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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
Marius Bakke 2021-07-29 22:34:57 +02:00
parent bc55f3091b ffb381856d
commit b029be2ee0
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100 changed files with 5664 additions and 43929 deletions
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4
Makefile.am
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@ -371,10 +371,6 @@ AUX_FILES = \
gnu/packages/aux-files/linux-libre/5.13-arm64.conf \
gnu/packages/aux-files/linux-libre/5.13-i686.conf \
gnu/packages/aux-files/linux-libre/5.13-x86_64.conf \
gnu/packages/aux-files/linux-libre/5.12-arm.conf \
gnu/packages/aux-files/linux-libre/5.12-arm64.conf \
gnu/packages/aux-files/linux-libre/5.12-i686.conf \
gnu/packages/aux-files/linux-libre/5.12-x86_64.conf \
gnu/packages/aux-files/linux-libre/5.10-arm.conf \
gnu/packages/aux-files/linux-libre/5.10-arm64.conf \
gnu/packages/aux-files/linux-libre/5.10-i686.conf \

45
doc/guix.texi
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@ -46,7 +46,7 @@ Copyright @copyright{} 2017 Federico Beffa@*
Copyright @copyright{} 2017, 2018 Carlo Zancanaro@*
Copyright @copyright{} 2017 Thomas Danckaert@*
Copyright @copyright{} 2017 humanitiesNerd@*
Copyright @copyright{} 2017, 2021 Christopher Lemmer Webber@*
Copyright @copyright{} 2017, 2021 Christine Lemmer-Webber@*
Copyright @copyright{} 2017, 2018, 2019, 2020 Marius Bakke@*
Copyright @copyright{} 2017, 2019, 2020 Hartmut Goebel@*
Copyright @copyright{} 2017, 2019, 2020, 2021 Maxim Cournoyer@*
@ -14108,8 +14108,8 @@ Linux @dfn{pluggable authentication module} (PAM) services.
@c FIXME: Add xref to PAM services section.
@item @code{setuid-programs} (default: @code{%setuid-programs})
List of string-valued G-expressions denoting setuid programs.
@xref{Setuid Programs}.
List of @code{<setuid-program>}. @xref{Setuid Programs}, for more
information.
@item @code{sudoers-file} (default: @code{%sudoers-specification})
@cindex sudoers file
@ -32598,20 +32598,47 @@ the store, we let the system administrator @emph{declare} which programs
should be setuid root.
The @code{setuid-programs} field of an @code{operating-system}
declaration contains a list of G-expressions denoting the names of
programs to be setuid-root (@pxref{Using the Configuration System}).
For instance, the @command{passwd} program, which is part of the Shadow
package, can be designated by this G-expression (@pxref{G-Expressions}):
declaration contains a list of @code{<setuid-program>} denoting the
names of programs to have a setuid or setgid bit set (@pxref{Using the
Configuration System}). For instance, the @command{passwd} program,
which is part of the Shadow package, with a setuid root can be
designated like this:
@example
#~(string-append #$shadow "/bin/passwd")
(setuid-program
(program (file-append #$shadow "/bin/passwd")))
@end example
@deftp {Data Type} setuid-program
This data type represents a program with a setuid or setgid bit set.
@table @asis
@item @code{program}
A file-like object having its setuid and/or setgid bit set.
@item @code{setuid?} (default: @code{#t})
Whether to set user setuid bit.
@item @code{setgid?} (default: @code{#f})
Whether to set group setgid bit.
@item @code{user} (default: @code{0})
UID (integer) or user name (string) for the user owner of the program,
defaults to root.
@item @code{group} (default: @code{0})
GID (integer) goup name (string) for the group owner of the program,
defaults to root.
@end table
@end deftp
A default set of setuid programs is defined by the
@code{%setuid-programs} variable of the @code{(gnu system)} module.
@defvr {Scheme Variable} %setuid-programs
A list of G-expressions denoting common programs that are setuid-root.
A list of @code{<setuid-program>} denoting common programs that are
setuid-root.
The list includes commands such as @command{passwd}, @command{ping},
@command{su}, and @command{sudo}.

38
gnu/build/activation.scm
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@ -6,6 +6,8 @@
;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be>
;;; Copyright © 2020 Christine Lemmer-Webber <cwebber@dustycloud.org>
;;; Copyright © 2021 Brice Waegeneire <brice@waegenei.re>
;;;
;;; This file is part of GNU Guix.
;;;
@ -24,6 +26,7 @@
(define-module (gnu build activation)
#:use-module (gnu system accounts)
#:use-module (gnu system setuid)
#:use-module (gnu build accounts)
#:use-module (gnu build linux-boot)
#:use-module (guix build utils)
@ -279,14 +282,17 @@ they already exist."
"/run/setuid-programs")
(define (activate-setuid-programs programs)
"Turn PROGRAMS, a list of file names, into setuid programs stored under
%SETUID-DIRECTORY."
(define (make-setuid-program prog)
"Turn PROGRAMS, a list of file setuid-programs record, into setuid programs
stored under %SETUID-DIRECTORY."
(define (make-setuid-program program setuid? setgid? uid gid)
(let ((target (string-append %setuid-directory
"/" (basename prog))))
(copy-file prog target)
(chown target 0 0)
(chmod target #o4555)))
"/" (basename program)))
(mode (+ #o0555 ; base permissions
(if setuid? #o4000 0) ; setuid bit
(if setgid? #o2000 0)))) ; setgid bit
(copy-file program target)
(chown target uid gid)
(chmod target mode)))
(format #t "setting up setuid programs in '~a'...~%"
%setuid-directory)
@ -302,15 +308,27 @@ they already exist."
(for-each (lambda (program)
(catch 'system-error
(lambda ()
(make-setuid-program program))
(let* ((program-name (setuid-program-program program))
(setuid? (setuid-program-setuid? program))
(setgid? (setuid-program-setgid? program))
(user (setuid-program-user program))
(group (setuid-program-group program))
(uid (match user
((? string?) (passwd:uid (getpwnam user)))
((? integer?) user)))
(gid (match group
((? string?) (group:gid (getgrnam group)))
((? integer?) group))))
(make-setuid-program program-name setuid? setgid? uid gid)))
(lambda args
;; If we fail to create a setuid program, better keep going
;; so that we don't leave %SETUID-DIRECTORY empty or
;; half-populated. This can happen if PROGRAMS contains
;; incorrect file names: <https://bugs.gnu.org/38800>.
(format (current-error-port)
"warning: failed to make '~a' setuid-root: ~a~%"
program (strerror (system-error-errno args))))))
"warning: failed to make ~s setuid/setgid: ~a~%"
(setuid-program-program program)
(strerror (system-error-errno args))))))
programs))
(define (activate-special-files special-files)

5
gnu/local.mk
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@ -451,6 +451,7 @@ GNU_SYSTEM_MODULES = \
%D%/packages/php.scm \
%D%/packages/piet.scm \
%D%/packages/pkg-config.scm \
%D%/packages/plan9.scm \
%D%/packages/plotutils.scm \
%D%/packages/poedit.scm \
%D%/packages/polkit.scm \
@ -559,6 +560,7 @@ GNU_SYSTEM_MODULES = \
%D%/packages/tmux.scm \
%D%/packages/tor.scm \
%D%/packages/tv.scm \
%D%/packages/uglifyjs.scm \
%D%/packages/uml.scm \
%D%/packages/unicode.scm \
%D%/packages/unrtf.scm \
@ -994,6 +996,7 @@ dist_patch_DATA = \
%D%/packages/patches/enjarify-setup-py.patch \
%D%/packages/patches/enlightenment-fix-setuid-path.patch \
%D%/packages/patches/erlang-man-path.patch \
%D%/packages/patches/esmtp-add-lesmtp.patch \
%D%/packages/patches/eudev-rules-directory.patch \
%D%/packages/patches/evilwm-lost-focus-bug.patch \
%D%/packages/patches/evolution-CVE-2020-11879.patch \
@ -1257,6 +1260,7 @@ dist_patch_DATA = \
%D%/packages/patches/jfsutils-gcc-compat.patch \
%D%/packages/patches/jfsutils-include-systypes.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 \
@ -1389,6 +1393,7 @@ dist_patch_DATA = \
%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 \

36
gnu/packages/admin.scm
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@ -1307,6 +1307,38 @@ tools: server, client, and relay agent.")
(license license:mpl2.0)
(properties '((cpe-name . "dhcp"))))))
(define-public radvd
(package
(name "radvd")
(version "2.19")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/radvd-project/radvd")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1df827m3vkjq2bcs5y9wg2cygvpdwl8ppl446qqhyym584gz54nl"))))
(build-system gnu-build-system)
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("bison" ,bison)
("check" ,check)
("flex" ,flex)
("pkg-config" ,pkg-config)))
(arguments
`(#:configure-flags '("--with-check")))
(home-page "https://radvd.litech.org/")
(synopsis "IPv6 Router Advertisement Daemon")
(description
"The Router Advertisement Daemon (radvd) is run on systems acting as IPv6
routers. It sends Router Advertisement messages specified by RFC 2461
periodically and when requested by a node sending a Router Solicitation
message. These messages are required for IPv6 stateless autoconfiguration.")
(license (license:non-copyleft "file://COPYRIGHT"))))
(define-public libpcap
(package
(name "libpcap")
@ -1614,7 +1646,7 @@ system administrator.")
(define-public sudo
(package
(name "sudo")
(version "1.9.7p1")
(version "1.9.7p2")
(source (origin
(method url-fetch)
(uri
@ -1624,7 +1656,7 @@ system administrator.")
version ".tar.gz")))
(sha256
(base32
"1kyqj45nmykwj38sc5kx7mi0vf6x637hzvbd1jv22lg5aks3251r"))
"1a7w99mlpa7kb7zfqkhvafli0a3xhz50kws25y2sg2dzbmrfxd98"))
(modules '((guix build utils)))
(snippet
'(begin

20
gnu/packages/algebra.scm
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@ -237,7 +237,7 @@ the real span of the lattice.")
(define-public pari-gp
(package
(name "pari-gp")
(version "2.13.1")
(version "2.13.2")
(source (origin
(method url-fetch)
(uri (string-append
@ -245,7 +245,7 @@ the real span of the lattice.")
version ".tar.gz"))
(sha256
(base32
"1cgwdpw8b797883z9y92ixxjkv72kiy65zsw2qqf5and1kbzgv41"))))
"095s7vdlsxmxa0n0l1a082m6gjaypqfqkaj99z8j7dx0ji89hy8n"))))
(build-system gnu-build-system)
(native-inputs
`(("texlive" ,(texlive-updmap.cfg
@ -343,7 +343,7 @@ precision.")
(define-public giac
(package
(name "giac")
(version "1.7.0-17")
(version "1.7.0-21")
(source
(origin
(method url-fetch)
@ -355,7 +355,7 @@ precision.")
"~parisse/debian/dists/stable/main/source/"
"giac_" version ".tar.gz"))
(sha256
(base32 "0yh556wlgs9hfyp5j2xz4nlrd2dma63cicrc3dhahyl96y1aw6mr"))))
(base32 "1w8wyz559ljsjxf5xjkjvgkac1xpj71qzy6sycnbsqza4m0j28l5"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((ice-9 ftw)
@ -368,14 +368,12 @@ precision.")
(lambda _
(substitute* (cons "micropython-1.12/xcas/Makefile"
(find-files "doc" "^Makefile"))
(("/bin/cp") (which "cp")))
#t))
(("/bin/cp") (which "cp")))))
(add-after 'unpack 'disable-failing-test
;; FIXME: Test failing. Not sure why.
(lambda _
(substitute* "check/Makefile.in"
(("chk_fhan11") ""))
#t))
(("chk_fhan11") ""))))
(add-after 'install 'fix-doc
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
@ -388,13 +386,11 @@ precision.")
;; Remove duplicate documentation in
;; "%out/share/doc/giac/", where Xcas does not expect
;; to find it.
(delete-file-recursively (string-append out "/share/doc/giac"))
#t)))
(delete-file-recursively (string-append out "/share/doc/giac")))))
(add-after 'install 'remove-unnecessary-executable
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(delete-file (string-append out "/bin/xcasnew"))
#t))))))
(delete-file (string-append out "/bin/xcasnew"))))))))
(inputs
;; TODO: Add libnauty, unbundle "libmicropython.a".
`(("fltk" ,fltk)

8
gnu/packages/audio.scm
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@ -4914,7 +4914,7 @@ in the package.")
(origin
(method git-fetch)
(uri (git-reference
(url "https://git.zrythm.org/git/libaudec")
(url "https://git.zrythm.org/zrythm/libaudec")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@ -4934,7 +4934,7 @@ in the package.")
(description "libaudec is a wrapper library over ffmpeg, sndfile and
libsamplerate for reading and resampling audio files, based on Robin Gareus'
@code{audio_decoder} code.")
(home-page "https://git.zrythm.org/cgit/libaudec")
(home-page "https://git.zrythm.org/zrythm/libaudec")
(license license:agpl3+)))
(define-public lv2lint
@ -5013,7 +5013,7 @@ with the provided metadata and adhere to well-known best practices.")
(origin
(method git-fetch)
(uri (git-reference
(url "https://git.zrythm.org/git/ztoolkit")
(url "https://git.zrythm.org/zrythm/ztoolkit")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@ -5034,7 +5034,7 @@ the user and provides a high-level API for managing the UI and custom
widgets. ZToolkit is written in C and was created to be used for building
audio plugin UIs, where the dependencies often need to be kept to a
minimum.")
(home-page "https://git.zrythm.org/cgit/ztoolkit/")
(home-page "https://git.zrythm.org/zrythm/ztoolkit")
(license license:agpl3+)))
(define-public libinstpatch

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46
gnu/packages/bioconductor.scm
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@ -2743,14 +2743,14 @@ CAGE.")
(define-public r-ensembldb
(package
(name "r-ensembldb")
(version "2.16.2")
(version "2.16.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ensembldb" version))
(sha256
(base32
"0mbdfxic2vkfwm6b16353zr0qg8ylwf1vrxry85j2lgzl1qyyras"))))
"1y3d6mx59531ixr8nzq57sa5nwimq3qyy1xabk52vvdbkl2aa52x"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@ -3814,14 +3814,14 @@ region sets and other genomic features.")
(define-public r-reportingtools
(package
(name "r-reportingtools")
(version "2.32.0")
(version "2.32.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ReportingTools" version))
(sha256
(base32
"0v6wzfswwcd1xdxgwa9gzlkmavr4p55jy11k84anh0rs0xx3dmmj"))))
"0wq9y649dh1am6djzz0xlz42428xsgw2bdx1dknhdw2xbydmmx47"))))
(properties
`((upstream-name . "ReportingTools")))
(build-system r-build-system)
@ -4221,20 +4221,20 @@ graph construction.")
(define-public r-structuralvariantannotation
(package
(name "r-structuralvariantannotation")
(version "1.8.0")
(version "1.8.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "StructuralVariantAnnotation" version))
(sha256
(base32
"10h63h1v87nvm3bfyr6dsjlbmzxf1vks30d0xz6q4hssqq9xlzgv"))))
(base32 "13q6zbdkpx1iw6n75pggg50f9q3zb7k3dxjdra8mhi6zin7018j8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
("r-biocgenerics" ,r-biocgenerics)
("r-biostrings" ,r-biostrings)
("r-dplyr" ,r-dplyr)
("r-genomicfeatures" ,r-genomicfeatures)
("r-genomicranges" ,r-genomicranges)
("r-rlang" ,r-rlang)
("r-rtracklayer" ,r-rtracklayer)
@ -5013,14 +5013,14 @@ determining dependencies between variables, code improvement suggestions.")
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
(version "3.26.0")
(version "3.26.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
"1wnmsdrb4wz2qprj5mnd3h0wx32y2mpy3xg7mjbgwlqn9bzpw3gk"))))
"003550ygh0haxyyypsss7s03jlsx7cqkhly4fcz10maczi6j4l30"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
@ -6541,14 +6541,14 @@ distributions.")
(define-public r-scone
(package
(name "r-scone")
(version "1.16.0")
(version "1.16.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scone" version))
(sha256
(base32
"1wlky6nkdpz8fya81l6zaxlxc30wyp2gkyh94y5995jwddll38z5"))))
"0zw8g4mql7b02xqwhc1i0bnhm20c1q9xqc7yz84j98pqbi996vi5"))))
(build-system r-build-system)
(propagated-inputs
`(("r-aroma-light" ,r-aroma-light)
@ -7795,12 +7795,12 @@ frequency matrices from nine public sources, for multiple organisms.")
(define-public r-motifbreakr
(package
(name "r-motifbreakr")
(version "2.6.0")
(version "2.6.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "motifbreakR" version))
(sha256
(base32 "0i18qriznad4lr6ynzmz01k5yavs5m3h7hd0adbyg8lppbzm6hh4"))))
(base32 "1n6v8a7c27aswmbrlcwcpghf27aplkc6nn923imglc3c0sh2lkrz"))))
(properties `((upstream-name . "motifbreakR")))
(build-system r-build-system)
(propagated-inputs
@ -8612,14 +8612,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
(define-public r-xcms
(package
(name "r-xcms")
(version "3.14.0")
(version "3.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "xcms" version))
(sha256
(base32
"1fs72lkgz1jik1smi6bb4f8jh6rrlpxdh3a5hydrnnndfxkz5kwx"))))
"1g8k90p0sbcb3rdrbldj5bcjp2piy5ldni4jplyr78vjpmrmvqk7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@ -9329,14 +9329,14 @@ datasets.")
(define-public r-annotatr
(package
(name "r-annotatr")
(version "1.18.0")
(version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotatr" version))
(sha256
(base32
"0pcf4jrq05bmfxph41hmdx1x147k1ay5fl2h488y1s4h8qm3c67p"))))
"1ls1qdfppcxysggi3bghrnspb5a3s40pm2mj4x0whc7c40cf90mg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@ -9370,14 +9370,14 @@ annotations.")
(define-public r-rsubread
(package
(name "r-rsubread")
(version "2.6.3")
(version "2.6.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rsubread" version))
(sha256
(base32
"04nz85vr184fjmf2k0kc5sy2hjzpfazfkxlhlgax50rnkn98va5x"))))
"043m4512q73x6q529hqfgrap0fq5anvny4va085nafia06b805pi"))))
(properties `((upstream-name . "Rsubread")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
@ -9932,14 +9932,14 @@ self-organizing map clustering and minimal spanning trees.")
(define-public r-mixomics
(package
(name "r-mixomics")
(version "6.16.1")
(version "6.16.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mixOmics" version))
(sha256
(base32
"0fiwf86hvkidxwkdcw0x7lk3bk2fsxqng43b1js7klifm3gfcf91"))))
"0kbljjwm5caf2znqnkhrbmcfsv1mhppp9h491210q477y8bjlkja"))))
(properties `((upstream-name . "mixOmics")))
(build-system r-build-system)
(propagated-inputs
@ -13010,14 +13010,14 @@ relevant, and the minimum expression of the most abundant condition.")
(define-public r-catalyst
(package
(name "r-catalyst")
(version "1.16.1")
(version "1.16.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CATALYST" version))
(sha256
(base32
"12frw4myqr8y3ff4n74ld4478ndpmfj5ynr6gnigbr1h61b94m3v"))))
"1vw8x54hwgcyn29k81zcvawawy2iy2qgp49gjpb830q04gx6yc6h"))))
(properties `((upstream-name . "CATALYST")))
(build-system r-build-system)
(propagated-inputs

359
gnu/packages/bioinformatics.scm
View File

@ -388,10 +388,10 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1.
(license (list license:gpl3+ license:expat))))
(define-public bcftools-1.9
(define-public bcftools-1.10
(package (inherit bcftools)
(name "bcftools")
(version "1.9")
(version "1.10")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/samtools/bcftools/"
@ -399,15 +399,15 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
version "/bcftools-" version ".tar.bz2"))
(sha256
(base32
"1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg"))
"10xgwfdgqb6dsmr3ndnpb77mc3a38dy8kh2c6czn6wj7jhdp4dra"))
(modules '((guix build utils)))
(snippet '(begin
;; Delete bundled htslib.
(delete-file-recursively "htslib-1.9")
(delete-file-recursively "htslib-1.10")
#t))))
(build-system gnu-build-system)
(native-inputs
`(("htslib" ,htslib-1.9)
`(("htslib" ,htslib-1.10)
("perl" ,perl)))))
(define-public bedops
@ -1213,14 +1213,14 @@ sequencing.")
(define-public python-biopython
(package
(name "python-biopython")
(version "1.70")
(version "1.73")
(source (origin
(method url-fetch)
;; use PyPi rather than biopython.org to ease updating
(uri (pypi-uri "biopython" version))
(sha256
(base32
"0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a"))))
"1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh"))))
(build-system python-build-system)
(arguments
`(#:phases
@ -2043,7 +2043,7 @@ has several key features:
(define-public python-pysam
(package
(name "python-pysam")
(version "0.15.1")
(version "0.16.0.1")
(source (origin
(method git-fetch)
;; Test data is missing on PyPi.
@ -2053,7 +2053,7 @@ has several key features:
(file-name (git-file-name name version))
(sha256
(base32
"1vj367w6xbn9bpmksm162l1aipf7cj97h1q83y7jcpm33ihwpf7x"))
"168bwwm8c2k22m7paip8q0yajyl7xdxgnik0bgjl7rhqg0majz0f"))
(modules '((guix build utils)))
(snippet '(begin
;; Drop bundled htslib. TODO: Also remove samtools
@ -2073,36 +2073,37 @@ has several key features:
(setenv "LDFLAGS" "-lncurses")
(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)
;; 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")))))))
(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)
("zlib" ,zlib)))
(native-inputs
`(("python-cython" ,python-cython)
("python-pytest" ,python-pytest)
;; Dependencies below are are for tests only.
("samtools" ,samtools-1.9)
("bcftools" ,bcftools-1.9)
("samtools" ,samtools-1.10)
("bcftools" ,bcftools-1.10)
("python-nose" ,python-nose)))
(home-page "https://github.com/pysam-developers/pysam")
(synopsis "Python bindings to the SAMtools C API")
@ -3589,7 +3590,7 @@ results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)
("seqan" ,seqan)))
("seqan" ,seqan-2)))
(home-page "https://github.com/seqan/flexbar")
(synopsis "Barcode and adapter removal tool for sequencing platforms")
(description
@ -4603,6 +4604,19 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and
;; the rest is released under the Expat license
(license (list license:expat license:bsd-3))))
(define-public htslib-1.10
(package (inherit htslib)
(name "htslib")
(version "1.10")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/samtools/htslib/releases/download/"
version "/htslib-" version ".tar.bz2"))
(sha256
(base32
"0wm9ay7qgypj3mwx9zl1mrpnr36298b1aj5vx69l4k7bzbclvr3s"))))))
(define-public htslib-1.9
(package (inherit htslib)
(name "htslib")
@ -6051,10 +6065,10 @@ variant calling (in conjunction with bcftools), and a simple alignment
viewer.")
(license license:expat)))
(define-public samtools-1.9
(define-public samtools-1.10
(package (inherit samtools)
(name "samtools")
(version "1.9")
(version "1.10")
(source
(origin
(method url-fetch)
@ -6063,14 +6077,14 @@ viewer.")
version "/samtools-" version ".tar.bz2"))
(sha256
(base32
"10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8"))
"119ms0dpydw8dkh3zc4yyw9zhdzgv12px4l2kayigv31bpqcb7kv"))
(modules '((guix build utils)))
(snippet '(begin
;; Delete bundled htslib.
(delete-file-recursively "htslib-1.9")
(delete-file-recursively "htslib-1.10")
#t))))
(inputs
`(("htslib" ,htslib-1.9)
`(("htslib" ,htslib-1.10)
("ncurses" ,ncurses)
("perl" ,perl)
("python" ,python)
@ -6706,6 +6720,39 @@ writing files into the .sra format.")
(define-public seqan
(package
(name "seqan")
(version "3.0.3")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/seqan/seqan3/releases/"
"download/" version "/seqan3-"
version "-Source.tar.xz"))
(sha256
(base32
"1h2z0cvgidhkmh5xsbw75waqbrqbbv6kkrvb0b92xfh3gqpaiz22"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _
(invoke "ctest" "test" "--output-on-failure"))))))
(native-inputs
`(("bzip2" ,bzip2)
("cereal" ,cereal)
("zlib" ,zlib)))
(home-page "https://www.seqan.de")
(synopsis "Library for nucleotide sequence analysis")
(description
"SeqAn is a C++ library of efficient algorithms and data structures for
the analysis of sequences with the focus on biological data. It contains
algorithms and data structures for string representation and their
manipulation, online and indexed string search, efficient I/O of
bioinformatics file formats, sequence alignment, and more.")
(license license:bsd-3)))
(define-public seqan-2
(package
(inherit seqan)
(version "2.4.0")
(source (origin
(method url-fetch)
@ -6737,16 +6784,7 @@ writing files into the .sra format.")
(native-inputs
`(("source" ,source)
("tar" ,tar)
("xz" ,xz)))
(home-page "https://www.seqan.de")
(synopsis "Library for nucleotide sequence analysis")
(description
"SeqAn is a C++ library of efficient algorithms and data structures for
the analysis of sequences with the focus on biological data. It contains
algorithms and data structures for string representation and their
manipulation, online and indexed string search, efficient I/O of
bioinformatics file formats, sequence alignment, and more.")
(license license:bsd-3)))
("xz" ,xz)))))
(define-public seqan-1
(package (inherit seqan)
@ -9310,6 +9348,54 @@ using nucleotide or amino-acid sequence data.")
;; GPLv3 only
(license license:gpl3)))
(define-public segemehl
(package
(name "segemehl")
(version "0.3.4")
(source (origin
(method url-fetch)
(uri (string-append "https://www.bioinf.uni-leipzig.de/Software"
"/segemehl/downloads/segemehl-"
version ".tar.gz"))
(sha256
(base32
"0lbzbb7i8zadsn9b99plairhq6s2h1z8qdn6n7djclfis01nycz4"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags
(list (string-append "CC=" ,(cc-for-target))
"all")
#:tests? #false ; there are none
#:phases
(modify-phases %standard-phases
(delete 'configure)
;; There is no installation target
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(exes (list "segemehl.x" "haarz.x")))
(mkdir-p bin)
(for-each (lambda (exe)
(install-file exe bin))
exes)))))))
(inputs
`(("htslib" ,htslib)
("ncurses" ,ncurses)
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "https://www.bioinf.uni-leipzig.de/Software/segemehl")
(synopsis "Map short sequencer reads to reference genomes")
(description "Segemehl is software to map short sequencer reads to
reference genomes. Segemehl implements a matching strategy based on enhanced
suffix arrays (ESA). It accepts fasta and fastq queries (gzip'ed and
bgzip'ed). In addition to the alignment of reads from standard DNA- and
RNA-seq protocols, it also allows the mapping of bisulfite converted
reads (Lister and Cokus) and implements a split read mapping strategy. The
output of segemehl is a SAM or BAM formatted alignment file.")
(license license:gpl3+)))
(define-public kallisto
(package
(name "kallisto")
@ -12991,28 +13077,32 @@ downstream analysis.")
("taxtastic" ,taxtastic)))
(synopsis "Pplacer Python scripts")))
(define-public python2-checkm-genome
(define-public checkm
(package
(name "python2-checkm-genome")
(version "1.0.13")
(name "checkm")
(version "1.1.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "checkm-genome" version))
(sha256
(base32
"0bm8gpxjmzxsxxl8lzwqhgx8g1dlnmp6znz7wv3hgb0gdjbf9dzz"))))
"0i2nnki639hgjag17wlva2x0ymn37b4krqsf6akxddykhfbkdnkz"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:tests? #f)) ; some tests are interactive
(propagated-inputs
`(("python-dendropy" ,python2-dendropy)
("python-matplotlib" ,python2-matplotlib)
("python-numpy" ,python2-numpy)
("python-pysam" ,python2-pysam)
("python-scipy" ,python2-scipy)))
(home-page "https://pypi.org/project/Checkm/")
`(#:tests? #f ; Some tests fail for unknown reasons.
#:phases
(modify-phases %standard-phases
(add-before 'check 'set-HOME
(lambda _
(setenv "HOME" "/tmp"))))))
(inputs
`(("python-dendropy" ,python-dendropy)
("python-matplotlib" ,python-matplotlib)
("python-numpy" ,python-numpy)
("python-pysam" ,python-pysam)
("python-scipy" ,python-scipy)))
(home-page "https://ecogenomics.github.io/CheckM/")
(synopsis "Assess the quality of putative genome bins")
(description
"CheckM provides a set of tools for assessing the quality of genomes
@ -13027,6 +13117,9 @@ on marker set compatibility, similarity in genomic characteristics, and
proximity within a reference genome.")
(license license:gpl3+)))
(define-public python2-checkm-genome
(deprecated-package "python2-checkm-genome" checkm))
(define-public umi-tools
(package
(name "umi-tools")
@ -14490,3 +14583,155 @@ quantifying single-cell chromatin data, computing per-cell quality control
metrics, dimension reduction and normalization, visualization, and DNA
sequence motif analysis.")
(license license:expat))))
(define-public tombo
(package
(name "tombo")
(version "1.5.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ont-tombo" version))
(sha256
(base32
"1023hadgcsgi53kz53ql45207hfizf9sw57z0qij3ay1bx68zbpm"))))
(build-system python-build-system)
(native-inputs
`(("python-cython" ,python-cython)
("python-nose2" ,python-nose2)))
;; The package mainly consists of a command-line tool, but also has a
;; Python-API. Thus these must be propagated.
(propagated-inputs
`(("python-future" ,python-future)
("python-h5py" ,python-h5py)
("python-mappy" ,python-mappy)
("python-numpy" ,python-numpy)
("python-scipy" ,python-scipy)
("python-tqdm" ,python-tqdm)
("python-rpy2" ,python-rpy2)))
(home-page "https://github.com/nanoporetech/tombo")
(synopsis "Analysis of raw nanopore sequencing data")
(description "Tombo is a suite of tools primarily for the identification of
modified nucleotides from nanopore sequencing data. Tombo also provides tools
for the analysis and visualization of raw nanopore signal.")
;; Some parts may be BSD-3-licensed.
(license license:mpl2.0)))
(define-public python-pyvcf
(package
(name "python-pyvcf")
(version "0.6.8")
;; Use git, because the PyPI tarballs lack test data.
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/jamescasbon/PyVCF.git")
;; Latest release is not tagged.
(commit "bfcedb9bad1a14074ac4526ffdb610611e073810")))
(file-name (git-file-name name version))
(sha256
(base32
"0c7lsssns3zp8fh2ibllzzra003srg9vbxqzmq6654akbzdb7lrf"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'install 'remove-installed-tests
;; Do not install test files.
(lambda* (#:key inputs outputs #:allow-other-keys)
(delete-file-recursively (string-append
(site-packages inputs outputs)
"vcf/test"))
#t)))))
(native-inputs `(("python-cython" ,python-cython)))
(propagated-inputs
`(("python-pysam" ,python-pysam)
("python-rpy2" ,python-rpy2)))
(home-page "https://github.com/jamescasbon/PyVCF")
(synopsis "Variant Call Format parser for Python")
(description "This package provides a @acronym{VCF,Variant Call Format}
parser for Python.")
(license license:expat)))
(define-public nanosv
(package
(name "nanosv")
(version "1.2.4")
(source (origin
(method url-fetch)
(uri (pypi-uri "NanoSV" version))
(sha256
(base32
"1wl2daj0bwrl8fx5xi8j8hfs3mp3vg3qycy66538n032v1qkc6xg"))))
(build-system python-build-system)
(inputs
`(("python-configparser" ,python-configparser)
("python-pysam" ,python-pysam)
("python-pyvcf" ,python-pyvcf)))
(home-page "https://github.com/mroosmalen/nanosv")
(synopsis "Structural variation detection tool for Oxford Nanopore data.")
(description "NanoSV is a software package that can be used to identify
structural genomic variations in long-read sequencing data, such as data
produced by Oxford Nanopore Technologies’ MinION, GridION or PromethION
instruments, or Pacific Biosciences RSII or Sequel sequencers.")
(license license:expat)))
(define-public r-ascat
(package
(name "r-ascat")
(version "2.5.2")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Crick-CancerGenomics/ascat.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0cc0y3as6cb64iwnx0pgbajiig7m4z723mns9d5i4j09ccid3ccm"))))
(build-system r-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'move-to-ascat-dir
(lambda _
(chdir "ASCAT"))))))
(propagated-inputs
`(("r-rcolorbrewer" ,r-rcolorbrewer)))
(home-page "https://github.com/VanLoo-lab/ascat/")
(synopsis "Allele-Specific Copy Number Analysis of Tumors in R")
(description "This package provides the @acronym{ASCAT,Allele-Specific Copy
Number Analysis of Tumors} R package that can be used to infer tumour purity,
ploidy and allele-specific copy number profiles.")
(license license:gpl3)))
(define-public r-battenberg
(package
(name "r-battenberg")
(version "2.2.9")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Wedge-lab/battenberg.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0nmcq4c7y5g8h8lxsq9vadz9bj4qgqn118alip520ny6czaxki4h"))))
(build-system r-build-system)
(propagated-inputs
`(("r-devtools" ,r-devtools)
("r-readr" ,r-readr)
("r-doparallel" ,r-doparallel)
("r-ggplot2" ,r-ggplot2)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-gridextra" ,r-gridextra)
("r-gtools" ,r-gtools)
("r-ascat" ,r-ascat)))
(home-page "https://github.com/Wedge-lab/battenberg")
(synopsis "Subclonal copy number estimation in R")
(description "This package contains the Battenberg R package for subclonal
copy number estimation, as described by
@url{doi:10.1016/j.cell.2012.04.023,Nik-Zainal et al.}")
(license license:gpl3)))

10
gnu/packages/cmake.scm
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@ -11,6 +11,7 @@
;;; Copyright © 2019, 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2019 Pierre-Moana Levesque <pierre.moana.levesque@gmail.com>
;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -327,6 +328,15 @@ and workspaces that can be used in the compiler environment of your choice.")
(package
(inherit cmake-minimal)
(name "cmake")
(version "3.21.1")
(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"))))
(arguments
(substitute-keyword-arguments (package-arguments cmake-minimal)
;; Use cmake-minimal this time.

10
gnu/packages/code.scm
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@ -2,7 +2,7 @@
;;; Copyright © 2013, 2015, 2018, 2020, 2021 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2015, 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2017, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2017 Andy Wingo <wingo@igalia.com>
@ -127,14 +127,14 @@ highlighting your own code that seemed comprehensible when you wrote it.")
(define-public global ; a global variable
(package
(name "global")
(version "6.6.6")
(version "6.6.7")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/global/global-"
version ".tar.gz"))
(sha256
(base32
"0pad5p31rdspyrzqky3ppgx7f6gdlfnwg1c7qm8w1m4qzyppi03m"))))
"0g4aslm2zajq605py11s4rs1wdnzcqhkh7bc2xl5az42adzzg839"))))
(build-system gnu-build-system)
(inputs `(("coreutils" ,coreutils)
("ncurses" ,ncurses)
@ -163,7 +163,9 @@ highlighting your own code that seemed comprehensible when you wrote it.")
(let* ((out (assoc-ref outputs "out"))
(data (string-append out "/share/gtags"))
(vim (string-append out "/share/vim/vimfiles/plugin"))
(lisp (string-append out "/share/emacs/site-lisp")))
(lisp (string-append out "/share/emacs/site-lisp/"
,(package-name this-package) "-"
,(package-version this-package))))
(mkdir-p lisp)
(mkdir-p vim)
(rename-file (string-append data "/gtags.el")

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gnu/packages/curl.scm
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@ -12,6 +12,7 @@
;;; 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.
;;;
@ -46,6 +47,7 @@
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages ssh)
#:use-module (gnu packages tls)
#:use-module (gnu packages web)
#:use-module (srfi srfi-1))
@ -146,6 +148,17 @@ tunneling, and so on.")
(define-public curl-minimal
(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 kurly
(package
(name "kurly")

91
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@ -52,6 +52,7 @@
;;; Copyright © 2021 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@bonfacemunyoki.com>
;;; Copyright © 2021 Simon Streit <simon@netpanic.org>
;;; Copyright © 2021 Alexandre Hannud Abdo <abdo@member.fsf.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -88,11 +89,14 @@
#:use-module (gnu packages dbm)
#:use-module (gnu packages emacs)
#:use-module (gnu packages flex)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gettext)
#:use-module (gnu packages glib)
#:use-module (gnu packages gnome)
#:use-module (gnu packages gnupg)
#:use-module (gnu packages golang)
#:use-module (gnu packages gtk)
#:use-module (gnu packages guile)
#:use-module (gnu packages icu4c)
#:use-module (gnu packages jemalloc)
@ -109,6 +113,7 @@
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages onc-rpc)
#:use-module (gnu packages pantheon)
#:use-module (gnu packages parallel)
#:use-module (gnu packages pcre)
#:use-module (gnu packages perl)
@ -130,6 +135,7 @@
#:use-module (gnu packages ruby)
#:use-module (gnu packages serialization)
#:use-module (gnu packages sphinx)
#:use-module (gnu packages ssh)
#:use-module (gnu packages sqlite)
#:use-module (gnu packages tcl)
#:use-module (gnu packages terminals)
@ -148,6 +154,7 @@
#:use-module (guix build-system emacs)
#:use-module (guix build-system gnu)
#:use-module (guix build-system go)
#:use-module (guix build-system meson)
#:use-module (guix build-system perl)
#:use-module (guix build-system python)
#:use-module (guix build-system ruby)
@ -3638,7 +3645,7 @@ the SQL language using a syntax that reflects the resulting query.")
(define-public apache-arrow
(package
(name "apache-arrow")
(version "4.0.1")
(version "5.0.0")
(source
(origin
(method git-fetch)
@ -3648,7 +3655,7 @@ the SQL language using a syntax that reflects the resulting query.")
(file-name (git-file-name name version))
(sha256
(base32
"1lcd9gdpwlrr92rm812a5p4l6zx0arwd0zj72a4ga699s1psz8yv"))))
"0275aayzy78nbxzbj93w5152sv5q2c7020ijxnf8b58v9qwfxzz0"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f
@ -3770,13 +3777,34 @@ algorithm implementations.")
(modify-phases %standard-phases
(delete 'build) ; XXX the build is performed again during the install phase
(add-after 'unpack 'enter-source-directory
(lambda _ (chdir "python") #t))
(lambda _ (chdir "python")))
(add-after 'unpack 'make-git-checkout-writable
(lambda _
(for-each make-file-writable (find-files "."))
#t)))))
(for-each make-file-writable (find-files "."))))
(add-before 'install 'patch-cmake-variables
(lambda* (#:key inputs #:allow-other-keys)
;; Replace cmake locations with hardcoded guix links for the
;; underlying C++ library and headers. This is a pretty awful
;; hack.
(substitute* "cmake_modules/FindParquet.cmake"
(("# Licensed to the Apache Software Foundation" m)
(string-append "set(PARQUET_INCLUDE_DIR \""
(assoc-ref inputs "apache-arrow:include")
"/share/include\")\n" m))
(("find_package_handle_standard_args" m)
(string-append "set(PARQUET_LIB_DIR \""
(assoc-ref inputs "apache-arrow:lib")
"/lib\")\n" m)))))
(add-before 'install 'patch-parquet-library
(lambda _
(substitute* "CMakeLists.txt"
(("parquet_shared") "parquet"))))
(add-before 'install 'set-PYARROW_WITH_PARQUET
(lambda _
(setenv "PYARROW_WITH_PARQUET" "1"))))))
(propagated-inputs
`(("apache-arrow" ,apache-arrow "lib")
`(("apache-arrow:lib" ,apache-arrow "lib")
("apache-arrow:include" ,apache-arrow "include")
("python-numpy" ,python-numpy)
("python-pandas" ,python-pandas)
("python-six" ,python-six)))
@ -3968,3 +3996,54 @@ PostreSQL, SQLite, ODBC and MySQL.")
"FreeTDS is an implementation of the Tabular DataStream protocol, used for
connecting to MS SQL and Sybase servers over TCP/IP.")
(license license:lgpl2.0+)))
(define-public sequeler
(package
(name "sequeler")
(version "0.8.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Alecaddd/sequeler")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1q1vzc3likpiwfh6blkyiz0wr0aarj9xrm8gbi7m3p1wslkpah7c"))))
(build-system meson-build-system)
(arguments
'(#:glib-or-gtk? #t
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'skip-gtk-update-icon-cache
;; Don't create 'icon-theme.cache'.
(lambda _
(substitute* "build-aux/meson_post_install.py"
(("gtk-update-icon-cache") "true")
(("update-desktop-database") "true"))
#t)))))
(native-inputs
`(;("appstream-glib" ,appstream-glib) ; validation fails for lack of network
("gettext-minimal" ,gettext-minimal)
("glib:bin" ,glib "bin") ; for glib-compile-resources
("gtk+" ,gtk+ "bin")
("pkg-config" ,pkg-config)
("vala" ,vala)))
(inputs
`(("glib" ,glib)
("granite" ,granite)
("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
("gtk+" ,gtk+)
("gtksourceview-3" ,gtksourceview-3)
("libgda" ,libgda)
("libgee" ,libgee)
("libsecret" ,libsecret)
("libssh2" ,libssh2)
("libxml2" ,libxml2)))
(synopsis "Friendly SQL Client")
(description "Sequeler is a native Linux SQL client built in Vala and
Gtk. It allows you to connect to your local and remote databases, write SQL in
a handy text editor with language recognition, and visualize SELECT results in
a Gtk.Grid Widget.")
(home-page "https://github.com/Alecaddd/sequeler")
(license license:gpl2+)))

4
gnu/packages/ebook.scm
View File

@ -116,7 +116,7 @@ with Microsoft Compiled HTML (CHM) files")
(define-public calibre
(package
(name "calibre")
(version "5.14.0")
(version "5.21.0")
(source
(origin
(method url-fetch)
@ -125,7 +125,7 @@ with Microsoft Compiled HTML (CHM) files")
version ".tar.xz"))
(sha256
(base32
"0w8j9r9qa56r8gm9b10dwh8zrzqlv79s2br82jqg02lrnrbwwv0q"))
"0mq2w8blq6ykaml812axakwkqcw85qcpfwijdikn7kvbrhnnp2s5"))
(modules '((guix build utils)))
(snippet
'(begin

7
gnu/packages/education.scm
View File

@ -330,7 +330,7 @@ easy.")
(define-public snap
(package
(name "snap")
(version "6.6.0")
(version "6.9.0")
(source
(origin
(method git-fetch)
@ -339,7 +339,7 @@ easy.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1k0j0sp6zz2hnh7zc7f086zc3sld01h7sk277j6fak914yv6slzy"))))
(base32 "1wppz57lrrribrfnaiv6jrrf703w7i6ja0dnz8yx8naxhbsglwyf"))))
(build-system trivial-build-system)
(arguments
`(#:modules ((guix build utils))
@ -368,8 +368,7 @@ easy.")
(call-with-output-file script
(lambda (port)
(format port "#!~a\n~a '~a'" bash xdg-open snap)))
(chmod script #o555)))
#t)))
(chmod script #o555))))))
(inputs
`(("bash" ,bash-minimal)
("js-filesaver" ,js-filesaver)

365
gnu/packages/emacs-xyz.scm
View File

@ -101,6 +101,7 @@
;;; Copyright © 2021 David Dashyan <mail@davie.li>
;;; Copyright © 2021 Dhruvin Gandhi <contact@dhruvin.dev>
;;; Copyright © 2021 Matthew James Kraai <kraai@ftbfs.org>
;;; Copyright © 2021 Noisytoot <noisytoot@disroot.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -155,6 +156,7 @@
#:use-module (gnu packages ibus)
#:use-module (gnu packages java)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages networking)
#:use-module (gnu packages python)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages telephony)
@ -1197,8 +1199,8 @@ handful of functions that are not resource-specific.")
(define-public emacs-typit
;; Last release is from 2017.
(let ((commit "231cb7df43253b84323520b8ed70f128d37003af")
(revision "1"))
(let ((commit "fa125bf43757737fbcf91958b76c38b440d54b4c")
(revision "2"))
(package
(name "emacs-typit")
(version (git-version "0.2.1" revision commit))
@ -1210,20 +1212,10 @@ handful of functions that are not resource-specific.")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1savrxs7xl92ifyxpxkkzv2didr7lb405h0dwz1bs1wldr5fb53f"))))
(base32 "1l0qb8gjgsmjjdvxlma7g6fn2z6rj246p2kczrikq8ajg1xh61sr"))))
(build-system emacs-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'install 'install-dictionaries
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(site-lisp
(string-append
out "/share/emacs/site-lisp/dict")))
(mkdir-p site-lisp)
(copy-recursively "dict" site-lisp)
#t))))))
'(#:include (cons "^dict/" %default-include)))
(propagated-inputs
`(("emacs-f" ,emacs-f)
("emacs-mmt" ,emacs-mmt)))
@ -2348,14 +2340,14 @@ also includes a pairing agent.")
(define-public emacs-aggressive-indent
(package
(name "emacs-aggressive-indent")
(version "1.8.3")
(version "1.10.0")
(source (origin
(method url-fetch)
(uri (string-append "https://elpa.gnu.org/packages/"
"aggressive-indent-" version ".el"))
"aggressive-indent-" version ".tar"))
(sha256
(base32
"0jnzccl50x0wapprgwxinp99pwwa6j43q6msn4gv437j7swy8wnj"))))
"166jk1z0vw481lfi3gbg7f9vsgwfv8fiyxpkfphgvgcmf5phv4q1"))))
(build-system emacs-build-system)
(home-page "https://elpa.gnu.org/packages/aggressive-indent.html")
(synopsis "Minor mode to aggressively keep your code always indented")
@ -2452,8 +2444,8 @@ configuration language. It features:
(define-public emacs-link-hint
;; Last release was in 2015.
(let ((commit "ae73db6a5948c8d109fc1d570760bcafa3f07175")
(revision "2"))
(let ((commit "9fbf196d155016d9b8471a99318ed67a086cf257")
(revision "3"))
(package
(name "emacs-link-hint")
(version (git-version "0.1" revision commit))
@ -2466,7 +2458,7 @@ configuration language. It features:
(file-name (git-file-name name version))
(sha256
(base32
"1rlbxlh9a0hnlaxpgfjvjjvmhnzwc84p9xiqi740xv82cd27wcnl"))))
"0v2g9gzf2v88ag59q1pf5vhd4qjnz3g4i6gzl27k6fi7pvlxdn39"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-avy" ,emacs-avy)))
@ -2815,16 +2807,16 @@ of bibliographic references.")
(define-public emacs-corfu
(package
(name "emacs-corfu")
(version "0.9")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/minad/corfu")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0265kld5vg870n1zaks42qdawl03zi6rjhffrkkngwgs9i9ap30i"))))
(version "0.10")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/minad/corfu")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1z61qrwjg1d28vhh39yrbrxsjbmnqws74bs3dwbw7d854d5wsy9q"))))
(build-system emacs-build-system)
(home-page "https://github.com/minad/corfu")
(synopsis "Completion overlay region function")
@ -4954,7 +4946,7 @@ displays the priority part of a heading as your preferred string value.")
(define-public emacs-org-fragtog
(package
(name "emacs-org-fragtog")
(version "0.3.2")
(version "0.3.3")
(source
(origin
(method git-fetch)
@ -4963,7 +4955,7 @@ displays the priority part of a heading as your preferred string value.")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0cw8903nw0mrn9kppwlypsb6h9m54zrb6y969yj0gnkza6gqy36c"))))
(base32 "02g4a5lsmalc5mcybimx7ils43w3ac6269n9kzcnw59bj0i5kkcj"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-org" ,emacs-org)))
@ -5481,7 +5473,7 @@ for Flow files.")
(define-public emacs-flycheck-grammalecte
(package
(name "emacs-flycheck-grammalecte")
(version "1.4")
(version "2.0")
(source
(origin
(method git-fetch)
@ -5490,7 +5482,7 @@ for Flow files.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "18yiv09hzbclf9rjp61lxlia2m1qbvmwkiqxxs9jjpac28x7ypjf"))))
(base32 "040mb9djj4cxpjsjch9i30pi36a2z7grkhnsnfdi5qyh341p4pq0"))))
(build-system emacs-build-system)
(arguments
`(#:include (cons "\\.py$" %default-include)
@ -5502,29 +5494,27 @@ for Flow files.")
;; Hard-code python3 executable location in the library.
(lambda* (#:key inputs #:allow-other-keys)
(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"
(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)))
@ -5844,6 +5834,29 @@ minibuffer to enable editing the minibuffer input in another buffer with
source code using IPython.")
(license license:gpl3+)))
(define-public emacs-ob-async
(package
(name "emacs-ob-async")
(version "1.0.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/astahlman/ob-async")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "10x4hxrjm4pr6vg42a961h9ilqzyd0l0fv7fsbq9clxi439f1nd6"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-async" ,emacs-async)
("emacs-dash" ,emacs-dash)))
(home-page "https://github.com/astahlman/ob-async")
(synopsis "Asynchronous src_block execution for org-babel")
(description "@code{ob-async} enables asynchronous execution of org-babel
src blocks.")
(license license:gpl3+)))
(define-public emacs-debbugs
(package
(name "emacs-debbugs")
@ -5961,6 +5974,51 @@ view the build status of those servers' build jobs, and possibly to trigger
build jobs.")
(license license:gpl3+)))
(define-public emacs-zmq
(package
(name "emacs-zmq")
(version "0.10.10")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/nnicandro/emacs-zmq")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0ngxm5mm0kqgvn8977ryrngamx0khzlw86d8vz5s0jhm2kgwnqp8"))))
(build-system emacs-build-system)
(arguments
`(#:tests? #f ; no tests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'configure
(lambda _
(invoke "make" "src/configure")
(substitute* "src/configure"
(("/bin/sh") (which "sh"))
(("/usr/bin/file") (which "file")))
(invoke "make")))
(add-after 'install 'install-shared-object
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(site-lisp (string-append out "/share/emacs/site-lisp"))
(libdir (string-append site-lisp "/zmq-0.10.10")))
(copy-file "emacs-zmq.so"
(string-append libdir "/emacs-zmq.so"))))))))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("libtool" ,libtool)
("pkg-config" ,pkg-config)))
(inputs
`(("zeromq" ,zeromq)))
(home-page "https://github.com/nnicandro/emacs-zmq")
(synopsis "Emacs bindings to ØMQ")
(description "This package provides Emacs bindings to ØMQ.")
(license (list license:gpl2+ ;zmq.el
license:gpl3+)))) ;src/emacs-module.h
(define-public emacs-tup-mode
(package
(name "emacs-tup-mode")
@ -6366,7 +6424,7 @@ succeeds.")
(define-public emacs-nswbuff
(package
(name "emacs-nswbuff")
(version "1.2.1")
(version "1.3")
(source
(origin
(method git-fetch)
@ -6375,7 +6433,7 @@ succeeds.")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1sswhr52rp8c4v4fv30sww1gadbdrlk3l35j8xmqfw6hbgzxb5dn"))))
(base32 "0bkx7mwy3zbb0ixawvn4cysxk3jjc7ahssvdprvw19ls9xx3wbsp"))))
(build-system emacs-build-system)
(home-page "https://github.com/joostkremers/nswbuff")
(synopsis "Quickly switch between buffers")
@ -7808,6 +7866,33 @@ Sublime Text. It features a dark blue/gray background and soft blue, green,
orange and red as accent colors.")
(license license:expat)))) ; MIT license
(define-public emacs-org-cv
;; There are no tagged releases.
(let ((commit "24bcd82348d441d95c2c80fb8ef8b5d6d4b80d95")
(revision "0"))
(package
(name "emacs-org-cv")
(version (git-version "0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://gitlab.com/Titan-C/org-cv")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0zcnbxvlwi4d6vzsm3ag7z74qphdigmx303gppb9d614jnsfsdg2"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-ox-hugo" ,emacs-ox-hugo)))
(home-page "https://titan-c.gitlab.io/org-cv/")
(synopsis "Collection of export backends for Org to generate a CV")
(description
"This project exports an Org file with reasonably structured items into
a LaTeX file, which compiles into a nice CV. In the same spirit, the Org file
may export to Markdown so that it can be used for a web based CV.")
(license license:gpl3+))))
(define-public emacs-2048-game
(package
(name "emacs-2048-game")
@ -7913,7 +7998,7 @@ single theme but a set of guidelines with numerous implementations.")
(define-public emacs-solaire-mode
(package
(name "emacs-solaire-mode")
(version "2.0.0")
(version "2.0.2")
(source
(origin
(method git-fetch)
@ -7922,7 +8007,7 @@ single theme but a set of guidelines with numerous implementations.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0aigavrqfi2dy4q5vrfs48n5k7839gqnafq7mp14cmcbrzcwadrd"))))
(base32 "01c1lkr21y0cd6gixzd38mql89k70jn049jr0xhazgz16cnw1g7j"))))
(build-system emacs-build-system)
(home-page "https://github.com/hlissner/emacs-solaire-mode")
(synopsis "Change background of file-visiting buffers in Emacs")
@ -11250,7 +11335,7 @@ Lua programming language}.")
(define-public emacs-ebuild-mode
(package
(name "emacs-ebuild-mode")
(version "1.52")
(version "1.53")
(source
(origin
(method url-fetch)
@ -11259,7 +11344,7 @@ Lua programming language}.")
"ebuild-mode-" version ".tar.xz"))
(file-name (string-append name "-" version ".tar.xz"))
(sha256
(base32 "10nikbbwh612qlnms2i31963a0h3ccyg85vrxlizdpsqs4cjpg6h"))))
(base32 "1l740qp71df9ids0c49kvp942rk8k1rfkg1hyv7ysfns5shk7b9l"))))
(build-system emacs-build-system)
(arguments
'(#:phases
@ -13342,16 +13427,16 @@ reached with the right hand.")
(define-public emacs-csharp-mode
(package
(name "emacs-csharp-mode")
(version "0.11.0")
(version "0.12.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/josteink/csharp-mode")
(commit (string-append "v" version))))
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0aq6ln92jr3hcrd1592n4s5cb079fly7qaj2hm510p9zckyfx230"))))
(base32 "1x40xm9d5sbxbnyxl12ppkzlgxzyn0bjg2vmc139jpkazmmw7r7k"))))
(build-system emacs-build-system)
(home-page "https://github.com/josteink/csharp-mode")
(synopsis "Major mode for C# code")
@ -13445,13 +13530,13 @@ containing words from the Rime project.")
(define-public emacs-pyim
(package
(name "emacs-pyim")
(version "3.9.2")
(version "3.9.3")
(source
(origin
(method url-fetch)
(uri (string-append "https://elpa.gnu.org/packages/pyim-" version ".tar"))
(sha256
(base32 "18m5wni1zns8fad2ll9flbfgxfy14gi03apnycajdbqxsqfp65j9"))))
(base32 "0rjaimvbh0fadbqiq4ggyxr0y4pfzld76wb64v7l5874qczn8dfr"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-async" ,emacs-async)
@ -15858,7 +15943,7 @@ the format.")
(define-public emacs-nov-el
(package
(name "emacs-nov-el")
(version "0.3.3")
(version "0.3.4")
(source
(origin
(method git-fetch)
@ -15868,10 +15953,11 @@ the format.")
(file-name (git-file-name name version))
(sha256
(base32
"116klnjyggwfwvs9nqhpv97m00k63q6lg41ph41kywsqkfy42dlk"))))
"0va9xjrq30cv5kb59a4rq5mcm83ggnv774r8spmskff3hj8012wf"))))
(build-system emacs-build-system)
(arguments
`(#:phases
`(#:emacs ,emacs ;need libxml
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'embed-path-to-unzip
(lambda _
@ -15949,6 +16035,34 @@ Features:
the pipeline, featuring the support for running @code{emacsclient}.")
(license license:gpl3+)))
(define-public emacs-jupyter
(package
(name "emacs-jupyter")
(version "0.8.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/nnicandro/emacs-jupyter")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1sr007wsl2y6wqpzkmv3inbpwhvgdcb2nmqzgfg7w1awapi2r13p"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-company" ,emacs-company) ;optional
("emacs-markdown-mode" ,emacs-markdown-mode) ;optional
("emacs-simple-httpd" ,emacs-simple-httpd)
("emacs-websocket" ,emacs-websocket)
("emacs-zmq" ,emacs-zmq)))
(home-page "https://github.com/nnicandro/emacs-jupyter")
(synopsis "Emacs interface to communicate with Jupyter kernels")
(description "This package provides an Emacs interface to communicate with
Jupyter kernels. It provides REPL and @code{org-mode} source code block
frontends to Jupyter kernels and kernel interactions integrated with Emacs'
built-in features.")
(license license:gpl3+)))
(define-public emacs-hcl-mode
(package
(name "emacs-hcl-mode")
@ -24406,7 +24520,7 @@ previewed by scrolling up and down within a @code{dired} buffer.")
(define-public emacs-counsel-etags
(package
(name "emacs-counsel-etags")
(version "1.9.16")
(version "1.9.17")
(source
(origin
(method git-fetch)
@ -24415,13 +24529,13 @@ previewed by scrolling up and down within a @code{dired} buffer.")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "01si554r0s6m7ypx1m2n0z6j6q6yihifz76dha6q6v56ixdlv626"))))
(base32 "07445bbr68q1pnwpj5bwqmml9ky1gq67g24zswv8fylnzjkhy9wc"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-counsel" ,emacs-counsel)))
(arguments
`(#:tests? #t
#:test-command '("make" "test")))
`(#:tests? #f ;require internet access
#:test-command '("make test")))
(home-page "https://github.com/redguardtoo/counsel-etags")
(synopsis "Fast @code{Ctags}/@code{Etags} solution with @code{ivy-mode}")
(description "This package uses @code{ivy-mode} to facilitate navigating
@ -25264,37 +25378,40 @@ it forcibly
(license license:gpl3+))))
(define-public emacs-elpher
(package
(name "emacs-elpher")
(version "2.10.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "git://thelambdalab.xyz/elpher.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0xqiisirpvw4ka9417pq4r73x937wl3qbf8cpn2i03akm8d58smd"))))
(build-system emacs-build-system)
(native-inputs
`(("texinfo" ,texinfo)))
(arguments
`(#:phases
(modify-phases %standard-phases
(add-before 'install 'build-doc
(lambda _
(invoke "makeinfo" "elpher.texi"))))))
(home-page "gopher://thelambdalab.xyz/1/projects/elpher/")
(synopsis "Gopher and gemini client for Emacs")
(description "Elpher is a full-featured gopher and gemini client for
;; No tagged release upstream, but the commit below corresponds to the 2.10.3
;; release.
(let ((commit "b0272de36cea3e1cd41cd15a012c8141b4b04575"))
(package
(name "emacs-elpher")
(version "2.10.3")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "git://thelambdalab.xyz/elpher.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1m6lq47i4j6k76f81vcch6akab9mqph7kna3fn356295fvgm7j7q"))))
(build-system emacs-build-system)
(native-inputs
`(("texinfo" ,texinfo)))
(arguments
`(#:phases
(modify-phases %standard-phases
(add-before 'install 'build-doc
(lambda _
(invoke "makeinfo" "elpher.texi"))))))
(home-page "gopher://thelambdalab.xyz/1/projects/elpher/")
(synopsis "Gopher and gemini client for Emacs")
(description "Elpher is a full-featured gopher and gemini client for
Emacs. Its features include intuitive keyboard and mouse-driven browsing,
out-of-the-box compatibility with evil-mode, clickable links in plain text,
caching of visited sites, pleasant and configurable visualization of Gopher
directories, direct visualisation of image files, jumping directly to links by
name (with autocompletion), a simple bookmark management system and
connections using TLS encryption.")
(license license:gpl3+)))
(license license:gpl3+))))
(define-public emacs-zerodark-theme
(package
@ -25529,14 +25646,14 @@ federated microblogging social network.")
(define-public emacs-ebdb
(package
(name "emacs-ebdb")
(version "0.6.24")
(version "0.7")
(source
(origin
(method url-fetch)
(uri (string-append "https://elpa.gnu.org/packages/"
"ebdb-" version ".tar"))
(sha256
(base32 "0156rh6fkv2yp509h6i8qzh4gsda2mcmfrxl4r6ywn1z5ahijc3r"))))
(base32 "0q4ywgh87d6hjac3031s21w91gld2hh7s8nbva94dnzwn6y9d0v1"))))
(build-system emacs-build-system)
(home-page "https://github.com/girzel/ebdb")
(synopsis "EIEIO port of BBDB, Emacs's contact-management package")
@ -25880,7 +25997,7 @@ Emacs that integrate with major modes like Org-mode.")
(define-public emacs-modus-themes
(package
(name "emacs-modus-themes")
(version "1.4.0")
(version "1.5.0")
(source
(origin
(method git-fetch)
@ -25889,7 +26006,7 @@ Emacs that integrate with major modes like Org-mode.")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1lw3spg7r7ga8sl2pnr1snviqgbvhxayl1mm7dny720a8mgv49f0"))))
(base32 "1yz5yr3acc601xcms7vr2jbj4bq6dqz8n5ymyfyxldid0n5ykzy4"))))
(build-system emacs-build-system)
(home-page "https://protesilaos.com/modus-themes/")
(synopsis "Accessible themes (WCAG AAA)")
@ -27807,7 +27924,7 @@ snippets for Emacs.")
(define-public emacs-org-roam
(package
(name "emacs-org-roam")
(version "1.2.4")
(version "2.0.0")
(source
(origin
(method git-fetch)
@ -27816,7 +27933,7 @@ snippets for Emacs.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "10jrnjq65lpg1x8d7lqc537yai9m6pdnfbzwr87fcyv6f8yii8xn"))))
(base32 "0mslrdgd41czay3w7znz4qsv1h0p3zqfsq6bkyxmxfyd2w5z82zf"))))
(build-system emacs-build-system)
(arguments
`(#:phases
@ -27839,6 +27956,7 @@ snippets for Emacs.")
`(("emacs-dash" ,emacs-dash)
("emacs-emacsql-sqlite3" ,emacs-emacsql-sqlite3)
("emacs-f" ,emacs-f)
("emacs-magit" ,emacs-magit)
("emacs-org" ,emacs-org)
("emacs-s" ,emacs-s)))
(home-page "https://github.com/org-roam/org-roam/")
@ -27853,7 +27971,7 @@ personal wiki.")
(define-public emacs-org-roam-bibtex
(package
(name "emacs-org-roam-bibtex")
(version "0.6.0-pre.2")
(version "0.6.0")
(source
(origin
(method git-fetch)
@ -27862,7 +27980,7 @@ personal wiki.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0cjj7lx73qg4yw84r3b8fqhp5r74bzi57nvnvbvbck4i33ywqwx5"))))
(base32 "04vc2w7x2lyamp0qa1y274smsf9x2qxr1igrpz9f4y5ha5332px5"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-helm-bibtex" ,emacs-helm-bibtex)
@ -28899,3 +29017,54 @@ to the @url{https://multitran.com} online dictionary.")
"Kibit Helper provides functions to work with the Kibit Leiningen plugin
for detecting and improve non-idiomatic Clojure source code.")
(license license:gpl3+)))
(define-public emacs-seeing-is-believing
(let ((version "1.2.0") ; from .el file
(commit "fbbe246c0fda87bb26227bb826eebadb418a220f")
(revision "0"))
(package
(name "emacs-seeing-is-believing")
(home-page "https://github.com/jcinnamond/seeing-is-believing")
(version (git-version version revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url home-page)
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1h1b48s2iirswdlvfz41jbflm4x09ksc2lycrc1awzlwd6r8hdhg"))))
(build-system emacs-build-system)
(synopsis
"Minor mode for running the seeing-is-believing Ruby gem")
(description
"@uref{https://github.com/JoshCheek/seeing_is_believing,Seeing Is
Believing} is a ruby gem to evaluate Ruby code, recording the results of each
line. This minor mode provides an easy way to run it from Emacs on the
current region or entire buffer.")
(license license:gpl3+))))
(define-public emacs-nasm-mode
(package
(name "emacs-nasm-mode")
(version "1.1.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/skeeto/nasm-mode")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1dyc50a1zskx9fqxl2iy2x74f3bkb2ccz908v0aj13rqfqqnns9j"))))
(build-system emacs-build-system)
(home-page "https://github.com/skeeto/nasm-mode")
(synopsis "NASM x86 assembly major mode")
(description
"NASM mode is a major mode for editing NASM x86 assembly programs.
It includes syntax highlighting, automatic indentation, and imenu integration.
Unlike Emacs' generic ASM mode, it understands NASM-specific syntax.")
(license license:unlicense)))

58
gnu/packages/emulators.scm
View File

@ -722,7 +722,7 @@ The following systems are supported:
(define-public mgba
(package
(name "mgba")
(version "0.9.1")
(version "0.9.2")
(source
(origin
(method git-fetch)
@ -731,7 +731,7 @@ The following systems are supported:
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "163azad5y4zxwzxyrb481rwfc2p86v99pf7nvdr6bavzq98x2z8h"))
(base32 "16kngkzf08jflqxwbgafb47091vqqb9pbhazg9cd94cy81ahz3q3"))
(modules '((guix build utils)))
(snippet
;; Make sure we don't use the bundled software.
@ -740,29 +740,30 @@ The following systems are supported:
(lambda (subdir)
(let ((lib-subdir (string-append "src/third-party/" subdir)))
(delete-file-recursively lib-subdir)))
'("libpng" "lzma" "sqlite3" "zlib"))
#t))))
'("libpng" "lzma" "sqlite3" "zlib"))))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ;no "test" target
#:configure-flags
(list "-DUSE_LZMA=OFF" ;do not use bundled LZMA
"-DUSE_LIBZIP=OFF"))) ;use "zlib" instead
(native-inputs `(("pkg-config" ,pkg-config)
("qttools" ,qttools)))
(inputs `(("ffmpeg" ,ffmpeg)
("libedit" ,libedit)
("libelf" ,libelf)
("libepoxy" ,libepoxy)
("libpng" ,libpng)
("mesa" ,mesa)
("minizip" ,minizip)
("ncurses" ,ncurses)
("qtbase" ,qtbase-5)
("qtmultimedia" ,qtmultimedia)
("sdl2" ,sdl2)
("sqlite" ,sqlite)
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)
("qttools" ,qttools)))
(inputs
`(("ffmpeg" ,ffmpeg)
("libedit" ,libedit)
("libelf" ,libelf)
("libepoxy" ,libepoxy)
("libpng" ,libpng)
("mesa" ,mesa)
("minizip" ,minizip)
("ncurses" ,ncurses)
("qtbase" ,qtbase-5)
("qtmultimedia" ,qtmultimedia)
("sdl2" ,sdl2)
("sqlite" ,sqlite)
("zlib" ,zlib)))
(home-page "https://mgba.io")
(synopsis "Game Boy Advance emulator")
(description
@ -1769,7 +1770,7 @@ This is a part of the TiLP project.")
(define-public mame
(package
(name "mame")
(version "0.233")
(version "0.234")
(source
(origin
(method git-fetch)
@ -1778,7 +1779,7 @@ This is a part of the TiLP project.")
(commit (apply string-append "mame" (string-split version #\.)))))
(file-name (git-file-name name version))
(sha256
(base32 "1zq7hvss004mwczk3jvyalkj9c5v6npswhkc2wj7dxyxz770clb3"))
(base32 "010ing14pfwc0j7jnghjdcvq0qr7g4dplnggl545apyy61zigdkn"))
(modules '((guix build utils)))
(snippet
;; Remove bundled libraries.
@ -1787,8 +1788,7 @@ This is a part of the TiLP project.")
(for-each delete-file-recursively
'("asio" "expat" "glm" "libflac" "libjpeg" "lua"
"portaudio" "portmidi" "pugixml" "rapidjson" "SDL2"
"SDL2-override" "sqlite3" "utf8proc" "zlib")))
#t))))
"SDL2-override" "sqlite3" "utf8proc" "zlib")))))))
(build-system gnu-build-system)
(arguments
`(#:make-flags
@ -1826,16 +1826,14 @@ This is a part of the TiLP project.")
(install-file "uismall.bdf" fonts))
(when (file-exists? "mame64")
(rename-file "mame64" "mame"))
(install-file "mame" (string-append out "/bin")))
#t))
(install-file "mame" (string-append out "/bin")))))
(add-after 'install 'install-documentation
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(man (string-append out "/share/man/man1"))
(info (string-append out "/share/info")))
(install-file "docs/build/man/MAME.1" man)
(install-file "docs/build/texinfo/MAME.info" info))
#t))
(install-file "docs/build/texinfo/MAME.info" info))))
(add-after 'install 'install-ini-file
;; Generate an ini file so as to set some directories (e.g., roms)
;; to a writable location, i.e., "$HOME/.mame/" and "$HOME/mame/".
@ -1894,8 +1892,7 @@ This is a part of the TiLP project.")
select_directory $HOME/mame/select~@
icons_directory $HOME/mame/icons~@
covers_directory $HOME/mame/covers~@
ui_path $HOME/.mame/ui~%")))
#t)))
ui_path $HOME/.mame/ui~%"))))))
(add-after 'install 'install-desktop-file
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@ -1914,8 +1911,7 @@ This is a part of the TiLP project.")
Type=Application~@
Categories=Game;Emulator;~@
Keywords=Game;Emulator;Arcade;~%"
executable)))
#t))))))
executable)))))))))
(native-inputs
`(("pkg-config" ,pkg-config)
("sphinx" ,python-sphinx)

11
gnu/packages/enlightenment.scm
View File

@ -571,17 +571,22 @@ directories.
(define-public evisum
(package
(name "evisum")
(version "0.5.11")
(version "0.5.13")
(source
(origin
(method url-fetch)
(uri (string-append "https://download.enlightenment.org/rel/apps/"
"evisum/evisum-" version ".tar.xz"))
(sha256
(base32 "0cbfg393nlf0k91a2hdlyakns3dpzvs3isd95dm3zizydyf9h8wc"))))
(base32 "1rjqvida4anh7gqjp6xrpk6kmhqb66r733yyr2ixphgxn33p3iac"))))
(build-system meson-build-system)
(arguments
'(#:tests? #f)) ; no tests
'(#:tests? #f ; no tests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'set-homedir
(lambda _
(setenv "HOME" (getcwd)))))))
(native-inputs
`(("gettext" ,gettext-minimal)
("pkg-config" ,pkg-config)))

45
gnu/packages/freedesktop.scm
View File

@ -75,6 +75,7 @@
#:use-module (gnu packages glib) ;intltool
#:use-module (gnu packages gnome)
#:use-module (gnu packages gperf)
#:use-module (gnu packages graph)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages gstreamer)
#:use-module (gnu packages gtk)
@ -96,6 +97,7 @@
#:use-module (gnu packages python)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages rdesktop)
#:use-module (gnu packages samba)
#:use-module (gnu packages sqlite)
#:use-module (gnu packages valgrind)
@ -1065,7 +1067,7 @@ protocol either in Wayland core, or some other protocol in wayland-protocols.")
(define-public weston
(package
(name "weston")
(version "6.0.1")
(version "9.0.0")
(source (origin
(method url-fetch)
(uri (string-append
@ -1073,43 +1075,60 @@ protocol either in Wayland core, or some other protocol in wayland-protocols.")
"weston-" version ".tar.xz"))
(sha256
(base32
"1d2m658ll8x7prlsfk71qgw89c7dz6y7d6nndfxwl49fmrd6sbxz"))))
"1zlql0xgiqc3pvgbpnnvj4xvpd91pwva8qf83xfb23if377ddxaw"))))
(build-system meson-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)
`(("mscgen" ,mscgen)
("pkg-config" ,pkg-config)
("xorg-server" ,xorg-server)))
(inputs
`(("cairo" ,cairo-xcb)
("colord" ,colord)
("dbus" ,dbus)
("elogind" ,elogind)
("freerdp" ,freerdp)
("glib" ,glib)
("gstreamer" ,gstreamer)
("gst-plugins-base" ,gst-plugins-base)
("lcms" ,lcms)
("libdrm" ,libdrm)
("libevdev" ,libevdev)
("libinput" ,libinput-minimal)
("libjpeg" ,libjpeg-turbo)
("libpng" ,libpng)
("libunwind" ,libunwind)
("libva" ,libva)
("libwebp" ,libwebp)
("libx11" ,libx11)
("libxcb" ,libxcb)
("libxcursor" ,libxcursor)
("libxkbcommon" ,libxkbcommon)
("libxml2" ,libxml2)
("mesa" ,mesa)
("mtdev" ,mtdev)
("linux-pam" ,linux-pam)
("pango" ,pango)
("wayland" ,wayland)
("pipewire" ,pipewire)
("wayland-protocols" ,wayland-protocols)
("xorg-server-xwayland" ,xorg-server-xwayland)))
(propagated-inputs
`(("libxkbcommon" ,libxkbcommon)
("pixman" ,pixman)
("wayland" ,wayland)))
(arguments
`(#:configure-flags
(list "-Dbackend-rdp=false" ; TODO: Enable.
"-Dremoting=false" ; TODO: Enable.
"-Dsimple-dmabuf-drm=auto"
"-Dsystemd=false"
(string-append "-Dxwayland-path="
(assoc-ref %build-inputs "xorg-server-xwayland")
"/bin/Xwayland"))
#:parallel-tests? #f ; Parallel tests cause failures.
(list
;; Otherwise, the RUNPATH will lack the final path component.
(string-append "-Dc_link_args=-Wl,-rpath="
(assoc-ref %outputs "out") "/lib:"
(assoc-ref %outputs "out") "/lib/weston:"
(assoc-ref %outputs "out") "/lib/libweston-"
,(version-major (package-version this-package)))
"-Dbackend-default=auto"
"-Dsystemd=false"
(string-append "-Dxwayland-path="
(assoc-ref %build-inputs "xorg-server-xwayland")
"/bin/Xwayland"))
#:parallel-tests? #f ; Parallel tests cause failures.
#:phases
(modify-phases %standard-phases
(add-before 'configure 'use-elogind

55
gnu/packages/geo.scm
View File

@ -9,7 +9,7 @@
;;; Copyright © 2018, 2019, 2020 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2019, 2020, 2021 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
;;; Copyright © 2019, 2021 Wiktor Żelazny <wzelazny@vurv.cz>
;;; Copyright © 2019, 2020 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2020 Christopher Baines <mail@cbaines.net>
@ -210,7 +210,7 @@ topology functions.")
(define-public gnome-maps
(package
(name "gnome-maps")
(version "3.36.7")
(version "3.38.5")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/" name "/"
@ -218,7 +218,7 @@ topology functions.")
name "-" version ".tar.xz"))
(sha256
(base32
"09rgw8hq3ligap1zzjhx25q354ficpbiw1z9ramghhcqbpylsxdh"))))
"1llgzm2ni3iy31dznqkc81vadv0fpqgpz2l9zzrj5jshvyq0akgh"))))
(build-system meson-build-system)
(arguments
`(#:glib-or-gtk? #t
@ -236,6 +236,15 @@ topology functions.")
(("@pkgdatadir@/org.gnome.Maps")
(string-append (assoc-ref outputs "out") "/bin/gnome-maps")))
#t))
(add-after 'unpack 'fix-broken-tests
(lambda _
;; For some reason setting LC_ALL=C and LANG=C as done in the
;; build system does not prevent these gratuitous commas from
;; being inserted.
(substitute* "tests/utilsTest.js"
(("1001 m") "1,001 m")
(("1000 ft") "1,000 ft")
(("5282 ft") "5,282 ft"))))
(add-after 'install 'wrap
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
@ -2412,3 +2421,43 @@ web services. @code{geopy} makes it easy for Python developers to locate the
coordinates of addresses, cities, countries, and landmarks across the globe
using third-party geocoders and other data sources.")
(license license:expat)))
(define-public marble-qt
(let ((release "17.08")
(commit "fc7166eeef784732033c999ba605364f9c82d21c")
(revision "1"))
(package
(name "marble-qt")
(version (git-version release revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://invent.kde.org/education/marble.git/")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0m0sf3sddaib7vc5lhbmh7ziw07p1hahg02f65sgfylyl5f5kj92"))
(patches (search-patches
"marble-qt-add-qt-headers.patch"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ; libmarblewidget-qt5.so.28 not found
#:configure-flags
'("-DCMAKE_BUILD_TYPE=Release"
"-DWITH_KF5=FALSE")))
(native-inputs
`(("qttools" ,qttools)))
(inputs
`(("qtbase" ,qtbase-5)
("qtsvg" ,qtsvg)
("qtdeclarative" ,qtdeclarative)
("qtwebkit" ,qtwebkit)
("qtlocation" ,qtlocation)))
(home-page "https://marble.kde.org/")
(synopsis "Virtual globe and world atlas")
(description "Marble is similar to a desktop globe. At closer scale it
becomes a world atlas, while OpenStreetMap takes the user to street level. It
supports searching for places of interest, viewing Wikipedia articles,
creating routes by drag and drop and more.")
(license license:gpl3))))

25
gnu/packages/gl.scm
View File

@ -15,6 +15,7 @@
;;; 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.
;;;
@ -484,10 +485,26 @@ from software emulation to complete hardware acceleration for modern GPUs.")
(package/inherit mesa-opencl
(name "mesa-opencl-icd")
(arguments
(substitute-keyword-arguments (package-arguments mesa)
((#:configure-flags flags)
`(cons "-Dgallium-opencl=icd"
,(delete "-Dgallium-opencl=standalone" flags)))))))
(substitute-keyword-arguments (package-arguments mesa)
((#:configure-flags flags)
`(cons "-Dgallium-opencl=icd"
,(delete "-Dgallium-opencl=standalone" flags)))
((#:phases phases)
`(modify-phases ,phases
(add-after 'install 'mesa-icd-absolute-path
(lambda _
;; Use absolute path for OpenCL platform library.
;; Otherwise we would have to set LD_LIBRARY_PATH=LIBRARY_PATH
;; for ICD in our applications to find OpenCL platform.
(use-modules (guix build utils)
(ice-9 textual-ports))
(let* ((out (assoc-ref %outputs "out"))
(mesa-icd (string-append out "/etc/OpenCL/vendors/mesa.icd"))
(old-path (call-with-input-file mesa-icd get-string-all))
(new-path (string-append out "/lib/" (string-trim-both old-path))))
(if (file-exists? new-path)
(call-with-output-file mesa-icd
(lambda (port) (format port "~a\n" new-path)))))))))))))
(define-public mesa-headers
(package/inherit mesa

70
gnu/packages/gnome.scm
View File

@ -3926,67 +3926,6 @@ graphical interfaces described in glade files and for accessing the
widgets built in the loading process.")
(license license:gpl2+))) ; This is correct. GPL not LGPL
(define-public libgnomeprint
;; This library has been deprecated since 2006; see
;; <https://mail.gnome.org/archives/devel-announce-list/2006-August/msg00005.html>.
(package
(name "libgnomeprint")
(version "2.18.8")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/" name "/"
(version-major+minor version) "/"
name "-" version ".tar.bz2"))
(sha256
(base32
"14cnimvlc7ky22g2snyf4362412k3jk1syjf8b9887q5a63fqd0h"))))
(build-system gnu-build-system)
(inputs
`(("popt" ,popt)
("libart-lgpl" ,libart-lgpl)
("gtk+" ,gtk+-2)
("libxml2" ,libxml2)))
(native-inputs
`(("intltool" ,intltool)
("glib" ,glib "bin") ; for glib-genmarshal, etc.
("pkg-config" ,pkg-config)))
(home-page "https://projects.gnome.org/gnome-print/home/faq.html")
(synopsis "Printing framework for GNOME")
(description
"GNOME-print was a printing framework for GNOME. It has been deprecated
since ca. 2006, when GTK+ itself incorporated printing support.")
(license license:lgpl2.0+)))
(define-public libgnomeprintui
;; Deprecated; see libgnomeprint.
(package
(name "libgnomeprintui")
(version "2.18.6")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/" name "/"
(version-major+minor version) "/"
name "-" version ".tar.bz2"))
(sha256
(base32
"0spl8vinb5n6n1krnfnr61dwaxidg67h8j94z9p59k2xdsvfashm"))))
(build-system gnu-build-system)
;; Mentioned as Required in the .pc file
(propagated-inputs `(("libgnomeprint" ,libgnomeprint)))
(inputs `(("gtk+" ,gtk+-2)
("glib" ,glib)
("gnome-icon-theme" ,gnome-icon-theme)
("libgnomecanvas" ,libgnomecanvas)
("libxml2" ,libxml2)))
(native-inputs
`(("intltool" ,intltool)
("pkg-config" ,pkg-config)))
(home-page "https://projects.gnome.org/gnome-print/home/faq.html")
(synopsis "Printing framework for GNOME")
(description (package-description libgnomeprint))
(license license:lgpl2.0+)))
(define-public libbonoboui
(package
(name "libbonoboui")
@ -10198,9 +10137,7 @@ that support the Assistive Technology Service Provider Interface (AT-SPI).")
(setenv "ASPELL_DICT_DIR"
(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)
@ -10212,7 +10149,10 @@ that support the Assistive Technology Service Provider Interface (AT-SPI).")
("aspell-dict-en" ,aspell-dict-en)
("xorg-server" ,xorg-server-for-tests)))
(propagated-inputs
`(("enchant" ,enchant))) ;enchant.pc is required by gspell-1.pc
;; Referred by .pc file.
`(("enchant" ,enchant)
("glib" ,glib)
("gtk+" ,gtk+)))
(home-page "https://wiki.gnome.org/Projects/gspell")
(synopsis "GNOME's alternative spell checker")
(description

8
gnu/packages/gnuzilla.scm
View File

@ -1304,11 +1304,11 @@ standards of the IceCat project.")
(cpe-version . ,(first (string-split version #\-)))))))
;; Update this together with icecat!
(define %icedove-build-id "20210601000000") ;must be of the form YYYYMMDDhhmmss
(define %icedove-build-id "20210713000000") ;must be of the form YYYYMMDDhhmmss
(define-public icedove
(package
(name "icedove")
(version "78.11.0")
(version "78.12.0")
(source icecat-source)
(properties
`((cpe-name . "thunderbird_esr")))
@ -1592,7 +1592,7 @@ standards of the IceCat project.")
;; in the Thunderbird release tarball. We don't use the release
;; tarball because it duplicates the Icecat sources and only adds the
;; "comm" directory, which is provided by this repository.
,(let ((changeset "1717d8d5fbd359aab7a4a0a15f4d15c72a7e6afc"))
,(let ((changeset "6796ff47626a009d169a1e9fd1f307a6c14b7ed5"))
(origin
(method hg-fetch)
(uri (hg-reference
@ -1601,7 +1601,7 @@ standards of the IceCat project.")
(file-name (string-append "thunderbird-" version "-checkout"))
(sha256
(base32
"10l042dd7b8rvla0cbiks5kjrz2b28yy7hr8sr169wlx202hxa01")))))
"1nnz90h5w9skpdwm8ilndcwfx9d7k9cn6gzh32y4jil95da13813")))))
("autoconf" ,autoconf-2.13)
("cargo" ,rust "cargo")
("clang" ,clang)

11
gnu/packages/gpodder.scm
View File

@ -30,6 +30,7 @@
#:use-module (gnu packages)
#:use-module (gnu packages autotools)
#:use-module (gnu packages base)
#:use-module (gnu packages bash)
#:use-module (gnu packages check)
#:use-module (gnu packages curl)
#:use-module (gnu packages freedesktop)
@ -37,6 +38,7 @@
#:use-module (gnu packages gtk)
#:use-module (gnu packages groff)
#:use-module (gnu packages mp3)
#:use-module (gnu packages music)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
@ -68,12 +70,14 @@
("python-pytest-httpserver" ,python-pytest-httpserver)
("which" ,which)))
(inputs
`(("gtk+" ,gtk+)
`(("bash-minimal" ,bash-minimal)
("gtk+" ,gtk+)
("python-pygobject" ,python-pygobject)
("python-pycairo" ,python-pycairo)
("python-requests" ,python-requests)
("python-dbus" ,python-dbus)
("python-html5lib" ,python-html5lib)
("python-mutagen" ,python-mutagen)
("python-mygpoclient" ,python-mygpoclient)
("python-podcastparser" ,python-podcastparser)
("youtube-dl" ,youtube-dl)
@ -89,8 +93,9 @@
(("xdg-open") (string-append xdg-utils "/bin/xdg-open")))
#t)))
(replace 'check
(lambda _
(invoke "make" "unittest")))
(lambda* (#:key tests? #:allow-other-keys)
(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

24
gnu/packages/graph.scm
View File

@ -539,7 +539,7 @@ transformed into common image formats for display or printing.")
(define-public python-graph-tool
(package
(name "python-graph-tool")
(version "2.37")
(version "2.43")
(source (origin
(method url-fetch)
(uri (string-append
@ -547,7 +547,7 @@ transformed into common image formats for display or printing.")
version ".tar.bz2"))
(sha256
(base32
"0w2i4d4zyk051zkykcg0ksngspajznwmp523hbsx50xnxc6jliyz"))))
"0v58in4rwk9fhjarjw6xfxpx5zz2z13sy3yvd14b5kr0884yw6sz"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
@ -563,23 +563,23 @@ transformed into common image formats for display or printing.")
"python"))))
"/site-packages/"))))
(native-inputs
`(("pkg-config" ,pkg-config)
("gcc-10" ,gcc-10)
("ncurses" ,ncurses)))
`(("gcc-10" ,gcc-10)
("ncurses" ,ncurses)
("pkg-config" ,pkg-config)))
(inputs
`(("python" ,python-wrapper)
("boost" ,boost)
`(("boost" ,boost)
("cairomm" ,cairomm)
("cgal" ,cgal)
("expat" ,expat)
("gmp" ,gmp)
("cgal" ,cgal)
("sparsehash" ,sparsehash)
("gtk+" ,gtk+)
("cairomm" ,cairomm)))
("python" ,python-wrapper)
("sparsehash" ,sparsehash)))
(propagated-inputs
`(("python-scipy" ,python-scipy)
`(("python-matplotlib" ,python-matplotlib)
("python-numpy" ,python-numpy)
("python-pycairo" ,python-pycairo)
("python-matplotlib" ,python-matplotlib)))
("python-scipy" ,python-scipy)))
(synopsis "Manipulate and analyze graphs with Python efficiently")
(description "Graph-tool is an efficient Python module for manipulation
and statistical analysis of graphs (a.k.a. networks). Contrary to most other

2
gnu/packages/graphviz.scm
View File

@ -118,7 +118,7 @@
("swig" ,swig)
("pkg-config" ,pkg-config)))
(outputs '("out" "doc")) ; 5 MiB of html + pdfs
(home-page "http://www.graphviz.org/")
(home-page "https://www.graphviz.org/")
(synopsis "Graph visualization software")
(description
"Graphviz is a graph visualization tool suite. Graph visualization is a

4
gnu/packages/guile.scm
View File

@ -805,7 +805,7 @@ type system, elevating types to first-class status.")
(define-public guile-git
(package
(name "guile-git")
(version "0.5.1")
(version "0.5.2")
(home-page "https://gitlab.com/guile-git/guile-git.git")
(source (origin
(method git-fetch)
@ -815,7 +815,7 @@ type system, elevating types to first-class status.")
(file-name (git-file-name name version))
(sha256
(base32
"1x3wa6la4j1wcfxyhhjlmd7yp85wwpny0y6lrzpz803i9z5fwagc"))))
"11a51acibwi2hpaygmrpn6nwbr4lqalc87ihrgj3mhz6swbsk9n7"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags '("GUILE_AUTO_COMPILE=0"))) ; to prevent guild warnings

4
gnu/packages/haskell-apps.scm
View File

@ -344,14 +344,14 @@ to @code{cabal repl}).")
(define-public git-annex
(package
(name "git-annex")
(version "8.20210630")
(version "8.20210714")
(source
(origin
(method url-fetch)
(uri (string-append "https://hackage.haskell.org/package/"
"git-annex/git-annex-" version ".tar.gz"))
(sha256
(base32 "0mxzddaf7ra807aazx9gd4rl5565xzky0hwiyby0a06yqnf02266"))))
(base32 "0pkzqa8qmckv4fcc9pndlplz4w0ndlqkp18hx6pyycckycljdyzy"))))
(build-system haskell-build-system)
(arguments
`(#:configure-flags

12
gnu/packages/haskell.scm
View File

@ -20,6 +20,7 @@
;;; Copyright © 2019 Robert Vollmert <rob@vllmrt.net>
;;; Copyright © 2019 Jacob MacDonald <jaccarmac@gmail.com>
;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2021 Matthew James Kraai <kraai@ftbfs.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -612,14 +613,14 @@ interactive environment for the functional language Haskell.")
(define-public ghc-8.8
(package (inherit ghc-8.6)
(name "ghc")
(version "8.8.3")
(version "8.8.4")
(source
(origin
(method url-fetch)
(uri (string-append "https://www.haskell.org/ghc/dist/"
version "/ghc-" version "-src.tar.xz"))
(sha256
(base32 "128g932i3wix6ic03v04nh5755vyjiidzri9iybwad72yfmc1p70"))))
(base32 "0bgwbxxvdn56l91bp9p5d083gzcfdi6z8l8b17qzjpr3n8w5wl7h"))))
(native-inputs
`(("ghc-bootstrap" ,ghc-8.6)
("ghc-testsuite"
@ -631,7 +632,7 @@ interactive environment for the functional language Haskell.")
(patches (search-patches "ghc-testsuite-dlopen-pie.patch"))
(sha256
(base32
"1l32mp94ll72skfsq1g2fqax4bkiw8b85gr3wd0bbqsqyi9a9jpr"))))
"0c55pj2820q26rikhpf636sn4mjgqsxjrl94vsywrh79dxp3k14z"))))
("git" ,git) ; invoked during tests
,@(filter (match-lambda
(("ghc-bootstrap" . _) #f)
@ -642,6 +643,11 @@ interactive environment for the functional language Haskell.")
(substitute-keyword-arguments (package-arguments ghc-8.6)
((#:phases phases '%standard-phases)
`(modify-phases ,phases
(add-after 'fix-references 'fix-cc-reference
(lambda _
(substitute* "utils/hsc2hs/Common.hs"
(("\"cc\"") "\"gcc\""))
#t))
(add-after 'unpack-testsuite 'skip-more-tests
(lambda _
;; XXX: This test fails because our ld-wrapper script

18
gnu/packages/java.scm
View File

@ -7955,14 +7955,14 @@ This is a part of the Apache Commons Project.")
(define-public java-commons-codec
(package
(name "java-commons-codec")
(version "1.14")
(version "1.15")
(source (origin
(method url-fetch)
(uri (string-append "mirror://apache/commons/codec/source/"
"commons-codec-" version "-src.tar.gz"))
(sha256
(base32
"11xr0agckkhm91pb5akf2mbk84yd54gyr178wj57gsm97fi7nkh9"))))
"01z9qmg8fd8d7p7xxipwj1vi9bmvpgqyi29kldjz2x6vzwm171jj"))))
(build-system ant-build-system)
(arguments
`(#:jar-name "java-commons-codec.jar"
@ -7974,13 +7974,19 @@ This is a part of the Apache Commons Project.")
(add-before 'build 'copy-resources
(lambda _
(copy-recursively "src/main/resources"
"build/classes")
#t))
"build/classes")))
(add-before 'check 'copy-test-resources
(lambda _
(copy-recursively "src/test/resources"
"build/test-classes")
#t))
"build/test-classes")))
(add-before 'check 'skip-ravenous-test
(lambda _
;; This test admits to being "memory hungry", but reliably fails
;; even on a machine that should have plenty (12 GiB). Skip it.
(substitute*
"src/test/java/org/apache/commons/codec/binary/BaseNCodecTest.java"
(("\\bassertEnsureBufferSizeExpandsToMaxBufferSize.*;")
"return;"))))
(replace 'install (install-from-pom "pom.xml")))))
(native-inputs
`(("java-commons-lang3" ,java-commons-lang3)

3
gnu/packages/julia-jll.scm
View File

@ -40,6 +40,7 @@
#:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages julia)
#:use-module (gnu packages julia-xyz)
#:use-module (gnu packages libffi)
#:use-module (gnu packages linux)
#:use-module (gnu packages maths)
@ -639,6 +640,8 @@ rendering library.")
(("return joinpath.*") "return $override\n"))
#t)))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-preferences" ,julia-preferences)))
(home-page "https://github.com/JuliaPackaging/JLLWrappers.jl")
(synopsis "Julia macros used by JLL packages")
(description "This package contains Julia macros that enable JLL packages

302
gnu/packages/julia-xyz.scm
View File

@ -21,6 +21,7 @@
(define-module (gnu packages julia-xyz)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
#:use-module (guix packages)
#:use-module (guix git-download)
#:use-module (guix build-system julia)
@ -120,7 +121,7 @@ provides functions to run a few automatable checks for Julia packages.")
(define-public julia-arrayinterface
(package
(name "julia-arrayinterface")
(version "3.1.17")
(version "3.1.19")
(source
(origin
(method git-fetch)
@ -129,7 +130,7 @@ provides functions to run a few automatable checks for Julia packages.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1yfl7wsciqm8ggfs6grxdrvpkxniy4c63d05f65v2j0c55z8a6mn"))))
(base32 "0cmldnzvdgmfnrnrzgj6v1mfr2rvk5096392rwmhd3iyx7v0pq33"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-ifelse" ,julia-ifelse)
@ -156,7 +157,7 @@ no issues with the upgrade.")
(define-public julia-arraylayouts
(package
(name "julia-arraylayouts")
(version "0.7.0")
(version "0.7.3")
(source
(origin
(method git-fetch)
@ -165,7 +166,7 @@ no issues with the upgrade.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "01725v4jp8h8zwn85splw907r206h1hnp205pchmzjin7h4659xz"))))
(base32 "0ri05xhfrj2909c6yy09qm6zi8v8s5fvmbbwbg8qgjq0yxnviw32"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-fillarrays" ,julia-fillarrays)))
@ -204,7 +205,7 @@ axis (dimension).")
(define-public julia-axisarrays
(package
(name "julia-axisarrays")
(version "0.4.3")
(version "0.4.4")
(source
(origin
(method git-fetch)
@ -213,7 +214,7 @@ axis (dimension).")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "079rj7wvh9ks293g2ih1yah5k0sg8wazw08z3vg2bxj4s16wr64p"))))
(base32 "03kzan1lm4fxfhzv1xjg3ysf6y7nagcc61vfz15kvdrp1dqxlynk"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-rangearrays" ,julia-rangearrays)
@ -235,7 +236,7 @@ axes, allowing column names or interval selections.")
(define-public julia-bandedmatrices
(package
(name "julia-bandedmatrices")
(version "0.16.9")
(version "0.16.10")
(source
(origin
(method git-fetch)
@ -244,7 +245,7 @@ axes, allowing column names or interval selections.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "105y5d3208s0byk3p0469sfy79lhjpdblk6karbwj8x7hl26na00"))))
(base32 "0rlfj9gr9ss621v5kw5b06206yaak21s2vq9vk7r8a7p2ylncism"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-arraylayouts" ,julia-arraylayouts)
@ -260,7 +261,7 @@ the entries on the bands.")
(define-public julia-benchmarktools
(package
(name "julia-benchmarktools")
(version "0.7.0")
(version "1.1.1")
(source
(origin
(method git-fetch)
@ -269,7 +270,7 @@ the entries on the bands.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "000izw9pj7cbh9r35nnwg2ijkb9dpfd5nkl2889b8b2dpsh4fi63"))))
(base32 "1xz3kdrphp4b158pg7dwkiry49phs2fjjpdvk1hjpww5ykxacks8"))))
(build-system julia-build-system)
(propagated-inputs `(("julia-json" ,julia-json)))
(home-page "https://github.com/JuliaCI/BenchmarkTools.jl")
@ -282,7 +283,7 @@ benchmarks as well as comparing benchmark results.")
(define-public julia-blockarrays
(package
(name "julia-blockarrays")
(version "0.15.3")
(version "0.16.3")
(source
(origin
(method git-fetch)
@ -291,7 +292,7 @@ benchmarks as well as comparing benchmark results.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "15nd493bfkx92ihnr8dj8mb155dj44iqw266igv0qr5q0wad2bfr"))))
(base32 "1f9pnnfv97vww2dxklpx8pa2k85fw2l3pzsj7n28nws1xlwnj96c"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-arraylayouts" ,julia-arraylayouts)
@ -318,7 +319,7 @@ access to the full matrix to use in in for example a linear solver.")
(define-public julia-blockbandedmatrices
(package
(name "julia-blockbandedmatrices")
(version "0.10.6")
(version "0.10.7")
(source
(origin
(method git-fetch)
@ -327,7 +328,7 @@ access to the full matrix to use in in for example a linear solver.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0q9ni4pgdkb00jb42fdzlhx745852xx2666vr96k0c4l0cn5mi0y"))))
(base32 "10n1r6kmmv2wa307jfg9y2m6p16j8hngjp3fjavpbdy1r5haasm9"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-arraylayouts" ,julia-arraylayouts)
@ -428,7 +429,7 @@ variables, both with unordered (nominal variables) and ordered categories
(define-public julia-chainrules
(package
(name "julia-chainrules")
(version "0.7.65")
(version "1.1.0")
(source
(origin
(method git-fetch)
@ -437,7 +438,7 @@ variables, both with unordered (nominal variables) and ordered categories
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0697m5y5ryqnhw6cbk90rlydrxan2b308pzbl86qz4mzhypyk7yi"))))
(base32 "0if93pd3b3scg2x3gmk1cbwjk0ax1n792vy8c38y3xl7jpd5cb70"))))
(build-system julia-build-system)
(inputs ;required for test
`(("julia-chainrulestestutils" ,julia-chainrulestestutils)
@ -459,7 +460,7 @@ execute forward-, reverse-, and mixed-mode primitives.")
(define-public julia-chainrulescore
(package
(name "julia-chainrulescore")
(version "0.9.43")
(version "1.0.2")
(source
(origin
(method git-fetch)
@ -468,7 +469,7 @@ execute forward-, reverse-, and mixed-mode primitives.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "12by6zcxv0ivpf0f22gc9i067360syda9m2lxk0rhypxq4smj8w4"))))
(base32 "1866xv30h1bi7f2m993nljzf58wwmv8zlgn6ffn9j3wckch1nfpb"))))
(build-system julia-build-system)
(inputs ;required for tests
`(("julia-benchmarktools" ,julia-benchmarktools)
@ -484,7 +485,7 @@ sensitivities for functions without the need to depend on ChainRules itself.")
(define-public julia-chainrulestestutils
(package
(name "julia-chainrulestestutils")
(version "0.6.11")
(version "1.0.0")
(source
(origin
(method git-fetch)
@ -493,7 +494,7 @@ sensitivities for functions without the need to depend on ChainRules itself.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1nx2fzxhh3q8znnjfjbgf7776scszixmigwna3hvmdfixsk58x0i"))))
(base32 "07l4sjc7avmmp4v1dsym1jyb46q4jsvv7i0yzszf72gj8d9k6lwa"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-chainrulescore" ,julia-chainrulescore)
@ -542,7 +543,7 @@ color scales for graphics.")
(define-public julia-colorschemes
(package
(name "julia-colorschemes")
(version "3.12.1")
(version "3.13.0")
(source
(origin
(method git-fetch)
@ -551,8 +552,7 @@ color scales for graphics.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"08k39hbdf3jn0001f7qxa99xvagrnh9764911hs6cmxkvp061sa4"))))
(base32 "13gy1njxlkfnxmpj2z6aj1bzbzn7jipaxr9fgkv41yiy0xjhqiyh"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-colors" ,julia-colors)
@ -663,7 +663,7 @@ common subexpression elimination.")
(define-public julia-compat
(package
(name "julia-compat")
(version "3.30.0")
(version "3.32.0")
(source
(origin
(method git-fetch)
@ -672,7 +672,7 @@ common subexpression elimination.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1qs6fm58dicdjy69qk5p0ndj2b7qsvg7rmydq7igvrvirad55v56"))))
(base32 "1zif3dj0a85w7xqbg0chrdhw8dk410zxcqbnkf764xmylwbps498"))))
(build-system julia-build-system)
(home-page "https://github.com/JuliaLang/Compat.jl")
(synopsis "Compatibility across Julia versions")
@ -685,7 +685,7 @@ way.")
(define-public julia-constructionbase
(package
(name "julia-constructionbase")
(version "1.2.1")
(version "1.3.0")
(source
(origin
(method git-fetch)
@ -694,7 +694,7 @@ way.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1bmx5c5z9jxmyf2xjwwl5lhs9czmwq4isl0bkr78fak4j8brqr4n"))))
(base32 "1jk3h446vkv4yaavgm1hf1az7cwhppvhklvr08s49hhg02cm750q"))))
(build-system julia-build-system)
(home-page "https://juliaobjects.github.io/ConstructionBase.jl/dev/")
(synopsis "Primitive functions for construction of objects")
@ -762,7 +762,7 @@ styles available to terminals.")
(define-public julia-dataapi
(package
(name "julia-dataapi")
(version "1.6.0")
(version "1.7.0")
(source
(origin
(method git-fetch)
@ -771,7 +771,7 @@ styles available to terminals.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "14sfvkz169zcbap3gdwpj16qsap783h86fd07flfxk822abam11w"))))
(base32 "0swk31p83fycz5cdj4fg6b0wfqj473lnx94q2fl7ybxkkc6afba7"))))
(build-system julia-build-system)
(home-page "https://github.com/JuliaData/DataAPI.jl")
(synopsis "Data-focused namespace for packages to share functions")
@ -842,7 +842,8 @@ without having to take direct dependencies.")
(base32 "15j3hrqq6nazn533bfsvg32xznacbzsl303j1qs48av59ppnvhhv"))))
(build-system julia-build-system)
(arguments
`(#:phases
`(#:tests? #f ; Tests need upgrading with newer Julia version.
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'skip-known-failing-tests
(lambda _
@ -886,7 +887,7 @@ dictionaries where values associated with a particular key may change,
(define-public julia-dictionaries
(package
(name "julia-dictionaries")
(version "0.3.8")
(version "0.3.10")
(source
(origin
(method git-fetch)
@ -895,7 +896,7 @@ dictionaries where values associated with a particular key may change,
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1j88f6qa5hqm64n5q3jy08a02gwp7by401s03n5x7575p58iqqh2"))))
(base32 "1mm43hm8hd6sgmkkpqhbqhvap7mpkjwzmz5algxi6manp580gkr5"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-indexing" ,julia-indexing)))
@ -924,10 +925,13 @@ dictionaries in Julia, for improved productivity and performance.")
(modify-phases %standard-phases
(add-after 'unpack 'skip-flakey-tests
(lambda _
;; Some combination of these tests fail nondeterministically
;; each of the times this package is built.
(substitute* "test/test_dists.jl"
(("test dyz ≥") "test_nowarn dyz ≥")
(("test dist\\(y, x") "test_nowarn dist(y, x")
(("test dist\\(z, x") "test_nowarn dist(z, x")))))))
(("test dist\\(z, x") "test_nowarn dist(z, x")
(("test dist\\(z, y") "test_nowarn dist(z, y")))))))
(propagated-inputs
`(("julia-statsapi" ,julia-statsapi)))
(native-inputs
@ -955,6 +959,8 @@ straightforward loop implementation.")
(sha256
(base32 "0fy4kfnfacyfmlly6nqxn77dk2gqw80b69zb4m1i0i39zv3cpqfb"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f)) ; Tests try to read SSL certificates.
(home-page "https://juliadocs.github.io/DocStringExtensions.jl/latest/")
(synopsis "Extensions for Julia's docsystem")
(description "This package provides a collection of useful extensions for
@ -1079,6 +1085,14 @@ combinations of dual numbers with predefined Julia numeric types.")
(sha256
(base32 "0py46kxl702r8pw3v7x4cqllf7yc91b0dr7vb60xh2qi7d6y3jc7"))))
(build-system julia-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'adjust-test-suite
(lambda _
(substitute* "test/runtests.jl"
;; Seems to not play nicely with Julia-1.6.
((".*basic.jl.*") "")))))))
(propagated-inputs
`(("julia-arrayinterface" ,julia-arrayinterface)))
(home-page "https://github.com/ChrisRackauckas/EllipsisNotation.jl")
@ -1111,7 +1125,7 @@ before (or after)\".")
(define-public julia-exprtools
(package
(name "julia-exprtools")
(version "0.1.3")
(version "0.1.6")
(source
(origin
(method git-fetch)
@ -1120,7 +1134,7 @@ before (or after)\".")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1lwxi9fx9farf1jdv42gv43xs3f3i3js2xnvr5gf6d0xfx0g6b6a"))))
(base32 "058ax5d96jpym5w3g37ah1c4xq3fskwpjdhchakzax15vqzy7ab4"))))
(build-system julia-build-system)
(home-page "https://github.com/invenia/ExprTools.jl")
(synopsis "Light-weight expression manipulation tools")
@ -1228,7 +1242,7 @@ working with filesystem paths in Julia.")
(define-public julia-fillarrays
(package
(name "julia-fillarrays")
(version "0.11.7")
(version "0.12.1")
(source
(origin
(method git-fetch)
@ -1237,7 +1251,7 @@ working with filesystem paths in Julia.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1q1qn9pb5dmppddnmf8gggdqyvivqh3ffvbblhn37smcf9r5sy7d"))))
(base32 "1va8vvcxbxcy5xp487hdqfp0ps3m8q0819xrxygsf5135azp3qrh"))))
(build-system julia-build-system)
(inputs ;required by tests
`(("julia-staticarrays" ,julia-staticarrays)))
@ -1252,7 +1266,7 @@ following types: @code{Eye}, @code{Fill}, @code{Ones}, @code{Zeros},
(define-public julia-finitediff
(package
(name "julia-finitediff")
(version "2.8.0")
(version "2.8.1")
(source
(origin
(method git-fetch)
@ -1261,7 +1275,7 @@ following types: @code{Eye}, @code{Fill}, @code{Ones}, @code{Zeros},
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0ndazn02wn8ddwgjh1i32y7pbaqpw06f42ccilz5ya78cyrjhq2m"))))
(base32 "105f6r0hq97n9mxf1nacmz94dpca66vzqj5p3zh4h0brshmggqnq"))))
(build-system julia-build-system)
(arguments
`(#:phases
@ -1291,7 +1305,7 @@ types and sparsity.")
(define-public julia-finitedifferences
(package
(name "julia-finitedifferences")
(version "0.12.6")
(version "0.12.17")
(source
(origin
(method git-fetch)
@ -1300,7 +1314,7 @@ types and sparsity.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0kg8snnspn48i2rr99mwy0an3hzlgrnic7xnh3whj2ws2znw46hr"))))
(base32 "09nsf9cgk49yrvprflnhd9h5rrgs280rgj8sad3csghxdx6jqk5c"))))
(build-system julia-build-system)
(inputs
`(("julia-benchmarktools" ,julia-benchmarktools)))
@ -1443,6 +1457,13 @@ arbitrary functions.")
(sha256
(base32 "07sv88c472n6w4x7diy952igbcfm1s104ysnnvprld83312siw06"))))
(build-system julia-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'skip-failing-test
(lambda _
(substitute* "test/runtests.jl"
((".*RPLE.*") "")))))))
(home-page "https://github.com/JunoLab/FuzzyCompletions.jl")
(synopsis "Fuzzy completion provider for Julia")
(description
@ -1483,7 +1504,7 @@ algebra routines written in Julia (except for optimized BLAS).")
(define-public julia-genericschur
(package
(name "julia-genericschur")
(version "0.5.0")
(version "0.5.1")
(source
(origin
(method git-fetch)
@ -1492,7 +1513,7 @@ algebra routines written in Julia (except for optimized BLAS).")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0kklc2niylvynhq0v49kdmy58m9jmr5jxjf287k1wr9r81fya3sz"))))
(base32 "12x6lxzxm91y3k6s9dam46dq5hrby5sr0gy0fdfnp0xhjzdy2j0d"))))
(build-system julia-build-system)
(arguments
`(#:phases
@ -1566,7 +1587,7 @@ library for parsing HTML.")
(define-public julia-http
(package
(name "julia-http")
(version "0.9.2")
(version "0.9.12")
(source
(origin
(method git-fetch)
@ -1575,7 +1596,7 @@ library for parsing HTML.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0ij0yci13c46p92m4zywvcs02nn8pm0abyfffiyhxvva6hq48lyl"))))
(base32 "1jsyk3mhnwj4h19cxclx26igdqdrw51fd3k1hgav0nm67dy4cxyk"))))
(build-system julia-build-system)
(arguments
`(#:phases
@ -1729,7 +1750,7 @@ dependencies.")
(define-public julia-imagecore
(package
(name "julia-imagecore")
(version "0.9.0")
(version "0.9.1")
(source
(origin
(method git-fetch)
@ -1738,7 +1759,7 @@ dependencies.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0d844lrilw7zjpax8zr5272a9s292wg4qk53mvm0n88yai598zd6"))))
(base32 "0h9m3pl3wic1jrgaqkdifz24cya5vxd3m6qdmm37pxg2y2ii2vcq"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f)) ; Cycle with ImageMagick.jl.
@ -1771,7 +1792,7 @@ of packages designed to support image processing and computer vision.")
(define-public julia-imageinterminal
(package
(name "julia-imageinterminal")
(version "0.4.6")
(version "0.4.7")
(source
(origin
(method git-fetch)
@ -1780,17 +1801,19 @@ of packages designed to support image processing and computer vision.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1mqbv27qmnsr6wqvklzb4gawi7hp4wnaspszhaxny1m53q6wbifl"))))
(base32 "0bbpzi7bv8jdiggq1wmcn67vnf96qagvwg0fk95s125wy5980xsl"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f)) ; Cycle with ReferenceTests.jl.
(propagated-inputs
`(("julia-crayons" ,julia-crayons)
("julia-imagebase" ,julia-imagebase)
("julia-imagecore" ,julia-imagecore)
("julia-imagetransformations" ,julia-imagetransformations)))
("julia-requires" ,julia-requires)))
;(native-inputs
; `(("julia-coordinatetransformations" ,julia-coordinatetransformations)
; ("julia-imagemagick" ,julia-imagemagick)
; ("julia-imagetransformations" ,julia-imagetransformations)
; ("julia-offsetarrays" ,julia-offsetarrays)
; ("julia-referencetests" ,julia-referencetests)
; ("julia-rotations" ,julia-rotations)
@ -2024,7 +2047,7 @@ interfaces with @file{.ini} files.")
(define-public julia-interpolations
(package
(name "julia-interpolations")
(version "0.13.2")
(version "0.13.3")
(source
(origin
(method git-fetch)
@ -2033,19 +2056,21 @@ interfaces with @file{.ini} files.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "06wh4fc7hy20kq9iipk3w8v50vd09k7vkii43k8z1vw036f6l7x3"))))
(base32 "1236c20k388qlh7k74mhf7hkbn0vf7ss8b1rgh1a6aj0234ayfnc"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-axisalgorithms" ,julia-axisalgorithms)
("julia-offsetarrays" ,julia-offsetarrays)
("julia-ratios" ,julia-ratios)
("julia-requires" ,julia-requires)
("julia-staticarrays" ,julia-staticarrays)
("julia-woodburymatrices" ,julia-woodburymatrices)))
(native-inputs
`(("julia-dualnumbers" ,julia-dualnumbers)
("julia-forwarddiff" ,julia-forwarddiff)
("julia-offsetarrays" ,julia-offsetarrays)
("julia-unitful" ,julia-unitful)))
("julia-unitful" ,julia-unitful)
("julia-zygote" ,julia-zygote)))
(home-page "https://github.com/JuliaMath/Interpolations.jl")
(synopsis "Continuous interpolation of discrete datasets")
(description "This package implements a variety of interpolation schemes for
@ -2126,7 +2151,7 @@ as a string together with the return value.")
(define-public julia-irtools
(package
(name "julia-irtools")
(version "0.4.2")
(version "0.4.3")
(source
(origin
(method git-fetch)
@ -2135,7 +2160,7 @@ as a string together with the return value.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0wwzy77jcdnffnd5fr6xan7162g4wydz67igrq82wflwnrhlcx5y"))))
(base32 "11334fcg2slpwcj0raxf457brhf7pxglgxc6cy8q58ggrpxqfqql"))))
(arguments
'(#:tests? #f)) ;require Documenter, not packaged yet
(build-system julia-build-system)
@ -2217,7 +2242,7 @@ and printing JSON documents.")
(define-public julia-json3
(package
(name "julia-json3")
(version "1.8.2")
(version "1.9.0")
(source
(origin
(method git-fetch)
@ -2226,7 +2251,7 @@ and printing JSON documents.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1mc3byqm6ygg4mjpdrx6grkr4gn06p25nr7050jgq1k2cf06iqba"))))
(base32 "11z5maz7v50wd99id8z7838higza0cllh2amkdkrlskbri3v2f17"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-parsers" ,julia-parsers)
@ -2240,7 +2265,7 @@ focus on speed and slick struct mapping.")
(define-public julia-lazyarrays
(package
(name "julia-lazyarrays")
(version "0.21.6")
(version "0.21.11")
(source
(origin
(method git-fetch)
@ -2249,7 +2274,7 @@ focus on speed and slick struct mapping.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0zm1ihvi8v2823ap59ajqcs46s5z0nai8l70n51f6j9dzp8lc3cy"))))
(base32 "1vdli4zr94xhrx5bpvrqiysz21nzlcgmqz0zhza1ayw0zjgzihfw"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-arraylayouts" ,julia-arraylayouts)
@ -2346,7 +2371,7 @@ comes from the fact that @code{M == map(f, A)}.")
(define-public julia-matrixfactorizations
(package
(name "julia-matrixfactorizations")
(version "0.8.3")
(version "0.8.4")
(source
(origin
(method git-fetch)
@ -2355,7 +2380,7 @@ comes from the fact that @code{M == map(f, A)}.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "14c6w1vhyf4pi4454pdp6ryczsxn9pgjg99fg9bkdj03xg5fsxb8"))))
(base32 "15zvcv2l4iqmjpnqjyx2kry7a85p652nbjy9pj3wq0piksqcz4jb"))))
(build-system julia-build-system)
(arguments
`(#:phases
@ -2529,7 +2554,7 @@ Julia, with type-driven, overloadable packing/unpacking functionality.")
(define-public julia-mutablearithmetics
(package
(name "julia-mutablearithmetics")
(version "0.2.19")
(version "0.2.20")
(source
(origin
(method git-fetch)
@ -2538,7 +2563,7 @@ Julia, with type-driven, overloadable packing/unpacking functionality.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1zjfq5sh0rc941pbc9kvnr6a2lpr4yd276mw62vbncbz9jg52rrg"))))
(base32 "1isyj8h4nx96cr6892d154v8pw1nhr7mjyz5bd6ffr2mkzb2bq4f"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-offsetarrays" ,julia-offsetarrays)))
@ -2604,7 +2629,7 @@ interface to interact with these types.")
(define-public julia-nnlib
(package
(name "julia-nnlib")
(version "0.7.19")
(version "0.7.25")
(source
(origin
(method git-fetch)
@ -2613,10 +2638,11 @@ interface to interact with these types.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "163v7hkmbxxgnq7qigmqjdqcdywi2njxbh54w8v0hf4bddnalbba"))))
(base32 "0vp4kcn9ivkhmqgkyvnabcdqi6pv7ghbmjc1llkwv1kzhylyf86p"))))
(build-system julia-build-system)
(arguments
`(#:phases
`(#:tests? #f ; Test suite not updated for ChainRulesTestUtils-1.0.
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'drop-cuda-support
(lambda _
@ -2685,7 +2711,7 @@ which they were added to the collection.")
(define-public julia-offsetarrays
(package
(name "julia-offsetarrays")
(version "1.9.2")
(version "1.10.3")
(source
(origin
(method git-fetch)
@ -2694,7 +2720,7 @@ which they were added to the collection.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "10mycjmjlp80c1bsdmk1hnb5hg81zqd2dcxyaa9p55ykla051a9q"))))
(base32 "0j5a8ar8yc0j9h87gwfyrcqm23wpyv5yv5gn8vzilpg4vr0fiasc"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-adapt" ,julia-adapt)))
@ -2829,7 +2855,7 @@ actual computation.")
(define-public julia-plotutils
(package
(name "julia-plotutils")
(version "1.0.10")
(version "1.0.11")
(source
(origin
(method git-fetch)
@ -2838,8 +2864,7 @@ actual computation.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1jimdkp590g7s33w7i431nn7mp1phjy9gdjs88zyqsmq5hxldacg"))))
(base32 "0pqd3yvs3w48sr50c8rcqk5pzvpdy9nf4kimcvyz9dvwc3jgh6rd"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-colors" ,julia-colors)
@ -2902,6 +2927,31 @@ Hessian and g the gradient) may not be a descent direction if H is not positive
definite.")
(license license:expat)))
(define-public julia-preferences
(package
(name "julia-preferences")
(version "1.2.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaPackaging/Preferences.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1cail43iqzbi6m9v6981rhz47zf2lcvhs5ds5gdqvc9nx5frghxq"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f)) ; Tests try to mkdir /.julia
(home-page "https://github.com/JuliaPackaging/Preferences.jl")
(synopsis "Store configuration switches to TOML files")
(description "The @code{Preferences} package provides an integrated way for
packages to store configuration switches to persistent TOML files, and use those
pieces of information at both run time and compile time in Julia. This enables
the user to modify the behavior of a package, and have that choice reflected in
everything from run time algorithm choice to code generation at compile time.")
(license license:expat)))
(define-public julia-prettytables
(package
(name "julia-prettytables")
@ -3087,7 +3137,7 @@ more complex visualizations.")
(define-public julia-recipespipeline
(package
(name "julia-recipespipeline")
(version "0.3.2")
(version "0.3.4")
(source
(origin
(method git-fetch)
@ -3096,8 +3146,7 @@ more complex visualizations.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0wa342m2d9k4kihr6g9i0wpbsipp0n11kh9jmlw4pc5msmz4rxr0"))))
(base32 "0zq4bzxvq36zr0va6iip3x97mgq5b4fwza8avszx1ryfqm3lg1f7"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f)) ; Cycle with Plots.jl.
@ -3118,7 +3167,7 @@ recipes to full specifications for a plot.")
(define-public julia-recursivearraytools
(package
(name "julia-recursivearraytools")
(version "2.11.4")
(version "2.16.1")
(source
(origin
(method git-fetch)
@ -3127,15 +3176,16 @@ recipes to full specifications for a plot.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "14wh39g3l0fzzrkxgxijklilqcgpxsk1d44dfpfl48gsp0n6icjm"))))
(base32 "0vx8ndxrii53na7jsc2lki47wfpi77rn3y2r6xhiysx1qwr14msf"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f)) ; Cycle with OrdinaryDiffEq.jl.
(propagated-inputs
`(("julia-arrayinterface" ,julia-arrayinterface)
("julia-chainrulescore" ,julia-chainrulescore)
("julia-docstringextensions" ,julia-docstringextensions)
("julia-requires" ,julia-requires)
("julia-recipesbase" ,julia-recipesbase)
("julia-requires" ,julia-requires)
("julia-staticarrays" ,julia-staticarrays)
("julia-zygoterules" ,julia-zygoterules)))
;(native-inputs
@ -3143,7 +3193,6 @@ recipes to full specifications for a plot.")
; ("julia-nlsolve" ,julia-nlsolve)
; ("julia-ordinarydiffeq" ,julia-ordinarydiffeq)
; ("julia-structarrays" ,julia-structarrays)
; ("julia-unitful" ,julia-unitful)
; ("julia-zygote" ,julia-zygote)))
(home-page "https://github.com/SciML/RecursiveArrayTools.jl")
(synopsis "Tools for handling objects like arrays of arrays and deeper nestings")
@ -3296,33 +3345,36 @@ other power series in @code{h}.")
(license license:expat)))
(define-public julia-rotations
(package
(name "julia-rotations")
(version "1.0.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaGeometry/Rotations.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1l1a3bnrpv9qdksnk3c8j82ik3yrnpsmnyxyiy3gc1yjya5pajqj"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-staticarrays" ,julia-staticarrays)))
(native-inputs
`(("julia-benchmarktools" ,julia-benchmarktools)
("julia-forwarddiff" ,julia-forwarddiff)
("julia-unitful" ,julia-unitful)))
(home-page "https://github.com/JuliaGeometry/Rotations.jl")
(synopsis "Julia implementations for different rotation parameterisations")
(description "This package implements various 3D rotation parameterizations
;; This is the first commit with support for julia-1.6.
(let ((commit "b599102535bc3534252c76f3fd4cf521f4741788")
(revision "1"))
(package
(name "julia-rotations")
(version (git-version "1.0.2" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaGeometry/Rotations.jl")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "01wwqbdmj61yiz7rkmams4xg7gb9hbmg325173846ky4b9x1wb19"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-staticarrays" ,julia-staticarrays)))
(native-inputs
`(("julia-benchmarktools" ,julia-benchmarktools)
("julia-forwarddiff" ,julia-forwarddiff)
("julia-unitful" ,julia-unitful)))
(home-page "https://github.com/JuliaGeometry/Rotations.jl")
(synopsis "Julia implementations for different rotation parameterisations")
(description "This package implements various 3D rotation parameterizations
and defines conversions between them. At their heart, each rotation
parameterization is a 3×3 unitary (orthogonal) matrix (based on the
@code{StaticArrays.jl} package), and acts to rotate a 3-vector about the origin
through matrix-vector multiplication.")
(license license:expat)))
(license license:expat))))
(define-public julia-safetestsets
;; The only release tag is the first commit in the repository.
@ -3403,7 +3455,7 @@ in @code{Gadfly}, @code{Plots} and @code{Makie} to label axes and keys.")
(define-public julia-simpletraits
(package
(name "julia-simpletraits")
(version "0.9.3")
(version "0.9.4")
(source
(origin
(method git-fetch)
@ -3412,7 +3464,7 @@ in @code{Gadfly}, @code{Plots} and @code{Makie} to label axes and keys.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1aaq91klwxb0r3ckwihf7rd7jvg70757nkhp5ip4cc3lspnnip23"))))
(base32 "1qvmkqcvhc2nilvkk36szccxdlcv9ls2i0ksxgl2yfjr3b3qlr05"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-macrotools" ,julia-macrotools)))
@ -3428,18 +3480,16 @@ types are fixed after creation.")
(define-public julia-sortingalgorithms
(package
(name "julia-sortingalgorithms")
(version "1.0.0")
(version "1.0.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaCollections/SortingAlgorithms.jl")
;; Tagging releases is hard:
;; https://github.com/JuliaCollections/SortingAlgorithms.jl/issues/41#issuecomment-840587380
(commit "aa2b98d384ddd132aae0219e68fb63b92513cb35")))
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "13zbx18psxrg4fvkqgp0m7g484vrama2xm6902bbls30801hgljg"))))
(base32 "173x77a80xnh99viqa3r7rgdaksvxaw8xyfqw09gwvp4p2zrxivb"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f)) ; cycle with StatsBase.jl
@ -3457,7 +3507,7 @@ timsort and radixsort.")
(define-public julia-specialfunctions
(package
(name "julia-specialfunctions")
(version "1.3.0")
(version "1.6.0")
(source
(origin
(method git-fetch)
@ -3466,12 +3516,13 @@ timsort and radixsort.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1rfhrrkzi3ils7fklbn35ki1yp5x88fi71qknfwqyw4pk8cf8p80"))))
(base32 "0nfpnglx7zl9g20w2mgfkg17hcw9ri0shaq2rwplj0ij5pwz8yf0"))))
(build-system julia-build-system)
(inputs
`(("julia-chainrulestestutils" ,julia-chainrulestestutils)))
(propagated-inputs
`(("julia-chainrulescore" ,julia-chainrulescore)
("julia-logexpfunctions" ,julia-logexpfunctions)
("julia-openspecfun-jll" ,julia-openspecfun-jll)))
(home-page "https://github.com/JuliaMath/SpecialFunctions.jl")
(synopsis "Special mathematical functions")
@ -3573,7 +3624,7 @@ There are multiple ways to understand @code{StackView}:
(define-public julia-static
(package
(name "julia-static")
(version "0.2.5")
(version "0.3.0")
(source
(origin
(method git-fetch)
@ -3582,7 +3633,7 @@ There are multiple ways to understand @code{StackView}:
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1sxfp169c7caaklpp7mz8770ayk9w8xw133m95kf7v11sya1lb7v"))))
(base32 "19k7h47zhz3zz28i0l4b3cc0r07pzp8kf35z0yammpy361b644l2"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-ifelse" ,julia-ifelse)))
@ -3597,7 +3648,7 @@ types and a common interface that is shared between them.")
(define-public julia-staticarrays
(package
(name "julia-staticarrays")
(version "1.2.0")
(version "1.2.9")
(source
(origin
(method git-fetch)
@ -3606,7 +3657,7 @@ types and a common interface that is shared between them.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0z4g1kk6gy514dyafb559gcp4264ffx6h28ffczdvkyk8gm9j0m7"))))
(base32 "1902bl9p96mfq7d1rbilwp98wz2g82ml9svcgx7sczglyjbs4nsk"))))
(build-system julia-build-system)
(inputs
`(("julia-benchmarktools" ,julia-benchmarktools)))
@ -3762,7 +3813,7 @@ the @code{Pluto.jl} tabular data import functionality.")
(define-public julia-tables
(package
(name "julia-tables")
(version "1.4.3")
(version "1.4.4")
(source
(origin
(method git-fetch)
@ -3771,7 +3822,7 @@ the @code{Pluto.jl} tabular data import functionality.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0yfjl4v1vglsk9wr7gbqgya4kk3a0q0i6zhi9xdgvnqsqzqrsc7c"))))
(base32 "1sqqagzqvav8b1rv5ywwbgy9ixvlmipq95fkwfwn0m8769i8jwzb"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-dataapi" ,julia-dataapi)
@ -3907,7 +3958,8 @@ package.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1s4mdywbp7nli7z985fqaj1rs4i6d92b1jx3lhg0qhk1s5wc0v8j"))))
(base32 "1s4mdywbp7nli7z985fqaj1rs4i6d92b1jx3lhg0qhk1s5wc0v8j"))
(patches (search-patches "julia-tracker-16-compat.patch"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-adapt" ,julia-adapt)
@ -3929,7 +3981,7 @@ automatic differentiation for its machine learning platform.")
(define-public julia-typedtables
(package
(name "julia-typedtables")
(version "1.2.4")
(version "1.4.0")
(source
(origin
(method git-fetch)
@ -3938,7 +3990,7 @@ automatic differentiation for its machine learning platform.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "06k5h7ybsh29b6kiy0p62rp9b2q3xi9jk8p9wf0kq907p5kvfnfy"))))
(base32 "0nk6zhqvl2r8yhjdhb59kxq0srd3vy4ysg4d8rszj9a43dnn3w3i"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-adapt" ,julia-adapt)
@ -4009,7 +4061,7 @@ working with @acronym{URIs,Uniform Resource Identifiers}, as defined in RFC
(define-public julia-unitful
(package
(name "julia-unitful")
(version "1.8.0")
(version "1.9.0")
(source
(origin
(method git-fetch)
@ -4018,7 +4070,7 @@ working with @acronym{URIs,Uniform Resource Identifiers}, as defined in RFC
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0n9z4skj04h033qbn22cn6f5jby6584j6pizvs7bdbk93h39ch1g"))))
(base32 "10qwscd15dnmvx116dwvg99m7kmwgmj5ahdkq7psiq48lcc554gq"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-constructionbase" ,julia-constructionbase)))
@ -4056,7 +4108,7 @@ useful in order to support @code{VersionNumber} comparisons applied to
(define-public julia-weakrefstrings
(package
(name "julia-weakrefstrings")
(version "1.0.0")
(version "1.1.0")
(source
(origin
(method git-fetch)
@ -4065,7 +4117,7 @@ useful in order to support @code{VersionNumber} comparisons applied to
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1p8q62zsmi02vyckgy25ddmxns223xrhx575x9lfgvr7jrw1kl2p"))))
(base32 "14h1vdnc3rx87w6v2rr59lgb4kai2hd1wzqpxhmzsi8karg2z219"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-dataapi" ,julia-dataapi)
@ -4147,7 +4199,7 @@ Zygote, without depending on Zygote itself.")
(define-public julia-zygote
(package
(name "julia-zygote")
(version "0.6.10")
(version "0.6.17")
(source
(origin
(method git-fetch)
@ -4156,7 +4208,7 @@ Zygote, without depending on Zygote itself.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0qqjzhiqghj07mab24b0n0h4xfzq8r1s9hccrmx1lwjkkskhc5f9"))))
(base32 "1cx66sp30s34ln6p0fpqk1ggjxfxg2gp8791zz3cl85dmk4dl14b"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f)) ;require CUDA, not packaged yet

431
gnu/packages/julia.scm
View File

@ -1,9 +1,11 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
;;; Copyright © 2020, 2021 Nicolò Balzarotti <nicolo@nixo.xyz>
;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com>
;;; Copyright © 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -30,6 +32,7 @@
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
#:use-module (gnu packages certs)
#:use-module (gnu packages compression)
#:use-module (gnu packages curl)
#:use-module (gnu packages elf)
@ -48,14 +51,15 @@
#:use-module (gnu packages ssh)
#:use-module (gnu packages tls)
#:use-module (gnu packages version-control)
#:use-module (gnu packages web)
#:use-module (gnu packages wget)
#:use-module (ice-9 match))
(define libuv-julia
(let ((commit "1fcc6d66f9df74189c74d3d390f02202bb7db953")
(revision "2"))
(let ((commit "fb3e3364c33ae48c827f6b103e05c3f0e78b79a9")
(revision "3"))
;; When upgrading Julia, also upgrade this. Get the commit from
;; https://github.com/JuliaLang/julia/blob/v1.5.2/deps/libuv.version
;; https://github.com/JuliaLang/julia/blob/v1.6.1/deps/libuv.version
(package
(inherit libuv)
(name "libuv-julia")
@ -65,16 +69,10 @@
(uri (git-reference
(url "https://github.com/JuliaLang/libuv")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(file-name (git-file-name name version))
(sha256
(base32
"040l7f1hk7xyza11sry5cj4fhw05na949865axqqhxnifdvnmfji"))))
(build-system gnu-build-system)
(arguments
(substitute-keyword-arguments (package-arguments libuv)
((#:phases phases)
`(modify-phases ,phases
(delete 'autogen)))))
"1kqpn19d20aka30h6q5h8lnzyp0vw0xzgx0wm4w2r5j6yf76m2hr"))))
(home-page "https://github.com/JuliaLang/libuv"))))
(define libunwind-julia
@ -97,7 +95,9 @@
(julia-patch "libunwind-prefer-extbl"
"0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1")
(julia-patch "libunwind-static-arm"
"1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq")))))
"1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq")
(julia-patch "libunwind-cfa-rsp"
"1aswjhvysahhldbzh1afbf0hsjxrvs6xidsz2i7s1cjkjbdiia1z")))))
(home-page "https://github.com/JuliaLang/tree/master/deps/")))
(define (julia-patch-url version name)
@ -105,7 +105,7 @@
"/deps/patches/" name ".patch"))
(define (julia-patch name sha)
(let ((version "1.5.3"))
(let ((version "1.6.1"))
(origin (method url-fetch)
(uri (julia-patch-url version name))
(sha256 (base32 sha))
@ -113,10 +113,10 @@
(define llvm-julia
(package
(inherit llvm-9)
(inherit llvm-11)
(name "llvm-julia")
(source (origin
(inherit (package-source llvm-9))
(inherit (package-source llvm-11))
;; Those patches are inside the Julia source repo.
;; They are _not_ Julia specific (https://github.com/julialang/julia#llvm)
;; but they are required to build Julia.
@ -132,37 +132,72 @@
"19spqc3xsazn1xs9gpcgv9ldadfkv49rmc5khl7sf1dlmhgi4602")
'("llvm-7.0-D44650"
"1h55kkmkiisfj6sk956if2bcj9s0v6n5czn8dxb870vp5nccj3ir")
'("llvm-6.0-DISABLE_ABI_CHECKS"
"014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg")
'("llvm9-D50010-VNCoercion-ni"
"1s1d3sjsiq4vxg7ncy5cz56zgy5vcq6ls3iqaiqkvr23wyryqmdx")
'("llvm-exegesis-mingw"
"0ph1cj1j7arvf1xq2xcr7qf9g0cpdl14fincgr67vpi520zvd3vp")
'("llvm-test-plugin-mingw"
"12z738cnahbf6n381im7i0hxp1m6k9hrnfjlmq9sac46nxly9gnj")
'("llvm7-revert-D44485"
"0f59kq3p3mpwsbmskypbi4zn01l6ig0x7v2rjp08k2r8z8m6fa8n")
'("llvm-8.0-D66657-codegen-degenerate"
"1n1ddx19h90bbpimdyd9dh8fsm6gb93xxyqm4ljkxa1k3cx2vm72")
'("llvm-8.0-D71495-vectorize-freduce"
"1zff08wvji9lnpskk4b3p5zyjsy5hhy23ynxjqlj9dw7jvvfrf0p")
'("llvm-D75072-SCEV-add-type"
"029a3fywsm233vf48mscina24idd50dc75wr70lmimrhwnw27p0z")
'("llvm-9.0-D65174-limit-merge-stores"
"04bff1mnblfj9mxfdwr1qdnw3i3szmp60gnhxwas5y68qg33z6j0")
'("llvm9-D71443-PPC-MC-redef-symbol"
"1c93nv7rgc9jg5mqrnvv08xib1789qvlql94fwggh18mp3b9hbgy")
'("llvm-9.0-D78196"
"08a43hyg7yyqjq2vmfsmppf34xcz60wq6y9zw5fdyhw2h1mcnmns")
'("llvm-11-D75072-SCEV-add-type"
"176xi1lnbnv2rcs05ywhyb7pd0xgmibayvwzksksg44wg2dh8mbx")
'("llvm-julia-tsan-custom-as"
"0awh40kf6lm4wn1nsjd1bmhfwq7rqj811szanp2xkpspykw9hg9s")
'("llvm-9.0-D85499"
"0vxlr35srvbvihlgrxq15v6dylp90vgi0qahj22j01jgqmdasjkm"))))
'("llvm-D80101"
"1gsdwmgmpbignvqyxcnlprj899259p3dvdznlncd84ss445qgq3j")
'("llvm-D84031"
"0nks9sbk7p0r5gyr0idrmm93a5fmdai8kihz9532dx4zhcvvqbjc")
'("llvm-10-D85553"
"1zjq7j9q2qp56hwkc8yc8f0z7kvam3j7hj8sb7qyd77r255ff78l")
'("llvm-10-unique_function_clang-sa"
"1jys9w2zqk3dasnxqh0qz5ij7rxi6mkgq9pqjsclmamr5169zyan")
;'("llvm-D88630-clang-cmake"
; "0rs6s71nqnjkny7i69gqazhqj5jqfdr0bkxs2v5a55sfx8fa1k54")
'("llvm-11-D85313-debuginfo-empty-arange"
"1f672d5385xpgb8yrim8d3b7wg2z1l81agnshm1q61kdvjixqx32")
'("llvm-11-D90722-rtdyld-absolute-relocs"
"0kmnai229yyxkmpk9lxd180mcnhk2i8d87k2sg89gc8as18w10r6")
'("llvm-invalid-addrspacecast-sink"
"1n1b7j4s80vj7x5377aj9vyphmxx1q6bm0chhkxp6zsy3mx3g2ry")
'("llvm-11-D92906-ppc-setjmp"
"0cmd4dsblp7a8m03j16dqxws0ijh55zf4jzzxmj341qxa1gamdp9")
'("llvm-11-PR48458-X86ISelDAGToDAG"
"0vwzvlhsdazhxg4gj8g2f00a4f8qc5cgac23w575xk3pgba1jh6y")
'("llvm-11-D93092-ppc-knownbits"
"1748bypsc7c9lbs3fnkv0kwvch6bn85kj98j4jdaz254ig0wa6xj")
'("llvm-11-D93154-globalisel-as"
"1k5wd4z3pa7zj0gyjkif7viqj906dhqlbb7dc95gig40nbxv6zpj")
'("llvm-11-ppc-half-ctr"
"0piywisfz6cmw3133kz7vzhiqflq2y7igakqxlym0gi8pqylv7w9")
'("llvm-11-ppc-sp-from-bp"
"1wmg3485cx5f9pbykyl3jibk1wwv4w1x30hl4jyfndzr2yh8azf9")
'("llvm-rGb498303066a6-gcc11-header-fix"
"0hkd4rwhvh8g2yh13g29wiwnjpv2yd1hdyiv1ryw8izl25bz9c67")
'("llvm-11-D94813-mergeicmps"
"0cmy0ywkgyrdcvr9bd6pd912lyd4gcsrib4z0v05dwgcdxhk7y29")
'("llvm-11-D94980-CTR-half"
"1yf8cxib3z8hz7zi9n6v2g2c6vpfr4slq9hpx8m8yq8f1jbyw3fw")
'("llvm-11-D94058-sext-atomic-ops"
"1x6p6k6q651z5jcqxx8vj17cxnv196mka7mwn7dpp6c23lwgfdpb")
'("llvm-11-D96283-dagcombine-half"
"0lv4iq2f8qrcz1xyxfic3bcr5p0aqam3a7c6pp6fnw3riixm096k"))))
(patch-flags '("-p1"))))
(arguments
(substitute-keyword-arguments (package-arguments llvm-9)
(substitute-keyword-arguments (package-arguments llvm-11)
((#:phases phases)
`(modify-phases ,phases
(add-after 'unpack 'patch-round-two
;; We have to do the patching in two rounds because we can't
;; pass '-p1' and '-p2' in the source field.
(lambda* (#:key inputs #:allow-other-keys)
(map (lambda (patchname)
(invoke "patch" patchname "-p2"))
(list "llvm-11-AArch64-FastIsel-bug"
"llvm-11-D97435-AArch64-movaddrreg"
"llvm-11-D97571-AArch64-loh"
"llvm-11-aarch64-addrspace"))))))
((#:build-type _) "Release")
((#:configure-flags flags)
`(list ;; Taken from NixOS. Only way I could get libLLVM-6.0.so
"-DCMAKE_BUILD_TYPE=Release"
`(list
;; Build a native compiler and the NVPTX backend (NVIDIA) since
;; Julia insists on it, nothing more. This reduces build times and
;; disk usage.
@ -177,7 +212,22 @@
;; "-DLLVM_DEFAULT_TARGET_TRIPLE=${stdenv.hostPlatform.config}"
;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly"
"-DLLVM_ENABLE_DUMP=ON"
"-DLLVM_LINK_LLVM_DYLIB=ON"))))))
"-DLLVM_LINK_LLVM_DYLIB=ON"))))
(inputs
(append
(package-inputs llvm-11)
`(("llvm-11-AArch64-FastIsel-bug"
,(julia-patch "llvm-11-AArch64-FastIsel-bug"
"1m2vddj1mw4kbij8hbrx82piyy6bvr2x7wwdnlxfaqcm72ipzyh9"))
("llvm-11-D97435-AArch64-movaddrreg"
,(julia-patch "llvm-11-D97435-AArch64-movaddrreg"
"10jnavq9ljkj7j2gqj2zd1pwqpqb5zs3zp9h96pmz0djbmxwa86y"))
("llvm-11-D97571-AArch64-loh"
,(julia-patch "llvm-11-D97571-AArch64-loh"
"128zcbg1w1j7hngsf7z1a7alc6lig6l2rqgjp6i8nk3k3f842v6n"))
("llvm-11-aarch64-addrspace"
,(julia-patch "llvm-11-aarch64-addrspace"
"0ckbzgfirxrf2d5bpinpngp7gnilbjrk0cbdfyl3h6f5v6i6xj6m")))))))
(define-public libwhich
(package
@ -223,7 +273,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
(define-public julia
(package
(name "julia")
(version "1.5.3")
(version "1.6.1")
(source (origin
(method url-fetch)
(uri (string-append
@ -231,7 +281,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
version "/julia-" version ".tar.gz"))
(sha256
(base32
"1zmim82x9kkdcgn0cdi01hmzi59zbszy1sqlygb86xq4hc1n66dy"))
"1mfzbjyqcmx7wb1sa7qab5fl78yzd7ap088krqbphbwvpn880srn"))
(patches
(search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch"))))
(build-system gnu-build-system)
@ -241,6 +291,10 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
(guix build gnu-build-system)
(guix build utils))
;; The test suite takes many times longer than building and
;; can easily fail on smaller machines when they run out of memory.
#:tests? ,(not (target-aarch64?))
;; Do not strip binaries to keep support for full backtraces.
;; See https://github.com/JuliaLang/julia/issues/17831
#:strip-binaries? #f
@ -259,14 +313,13 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
(string-join (map (lambda (pkg)
(string-append (assoc-ref inputs pkg)
"/lib"))
'("arpack-ng" "curl" "dsfmt"
'("curl" "dsfmt"
"gmp" "lapack"
"libssh2" "libgit2"
"libssh2" "libnghttp2" "libgit2"
"mbedtls" "mpfr"
"openblas" "openlibm" "pcre2"
"suitesparse"))
":"))
#t))
"suitesparse" "gfortran:lib"))
":"))))
;; FIXME: Building the documentation requires Julia packages that
;; would be downloaded from the Internet. We should build them in a
;; separate build phase.
@ -304,7 +357,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
"$(BUILDDIR)/$(EXENAME)-debug\\$\\(EXE\\): $(DOBJS) $(LLT_debug)"))
;; The REPL must be linked with libuv.
(substitute* "ui/Makefile"
(substitute* "cli/Makefile"
(("JLDFLAGS \\+= ")
(string-append "JLDFLAGS += "
(assoc-ref %build-inputs "libuv")
@ -318,27 +371,99 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
(substitute* "base/client.jl"
(("/bin/sh") (which "sh")))
#t))
(add-before 'build 'fix-precompile
(lambda _
(substitute* "base/loading.jl"
(("something(Base.active_project(), \"\")") "\"\""))
#t))
(add-before 'build 'shared-objects-paths
(lambda* (#:key inputs #:allow-other-keys)
(let ((jlpath
(lambda (pkgname)
(string-append
"stdlib/" pkgname "_jll/src/" pkgname "_jll.jl")))
(from
(lambda (libname)
(string-append "const " libname " = .*\\.so")))
(to
(lambda* (pkg libname #:optional libname_jl)
(string-append
"const " (or libname_jl libname) "= \""
(assoc-ref inputs pkg) "/lib/" libname ".so"))))
(substitute* (jlpath "dSFMT")
(((from "libdSFMT")) (to "dsfmt" "libdSFMT")))
(substitute* (jlpath "GMP")
(((from "libgmp")) (to "gmp" "libgmp"))
(((from "libgmpxx")) (to "gmp" "libgmpxx")))
(substitute* (jlpath "libLLVM")
(((from "libLLVM")) (to "llvm" "libLLVM")))
(substitute* (jlpath "LibCURL")
(((from "libcurl")) (to "curl" "libcurl")))
(substitute* (jlpath "LibGit2")
(((from "libgit2")) (to "libgit2" "libgit2")))
(substitute* (jlpath "LibSSH2")
(((from "libssh2")) (to "libssh2" "libssh2")))
(substitute* (jlpath "LibUV")
(((from "libuv")) (to "libuv" "libuv")))
(substitute* (jlpath "LibUnwind")
(((from "libunwind")) (to "libunwind" "libunwind")))
(substitute* (jlpath "MPFR")
(((from "libmpfr")) (to "mpfr" "libmpfr")))
(substitute* (jlpath "MbedTLS")
;; For the newer version of mbedtls-apache:
(("libmbedcrypto.so.5") "libmbedcrypto.so.6")
(((from "libmbedcrypto")) (to "mbedtls" "libmbedcrypto"))
(((from "libmbedtls")) (to "mbedtls" "libmbedtls"))
(((from "libmbedx509")) (to "mbedtls" "libmbedx509")))
(substitute* (jlpath "nghttp2")
(((from "libnghttp2")) (to "libnghttp2" "libnghttp2")))
(substitute* (jlpath "OpenBLAS")
(((from "libopenblas")) (to "openblas" "libopenblas")))
(substitute* (jlpath "OpenLibm")
(((from "libopenlibm")) (to "openlibm" "libopenlibm")))
(substitute* (jlpath "PCRE2")
(((from "libpcre2")) (to "pcre2" "libpcre2" "libpcre2_8")))
(substitute* (jlpath "SuiteSparse")
(((from "libamd")) (to "suitesparse" "libamd"))
(((from "libbtf")) (to "suitesparse" "libbtf"))
(((from "libcamd")) (to "suitesparse" "libcamd"))
(((from "libccolamd")) (to "suitesparse" "libccolamd"))
(((from "libcholmod")) (to "suitesparse" "libcholmod"))
(((from "libcolamd")) (to "suitesparse" "libcolamd"))
(((from "libklu")) (to "suitesparse" "libklu"))
(((from "libldl")) (to "suitesparse" "libldl"))
(((from "librbio")) (to "suitesparse" "librbio"))
(((from "libspqr")) (to "suitesparse" "libspqr"))
(((from "libsuitesparse")) (to "suitesparse" "libsuitesparse"))
(((from "libsuitesparseconfig"))
(to "suitesparse" "libsuitesparseconfig"))
(((from "libumfpack")) (to "suitesparse" "libumfpack")))
(substitute* (jlpath "Zlib")
(((from "libz")) (to "zlib" "libz"))))
#t))
(add-after 'unpack 'adjust-test-suite
(lambda* (#:key inputs #:allow-other-keys)
(let (;(pcre2 (assoc-ref inputs "pcre2"))
(mbedtls-apache (assoc-ref inputs "mbedtls"))
(mpfr (assoc-ref inputs "mpfr"))
(suitesparse (assoc-ref inputs "suitesparse")))
;; Some tests only check to see if the input is the correct version.
;(substitute* "stdlib/PCRE2_jll/test/runtests.jl"
; (("10.36.0") ,(package-version pcre2)))
(substitute* "stdlib/MbedTLS_jll/test/runtests.jl"
(("2.24.0") ,(package-version mbedtls-apache)))
(substitute* "stdlib/MPFR_jll/test/runtests.jl"
(("4.1.0") ,(package-version mpfr)))
(substitute* "stdlib/SuiteSparse_jll/test/runtests.jl"
(("5004") ,(string-replace-substring
(version-major+minor
(package-version suitesparse)) "." "0")))
#t)))
(add-before 'check 'disable-broken-tests
(lambda _
;; disabling REPL tests because they require a stdin
;; There are some read-only precompile issues in the 1.6 series.
;; https://github.com/JuliaLang/julia/pull/41614
;; https://github.com/JuliaLang/julia/issues/41156
(substitute* "test/choosetests.jl"
(("tests = testnames")
;; Those failings are not deterministic. They depends on the
;; running order. I think it depends on the number of
;; runners, disabling it for now
;; https://github.com/JuliaLang/julia/issues/34330
"tests = filter(e->!in(e,[\"backtrace\",\"exceptions\",\"precompile\",
\"client\",\"stacktraces\"]),
testnames)"))
;; Marking the test as broken as it's a known bug:
;; https://github.com/JuliaLang/julia/issues/32377
(substitute* "stdlib/REPL/test/replcompletions.jl"
(("@test count") "@test_broken count"))
;; Dates has a similar bug:
(("skip_tests = \\[\\]")
"skip_tests = [\"REPL\", \"precompile\"]"))
;; Dates/io tests fail on master when networking is unavailable
;; https://github.com/JuliaLang/julia/issues/34655
(substitute* "stdlib/Dates/test/io.jl"
(("\"Dates.Date") "\"Date")
@ -347,11 +472,67 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
;; https://github.com/JuliaLang/julia/issues/35785
(substitute* "test/file.jl"
(("@test dirname\\(t\\) == d") "@test_broken dirname(t) == d"))
;; Deprecation test fails with --depwarn=no
;; https://github.com/JuliaLang/julia/issues/37673
(substitute* "test/Makefile"
(("./runtests.jl") "--depwarn=error ./runtests.jl"))
;; julia embeds a certificate, we are not doing that
(substitute* "stdlib/MozillaCACerts_jll/test/runtests.jl"
(("@test isfile\\(MozillaCACerts_jll.cacert\\)")
"@test_broken isfile(MozillaCACerts_jll.cacert)"))
;; since certificate is not present some tests are failing in network option
(substitute* "usr/share/julia/stdlib/v1.6/NetworkOptions/test/runtests.jl"
(("@test isfile\\(bundled_ca_roots\\(\\)\\)")
"@test_broken isfile(bundled_ca_roots())")
(("@test ispath\\(ca_roots_path\\(\\)\\)")
"@test_broken ispath(ca_roots_path())")
(("@test ca_roots_path\\(\\) \\!= bundled_ca_roots\\(\\)")
"@test_broken ca_roots_path() != bundled_ca_roots()"))
;; Some digraphs are too wide for some terminals during testing.
(substitute* "stdlib/Unicode/test/runtests.jl"
(("test collect\\(graphemes") "test_broken collect(grapemes"))
;; WARNING: failed to select UTF-8 encoding, using ASCII
;; Using 'setlocale' doesn't affect the test failures.
;(setlocale LC_ALL "en_US.utf8")
;(setenv "LC_ALL" "en_US.utf8")
(substitute* "test/cmdlineargs.jl"
(("test v\\[3") "test_broken v[3")
(("test isempty\\(v\\[3") "test_broken isempty(v[3"))
#t))
(add-before 'install 'symlink-libraries
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((link
(lambda (pkgname dir pred)
(map (lambda (file)
(unless (file-exists?
(string-append dir (basename file)))
(symlink file (string-append dir (basename file)))))
(find-files (string-append (assoc-ref inputs pkgname)
"/lib") pred)))))
(link "curl" "usr/lib/" "\\.so") ; missing libpthreads libLLVM-11jl
(link "suitesparse" "usr/lib/julia/" "libbtf\\.so")
(link "suitesparse" "usr/lib/julia/" "libklu\\.so")
(link "suitesparse" "usr/lib/julia/" "libldl\\.so")
(link "suitesparse" "usr/lib/julia/" "librbio\\.so")
(link "gmp" "usr/lib/julia/" "libgmpxx\\.so")
(link "libuv" "usr/lib/julia/" "libuv\\.so")
(link "zlib" "usr/lib/julia/" "libz\\.so")
(link "libunwind" "usr/lib/julia/" "libunwind\\.so")
(symlink (string-append (assoc-ref inputs "p7zip") "/bin/7z")
"usr/libexec/7z")
#t)))
(add-after 'install 'symlink-llvm-utf8proc
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(link
(lambda (pkgname pred)
(map (lambda (file)
(unless (file-exists?
(string-append out "/lib/julia/"
(basename file)))
(symlink file (string-append out "/lib/julia/"
(basename file)))))
(find-files (string-append (assoc-ref inputs pkgname)
"/lib") pred)))))
(link "llvm" "libLLVM-11\\.so")
(link "utf8proc" "libutf8proc\\.so")
#t)))
(add-after 'install 'make-wrapper
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@ -360,8 +541,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
(with-directory-excursion bin
(wrap-program program
`("JULIA_LOAD_PATH" ":" prefix
("" "$JULIA_LOAD_PATH")))
(wrap-program program
("" "$JULIA_LOAD_PATH"))
`("JULIA_DEPOT_PATH" ":" prefix
("" "$JULIA_DEPOT_PATH"))))
#t))))
@ -369,11 +549,14 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
(list
(string-append "prefix=" (assoc-ref %outputs "out"))
;; Passing the MARCH flag is necessary to build binary substitutes for
;; the supported architectures.
;; Passing the MARCH or JULIA_CPU_TARGET flag is necessary to build
;; binary substitutes for the supported architectures. See also
;; https://docs.julialang.org/en/v1/devdocs/sysimg/#Specifying-multiple-system-image-targets
,(match (or (%current-target-system)
(%current-system))
("x86_64-linux" "MARCH=x86-64")
("x86_64-linux"
;; These are the flags that upstream uses for their binaries.
"JULIA_CPU_TARGET=generic;generic,-cx16,clone_all;sandybridge,-xsaveopt,clone_all;haswell,-rdrnd,base(1)")
("i686-linux" "MARCH=pentium4")
("armhf-linux" "JULIA_CPU_TARGET=armv7-a,neon")
("powerpc64le-linux" "JULIA_CPU_TARGET=pwr8")
@ -382,81 +565,87 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
;; and also of targeting the builder's architecture.
(_ "JULIA_CPU_TARGET=generic"))
"CONFIG_SHELL=bash" ;needed to build bundled libraries
;; list of "USE_SYSTEM_*" is here:
;; https://github.com/JuliaLang/julia/blob/v1.3.1/Make.inc
"CONFIG_SHELL=bash -x" ; needed to build bundled libraries
"USE_BINARYBUILDER=0"
;; list (and order!) of "USE_SYSTEM_*" is here:
;; https://github.com/JuliaLang/julia/blob/v1.6.0/Make.inc
"USE_SYSTEM_CSL=1"
"USE_SYSTEM_LLVM=1"
"USE_SYSTEM_LIBUNWIND=1"
"USE_SYSTEM_PCRE=1"
"USE_SYSTEM_OPENLIBM=1"
"USE_SYSTEM_DSFMT=1"
"USE_SYSTEM_P7ZIP=1"
"USE_SYSTEM_LAPACK=1"
"USE_SYSTEM_BLAS=1"
"USE_BLAS64=0" ;needed when USE_SYSTEM_BLAS=1
"USE_SYSTEM_LAPACK=1"
"USE_SYSTEM_GMP=1"
"USE_SYSTEM_MPFR=1"
"USE_SYSTEM_SUITESPARSE=1"
"USE_SYSTEM_LIBUV=1"
"USE_SYSTEM_UTF8PROC=1"
"USE_SYSTEM_MBEDTLS=1"
"USE_SYSTEM_LIBSSH2=1"
"USE_SYSTEM_NGHTTP2=1"
"USE_SYSTEM_CURL=1"
"USE_SYSTEM_LIBGIT2=1"
"USE_SYSTEM_PATCHELF=1"
"USE_SYSTEM_ZLIB=1"
"USE_SYSTEM_P7ZIP=1"
"NO_GIT=1" ; build from release tarball.
"USE_BLAS64=0" ; needed when USE_SYSTEM_BLAS=1
"LIBBLAS=-lopenblas"
"LIBBLASNAME=libopenblas"
"USE_SYSTEM_SUITESPARSE=1"
(string-append "SUITESPARSE_INC=-I "
(assoc-ref %build-inputs "suitesparse")
"/include")
"USE_GPL_LIBS=1" ;proudly
"USE_SYSTEM_UTF8PROC=1"
"USE_GPL_LIBS=1" ; proudly
(string-append "UTF8PROC_INC="
(assoc-ref %build-inputs "utf8proc")
"/include")
"USE_SYSTEM_LLVM=1"
"LLVM_VER=9.0.1"
"LLVM_VER=11.0.0"
"USE_LLVM_SHLIB=1"
"USE_SYSTEM_LIBUNWIND=1"
"USE_SYSTEM_LIBUV=1"
(string-append "LIBUV="
(assoc-ref %build-inputs "libuv")
"/lib/libuv.so")
(string-append "LIBUV_INC="
(assoc-ref %build-inputs "libuv")
"/include")
"USE_SYSTEM_PATCHELF=1"
"USE_SYSTEM_PCRE=1"
"USE_SYSTEM_OPENLIBM=1"
"USE_SYSTEM_MBEDTLS=1"
"USE_SYSTEM_LIBSSH2=1"
"USE_SYSTEM_GMP=1"
"USE_SYSTEM_MPFR=1"
"USE_SYSTEM_ARPACK=1"
"USE_SYSTEM_LIBGIT2=1"
"USE_SYSTEM_ZLIB=1")))
"/include"))))
(inputs
`(("llvm" ,llvm-julia)
("p7zip" ,p7zip)
;; The bundled version is 3.3.0 so stick to that version. With other
;; versions, we get test failures in 'linalg/arnoldi' as described in
;; <https://bugs.gnu.org/30282>.
("arpack-ng" ,arpack-ng-3.3.0)
("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
`(("coreutils" ,coreutils) ; for bindings to "mkdir" and the like
("curl" ,curl-ssh)
("gfortran" ,gfortran)
;; required for libgcc_s.so
("gfortran:lib" ,gfortran "lib")
("gmp" ,gmp)
("lapack" ,lapack)
("openblas" ,openblas) ;Julia does not build with Atlas
("libunwind" ,libunwind-julia)
("openlibm" ,openlibm)
("mbedtls" ,mbedtls-apache)
("curl" ,curl)
("libgit2" ,libgit2-0.28)
("libgit2" ,libgit2)
("libnghttp2" ,nghttp2 "lib")
("libssh2" ,libssh2)
("fortran" ,gfortran)
("libunwind" ,libunwind-julia)
("libuv" ,libuv-julia)
("pcre2" ,pcre2)
("utf8proc" ,utf8proc)
("llvm" ,llvm-julia)
("mbedtls" ,mbedtls-apache)
("mpfr" ,mpfr)
("openblas" ,openblas)
("openlibm" ,openlibm)
("p7zip" ,p7zip)
;; pcre2-10.35 has a bug with the JIT regex parser:
;; https://github.com/JuliaLang/julia/issues/40231#issuecomment-812753324
("pcre2" ,pcre2-10.36)
("suitesparse" ,suitesparse)
("utf8proc" ,utf8proc-2.6.1)
("wget" ,wget)
("which" ,which)
("zlib" ,zlib)
("gmp" ,gmp)
("suitesparse" ,suitesparse)
;; Find dependencies versions here:
;; https://raw.githubusercontent.com/JuliaLang/julia/v1.3.0/deps/Versions.make
("libwhich" ,libwhich)
("dsfmt" ,dsfmt)))
;; https://raw.githubusercontent.com/JuliaLang/julia/v1.6.0/deps/Versions.make
("dsfmt" ,dsfmt)
("libwhich" ,libwhich)))
(native-inputs
`(("openssl" ,openssl)
`(("nss-certs" ,nss-certs)
("openssl" ,openssl)
("perl" ,perl)
("patchelf" ,patchelf)
("pkg-config" ,pkg-config)

88
gnu/packages/jupyter.scm
View File

@ -25,6 +25,7 @@
#:use-module (guix git-download)
#:use-module (guix build-system cmake)
#:use-module (guix build-system python)
#:use-module (gnu packages bash)
#:use-module (gnu packages check)
#:use-module (gnu packages cpp)
#:use-module (gnu packages linux)
@ -35,6 +36,7 @@
#:use-module (gnu packages python-check)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages python-web)
#:use-module (gnu packages rdf)
#:use-module (gnu packages time)
#:use-module (gnu packages xml)
#:use-module (gnu packages tls)
@ -382,3 +384,89 @@ used to explore a repository locally by building and executing the constructed
image of the repository, or as a means of building images that are pushed to a
Docker registry.")
(license license:bsd-3)))
(define-public python-bash-kernel
(package
(name "python-bash-kernel")
(version "0.7.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "bash_kernel" version))
(sha256
(base32
"0w0nbr3iqqsgpk83rgd0f5b02462bkyj2n0h6i9dwyc1vpnq9350"))))
(build-system python-build-system)
(arguments
`(#:tests? #f
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'bash-references
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "bash_kernel/kernel.py"
(("\"bash\"")
(string-append "\"" (assoc-ref inputs "bash") "/bin/bash\""))
(("\\['bash', ")
(string-append "['" (assoc-ref inputs "bash") "/bin/bash', ")))
#t))
(add-after 'install 'install-kernelspec
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(setenv "HOME" "/tmp")
(invoke "python" "-m" "bash_kernel.install" "--prefix" out)
#t))))))
(inputs
`(("bash" ,bash)))
(propagated-inputs
`(("python-pexpect" ,python-pexpect)
("python-ipykernel" ,python-ipykernel)
("python-jupyter-client" ,python-jupyter-client)))
(home-page "https://github.com/takluyver/bash_kernel")
(synopsis "Jupyter kernel for Bash")
(description "A bash shell kernel for Jupyter.")
(license license:expat)))
(define-public python-sparqlkernel
(package
(name "python-sparqlkernel")
(version "1.3.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "sparqlkernel" version))
(sha256
(base32
"004v22nyi5cnpxq4fiws89p7i5wcnzv45n3n70axdd6prh6rkapx"))))
(build-system python-build-system)
(arguments
`(#:tests? #f
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'no-custom-css
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "sparqlkernel/install.py"
(("install_custom_css\\( destd, PKGNAME \\)") ""))
#t))
(add-after 'install 'install-kernelspec
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(setenv "HOME" "/tmp")
(add-installed-pythonpath inputs outputs)
(invoke
(string-append out "/bin/jupyter-sparqlkernel")
"install"
(string-append "--InstallKernelSpec.prefix=" out))
#t))))))
(native-inputs
`(("python-traitlets" ,python-traitlets)
("python-jupyter-client" ,python-jupyter-client)
("python-notebook" ,python-notebook)
("python-ipykernel" ,python-ipykernel)
("python-html5lib" ,python-html5lib-0.9)))
(propagated-inputs
`(("python-sparqlwrapper" ,python-sparqlwrapper)
("python-pygments" ,python-pygments)))
(home-page "https://github.com/paulovn/sparql-kernel")
(synopsis "Jupyter kernel for SPARQL")
(description "This module installs a Jupyter kernel for SPARQL. It allows
sending queries to an SPARQL endpoint and fetching & presenting the results in
a notebook.")
(license license:bsd-3)))

156
gnu/packages/linux.scm
View File

@ -52,6 +52,7 @@
;;; Copyright © 2020 David Dashyan <mail@davie.li>
;;; Copyright © 2020 pukkamustard <pukkamustard@posteo.net>
;;; Copyright © 2021 B. Wilson <elaexuotee@wilsonb.com>
;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru>
;;;
;;; This file is part of GNU Guix.
;;;
@ -355,49 +356,36 @@ 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-5.13-version "5.13.2")
(define-public linux-libre-5.13-version "5.13.6")
(define deblob-scripts-5.13
(linux-libre-deblob-scripts
linux-libre-5.13-version
(base32 "1mhc215a1y8bxip2f0sqmyl0rf7cgw22cmg26hg9x0pfm9li2c95")
(base32 "1hkbkyy3myraczaj982z72m0p1yxjwigqhsz2kx9g74qkap0xy9d")))
(base32 "08xai5zqgk0y0rwhssf81lf8vivjg12wjkv7855l3ljkivgjclbf")
(base32 "153jf5l5x4438zgxwggaky2ahjlfl48j438vhpzks6h77lzc51a5")))
(define-public linux-libre-5.13-pristine-source
(let ((version linux-libre-5.13-version)
(hash (base32 "0dx9khk7fh003xyb3xix0kc0rmjncg7ric5p830zhadnrw4hv563")))
(hash (base32 "0xjjl8dmilp425b1cp977v26qxlg1147gh54kni949pzxwh1fb56")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-5.13)))
(define-public linux-libre-5.12-version "5.12.17")
(define deblob-scripts-5.12
(linux-libre-deblob-scripts
linux-libre-5.12-version
(base32 "1vdsr9y4gckknrbqcjyfakwva3k0vb5zcivzk3k1s9mh7qp9dils")
(base32 "1kb98sbn6lgf5cpd2f8mav93hxh0aywybfjzxx35294ipll1264y")))
(define-public linux-libre-5.12-pristine-source
(let ((version linux-libre-5.12-version)
(hash (base32 "1ghyqxfxslxzr7273vj2yn14pkdnkja3wk50xxhavpvf87i8c40j")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-5.12)))
;; 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-5.10-version "5.10.50")
(define-public linux-libre-5.10-version "5.10.54")
(define deblob-scripts-5.10
(linux-libre-deblob-scripts
linux-libre-5.10-version
(base32 "1rmnx1px4sizs2lq831yd2g9dyflg0vmykz3cv9443x2a2vwy81f")
(base32 "1fdvjhc048nk8v27bgir0fdjqm8hn4yfdgd3mdjird4ary80ywb2")))
(base32 "16w9r5h8r8j5ckq2brr15xgdq3ksr2pgwcmjx5a7bqry8a60i3m4")
(base32 "0c9x07gplzajm0h5if3fpw2rvfb7psw3yp7i2n6ws7ggq1dvmki2")))
(define-public linux-libre-5.10-pristine-source
(let ((version linux-libre-5.10-version)
(hash (base32 "0dmlpy9k7am99495bxcm46i4y6g34d1fzdkzz3wgzb4mgmx35nlb")))
(hash (base32 "0i5y56v34gm0djgmh2bld4hmndf1ymfkwyd1lkn8fwc4c4rccl5z")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-5.10)))
(define-public linux-libre-5.4-version "5.4.132")
(define-public linux-libre-5.4-version "5.4.136")
(define deblob-scripts-5.4
(linux-libre-deblob-scripts
linux-libre-5.4-version
@ -405,12 +393,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(base32 "1xghbbnaisjd0k1klbyn1p7r6r4x5a1bpmkm56a3gh2zvw4s7mj8")))
(define-public linux-libre-5.4-pristine-source
(let ((version linux-libre-5.4-version)
(hash (base32 "1vq0dmrn7gl2vprm08l8by5ja3xjgggrcd38vqg7b7jpnfzssrl4")))
(hash (base32 "05mdkgscnfvhanspipd9ka0phfqzdlcxzm5j1x0jvf46pwvds8j3")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-5.4)))
(define-public linux-libre-4.19-version "4.19.197")
(define-public linux-libre-4.19-version "4.19.199")
(define deblob-scripts-4.19
(linux-libre-deblob-scripts
linux-libre-4.19-version
@ -418,12 +406,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(base32 "1jiaw0as1ippkrjdpd52657w5mz9qczg3y2hlra7m9k0xawwiqlf")))
(define-public linux-libre-4.19-pristine-source
(let ((version linux-libre-4.19-version)
(hash (base32 "10kj442qaky6rpl65k5rrvd3p6mdgz4p321zvf4s312ixfdja0g6")))
(hash (base32 "16iawii33rpc7lgf4ri3idwj32g88p3k3s4lznvmbn66s3wanyrx")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.19)))
(define-public linux-libre-4.14-version "4.14.239")
(define-public linux-libre-4.14-version "4.14.241")
(define deblob-scripts-4.14
(linux-libre-deblob-scripts
linux-libre-4.14-version
@ -431,12 +419,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(base32 "1qij18inijj6c3ma8hv98yjagnzxdxyn134da9fd23ky8q6hbvky")))
(define-public linux-libre-4.14-pristine-source
(let ((version linux-libre-4.14-version)
(hash (base32 "167zwm3giizv42m0xjz71xnb2swlwiaw0xw0dg8j8mb74hz1drx0")))
(hash (base32 "0zczi2hv6ib67niycn6s2gaw73y0nxz0c75w11xa4jqmf2xh9fxm")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.14)))
(define-public linux-libre-4.9-version "4.9.275")
(define-public linux-libre-4.9-version "4.9.277")
(define deblob-scripts-4.9
(linux-libre-deblob-scripts
linux-libre-4.9-version
@ -444,12 +432,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(base32 "0fxajshb75siq39lj5h8xvhdj8lcmddkslwlyj65rhlwk6g2r4b2")))
(define-public linux-libre-4.9-pristine-source
(let ((version linux-libre-4.9-version)
(hash (base32 "08mz7mzmhk5n1gwadrc5fw8s40jk0rayvdpjcricl4sv56574lb6")))
(hash (base32 "1pkjcz9llc7hkmzfyjcx20b5njnqbkwlzyy1ncc8na71nn6rvsg6")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.9)))
(define-public linux-libre-4.4-version "4.4.275")
(define-public linux-libre-4.4-version "4.4.277")
(define deblob-scripts-4.4
(linux-libre-deblob-scripts
linux-libre-4.4-version
@ -457,7 +445,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(base32 "0hhin1jpfkd6nwrb6xqxjzl3hdxy4pn8a15hy2d3d83yw6pflbsf")))
(define-public linux-libre-4.4-pristine-source
(let ((version linux-libre-4.4-version)
(hash (base32 "1aiwq6019sibsw5smj6ii28cr64dv24c19k4n8c09nakhmhcg94i")))
(hash (base32 "1m5zkssh523f15fvy80rcvfwqzdkldz3jhny6vbaj8q0zvk3w5r5")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.4)))
@ -498,14 +486,6 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(search-patch
"linux-libre-arm64-generic-pinebook-lcd.patch"))))
(define-public linux-libre-5.12-source
(source-with-patches linux-libre-5.12-pristine-source
(list %boot-logo-patch
%linux-libre-arm-export-__sync_icache_dcache-patch
;; Pinebook Pro patch to fix LCD display
(search-patch
"linux-libre-arm64-generic-pinebook-lcd.patch"))))
(define-public linux-libre-5.10-source
(source-with-patches linux-libre-5.10-pristine-source
(list %boot-logo-patch
@ -620,10 +600,6 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(make-linux-libre-headers* linux-libre-5.13-version
linux-libre-5.13-source))
(define-public linux-libre-headers-5.12
(make-linux-libre-headers* linux-libre-5.12-version
linux-libre-5.12-source))
(define-public linux-libre-headers-5.10
(make-linux-libre-headers* linux-libre-5.10-version
linux-libre-5.10-source))
@ -925,16 +901,10 @@ It has been modified to remove all non-free binary blobs.")
'("x86_64-linux" "i686-linux" "armhf-linux" "aarch64-linux" "riscv64-linux")
#:configuration-file kernel-config))
(define-public linux-libre-5.12
(make-linux-libre* linux-libre-5.12-version
linux-libre-5.12-source
'("x86_64-linux" "i686-linux" "armhf-linux" "aarch64-linux" "riscv64-linux")
#:configuration-file kernel-config))
(define-public linux-libre-version linux-libre-5.12-version)
(define-public linux-libre-pristine-source linux-libre-5.12-pristine-source)
(define-public linux-libre-source linux-libre-5.12-source)
(define-public linux-libre linux-libre-5.12)
(define-public linux-libre-version linux-libre-5.13-version)
(define-public linux-libre-pristine-source linux-libre-5.13-pristine-source)
(define-public linux-libre-source linux-libre-5.13-source)
(define-public linux-libre linux-libre-5.13)
(define-public linux-libre-5.10
(make-linux-libre* linux-libre-5.10-version
@ -1148,8 +1118,8 @@ It has been modified to remove all non-free binary blobs.")
(define-public linux-libre-with-bpf
(let ((base-linux-libre
(make-linux-libre*
linux-libre-5.12-version
linux-libre-5.12-source
linux-libre-5.13-version
linux-libre-5.13-source
'("x86_64-linux" "i686-linux" "armhf-linux"
"aarch64-linux" "riscv64-linux")
#:extra-version "bpf"
@ -1654,6 +1624,31 @@ at login. Local and dynamic reconfiguration are its key features.")
;;; Miscellaneous.
;;;
(define-public powercap
(package
(name "powercap")
(version "0.4.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/powercap/powercap")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1hp2i1d195v0n4jgvgaymkxlpgyhn07ic273gkda95lz65cdfcgm"))))
(build-system cmake-build-system)
(arguments
'(#:configure-flags
'("-DBUILD_SHARED_LIBS=ON")))
(home-page "https://github.com/powercap/powercap")
(synopsis "Utilities for accessing the powercap Linux kernel feature")
(description "This package contains utilities for accessing the powercap
Linux kernel feature through sysfs. It includes an implementation for working
with Intel @acronym{RAPL, Running Average Power Limit}.
It provides the commands @code{powercap-info} and @code{powercap-set}.")
(license license:bsd-3)))
(define-public powerstat
(package
(name "powerstat")
@ -3790,7 +3785,7 @@ devices that can inject events directly into the input subsystem.")
(define-public interception-dual-function-keys
(package
(name "interception-dual-function-keys")
(version "1.3.0")
(version "1.4.0")
(home-page "https://gitlab.com/interception/linux/plugins/dual-function-keys")
(source (origin
(method git-fetch)
@ -3800,14 +3795,15 @@ devices that can inject events directly into the input subsystem.")
(file-name (git-file-name name version))
(sha256
(base32
"1gvhkmwzl5fyyc7k8rc4rf2b9mzh05wa8wcybf9hz2x1mqkc7lmz"))))
"0s49vbg3j4rwh78i8rx8qr7myql09p7b3lhrjl0p7dd98xp6ann6"))))
(build-system gnu-build-system)
(inputs
`(("libevdev" ,libevdev)
("yaml-cpp" ,yaml-cpp)))
(arguments
`(#:make-flags (list "CC=gcc" "CXX=g++"
(string-append "PREFIX=" (assoc-ref %outputs "out")))
`(#:make-flags (list ,(string-append "CC=" (cc-for-target))
,(string-append "CXX=" (cxx-for-target))
(string-append "PREFIX=" %output))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-libevdev-path
@ -3818,9 +3814,9 @@ devices that can inject events directly into the input subsystem.")
(string-append libevdev "/include/libevdev-1.0")))
#t)))
;; No configure script
(delete 'configure)
;; No target 'check'
(delete 'check))))
(delete 'configure))
;; No tests are included.
#:tests? #f))
(synopsis "Tap for one key, hold for another")
(description
"Dual Function Keys is a plugin for @code{interception-tools} that allows
@ -8348,3 +8344,39 @@ Availability and Serviceability} reports from Linux kernel trace events.
These trace events are logged in @file{/sys/kernel/debug/tracing} and reported
through standard log mechanisms like syslog.")
(license license:gpl2)))
(define-public libgpiod
(package
(name "libgpiod")
(version "1.6.3")
(source
(origin
(method git-fetch)
(uri
(git-reference
(url "https://git.kernel.org/pub/scm/libs/libgpiod/libgpiod.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256 (base32 "0rv8a11hx3pc6sdw6nfc6k35hkp2clb3v53n1381cvip8fzhbsad"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
'("--enable-tools=yes"
"--enable-bindings-cxx"
"--enable-bindings-python")))
(native-inputs
`(("automake" ,automake)
("autoconf" ,autoconf)
("libtool" ,libtool)
("autoconf-archive" ,autoconf-archive)
("pkg-config" ,pkg-config)
("python" ,python-3)))
(synopsis "Interact with the Linux GPIO character device")
(description
"This package provides a C library with C++/Python bindings and
command-line tools for interacting with GPIO devices that avoids the usage of
older system-wide @file{/sys} interface.")
(home-page "https://git.kernel.org/pub/scm/libs/libgpiod/libgpiod.git/")
(license (list license:lgpl2.1+ ;; libgpiod
license:gpl2+ ;; gpio-tools
license:lgpl3+)))) ;; C++ bindings

132
gnu/packages/lisp-xyz.scm
View File

@ -91,6 +91,7 @@
#:use-module (gnu packages web)
#:use-module (gnu packages webkit)
#:use-module (gnu packages xdisorg)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
#:use-module (ice-9 match)
#:use-module (srfi srfi-1)
@ -16516,11 +16517,11 @@ for Common Lisp.")
(sbcl-package->cl-source-package sbcl-bknr-datastore))
(define-public sbcl-authentic
(let ((commit "d5ff2f4666ce24e41fb4ca22476c782c070e6f6e")
(revision "1"))
(let ((commit "4e9194dda227b98f56dda1c2a2480efcc2d1f973")
(revision "2"))
(package
(name "sbcl-authentic")
(version (git-version "0.1.0" revision commit))
(version (git-version "0.1.2" revision commit))
(source
(origin
(method git-fetch)
@ -16529,7 +16530,7 @@ for Common Lisp.")
(commit commit)))
(file-name (git-file-name "cl-authentic" version))
(sha256
(base32 "1dmi9lw1ickx0i41lh9sfchalvy7km6wc9w3szfjlvny7svwf6qp"))))
(base32 "0ncsxrybnx0pjsndv3j8w4lphlpcsld8sxg3c5b46fb3a8nd4ssf"))))
(build-system asdf-build-system/sbcl)
(native-inputs
`(("fiveam" ,sbcl-fiveam)))
@ -18543,3 +18544,126 @@ semantics in Lisp and Parenscript.
(define-public cl-spinneret
(sbcl-package->cl-source-package sbcl-spinneret))
(define-public sbcl-cl-libxml2
(let ((commit "8d03110c532c1a3fe15503fdfefe82f60669e4bd"))
(package
(name "sbcl-cl-libxml2")
(version (git-version "0.3.4" "1" commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/archimag/cl-libxml2")
(commit commit)))
(file-name (git-file-name "cl-libxml2" version))
(sha256
(base32 "09049c13cfp5sc6x9lrw762jd7a9qkfq5jgngqgrzn4kn9qscarw"))))
(build-system asdf-build-system/sbcl)
(inputs
`(("alexandria" ,sbcl-alexandria)
("cffi" ,sbcl-cffi)
("flexi-streams" ,sbcl-flexi-streams)
("garbage-pools" ,sbcl-garbage-pools)
("iterate" ,sbcl-iterate)
("metabang-bind" ,sbcl-metabang-bind)
("puri" ,sbcl-puri)
;; Non-Lisp inputs:
("libxml2" ,libxml2)
("libxslt" ,libxslt)))
(native-inputs
`(("gcc" ,sbcl-lift)
("lift" ,sbcl-lift)))
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-paths
(lambda* (#:key inputs outputs #:allow-other-keys)
(substitute* "tree/xtree.lisp"
(("libxml2.so.2")
(string-append (assoc-ref inputs "libxml2") "/lib/libxml2.so")))
(let ((libxslt (assoc-ref inputs "libxslt")))
(substitute* "xslt/xslt.lisp"
(("libxslt.so.1")
(string-append libxslt "/lib/libxslt.so"))
(("libexslt.so.0")
(string-append libxslt "/lib/libexslt.so"))
(("cllibxml2.so")
(string-append (assoc-ref outputs "out") "/lib/cllibxml2.so"))))
#t))
(add-before 'build 'build-helper-library
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((prefix-dir (string-append (assoc-ref outputs "out"))))
(mkdir-p (string-append prefix-dir "/lib"))
(invoke "make" "-C" "foreign" "install"
"INSOPTS="
(string-append "PREFIX=" prefix-dir))
#t)))
(add-after 'unpack 'fix-tests
(lambda _
(substitute* '("cl-libxml2.asd" "cl-libxslt.asd" "xfactory.asd")
((" :force t") ""))
#t)))))
(home-page "https://web.archive.org/web/20160121073421/http://cl-libxml2.googlecode.com/svn/doc/index.html")
(synopsis "High-level wrapper around libxml2 and libxslt libraries")
(description
"cl-libxml2 is high-level Common Lisp wrapper around the @code{libxml2}
and @code{libxslt} libraries.
@itemize
@item Interfaces for tree manipulation (like @code{cxml-stp}).
@item Interface for HTML 4.0 non-validating parsers.
@item Specific APIs to process HTML trees, especially serialization.
@item XPath API.
@item XSLT API.
@item Custom URL resolvers.
@item XPath extension functions.
@item XSLT extension elements.
@item Translates @code{libxml2} and @code{libxslt} errors to Lisp conditions.
@item Extends the Common Lisp @code{iterate} library with custom drivers for
child nodes enumeration, etc.
@item The @code{XFACTORY} system provides a simple and compact syntax for XML generation.
@end itemize\n")
(license license:llgpl))))
(define-public ecl-cl-libxml2
(sbcl-package->ecl-package sbcl-cl-libxml2))
(define-public cl-libxml2
(sbcl-package->cl-source-package sbcl-cl-libxml2))
(define-public sbcl-feeder
;; No release.
(let ((commit "b05f517d7729564575cc809e086c262646a94d34")
(revision "1"))
(package
(name "sbcl-feeder")
(version (git-version "1.0.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Shinmera/feeder")
(commit commit)))
(file-name (git-file-name "feeder" version))
(sha256
(base32 "1dpbzhycg50snl3j01c8dh8gdvhfhz0hnfl54xy55a3wbr3m6rp7"))))
(build-system asdf-build-system/sbcl)
(inputs
`(("documentation-utils" ,sbcl-documentation-utils)
("local-time" ,sbcl-local-time)
("plump" ,sbcl-plump)))
(home-page "https://shinmera.github.io/feeder/")
(synopsis "RSS, Atom and general feed parsing and generating")
(description
"Feeder is a syndication feed library. It presents a general protocol
for representation of feed items, as well as a framework to translate these
objects from and to external formats. It also implements the RSS 2.0 and Atom
formats within this framework.")
(license license:zlib))))
(define-public ecl-feeder
(sbcl-package->ecl-package sbcl-feeder))
(define-public cl-feeder
(sbcl-package->cl-source-package sbcl-feeder))

118
gnu/packages/lisp.scm
View File

@ -18,6 +18,7 @@
;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2020 Zhu Zihao <all_but_last@163.com>
;;; Copyright © 2021 Sharlatan Hellseher <sharlatanus@gmail.com>
;;; Copyright © 2021 Paul A. Patience <paul@apatience.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -53,14 +54,17 @@
#:use-module (guix build-system trivial)
#:use-module (gnu packages admin)
#:use-module (gnu packages base)
#:use-module (gnu packages bash)
#:use-module (gnu packages bdw-gc)
#:use-module (gnu packages compression)
#:use-module (gnu packages ed)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gettext)
#:use-module (gnu packages ghostscript)
#:use-module (gnu packages gl)
#:use-module (gnu packages glib)
#:use-module (gnu packages groff)
#:use-module (gnu packages m4)
#:use-module (gnu packages maths)
#:use-module (gnu packages multiprecision)
@ -842,10 +846,64 @@ enough to play the original mainframe Zork all the way through.")
(home-page "http://www.russotto.net/git/mrussotto/confusion/src/master/src/README")
(license license:gpl3+))))
(define man-for-txr
(let ((commit "dfbf19b9a96474b8c1bacac85e43605e5691ceb2")
;; Number of additional commits since the last tag (see the output of
;; "git describe --tags").
(revision "41"))
(package
(name "man-for-txr")
(version (git-version "1.6g" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "http://www.kylheku.com/git/man/")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1zy0g8fj9nsfwzvg88hyaiy94r8j14xhs8vy2ln2niqdm6x2lvy2"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; There are no tests.
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-man2html-makefile
(lambda _
(substitute* "man2html/Makefile.in"
;; It inadvertently ignores @bindir@.
(("^(bindir = \\$\\(DESTDIR\\)\\$\\(PREFIX\\)).*" _ prefix)
(string-append prefix "@bindir@\n")))
#t))
(add-after 'unpack 'delete-generated-files
(lambda _
(for-each delete-file
(append
(list "conf_script")
(map (lambda (d) (string-append d "/Makefile"))
'("." "man" "man2html" "src"))
(map (lambda (f) (string-append "src/" f))
'("makewhatis.in" "man.conf"
"paths.h" "version.h"))))
#t))
(replace 'configure
(lambda* (#:key outputs #:allow-other-keys)
(setenv "CC" ,(cc-for-target))
;; Humor the manually written configure script.
(invoke "./configure" "+lang" "en" "+fhs"
(string-append "-prefix=" (assoc-ref outputs "out")))
#t)))))
(home-page "http://www.kylheku.com/cgit/man/")
(synopsis "Modifications to the man utilities, specifically man2html")
(description
"This is a fork of the man utilities intended specifically for building
the HTML documentation of TXR.")
(license license:gpl2))))
(define-public txr
(package
(name "txr")
(version "263")
(version "266")
(source
(origin
(method git-fetch)
@ -854,8 +912,16 @@ enough to play the original mainframe Zork all the way through.")
(commit (string-append "txr-" version))))
(file-name (git-file-name name version))
(sha256
(base32 "14zaziymnbr2ld79x4h7sf88bzzzj82w3xpavmcx7mhwannb2swh"))))
(base32 "1k9mj3zaxdsylgnb8g6cq0cmp6420x7fp3nnsqdmds4gh8ib95wn"))))
(build-system gnu-build-system)
(native-inputs
;; Required to build the documentation.
`(("ghostscript" ,ghostscript)
("groff" ,groff)
("man2html" ,man-for-txr)))
(inputs
`(("bash" ,bash-minimal)
("libffi" ,libffi)))
(arguments
`(#:configure-flags
(list ,(string-append "cc=" (cc-for-target))
@ -863,6 +929,38 @@ enough to play the original mainframe Zork all the way through.")
#:test-target "tests"
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-license-installation
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "Makefile"
(("INSTALL(,.*LICENSE,.*)\\$\\(datadir\\)" _ match)
(string-append "INSTALL" match
(assoc-ref outputs "out")
"/share/doc/" ,name "-" ,version)))
#t))
(delete 'install-license-files)
(add-after 'unpack 'inhibit-doc-syms-generation
(lambda _
(substitute* "genman.txr"
;; Exit from genman.txr before it tries to write to
;; stdlib/doc-syms.tl, which is anyway kept up to date with
;; each release (and is already compiled to stdlib/doc-syms.tlo
;; when genman.txr is run).
(("^@\\(output \"stdlib/doc-syms\\.tl\"\\).*" line)
(string-append "@(do (exit))\n" line)))
#t))
(add-after 'unpack 'fix-paths
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "stream.c"
(("/bin/sh")
(string-append (assoc-ref inputs "bash") "/bin/bash")))))
(add-after 'unpack 'fix-tests
(lambda _
(substitute* (list "tests/017/realpath.tl"
"tests/017/realpath.expected")
(("/usr/bin") "/"))
(substitute* "tests/018/path-test.tl"
(("/bin") (dirname (which "sh"))))
#t))
(replace 'configure
;; ./configure is a hand-written script that can't handle standard
;; autotools arguments like CONFIG_SHELL.
@ -870,14 +968,18 @@ enough to play the original mainframe Zork all the way through.")
(setenv "txr_shell" (which "bash"))
(apply invoke "./configure" configure-flags)
#t))
(add-after 'configure 'fix-tests
(add-after 'build 'build-doc
(lambda _
(substitute* (list "tests/017/realpath.tl"
"tests/017/realpath.expected")
(("/usr/bin") "/"))
(setenv "GS_GENERATE_UUIDS" "0")
(invoke "make" "txr-manpage.html" "txr-manpage.pdf")
#t))
(add-after 'install 'install-doc
(lambda* (#:key outputs #:allow-other-keys)
(let ((doc (string-append (assoc-ref outputs "out")
"/share/doc/" ,name "-" ,version)))
(for-each (lambda (f) (install-file f doc))
'("txr-manpage.html" "txr-manpage.pdf")))
#t)))))
(inputs
`(("libffi" ,libffi)))
(synopsis "General-purpose, multi-paradigm programming language")
(description
"TXR is a general-purpose, multi-paradigm programming language. It

51
gnu/packages/machine-learning.scm
View File

@ -1189,6 +1189,57 @@ Models, is a program for performing both single-SNP and SNP-set genome-wide
association studies (GWAS) on extremely large data sets.")
(license license:asl2.0)))
(define-public python-hyperopt
(package
(name "python-hyperopt")
(version "0.2.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "hyperopt" version))
(sha256
(base32 "1k4ma8ci0bxghw7g4ms944zak1pi83yv2d6bxd7fcslm1zalfq5w"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
(when tests?
(add-installed-pythonpath inputs outputs)
(invoke "python" "-m" "pytest" "--ignore"
;; Needs python-pyspark.
"hyperopt/tests/test_spark.py"
;; Needs both python-scikit-learn and python-lightgbm.
"--ignore" "hyperopt/tests/test_atpe_basic.py"
;; The tests below need python-lightgbm.
"-k" (string-append "not test_branin"
" and not test_distractor"
" and not test_q1lognormal"
" and not test_quadratic1"
" and not test_twoarms"))))))))
(propagated-inputs
`(("python-cloudpickle" ,python-cloudpickle)
("python-future" ,python-future)
("python-networkx" ,python-networkx)
("python-numpy" ,python-numpy)
("python-scipy" ,python-scipy)
("python-six" ,python-six)
("python-tqdm" ,python-tqdm)))
(native-inputs
`(("python-black" ,python-black)
("python-ipython" ,python-ipython)
("python-ipyparallel" ,python-ipyparallel)
("python-nose" ,python-nose)
("python-pymongo" ,python-pymongo)
("python-pytest" ,python-pytest)))
(home-page "https://hyperopt.github.io/hyperopt/")
(synopsis "Library for hyperparameter optimization")
(description "Hyperopt is a Python library for serial and parallel
optimization over awkward search spaces, which may include real-valued,
discrete, and conditional dimensions.")
(license license:bsd-3)))
;; There have been no proper releases yet.
(define-public kaldi
(let ((commit "d4791c0f3fc1a09c042dac365e120899ee2ad21e")

19
gnu/packages/mail.scm
View File

@ -534,7 +534,7 @@ aliasing facilities to work just as they would on normal mail.")
(define-public mutt
(package
(name "mutt")
(version "2.1.0")
(version "2.1.1")
(source (origin
(method url-fetch)
(uri (list
@ -544,7 +544,7 @@ aliasing facilities to work just as they would on normal mail.")
version ".tar.gz")))
(sha256
(base32
"0dqd6gg1wwhxjgdfl8j0kf93mw43kvd6wrwrzkscq2wjrsy5p0w0"))
"0jjjvqkqmpj55v111p1a1i2ry7mpd1bpphn1bhvlr18rgw7xdrja"))
(patches (search-patches "mutt-store-references.patch"))))
(build-system gnu-build-system)
(inputs
@ -1628,6 +1628,16 @@ compresses it.")
"gtk_update_icon_cache=true")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-source
(lambda* (#:key inputs #:allow-other-keys)
;; Use absolute paths to referenced programs.
(let* ((mailutils (assoc-ref inputs "mailutils"))
(inc (string-append mailutils "/bin/mu-mh/inc"))
(send-mail (assoc-ref inputs "sendmail"))
(sendmail (string-append send-mail "/usr/sbin/sendmail")))
(substitute* "src/common/defs.h"
(("/usr/bin/mh/inc") inc)
(("/usr/sbin/sendmail") sendmail)))))
(add-before 'build 'patch-mime
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "src/procmime.c"
@ -1673,6 +1683,7 @@ compresses it.")
("libsm" ,libsm)
("libsoup" ,libsoup)
("libxml2" ,libxml2)
("mailutils" ,mailutils)
("nettle" ,nettle)
("network-manager" ,network-manager)
("openldap" ,openldap)
@ -1680,6 +1691,7 @@ compresses it.")
("poppler" ,poppler)
("python" ,python)
("python-pygobject" ,python-pygobject)
("sendmail" ,sendmail)
("shared-mime-info" ,shared-mime-info)
("startup-notification" ,startup-notification)
;;("webkitgtk" ,webkitgtk)
@ -2386,7 +2398,8 @@ be expected from a simple client.")
(sha256
(base32
"1ay282rrl92h0m0m8z5zzjnwiiagi7c78aq2qvhia5mw7prwfyw2"))
(file-name (string-append name "-" version "-checkout"))))
(file-name (string-append name "-" version "-checkout"))
(patches (search-patches "esmtp-add-lesmtp.patch"))))
(arguments
`(#:phases (modify-phases %standard-phases
(replace 'bootstrap

282
gnu/packages/maths.scm
View File

@ -47,6 +47,7 @@
;;; Copyright © 2021 Philip McGrath <philip@philipmcgrath.com>
;;; Copyright © 2021 Paul A. Patience <paul@apatience.com>
;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru>
;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
;;;
;;; This file is part of GNU Guix.
;;;
@ -1800,6 +1801,154 @@ large-scale nonlinear optimization. It provides C++, C, and Fortran
interfaces.")
(license license:epl2.0)))
(define-public nomad-optimizer
(package
(name "nomad-optimizer")
(version "4.1.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/bbopt/nomad/")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0w386d8r5ldbvnv0c0g7vz95pfpvwdxis26vaalk2amsa5akl775"))))
(build-system cmake-build-system)
(native-inputs
`(("python" ,python-wrapper)
("python-cython" ,python-cython)))
(arguments
`(#:imported-modules ((guix build python-build-system)
,@%cmake-build-system-modules)
#:modules (((guix build python-build-system)
#:select (python-version site-packages))
(guix build cmake-build-system)
(guix build utils))
#:configure-flags
'("-DBUILD_INTERFACES=ON"
"-DBUILD_TESTS=ON")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-sources-for-build
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "CMakeLists.txt"
;; CMAKE_INSTALL_PREFIX is accidentally hardcoded.
(("set\\(CMAKE_INSTALL_PREFIX .* FORCE\\)") "")
;; Requiring GCC version 8 or later is unwarranted.
(("message\\(FATAL_ERROR \"GCC version < 8")
"message(STATUS \"GCC version < 8"))
(let ((out (assoc-ref outputs "out")))
(substitute* "interfaces/PyNomad/CMakeLists.txt"
;; We don't want to build in-place, and anyway the install
;; command further below runs build_ext as a prerequisite.
(("COMMAND python setup_PyNomad\\.py .* build_ext --inplace\n")
"")
;; Don't install locally.
(("COMMAND python (setup_PyNomad\\.py .* install) --user\n"
_ args)
(string-append "COMMAND ${CMAKE_COMMAND} -E env"
" CC=" ,(cc-for-target)
" CXX=" ,(cxx-for-target)
" " (which "python")
" " args
" --prefix=" out
"\n")))
;; Fix erroneous assumptions about the paths of the include and
;; library directories.
(substitute* "interfaces/PyNomad/setup_PyNomad.py"
(("^( +os_include_dirs = ).*" _ prefix)
(string-append prefix "[\"../../src\"]\n"))
(("^(installed_lib_dir = ).*" _ prefix)
(string-append prefix "\"" out "/lib\"\n"))))
#t))
;; Fix the tests so they run in out-of-source builds.
(add-after 'fix-sources-for-build 'fix-sources-for-tests
(lambda _
(substitute*
(map (lambda (d) (string-append "examples/" d "/CMakeLists.txt"))
(append
(map (lambda (d) (string-append "basic/library/" d))
'("example1" "example2" "example3"
"single_obj_parallel"))
(map (lambda (d) (string-append "advanced/library/" d))
'("FixedVariable" "NMonly" "PSDMads" "Restart"
"c_api/example1" "c_api/example2"
"exampleSuggestAndObserve"))))
;; The built examples are assumed to be in the source tree
;; (which isn't the case here).
(("(COMMAND \\$\\{CMAKE_BINARY_DIR\\}/examples/runExampleTest\\.sh )\\.(/.*)"
_ command test)
(string-append command "${CMAKE_CURRENT_BINARY_DIR}" test)))
;; (Unrelated to support for out-of-source testing.)
(make-file-writable
"examples/advanced/library/exampleSuggestAndObserve/cache0.txt")
(let* ((builddir (string-append (getcwd) "/../build"))
;; The BB_EXE and SURROGATE_EXE paths are interpreted
;; relative to the configuration file provided to NOMAD.
;; However, the configuration files are all in the source
;; tree rather than in the build tree (unlike the compiled
;; executables).
(fix-exe-path (lambda* (dir #:optional
(file "param.txt")
(exe-opt "BB_EXE"))
(substitute* (string-append dir "/" file)
(((string-append "^" exe-opt " +"))
;; The $ prevents NOMAD from prefixing
;; the executable with the path of the
;; parent directory of the configuration
;; file NOMAD was provided with as
;; argument (param.txt or some such).
(string-append exe-opt " $"
builddir "/" dir "/"))))))
(for-each
(lambda (dir)
(let ((dir (string-append "examples/" dir)))
(substitute* (string-append dir "/CMakeLists.txt")
;; The install phase has not yet run.
(("COMMAND \\$\\{CMAKE_INSTALL_PREFIX\\}/bin/nomad ")
"COMMAND ${CMAKE_BINARY_DIR}/src/nomad "))
(fix-exe-path dir)
(when (equal? dir "examples/basic/batch/surrogate_sort")
(fix-exe-path dir "param.txt" "SURROGATE_EXE"))))
(append (map (lambda (d) (string-append "basic/batch/" d))
'("example1" "example2"
"single_obj" "single_obj_parallel"
"surrogate_sort"))
'("advanced/batch/LHonly")))
(let ((dir "examples/advanced/batch/FixedVariable"))
(substitute* (string-append dir "/runFixed.sh")
;; Hardcoded path to NOMAD executable.
(("^\\.\\./\\.\\./\\.\\./\\.\\./bin/nomad ")
(string-append builddir "/src/nomad ")))
(for-each
(lambda (f) (fix-exe-path dir f))
'("param1.txt" "param2.txt" "param3.txt" "param10.txt"))))
#t))
;; The information in the .egg-info file is not kept up to date.
(add-after 'install 'delete-superfluous-egg-info
(lambda* (#:key inputs outputs #:allow-other-keys)
(delete-file (string-append
(site-packages inputs outputs)
"PyNomad-0.0.0-py"
(python-version (assoc-ref inputs "python"))
".egg-info"))
#t)))))
(home-page "https://www.gerad.ca/nomad/")
(synopsis "Nonlinear optimization by mesh-adaptive direct search")
(description
"NOMAD is a C++ implementation of the mesh-adaptive direct search (MADS)
algorithm, designed for difficult blackbox optimization problems. These
problems occur when the functions defining the objective and constraints are
the result of costly computer simulations.")
(license license:lgpl3+)))
(define-public cbc
(package
(name "cbc")
@ -3553,31 +3702,32 @@ processor cores.")
(synopsis "Parallel adaptive mesh refinement on forests of octrees")))
(define-public gsegrafix
;; This is an old and equally dead "experimental fork" of the longer-dead
;; original. At least it no longer requires the even-deader libgnomeprint{,ui}
;; libraries, instead rendering plots with Pango.
(package
(name "gsegrafix")
(version "1.0.6")
(version "1.0.7.2")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://gnu/" name "/" name "-"
version ".tar.gz"))
(sha256
(base32
"1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
(method url-fetch)
(uri (string-append "mirror://savannah/gsegrafix-experimental/"
"gsegrafix-experimental-" version ".tar.gz"))
(sha256
(base32 "0fwh6719xy2zasmqlp0vdx6kzm45hn37ga88xmw5cz0yx7xw4j6f"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags '("LDFLAGS=-lm")))
`(#:configure-flags
(list "--disable-static")))
(inputs
`(("libgnomecanvas" ,libgnomecanvas)
("libbonoboui" ,libbonoboui)
("libgnomeui" ,libgnomeui)
("libgnomeprintui" ,libgnomeprintui)
("popt" ,popt)))
`(("glib" ,glib)
("gtk+" ,gtk+)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "https://www.gnu.org/software/gsegrafix/")
(synopsis "GNOME application to create scientific and engineering plots")
(description "GSEGrafix is an application which produces high-quality graphical
(description
"GSEGrafix is an application which produces high-quality graphical
plots for science and engineering. Plots are specified via simple ASCII
parameter files and data files and are presented in an anti-aliased GNOME
canvas. The program supports rectangular two-dimensional plots, histograms,
@ -4033,7 +4183,7 @@ access to BLIS implementations via traditional BLAS routine calls.")
(define-public openlibm
(package
(name "openlibm")
(version "0.6.0")
(version "0.7.4")
(source
(origin
(method git-fetch)
@ -4042,11 +4192,12 @@ access to BLIS implementations via traditional BLAS routine calls.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "08wfchmmr5200fvmn1kwq9byc1fhsq46hn0y5k8scdl74771c7gh"))))
(base32 "1azms0lpxb7vxb3bln5lyz0wpwx6jnzbffkclclpq2v5aiw8d14i"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags
(list (string-append "prefix=" (assoc-ref %outputs "out")))
(list (string-append "prefix=" (assoc-ref %outputs "out"))
,(string-append "CC=" (cc-for-target)))
#:phases
;; no configure script
(modify-phases %standard-phases (delete 'configure))
@ -4461,40 +4612,75 @@ revised simplex and the branch-and-bound methods.")
(define-public dealii
(package
(name "dealii")
(version "9.2.0")
(version "9.3.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/dealii/dealii/releases/"
"download/v" version "/dealii-" version ".tar.gz"))
(sha256
(base32
"0fm4xzrnb7dfn4415j24d8v3jkh0lssi86250x2f5wgi83xq4nnh"))
(base32 "1f0sqvlxvl0myqcn0q6xrn1vnp5pgx143lai4a4jkh1dmdv4cbx6"))
(modules '((guix build utils)))
(snippet
;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
'(begin
;; Remove bundled boost, muparser, TBB and UMFPACK.
(delete-file-recursively "bundled")
#t))))
(build-system cmake-build-system)
(outputs '("out" "doc"))
(native-inputs
;; Required to build the documentation.
`(("dot" ,graphviz)
("doxygen" ,doxygen)
("perl" ,perl)))
(inputs
`(("tbb" ,tbb)
("zlib" ,zlib)
("boost" ,boost)
("p4est" ,p4est)
`(("arpack" ,arpack-ng)
("blas" ,openblas)
("lapack" ,lapack)
("arpack" ,arpack-ng)
("muparser" ,muparser)
("gfortran" ,gfortran)
("suitesparse" ,suitesparse))) ;for UMFPACK
("lapack" ,lapack)
("muparser" ,muparser)
("zlib" ,zlib)))
(propagated-inputs
;; Some scripts are installed into share/deal.II/scripts that require
;; perl and python, but they are not executable (and some are missing the
;; shebang line) and therefore must be explicitly passed to the
;; interpreter.
;; Anyway, they are meant to be used at build time, so rather than adding
;; the interpreters here, any package depending on them should just add
;; the requisite interpreter to its native inputs.
`(("boost" ,boost)
("hdf5" ,hdf5)
("suitesparse" ,suitesparse) ; For UMFPACK.
("tbb" ,tbb)))
(arguments
`(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
`(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease.
;; The tests take too long and must be explicitly enabled with "make
;; setup_tests".
;; See https://www.dealii.org/developer/developers/testsuite.html.
;; (They can also be run for an already installed deal.II.)
#:tests? #f
#:configure-flags
;; Work around a bug in libsuitesparseconfig linking
;; see https://github.com/dealii/dealii/issues/4745
'("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
(home-page "https://www.dealii.org")
(let ((doc (string-append (assoc-ref %outputs "doc")
"/share/doc/" ,name "-" ,version)))
`("-DDEAL_II_COMPONENT_DOCUMENTATION=ON"
,(string-append "-DDEAL_II_DOCREADME_RELDIR=" doc)
,(string-append "-DDEAL_II_DOCHTML_RELDIR=" doc "/html")
;; Don't compile the examples because the source and CMakeLists.txt
;; are installed anyway, allowing users to do so for themselves.
"-DDEAL_II_COMPILE_EXAMPLES=OFF"
,(string-append "-DDEAL_II_EXAMPLES_RELDIR=" doc "/examples")))
#:phases
(modify-phases %standard-phases
(add-after 'install 'remove-build-logs
;; These build logs leak the name of the build directory by storing
;; the values of CMAKE_SOURCE_DIR and CMAKE_BINARY_DIR.
(lambda* (#:key outputs #:allow-other-keys)
(let ((doc (string-append (assoc-ref outputs "doc")
"/share/doc/" ,name "-" ,version)))
(for-each delete-file (map (lambda (f) (string-append doc "/" f))
'("detailed.log" "summary.log"))))
#t)))))
(home-page "https://www.dealii.org/")
(synopsis "Finite element library")
(description
"Deal.II is a C++ program library targeted at the computational solution
@ -4505,30 +4691,24 @@ in finite element programs.")
(license license:lgpl2.1+)))
(define-public dealii-openmpi
(package (inherit dealii)
(package/inherit dealii
(name "dealii-openmpi")
(inputs
`(("mpi" ,openmpi)
;;Supported only with MPI:
("hdf5" ,hdf5-parallel-openmpi) ;TODO: have petsc-openmpi propagate?
`(("arpack" ,arpack-ng-openmpi)
("metis" ,metis)
("scalapack" ,scalapack)
,@(alist-delete "arpack" (package-inputs dealii))))
(propagated-inputs
`(("hdf5" ,hdf5-parallel-openmpi)
("mpi" ,openmpi)
("p4est" ,p4est-openmpi)
("petsc" ,petsc-openmpi)
("slepc" ,slepc-openmpi)
("metis" ,metis) ;for MUMPS
("scalapack" ,scalapack) ;for MUMPS
("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
("arpack" ,arpack-ng-openmpi)
,@(fold alist-delete (package-inputs dealii)
'("p4est" "arpack"))))
,@(alist-delete "hdf5" (package-propagated-inputs dealii))))
(arguments
(substitute-keyword-arguments (package-arguments dealii)
((#:configure-flags cf)
`(cons "-DDEAL_II_WITH_MPI:BOOL=ON"
,cf))
((#:phases phases '%standard-phases)
`(modify-phases ,phases
(add-before 'check 'mpi-setup
,%openmpi-setup)))))
((#:configure-flags flags)
`(cons "-DDEAL_II_WITH_MPI=ON" ,flags))))
(synopsis "Finite element library (with MPI support)")))
(define-public flann

40
gnu/packages/messaging.scm
View File

@ -73,6 +73,7 @@
#:use-module (gnu packages glib)
#:use-module (gnu packages gnome)
#:use-module (gnu packages gnupg)
#:use-module (gnu packages golang)
#:use-module (gnu packages gperf)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages gstreamer)
@ -139,6 +140,45 @@
#:use-module (guix packages)
#:use-module (guix utils))
(define-public omemo-wget
(package
(name "omemo-wget")
(version "0.3.0")
(source
(origin
(method git-fetch)
(uri
(git-reference
(url "https://github.com/roobre/omemo-wget")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0s3vfaicw5xbjl9yiyr4ckrzhzqbvfh1w2ih1igavlfpgw4v7kva"))))
(build-system go-build-system)
(arguments
`(#:import-path "github.com/roobre/omemo-wget"
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch
(lambda* (#:key inputs #:allow-other-keys)
(let* ((xdg-utils (assoc-ref inputs "xdg-utils"))
(xdg-open (string-append xdg-utils "/bin/xdg-open")))
(substitute* (find-files "." "\\.go$")
;; Correct the import path of 'aesgcm' package.
(("roob\\.re/omemo-wget/aesgcm")
"github.com/roobre/omemo-wget/aesgcm")
;; Use absolute path of 'xdg-open' program.
(("xdg-open") xdg-open))))))))
(inputs
`(("go-github-com-pkg-errors" ,go-github-com-pkg-errors)
("xdg-utils" ,xdg-utils)))
(home-page "https://roob.re/omemo-wget")
(synopsis "Program to download and decrypt @code{aesgcm://} URLs")
(description "OMEMO-wget is a tool to handle cryptographic URLs, generated
by @acronym{OMEMO, OMEMO Multi-End Message and Object Encryption}, during
XMPP-based sessions.")
(license license:lgpl3+)))
(define-public psi
(package
(name "psi")

219
gnu/packages/music.scm
View File

@ -847,7 +847,7 @@ MusePack, Monkey's Audio, and WavPack files.")
(define-public extempore
(package
(name "extempore")
(version "0.8.6")
(version "0.8.9")
(source (origin
(method git-fetch)
(uri (git-reference
@ -855,7 +855,7 @@ MusePack, Monkey's Audio, and WavPack files.")
(commit (string-append "v" version))))
(sha256
(base32
"182jy23qv115dipny7kglwbn21z55dp253w1ykm0kh8n6vkgs7gp"))
"16i12zl3g1zpx6lhg5pg821xirdf9rxx5m11b68inf83wn6hknhb"))
(file-name (git-file-name name version))
(patches (search-patches
"extempore-unbundle-external-dependencies.patch"))
@ -864,16 +864,12 @@ MusePack, Monkey's Audio, and WavPack files.")
'(begin
;; Remove bundled sources.
(map delete-file-recursively
'("src/portaudio"
"src/pcre"))
'("src/pcre"))
#t))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags (list "-DJACK=ON"
"-DPACKAGE=ON"
"-DEXTERNAL_SHLIBS_AUDIO=OFF"
"-DEXTERNAL_SHLIBS_GRAPHICS=OFF"
"-DCMAKE_BUILD_TYPE=Release"
(string-append "-DEXT_SHARE_DIR="
(assoc-ref %outputs "out")
"/share"))
@ -958,7 +954,12 @@ MusePack, Monkey's Audio, and WavPack files.")
(("COMMAND extempore" prefix)
(string-append prefix " --sharedir " (getcwd)
" --mcpu=generic --attr=none")))
#t)))))
#t))
(add-after 'unpack 'symlink-assets
(lambda* (#:key inputs #:allow-other-keys)
(let ((assets (assoc-ref inputs "extempore-assets")))
(symlink assets "assets")
#t))))))
(inputs
`(("llvm"
,(package
@ -972,6 +973,19 @@ MusePack, Monkey's Audio, and WavPack files.")
(sha256
(base32
"1svdl6fxn8l01ni8mpm0bd5h856ahv3h9sdzgmymr6fayckjvqzs"))))))
("extempore-assets"
,(let ((commit "0c9f32c18169b3fbc24bc1ad66283125b54a0c85")
(revision "0")
(version "0.0.0"))
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/extemporelang/extempore-assets")
(commit commit)))
(file-name (git-file-name "extempore-assets"
(git-version version revision commit)))
(sha256
(base32 "1pxmcbngd9qx8m71d5rfsmf4h31jnsnd3wjh8vb0rwskif22xz8l")))))
("libffi" ,libffi)
("jack" ,jack-1)
("libsndfile" ,libsndfile)
@ -1538,9 +1552,9 @@ Guile.")
;; more than an hour of silence, so double the max silent time.
(properties `((max-silent-time . 7200)))))
(define-public python-abjad
(define-public abjad
(package
(name "python-abjad")
(name "abjad")
(version "3.3")
(source
(origin
@ -1556,17 +1570,108 @@ Guile.")
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-source
(lambda _
(substitute* "setup.py"
(("uqbar>=0.5.1, <0.5.0") "uqbar>=0.5.0"))
#t))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
;; See: https://stackoverflow.com/a/34140498
(invoke "python" "-m" "pytest" "tests")
#t))))))
(native-inputs
`(("python-black" ,python-black)
("python-flake8" ,python-flake8)
("python-iniconfig" ,python-iniconfig)
("python-isort" ,python-isort)
("python-mypy" ,python-mypy)
("python-pytest" ,python-pytest)
("python-pytest-cov" ,python-pytest-cov)
("python-sphinx-autodoc-typehints" ,python-sphinx-autodoc-typehints)))
(inputs
`(("lilypond" ,lilypond)))
(propagated-inputs
`(("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
"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)
("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)
@ -1574,19 +1679,64 @@ Guile.")
("python-iniconfig" ,python-iniconfig)
("python-isort" ,python-isort)
("python-mypy" ,python-mypy)
("python-ply" ,python-ply)
("python-pytest" ,python-pytest)
("python-pytest-cov" ,python-pytest-cov)
("python-sphinx-autodoc-typehints" ,python-sphinx-autodoc-typehints)))
("python-pytest-helpers-namespace" ,python-pytest-helpers-namespace)))
(propagated-inputs
`(("python-quicktions" ,python-quicktions)
("python-roman" ,python-roman)
("python-six" ,python-six)
("python-uqbar" ,python-uqbar)))
`(("abjad" ,abjad)))
(home-page "https://abjad.github.io")
(synopsis "Python API for building LilyPond files")
(synopsis "Abjad quantization extension, based on Paul Nauert's Q-Grids")
(description
"This package provides a Python API for building LilyPond files.")
"@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)
("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
@ -4963,14 +5113,15 @@ specification and header.")
(define-public rosegarden
(package
(name "rosegarden")
(version "21.06")
(version "21.06.1")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/rosegarden/rosegarden/"
version "/rosegarden-" version ".tar.bz2"))
(version-major+minor version) "/"
"rosegarden-" version ".tar.bz2"))
(sha256
(base32 "0rhbmygzh62hc3mkq60lh9r28wvfkhzzd5kspl1ll0h1ipjgvr6d"))))
(base32 "0yir279gxc5b298sr0fg9jxgdi75bb1gvvy4mh3pxqjsnp00sxc7"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release")
@ -4981,8 +5132,7 @@ specification and header.")
(substitute* "CMakeLists.txt"
(("BUILD_TESTING OFF") "BUILD_TESTING ON")
;; Make tests work.
((" -fvisibility=hidden") ""))
#t))
((" -fvisibility=hidden") ""))))
(add-after 'unpack 'fix-references
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "src/gui/general/ProjectPackager.cpp"
@ -5000,8 +5150,7 @@ specification and header.")
(("\"convert-ly\\>")
(string-append "\"" (assoc-ref inputs "lilypond") "/bin/convert-ly"))
(("\"lilypond\\>")
(string-append "\"" (assoc-ref inputs "lilypond") "/bin/lilypond")))
#t))
(string-append "\"" (assoc-ref inputs "lilypond") "/bin/lilypond")))))
(add-after 'unpack 'make-reproducible
(lambda _
;; Prevent Last-Modified from being written.
@ -5016,16 +5165,14 @@ specification and header.")
;; "qt5_add_resources(rg_SOURCES ../data/data.qrc OPTIONS --format-version 1)")
)
;; Make hashtable traversal order predicable.
(setenv "QT_RCC_TEST" "1") ; important
#t))
(setenv "QT_RCC_TEST" "1"))) ; important
(add-before 'check 'prepare-check
(lambda _
(setenv "QT_QPA_PLATFORM" "offscreen")
;; Tests create files in $HOME/.local/share/rosegarden .
(mkdir-p "/tmp/foo")
(setenv "HOME" "/tmp/foo")
(setenv "XDG_RUNTIME_DIR" "/tmp/foo")
#t)))))
(setenv "XDG_RUNTIME_DIR" "/tmp/foo"))))))
(inputs
`(("alsa-lib" ,alsa-lib)
("bash" ,bash)
@ -5045,7 +5192,7 @@ specification and header.")
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)
("qtlinguist" ,qttools)))
("qttools" ,qttools))) ;for qtlinguist
(synopsis "Music composition and editing environment based around a MIDI
sequencer")
(description "Rosegarden is a music composition and editing environment
@ -6332,7 +6479,7 @@ as JACK standalone applications.")
(method git-fetch)
(uri
(git-reference
(url "https://git.zrythm.org/git/zplugins")
(url "https://git.zrythm.org/zrythm/zplugins")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256

11
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View File

@ -43,6 +43,7 @@
;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
;;; Copyright © 2021 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2021 Justin Veilleux <terramorpha@cock.li>
;;; Copyright © 2021 Vinicius Monego <monego@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -1027,7 +1028,8 @@ transparently check connection attempts against an access control list.")
(sha256
(base32 "1rf3jmi36ms8jh2g5cvi253h43l6xdfq0r7mvp95va7mi4d014y5"))))
(build-system gnu-build-system)
(arguments '(#:configure-flags '("--disable-static")))
(arguments '(#:configure-flags '("--disable-static"
"--enable-drafts")))
(home-page "https://zeromq.org")
(synopsis "Library for message-based applications")
(description
@ -1441,14 +1443,14 @@ of the same name.")
(define-public wireshark
(package
(name "wireshark")
(version "3.4.6")
(version "3.4.7")
(source
(origin
(method url-fetch)
(uri (string-append "https://www.wireshark.org/download/src/wireshark-"
version ".tar.xz"))
(sha256
(base32 "0a26kcj3n1a2kw1f3fc6s1x3rw3f3bj2cq6rp7k0kc4ciwh7i9hj"))))
(base32 "17d00kl0s010wg2dfhy7sdbr2qm54lsi317fmbcvjz4rxx8ywk3c"))))
(build-system cmake-build-system)
(arguments
`(#:phases
@ -1461,8 +1463,7 @@ of the same name.")
(lambda _
(substitute* "CMakeLists.txt"
(("suite_unittests" all) (string-append "# " all))
(("suite_extcaps" all) (string-append "# " all)))
#t)))
(("suite_extcaps" all) (string-append "# " all))))))
;; Build process chokes during `validate-runpath' phase.
;;
;; Errors are like the following:

27
gnu/packages/node-xyz.scm
View File

@ -2,6 +2,7 @@
;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2020 Giacomo Leidi <goodoldpaul@autistici.org>
;;; Copyright © 2021 Noisytoot <noisytoot@disroot.org>
;;; Copyright © 2021 Charles <charles.b.jackson@protonmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -24,6 +25,32 @@
#:use-module (guix git-download)
#:use-module (guix build-system node))
(define-public node-acorn
(package
(name "node-acorn")
(version "8.4.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/acornjs/acorn")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "068h5gysz8bbslq31dva8f223rdf8l7w6nxcxjnv4zdprwkzkhaa"))))
(build-system node-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'change-directory
(lambda _
(chdir "acorn"))))))
(home-page "https://github.com/acornjs/acorn/tree/master/acorn")
(synopsis "Javascript-based Javascript parser")
(description "Acornjs is a Javascrip parser with many options and an
architecture supporting plugins.")
(license license:expat)))
(define-public node-color-name
(package
(name "node-color-name")

121
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@ -17,6 +17,7 @@
;;; Copyright © 2020 Jesse Gibbons <jgibbons2357+guix@gmail.com>
;;; Copyright © 2020 Martin Becze <mjbecze@riseup.net>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru>
;;;
;;; This file is part of GNU Guix.
;;;
@ -52,6 +53,7 @@
#:use-module (gnu packages crypto)
#:use-module (gnu packages curl)
#:use-module (gnu packages databases)
#:use-module (gnu packages dejagnu)
#:use-module (gnu packages dbm)
#:use-module (gnu packages docbook)
#:use-module (gnu packages file)
@ -64,6 +66,7 @@
#:use-module (gnu packages guile)
#:use-module (gnu packages guile-xyz)
#:use-module (gnu packages hurd)
#:use-module (gnu packages less)
#:use-module (gnu packages libedit)
#:use-module (gnu packages linux)
#:use-module (gnu packages lisp)
@ -83,6 +86,7 @@
#:use-module (gnu packages serialization)
#:use-module (gnu packages sqlite)
#:use-module (gnu packages ssh)
#:use-module (gnu packages tcl)
#:use-module (gnu packages texinfo)
#:use-module (gnu packages time)
#:use-module (gnu packages tls)
@ -1155,7 +1159,7 @@ outputs of those builds.")
(define-public guix-jupyter
(package
(name "guix-jupyter")
(version "0.2.1")
(version "0.2.2")
(home-page "https://gitlab.inria.fr/guix-hpc/guix-kernel")
(source (origin
(method git-fetch)
@ -1163,7 +1167,7 @@ outputs of those builds.")
(commit (string-append "v" version))))
(sha256
(base32
"1kqwfp5h95s6mirq5nbydsbmlhsinn32grz1ld5mbxvhl6sn2i0j"))
"17m6970wnvwlbarq4gxz5bakhzyhq5ch8qd8jw55ydccpv6473kq"))
(file-name (string-append "guix-jupyter-" version "-checkout"))))
(build-system gnu-build-system)
(arguments
@ -1494,3 +1498,116 @@ It is mainly meant for programmers who develop portable programs or libraries in
but could potentially work for end-users of those programs. It also has a translator
from R7RS, which allows most R7RS code to run on R6RS implementations.")
(license license:gpl3+)))
(define-public modules
(package
(name "modules")
(version "4.8.0")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/modules/Modules/modules-"
version "/modules-" version ".tar.bz2"))
(sha256 (base32 "1amz8qdqbvfdc8jv0j4720vywbz2gi7l3sr1lh37ilfbxy9lq9g9"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
(list (string-append "--with-bin-search-path="
(assoc-ref %build-inputs "tcl") "/bin" ":"
(assoc-ref %build-inputs "procps") "/bin" ":"
(assoc-ref %build-inputs "less") "/bin" ":"
(assoc-ref %build-inputs "coreutils") "/bin")
(string-append "--with-tcl=" (assoc-ref %build-inputs "tcl") "/lib")
"--disable-compat-version")
#:test-target "test"
#:phases
(modify-phases %standard-phases
(add-before 'configure 'patch-add-modules
(lambda* (#:key inputs #:allow-other-keys)
(let ((coreutils (assoc-ref inputs "coreutils")))
(substitute* "script/add.modules.in"
(("/bin/(cat|cp|rm)" _ command)
(string-append coreutils "/bin/" command))
(("/bin/echo")
"echo")))))
(add-before 'configure 'patch-scripts-for-python-3
(lambda _
;; Patch the script for python-3.
(substitute* "script/createmodule.py.in"
(("pathkeys.sort\\(\\)") "pathkeys = sorted(pathkeys)")
(("print\\(\"\\\\t\"\\*") "print(\"\\t\"*int")
(("@PYTHON@") (which "python3")))))
(add-before 'check 'patch-/bin/sh-and-nixbld-groups-in-tests
(lambda _
(use-modules (srfi srfi-1))
(let* ((groups-file (string-append (getcwd) "/nixbld-groups"))
(groups-file-z (string-append groups-file "-z"))
(nixbld-groups
(fold
(lambda (id prev)
(catch #t
(lambda () (cons (group:name (getgrnam id)) prev))
(lambda _ prev)))
'()
(vector->list (getgroups)))))
;; Simulate "id -G -n" command output.
(call-with-output-file groups-file
(lambda (port)
(display (string-join nixbld-groups " ") port)
(display #\newline port)))
;; Simulate "id -G -n -z" command output.
(call-with-output-file groups-file-z
(lambda (port)
(for-each
(lambda (group-name)
(display group-name port)
(display #\null port))
nixbld-groups)))
;; Generate "modulecmd-test.tcl" before running "make test".
(invoke "make" "modulecmd-test.tcl")
;; Substitute shell.
(substitute*
'("modulecmd-test.tcl"
"modulecmd.tcl"
"testsuite/modules.70-maint/380-edit.exp"
"compat/init/filter")
(("/bin/sh") (which "sh")))
;; Skip tests that use supplementary groups.
(for-each
delete-file
'("testsuite/modules.20-locate/112-hide-user-group.exp"
"testsuite/modules.20-locate/117-forbid-user-group.exp"
"testsuite/modules.20-locate/119-hide-cascading.exp"
"testsuite/modules.50-cmds/140-system.exp"
"testsuite/modules.50-cmds/287-info-usergroups.exp"
"testsuite/modules.50-cmds/440-module-tag.exp"
"testsuite/modules.70-maint/220-config.exp"))
(for-each
(lambda (file)
(substitute* file
(("/bin/sh") (which "bash"))
;; For some reason "kvm" group cannot be resolved for
;; "nixbld" user. We replace "id ..." commands with
;; "cat ..." that simulates them.
(("exec id -G -n -z") (string-append "exec cat " groups-file-z))
(("exec id -G -n") (string-append "exec cat " groups-file))))
'("testsuite/modules.00-init/005-init_ts.exp"
"testsuite/install.00-init/005-init_ts.exp"
"modulecmd-test.tcl"))))))))
(native-inputs
`(("dejagnu" ,dejagnu)
("autoconf" ,autoconf)
("which" ,which)))
(inputs
`(("tcl" ,tcl)
("less" ,less)
("procps" ,procps)
("coreutils" ,coreutils)
("python" ,python-3)))
(home-page "http://modules.sourceforge.net/")
(synopsis "Shell environment variables and aliases management")
(description "Modules simplify shell initialization and let users
modify their environment during the session with modulefiles. Modules are
used on high-performance clusters to dynamically add and remove paths
to specific versions of applications.")
(license license:gpl2+)))

37
gnu/packages/patches/esmtp-add-lesmtp.patch 100644
View File

@ -0,0 +1,37 @@
From 9b09ff673954c459218e2c664386286ca68aae51 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 24 Jul 2021 23:55:26 +0200
Subject: [PATCH] gnu: esmtp: Always assume that -lesmtp will work.
libesmtp 1.1.0 removed the libesmtp-config helper in favour of pkg-config.
This does not use that (I lack the chops and the patience). Assume that
the build environment has everything set up for us, which is true on Guix.
---
configure.ac | 11 ++---------
1 file changed, 2 insertions(+), 9 deletions(-)
diff --git a/configure.ac b/configure.ac
index 9252ec2..7ccf71a 100644
--- a/configure.ac
+++ b/configure.ac
@@ -32,15 +32,8 @@ then
AC_CHECK_HEADER(libesmtp.h, ,[AC_MSG_ERROR([libesmtp.h not found in $with_libesmtp])])
fi
AC_MSG_CHECKING(for libESMTP)
-if libesmtp-config --version > /dev/null 2>&1
-then
- AC_MSG_RESULT(yes)
- CFLAGS="$CFLAGS `libesmtp-config --cflags`"
- LIBS="$LIBS `libesmtp-config --libs`"
-else
- AC_MSG_RESULT(no)
- AC_MSG_ERROR(libESMTP library not found)
-fi
+AC_MSG_RESULT(assumed)
+LIBS="$LIBS -lesmtp"
jrf_FUNC_GETOPT
--
2.32.0

320
gnu/packages/patches/extempore-unbundle-external-dependencies.patch
View File

@ -1,19 +1,27 @@
Remove build machinery for bundled dependencies.
From b48ef9af13a154939acc245c32d72358001d00f1 Mon Sep 17 00:00:00 2001
From: Giacomo Leidi <goodoldpaul@autistici.org>
Date: Sun, 20 Jun 2021 12:53:27 +0200
Subject: [PATCH] Remove build machinery for bundled dependencies.
---
CMakeLists.txt | 192 +------------------------------------------------
1 file changed, 1 insertion(+), 191 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 89e6125e..c5e90750 100644
index 17d13d7c..2a7206ed 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -36,7 +36,7 @@ endif()
if(PACKAGE)
# this needs to be set before project() is called
set(CMAKE_OSX_DEPLOYMENT_TARGET 10.12)
- set(ASSETS ON) # necessary for packaging
+ set(ASSETS OFF) # necessary for packaging
message(STATUS "Building Extempore for binary distribution (assets directory will be downloaded)")
endif()
@@ -1,9 +1,6 @@
cmake_minimum_required(VERSION 3.1) # we use target_sources()
project(Extempore VERSION 0.8.9)
@@ -134,71 +134,6 @@ else()
-# for backwards compatibility with CMake older than 3.19
-cmake_policy(SET CMP0114 OLD)
-
option(ASSETS "download multimedia assets (approx 500MB)" OFF)
option(BUILD_TESTS "build test targets (including examples)" ON)
option(PACKAGE "set up install targets for packaging" OFF)
@@ -142,55 +139,6 @@ else()
message(FATAL_ERROR "Sorry, Extempore isn't supported on this platform - macOS, Linux & Windows only.")
endif()
@ -51,90 +59,224 @@ index 89e6125e..c5e90750 100644
-# portaudio #
-#############
-
-add_library(portaudio STATIC
- src/portaudio/src/common/pa_allocation.c
- src/portaudio/src/common/pa_allocation.h
- src/portaudio/src/common/pa_converters.c
- src/portaudio/src/common/pa_converters.h
- src/portaudio/src/common/pa_cpuload.c
- src/portaudio/src/common/pa_cpuload.h
- src/portaudio/src/common/pa_debugprint.c
- src/portaudio/src/common/pa_debugprint.h
- src/portaudio/src/common/pa_dither.c
- src/portaudio/src/common/pa_dither.h
- src/portaudio/src/common/pa_endianness.h
- src/portaudio/src/common/pa_front.c
- src/portaudio/src/common/pa_hostapi.h
- src/portaudio/src/common/pa_memorybarrier.h
- src/portaudio/src/common/pa_process.c
- src/portaudio/src/common/pa_process.h
- src/portaudio/src/common/pa_ringbuffer.c
- src/portaudio/src/common/pa_ringbuffer.h
- src/portaudio/src/common/pa_stream.c
- src/portaudio/src/common/pa_stream.h
- src/portaudio/src/common/pa_trace.c
- src/portaudio/src/common/pa_trace.h
- src/portaudio/src/common/pa_types.h
- src/portaudio/src/common/pa_util.h
- )
-include(ExternalProject)
-
-target_include_directories(portaudio
- PRIVATE src/portaudio/include
- PRIVATE src/portaudio/src/common)
-ExternalProject_Add(portaudio_static
- PREFIX portaudio
- URL https://github.com/PortAudio/portaudio/archive/3f7bee79a65327d2e0965e8a74299723ed6f072d.zip
- URL_MD5 182b76e05f6ef21d9f5716da7489905d
- CMAKE_ARGS
- -DPA_BUILD_STATIC=ON
- -DPA_BUILD_SHARED=OFF
- -DPA_LIBNAME_ADD_SUFFIX=OFF
- -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
- -DCMAKE_C_FLAGS=${EXT_DEPS_C_FLAGS}
- -DCMAKE_CXX_FLAGS=${EXT_DEPS_CXX_FLAGS}
- -DCMAKE_INSTALL_PREFIX=${CMAKE_BINARY_DIR}/portaudio)
-
# platform-specific
if(APPLE)
@@ -224,25 +159,8 @@ if(APPLE)
elseif(UNIX AND NOT APPLE)
# use ALSA on Linux
- target_sources(portaudio
- PRIVATE src/portaudio/src/hostapi/alsa/pa_linux_alsa.c
- PRIVATE src/portaudio/src/os/unix/pa_unix_hostapis.c
- PRIVATE src/portaudio/src/os/unix/pa_unix_util.c
- )
- target_include_directories(portaudio
- PRIVATE src/portaudio/src/os/unix)
- target_compile_definitions(portaudio
- PRIVATE -DPA_USE_ALSA)
- target_link_libraries(portaudio
- PRIVATE asound)
if(JACK)
- target_sources(portaudio
- PRIVATE src/portaudio/src/hostapi/jack/pa_jack.c)
- target_compile_definitions(portaudio
- PRIVATE -DPA_USE_JACK)
- target_link_libraries(portaudio
- PRIVATE jack)
endif()
elseif(WIN32)
@@ -292,8 +210,6 @@ if(ASIO)
endif()
if(PACKAGE)
- target_compile_options(portaudio
- PRIVATE -mtune=generic)
endif()
##############
@@ -411,8 +327,6 @@ endif()
# LLVM 3.8.0 #
##############
@@ -323,11 +271,6 @@ if(UNIX)
set_source_files_properties(src/Scheme.cpp PROPERTIES COMPILE_FLAGS -Wno-switch)
endif()
# dependencies
-add_dependencies(extempore pcre portaudio)
-# static extempore build dependencies
-
-add_dependencies(extempore pcre)
-add_dependencies(extempore portaudio_static)
-
if(BUILD_LLVM)
if(WIN32)
add_dependencies(extempore LLVM-install)
@@ -553,7 +467,7 @@ else()
install(TARGETS extempore
RUNTIME
DESTINATION ".")
- install(DIRECTORY assets runtime libs examples tests
+ install(DIRECTORY runtime libs examples
DESTINATION "."
PATTERN ".DS_Store" EXCLUDE)
@@ -342,12 +285,9 @@ endif()
target_include_directories(extempore
PRIVATE
- src/pcre
- ${CMAKE_BINARY_DIR}/portaudio/include # installed by ExternalProject
${EXT_LLVM_DIR}/include)
-target_link_directories(extempore PRIVATE ${CMAKE_BINARY_DIR}/portaudio/lib)
-target_link_libraries(extempore PRIVATE pcre portaudio${CMAKE_STATIC_LIBRARY_SUFFIX} ${LLVM_LIBRARIES})
+target_link_libraries(extempore PRIVATE pcre portaudio ${LLVM_LIBRARIES})
if(UNIX AND NOT APPLE)
target_link_libraries(extempore PRIVATE asound)
endif()
@@ -425,7 +365,6 @@ elseif(APPLE) # macOS
PRIVATE "-framework AudioToolbox")
elseif(UNIX AND NOT APPLE) # Linux
- set_property(TARGET pcre PROPERTY POSITION_INDEPENDENT_CODE ON)
set_property(TARGET extempore PROPERTY POSITION_INDEPENDENT_CODE ON)
# target_link_libraries(extempore PRIVATE --export-dynamic)
target_link_libraries(extempore PRIVATE dl)
@@ -529,7 +468,6 @@ else(WIN32)
DEPENDS ${filename} extempore)
set_target_properties(${targetname} PROPERTIES FOLDER AOT)
if(NOT ${group} STREQUAL "core")
- add_dependencies(${targetname} external_shlibs_${group})
add_dependencies(aot_external_${group} ${targetname})
endif()
foreach(dep ${ARGN})
@@ -568,59 +506,6 @@ add_custom_target(clean_aot
if(UNIX)
if(EXTERNAL_SHLIBS_AUDIO)
- # first, download & build the shared libraries themselves (these are all external to Extempore)
-
- ExternalProject_Add(portmidi
- PREFIX portmidi
- URL https://github.com/extemporelang/portmidi/archive/8602f548f71daf5ef638b2f7d224753400cb2158.zip
- CMAKE_ARGS
- -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
- -DCMAKE_C_FLAGS=${EXT_DEPS_C_FLAGS}
- -DCMAKE_CXX_FLAGS=${EXT_DEPS_CXX_FLAGS}
- -DCMAKE_INSTALL_PREFIX=${EXT_DEPS_INSTALL_DIR})
- set_target_properties(portmidi PROPERTIES FOLDER EXTERNAL_SHLIBS)
-
- ExternalProject_Add(rtmidi
- PREFIX rtmidi
- URL https://github.com/thestk/rtmidi/archive/84d130bf22d878ff1b0e224346e2e0f9e3ba8099.zip
- URL_MD5 d932b9fef01b859a1b8b86a3c8dc6621
- CMAKE_ARGS
- -DRTMIDI_BUILD_TESTING=OFF
- -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
- -DCMAKE_C_FLAGS=${EXT_DEPS_C_FLAGS}
- -DCMAKE_CXX_FLAGS=${EXT_DEPS_CXX_FLAGS}
- -DCMAKE_INSTALL_PREFIX=${EXT_DEPS_INSTALL_DIR})
- set_target_properties(rtmidi PROPERTIES FOLDER EXTERNAL_SHLIBS)
-
- ExternalProject_Add(kiss_fft
- PREFIX kiss_fft
- URL https://github.com/extemporelang/kiss_fft/archive/1.3.0.zip
- CMAKE_ARGS
- -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
- -DCMAKE_C_FLAGS=${EXT_DEPS_C_FLAGS}
- -DCMAKE_CXX_FLAGS=${EXT_DEPS_CXX_FLAGS}
- -DCMAKE_INSTALL_PREFIX=${EXT_DEPS_INSTALL_DIR})
- set_target_properties(kiss_fft PROPERTIES FOLDER EXTERNAL_SHLIBS)
-
- # build with as few deps as we can get away with
-
- ExternalProject_Add(sndfile
- PREFIX libsndfile
- URL https://github.com/erikd/libsndfile/archive/ae64caf9b5946d365971c550875000342e763de6.zip
- CMAKE_ARGS
- -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
- -DCMAKE_C_FLAGS=${EXT_DEPS_C_FLAGS}
- -DCMAKE_CXX_FLAGS=${EXT_DEPS_CXX_FLAGS}
- -DCMAKE_INSTALL_PREFIX=${EXT_DEPS_INSTALL_DIR}
- -DBUILD_SHARED_LIBS=ON
- -DBUILD_PROGRAMS=OFF
- -DBUILD_EXAMPLES=OFF
- -DENABLE_EXTERNAL_LIBS=OFF
- -DBUILD_TESTING=OFF
- -DENABLE_CPACK=OFF
- -DENABLE_PACKAGE_CONFIG=OFF)
- set_target_properties(sndfile PROPERTIES FOLDER EXTERNAL_SHLIBS)
-
add_custom_target(aot_external_audio ALL)
set_target_properties(aot_external_audio PROPERTIES FOLDER AOT)
aotcompile_lib(libs/external/fft.xtm audio base math)
@@ -629,76 +514,13 @@ if(UNIX)
aotcompile_lib(libs/external/instruments_ext.xtm audio base sndfile instruments)
aotcompile_lib(libs/external/portmidi.xtm audio base)
- add_custom_target(external_shlibs_audio
- COMMENT "moving shared libs into ${EXT_PLATFORM_SHLIBS_DIR}"
- DEPENDS LLVM sndfile kiss_fft portmidi rtmidi
- COMMAND ${CMAKE_COMMAND} -E make_directory ${EXT_PLATFORM_SHLIBS_DIR}
- COMMAND ${CMAKE_COMMAND} -E copy libkiss_fft${CMAKE_SHARED_LIBRARY_SUFFIX} ${EXT_PLATFORM_SHLIBS_DIR}
- COMMAND ${CMAKE_COMMAND} -E copy libportmidi${CMAKE_SHARED_LIBRARY_SUFFIX} ${EXT_PLATFORM_SHLIBS_DIR}
- COMMAND ${CMAKE_COMMAND} -E copy librtmidi${CMAKE_SHARED_LIBRARY_SUFFIX} ${EXT_PLATFORM_SHLIBS_DIR}
- COMMAND ${CMAKE_COMMAND} -E copy libsndfile${CMAKE_SHARED_LIBRARY_SUFFIX} ${EXT_PLATFORM_SHLIBS_DIR}
- WORKING_DIRECTORY ${EXT_DEPS_INSTALL_DIR}/lib)
- set_target_properties(external_shlibs_audio PROPERTIES FOLDER EXTERNAL_SHLIBS)
-
add_dependencies(aot_external_audio extempore)
- add_dependencies(aot_external_audio external_shlibs_audio)
endif(EXTERNAL_SHLIBS_AUDIO)
if(EXTERNAL_SHLIBS_GRAPHICS)
- ExternalProject_Add(nanovg
- PREFIX nanovg
- URL https://github.com/extemporelang/nanovg/archive/3c60175fcc2e5fe305b04355cdce35d499c80310.tar.gz
- CMAKE_ARGS
- -DEXTEMPORE_LIB_PATH=${CMAKE_SOURCE_DIR}/libs/platform-shlibs/extempore.lib
- -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
- -DCMAKE_C_FLAGS=${EXT_DEPS_C_FLAGS}
- -DCMAKE_CXX_FLAGS=${EXT_DEPS_CXX_FLAGS}
- -DCMAKE_INSTALL_PREFIX=${EXT_DEPS_INSTALL_DIR})
- set_target_properties(nanovg PROPERTIES FOLDER EXTERNAL_SHLIBS)
-
- add_dependencies(nanovg extempore)
-
- ExternalProject_Add(stb_image
- PREFIX stb_image
- URL https://github.com/extemporelang/stb/archive/152a250a702bf28951bb0220d63bc0c99830c498.zip
- CMAKE_ARGS
- -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
- -DCMAKE_C_FLAGS=${EXT_DEPS_C_FLAGS}
- -DCMAKE_CXX_FLAGS=${EXT_DEPS_CXX_FLAGS}
- -DCMAKE_INSTALL_PREFIX=${EXT_DEPS_INSTALL_DIR})
- set_target_properties(nanovg PROPERTIES FOLDER EXTERNAL_SHLIBS)
-
- ExternalProject_Add(glfw3
- PREFIX glfw3
- URL https://github.com/glfw/glfw/releases/download/3.2.1/glfw-3.2.1.zip
- CMAKE_ARGS
- -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
- -DCMAKE_C_FLAGS=${EXT_DEPS_C_FLAGS}
- -DCMAKE_CXX_FLAGS=${EXT_DEPS_CXX_FLAGS}
- -DBUILD_SHARED_LIBS=ON
- -DGLFW_BUILD_EXAMPLES=OFF
- -DGLFW_BUILD_TESTS=OFF
- -DCMAKE_INSTALL_PREFIX=${EXT_DEPS_INSTALL_DIR})
- set_target_properties(glfw3 PROPERTIES FOLDER EXTERNAL_SHLIBS)
-
- ExternalProject_Add(assimp
- PREFIX assimp
- URL https://github.com/assimp/assimp/archive/v3.2.zip
- CMAKE_ARGS
- -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
- -DCMAKE_C_FLAGS=${EXT_DEPS_C_FLAGS}
- -DCMAKE_CXX_FLAGS=${EXT_DEPS_CXX_FLAGS}
- -DCMAKE_DEBUG_POSTFIX=
- -DASSIMP_BUILD_ASSIMP_TOOLS=OFF
- -DASSIMP_BUILD_SAMPLES=OFF
- -DASSIMP_BUILD_TESTS=OFF
- -DCMAKE_INSTALL_PREFIX=${EXT_DEPS_INSTALL_DIR})
- set_target_properties(assimp PROPERTIES FOLDER EXTERNAL_SHLIBS)
-
add_custom_target(aot_external_graphics ALL)
- set_target_properties(assimp PROPERTIES FOLDER AOT)
aotcompile_lib(libs/external/stb_image.xtm graphics base)
aotcompile_lib(libs/external/glfw3.xtm graphics base)
@@ -715,20 +537,8 @@ if(UNIX)
aotcompile_lib(libs/external/assimp.xtm graphics base stb_image graphics-pipeline)
aotcompile_lib(libs/external/gl/glcompat-${GL_BIND_METHOD}.xtm graphics base)
- add_custom_target(external_shlibs_graphics
- COMMENT "moving shared libs into ${EXT_PLATFORM_SHLIBS_DIR}"
- DEPENDS LLVM assimp glfw3 stb_image nanovg
- COMMAND ${CMAKE_COMMAND} -E make_directory ${EXT_PLATFORM_SHLIBS_DIR}
- COMMAND ${CMAKE_COMMAND} -E copy libassimp${CMAKE_SHARED_LIBRARY_SUFFIX} ${EXT_PLATFORM_SHLIBS_DIR}
- COMMAND ${CMAKE_COMMAND} -E copy libglfw${CMAKE_SHARED_LIBRARY_SUFFIX} ${EXT_PLATFORM_SHLIBS_DIR}
- COMMAND ${CMAKE_COMMAND} -E copy libnanovg${CMAKE_SHARED_LIBRARY_SUFFIX} ${EXT_PLATFORM_SHLIBS_DIR}
- COMMAND ${CMAKE_COMMAND} -E copy libstb_image${CMAKE_SHARED_LIBRARY_SUFFIX} ${EXT_PLATFORM_SHLIBS_DIR}
- WORKING_DIRECTORY ${EXT_DEPS_INSTALL_DIR}/lib)
- set_target_properties(external_shlibs_graphics PROPERTIES FOLDER EXTERNAL_SHLIBS)
-
# set up these libs for AOT compilation
add_dependencies(aot_external_graphics extempore)
- add_dependencies(aot_external_graphics external_shlibs_graphics)
endif(EXTERNAL_SHLIBS_GRAPHICS)
endif(UNIX)
--
2.32.0

28
gnu/packages/patches/glibc-bootstrap-system.patch
View File

@ -14,7 +14,7 @@ index ebc381ed7c..e0d3ed1bc3 100644
}
- if (__posix_spawn (&((_IO_proc_file *) fp)->pid, _PATH_BSHELL, fa, 0,
+ if (posix_spawnp (&((_IO_proc_file *) fp)->pid, "sh", fa, 0,
+ if (__posix_spawnp (&((_IO_proc_file *) fp)->pid, "sh", fa, 0,
(char *const[]){ (char*) "sh", (char*) "-c",
(char *) command, NULL }, __environ) != 0)
return false;
@ -36,7 +36,31 @@ index a03f478fc7..94da6facf3 100644
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)

40
gnu/packages/patches/julia-tracker-16-compat.patch 100644
View File

@ -0,0 +1,40 @@
https://github.com/FluxML/Tracker.jl/commit/f6550ba38a9ea5802e2de4fa9c939929ba711f0d.patch
from an upstream pull request
https://github.com/FluxML/Tracker.jl/pull/94
From f6550ba38a9ea5802e2de4fa9c939929ba711f0d Mon Sep 17 00:00:00 2001
From: Michael Abbott <me@escbook>
Date: Wed, 3 Feb 2021 22:58:33 +0100
Subject: [PATCH] two fixes for 1.6
---
src/lib/array.jl | 2 +-
src/lib/real.jl | 1 +
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/src/lib/array.jl b/src/lib/array.jl
index 92f2b39..f8cbbac 100644
--- a/src/lib/array.jl
+++ b/src/lib/array.jl
@@ -298,7 +298,7 @@ Base.reverse(xs::TrackedArray; dims) = track(reverse, xs, dims = dims)
@grad reverse(xs; dims) = reverse(data(xs), dims = dims), Δ -> (reverse(Δ, dims = dims), nothing)
Base.reverse(xs::TrackedVector) = track(reverse, xs)
@grad reverse(xs::TrackedVector) = reverse(data(xs)), Δ -> (reverse(Δ),)
-Base.reverse(xs::TrackedVector, start, stop) = track(reverse, xs, start, stop)
+Base.reverse(xs::TrackedVector, start::Integer, stop::Integer) = track(reverse, xs, start, stop)
@grad reverse(xs, start, stop) = reverse(data(xs), start, stop), Δ -> (reverse(Δ, start, stop), nothing, nothing)
function _kron(mat1::AbstractMatrix,mat2::AbstractMatrix)
diff --git a/src/lib/real.jl b/src/lib/real.jl
index 737afd8..e1975ac 100644
--- a/src/lib/real.jl
+++ b/src/lib/real.jl
@@ -55,6 +55,7 @@ for f in :[isinf, isnan, isfinite].args
end
Printf.fix_dec(x::TrackedReal, n::Int, a...) = Printf.fix_dec(data(x), n, a...)
+Printf.tofloat(x::TrackedReal) = Printf.tofloat(data(x))
Base.float(x::TrackedReal) = x

189
gnu/packages/patches/marble-qt-add-qt-headers.patch 100644
View File

@ -0,0 +1,189 @@
Adapted from Debian: https://salsa.debian.org/qt-kde-team/kde/marble/-/blob/debian/4%2517.08.3-3.1/debian/patches/qt5.11.patch
Upstream status: Probably irrelevant, as this is an old version of this software.
diff --git a/src/lib/marble/MergedLayerDecorator.cpp b/src/lib/marble/MergedLayerDecorator.cpp
index 40f3ddb..bafff50 100644
--- a/src/lib/marble/MergedLayerDecorator.cpp
+++ b/src/lib/marble/MergedLayerDecorator.cpp
@@ -36,6 +36,7 @@
#include <QPointer>
#include <QPainter>
+#include <QPainterPath>
using namespace Marble;
diff --git a/src/lib/marble/VisiblePlacemark.cpp b/src/lib/marble/VisiblePlacemark.cpp
index cfe08af..1a84006 100644
--- a/src/lib/marble/VisiblePlacemark.cpp
+++ b/src/lib/marble/VisiblePlacemark.cpp
@@ -22,6 +22,7 @@
#include <QApplication>
#include <QPainter>
+#include <QPainterPath>
#include <QPalette>
#include <QPixmapCache>
diff --git a/src/lib/marble/graphicsview/FrameGraphicsItem.cpp b/src/lib/marble/graphicsview/FrameGraphicsItem.cpp
index 8a90526..065f245 100644
--- a/src/lib/marble/graphicsview/FrameGraphicsItem.cpp
+++ b/src/lib/marble/graphicsview/FrameGraphicsItem.cpp
@@ -18,6 +18,7 @@
// Qt
#include <QSizeF>
#include <QPainter>
+#include <QPainterPath>
#include <QPixmapCache>
#include <QMargins>
#include <qdrawutil.h>
diff --git a/src/lib/marble/layers/GroundLayer.cpp b/src/lib/marble/layers/GroundLayer.cpp
index 58d409f..df6d226 100644
--- a/src/lib/marble/layers/GroundLayer.cpp
+++ b/src/lib/marble/layers/GroundLayer.cpp
@@ -14,6 +14,9 @@
#include "ViewportParams.h"
#include "RenderState.h"
+#include <QPainter>
+#include <QPainterPath>
+
namespace Marble
{
diff --git a/src/plugins/render/compass/CompassFloatItem.cpp b/src/plugins/render/compass/CompassFloatItem.cpp
index d8dc021..66095cc 100644
--- a/src/plugins/render/compass/CompassFloatItem.cpp
+++ b/src/plugins/render/compass/CompassFloatItem.cpp
@@ -19,6 +19,7 @@
#include <QRect>
#include <QColor>
#include <QPainter>
+#include <QPainterPath>
#include <QPushButton>
#include <QSvgRenderer>
diff --git a/src/plugins/render/elevationprofilefloatitem/ElevationProfileFloatItem.cpp b/src/plugins/render/elevationprofilefloatitem/ElevationProfileFloatItem.cpp
index a790c16..96f5bed 100644
--- a/src/plugins/render/elevationprofilefloatitem/ElevationProfileFloatItem.cpp
+++ b/src/plugins/render/elevationprofilefloatitem/ElevationProfileFloatItem.cpp
@@ -31,6 +31,7 @@
#include <QContextMenuEvent>
#include <QRect>
#include <QPainter>
+#include <QPainterPath>
#include <QPushButton>
#include <QMenu>
#include <QMouseEvent>
diff --git a/src/plugins/render/foursquare/FoursquareItem.cpp b/src/plugins/render/foursquare/FoursquareItem.cpp
index d9e1f57..ef80472 100644
--- a/src/plugins/render/foursquare/FoursquareItem.cpp
+++ b/src/plugins/render/foursquare/FoursquareItem.cpp
@@ -13,6 +13,8 @@
#include "ViewportParams.h"
#include <QFontMetrics>
+#include <QPainter>
+#include <QPainterPath>
namespace Marble
{
diff --git a/src/plugins/render/gpsinfo/GpsInfo.cpp b/src/plugins/render/gpsinfo/GpsInfo.cpp
index 522e907..20fd75a 100644
--- a/src/plugins/render/gpsinfo/GpsInfo.cpp
+++ b/src/plugins/render/gpsinfo/GpsInfo.cpp
@@ -21,6 +21,8 @@
#include "ViewportParams.h"
#include "GeoDataAccuracy.h"
+#include <QIcon>
+
namespace Marble
{
diff --git a/src/plugins/render/license/License.cpp b/src/plugins/render/license/License.cpp
index 511dfc0..9436083 100644
--- a/src/plugins/render/license/License.cpp
+++ b/src/plugins/render/license/License.cpp
@@ -23,6 +23,7 @@
#include <QCommonStyle>
#include <QContextMenuEvent>
#include <QPainter>
+#include <QPainterPath>
#include <QLabel>
#include <QMenu>
#include <QMouseEvent>
diff --git a/src/plugins/render/notes/NotesItem.cpp b/src/plugins/render/notes/NotesItem.cpp
index 9d0961f..0c9fe99 100644
--- a/src/plugins/render/notes/NotesItem.cpp
+++ b/src/plugins/render/notes/NotesItem.cpp
@@ -9,6 +9,7 @@
#include "MarbleDirs.h"
#include <QPainter>
+#include <QPainterPath>
#include <QRect>
using namespace Marble;
diff --git a/src/plugins/render/postalcode/PostalCodeItem.cpp b/src/plugins/render/postalcode/PostalCodeItem.cpp
index 772c0b2..0ff7957 100644
--- a/src/plugins/render/postalcode/PostalCodeItem.cpp
+++ b/src/plugins/render/postalcode/PostalCodeItem.cpp
@@ -17,6 +17,7 @@
// Qt
#include <QFontMetrics>
#include <QPainter>
+#include <QPainterPath>
using namespace Marble;
diff --git a/src/plugins/render/progress/ProgressFloatItem.cpp b/src/plugins/render/progress/ProgressFloatItem.cpp
index a465857..6e2452c 100644
--- a/src/plugins/render/progress/ProgressFloatItem.cpp
+++ b/src/plugins/render/progress/ProgressFloatItem.cpp
@@ -22,6 +22,7 @@
#include <QColor>
#include <QPaintDevice>
#include <QPainter>
+#include <QPainterPath>
namespace Marble
{
diff --git a/src/plugins/render/satellites/SatellitesPlugin.cpp b/src/plugins/render/satellites/SatellitesPlugin.cpp
index 04d8321..0a43d24 100644
--- a/src/plugins/render/satellites/SatellitesPlugin.cpp
+++ b/src/plugins/render/satellites/SatellitesPlugin.cpp
@@ -25,6 +25,7 @@
#include "ui_SatellitesConfigDialog.h"
+#include <QAction>
#include <QUrl>
#include <QMouseEvent>
diff --git a/src/plugins/render/speedometer/Speedometer.cpp b/src/plugins/render/speedometer/Speedometer.cpp
index 6e9c532..f40a174 100644
--- a/src/plugins/render/speedometer/Speedometer.cpp
+++ b/src/plugins/render/speedometer/Speedometer.cpp
@@ -19,6 +19,8 @@
#include "MarbleGraphicsGridLayout.h"
#include "ViewportParams.h"
+#include <QIcon>
+
namespace Marble
{
diff --git a/src/plugins/render/stars/StarsPlugin.cpp b/src/plugins/render/stars/StarsPlugin.cpp
index 6599545..482680f 100644
--- a/src/plugins/render/stars/StarsPlugin.cpp
+++ b/src/plugins/render/stars/StarsPlugin.cpp
@@ -19,6 +19,8 @@
#include <QContextMenuEvent>
#include <QMenu>
#include <QColorDialog>
+#include <QPainter>
+#include <QPainterPath>
#include <qmath.h>
#include "MarbleClock.h"

15
gnu/packages/pcre.scm
View File

@ -7,6 +7,8 @@
;;; Copyright © 2017 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -119,3 +121,16 @@ own native API, as well as a set of wrapper functions that correspond to the
POSIX regular expression API.")
(license license:bsd-3)
(home-page "https://www.pcre.org/")))
(define-public pcre2-10.36
(package
(inherit pcre2)
(name "pcre2")
(version "10.36")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/pcre/pcre2/"
version "/pcre2-" version ".tar.bz2"))
(sha256
(base32
"0p3699msps07p40g9426lvxa3b41rg7k2fn7qxl2jm0kh4kkkvx9"))))))

19
gnu/packages/pdf.scm
View File

@ -78,6 +78,7 @@
#:use-module (gnu packages libffi)
#:use-module (gnu packages linux)
#:use-module (gnu packages lua)
#:use-module (gnu packages man)
#:use-module (gnu packages pcre)
#:use-module (gnu packages perl)
#:use-module (gnu packages photo)
@ -898,7 +899,7 @@ using a stylus.")
(define-public xournalpp
(package
(name "xournalpp")
(version "1.0.20")
(version "1.1.0")
(source
(origin
(method git-fetch)
@ -907,7 +908,7 @@ using a stylus.")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1c7n03xm3m4lwcwxgplkn25i8c6s3i7rijbkcx86br1j4jadcs3k"))))
(base32 "0ldf58l5sqy52x5dqfpdjdh7ldjilj9mw42jzsl5paxg0md2k0hl"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags (list "-DENABLE_CPPUNIT=ON") ;enable tests
@ -921,31 +922,31 @@ using a stylus.")
(add-after 'unpack 'fix-permissions-on-po-files
(lambda _
;; Make sure 'msgmerge' can modify the PO files.
(for-each (lambda (po) (chmod po #o666))
(find-files "." "\\.po$"))
#t))
(for-each make-file-writable
(find-files "." "\\.po$"))))
;; Fix path to addr2line utility, which the crash reporter uses.
(add-after 'unpack 'fix-paths
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "src/util/Stacktrace.cpp"
;; Match only the commandline.
(("\"addr2line ")
(string-append "\"" (which "addr2line") " ")))
#t))
(string-append "\"" (which "addr2line") " ")))))
(add-after 'install 'glib-or-gtk-wrap
(assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))))
(native-inputs
`(("cppunit" ,cppunit)
("gcc" ,gcc-8)
("gettext" ,gettext-minimal)
("help2man" ,help2man)
("pkg-config" ,pkg-config)))
(inputs
`(("alsa-lib" ,alsa-lib)
("glib" ,glib)
("gtk+" ,gtk+)
("librsvg" ,librsvg)
("libsndfile" ,libsndfile)
("libxml2" ,libxml2)
("libzip" ,libzip)
("lua" ,lua) ;FIXME: It cannot find the Lua library.
("lua" ,lua)
("poppler" ,poppler)
("portaudio" ,portaudio)
("texlive-bin" ,texlive-bin)))

16
gnu/packages/php.scm
View File

@ -36,7 +36,6 @@
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gd)
#:use-module (gnu packages gettext)
#:use-module (gnu packages glib)
#:use-module (gnu packages gnupg)
#:use-module (gnu packages icu4c)
#:use-module (gnu packages image)
@ -61,7 +60,7 @@
(define-public php
(package
(name "php")
(version "7.4.20")
(version "7.4.22")
(home-page "https://secure.php.net/")
(source (origin
(method url-fetch)
@ -69,7 +68,7 @@
"php-" version ".tar.xz"))
(sha256
(base32
"0db3nqfbfqfd8fkvrw1k8l6698qcbzv1v5j8rgr0ny0dg6k6r90z"))
"1s5xjy1cchlg0vfxic73wy2wip8spfjr094hzzyc76plsbbqq1wf"))
(modules '((guix build utils)))
(snippet
'(with-directory-excursion "ext"
@ -146,13 +145,11 @@
;; This file has ISO-8859-1 encoding.
(with-fluids ((%default-port-encoding "ISO-8859-1"))
(substitute* "main/build-defs.h.in"
(("@CONFIGURE_COMMAND@") "(omitted)")))
#t))
(("@CONFIGURE_COMMAND@") "(omitted)")))))
(add-before 'build 'patch-/bin/sh
(lambda _
(substitute* '("run-tests.php" "ext/standard/proc_open.c")
(("/bin/sh") (which "sh")))
#t))
(("/bin/sh") (which "sh")))))
(add-before 'check 'prepare-tests
(lambda _
;; Some of these files have ISO-8859-1 encoding, whereas others
@ -345,8 +342,7 @@
(setenv "REPORT_EXIT_STATUS" "1")
;; Skip tests requiring I/O facilities that are unavailable in the
;; build environment
(setenv "SKIP_IO_CAPTURE_TESTS" "1")
#t)))
(setenv "SKIP_IO_CAPTURE_TESTS" "1"))))
#:test-target "test"))
(inputs
`(("aspell" ,aspell)
@ -378,7 +374,7 @@
(native-inputs
`(("pkg-config" ,pkg-config)
("bison" ,bison)
("intltool" ,intltool)
("gettext" ,gettext-minimal)
("procps" ,procps))) ; for tests
(synopsis "PHP programming language")
(description

66
gnu/packages/plan9.scm 100644
View File

@ -0,0 +1,66 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2021 宋文武 <iyzsong@member.fsf.org>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages plan9)
#:use-module (guix build-system gnu)
#:use-module (guix git-download)
#:use-module (guix packages)
#:use-module (guix utils)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages xorg))
(define-public drawterm
(let ((revision "1")
(commit "c97fe4693f6112504d6f13fab46f7cc8b27685c1"))
(package
(name "drawterm")
(version (git-version "20210628" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "git://git.9front.org/plan9front/drawterm")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "059sl60ap6c9lz8k91k6bd34694a290wm0s93b2vfszzzv683spw"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags (list "CONF=unix"
(string-append "CC=" ,(cc-for-target)))
#:tests? #f ; no tests
#:phases
(modify-phases %standard-phases
(delete 'configure) ; no configure script
(replace 'install ; no install target
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin/"))
(man (string-append out "/share/man/man1/")))
(install-file "drawterm" bin)
(install-file "drawterm.1" man)))))))
(inputs
`(("libx11" ,libx11)
("libxt" ,libxt)))
(synopsis "Connect to Plan 9 systems")
(home-page "http://drawterm.9front.org")
(description
"@command{drawterm} is a client for connecting venerable systems to
Plan 9 systems. It behaves like a Plan 9 kernel and will attempt to
reconstruct a Plan 9 terminal-like experience from a non-Plan 9 system.")
(license license:expat))))

210
gnu/packages/python-science.scm
View File

@ -35,6 +35,7 @@
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages check)
#:use-module (gnu packages databases)
#:use-module (gnu packages gcc)
#:use-module (gnu packages image-processing)
#:use-module (gnu packages machine-learning)
@ -44,6 +45,7 @@
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-check)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
@ -327,49 +329,55 @@ of the SGP4 satellite tracking algorithm.")
(define-public python-pandas
(package
(name "python-pandas")
(version "1.0.5")
(version "1.3.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pandas" version))
(sha256
(base32 "1a2gv3g6jr6vb5ca43fkwjl5xf86wpfz8y3zcy787adjl0hdkib9"))))
(base32 "1qi2cv450m05dwccx3p1s373k5b4ncvwi74plnms2pidrz4ycm65"))))
(build-system python-build-system)
(arguments
`(#:modules ((guix build utils)
(guix build python-build-system)
(ice-9 ftw)
(srfi srfi-1)
(srfi srfi-26))
#:phases (modify-phases %standard-phases
(add-after 'unpack 'patch-which
(lambda* (#:key inputs #:allow-other-keys)
(let ((which (assoc-ref inputs "which")))
(substitute* "pandas/io/clipboard/__init__.py"
(("^WHICH_CMD = .*")
(string-append "WHICH_CMD = \"" which "\"\n"))))
#t))
(add-before 'check 'prepare-x
(lambda _
(system "Xvfb &")
(setenv "DISPLAY" ":0")
;; xsel needs to write a log file.
(setenv "HOME" "/tmp")
#t))
(replace 'check
(lambda _
(let ((build-directory
(string-append
(getcwd) "/build/"
(car (scandir "build"
(cut string-prefix? "lib." <>))))))
;; Disable the "strict data files" option which causes
;; the build to error out if required data files are
;; not available (as is the case with PyPI archives).
(substitute* "setup.cfg"
(("addopts = --strict-data-files") "addopts = "))
(with-directory-excursion build-directory
(invoke "pytest" "-vv" "pandas" "--skip-slow"
"--skip-network"))))))))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-which
(lambda* (#:key inputs #:allow-other-keys)
(let ((which (assoc-ref inputs "which")))
(substitute* "pandas/io/clipboard/__init__.py"
(("^WHICH_CMD = .*")
(string-append "WHICH_CMD = \"" which "\"\n"))))))
(add-before 'check 'prepare-x
(lambda _
(system "Xvfb &")
(setenv "DISPLAY" ":0")
;; xsel needs to write a log file.
(setenv "HOME" "/tmp")))
(replace 'check
(lambda _
(let ((build-directory
(string-append
(getcwd) "/build/"
(first (scandir "build"
(cut string-prefix? "lib." <>))))))
(with-directory-excursion build-directory
(invoke "pytest" "-vv" "pandas" "--skip-slow"
"--skip-network"
"-k"
;; These tets access the internet:
;; pandas/tests/io/xml/test_xml.py::test_wrong_url[lxml]
;; pandas/tests/io/xml/test_xml.py::test_wrong_url[etree]
;; TODO: the excel tests fail for unknown reasons
(string-append "not test_wrong_url"
" and not test_excelwriter_fspath"
" and not test_ExcelWriter_dispatch"
;; TODO: Missing input
" and not TestS3"
" and not s3")))))))))
(propagated-inputs
`(("python-jinja2" ,python-jinja2)
("python-numpy" ,python-numpy)
@ -835,3 +843,141 @@ and more
@end itemize")
(license license:gpl3)))
(define-public python-distributed
(package
(name "python-distributed")
(version "2021.07.1")
(source
(origin
;; The test files are not included in the archive on pypi
(method git-fetch)
(uri (git-reference
(url "https://github.com/dask/distributed")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0i55zf3k55sqjxnwlzsyj3h3v1588fn54ng4mj3dfiqzh3nlj0dg"))))
(build-system python-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-references
(lambda* (#:key outputs #:allow-other-keys)
(substitute* '("distributed/comm/tests/test_ucx_config.py"
"distributed/tests/test_client.py"
"distributed/tests/test_queues.py"
"distributed/tests/test_variable.py"
"distributed/cli/tests/test_tls_cli.py"
"distributed/cli/tests/test_dask_spec.py"
"distributed/cli/tests/test_dask_worker.py"
"distributed/cli/tests/test_dask_scheduler.py")
(("\"dask-scheduler\"")
(format #false "\"~a/bin/dask-scheduler\""
(assoc-ref outputs "out")))
(("\"dask-worker\"")
(format #false "\"~a/bin/dask-worker\""
(assoc-ref outputs "out"))))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(setenv "DISABLE_IPV6" "1")
(invoke "pytest" "-vv" "distributed"
"-m" "not slow and not gpu and not ipython and not avoid_ci"
"-k"
;; TODO: These tests fail for unknown reasons:
;; Assertion error.
(string-append
"not test_version_option"
;; "The 'distributed' distribution was not found"
" and not test_register_backend_entrypoint"
;; "AttributeError: module 'distributed.dashboard' has no attribute 'scheduler'"
" and not test_get_client_functions_spawn_clusters"))))))))
(propagated-inputs
`(("python-click" ,python-click)
("python-cloudpickle" ,python-cloudpickle)
("python-cryptography" ,python-cryptography)
("python-dask" ,python-dask)
("python-msgpack" ,python-msgpack)
("python-psutil" ,python-psutil)
("python-pyyaml" ,python-pyyaml)
("python-setuptools" ,python-setuptools)
("python-sortedcontainers" ,python-sortedcontainers)
("python-tblib" ,python-tblib)
("python-toolz" ,python-toolz)
("python-tornado" ,python-tornado-6)
("python-zict" ,python-zict)))
(native-inputs
`(("python-pytest" ,python-pytest)))
(home-page "https://distributed.dask.org")
(synopsis "Distributed scheduler for Dask")
(description "Dask.distributed is a lightweight library for distributed
computing in Python. It extends both the @code{concurrent.futures} and
@code{dask} APIs to moderate sized clusters.")
(license license:bsd-3)))
(define-public python-modin
(package
(name "python-modin")
(version "0.10.1")
(source
(origin
;; The archive on pypi does not include all required files.
(method git-fetch)
(uri (git-reference
(url "https://github.com/modin-project/modin")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"128ghfb9ncmnn8km409xjcdppvn9nr9jqw8rkvsfavh7wnwlk509"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'make-files-writable
(lambda _
(for-each make-file-writable (find-files "."))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(setenv "MODIN_ENGINE" "dask")
(invoke "python" "-m" "pytest"
"modin/pandas/test/test_concat.py")
(setenv "MODIN_ENGINE" "python")
(invoke "python" "-m" "pytest"
"modin/pandas/test/test_concat.py")))))))
(propagated-inputs
`(("python-cloudpickle" ,python-cloudpickle)
("python-dask" ,python-dask)
("python-distributed" ,python-distributed)
("python-numpy" ,python-numpy)
("python-packaging" ,python-packaging)
("python-pandas" ,python-pandas)))
(native-inputs
`(("python-coverage" ,python-coverage)
("python-jinja2" ,python-jinja2)
("python-lxml" ,python-lxml)
("python-matplotlib" ,python-matplotlib)
("python-msgpack" ,python-msgpack)
("python-openpyxl" ,python-openpyxl)
("python-psutil" ,python-psutil)
("python-pyarrow" ,python-pyarrow)
("python-pytest" ,python-pytest)
("python-pytest-benchmark" ,python-pytest-benchmark)
("python-pytest-cov" ,python-pytest-cov)
("python-pytest-xdist" ,python-pytest-xdist)
("python-scipy" ,python-scipy)
("python-sqlalchemy" ,python-sqlalchemy)
("python-tables" ,python-tables)
("python-tqdm" ,python-tqdm)
("python-xarray" ,python-xarray)
("python-xlrd" ,python-xlrd)))
(home-page "https://github.com/modin-project/modin")
(synopsis "Make your pandas code run faster")
(description
"Modin uses Ray or Dask to provide an effortless way to speed up your
pandas notebooks, scripts, and libraries. Unlike other distributed DataFrame
libraries, Modin provides seamless integration and compatibility with existing
pandas code.")
(license license:asl2.0)))

25
gnu/packages/python-web.scm
View File

@ -1051,6 +1051,31 @@ Origin Resource Sharing}, making cross-origin AJAX possible.")
into Jinja2 by default.")
(license license:bsd-3)))
(define-public python-flask-misaka
(package
(name "python-flask-misaka")
(version "1.0.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "Flask-Misaka" version))
(sha256
(base32
"12gm6hq3lvlj0ddw8p6lk5pky8jk3pw758ihffjl49shnnzc68zl"))))
(build-system python-build-system)
(native-inputs
`(("python-coverage" ,python-coverage)
("python-mock" ,python-mock)))
(propagated-inputs
`(("python-flask" ,python-flask)
("python-misaka" ,python-misaka)))
(home-page "https://github.com/singingwolfboy/flask-misaka/")
(synopsis "Flask interface to Misaka, a Markdown parsing library")
(description
"This package provides an interface between the Flask web framework and
the Misaka Markdown parser.")
(license license:expat)))
(define-public python-flask-session
(package
(name "python-flask-session")

218
gnu/packages/python-xyz.scm
View File

@ -66,7 +66,7 @@
;;; Copyright © 2019 Jacob MacDonald <jaccarmac@gmail.com>
;;; Copyright © 2019, 2020 Giacomo Leidi <goodoldpaul@autistici.org>
;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
;;; Copyright © 2019, 2020 Tanguy Le Carrour <tanguy@bioneland.org>
;;; Copyright © 2019, 2020, 2021 Tanguy Le Carrour <tanguy@bioneland.org>
;;; Copyright © 2019, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2020 Riku Viitanen <riku.viitanen@protonmail.com>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
@ -105,6 +105,7 @@
;;; Copyright © 2021 Danial Behzadi <dani.behzi@ubuntu.com>
;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be>
;;; Copyright © 2021 Hugo Lecomte <hugo.lecomte@inria.fr>
;;; Copyright © 2021 Franck Pérignon <franck.perignon@univ-grenoble-alpes.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@ -5534,14 +5535,14 @@ that client code uses to construct the grammar directly in Python code.")
(define-public python-numexpr
(package
(name "python-numexpr")
(version "2.6.5")
(version "2.7.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "numexpr" version))
(sha256
(base32
"1frnbcwmsi312154x274xl28xazr1k8vjby83fwyla2n10a81bgq"))))
"09d8yfsx33ddwfkpn8805w2mxnn4cvf47yc66g4azldpz4lnaqa3"))))
(build-system python-build-system)
(arguments `(#:tests? #f)) ; no tests included
(propagated-inputs
@ -6321,13 +6322,13 @@ the OleFileIO module from PIL, the Python Image Library.")
(define-public python-pikepdf
(package
(name "python-pikepdf")
(version "2.14.2")
(version "2.16.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pikepdf" version))
(sha256
(base32 "01f173af5j0fmrzg6czfr92d331bqdbs3dkch7p41ykyv4fsv6kn"))))
(base32 "1phdpi9cm2pbvgcxqvwr8ck327sxhdw4dnxmzhrbf7hzydmgykg2"))))
(build-system python-build-system)
(arguments
`(#:tests? #false)) ;require python-xmp-toolkit
@ -10350,6 +10351,26 @@ your package is installed, via @code{pkg_resources} (part of
primary use case is APIs defined before keyword-only parameters existed.")
(license license:gpl3+)))
(define-public python-langdetect
(package
(name "python-langdetect")
(version "1.0.9")
(source
(origin
(method url-fetch)
(uri (pypi-uri "langdetect" version))
(sha256
(base32 "1805svvb7xjm4sf1j7b6nc3409x37pd1xmabfwwjf1ldkzwgxhfb"))))
(build-system python-build-system)
(propagated-inputs
`(("python-six" ,python-six)))
(home-page "https://github.com/Mimino666/langdetect")
(synopsis "Language detection library")
(description
"This library is a port of Nakatani Shuyo's language-detection library
(version from 03/03/2014) to Python.")
(license license:expat)))
(define-public python-pyasn1
(package
(name "python-pyasn1")
@ -19391,6 +19412,50 @@ and works only with Python 2 and NumPy < 1.9.")
(define-public python2-phonenumbers
(package-with-python2 python-phonenumbers))
(define-public python-heapdict
(package
(name "python-heapdict")
(version "1.0.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "HeapDict" version))
(sha256
(base32
"1dnd7v9adqd21bf4ih2wzn9a7b41m0nccb0vbxny9n037rxzb5c4"))))
(build-system python-build-system)
(home-page "http://stutzbachenterprises.com/")
(synopsis "Heap with decrease-key and increase-key operations")
(description
"heapdict implements the MutableMapping ABC, meaning it works pretty much
like a regular Python @code{dict}. It’s designed to be used as a priority
queue.")
(license license:bsd-3)))
(define-public python-zict
(package
(name "python-zict")
(version "2.0.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "zict" version))
(sha256
(base32
"05pd1hyhqvpw87rnbvl3vdyf619snpyccbswaxisdj17frwnjacf"))))
(build-system python-build-system)
(propagated-inputs
`(("python-heapdict" ,python-heapdict)))
(native-inputs
`(("python-pytest" ,python-pytest)))
(home-page "https://zict.readthedocs.io/en/latest/")
(synopsis "Composable mutable mapping tools")
(description "This package provides abstract @code{MutableMapping} classes
that consume and build on other @code{MutableMappings}. Several of these can
be composed with one another to form intuitive interfaces over complex storage
systems policies.")
(license license:bsd-3)))
(define-public python-send2trash
(package
(name "python-send2trash")
@ -20726,6 +20791,43 @@ Public Suffix List's private domains as well.")
(define-public python2-tldextract
(package-with-python2 python-tldextract))
(define-public python-tldr
(package
(name "python-tldr")
(version "1.2.1")
(source
(origin
;; There's no test in PyPI.
(method git-fetch)
(uri (git-reference
(url "https://github.com/tldr-pages/tldr-python-client")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0n9wqvjxspm18vlxf9j9slrcydshk4rkv5nwkrqhfq606n6zvks4"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
;; This test fails. It tries to open a network socket.
(invoke "pytest" "-vv" "-k" "not test_error_message")))))))
(native-inputs
`(("python-pytest" ,python-pytest)
("python-pytest-runner" ,python-pytest-runner)))
(inputs
`(("python-argcomplete" ,python-argcomplete)
("python-colorama" ,python-colorama)
("python-termcolor" ,python-termcolor)))
(home-page "https://github.com/tldr-pages/tldr-python-client")
(synopsis "Python command-line client for tldr pages")
(description "This package provides the @code{tldr} command allowing users
to view @code{tldr} pages from a shell. The @code{tldr} pages are a community
effort to simplify the man pages with practical examples.")
(license license:expat))) ; MIT license
(define-public python-nodeenv
(package
(name "python-nodeenv")
@ -21250,30 +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
(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
@ -21288,9 +21416,20 @@ data.")
(define-public python2-cloudpickle
(let ((base (package-with-python2 (strip-python2-variant python-cloudpickle))))
(package/inherit base
(version "1.3.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cloudpickle" version))
(sha256
(base32
"0lx7gy9clp427qwcm7b23zdsldpr03gy3vxxhyi8fpbhwz859brq"))))
(native-inputs
`(("python-mock" ,python2-mock)
,@(package-native-inputs base)))
`(;; For tests.
("python-mock" ,python2-mock)
("python-psutil" ,python2-psutil)
("python-pytest" ,python2-pytest)
("python-tornado" ,python2-tornado)))
(propagated-inputs
`(("python-futures" ,python2-futures)
,@(package-propagated-inputs base))))))
@ -21354,14 +21493,14 @@ This Python package wraps the Blosc library.")
(define-public python-partd
(package
(name "python-partd")
(version "0.3.9")
(version "1.2.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "partd" version))
(sha256
(base32
"0sz6rwlnl4fqq220pyz863cnv0gjdxl4m7lscl71ishl5z0xkmhz"))))
"1sy3vdfyyx3bc5590zb7gwpsmimqz8m992x9hsydq8nmhixqjrxa"))))
(build-system python-build-system)
(propagated-inputs
`(("python-blosc" ,python-blosc)
@ -21401,13 +21540,13 @@ decisions with any given backend.")
(define-public python-dask
(package
(name "python-dask")
(version "2.14.0")
(version "2021.7.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "dask" version))
(sha256
(base32 "031j0j26s0675v0isyps2dphm03330n7dy8ifdy70jgvf78d119q"))))
(base32 "131c1bp193d7wp4gx09j6wark1c322c8sqjy22i0jaafl5rqfbz7"))))
(build-system python-build-system)
(arguments
`(#:phases
@ -21418,14 +21557,7 @@ decisions with any given backend.")
(substitute* "dask/tests/test_threaded.py"
(("def test_interrupt\\(\\)" m)
(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
m)))
;; This one fails with a type error:
;; TypeError: Already tz-aware, use tz_convert to convert.
(substitute* "dask/dataframe/tests/test_shuffle.py"
(("def test_set_index_timestamp\\(\\)" m)
(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
m)))
#t))
m)))))
(replace 'check
(lambda _ (invoke "pytest" "-vv"))))))
(propagated-inputs
@ -25878,3 +26010,25 @@ result.")
"This packages provides a docutils-compatibility bridge to CommonMark,
enabling you to write CommonMark inside of Docutils & Sphinx projects.")
(license license:expat)))
(define-public python-pyhull
(package
(name "python-pyhull")
(version "2015.2.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyhull" version))
(sha256
(base32
"091sph52c4yk1jlm5w8xidxpzbia9r7s42bnb23q4m4b56ihmzyj"))))
(build-system python-build-system)
(propagated-inputs
`(("python-numpy" ,python-numpy)))
(home-page "https://github.com/materialsvirtuallab/pyhull")
(synopsis "Python wrapper to Qhull")
(description
"This package provides a Python wrapper to @uref{http://www.qhull.org/,
Qhull} for the computation of the convex hull, Delaunay triangulation, and
Voronoi diagram.")
(license license:expat)))

7
gnu/packages/rdesktop.scm
View File

@ -108,7 +108,6 @@ to remotely control a user's Windows desktop.")
("libjpeg" ,libjpeg-turbo)
("libusb" ,libusb)
("libx11" ,libx11)
("libxkbcommon" ,libxkbcommon)
("libxkbfile" ,libxkbfile)
("libxcursor" ,libxcursor)
("libxext" ,libxext)
@ -118,10 +117,12 @@ to remotely control a user's Windows desktop.")
("libxrender" ,libxrender)
("libxinerama" ,libxinerama)
("libxshmfence" ,libxshmfence)
("openssl" ,openssl)
("pulseaudio" ,pulseaudio)
("wayland" ,wayland)
("zlib" ,zlib)))
(propagated-inputs
`(("libxkbcommon" ,libxkbcommon)
("openssl" ,openssl)
("wayland" ,wayland)))
(arguments
`(#:build-type "RELEASE"
#:configure-flags

27
gnu/packages/rdf.scm
View File

@ -443,3 +443,30 @@ parser and serializer.")
RDF data that can also be queried for Triple Patterns. This package provides a
C++ library as well as various command-line tools to to work with HDT.")
(license license:lgpl2.1+)))
(define-public python-sparqlwrapper
(package
(name "python-sparqlwrapper")
(version "1.8.5")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/RDFLib/sparqlwrapper.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1ia5h06zf6kpw6gdi7f80pzx10m79brj08zrbffb5wn9hzz8x528"))))
(build-system python-build-system)
(arguments
'(#:tests? #f)) ; The test suite simply queries external HTTP endpoints.
(native-inputs
`(("python-nose" ,python-nose)))
(propagated-inputs
`(("python-rdflib" ,python-rdflib)))
(home-page "https://rdflib.dev/sparqlwrapper/")
(synopsis "SPARQL Endpoint interface to Python")
(description "Python wrapper around a SPARQL service. It helps in creating
the query URI and, possibly, convert the result into a more manageable
format.")
(license license:w3c)))

27
gnu/packages/ruby.scm
View File

@ -8,7 +8,7 @@
;;; Copyright © 2017 Nikita <nikita@n0.is>
;;; Copyright © 2017, 2019, 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017, 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017, 2018, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2017, 2018, 2019 Christopher Baines <mail@cbaines.net>
;;; Copyright © 2018 Vasile Dumitrascu <va511e@yahoo.com>
@ -7676,15 +7676,26 @@ navigation capabilities to @code{pry}, using @code{byebug}.")
(define-public ruby-stackprof
(package
(name "ruby-stackprof")
(version "0.2.16")
(version "0.2.17")
(source
(origin
(method url-fetch)
(uri (rubygems-uri "stackprof" version))
(sha256
(base32
"147rb66p3n062vc433afqhkd99iazvkrqnghxgh871r62yhha93f"))))
(origin
(method url-fetch)
(uri (rubygems-uri "stackprof" version))
(sha256
(base32 "06lz70k8c0r7fyxk1nc3idh14x7nvsr21ydm1bsmbj00jyhmfzsn"))))
(build-system ruby-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-before 'check 'skip-dubious-test
;; This unreliable test can fail with "Expected 0 to be >= 1."
(lambda _
(substitute* "test/test_stackprof.rb"
(("def test_(cputime)" _ name)
(string-append "def skip_" name)))))
(add-before 'check 'build-tests
(lambda _
(invoke "rake" "compile"))))))
(native-inputs
`(("ruby-mocha" ,ruby-mocha)
("ruby-rake-compiler" ,ruby-rake-compiler)))

7
gnu/packages/rust-apps.scm
View File

@ -88,14 +88,14 @@ low-end hardware and serving many concurrent requests.")
(define-public bat
(package
(name "bat")
(version "0.18.1")
(version "0.18.2")
(source
(origin
(method url-fetch)
(uri (crate-uri "bat" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32 "0nvqkddpjxsmd27gqn8czql07faad50mihin5ivb9sxxnni28wnc"))))
(base32 "01zdamn1rd6d4xwwba1a8nfh06nmg7a0lakzgq8yfj5hsdgj9rdm"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
@ -113,6 +113,7 @@ low-end hardware and serving many concurrent requests.")
("rust-error-chain" ,rust-error-chain-0.12)
("rust-git2" ,rust-git2-0.13)
("rust-globset" ,rust-globset-0.4)
("rust-grep-cli" ,rust-grep-cli-0.1)
("rust-lazy-static" ,rust-lazy-static-1)
("rust-path-abs" ,rust-path-abs-0.5)
("rust-semver" ,rust-semver-0.11)
@ -124,7 +125,7 @@ low-end hardware and serving many concurrent requests.")
("rust-wild" ,rust-wild-2))
#:cargo-development-inputs
(("rust-assert-cmd" ,rust-assert-cmd-1)
("rust-nix" ,rust-nix-0.20)
("rust-nix" ,rust-nix-0.21)
("rust-predicates" ,rust-predicates-1)
("rust-serial-test" ,rust-serial-test-0.5)
("rust-tempfile" ,rust-tempfile-3)

53
gnu/packages/search.scm
View File

@ -6,6 +6,7 @@
;;; Copyright © 2018, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
;;; Copyright © 2020 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2021 Vinicius Monego <monego@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -24,7 +25,7 @@
(define-module (gnu packages search)
#:use-module ((guix licenses)
#:select (gpl2 gpl2+ gpl3+ lgpl2.1+ bsd-3 x11 perl-license))
#:select (gpl2 gpl2+ gpl3+ agpl3+ lgpl2.1+ bsd-3 x11 perl-license))
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-download)
@ -43,9 +44,11 @@
#:use-module (gnu packages perl)
#:use-module (gnu packages pdf)
#:use-module (gnu packages python)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages sphinx)
#:use-module (gnu packages time)
#:use-module (gnu packages web)
#:use-module (gnu packages xdisorg)
#:use-module (gnu packages xml))
@ -207,6 +210,54 @@ files and directories.")
command line tool for interacting with libtocc.")
(license gpl3+)))
(define-public searx
(package
(name "searx")
(version "1.0.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/searx/searx")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0ghkx8g8jnh8yd46p4mlbjn2zm12nx27v7qflr4c8xhlgi0px0mh"))))
(build-system python-build-system)
(arguments
`(#:tests? #f ;what tests do is make online requests to each engine
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'relax-requirements
(lambda _
;; These packages are outdated in Guix at the time of packaging.
;; When they are updated, remove corresponding substitutions.
;; Tests can run after build with 'searx-checker' tool in /bin.
(substitute* "requirements.txt"
(("flask-babel==2.0.0") "flask-babel>=1.0.0")
(("jinja2==2.11.3") "jinja2>=2.11.2")
(("lxml==4.6.3") "lxml>=4.4.2")
(("pygments==2.8.0") "pygments>=2.7.3")
(("requests\\[socks\\]==2.25.1") "requests>=2.25")
(("==") ">=")))))))
(propagated-inputs
`(("python-babel" ,python-babel)
("python-certifi" ,python-certifi)
("python-dateutil" ,python-dateutil)
("python-flask" ,python-flask)
("python-flask-babel" ,python-flask-babel)
("python-idna" ,python-idna)
("python-jinja2" ,python-jinja2)
("python-langdetect" ,python-langdetect)
("python-lxml" ,python-lxml)
("python-pygments" ,python-pygments)
("python-pyyaml" ,python-pyyaml)
("python-requests" ,python-requests)))
(home-page "https://searx.github.io/searx/")
(synopsis "Privacy-respecting metasearch engine")
(description "Searx is a privacy-respecting, hackable metasearch engine.")
(license agpl3+)))
(define-public bool
(package
(name "bool")

805
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81
gnu/packages/simulation.scm
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@ -43,6 +43,7 @@
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
#:use-module (gnu packages python-science)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages readline)
#:use-module (gnu packages tls)
@ -50,6 +51,7 @@
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix svn-download)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
@ -879,3 +881,82 @@ way the meshing of complex geometries using high-level abstractions is
made possible. The package provides a Python library together with a
command-line utility for mesh optimisation.")
(license license:lgpl3)))
(define-public python-dolfin-adjoint
(package
(name "python-dolfin-adjoint")
(version "2019.1.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/dolfin-adjoint/pyadjoint")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0xhy76a5f33hz94wc9g2mc5qmwkxfccbbc6yxl7psm130afp8lhn"))
(modules '((guix build utils)))
(snippet
'(begin
;; One of the migration tests attempts to call openmpi
;; recursively and fails. See
;; https://bitbucket.org/mpi4py/mpi4py/issues/95. Run the
;; test sequentially instead.
(with-directory-excursion "tests/migration/optimal_control_mms"
(substitute* "test_optimal_control_mms.py"
(("\\\"mpirun\\\", \\\"-n\\\", \\\"2\\\", ") "")))
;; Result files are regenerated in the check phase.
(delete-file-recursively
"tests/migration/viscoelasticity/test-results")
#t))))
(build-system python-build-system)
(inputs
`(("fenics" ,fenics)
("openmpi" ,openmpi)
("pybind11" ,pybind11)))
(native-inputs
`(("pkg-config" ,pkg-config)
("python-coverage" ,python-coverage)
("python-decorator" ,python-decorator)
("python-flake8" ,python-flake8)
("python-pkgconfig" ,python-pkgconfig)
("python-pytest" ,python-pytest)))
(propagated-inputs
`(("scipy" ,python-scipy)))
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'build 'mpi-setup
,%openmpi-setup)
(add-after 'install 'install-doc
(lambda* (#:key outputs #:allow-other-keys)
(let* ((doc (string-append (assoc-ref outputs "out")
"/share/doc/" ,name "-"
,version))
(examples (string-append doc "/examples")))
(mkdir-p examples)
(copy-recursively "examples" examples))
#t))
(replace 'check
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
(when tests?
(add-installed-pythonpath inputs outputs)
(setenv "HOME" (getcwd))
(and (invoke "py.test" "-v" "tests/fenics_adjoint")
(invoke "py.test" "-v" "tests/migration")
(invoke "py.test" "-v" "tests/pyadjoint")))
#t)))))
(home-page "http://www.dolfin-adjoint.org")
(synopsis "Automatic differentiation library")
(description "@code{python-dolfin-adjoint} is a solver of
differential equations associated with a governing system and a
functional of interest. Working from the forward model the solver
automatically derives the discrete adjoint and tangent linear models.
These additional models are key ingredients in many algorithms such as
data assimilation, optimal control, sensitivity analysis, design
optimisation and error estimation. The dolfin-adjoint project
provides the necessary tools and data structures for cases where the
forward model is implemented in @code{fenics} or
@url{https://firedrakeproject.org,firedrake}.")
(license license:lgpl3)))

138
gnu/packages/statistics.scm
View File

@ -214,11 +214,14 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
(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 ((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 _
@ -1041,14 +1044,14 @@ solution for sending email, including attachments, from within R.")
(define-public r-stringi
(package
(name "r-stringi")
(version "1.6.2")
(version "1.7.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "stringi" version))
(sha256
(base32
"1bidc1xzsv5nz2glf6z4sjxqlbs6zq595wwdmiq66sc2p7cis59s"))))
"0mhz7dkjdm8ap2zav1pmivhr8s0l6p2f6piij2hy08nwszqk51nr"))))
(build-system r-build-system)
(inputs `(("icu4c" ,icu4c)))
(native-inputs `(("pkg-config" ,pkg-config)))
@ -1513,19 +1516,19 @@ the execution time of R expressions.")
(define-public r-pryr
(package
(name "r-pryr")
(version "0.1.4")
(version "0.1.5")
(source (origin
(method url-fetch)
(uri (cran-uri "pryr" version))
(sha256
(base32
"06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k"))))
"02vp1y7zhv22id43j5c0gdcgn9171dyypqp8rqrlc3w5a7n565kv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-stringr" ,r-stringr)
("r-codetools" ,r-codetools)))
(native-inputs
`(("r-rcpp" ,r-rcpp)))
`(("r-codetools" ,r-codetools)
("r-lobstr" ,r-lobstr)
("r-rcpp" ,r-rcpp)
("r-stringr" ,r-stringr)))
(home-page "https://github.com/hadley/pryr")
(synopsis "Tools for computing on the R language")
(description
@ -1677,14 +1680,14 @@ like tidy evaluation.")
(define-public r-tibble
(package
(name "r-tibble")
(version "3.1.2")
(version "3.1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "tibble" version))
(sha256
(base32
"1vmwz1a756lar0jsigx6dhmj9mwk5mhywhq0prifwih3abhvszmn"))))
"1gpy90hg0bd4an0wqj0xx16a6x37fhc94z1v63y46dpiz231xfks"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ellipsis" ,r-ellipsis)
@ -2552,13 +2555,13 @@ time-of-day values, based on the @code{difftime} class.")
(define-public r-readr
(package
(name "r-readr")
(version "1.4.0")
(version "2.0.0")
(source (origin
(method url-fetch)
(uri (cran-uri "readr" version))
(sha256
(base32
"1fa67h4l9d30ig460xizgzl115i9pm3bk9dvsbrw6awbmf51ic82"))))
"1738nccg0msrhmzsasp19i0dpqi3m1nqbbg3nf1iiyp0mqc1dl8r"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
@ -2570,7 +2573,8 @@ time-of-day values, based on the @code{difftime} class.")
("r-tibble" ,r-tibble)
("r-r6" ,r-r6)
("r-rlang" ,r-rlang)
("r-bh" ,r-bh)))
("r-tzdb" ,r-tzdb)
("r-vroom" ,r-vroom)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/hadley/readr")
@ -2644,13 +2648,13 @@ well as additional utilities such as panel and axis annotation functions.")
(define-public r-rcpparmadillo
(package
(name "r-rcpparmadillo")
(version "0.10.5.0.0")
(version "0.10.6.0.0")
(source (origin
(method url-fetch)
(uri (cran-uri "RcppArmadillo" version))
(sha256
(base32
"059qi872f9h40ns65166qsq1i1jq1mvizm29a0xmqlyn7a5y9ca3"))))
"1bcx8fk5l5mmwb6cw36ndvld9v3amkz6vyc19059dw0xp7mxx04v"))))
(properties `((upstream-name . "RcppArmadillo")))
(build-system r-build-system)
(propagated-inputs
@ -2829,13 +2833,13 @@ that package, other packages are unaffected.")
(define-public r-blob
(package
(name "r-blob")
(version "1.2.1")
(version "1.2.2")
(source (origin
(method url-fetch)
(uri (cran-uri "blob" version))
(sha256
(base32
"1slb5mvxfyi92i8ifx2qa31hp57inilwhq1g9lzvgha6jrxbqm7g"))))
"1yn7f13icaix0apxp4drnciwdn8bx8xmbd129jd7ck4rcly0axj9"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rlang" ,r-rlang)
@ -3410,14 +3414,14 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
(define-public r-e1071
(package
(name "r-e1071")
(version "1.7-7")
(version "1.7-8")
(source
(origin
(method url-fetch)
(uri (cran-uri "e1071" version))
(sha256
(base32
"1phqrx787fkiamgx56sjjmzl9nh5wgpffah0mlwd7ijrf446qz3r"))))
"16lw0pr71h00whndkkv9zh2ixm6vc8bkp8m4i5wwhmihd9abdkdb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-class" ,r-class)
@ -3658,13 +3662,13 @@ t-probabilities, quantiles, random deviates and densities.")
(define-public r-matrixstats
(package
(name "r-matrixstats")
(version "0.59.0")
(version "0.60.0")
(source (origin
(method url-fetch)
(uri (cran-uri "matrixStats" version))
(sha256
(base32
"178baqrd7rbin3l10zyrkps5sda0q9mdqil9r12b3n99mlk8fhh7"))))
"08azjib5pwqs683dpgr3p5gid0silddcq6baqmvmazncrw1r7q0f"))))
(properties `((upstream-name . "matrixStats")))
(build-system r-build-system)
(arguments
@ -5444,14 +5448,14 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
(define-public r-ranger
(package
(name "r-ranger")
(version "0.12.1")
(version "0.13.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "ranger" version))
(sha256
(base32
"1vr5akgh388iivrxi0g4pl2npq9dc4cim3ljk4kjf637q058wc7w"))))
"02idcc6zbdz4wsi1mcwh7qyhmlbwvnzxwkdvvppxw7n2rh54z4v0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)
@ -6215,3 +6219,85 @@ various statistical models with linear predictors.")
factors for simple designs, including contingency tables, one- and two-sample
designs, one-way designs, general ANOVA designs, and linear regression.")
(license license:gpl2)))
(define-public r-norm
(package
(name "r-norm")
(version "1.0-9.5")
(source (origin
(method url-fetch)
(uri (cran-uri "norm" version))
(sha256
(base32
"01j1h412yfjx5r4dd0w8rhlf55997spgb6zd6pawy19rgw0byp1h"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(home-page "https://cran.r-project.org/web/packages/norm/")
(synopsis "Analysis of multivariate normal datasets with missing values")
(description "Multiple imputation of multivariate continuous data under a
normal model.")
;; Custom license, see https://cran.r-project.org/web/packages/norm/LICENSE.
(license (license:non-copyleft "file://LICENSE"))))
(define-public r-naniar
(package
(name "r-naniar")
(version "0.6.1")
(source (origin
(method url-fetch)
(uri (cran-uri "naniar" version))
(sha256
(base32
"0l3l2x85v3srilww483kpgp4zlwixyml257b0cqly8kcpwawlinm"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
("r-norm" ,r-norm)
("r-forcats" ,r-forcats)
("r-ggplot2" ,r-ggplot2)
("r-glue" ,r-glue)
("r-magrittr" ,r-magrittr)
("r-purrr" ,r-purrr)
("r-rlang" ,r-rlang)
("r-tibble" ,r-tibble)
("r-tidyr" ,r-tidyr)
("r-upsetr" ,r-upsetr)
("r-viridis" ,r-viridis)
("r-visdat" ,r-visdat)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/njtierney/naniar")
(synopsis
"Data structures, summaries, and visualisations for missing data")
(description
"Missing values are ubiquitous in data and need to be explored and
handled in the initial stages of analysis. The package provides data structures
and functions that facilitate the plotting of missing values and examination of
imputations. This allows missing data dependencies to be explored with minimal
deviation from the common work patterns of @code{ggplot2} and tidy data.")
(license license:expat)))
(define-public r-glinternet
(package
(name "r-glinternet")
(version "1.0.11")
(source
(origin
(method url-fetch)
(uri (cran-uri "glinternet" version))
(sha256
(base32
"1lqph2hj0h826gcfyk290ahkfalpnrd6jzymm60xi2qxia14lzk5"))))
(build-system r-build-system)
(home-page "http://web.stanford.edu/~hastie/Papers/glinternet_jcgs.pdf")
(synopsis "Learning interactions via hierarchical group-lasso regularization")
(description "Group-Lasso INTERaction-NET. Fits linear pairwise-interaction
models that satisfy strong hierarchy: if an interaction coefficient is estimated
to be nonzero, then its two associated main effects also have nonzero estimated
coefficients. Accommodates categorical variables (factors) with arbitrary
numbers of levels, continuous variables, and combinations thereof. Implements
the machinery described in the paper \"Learning interactions via hierarchical
group-lasso regularization\" (JCGS 2015, Volume 24, Issue 3).
Michael Lim & Trevor Hastie (2015)")
(license license:gpl2)))

21
gnu/packages/text-editors.scm
View File

@ -47,6 +47,7 @@
#:use-module (gnu packages aspell)
#:use-module (gnu packages assembly)
#:use-module (gnu packages autotools)
#:use-module (gnu packages base)
#:use-module (gnu packages boost)
#:use-module (gnu packages code)
#:use-module (gnu packages crates-io)
@ -524,27 +525,23 @@ Wordstar-, EMACS-, Pico, Nedit or vi-like key bindings. e3 can be used on
(native-inputs
`(("pkg-config" ,pkg-config)))
(inputs
`(("libbsd" ,libbsd)
`(("diffutils" ,diffutils)
("libbsd" ,libbsd)
("ncurses" ,ncurses)))
(arguments
;; No test suite available.
`(#:tests? #f
#:make-flags (list (string-append "prefix=" %output)
(string-append "CC=" ,(cc-for-target)))
(string-append "CC=" ,(cc-for-target))
(string-append "PKG_CONFIG=" ,(pkg-config-for-target)))
#:phases (modify-phases %standard-phases
(delete 'configure) ; no configure script
(add-before 'build 'correct-location-of-difftool
(lambda _
(add-before 'build 'correct-location-of-diff
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "buffer.c"
(("/usr/bin/diff")
(which "diff")))))
(add-before 'build 'pkg-config-for-cross-compiling-target
(lambda _
(substitute* "GNUmakefile"
(("pkg-config")
(or (which "pkg-config")
(string-append ,(%current-target-system)
"-pkg-config"))))))
(string-append (assoc-ref inputs "diffutils")
"/bin/diff")))))
(add-before 'install 'patch-tutorial-location
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "mg.1"

43
gnu/packages/textutils.scm
View File

@ -20,6 +20,8 @@
;;; Copyright © 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -63,6 +65,7 @@
#:use-module (gnu packages python-build)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages readline)
#:use-module (gnu packages ruby)
#:use-module (gnu packages slang)
#:use-module (gnu packages web))
@ -201,6 +204,46 @@ normalization, case-folding, and other operations for data in the UTF-8
encoding, supporting Unicode version 9.0.0.")
(license license:expat)))
(define-public utf8proc-2.6.1
(package
(inherit utf8proc)
(name "utf8proc")
(version "2.6.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaStrings/utf8proc")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1zqc6airkzkssbjxanx5v8blfk90180gc9id0dx8ncs54f1ib8w7"))))
(arguments
(substitute-keyword-arguments (package-arguments utf8proc)
((#:phases phases)
`(modify-phases ,phases
(replace 'check-data
(lambda* (#:key inputs native-inputs #:allow-other-keys)
(display native-inputs)
(for-each (lambda (i)
(copy-file (assoc-ref (or native-inputs inputs) i)
(string-append "data/" i)))
'("NormalizationTest.txt" "GraphemeBreakTest.txt"
"DerivedCoreProperties.txt"))))))))
(native-inputs
(append
(package-native-inputs utf8proc)
(let ((UNICODE_VERSION "13.0.0"))
`(("DerivedCoreProperties.txt"
,(origin
(method url-fetch)
(uri (string-append "https://www.unicode.org/Public/"
UNICODE_VERSION "/ucd/DerivedCoreProperties.txt"))
(sha256
(base32 "0j12x112cd8fpgazkc8izxnhhpia44p1m36ff8yapslxndcmzm55"))))
;; For tests
("ruby" ,ruby)))))))
(define-public libconfuse
(package
(name "libconfuse")

6
gnu/packages/tls.scm
View File

@ -593,13 +593,13 @@ netcat implementation that supports TLS.")
(package
(name "python-acme")
;; Remember to update the hash of certbot when updating python-acme.
(version "1.16.0")
(version "1.17.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "acme" version))
(sha256
(base32
"0mvqc8z30sxgr1m4p3yi3rm76sndnvl5khv4ybwx6zyq42403y51"))))
"03ij1wp7jwvppv70qbjkgdg7w824yh6j4gfb68jj20wicx08xx1a"))))
(build-system python-build-system)
(arguments
`(#:phases
@ -647,7 +647,7 @@ netcat implementation that supports TLS.")
(uri (pypi-uri "certbot" version))
(sha256
(base32
"0z90pcndbks8f62f47m5nkqcmkabb8r526by29lp30x4gjc0xs04"))))
"0wyipx6q78fmvngf1i6g50s01qpjqh07qlk1b5vyxwgl3080lhgg"))))
(build-system python-build-system)
(arguments
`(,@(substitute-keyword-arguments (package-arguments python-acme)

63
gnu/packages/tmux.scm
View File

@ -67,36 +67,39 @@ continue running in the background, then later reattached.")
(license license:isc)))
(define-public tmux-themepack
(let ((commit "03a372866f7677f7fe63bcee140b48b9fd372c48")
(revision "1"))
(package
(name "tmux-themepack")
(version (git-version "0.0.0" revision commit)) ; no version tags
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/jimeh/tmux-themepack")
(commit commit)))
(sha256
(base32
"1d3k87mq5lca042jbap5kxskjy3kg79wjhhpnm6jacbn3anc67zl"))
(file-name (git-file-name name version))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no test suite
#:phases (modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (string-append
(assoc-ref outputs "out")
"/share/" ,name "-" ,version)))
(copy-recursively "." out)))))))
(home-page "https://github.com/jimeh/tmux-themepack")
(synopsis "Collection of themes for Tmux")
(description "A collection of various themes for Tmux.")
(license license:wtfpl2))))
(package
(name "tmux-themepack")
(version "1.1.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/jimeh/tmux-themepack")
(commit version)))
(sha256
(base32
"00dmd16ngyag3n46rbnl9vy82ih6g0y02yfwkid32a1c8vdbvb3z"))
(file-name (git-file-name name version))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no test suite
#:phases (modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (string-append
(assoc-ref outputs "out")
"/share/" ,name)))
(copy-recursively "powerline" (string-append out "/powerline"))
(for-each (lambda (file) (copy-file file (string-append out "/" file)))
'("basic.tmuxtheme"
"default.tmuxtheme"
"themepack.tmux"))))))))
(home-page "https://github.com/jimeh/tmux-themepack")
(synopsis "Collection of themes for Tmux")
(description
"This package provides several themes for Tmux, the terminal multiplexer.")
(license license:wtfpl2)))
(define-public tmuxifier
(package

10
gnu/packages/tor.scm
View File

@ -45,6 +45,7 @@
#:use-module (gnu packages glib)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages python-check)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
@ -226,7 +227,7 @@ networks.")
(define-public onionshare-cli
(package
(name "onionshare-cli")
(version "2.3.1")
(version "2.3.2")
(source
(origin
(method git-fetch)
@ -235,13 +236,14 @@ networks.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1llvnvb676s2cs6a4y7isxdj75ddfvskw1p93v5m35vsw7f72kqz"))))
(base32 "1qk0zvbaws9md1lmi0al1jc8v86l65nf7n3w1s36iwsfzazc6clv"))))
(build-system python-build-system)
(native-inputs
`(("python-pytest" ,python-pytest)))
(inputs
;; TODO: obfs4proxy
`(("python-click" ,python-click)
("python-colorama" ,python-colorama)
("python-eventlet" ,python-eventlet)
("python-flask" ,python-flask)
("python-flask-httpauth" ,python-flask-httpauth)
@ -303,10 +305,14 @@ OnionShare.")
;; - test_autostart_timer_too_short
;; - test_autostop_timer_too_short
(substitute* "desktop/tests/test_gui_share.py"
(("import os" &)
(string-append "import pytest\n" &))
(("( *)def test_autost(art|op)_(timer(_too_short)?|and_[^(]*)\\(" & >)
(string-append > "@pytest.mark.skip\n" &)))
;; - test_13_quit_with_server_started_should_warn
(substitute* "desktop/tests/test_gui_tabs.py"
(("import os" &)
(string-append "import pytest\n" &))
(("( *)def test_13" & >)
(string-append > "@pytest.mark.skip\n" &)))
;; Remove multiline load-path adjustment, so that onionshare-cli

50
gnu/packages/uglifyjs.scm 100644
View File

@ -0,0 +1,50 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2021 Charles <charles.b.jackson@protonmail.com>
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages uglifyjs)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix git-download)
#:use-module (guix build-system node)
#:use-module (gnu packages node-xyz))
(define-public node-uglify-js
(package
(name "node-uglify-js")
(version "3.13.9")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mishoo/UglifyJS")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0q1f91xwwm829cl5v727d4qkxy4yh7wri3pgl89f0m3a4y1n7hi4"))))
(build-system node-build-system)
(native-inputs
`(("node-acorn" ,node-acorn)
("node-semver" ,node-semver)))
(home-page "https://lisperator.net/uglifyjs/")
(synopsis "JavaScript parser / mangler / compressor / beautifier toolkit")
(description "UglifyJS is a JavaScript compressor/minifier written in
JavaScript. It also contains tools that allow one to automate working with
JavaScript code: parser, code generator, compressor, mangler, scope analyzer,
tree walker, and tree transformer.")
(license license:bsd-2)))
(define-public uglifyjs node-uglify-js)

6
gnu/packages/video.scm
View File

@ -1057,7 +1057,11 @@ H.264 (MPEG-4 AVC) video streams.")
(modify-phases %standard-phases
(add-after 'unpack 'patch-source
(lambda* (#:key inputs #:allow-other-keys)
(substitute* (find-files "." ".*-viewer$")
(substitute* (find-files "lib" "\\.pm$")
(("\"youtube-dl\"")
(format #f "\"~a/bin/youtube-dl\""
(assoc-ref inputs "youtube-dl"))))
(substitute* (find-files "bin" ".*-viewer$")
(("'ffmpeg'")
(format #f "'~a/bin/ffmpeg'"
(assoc-ref inputs "ffmpeg")))

6
gnu/packages/vim.scm
View File

@ -899,16 +899,16 @@ through its msgpack-rpc API.")
(define-public vim-guix-vim
(package
(name "vim-guix-vim")
(version "0.2.1")
(version "0.3.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://gitlab.com/Efraim/guix.vim")
(url "https://gitlab.com/Efraim/guix.vim.git/")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1fyfwsvv787al88lqjgqcgykav8pcf4xgj5d4i0j7wjcfb3mh1vw"))))
"0bk2mnvbv1rfr0zzx4m8jjdw98wbbmdffx1h9svrjpg25lcvqv1b"))))
(build-system copy-build-system)
(arguments
'(#:install-plan

4
gnu/packages/visidata.scm
View File

@ -31,14 +31,14 @@
(define-public visidata
(package
(name "visidata")
(version "2.4")
(version "2.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "visidata" version))
(sha256
(base32
"1g9g4gd3mqi23damxghwj76zxi2ig9vf4jv8dnvl7q7ssb7gz60d"))))
"19fbjr9j91pcazcz0bqx3qrasmr8xdsb13haf5lfbpyxj23f7f1j"))))
(build-system python-build-system)
(arguments
'(#:phases

13
gnu/packages/web-browsers.scm
View File

@ -912,22 +912,19 @@ interface.")
(define-public telescope
(package
(name "telescope")
(version "0.3")
(version "0.4.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://git.omarpolo.com/telescope/snapshot/"
"telescope-" version ".tar.gz"))
(uri (string-append "https://github.com/omar-polo/telescope/releases/download/"
version "/telescope-" version ".tar.gz"))
(sha256
(base32 "1wg5x04n9iri7jx1lzhmd79j41grhjm3mpxn9qq9nf8n102wlvm3"))))
(base32 "086zps4nslv5isfw1b5gvms7vp3fglm7x1a6ks0h0wxarzj350bl"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f)) ;no tests
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("bison" ,bison)
("gettext" ,gettext-minimal)))
`(("gettext" ,gettext-minimal)))
(inputs
`(("libevent" ,libevent)
("libressl" ,libressl)

184
gnu/packages/web.scm
View File

@ -51,6 +51,7 @@
;;; Copyright © 2021 Stefan Reichör <stefan@xsteve.at>
;;; Copyright © 2021 la snesne <lasnesne@lagunposprasihopre.org>
;;; Copyright © 2021 Matthew James Kraai <kraai@ftbfs.org>
;;; Copyright © 2021 Sarah Morgensen <iskarian@mgsn.dev>
;;;
;;; This file is part of GNU Guix.
;;;
@ -96,6 +97,7 @@
#:use-module (gnu packages apr)
#:use-module (gnu packages autotools)
#:use-module (gnu packages base)
#:use-module (gnu packages bash)
#:use-module (gnu packages bison)
#:use-module (gnu packages bittorrent)
#:use-module (gnu packages boost)
@ -3482,14 +3484,14 @@ and multipart/form-data.")
(define-public perl-http-cookiejar
(package
(name "perl-http-cookiejar")
(version "0.010")
(version "0.012")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://cpan/authors/id/D/DA/DAGOLDEN/"
"HTTP-CookieJar-" version ".tar.gz"))
(sha256
(base32 "1l7mqsca4fmls7agzwmp6yq1x16y9jwq4114i6i75n654gl37qsn"))))
(base32 "0jk0ps4i67dhhhwaxwwa9nkv3n6n5w44xlnwyzvk59735pwvyjh0"))))
(build-system perl-build-system)
(native-inputs
`(("perl-test-deep" ,perl-test-deep)
@ -7692,87 +7694,83 @@ compressed JSON header blocks.
(license license:expat)))
(define-public hpcguix-web
(let ((commit "9de63562b06b4aef3a3afe5ecb18d3c91e57ee74")
(revision "5"))
(package
(name "hpcguix-web")
(version (git-version "0.0.1" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/UMCUGenetics/hpcguix-web")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0wjgj2s7v2cyz6dx24c111rxs99i84sfvxl4ch8brnh02j2606jz"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((guix build gnu-build-system)
(guix build utils)
(srfi srfi-26)
(ice-9 popen)
(ice-9 rdelim))
#:phases
(modify-phases %standard-phases
(add-before 'configure 'set-variables
(lambda _
;; This prevents a few warnings
(setenv "GUILE_AUTO_COMPILE" "0")
(setenv "XDG_CACHE_HOME" (getcwd))
#t))
(add-after 'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(guix (assoc-ref inputs "guix"))
(guile (assoc-ref inputs "guile"))
(gcrypt (assoc-ref inputs "guile-gcrypt"))
(git (assoc-ref inputs "guile-git"))
(bs (assoc-ref inputs "guile-bytestructures"))
(json (assoc-ref inputs "guile-json"))
(guile-cm (assoc-ref inputs
"guile-commonmark"))
(deps (list guile gcrypt git bs guile-cm guix json))
(effective
(read-line
(open-pipe* OPEN_READ
(string-append guile "/bin/guile")
"-c" "(display (effective-version))")))
(path (string-join
(map (cut string-append <>
"/share/guile/site/"
effective)
deps)
":"))
(gopath (string-join
(map (cut string-append <>
"/lib/guile/" effective
"/site-ccache")
deps)
":")))
(wrap-program (string-append out "/bin/run")
`("GUILE_LOAD_PATH" ":" prefix (,path))
`("GUILE_LOAD_COMPILED_PATH" ":" prefix (,gopath)))
#t))))))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("uglify-js" ,uglify-js)
("pkg-config" ,pkg-config)))
(inputs
`(("guile" ,@(assoc-ref (package-native-inputs guix) "guile"))
("guix" ,guix)))
(propagated-inputs
`(("guile" ,@(assoc-ref (package-native-inputs guix) "guile"))
("guile-commonmark" ,guile-commonmark)
("guile-json" ,guile-json-4)))
(home-page "https://github.com/UMCUGenetics/hpcguix-web")
(synopsis "Web interface for cluster deployments of Guix")
(description "Hpcguix-web provides a web interface to the list of packages
(package
(name "hpcguix-web")
(version "0.1.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/UMCUGenetics/hpcguix-web")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"02lz5k1hhkwfz3nr3lsd69icsz6n0q82z047d3svi09qpxw6y0cj"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((guix build gnu-build-system)
(guix build utils)
(srfi srfi-26)
(ice-9 popen)
(ice-9 rdelim))
#:phases
(modify-phases %standard-phases
(add-before 'configure 'set-variables
(lambda _
;; This prevents a few warnings
(setenv "GUILE_AUTO_COMPILE" "0")
(setenv "XDG_CACHE_HOME" (getcwd))))
(add-after 'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(guix (assoc-ref inputs "guix"))
(guile (assoc-ref inputs "guile"))
(gcrypt (assoc-ref inputs "guile-gcrypt"))
(git (assoc-ref inputs "guile-git"))
(bs (assoc-ref inputs "guile-bytestructures"))
(json (assoc-ref inputs "guile-json"))
(guile-cm (assoc-ref inputs
"guile-commonmark"))
(deps (list guile gcrypt git bs guile-cm guix json))
(effective
(read-line
(open-pipe* OPEN_READ
(string-append guile "/bin/guile")
"-c" "(display (effective-version))")))
(path (string-join
(map (cut string-append <>
"/share/guile/site/"
effective)
deps)
":"))
(gopath (string-join
(map (cut string-append <>
"/lib/guile/" effective
"/site-ccache")
deps)
":")))
(wrap-program (string-append out "/bin/hpcguix-web")
`("GUILE_LOAD_PATH" ":" prefix (,path))
`("GUILE_LOAD_COMPILED_PATH" ":" prefix (,gopath)))))))))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("uglify-js" ,uglify-js)
("pkg-config" ,pkg-config)))
(inputs
`(("guile" ,@(assoc-ref (package-native-inputs guix) "guile"))
("guix" ,guix)
("bash-minimal" ,bash-minimal))) ;for 'wrap-program'
(propagated-inputs
`(("guile" ,@(assoc-ref (package-native-inputs guix) "guile"))
("guile-commonmark" ,guile-commonmark)
("guile-json" ,guile-json-4)))
(home-page "https://github.com/UMCUGenetics/hpcguix-web")
(synopsis "Web interface for cluster deployments of Guix")
(description "Hpcguix-web provides a web interface to the list of packages
provided by Guix. The list of packages is searchable and provides
instructions on how to use Guix in a shared HPC environment.")
(license license:agpl3+))))
(license license:agpl3+)))
(define-public httrack
(package
@ -7967,8 +7965,8 @@ solution for any project's interface needs:
(license license:expat)))
(define-public gmnisrv
(let ((commit "d484ba0ab0020866535a44be5948c9482b8f2b8d")
(revision "1"))
(let ((commit "32854b79c73b278bf33eb5123abf1c36abdc7c01")
(revision "2"))
(package
(name "gmnisrv")
(version (git-version "0" revision commit))
@ -7980,24 +7978,22 @@ solution for any project's interface needs:
(commit commit)))
(sha256
(base32
"11phipixsxx1jgm42agp76p5s68l0zj65kgb41vzaymgwcq79ivn"))
"0lbb3ablwkdcgm1cjr1hikr55y8gpl420nh8b8g9wn4abhm2xgr9"))
(file-name (git-file-name name version))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-before 'configure 'set-variables
(lambda _
(setenv "CC" "gcc")
#t))
(delete 'check))))
`(#:tests? #f ; no check target
#:configure-flags (list "--sysconfdir=/etc"
(string-append "--with-mimedb="
(assoc-ref %build-inputs "mailcap")
"/etc/mime.types"))
#:make-flags (list (string-append "CC=" ,(cc-for-target)))))
(inputs
`(("openssl" ,openssl)))
`(("mailcap" ,mailcap)
("openssl" ,openssl)))
(native-inputs
`(("pkg-config" ,pkg-config)
("scdoc" ,scdoc)))
(propagated-inputs
`(("mailcap" ,mailcap)))
(synopsis "Simple Gemini protocol server")
(description "gmnisrv is a simple Gemini protocol server written in C.")
(license (list license:gpl3+

4
gnu/packages/webkit.scm
View File

@ -226,14 +226,14 @@ acceleration in mind, leveraging common 3D graphics APIs for best performance.")
(define-public webkitgtk
(package
(name "webkitgtk")
(version "2.32.1")
(version "2.32.3")
(source (origin
(method url-fetch)
(uri (string-append "https://www.webkitgtk.org/releases/"
"webkitgtk-" version ".tar.xz"))
(sha256
(base32
"05v9hgpkc6mi2klrd8nqql1n8xzq8rgdz3hvyy369xkhgwqifq8k"))
"1g1clppby019bng43ry50xd2dvzfzgrd9yv2xx6gwkk5mksrdx61"))
(patches (search-patches "webkitgtk-share-store.patch"
"webkitgtk-bind-all-fonts.patch"))))
(build-system cmake-build-system)

5
gnu/packages/xfce.scm
View File

@ -223,7 +223,7 @@ to share commonly used Xfce widgets among the Xfce applications.")
(define-public catfish
(package
(name "catfish")
(version "1.4.13")
(version "4.16.1")
(source (origin
(method url-fetch)
(uri (string-append "https://archive.xfce.org/src/apps/"
@ -231,7 +231,7 @@ to share commonly used Xfce widgets among the Xfce applications.")
"/catfish-" version ".tar.bz2"))
(sha256
(base32
"0fg89946z6n8njxn4mv29jksw8yavg8vypsljn9031pjwl3fmh2q"))))
"0md6ypirr97ch7x8qliwzixzwj6zzd68ivb2dzj90hm2lcn7wc8h"))))
(build-system python-build-system)
(arguments
'(#:phases
@ -263,6 +263,7 @@ to share commonly used Xfce widgets among the Xfce applications.")
("intltool" ,intltool)))
(inputs
`(("which" ,which)
("xfconf" ,xfconf)
("xdg-utils" ,xdg-utils)))
(propagated-inputs
`(("gtk+" ,gtk+)

8
gnu/packages/xml.scm
View File

@ -2071,8 +2071,9 @@ advantage of JIT JVMs.")
(version "2.1.10")
(source (origin
(method url-fetch)
(uri (string-append "http://www.extreme.indiana.edu/xgws/xsoap/"
"PullParser/PullParser" version ".tgz"))
;; Unfortunately, archive.org does not have a copy of this file.
(uri (string-append "https://ftp.fau.de/gentoo/distfiles/"
"PullParser" version ".tgz"))
(sha256
(base32
"1kw9nhyqb7bzhn2zjbwlpi5vp5rzj89amzi3hadw2acyh2dmd0md"))
@ -2088,7 +2089,8 @@ advantage of JIT JVMs.")
#:phases
(modify-phases %standard-phases
(replace 'install (install-jars "build/lib")))))
(home-page "http://www.extreme.indiana.edu/xgws/xsoap/xpp/")
(home-page (string-append "https://web.archive.org/web/20210225153105/"
"https://www.extreme.indiana.edu/"))
(synopsis "Streaming pull XML parser")
(description "Xml Pull Parser (in short XPP) is a streaming pull XML
parser and should be used when there is a need to process quickly and

18
gnu/packages/xorg.scm
View File

@ -31,6 +31,7 @@
;;; 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.
;;;
@ -60,6 +61,7 @@
#:use-module (gnu packages aidc)
#:use-module (gnu packages anthy)
#:use-module (gnu packages autotools)
#:use-module (gnu packages bash)
#:use-module (gnu packages bison)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
@ -1518,11 +1520,10 @@ treat it as part of their software base when porting.")
(build-system gnu-build-system)
(arguments
'(#:configure-flags '("--disable-static")))
(inputs
`(("libxext" ,libxext)
("libx11" ,libx11)))
(propagated-inputs
`(("xorgproto" ,xorgproto)))
`(("libx11" ,libx11)
("libxext" ,libxext)
("xorgproto" ,xorgproto)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "https://www.x.org/wiki/")
@ -6330,18 +6331,18 @@ basic eye-candy effects.")
(define-public xpra
(package
(name "xpra")
(version "4.2")
(version "4.2.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://www.xpra.org/src/xpra-"
version ".tar.gz"))
(sha256
(base32 "1yg9asi3i3wf73ibc006xv3g77axvbyp81lyinwq27syabh30i1a"))
(base32 "0gqdcw5cfk919jk8g0g4xjxbsvr5j9gskn8q3cmrz388pvfvm8x7"))
(patches (search-patches "xpra-4.2-systemd-run.patch"))))
(build-system python-build-system)
;; see also http://xpra.org/trac/wiki/Dependencies
(inputs `(
(inputs `(("bash-minimal" ,bash-minimal) ; for wrap-program
;; Essential dependencies.
("libjpeg" ,libjpeg-turbo)
("libwebp" ,libwebp)
@ -6473,7 +6474,8 @@ X11 servers, Windows, or macOS.")
`(("anthy" ,anthy)
("libedit" ,libedit)
("libxft" ,libxft)
("m17n-lib" ,m17n-lib)))
("m17n-lib" ,m17n-lib)
("ncurses" ,ncurses)))
(native-inputs
`(("emacs" ,emacs-minimal)
("intltool" ,intltool)

45
gnu/services.scm
View File

@ -4,6 +4,8 @@
;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
;;; Copyright © 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2021 raid5atemyhomework <raid5atemyhomework@protonmail.com>
;;; Copyright © 2020 Christine Lemmer-Webber <cwebber@dustycloud.org>
;;; Copyright © 2020, 2021 Brice Waegeneire <brice@waegenei.re>
;;;
;;; This file is part of GNU Guix.
;;;
@ -40,6 +42,7 @@
#:use-module (gnu packages base)
#:use-module (gnu packages bash)
#:use-module (gnu packages hurd)
#:use-module (gnu system setuid)
#:use-module (srfi srfi-1)
#:use-module (srfi srfi-9)
#:use-module (srfi srfi-9 gnu)
@ -801,15 +804,49 @@ directory."
FILES must be a list of name/file-like object pairs."
(service etc-service-type files))
(define (setuid-program->activation-gexp programs)
"Return an activation gexp for setuid-program from PROGRAMS."
(let ((programs (map (lambda (program)
;; FIXME This is really ugly, I didn't managed to use
;; "inherit"
(let ((program-name (setuid-program-program program))
(setuid? (setuid-program-setuid? program))
(setgid? (setuid-program-setgid? program))
(user (setuid-program-user program))
(group (setuid-program-group program)) )
#~(setuid-program
(setuid? #$setuid?)
(setgid? #$setgid?)
(user #$user)
(group #$group)
(program #$program-name))))
programs)))
(with-imported-modules (source-module-closure
'((gnu system setuid)))
#~(begin
(use-modules (gnu system setuid))
(activate-setuid-programs (list #$@programs))))))
(define (setuid-program-file-like-deprecated file-like)
(match file-like
((? file-like? program)
(warning
(G_ "representing setuid programs with '~a' is \
deprecated; use 'setuid-program' instead~%") program)
(setuid-program (program program)))
((? setuid-program? program)
program)))
(define setuid-program-service-type
(service-type (name 'setuid-program)
(extensions
(list (service-extension activation-service-type
(lambda (programs)
#~(activate-setuid-programs
(list #$@programs))))))
setuid-program->activation-gexp)))
(compose concatenate)
(extend append)
(extend (lambda (config extensions)
(map setuid-program-file-like-deprecated
(append config extensions))))
(description
"Populate @file{/run/setuid-programs} with the specified
executables, making them setuid-root.")))

13
gnu/services/dbus.scm
View File

@ -2,6 +2,7 @@
;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be>
;;; Copyright © 2021 Brice Waegeneire <brice@waegenei.re>
;;;
;;; This file is part of GNU Guix.
;;;
@ -21,6 +22,7 @@
(define-module (gnu services dbus)
#:use-module (gnu services)
#:use-module (gnu services shepherd)
#:use-module (gnu system setuid)
#:use-module (gnu system shadow)
#:use-module (gnu system pam)
#:use-module ((gnu packages glib) #:select (dbus))
@ -156,10 +158,12 @@ includes the @code{etc/dbus-1/system.d} directories of each package listed in
(shell (file-append shadow "/sbin/nologin")))))
(define dbus-setuid-programs
;; Return the file name of the setuid program that we need.
;; Return a list of <setuid-program> for the program that we need.
(match-lambda
(($ <dbus-configuration> dbus services)
(list (file-append dbus "/libexec/dbus-daemon-launch-helper")))))
(list (setuid-program
(program (file-append
dbus "/libexec/dbus-daemon-launch-helper")))))))
(define (dbus-activation config)
"Return an activation gexp for D-Bus using @var{config}."
@ -335,8 +339,9 @@ tuples, are all set as environment variables when the bus daemon launches it."
(define polkit-setuid-programs
(match-lambda
(($ <polkit-configuration> polkit)
(list (file-append polkit "/lib/polkit-1/polkit-agent-helper-1")
(file-append polkit "/bin/pkexec")))))
(map file-like->setuid-program
(list (file-append polkit "/lib/polkit-1/polkit-agent-helper-1")
(file-append polkit "/bin/pkexec"))))))
(define polkit-service-type
(service-type (name 'polkit)

26
gnu/services/desktop.scm
View File

@ -12,6 +12,7 @@
;;; Copyright © 2019 David Wilson <david@daviwil.com>
;;; Copyright © 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2020 Reza Alizadeh Majd <r.majd@pantherx.org>
;;; Copyright © 2021 Brice Waegeneire <brice@waegenei.re>
;;;
;;; This file is part of GNU Guix.
;;;
@ -40,6 +41,7 @@
#:use-module ((gnu system file-systems)
#:select (%elogind-file-systems file-system))
#:use-module (gnu system)
#:use-module (gnu system setuid)
#:use-module (gnu system shadow)
#:use-module (gnu system pam)
#:use-module (gnu packages glib)
@ -1034,14 +1036,15 @@ rules."
(define (enlightenment-setuid-programs enlightenment-desktop-configuration)
(match-record enlightenment-desktop-configuration
<enlightenment-desktop-configuration>
(enlightenment)
(list (file-append enlightenment
"/lib/enlightenment/utils/enlightenment_sys")
(file-append enlightenment
"/lib/enlightenment/utils/enlightenment_system")
(file-append enlightenment
"/lib/enlightenment/utils/enlightenment_ckpasswd"))))
<enlightenment-desktop-configuration>
(enlightenment)
(map file-like->setuid-program
(list (file-append enlightenment
"/lib/enlightenment/utils/enlightenment_sys")
(file-append enlightenment
"/lib/enlightenment/utils/enlightenment_system")
(file-append enlightenment
"/lib/enlightenment/utils/enlightenment_ckpasswd")))))
(define enlightenment-desktop-service-type
(service-type
@ -1204,8 +1207,11 @@ or setting its password with passwd.")))
;; Allow desktop users to also mount NTFS and NFS file systems
;; without root.
(simple-service 'mount-setuid-helpers setuid-program-service-type
(list (file-append nfs-utils "/sbin/mount.nfs")
(file-append ntfs-3g "/sbin/mount.ntfs-3g")))
(map (lambda (program)
(setuid-program
(program program)))
(list (file-append nfs-utils "/sbin/mount.nfs")
(file-append ntfs-3g "/sbin/mount.ntfs-3g"))))
;; The global fontconfig cache directory can sometimes contain
;; stale entries, possibly referencing fonts that have been GC'd,

9
gnu/services/docker.scm
View File

@ -4,6 +4,7 @@
;;; Copyright © 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2020 Jesse Dowell <jessedowell@gmail.com>
;;; Copyright © 2021 Brice Waegeneire <brice@waegenei.re>
;;;
;;; This file is part of GNU Guix.
;;;
@ -26,6 +27,7 @@
#:use-module (gnu services base)
#:use-module (gnu services dbus)
#:use-module (gnu services shepherd)
#:use-module (gnu system setuid)
#:use-module (gnu system shadow)
#:use-module (gnu packages docker)
#:use-module (gnu packages linux) ;singularity
@ -195,9 +197,10 @@ bundles in Docker containers.")
"-helper")))
'("action" "mount" "start")))))
(list (file-append helpers "/singularity-action-helper")
(file-append helpers "/singularity-mount-helper")
(file-append helpers "/singularity-start-helper")))
(map file-like->setuid-program
(list (file-append helpers "/singularity-action-helper")
(file-append helpers "/singularity-mount-helper")
(file-append helpers "/singularity-start-helper"))))
(define singularity-service-type
(service-type (name 'singularity)

6
gnu/services/networking.scm
View File

@ -17,6 +17,7 @@
;;; Copyright © 2021 Oleg Pykhalov <go.wigust@gmail.com>
;;; Copyright © 2021 Christopher Lemmer Webber <cwebber@dustycloud.org>
;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be>
;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -363,8 +364,9 @@ Protocol (DHCP) client, on all the non-loopback network interfaces.")))
(lambda _ (display ""))))
;; Validate the config.
(invoke/quiet
#$(file-append package "/sbin/dhcpd") "-t" "-cf"
#$config-file))))))
#$(file-append package "/sbin/dhcpd")
#$(string-append "-" version)
"-t" "-cf" #$config-file))))))
(define dhcpd-service-type
(service-type

4
gnu/services/web.scm
View File

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015 David Thompson <davet@gnu.org>
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Nikita <nikita@n0.is>
;;; Copyright © 2016, 2017, 2018 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2017 Christopher Baines <mail@cbaines.net>
@ -1163,7 +1163,7 @@ a webserver.")
(provision '(hpcguix-web))
(requirement '(networking))
(start #~(make-forkexec-constructor
(list #$(file-append hpcguix-web "/bin/run")
(list #$(file-append hpcguix-web "/bin/hpcguix-web")
(string-append "--config="
#$(scheme-file "hpcguix-web.scm" specs)))
#:user "hpcguix-web"

4
gnu/services/xorg.scm
View File

@ -8,6 +8,7 @@
;;; Copyright © 2020 shtwzrd <shtwzrd@protonmail.com>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;; Copyright © 2020 Alex Griffin <a@ajgrf.com>
;;; Copyright © 2021 Brice Waegeneire <brice@waegenei.re>
;;;
;;; This file is part of GNU Guix.
;;;
@ -29,6 +30,7 @@
#:use-module (gnu services)
#:use-module (gnu services shepherd)
#:use-module (gnu system pam)
#:use-module (gnu system setuid)
#:use-module (gnu system keyboard)
#:use-module (gnu services base)
#:use-module (gnu services dbus)
@ -681,7 +683,7 @@ reboot_cmd " shepherd "/sbin/reboot\n"
#:allow-empty-passwords? empty?)))))
(define screen-locker-setuid-programs
(compose list screen-locker-program))
(compose list file-like->setuid-program screen-locker-program))
(define screen-locker-service-type
(service-type (name 'screen-locker)

45
gnu/system.scm
View File

@ -7,7 +7,7 @@
;;; Copyright © 2019 Meiyo Peng <meiyo.peng@gmail.com>
;;; Copyright © 2019, 2020 Miguel Ángel Arruga Vivas <rosen644835@gmail.com>
;;; Copyright © 2020 Danny Milosavljevic <dannym@scratchpost.org>
;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
;;; Copyright © 2020, 2021 Brice Waegeneire <brice@waegenei.re>
;;; Copyright © 2020 Florian Pelz <pelzflorian@pelzflorian.de>
;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <jannek@gnu.org>
@ -74,6 +74,7 @@
#:use-module (gnu system locale)
#:use-module (gnu system pam)
#:use-module (gnu system linux-initrd)
#:use-module (gnu system setuid)
#:use-module (gnu system uuid)
#:use-module (gnu system file-systems)
#:use-module (gnu system mapped-devices)
@ -267,7 +268,7 @@
(pam-services operating-system-pam-services ; list of PAM services
(default (base-pam-services)))
(setuid-programs operating-system-setuid-programs
(setuid-programs %operating-system-setuid-programs
(default %setuid-programs)) ; list of string-valued gexps
(sudoers-file operating-system-sudoers-file ; file-like
@ -671,7 +672,7 @@ bookkeeping."
(operating-system-environment-variables os))
host-name procs root-fs
(service setuid-program-service-type
(operating-system-setuid-programs os))
(%operating-system-setuid-programs os))
(service profile-service-type
(operating-system-packages os))
other-fs
@ -701,7 +702,7 @@ bookkeeping."
(pam-root-service (operating-system-pam-services os))
(operating-system-etc-service os)
(service setuid-program-service-type
(operating-system-setuid-programs os))
(%operating-system-setuid-programs os))
(service profile-service-type (operating-system-packages os)))))
(define* (operating-system-services os)
@ -1065,25 +1066,31 @@ use 'plain-file' instead~%")
;; TODO: Remove when glibc@2.23 is long gone.
("GUIX_LOCPATH" . "/run/current-system/locale")))
(define (operating-system-setuid-programs os)
"Return the setuid programs for OS, as a list of setuid-program record."
(map file-like->setuid-program
(%operating-system-setuid-programs os)))
(define %setuid-programs
;; Default set of setuid-root programs.
(let ((shadow (@ (gnu packages admin) shadow)))
(list (file-append shadow "/bin/passwd")
(file-append shadow "/bin/sg")
(file-append shadow "/bin/su")
(file-append shadow "/bin/newgrp")
(file-append shadow "/bin/newuidmap")
(file-append shadow "/bin/newgidmap")
(file-append inetutils "/bin/ping")
(file-append inetutils "/bin/ping6")
(file-append sudo "/bin/sudo")
(file-append sudo "/bin/sudoedit")
(file-append fuse "/bin/fusermount")
(map file-like->setuid-program
(list (file-append shadow "/bin/passwd")
(file-append shadow "/bin/sg")
(file-append shadow "/bin/su")
(file-append shadow "/bin/newgrp")
(file-append shadow "/bin/newuidmap")
(file-append shadow "/bin/newgidmap")
(file-append inetutils "/bin/ping")
(file-append inetutils "/bin/ping6")
(file-append sudo "/bin/sudo")
(file-append sudo "/bin/sudoedit")
(file-append fuse "/bin/fusermount")
;; To allow mounts with the "user" option, "mount" and "umount" must
;; be setuid-root.
(file-append util-linux "/bin/mount")
(file-append util-linux "/bin/umount"))))
;; To allow mounts with the "user" option, "mount" and "umount" must
;; be setuid-root.
(file-append util-linux "/bin/mount")
(file-append util-linux "/bin/umount")))))
(define %sudoers-specification
;; Default /etc/sudoers contents: 'root' and all members of the 'wheel'

57
gnu/system/setuid.scm 100644
View File

@ -0,0 +1,57 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2021 Brice Waegeneire <brice@waegenei.re>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu system setuid)
#:use-module (guix records)
#:export (setuid-program
setuid-program?
setuid-program-program
setuid-program-setuid?
setuid-program-setgid?
setuid-program-user
setuid-program-group
file-like->setuid-program))
;;; Commentary:
;;;
;;; Data structures representing setuid/setgid programs. This is meant to be
;;; used both on the host side and at run time--e.g., in activation snippets.
;;;
;;; Code:
(define-record-type* <setuid-program>
setuid-program make-setuid-program
setuid-program?
;; Path to program to link with setuid permissions
(program setuid-program-program) ;file-like
;; Whether to set user setuid bit
(setuid? setuid-program-setuid? ;boolean
(default #t))
;; Whether to set group setgid bit
(setgid? setuid-program-setgid? ;boolean
(default #f))
;; The user this should be set to (defaults to root)
(user setuid-program-user ;integer or string
(default 0))
;; Group we want to set this to (defaults to root)
(group setuid-program-group ;integer or string
(default 0)))
(define (file-like->setuid-program program)
(setuid-program (program program)))

4
guix/build-system/minify.scm
View File

@ -46,8 +46,8 @@
(define (default-uglify-js)
"Return the default package to minify JavaScript source files."
;; Lazily resolve the binding to avoid a circular dependency.
(let ((mod (resolve-interface '(gnu packages lisp-xyz))))
(module-ref mod 'uglify-js)))
(let ((mod (resolve-interface '(gnu packages uglifyjs))))
(module-ref mod 'uglifyjs)))
(define* (lower name
#:key source inputs native-inputs outputs system

2
guix/build/minify-build-system.scm
View File

@ -40,7 +40,7 @@
(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 <>))
(match (close-pipe minified)

47
guix/derivations.scm
View File

@ -241,32 +241,29 @@ the store."
"Return a list of inputs, such that when INPUTS contains the same DRV twice,
they are coalesced, with their sub-derivations merged. This is needed because
Nix itself keeps only one of them."
(define (find pred lst) ;inlinable copy of 'find'
(let loop ((lst lst))
(match lst
(() #f)
((head . tail)
(if (pred head) head (loop tail))))))
(define table
(make-hash-table 25))
(fold (lambda (input result)
(match input
(($ <derivation-input> (= derivation-file-name path) sub-drvs)
;; XXX: quadratic
(match (find (match-lambda
(($ <derivation-input> (= derivation-file-name p)
s)
(string=? p path)))
result)
(#f
(cons input result))
((and dup ($ <derivation-input> drv sub-drvs2))
;; Merge DUP with INPUT.
(let ((sub-drvs (delete-duplicates
(append sub-drvs sub-drvs2))))
(cons (make-derivation-input drv (sort sub-drvs string<?))
(delq dup result))))))))
'()
inputs))
(for-each (lambda (input)
(let* ((drv (derivation-input-path input))
(sub-drvs (derivation-input-sub-derivations input)))
(match (hash-get-handle table drv)
(#f
(hash-set! table drv input))
((and handle (key . ($ <derivation-input> drv sub-drvs2)))
;; Merge DUP with INPUT.
(let* ((sub-drvs (delete-duplicates
(append sub-drvs sub-drvs2)))
(input
(make-derivation-input drv
(sort sub-drvs string<?))))
(set-cdr! handle input))))))
inputs)
(hash-fold (lambda (key input lst)
(cons input lst))
'()
table))
(define* (derivation-prerequisites drv #:optional (cut? (const #f)))
"Return the list of derivation-inputs required to build DRV, recursively.

6
guix/import/print.scm
View File

@ -69,9 +69,9 @@ when evaluated."
(if var
(symbol-append 'license: var)
`(license
(name ,(license-name lic))
(uri ,(license-uri lic))
(comment ,(license-comment lic))))))
,(license-name lic)
,(license-uri lic)
,(license-comment lic)))))
(define (search-path-specification->code spec)
`(search-path-specification

1
guix/utils.scm
View File

@ -1090,7 +1090,6 @@ bound by MAX-COLUMN-WIDTH."
(map (cut min <> max-column-width)
column-widths)))
(fmt (string-append (string-join column-formats "\t") "\t~a")))
(setvbuf (current-output-port) 'block) ;for better performance
(for-each (cut format #t "~?~%" fmt <>) rows)))
;;; Local Variables: