.scm | 4 +-
gnu/system.scm | 47 +-
gnu/system/setuid.scm | 57 +
guix/build-system/minify.scm | 4 +-
guix/build/minify-build-system.scm | 2 +-
guix/derivations.scm | 49 +-
guix/import/print.scm | 6 +-
guix/utils.scm | 1 -
100 files changed, 5651 insertions(+), 43916 deletions(-)
diff --cc gnu/local.mk
index 20f0b8f,c80a9af..812c997
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@@ -1256,7 -1287,9 +1259,8 @@@ dist_patch_DATA =
%D%/packages/patches/jfsutils-add-sysmacros.patch \
%D%/packages/patches/jfsutils-gcc-compat.patch \
%D%/packages/patches/jfsutils-include-systypes.patch \
- %D%/packages/patches/jsoncpp-fix-inverted-case.patch \
%D%/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch \
+ %D%/packages/patches/julia-tracker-16-compat.patch \
%D%/packages/patches/kdbusaddons-kinit-file-name.patch \
%D%/packages/patches/libblockdev-glib-compat.patch \
%D%/packages/patches/libffi-3.3-powerpc-fixes.patch \
@@@ -1389,8 -1421,8 +1393,9 @@@
%D%/packages/patches/lvm2-static-link.patch \
%D%/packages/patches/mailutils-fix-uninitialized-variable.patch \
%D%/packages/patches/make-impure-dirs.patch \
+ %D%/packages/patches/marble-qt-add-qt-headers.patch \
%D%/packages/patches/mariadb-CVE-2021-27928.patch \
+ %D%/packages/patches/mariadb-cmake-compat.patch \
%D%/packages/patches/mars-install.patch \
%D%/packages/patches/mars-sfml-2.3.patch \
%D%/packages/patches/maxima-defsystem-mkdir.patch \
diff --cc gnu/packages/algebra.scm
index 6e7ecda,6450ac8..1c7f94a
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@@ -245,11 -245,11 +245,11 @@@ the real span of the lattice."
version ".tar.gz"))
(sha256
(base32
- "1cgwdpw8b797883z9y92ixxjkv72kiy65zsw2qqf5and1kbzgv41"))))
+ "095s7vdlsxmxa0n0l1a082m6gjaypqfqkaj99z8j7dx0ji89hy8n"))))
(build-system gnu-build-system)
(native-inputs
- `(("texlive" ,(texlive-union
- (list texlive-amsfonts/patched)))))
+ `(("texlive" ,(texlive-updmap.cfg
+ (list texlive-amsfonts)))))
(inputs `(("gmp" ,gmp)
("libx11" ,libx11)
("perl" ,perl)
diff --cc gnu/packages/bioinformatics.scm
index 002b417,742b02c..0b87d37
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@@ -2071,29 -2104,36 +2071,29 @@@ has several key features
(setenv "HTSLIB_INCLUDE_DIR"
(string-append (assoc-ref inputs "htslib") "/include"))
(setenv "LDFLAGS" "-lncurses")
- (setenv "CFLAGS" "-D_CURSES_LIB=1")
- #t))
+ (setenv "CFLAGS" "-D_CURSES_LIB=1")))
(replace 'check
- (lambda _
- ;; This file contains tests that require a connection to the
- ;; internet.
- (delete-file "tests/tabix_test.py")
+ (lambda* (#:key tests? #:allow-other-keys)
- ;; Failing test removed in the next release.
+ ;; FIXME: These tests fail with "AttributeError: 'array.array'
+ ;; object has no attribute 'tostring'".
(delete-file "tests/AlignmentFile_test.py")
- (delete-file "tests/AlignedSegment_test.py")
- ;; Step out of source dir so python does not import from CWD.
- (with-directory-excursion "tests"
- (setenv "HOME" "/tmp")
- (invoke "make" "-C" "pysam_data")
- (invoke "make" "-C" "cbcf_data")
- ;; Running nosetests without explicitly asking for a single
- ;; process leads to a crash. Running with multiple processes
- ;; fails because the tests are not designed to run in parallel.
-
- ;; FIXME: tests keep timing out on some systems.
- (invoke "nosetests" "-v" "--processes" "1")))))))
- ;; Add first subdirectory of "build" directory to PYTHONPATH.
- (setenv "PYTHONPATH"
- (string-append
- (getenv "PYTHONPATH")
- ":" (getcwd) "/build/"
- (car (scandir "build"
- (negate (cut string-prefix? "." <>))))))
+ (when tests?
+ ;; Step out of source dir so python does not import from CWD.
+ (with-directory-excursion "tests"
+ (setenv "HOME" "/tmp")
+ (invoke "make" "-C" "pysam_data")
+ (invoke "make" "-C" "cbcf_data")
+ (invoke "pytest" "-k"
+ (string-append
+ ;; requires network access.
+ "not FileHTTP"
+ ;; bug in test suite with samtools update
+ ;;
https://github.com/pysam-developers/pysam/issues/961
+ " and not TestHeaderBAM"
+ " and not TestHeaderCRAM"
+ " and not test_text_processing")))))))))
(propagated-inputs
- `(("htslib" ,htslib-1.9))) ; Included from installed header files.
+ `(("htslib" ,htslib-1.10))) ; Included from installed header files.
(inputs
`(("ncurses" ,ncurses)
("curl" ,curl)
diff --cc gnu/packages/cmake.scm
index 68d215d,df8885b..f76ee3f
--- a/gnu/packages/cmake.scm
+++ b/gnu/packages/cmake.scm
@@@ -327,6 -335,39 +328,15 @@@ and workspaces that can be used in the
(package
(inherit cmake-minimal)
(name "cmake")
+ (version "3.21.1")
- ;; TODO: Move the following source field to the cmake-bootstrap package in
- ;; the next rebuild cycle.
+ (source (origin
+ (inherit (package-source cmake-bootstrap))
+ (uri (string-append "https://cmake.org/files/v";
+ (version-major+minor version)
+ "/cmake-" version ".tar.gz"))
+ (sha256
+ (base32
- "1m7y9j5lafkrfswsg2vkpx2fz6p6fqpp2pcp2dcz5pylf58r3hzs"))
- (snippet
- (match (origin-snippet (package-source cmake-bootstrap))
- ((_ _ exp ...)
- ;; Now we can delete the remaining software bundles.
- (append `(begin
- (define preserved-files
- '(,@%preserved-third-party-files
- ;; TODO: Move this file to the
- ;; %preserved-third-party-files variable in
- ;; the next rebuild cycle.
- "Utilities/cm3p" ;CMake header wrappers
- ;; Use the bundled JsonCpp during bootstrap
- ;; to work around a circular dependency.
- ;; TODO: JsonCpp can be built with Meson
- ;; instead of CMake, but meson-build-system
- ;; currently does not support
- ;; cross-compilation.
- "Utilities/cmjsoncpp"
- ;; LibUV is required to bootstrap the initial
- ;; build system.
- "Utilities/cmlibuv")))
- exp))))))
++ "1m7y9j5lafkrfswsg2vkpx2fz6p6fqpp2pcp2dcz5pylf58r3hzs"))))
(arguments
(substitute-keyword-arguments (package-arguments cmake-minimal)
;; Use cmake-minimal this time.
diff --cc gnu/packages/curl.scm
index 60eeb8f,e6f1bb0..39344b1
--- a/gnu/packages/curl.scm
+++ b/gnu/packages/curl.scm
@@@ -11,7 -11,7 +11,8 @@@
;;; Copyright © 2019, 2021 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;; Copyright © 2020 Dale Mellor <guix-devel-0brg6b@rdmp.org>
+;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
+ ;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
;;;
;;; This file is part of GNU Guix.
;;;
@@@ -143,9 -145,41 +145,20 @@@ 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-ssh
+ (package/inherit curl
+ (arguments
+ (substitute-keyword-arguments (package-arguments curl)
+ ((#:configure-flags flags)
+ `(cons "--with-libssh2" ,flags))))
+ (inputs
+ `(("libssh2" ,libssh2)
+ ,@(package-inputs curl)))
+ (properties `((hidden? . #t)))))
+
-(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"
- "curl-7.77-tls-priority-string.patch"))
- (sha256
- (base32
- "0jsrc97vbghvljic997r9nypc9qqddcil2lzvv032br8ahn5hr0g"))))))
-
(define-public kurly
(package
(name "kurly")
diff --cc gnu/packages/emacs-xyz.scm
index e92bf6b,d468abd..eb4902a
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@@ -5501,30 -5497,28 +5493,28 @@@ for Flow files."
(add-after 'unpack 'specify-python-location
;; Hard-code python3 executable location in the library.
(lambda* (#:key inputs #:allow-other-keys)
- (let ((python3 (string-append (assoc-ref inputs "python")
- "/bin/python3")))
+ (let ((python3 (search-input-file inputs "/bin/python3")))
- (substitute* "flycheck-grammalecte.el"
+ (substitute* '("flycheck-grammalecte.el" "grammalecte.el")
(("\"python3") (string-append "\"" python3)))
- (substitute* '("conjugueur.py" "flycheck-grammalecte.py")
- (("/usr/bin/env python3?") python3))
- #t)))
+ (substitute* '("conjugueur.py" "flycheck_grammalecte.py")
+ (("/usr/bin/env python3?") python3)))))
(add-after 'unpack 'specify-grammalecte-location
+ ;; Use our own Grammalecte.
(lambda* (#:key inputs #:allow-other-keys)
- (make-file-writable "flycheck-grammalecte.el")
- (emacs-substitute-variables "flycheck-grammalecte.el"
- ("flycheck-grammalecte-grammalecte-directory"
+ (make-file-writable "grammalecte.el")
+ (emacs-substitute-variables "grammalecte.el"
+ ("grammalecte-python-package-directory"
- (string-append (assoc-ref inputs "grammalecte")
- "/lib/python"
- ,(version-major+minor (package-version python))
- "/site-packages/grammalecte")))))
+ (search-input-directory
+ inputs
+ (string-append "lib/python"
+ ,(version-major+minor (package-version
python))
+ "/site-packages/grammalecte"))))))
(add-after 'unpack 'do-not-phone-home
- ;; The package wants to check upstream Grammalecte version to
- ;; decide if an update is in order. Always return version
- ;; installed so it doesn't phone home and doesn't install anything.
+ ;; Do not check for Grammalecte updates, ever.
(lambda _
- (substitute* "flycheck-grammalecte.el"
- (("\\(flycheck-grammalecte--grammalecte-upstream-version\\)")
- ,(format #f "\"~a\"" (package-version grammalecte)))))))))
+ (make-file-writable "grammalecte.el")
+ (emacs-substitute-variables "grammalecte.el"
+ ("grammalecte-check-upstream-version-delay" 0)))))))
(inputs
`(("grammalecte" ,grammalecte)
("python" ,python)))
diff --cc gnu/packages/gl.scm
index cc5131b,4a1a700..92c8b59
--- a/gnu/packages/gl.scm
+++ b/gnu/packages/gl.scm
@@@ -13,8 -13,8 +13,9 @@@
;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2020 Giacomo Leidi <goodoldpaul@autistici.org>
+;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2020 Kei Kebreau <kkebreau@posteo.net>
+ ;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru>
;;;
;;; This file is part of GNU Guix.
;;;
diff --cc gnu/packages/gnome.scm
index 57811ad,54ae54d..9df739f
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@@ -10196,11 -10190,11 +10135,9 @@@ that support the Assistive Technology S
;; Allow Enchant and its Aspell backend to find the en_US
;; dictionary.
(setenv "ASPELL_DICT_DIR"
- (string-append (assoc-ref inputs "aspell-dict-en")
- "/lib/aspell"))
- #t)))))
+ (search-input-directory inputs "/lib/aspell")))))))
(inputs
- `(("gtk+" ,gtk+)
- ("glib" ,glib)
- ("iso-codes" ,iso-codes)))
+ `(("iso-codes" ,iso-codes)))
(native-inputs
`(("glib" ,glib "bin")
("gobject-introspection" ,gobject-introspection)
diff --cc gnu/packages/gnuzilla.scm
index c562def,4231e2a..0872ca1
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@@ -1601,9 -1605,9 +1601,9 @@@ standards of the IceCat project."
(file-name (string-append "thunderbird-" version "-checkout"))
(sha256
(base32
- "10l042dd7b8rvla0cbiks5kjrz2b28yy7hr8sr169wlx202hxa01")))))
+ "1nnz90h5w9skpdwm8ilndcwfx9d7k9cn6gzh32y4jil95da13813")))))
("autoconf" ,autoconf-2.13)
- ("cargo" ,rust-1.41 "cargo")
+ ("cargo" ,rust "cargo")
("clang" ,clang)
("llvm" ,llvm)
("nasm" ,nasm)
diff --cc gnu/packages/gpodder.scm
index 245bca0,5a18a16..3b1db54
--- a/gnu/packages/gpodder.scm
+++ b/gnu/packages/gpodder.scm
@@@ -89,8 -93,12 +93,9 @@@
(("xdg-open") (string-append xdg-utils "/bin/xdg-open")))
#t)))
(replace 'check
- (lambda _
- (invoke "make" "unittest")))
+ (lambda* (#:key tests? #:allow-other-keys)
- ; The `unittest' target overrides the PYTHONPATH variable.
- (substitute* "makefile"
- (("PYTHONPATH=src/") "PYTHONPATH=${PYTHONPATH}:src/"))
+ (when tests?
+ (invoke "make" "unittest"))))
;; 'msgmerge' introduces non-determinism by resetting the
;; POT-Creation-Date in .po files.
(add-before 'install 'do-not-run-msgmerge
diff --cc gnu/packages/music.scm
index 492103b,dee17ac..6b544b6
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@@ -1574,19 -1592,161 +1582,161 @@@ Guile."
("python-iniconfig" ,python-iniconfig)
("python-isort" ,python-isort)
("python-mypy" ,python-mypy)
- ("python-ply" ,python-ply)
- ("python-pytest" ,python-pytest-6)
+ ("python-pytest" ,python-pytest)
("python-pytest-cov" ,python-pytest-cov)
("python-sphinx-autodoc-typehints" ,python-sphinx-autodoc-typehints)))
+ (inputs
+ `(("lilypond" ,lilypond)))
(propagated-inputs
- `(("python-quicktions" ,python-quicktions)
+ `(("python-ply" ,python-ply)
+ ("python-quicktions" ,python-quicktions)
("python-roman" ,python-roman)
("python-six" ,python-six)
("python-uqbar" ,python-uqbar)))
(home-page "https://abjad.github.io";)
(synopsis "Python API for building LilyPond files")
(description
- "This package provides a Python API for building LilyPond files.")
+ "Abjad helps composers build up complex pieces of music notation in
iterative
+ and incremental ways. Use Abjad to create a symbolic representation of all
the notes,
+ rests, chords, tuplets, beams and slurs in any score. Because Abjad extends
the Python
+ programming language, you can use Abjad to make systematic changes to music
as you work.
+ Because Abjad wraps the LilyPond music notation package, you can use Abjad to
control the
+ typographic detail of symbols on the page.")
+ (license license:expat)))
+
+ (define-public python-abjad
+ (deprecated-package "python-abjad" abjad))
+
+ (define-public abjad-ext-rmakers
+ (package
+ (name "abjad-ext-rmakers")
+ (version "3.3")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/Abjad/abjad-ext-rmakers";)
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "03nry8lzh3s81yq4lw8y6j63m7zdsl20q7rvx9cfmp3rmbvlaycs"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "python" "-m" "pytest" ".")
+ #t))))))
+ (native-inputs
+ `(("lilypond" ,lilypond)
+ ("python-black" ,python-black)
+ ("python-flake8" ,python-flake8)
+ ("python-iniconfig" ,python-iniconfig)
+ ("python-isort" ,python-isort)
+ ("python-mypy" ,python-mypy)
- ("python-pytest" ,python-pytest-6)
++ ("python-pytest" ,python-pytest)
+ ("python-pytest-cov" ,python-pytest-cov)
+ ("python-pytest-helpers-namespace" ,python-pytest-helpers-namespace)))
+ (propagated-inputs
+ `(("abjad" ,abjad)))
+ (home-page "https://abjad.github.io";)
+ (synopsis "Abjad rhythm-maker exension package")
+ (description
+ "@code{abjad-ext-rmakers} includes a collection of classes for creating
and
+ and manipulating rhythms such as accelerandi, taleas, and more.")
+ (license license:expat)))
+
+ (define-public abjad-ext-nauert
+ (package
+ (name "abjad-ext-nauert")
+ (version "3.3")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/Abjad/abjad-ext-nauert";)
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "07vgfjh32vmf652lcl2vrbzr0h6nld00qbgwbf9i1kk3xwhvklc9"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "python" "-m" "pytest" "tests")
+ #t))))))
+ (native-inputs
+ `(("lilypond" ,lilypond)
+ ("python-black" ,python-black)
+ ("python-flake8" ,python-flake8)
+ ("python-iniconfig" ,python-iniconfig)
+ ("python-isort" ,python-isort)
+ ("python-mypy" ,python-mypy)
- ("python-pytest" ,python-pytest-6)
++ ("python-pytest" ,python-pytest)
+ ("python-pytest-cov" ,python-pytest-cov)
+ ("python-pytest-helpers-namespace" ,python-pytest-helpers-namespace)))
+ (propagated-inputs
+ `(("abjad" ,abjad)))
+ (home-page "https://abjad.github.io";)
+ (synopsis "Abjad quantization extension, based on Paul Nauert's Q-Grids")
+ (description
+ "@code{abjad-ext-nauert} provides classes for dealing with composer and
+ music theorist Paul Nauert's quantization grids or Q-Grids, for short.")
+ (license license:expat)))
+
+ (define-public abjad-ext-ipython
+ (package
+ (name "abjad-ext-ipython")
+ (version "3.3")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/Abjad/abjad-ext-ipython";)
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1vv0alpiz0gf5lgjfvlh4km72dvrxfqkwzxl3k4amzci3i0jzbs2"))))
+ (build-system python-build-system)
+ (arguments
+ ;; UnboundLocalError: local variable 'output_path' referenced before
assignment
+ `(#:tests? #f
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? inputs outputs #:allow-other-keys)
+ (when tests?
+ (setenv "HOME" (getcwd))
+ (add-installed-pythonpath inputs outputs)
+ ;; From 'make jupyter-test'
+ (invoke "jupyter" "nbconvert" "--to=html"
+ "--ExecutePreprocessor.enabled=True" "tests/test.ipynb")))))))
+ (native-inputs
+ `(("lilypond" ,lilypond)
+ ("python-black" ,python-black)
+ ("python-flake8" ,python-flake8)
+ ("python-iniconfig" ,python-iniconfig)
+ ("python-isort" ,python-isort)
+ ("python-mypy" ,python-mypy)
- ("python-pytest" ,python-pytest-6)
++ ("python-pytest" ,python-pytest)
+ ("python-pytest-cov" ,python-pytest-cov)
+ ("python-pytest-helpers-namespace" ,python-pytest-helpers-namespace)))
+ (propagated-inputs
+ `(("abjad" ,abjad)
+ ("jupyter" ,jupyter)))
+ (home-page "https://abjad.github.io";)
+ (synopsis "Abjad IPython Extension")
+ (description
+ "@code{abjad-ext-ipython} makes it possible to embed music notation in
+ @code{jupyter} notebooks.")
(license license:expat)))
(define-public non-sequencer
diff --cc gnu/packages/patches/glibc-bootstrap-system.patch
index fcaf171,db6457e..9c0fac3
--- a/gnu/packages/patches/glibc-bootstrap-system.patch
+++ b/gnu/packages/patches/glibc-bootstrap-system.patch
@@@ -18,25 -25,27 +18,49 @@@ index ebc381ed7c..e0d3ed1bc3 10064
(char *const[]){ (char*) "sh", (char*) "-c",
(char *) command, NULL }, __environ) != 0)
return false;
+diff --git a/sysdeps/posix/system.c b/sysdeps/posix/system.c
+index a03f478fc7..94da6facf3 100644
+--- a/sysdeps/posix/system.c
++++ b/sysdeps/posix/system.c
+@@ -101,7 +101,7 @@ cancel_handler (void *arg)
+ static int
+ do_system (const char *line)
+ {
+- int status = -1;
++ int status = 0;
+ int ret;
+ pid_t pid;
+ struct sigaction sa;
+@@ -145,7 +145,7 @@ do_system (const char *line)
+ __posix_spawnattr_setflags (&spawn_attr,
+ POSIX_SPAWN_SETSIGDEF | POSIX_SPAWN_SETSIGMASK);
+
+- ret = __posix_spawn (&pid, SHELL_PATH, 0, &spawn_attr,
- + ret = posix_spawnp (&pid, SHELL_NAME, 0, &spawn_attr,
+++ ret = __posix_spawnp (&pid, SHELL_NAME, 0, &spawn_attr,
+ (char *const[]){ (char *) SHELL_NAME,
+ (char *) "-c",
+ (char *) line, NULL },
+
+ --- a/include/spawn.h
+ +++ b/include/spawn.h
+ @@ -5,6 +5,9 @@
+ __typeof (posix_spawn) __posix_spawn;
+ libc_hidden_proto (__posix_spawn)
+
+ +__typeof (posix_spawnp) __posix_spawnp;
+ +libc_hidden_proto (__posix_spawnp)
+ +
+ __typeof (posix_spawn_file_actions_addclose)
+ __posix_spawn_file_actions_addclose attribute_hidden;
+
+ --- a/posix/spawnp.c
+ +++ b/posix/spawnp.c
+ @@ -31,6 +31,7 @@ __posix_spawnp (pid_t *pid, const char *file,
+ SPAWN_XFLAGS_USE_PATH);
+ }
+ versioned_symbol (libc, __posix_spawnp, posix_spawnp, GLIBC_2_15);
+ +libc_hidden_def (__posix_spawnp)
+
+
+ #if SHLIB_COMPAT (libc, GLIBC_2_2, GLIBC_2_15)
+
diff --cc gnu/packages/python-xyz.scm
index 60a0ea5,4b2ed02..7f8764b
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@@ -21250,30 -21472,63 +21352,56 @@@ pure-Python."
(define-public python2-sortedcontainers
(package-with-python2 python-sortedcontainers))
- (define-public python-cloudpickle
+ (define python-cloudpickle-testpkg
(package
- (name "python-cloudpickle")
- (version "1.3.0")
+ (name "python-cloudpickle-testpkg")
+ (version "1.6.0")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "cloudpickle" version))
+ ;; Archive on pypi does not include test infrastructure.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/cloudpipe/cloudpickle";)
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0lx7gy9clp427qwcm7b23zdsldpr03gy3vxxhyi8fpbhwz859brq"))))
+ "1584d21d4rcpryn8yfz0pjnjprk4zm367m0razdcz8cjbsh0dxp6"))))
(build-system python-build-system)
(arguments
- '(#:phases (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (if tests?
- (invoke "pytest" "-s" "-vv")
- (format #t "test suite not run~%")))))))
+ '(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'chdir
+ (lambda _ (chdir "tests/cloudpickle_testpkg"))))))
+ (home-page "https://github.com/cloudpipe/cloudpickle";)
+ (synopsis "Extended pickling support for Python objects")
+ (description
+ "Cloudpickle makes it possible to serialize Python constructs not
+ supported by the default pickle module from the Python standard library. It
+ is especially useful for cluster computing where Python expressions are
+ shipped over the network to execute on remote hosts, possibly close to the
+ data.")
+ (license license:bsd-3)))
+
+ (define-public python-cloudpickle
+ (package
+ (inherit python-cloudpickle-testpkg)
+ (name "python-cloudpickle")
+ (build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
- (add-before 'check 'do-not-override-PYTHONPATH
- (lambda _
- ;; Append to PYTHONPATH instead of overriding it so
- ;; that dependencies from Guix can be found.
- (substitute* "tests/testutils.py"
- (("env\\['PYTHONPATH'\\] = pythonpath")
- "env['PYTHONPATH'] += os.pathsep + pythonpath"))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (if tests?
+ (invoke "pytest" "-s" "-vv")
+ (format #t "test suite not run~%")))))))
(native-inputs
`(;; For tests.
+ ("python-cloudpickle-testpkg" ,python-cloudpickle-testpkg)
("python-psutil" ,python-psutil)
("python-pytest" ,python-pytest)
- ("python-tornado" ,python-tornado)))
+ ("python-tornado" ,python-tornado-6)))
(home-page "https://github.com/cloudpipe/cloudpickle";)
(synopsis "Extended pickling support for Python objects")
(description
diff --cc gnu/packages/shells.scm
index 44a77e1,f2d5834..a694790
--- a/gnu/packages/shells.scm
+++ b/gnu/packages/shells.scm
@@@ -16,8 -16,8 +16,9 @@@
;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
;;; Copyright © 2020 Ryan Prior <rprior@protonmail.com>
;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2020 Marius Bakke <marius@gnu.org>
;;; Copyright © 2021 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+ ;;; Copyright © 2021 Felix Gruber <felgru@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
diff --cc gnu/packages/statistics.scm
index dd89653,7b50d28..b95a8d0
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@@ -214,11 -213,15 +214,14 @@@ This package also provides @command{xls
(substitute* "src/library/base/makebasedb.R"
(("compress = TRUE") "compress = FALSE"))
#t))
- (add-before 'configure 'patch-uname
+ (add-before 'configure 'patch-coreutils-paths
(lambda* (#:key inputs #:allow-other-keys)
- (let ((uname-bin (search-input-file inputs "/bin/uname")))
- (let* ((coreutils (assoc-ref inputs "coreutils"))
- (uname-bin (string-append coreutils "/bin/uname"))
- (rm-bin (string-append coreutils "/bin/rm")))
++ (let ((uname-bin (search-input-file inputs "/bin/uname"))
++ (rm-bin (search-input-file inputs "/bin/rm")))
(substitute* "src/scripts/R.sh.in"
- (("uname") uname-bin)))
+ (("uname") uname-bin))
+ (substitute* "src/unix/sys-std.c"
+ (("rm -Rf ") (string-append rm-bin " -Rf "))))
#t))
(add-after 'unpack 'build-reproducibly
(lambda _
diff --cc gnu/packages/xorg.scm
index 8d6dc21,6f96339..c82b020
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@@ -29,8 -29,8 +29,9 @@@
;;; Copyright © 2021 Nicolò Balzarotti <nicolo@nixo.xyz>
;;; Copyright © 2021 Matthew James Kraai <kraai@ftbfs.org>
;;; Copyright © 2021 Brice Waegeneire <brice@waegenei.re>
+;;; Copyright © 2021 Matthew James Kraai <kraai@ftbfs.org>
;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be>
+ ;;; Copyright © 2021 qblade <qblade@protonmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
diff --cc guix/build/minify-build-system.scm
index f7f51af,c5a8767..5789ca3
--- a/guix/build/minify-build-system.scm
+++ b/guix/build/minify-build-system.scm
@@@ -40,13 -39,10 +40,13 @@@
(format #t "minifying ~a\n" file)
(let* ((base (basename file ".js"))
(installed (or target (string-append directory base ".min.js")))
- (minified (open-pipe* OPEN_READ "uglify-js" file)))
+ (minified (open-pipe* OPEN_READ "uglifyjs" file)))
(call-with-output-file installed
(cut dump-port minified <>))
- #t))
+ (match (close-pipe minified)
+ (0 #t)
+ (status
+ (error "uglify-js failed" status)))))
(define* (build #:key javascript-files
#:allow-other-keys)