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Merge branch 'master' into core-updates

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Conflicts:
	gnu/local.mk
	gnu/packages/backup.scm
	gnu/packages/emacs-xyz.scm
	gnu/packages/guile.scm
	gnu/packages/lisp.scm
	gnu/packages/openldap.scm
	gnu/packages/package-management.scm
	gnu/packages/web.scm
	gnu/packages/xorg.scm
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Marius Bakke 2020-04-30 23:47:49 +02:00
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7
doc/guix-cookbook.texi
View file

@ -13,6 +13,7 @@ Copyright @copyright{} 2019 Efraim Flashner@*
Copyright @copyright{} 2019 Pierre Neidhardt@*
Copyright @copyright{} 2020 Oleg Pykhalov@*
Copyright @copyright{} 2020 Matthew Brooks@*
Copyright @copyright{} 2020 Marcin Karpezo@*
Permission is granted to copy, distribute and/or modify this document
under the terms of the GNU Free Documentation License, Version 1.3 or
@ -1575,7 +1576,7 @@ available for inclusion into the initrd.
@cindex stumpwm
You could install StumpWM with a Guix system by adding
@code{stumpwm-checkout} and optionally @code{`(,stumpwm-checkout "lib")}
@code{stumpwm} and optionally @code{`(,stumpwm "lib")}
packages to a system configuration file, e.g.@: @file{/etc/config.scm}.
An example configuration can look like this:
@ -1586,7 +1587,7 @@ An example configuration can look like this:
(operating-system
;; …
(packages (append (list sbcl stumpwm-checkout `(,stumpwm-checkout "lib"))
(packages (append (list sbcl stumpwm `(,stumpwm "lib"))
%base-packages)))
@end lisp
@ -1601,7 +1602,7 @@ module @code{sbcl-stumpwm-ttf-fonts}, adding it to Guix system packages:
(operating-system
;; …
(packages (append (list sbcl stumpwm-checkout `(,stumpwm-checkout "lib"))
(packages (append (list sbcl stumpwm `(,stumpwm "lib"))
sbcl-stumpwm-ttf-fonts font-dejavu %base-packages)))
@end lisp

15
doc/guix.texi
View file

@ -63,7 +63,7 @@ Copyright @copyright{} 2018, 2019 Florian Pelz@*
Copyright @copyright{} 2018 Laura Lazzati@*
Copyright @copyright{} 2018 Alex Vong@*
Copyright @copyright{} 2019 Josh Holland@*
Copyright @copyright{} 2019 Diego Nicola Barbato@*
Copyright @copyright{} 2019, 2020 Diego Nicola Barbato@*
Copyright @copyright{} 2019 Ivan Petkov@*
Copyright @copyright{} 2019 Jakob L. Kreuze@*
Copyright @copyright{} 2019 Kyle Andrews@*
@ -5118,7 +5118,7 @@ guix pack -f squashfs bash guile emacs geiser
@noindent
The result is a SquashFS file system image that can either be mounted or
directly be used as a file system container image with the
@uref{https://singularity.lbl.gov, Singularity container execution
@uref{https://www.sylabs.io/docs/, Singularity container execution
environment}, using commands like @command{singularity shell} or
@command{singularity exec}.
@ -8830,7 +8830,7 @@ $ guix environment --no-grafts -C foo --ad-hoc strace gdb
Here, @command{guix environment -C} creates a container and spawns a new
shell in it (@pxref{Invoking guix environment}). The @command{--ad-hoc
strace gdb} part adds the @command{strace} and @command{gdb} commands to
the container, which would may find handy while debugging. The
the container, which you may find handy while debugging. The
@option{--no-grafts} option makes sure we get the exact same
environment, with ungrafted packages (@pxref{Security Updates}, for more
info on grafts).
@ -16289,6 +16289,13 @@ This is the type for the @uref{https://www.pulseaudio.org/, PulseAudio}
sound server. It exists to allow system overrides of the default settings
via @code{pulseaudio-configuration}, see below.
@quotation Warning
This service overrides per-user configuration files. If you want
PulseAudio to honor configuraton files in @file{~/.config/pulse} you
have to unset the environment variables @code{PULSE_CONFIG} and
@code{PULSE_CLIENTCONFIG} in your @file{~/.bash_profile}.
@end quotation
@quotation Warning
This service on its own does not ensure, that the @code{pulseaudio} package
exists on your machine. It merely adds configuration files for it, as
@ -26592,7 +26599,7 @@ like
@lisp
(bootloader
(grub-configuration
(bootloader-configuration
;; @dots{}
(theme (grub-theme
(inherit %default-theme)

3
gnu/local.mk
View file

@ -10,7 +10,7 @@
# Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
# Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
# Copyright © 2016, 2017, 2018, 2019 Alex Vong <alexvong1995@gmail.com>
# Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
# Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
# Copyright © 2016, 2017, 2018, 2019, 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
# Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
# Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
@ -875,6 +875,7 @@ dist_patch_DATA = \
%D%/packages/patches/emacs-magit-log-format-author-margin.patch \
%D%/packages/patches/emacs-scheme-complete-scheme-r5rs-info.patch \
%D%/packages/patches/emacs-source-date-epoch.patch \
%D%/packages/patches/emacs-telega-test-env.patch \
%D%/packages/patches/emacs-undohist-ignored.patch \
%D%/packages/patches/emacs-wordnut-require-adaptive-wrap.patch \
%D%/packages/patches/emacs-zones-called-interactively.patch \

14
gnu/packages/admin.scm
View file

@ -152,24 +152,22 @@ (define-public ktsuss
(list "--enable-sudo=yes")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-sudo-path
(lambda* (#:key inputs #:allow-other-keys)
(add-after 'unpack 'patch-file-names
(lambda _
(substitute* "configure.ac"
(("supath=`which su 2>/dev/null`")
"supath=/run/setuid-programs/su")
(("sudopath=`which sudo 2>/dev/null`")
(string-append "sudopath="
(string-append (assoc-ref inputs "sudo")
"/bin/sudo"))))
"sudopath=/run/setuid-programs/sudo"))
#t)))))
(native-inputs
`(("autoconf" ,autoconf)
("autogen" ,autogen)
("automake" ,automake)
("libtool" ,libtool)
("pkg-config" ,pkg-config)))
(inputs
`(("glib" ,glib)
("gtk+" ,gtk+-2)
("sudo" ,sudo)))
("gtk+" ,gtk+-2)))
(synopsis "Graphical front end for @command{su}")
(description
"Ktsuss stands for ``Keep the @command{su} simple, stupid''.

8
gnu/packages/aspell.scm
View file

@ -8,6 +8,7 @@
;;; Copyright © 2016, 2017, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Jens Mølgaard <jens@zete.tk>
;;; Copyright © 2020 Timotej Lazar <timotej.lazar@araneo.si>
;;; Copyright © 2020 Marcin Karpezo <sirmacik@wioo.waw.pl>
;;;
;;; This file is part of GNU Guix.
;;;
@ -289,6 +290,13 @@ (define-public aspell-dict-nn
(base32
"0w2k5l5rbqpliripgqwiqixz5ghnjf7i9ggbrc4ly4vy1ia10rmc")))
(define-public aspell-dict-pl
(aspell-dictionary "pl" "Polish"
#:version "0.51-0"
#:sha256
(base32
"1a3ccji6k5gys7l3ilr2lh5pzxgzb7ipc5vb737svl6nqgdy8757")))
(define-public aspell-dict-pt-br
(aspell-dictionary "pt_BR" "Brazilian Portuguese"
#:version "20131030-12-0"

4
gnu/packages/astronomy.scm
View file

@ -157,7 +157,7 @@ (define-public gnuastro
(define-public stellarium
(package
(name "stellarium")
(version "0.19.3")
(version "0.20.1")
(source
(origin
(method url-fetch)
@ -165,7 +165,7 @@ (define-public stellarium
"/releases/download/v" version
"/stellarium-" version ".tar.gz"))
(sha256
(base32 "0p92rgclag0nkic9gk3p9vclb8xx9hv4zlgyij6cyh43s7c1avhp"))))
(base32 "034jkrdaaamvbrkfwi3qcl6h8hwfnw2nvf7a82faj55rskcpnkhm"))))
(build-system cmake-build-system)
(inputs
`(("qtbase" ,qtbase)

4
gnu/packages/audio.scm
View file

@ -1979,14 +1979,14 @@ (define-public lilv
(define-public lv2
(package
(name "lv2")
(version "1.16.0")
(version "1.18.0")
(source (origin
(method url-fetch)
(uri (string-append "http://lv2plug.in/spec/lv2-"
version ".tar.bz2"))
(sha256
(base32
"1ppippbpdpv13ibs06b0bixnazwfhiw0d0ja6hx42jnkgdyp5hyy"))))
"0gs7401xz23q9vajqr31aa2db8dvssgyh5zrvr4ipa6wig7yb8wh"))))
(build-system waf-build-system)
(arguments
`(#:tests? #f ; no check target

41
gnu/packages/backup.scm
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@ -11,10 +11,11 @@
;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2018 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2019 Alex Vong <alexvong1995@gmail.com>
;;; Copyright © 2019 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@ -37,6 +38,7 @@ (define-module (gnu packages backup)
#:use-module (guix git-download)
#:use-module (guix download)
#:use-module (guix utils)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system go)
#:use-module (guix build-system python)
@ -64,6 +66,7 @@ (define-module (gnu packages backup)
#:use-module (gnu packages pcre)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
@ -987,6 +990,42 @@ (define-public restic
@end itemize")
(license license:bsd-2)))
(define-public zbackup
(package
(name "zbackup")
(version "1.4.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/zbackup/zbackup.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "14l1kyxg7pccpax3d6qcpmdycb70kn3fxp1a59w64hqy2493hngl"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f)) ;no test
(inputs
`(("lzo" ,lzo)
("libressl" ,libressl)
("protobuf" ,protobuf)
("xz" ,xz)
("zlib" ,zlib)))
(home-page "http://zbackup.org")
(synopsis "Versatile deduplicating backup tool")
(description
"ZBackup is a globally-deduplicating backup tool, based on the
ideas found in Rsync. Feed a large @file{.tar} into it, and it will
store duplicate regions of it only once, then compress and optionally
encrypt the result. Feed another @file{.tar} file, and it will also
re-use any data found in any previous backups. This way only new
changes are stored, and as long as the files are not very different,
the amount of storage required is very low. Any of the backup files
stored previously can be read back in full at any time. The program
is format-agnostic, so you can feed virtually any files to it.")
(license license:gpl2+)))
(define-public burp
(package
(name "burp")

278
gnu/packages/bioconductor.scm
View file

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
;;;
@ -493,6 +493,30 @@ (define-public r-bsgenome-hsapiens-ucsc-hg19
by UCSC (hg19, February 2009) and stored in Biostrings objects.")
(license license:artistic2.0)))
(define-public r-bsgenome-hsapiens-ucsc-hg38
(package
(name "r-bsgenome-hsapiens-ucsc-hg38")
(version "1.4.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
version 'annotation))
(sha256
(base32
"1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
(properties
`((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
(build-system r-build-system)
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
"https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
(synopsis "Full genome sequences for Homo sapiens")
(description
"This package provides full genome sequences for Homo sapiens (Human)
as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
(license license:artistic2.0)))
(define-public r-ensdb-hsapiens-v75
(package
(name "r-ensdb-hsapiens-v75")
@ -718,6 +742,30 @@ (define-public r-illuminahumanmethylationepicmanifest
"This is a manifest package for Illumina's EPIC methylation arrays.")
(license license:artistic2.0)))
(define-public r-ideoviz
(package
(name "r-ideoviz")
(version "1.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IdeoViz" version))
(sha256
(base32
"0rsz6dawrx5qdrypxs2hgihmx3kbpdg1y73h876yxccgdlabvzil"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-iranges" ,r-iranges)
("r-genomicranges" ,r-genomicranges)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-rtracklayer" ,r-rtracklayer)
("r-genomeinfodb" ,r-genomeinfodb)))
(home-page "https://bioconductor.org/packages/IdeoViz/")
(synopsis "Plots data along a chromosomal ideogram")
(description "This package provides functions to plot data associated with
arbitrary genomic intervals along chromosomal ideogram.")
(license license:gpl2)))
;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
;; from Bioconductor.
(define-public r-deconstructsigs
@ -811,6 +859,32 @@ (define-public r-do-db
Disease Ontology.")
(license license:artistic2.0)))
(define-public r-pasilla
(package
(name "r-pasilla")
(version "1.14.0")
(source (origin
(method url-fetch)
(uri (string-append
"http://bioconductor.org/packages/release/data/experiment"
"/src/contrib/pasilla_" version ".tar.gz"))
(sha256
(base32
"0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocstyle" ,r-biocstyle)
("r-dexseq" ,r-dexseq)
("r-knitr" ,r-knitr)
("r-rmarkdown" ,r-rmarkdown)))
(home-page "https://www.bioconductor.org/packages/pasilla/")
(synopsis "Data package with per-exon and per-gene read counts")
(description "This package provides per-exon and per-gene read counts
computed for selected genes from RNA-seq data that were presented in the
article 'Conservation of an RNA regulatory map between Drosophila and mammals'
by Brooks et al., Genome Research 2011.")
(license license:lgpl2.1+)))
(define-public r-pfam-db
(package
(name "r-pfam-db")
@ -995,6 +1069,63 @@ (define-public r-affydata
package @code{affy}.")
(license license:gpl2+)))
(define-public r-coverageview
(package
(name "r-coverageview")
(version "1.24.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CoverageView" version))
(sha256
(base32
"0s47svs7xnr9jkylq0dxidqrigihdddiprcl0951vjr4w7kmb5nf"))))
(build-system r-build-system)
(propagated-inputs
`(("r-s4vectors" ,r-s4vectors)
("r-iranges" ,r-iranges)
("r-genomicranges" ,r-genomicranges)
("r-genomicalignments" ,r-genomicalignments)
("r-rtracklayer" ,r-rtracklayer)
("r-rsamtools" ,r-rsamtools)))
(home-page "https://bioconductor.org/packages/CoverageView/")
(synopsis "Coverage visualization package for R")
(description "This package provides a framework for the visualization of
genome coverage profiles. It can be used for ChIP-seq experiments, but it can
be also used for genome-wide nucleosome positioning experiments or other
experiment types where it is important to have a framework in order to inspect
how the coverage distributed across the genome.")
(license license:artistic2.0)))
(define-public r-cummerbund
(package
(name "r-cummerbund")
(version "2.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "cummeRbund" version))
(sha256
(base32
"1fjc3bcclm4gsvw4nq6cv3a1kbrldvrxbkyfb9306708si1n4dwk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-fastcluster", r-fastcluster)
("r-ggplot2" ,r-ggplot2)
("r-gviz" ,r-gviz)
("r-plyr" ,r-plyr)
("r-reshape2" ,r-reshape2)
("r-rsqlite" ,r-rsqlite)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)))
(home-page "https://bioconductor.org/packages/cummeRbund/")
(synopsis "Analyze Cufflinks high-throughput sequencing data")
(description "This package allows for persistent storage, access,
exploration, and manipulation of Cufflinks high-throughput sequencing
data. In addition, provides numerous plotting functions for commonly
used visualizations.")
(license license:artistic2.0)))
(define-public r-curatedtcgadata
(package
(name "r-curatedtcgadata")
@ -2533,6 +2664,41 @@ (define-public r-ebseq
gene and isoform level using RNA-seq data")
(license license:artistic2.0)))
(define-public r-karyoploter
(package
(name "r-karyoploter")
(version "1.12.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "karyoploteR" version))
(sha256
(base32
"03jmfgmw35hrgn3pc5lq6pblzhfx9fp4l6dx50rp303lr7kjxp9v"))))
(build-system r-build-system)
(propagated-inputs
`(("r-regioner" ,r-regioner)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-rsamtools" ,r-rsamtools)
("r-memoise" ,r-memoise)
("r-rtracklayer" ,r-rtracklayer)
("r-genomeinfodb" ,r-genomeinfodb)
("r-s4vectors" ,r-s4vectors)
("r-biovizbase" ,r-biovizbase)
("r-digest" ,r-digest)
("r-bezier" ,r-bezier)
("r-bamsignals" ,r-bamsignals)
("r-annotationdbi" ,r-annotationdbi)
("r-variantannotation" ,r-variantannotation)))
(home-page "https://bioconductor.org/packages/karyoploteR/")
(synopsis "Plot customizable linear genomes displaying arbitrary data")
(description "This package creates karyotype plots of arbitrary genomes and
offers a complete set of functions to plot arbitrary data on them. It mimicks
many R base graphics functions coupling them with a coordinate change function
automatically mapping the chromosome and data coordinates into the plot
coordinates.")
(license license:artistic2.0)))
(define-public r-lpsymphony
(package
(name "r-lpsymphony")
@ -3972,6 +4138,78 @@ (define-public r-motiv
distributions, modules and filter motifs.")
(license license:gpl2)))
(define-public r-motifdb
(package
(name "r-motifdb")
(version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "MotifDb" version))
(sha256
(base32 "0m5apkjlvdq9yhjdyds3hivfnkbm6f059hy2bkjhalrlhd2si2jc"))))
(properties `((upstream-name . "MotifDb")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-biostrings" ,r-biostrings)
("r-iranges" ,r-iranges)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-splitstackshape" ,r-splitstackshape)))
(home-page "https://www.bioconductor.org/packages/MotifDb/")
(synopsis "Annotated collection of protein-DNA binding sequence motifs")
(description "This package provides more than 2000 annotated position
frequency matrices from nine public sources, for multiple organisms.")
(license license:artistic2.0)))
(define-public r-motifbreakr
(package
(name "r-motifbreakr")
(version "2.0.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "motifbreakR" version))
(sha256
(base32 "190z8gj393qdpq5wz7gph96k0l8c1j9wd0p0llscysvk5kr1hf9n"))))
(properties `((upstream-name . "motifbreakR")))
(build-system r-build-system)
(propagated-inputs
`(("r-grimport" ,r-grimport)
("r-stringr" ,r-stringr)
("r-biocgenerics" ,r-biocgenerics)
("r-s4vectors" ,r-s4vectors)
("r-iranges" ,r-iranges)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicranges" ,r-genomicranges)
("r-biostrings" ,r-biostrings)
("r-bsgenome" ,r-bsgenome)
("r-rtracklayer" ,r-rtracklayer)
("r-variantannotation" ,r-variantannotation)
("r-biocparallel" ,r-biocparallel)
("r-motifstack" ,r-motifstack)
("r-gviz" ,r-gviz)
("r-matrixstats" ,r-matrixstats)
("r-tfmpvalue" ,r-tfmpvalue)
("r-motifdb" ,r-motifdb)))
(home-page "https://www.bioconductor.org/packages/motifbreakR/")
(synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
(description "This package allows biologists to judge in the first place
whether the sequence surrounding the polymorphism is a good match, and in
the second place how much information is gained or lost in one allele of
the polymorphism relative to another. This package gives a choice of
algorithms for interrogation of genomes with motifs from public sources:
@enumerate
@item a weighted-sum probability matrix;
@item log-probabilities;
@item weighted by relative entropy.
@end enumerate
This package can predict effects for novel or previously described variants in
public databases, making it suitable for tasks beyond the scope of its original
design. Lastly, it can be used to interrogate any genome curated within
Bioconductor.")
(license license:gpl2+)))
(define-public r-motifstack
(package
(name "r-motifstack")
@ -6368,6 +6606,44 @@ (define-public r-seqbias
genome sequence.")
(license license:lgpl3)))
(define-public r-snplocs-hsapiens-dbsnp144-grch37
(package
(name "r-snplocs-hsapiens-dbsnp144-grch37")
(version "0.99.20")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
version 'annotation))
(sha256
(base32
"1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
(build-system r-build-system)
;; As this package provides little more than a very large data file it
;; doesn't make sense to build substitutes.
(arguments `(#:substitutable? #f))
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-s4vectors" ,r-s4vectors)
("r-iranges" ,r-iranges)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicranges" ,r-genomicranges)
("r-bsgenome" ,r-bsgenome)
("r-biostrings" ,r-biostrings)))
(home-page
"https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
(synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
(description "This package provides SNP locations and alleles for Homo
sapiens extracted from NCBI dbSNP Build 144. The source data files used for
this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
the mitochondrion chromosome. Therefore, the SNPs in this package can be
injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
correct position but this injection will exclude chrM (i.e. nothing will be
injected in that sequence).")
(license license:artistic2.0)))
(define-public r-reqon
(package
(name "r-reqon")

169
gnu/packages/bioinformatics.scm
View file

@ -3,7 +3,7 @@
;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
@ -2334,6 +2334,62 @@ (define-public python-dnaio
files. The code was previously part of the cutadapt tool.")
(license license:expat)))
(define-public python-deeptoolsintervals
(package
(name "python-deeptoolsintervals")
(version "0.1.9")
(source (origin
(method url-fetch)
(uri (pypi-uri "deeptoolsintervals" version))
(sha256
(base32
"1xnl80nblysj6dylj4683wgrfa425rkx4dp5k65hvwdns9pw753x"))))
(build-system python-build-system)
(inputs
`(("zlib" ,zlib)))
(home-page "https://github.com/deeptools/deeptools_intervals")
(synopsis "Create GTF-based interval trees with associated meta-data")
(description
"This package provides a Python module creating/accessing GTF-based
interval trees with associated meta-data. It is primarily used by the
@code{deeptools} package.")
(license license:expat)))
(define-public python-deeptools
(package
(name "python-deeptools")
(version "3.4.3")
(source (origin
(method url-fetch)
(uri (pypi-uri "deepTools" version))
(sha256
(base32
"1azgjniss5ff6a90nicdjkxyjwqmi3gzfn09gra42hwlz19hipxb"))))
(build-system python-build-system)
(propagated-inputs
`(("python-matplotlib" ,python-matplotlib)
("python-numpy" ,python-numpy)
("python-numpydoc" ,python-numpydoc)
("python-py2bit" ,python-py2bit)
("python-pybigwig" ,python-pybigwig)
("python-pysam" ,python-pysam)
("python-scipy" ,python-scipy)
("python-deeptoolsintervals" ,python-deeptoolsintervals)
("python-plotly" ,python-plotly)))
(home-page "https://pypi.org/project/deepTools/")
(synopsis "Useful tools for exploring deep sequencing data")
(description "This package addresses the challenge of handling large amounts
of data that are now routinely generated from DNA sequencing centers.
@code{deepTools} contains useful modules to process the mapped reads data for
multiple quality checks, creating normalized coverage files in standard bedGraph
and bigWig file formats, that allow comparison between different files. Finally,
using such normalized and standardized files, deepTools can create many
publication-ready visualizations to identify enrichments and for functional
annotations of the genome.")
;; The file deeptools/cm.py is licensed under the BSD license. The
;; remainder of the code is licensed under the MIT license.
(license (list license:bsd-3 license:expat))))
(define-public cutadapt
(package
(name "cutadapt")
@ -4886,14 +4942,24 @@ (define-public python2-warpedlmm
"1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2)) ; requires Python 2.7
`(#:python ,python-2 ; requires Python 2.7
#:tests? #f ; test data are not included
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'use-weave
(lambda _
(substitute* "warpedlmm/util/linalg.py"
(("from scipy import linalg, weave")
"from scipy import linalg\nimport weave"))
#t)))))
(propagated-inputs
`(("python-scipy" ,python2-scipy)
("python-numpy" ,python2-numpy)
("python-matplotlib" ,python2-matplotlib)
("python-fastlmm" ,python2-fastlmm)
("python-pandas" ,python2-pandas)
("python-pysnptools" ,python2-pysnptools)))
("python-pysnptools" ,python2-pysnptools)
("python-weave" ,python2-weave)))
(native-inputs
`(("python-mock" ,python2-mock)
("python-nose" ,python2-nose)
@ -9102,6 +9168,46 @@ (define-public multiqc
common bioinformatics tools.")
(license license:gpl3+)))
(define-public variant-tools
(package
(name "variant-tools")
(version "3.1.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/vatlab/varianttools.git")
;; There is no tag corresponding to version 3.1.2
(commit "813ae4a90d25b69abc8a40f4f70441fe09015249")))
(file-name (git-file-name name version))
(sha256
(base32
"12ibdmksj7icyqhks4xyvd61bygk4pjmxn618kp6vgk1af01y34g"))))
(build-system python-build-system)
(inputs
`(("boost" ,boost)
("c-blosc" ,c-blosc)
("gsl" ,gsl)
("hdf5" ,hdf5)
("hdf5-blosc" ,hdf5-blosc)
("python-cython" ,python-cython)
("zlib" ,zlib)))
(propagated-inputs
`(("python-numpy" ,python-numpy)
("python-pycurl" ,python-pycurl)
("python-pyzmq" ,python-pyzmq)
("python-scipy" ,python-scipy)
("python-tables" ,python-tables)))
(home-page "https://vatlab.github.io/vat-docs/")
(synopsis "Analyze genetic variants from Next-Gen sequencing studies")
(description
"Variant tools is a tool for the manipulation, annotation,
selection, simulation, and analysis of variants in the context of next-gen
sequencing analysis. Unlike some other tools used for next-gen sequencing
analysis, variant tools is project based and provides a whole set of tools to
manipulate and analyze genetic variants.")
(license license:gpl3+)))
(define-public r-chipseq
(package
(name "r-chipseq")
@ -9660,13 +9766,13 @@ (define-public r-msnid
(define-public r-seurat
(package
(name "r-seurat")
(version "3.1.4")
(version "3.1.5")
(source (origin
(method url-fetch)
(uri (cran-uri "Seurat" version))
(sha256
(base32
"0lhjbjhv1hnx5i3gkx41k68i8ykay3f24708h30wx9xywww9lsvi"))))
"1lbq2pqhb6ih6iqawlnzdh05zff71pwbw1cpfv2sld3pd7kz0zkm"))))
(properties `((upstream-name . "Seurat")))
(build-system r-build-system)
(propagated-inputs
@ -9688,7 +9794,6 @@ (define-public r-seurat
("r-lmtest" ,r-lmtest)
("r-mass" ,r-mass)
("r-matrix" ,r-matrix)
("r-metap" ,r-metap)
("r-patchwork" ,r-patchwork)
("r-pbapply" ,r-pbapply)
("r-plotly" ,r-plotly)
@ -10634,14 +10739,14 @@ (define-public r-hitc
(define-public r-hdf5array
(package
(name "r-hdf5array")
(version "1.14.3")
(version "1.14.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "HDF5Array" version))
(sha256
(base32
"1z153a7nxmlml72pl1saasj2il9g5ahpynkpv3mkhhsvl5kbwbh6"))))
"0ib0grhd9zbrn0dkrm4aa7qj7h0y6z1dvyx1ab3w6vczw7xghsfb"))))
(properties `((upstream-name . "HDF5Array")))
(build-system r-build-system)
(inputs
@ -13152,7 +13257,7 @@ (define-public sjcount
(define-public minimap2
(package
(name "minimap2")
(version "2.10")
(version "2.17")
(source
(origin
(method url-fetch)
@ -13161,7 +13266,7 @@ (define-public minimap2
"minimap2-" version ".tar.bz2"))
(sha256
(base32
"080w9066irkbhbyr4nmf19pzkdd2s4v31hpzlajgq2y0drr6zcsj"))))
"0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are none
@ -13208,6 +13313,42 @@ (define-public minimap2
@end enumerate\n")
(license license:expat)))
(define-public miniasm
(package
(name "miniasm")
(version "0.3")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/lh3/miniasm/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0g89pa98dvh34idv7w1zv12bsbyr3a11c4qb1cdcz68gyda88s4v"))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)))
(arguments
`(#:tests? #f ; There are no tests.
#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "miniasm" bin)
(install-file "minidot" bin)))))))
(home-page "https://github.com/lh3/miniasm")
(synopsis "Ultrafast de novo assembly for long noisy reads")
(description "Miniasm is a very fast OLC-based de novo assembler for noisy
long reads. It takes all-vs-all read self-mappings (typically by minimap) as
input and outputs an assembly graph in the GFA format. Different from
mainstream assemblers, miniasm does not have a consensus step. It simply
concatenates pieces of read sequences to generate the final unitig sequences.
Thus the per-base error rate is similar to the raw input reads.")
(license license:expat)))
(define-public r-circus
(package
(name "r-circus")
@ -13366,14 +13507,14 @@ (define-public find-circ
(define-public python-scanpy
(package
(name "python-scanpy")
(version "1.4.5.1")
(version "1.4.6")
(source
(origin
(method url-fetch)
(uri (pypi-uri "scanpy" version))
(sha256
(base32
"14kh1ji70xxhmri5q8sgcibsidhr6f221wxrcw8a5xvibj5da17j"))))
"0s2b6cvaigx4wzw3850qb93sjwwxbzh22kpbp498zklc5rjpbz4l"))))
(build-system python-build-system)
(arguments
`(#:phases
@ -13383,6 +13524,7 @@ (define-public python-scanpy
;; These tests require Internet access.
(delete-file-recursively "scanpy/tests/notebooks")
(delete-file "scanpy/tests/test_clustering.py")
(delete-file "scanpy/tests/test_datasets.py")
;; TODO: I can't get the plotting tests to work, even with Xvfb.
(delete-file "scanpy/tests/test_plotting.py")
@ -13399,8 +13541,8 @@ (define-public python-scanpy
("python-h5py" ,python-h5py)
("python-igraph" ,python-igraph)
("python-joblib" ,python-joblib)
("python-louvain" ,python-louvain)
("python-legacy-api-wrap" ,python-legacy-api-wrap)
("python-louvain" ,python-louvain)
("python-matplotlib" ,python-matplotlib)
("python-natsort" ,python-natsort)
("python-networkx" ,python-networkx)
@ -13413,6 +13555,7 @@ (define-public python-scanpy
("python-seaborn" ,python-seaborn)
("python-statsmodels" ,python-statsmodels)
("python-tables" ,python-tables)
("python-tqdm" ,python-tqdm)
("python-umap-learn" ,python-umap-learn)))
(native-inputs
`(("python-pytest" ,python-pytest)

8
gnu/packages/chromium.scm
View file

@ -248,8 +248,8 @@ (define* (computed-origin-method gexp-promise hash-algo hash
#:system system
#:guile-for-build guile)))
(define %chromium-version "81.0.4044.122")
(define %ungoogled-revision "31d6e60c96481599b42072b4489e4468280198e3")
(define %chromium-version "81.0.4044.129")
(define %ungoogled-revision "c2a89fb6b5b559c826796c811741fa8ed3e11de8")
(define %debian-revision "debian/81.0.4044.92-1")
(define package-revision "0")
(define %package-version (string-append %chromium-version "-"
@ -264,7 +264,7 @@ (define %chromium-origin
%chromium-version ".tar.xz"))
(sha256
(base32
"0ahqh3vmzbpai4xwn7qybgw9phc8ssjdvfc7384mxqk9swqgv7qg"))))
"1ls663s1f74p912x42qp3zcvm17kmjiv1ij6yy1c14gdhcpmjx7z"))))
(define %ungoogled-origin
(origin
@ -275,7 +275,7 @@ (define %ungoogled-origin
(string-take %ungoogled-revision 7)))
(sha256
(base32
"1pj2vmzb2fagvypjsjn2kqf5n5k8vnhbisyb0snr6wqvpv09x0vv"))))
"0bbr4a2gkgm3ykdgpj8x58sd3dwam6qkifhzfs2997681g7b2v2q"))))
(define %debian-origin
(origin

65
gnu/packages/compression.scm
View file

@ -4,7 +4,7 @@
;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2015, 2016 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016, 2017, 2018, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2017, 2018 Leo Famulari <leo@famulari.name>
;;; Copyright © 2015 Jeff Mickey <j@codemac.net>
;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
@ -27,6 +27,7 @@
;;; Copyright © 2019 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2020 Lars-Dominik Braun <lars@6xq.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -52,6 +53,7 @@ (define-module (gnu packages compression)
#:use-module (guix build-system cmake)
#:use-module (guix build-system glib-or-gtk)
#:use-module (guix build-system gnu)
#:use-module (guix build-system go)
#:use-module (guix build-system python)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
@ -2126,3 +2128,64 @@ (define-public xarchiver
RAR, RPM, DEB, tar, and ZIP. It cannot perform functions for archives, whose
archiver is not installed.")
(license license:gpl2+)))
(define-public tarsplitter
(package
(name "tarsplitter")
(version "2.2.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/AQUAOSOTech/tarsplitter.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"17qkg95r97kcrs17b0mcqswx99280ni47j5yx8xa7nl3bdhm6325"))))
(build-system go-build-system)
(arguments
`(#:import-path "github.com/AQUAOSOTech/tarsplitter"
#:install-source? #f
#:phases
(modify-phases %standard-phases
(add-after 'install 'install-documentation
(lambda* (#:key import-path outputs #:allow-other-keys)
(let* ((source (string-append "src/" import-path))
(out (assoc-ref outputs "out"))
(doc (string-append out "/share/doc/" ,name "-" ,version)))
(with-directory-excursion source
(install-file "README.md" doc))
#t))))))
(home-page "https://github.com/AQUAOSOTech/tarsplitter")
(synopsis "Multithreaded tar utility")
(description
"Archive huge numbers of files, or split massive tar archives into smaller
chunks.")
(license license:expat)))
(define-public c-blosc
(package
(name "c-blosc")
(version "1.18.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Blosc/c-blosc.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1ywq8j70149859vvs19wgjq89d6xsvvmvm2n1dmkzpchxgrvnw70"))))
(build-system cmake-build-system)
(home-page "https://blosc.org")
(synopsis "Blocking, shuffling and lossless compression library")
(description
"Blosc is a high performance compressor optimized for binary data. It has
been designed to transmit data to the processor cache faster than the
traditional, non-compressed, direct memory fetch approach via a
@code{memcpy()} system call. Blosc is meant not only to reduce the size of
large datasets on-disk or in-memory, but also to accelerate memory-bound
computations.")
;; Blosc itself is released under BSD-3 but it incorporates code under
;; other non-copyleft licenses.
(license license:bsd-3)))

427
gnu/packages/cran.scm
View file

@ -2,7 +2,7 @@
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
@ -83,6 +83,25 @@ (define-module (gnu packages cran)
#:use-module (gnu packages web)
#:use-module (gnu packages xorg))
(define-public r-bezier
(package
(name "r-bezier")
(version "1.1.2")
(source (origin
(method url-fetch)
(uri (cran-uri "bezier" version))
(sha256
(base32
"1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/bezier/")
(synopsis "Bezier curve and spline toolkit")
(description
"This package is a toolkit for working with Bezier curves and splines.
The package provides functions for point generation, arc length estimation,
degree elevation and curve fitting.")
(license license:gpl2+)))
(define-public r-clipr
(package
(name "r-clipr")
@ -102,6 +121,36 @@ (define-public r-clipr
the system clipboards.")
(license license:gpl3)))
(define-public r-ggpmisc
(package
(name "r-ggpmisc")
(version "0.3.4")
(source (origin
(method url-fetch)
(uri (cran-uri "ggpmisc" version))
(sha256
(base32
"0xc1yp0kphipq23ri4ij93garx1x2nrf4i0lhs6m10pp9yz7fbmj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
("r-dplyr" ,r-dplyr)
("r-ggplot2" ,r-ggplot2)
("r-gridextra" ,r-gridextra)
("r-lubridate" ,r-lubridate)
("r-mass" ,r-mass)
("r-plyr" ,r-plyr)
("r-polynom" ,r-polynom)
("r-splus2r" ,r-splus2r)
("r-tibble" ,r-tibble)
("r-xts" ,r-xts)
("r-zoo" ,r-zoo)))
(home-page "https://www.r4photobiology.info/")
(synopsis "Miscellaneous Extensions to @code{ggplot2}")
(description "This package provides extensions to @code{ggplot2},
respecting the grammar of its graphics paradigm.")
(license license:gpl2+)))
(define-public r-oenb
(package
(name "r-oenb")
@ -177,6 +226,30 @@ (define-public r-pheatmap
control over dimensions and appearance.")
(license license:gpl2+)))
(define-public r-ecp
(package
(name "r-ecp")
(version "3.1.2")
(source (origin
(method url-fetch)
(uri (cran-uri "ecp" version))
(sha256
(base32
"11f9p869xr0zg779i46gmflxlq4xclk9wxbab0nj2fan26pn4sfy"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)))
(home-page "https://cran.r-project.org/web/packages/ecp/")
(synopsis "Multiple change-point analysis of multivariate data")
(description
"This package implements various procedures for finding multiple
change-points. Two methods make use of dynamic programming and pruning, with
no distributional assumptions other than the existence of certain absolute
moments in one method. Hierarchical and exact search methods are included.
All methods return the set of estimated change-points as well as other summary
information.")
(license license:gpl2+)))
(define-public r-ellipsis
(package
(name "r-ellipsis")
@ -449,6 +522,27 @@ (define-public r-reprex
such as copy/paste from an R session.")
(license license:expat)))
(define-public r-reordercluster
(package
(name "r-reordercluster")
(version "1.0")
(source (origin
(method url-fetch)
(uri (cran-uri "ReorderCluster" version))
(sha256
(base32
"0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
(build-system r-build-system)
(propagated-inputs
`(("r-gplots" ,r-gplots)
("r-rcpp" ,r-rcpp)))
(home-page "https://cran.r-project.org/web/packages/ReorderCluster")
(synopsis "Reordering the dendrogram according to the class labels")
(description "This package provides tools for performing the leaf reordering
for the dendrogram that preserves the hierarchical clustering result and at the
same time tries to group instances from the same class together.")
(license license:gpl3+)))
(define-public r-callr
(package
(name "r-callr")
@ -1027,13 +1121,13 @@ (define-public r-shinydashboard
(define-public r-shinyfiles
(package
(name "r-shinyfiles")
(version "0.7.5")
(version "0.8.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "shinyFiles" version))
(sha256
(base32 "1143m941hma9hc77c3xcw26c0ygfhn9ii2sbp9wrydxv4gc7mr8a"))))
(base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
(properties `((upstream-name . "shinyFiles")))
(build-system r-build-system)
(propagated-inputs
@ -1677,13 +1771,13 @@ (define-public r-ps
(define-public r-pkgbuild
(package
(name "r-pkgbuild")
(version "1.0.6")
(version "1.0.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "pkgbuild" version))
(sha256
(base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx"))))
(base32 "0wd9678yp6yi73n92f58wi9jc19gdq5cmbj65l6pifh2haikifr9"))))
(build-system r-build-system)
(propagated-inputs
`(("r-callr" ,r-callr)
@ -1910,17 +2004,19 @@ (define-public r-circlize
(define-public r-powerlaw
(package
(name "r-powerlaw")
(version "0.70.4")
(version "0.70.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "poweRlaw" version))
(sha256
(base32 "19zah9mx93az5lh9vicn3c8q1xb12g0w46dh5p901fbyimc32vwk"))))
(base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
(properties `((upstream-name . "poweRlaw")))
(build-system r-build-system)
(propagated-inputs
`(("r-vgam" ,r-vgam)))
`(("r-pracma" ,r-pracma)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/csgillespie/poweRlaw")
(synopsis "Tools for the analysis of heavy tailed distributions")
(description
@ -2029,14 +2125,14 @@ (define-public r-fastmatch
(define-public r-ff
(package
(name "r-ff")
(version "2.2-14")
(version "2.2-14.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "ff" version))
(sha256
(base32
"1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
"1r1pbrf5s4rdm3msxxr8fy1f2xjihqciclsnvxf59qzz6g1nmh7q"))))
(build-system r-build-system)
(propagated-inputs `(("r-bit" ,r-bit)))
(home-page "http://ff.r-forge.r-project.org/")
@ -2176,14 +2272,14 @@ (define-public r-ggally
(define-public r-proxy
(package
(name "r-proxy")
(version "0.4-23")
(version "0.4-24")
(source
(origin
(method url-fetch)
(uri (cran-uri "proxy" version))
(sha256
(base32
"17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
"0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/proxy")
(synopsis "Distance and similarity measures")
@ -2293,14 +2389,14 @@ (define-public r-lmoments
(define-public r-distillery
(package
(name "r-distillery")
(version "1.0-6")
(version "1.0-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "distillery" version))
(sha256
(base32
"1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
"0w72vb3p51m0hwms9icwgy1xg3dplmpjrxibl2s92lpdrv737249"))))
(build-system r-build-system)
(home-page "https://ral.ucar.edu/staff/ericg/")
(synopsis "Functions for confidence intervals and object information")
@ -2400,6 +2496,27 @@ (define-public r-inline
;; Any version of the LGPL.
(license license:lgpl3+)))
(define-public r-inum
(package
(name "r-inum")
(version "1.0-1")
(source (origin
(method url-fetch)
(uri (cran-uri "inum" version))
(sha256
(base32
"16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
(build-system r-build-system)
(propagated-inputs
`(("r-libcoin" ,r-libcoin)))
(home-page "https://cran.r-project.org/web/packages/inum/")
(synopsis "Interval and enum-type representation of vectors")
(description
"This package provides an enum-type representation of vectors and
representation of intervals, including a method of coercing variables
in data frames.")
(license license:gpl2)))
(define-public r-bdsmatrix
(package
(name "r-bdsmatrix")
@ -3105,14 +3222,14 @@ (define-public r-generics
(define-public r-broom
(package
(name "r-broom")
(version "0.5.5")
(version "0.5.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "broom" version))
(sha256
(base32
"0n7zd64263kfavdi28rl2bxrsa00c3m4vjhhjdrfwvvmrcxj39fx"))))
"0da3jsb02xckrk6alznicn6l5lnyvdhc64qklyarnd77miqgc1hb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-backports" ,r-backports)
@ -3124,6 +3241,8 @@ (define-public r-broom
("r-stringr" ,r-stringr)
("r-tibble" ,r-tibble)
("r-tidyr" ,r-tidyr)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/tidyverse/broom")
(synopsis "Convert statistical analysis objects into tidy data frames")
(description
@ -3926,14 +4045,14 @@ (define-public r-processx
(define-public r-tsp
(package
(name "r-tsp")
(version "1.1-9")
(version "1.1-10")
(source
(origin
(method url-fetch)
(uri (cran-uri "TSP" version))
(sha256
(base32
"183m6crb0dv17llj86059n3hbgsahbhfcqlx0ijdzkssg11i1cy7"))))
"0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
(properties `((upstream-name . "TSP")))
(build-system r-build-system)
(propagated-inputs `(("r-foreach" ,r-foreach)))
@ -4195,14 +4314,14 @@ (define-public r-uuid
(define-public r-tinytex
(package
(name "r-tinytex")
(version "0.21")
(version "0.22")
(source
(origin
(method url-fetch)
(uri (cran-uri "tinytex" version))
(sha256
(base32
"088zzc2v0izbcs45p19v547pi78vkr08ibpvvi1g9bkbya4x3mq9"))))
"0s9f62v3ps5f8903ar6kxlf1z3b4v78vlw1nb05bq55dgj8brg3b"))))
(build-system r-build-system)
(propagated-inputs
`(("r-xfun" ,r-xfun)))
@ -6456,14 +6575,14 @@ (define-public r-prediction
(define-public r-insight
(package
(name "r-insight")
(version "0.8.2")
(version "0.8.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "insight" version))
(sha256
(base32
"0fjf7dwpv1a7qfbzixppg348z1ksq19kdjm08vcb2am7w0k3plcj"))))
"0lm5a4r368mq1pwmxjk2xnz25lb9j4v7mdkl1bahk2alklxgb8yj"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
@ -6965,14 +7084,14 @@ (define-public r-proc
(define-public r-rootsolve
(package
(name "r-rootsolve")
(version "1.8.2")
(version "1.8.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "rootSolve" version))
(sha256
(base32
"0rj7c4zcrzgz7sb0vgvh7swpfafnw4040cxp7ypas3s8fnihn54l"))))
"0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
(properties `((upstream-name . "rootSolve")))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
@ -7313,14 +7432,14 @@ (define-public r-mosaicdata
(define-public r-raster
(package
(name "r-raster")
(version "3.0-12")
(version "3.1-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "raster" version))
(sha256
(base32
"0rrbsigkqxsdic8fly6nrsc79zsliwvr1x2b4xqpl9d34vr50dvg"))))
"010sq00ijpmwac280ip9rryw0pxk0al8g675v2lc9rdrbgaj4rnv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)
@ -8324,14 +8443,14 @@ (define-public r-multcomp
(define-public r-emmeans
(package
(name "r-emmeans")
(version "1.4.5")
(version "1.4.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "emmeans" version))
(sha256
(base32
"10fmvmd6q4zjr6b18hhc85mwrzv778qzj6lwl9kbs2fsfvsgw7mm"))))
"0mxk7ghlv4r6sna4897q1la2xgyn1dw3r9srhm9x4h5l4701avfa"))))
(build-system r-build-system)
(propagated-inputs
`(("r-estimability" ,r-estimability)
@ -8339,6 +8458,8 @@ (define-public r-emmeans
("r-numderiv" ,r-numderiv)
("r-plyr" ,r-plyr)
("r-xtable" ,r-xtable)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/rvlenth/emmeans")
(synopsis "Estimated marginal means, aka least-squares means")
(description
@ -8557,14 +8678,14 @@ (define-public r-glmmtmb
(define-public r-bayestestr
(package
(name "r-bayestestr")
(version "0.5.3")
(version "0.6.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "bayestestR" version))
(sha256
(base32
"1q24qh5p6bz4nbf4546kckh7d518x5pm1yhhbc8fwcnbca4kgqjz"))))
"0s7wdmk8avgaqk2b7fcf4bsh13isrkl1q4y7z2y8jhdagxxxnzd1"))))
(properties `((upstream-name . "bayestestR")))
(build-system r-build-system)
(propagated-inputs
@ -8611,14 +8732,14 @@ (define-public r-performance
(define-public r-ggeffects
(package
(name "r-ggeffects")
(version "0.14.2")
(version "0.14.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggeffects" version))
(sha256
(base32
"1y3yfb07jrr6vkc8hk6rp52l70dj7042jvqgjzllslzy7hx2jhyw"))))
"06p80bgjhjknzlb4vs4n41i9n9vv5agncakl9f92zkaahgyzd6sd"))))
(build-system r-build-system)
(propagated-inputs
`(("r-insight" ,r-insight)
@ -8799,14 +8920,14 @@ (define-public r-clisymbols
(define-public r-usethis
(package
(name "r-usethis")
(version "1.6.0")
(version "1.6.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "usethis" version))
(sha256
(base32
"12iyimqyza752anj29wpfisl8nz5r25kfcqbssybg24nb4wyy146"))))
"0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
@ -9395,14 +9516,14 @@ (define-public r-biocmanager
(define-public r-rgl
(package
(name "r-rgl")
(version "0.100.50")
(version "0.100.54")
(source
(origin
(method url-fetch)
(uri (cran-uri "rgl" version))
(sha256
(base32
"165p932ml7dpjkm41zc47p5cdxar69il0m5yvg0avi8q01vr17ay"))))
"1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
(build-system r-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))
@ -9534,14 +9655,14 @@ (define-public r-feature
(define-public r-arm
(package
(name "r-arm")
(version "1.10-1")
(version "1.11-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "arm" version))
(sha256
(base32
"0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
"0i2lnm09bqy1qw0ms5pw0rzw196xmnk5dxha3g8lc58lqpldp0kv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-abind" ,r-abind)
@ -11478,14 +11599,14 @@ (define-public r-rbamtools
(define-public r-protviz
(package
(name "r-protviz")
(version "0.6.3")
(version "0.6.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "protViz" version))
(sha256
(base32
"1ldciqh3f43xr9663yyhd9r6qwrg4c4vmkprlcancbnd460wakg7"))))
"1qq9bf4485x8cviry9fmhnv4hw9aw657w134003myzcv42c4pml6"))))
(properties `((upstream-name . "protViz")))
(build-system r-build-system)
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
@ -11528,14 +11649,14 @@ (define-public r-cmprsk
(define-public r-etm
(package
(name "r-etm")
(version "1.0.5.1")
(version "1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "etm" version))
(sha256
(base32
"0m41pm277sd50pharigcqzr1a2g92wnmdf6fcab6fx16ia2fzrm7"))))
"02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)
@ -11736,14 +11857,14 @@ (define-public r-globals
(define-public r-future
(package
(name "r-future")
(version "1.16.0")
(version "1.17.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "future" version))
(sha256
(base32
"1xaqh0b2knf5bp23mc0kriq0iqhqna31q3b7d960piqjhzrb03dm"))))
"0d4y7gwcgqx2z0y6h5bh4lrz0m7b0inii5cjcq0kk8za762bi8rg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
@ -11768,14 +11889,14 @@ (define-public r-future
(define-public r-future-apply
(package
(name "r-future-apply")
(version "1.4.0")
(version "1.5.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "future.apply" version))
(sha256
(base32
"1kgq6dv96hdy35kysqkn606nj7s9dp4ibgpm6n46gqhc5n75lzkk"))))
"095a681ngbwbp7v53ladwya7ar8fgwnlgr3r1yklf3vdxwd54xll"))))
(properties `((upstream-name . "future.apply")))
(build-system r-build-system)
(propagated-inputs
@ -13234,14 +13355,14 @@ (define-public r-deldir
(define-public r-sf
(package
(name "r-sf")
(version "0.9-1")
(version "0.9-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "sf" version))
(sha256
(base32
"1qghrskqwwlwxmmvkv7knhlr1a32ngyimycasy5gfazgviljsfn4"))))
"01xplgy5nlwy3ajfch4h1ssa1xhm7q0jzscpz04dmvgqfzwhhdfh"))))
(build-system r-build-system)
(inputs
`(("gdal" ,gdal)
@ -13730,17 +13851,19 @@ (define-public r-bookdown
(define-public r-optparse
(package
(name "r-optparse")
(version "1.6.4")
(version "1.6.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "optparse" version))
(sha256
(base32
"0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d"))))
"1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-getopt" ,r-getopt)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/trevorld/optparse")
(synopsis "Command line option parser")
(description
@ -14900,18 +15023,19 @@ (define-public r-downloader
(define-public r-rex
(package
(name "r-rex")
(version "1.1.2")
(version "1.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "rex" version))
(sha256
(base32
"0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
"0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lazyeval" ,r-lazyeval)
("r-magrittr" ,r-magrittr)))
`(("r-lazyeval" ,r-lazyeval)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/kevinushey/rex")
(synopsis "Friendly regular expressions")
(description
@ -15242,20 +15366,89 @@ (define-public r-dqrng
;; whole is distributed under the terms of the AGPL 3.
(license license:agpl3)))
(define-public r-ingredients
(package
(name "r-ingredients")
(version "1.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ingredients" version))
(sha256
(base32
"1q196y9xzn4wk44fa1bvh0hcbizgm93rwir82nyk31k5pgixk967"))))
(properties `((upstream-name . "ingredients")))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
("r-gridextra" ,r-gridextra)
("r-scales" ,r-scales)))
(native-inputs `(("r-knitr" ,r-knitr)))
(home-page "https://ModelOriented.github.io/ingredients/")
(synopsis "Effects and importances of model ingredients")
(description
"This is a collection of tools for assessment of feature importance and
feature effects. Key functions are:
@itemize
@item @code{feature_importance()} for assessment of global level feature
importance,
@item @code{ceteris_paribus()} for calculation of the what-if plots,
@item @code{partial_dependence()} for partial dependence plots,
@item @code{conditional_dependence()} for conditional dependence plots,
@item @code{accumulated_dependence()} for accumulated local effects plots,
@item @code{aggregate_profiles()} and @code{cluster_profiles()} for
aggregation of ceteris paribus profiles,
@item generic @code{print()} and @code{plot()} for better usability of
selected explainers,
@item generic @code{plotD3()} for interactive, D3 based explanations, and
@item generic @code{describe()} for explanations in natural language.
@end itemize\n")
(license license:gpl3)))
(define-public r-ibreakdown
(package
(name "r-ibreakdown")
(version "1.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "iBreakDown" version))
(sha256
(base32
"0y4zjpyn8j76jrs5phjzs5lfq3lqjspmrwcksqv9wq0rbdgh14vk"))))
(properties `((upstream-name . "iBreakDown")))
(build-system r-build-system)
(propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
(native-inputs `(("r-knitr" ,r-knitr)))
(home-page "https://ModelOriented.github.io/iBreakDown/")
(synopsis "Model agnostic instance level variable attributions")
(description
"This package provides a model agnostic tool for decomposition of
predictions from black boxes. It supports additive attributions and
attributions with interactions. The Break Down Table shows contributions of
every variable to a final prediction. The Break Down Plot presents variable
contributions in a concise graphical way. This package works for
classification and regression models.")
(license license:gpl3)))
(define-public r-dalex
(package
(name "r-dalex")
(version "1.0.1")
(version "1.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "DALEX" version))
(sha256
(base32
"1jbyn57vn6d281a5y15h5d8ljin8cdb9lr7lbgggc950blyfv4g0"))))
"0lx8nasm1zgh1ckz8nw3ysp6xjv3dsj39hzhr6k3xhh6i8pm9rxk"))))
(properties `((upstream-name . "DALEX")))
(build-system r-build-system)
(propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
("r-ibreakdown" ,r-ibreakdown)
("r-ingredients" ,r-ingredients)))
(home-page "https://pbiecek.github.io/DALEX/")
(synopsis "Descriptive machine learning explanations")
(description
@ -15317,14 +15510,14 @@ (define-public r-plot3d
(define-public r-ggfortify
(package
(name "r-ggfortify")
(version "0.4.9")
(version "0.4.10")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggfortify" version))
(sha256
(base32
"1p6knrbyaynaqwd939w09hpf1zz1gn95cb46sfgppl8l98krb2h5"))))
"0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
@ -15833,22 +16026,22 @@ (define-public r-covr
(define-public r-systemfonts
(package
(name "r-systemfonts")
(version "0.1.1")
(version "0.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "systemfonts" version))
(sha256
(base32
"0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z"))))
"0dna00xai0pw76b4830yy4r5j1hq7f7kla67v0iz39cjm4rq4ygq"))))
(properties `((upstream-name . "systemfonts")))
(build-system r-build-system)
(inputs
`(("fontconfig" ,fontconfig)
("freetype" ,freetype)
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)))
`(("pkg-config" ,pkg-config)
("r-knitr" ,r-knitr)))
(home-page "https://github.com/r-lib/systemfonts")
(synopsis "System native font finding")
(description
@ -15862,14 +16055,14 @@ (define-public r-systemfonts
(define-public r-graphlayouts
(package
(name "r-graphlayouts")
(version "0.6.0")
(version "0.7.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "graphlayouts" version))
(sha256
(base32
"1la016m37kp79zk8p1yx9kaha8y6d4w52w39h0mzv1mfsi6d75w0"))))
"17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0"))))
(properties `((upstream-name . "graphlayouts")))
(build-system r-build-system)
(propagated-inputs
@ -16756,28 +16949,61 @@ (define-public r-abstractr
included.")
(license license:gpl3)))
(define-public r-qgam
(package
(name "r-qgam")
(version "1.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "qgam" version))
(sha256
(base32
"0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
(properties `((upstream-name . "qgam")))
(build-system r-build-system)
(propagated-inputs
`(("r-doparallel" ,r-doparallel)
("r-mgcv" ,r-mgcv)
("r-plyr" ,r-plyr)
("r-shiny" ,r-shiny)))
(native-inputs `(("r-knitr" ,r-knitr)))
(home-page "https://cran.r-project.org/web/packages/qgam/")
(synopsis "Smooth additive quantile regression models")
(description
"This package provides smooth additive quantile regression models, fitted
using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
the smoothing parameters are estimated automatically by marginal loss
minimization, while the regression coefficients are estimated using either
PIRLS or Newton algorithm. The learning rate is determined so that the
Bayesian credible intervals of the estimated effects have approximately the
correct coverage. The main function is @code{qgam()} which is similar to
@code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
regression models.")
(license license:gpl2+)))
(define-public r-abtest
(package
(name "r-abtest")
(version "0.2.0")
(version "0.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "abtest" version))
(sha256
(base32
"1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws"))))
"1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
(properties `((upstream-name . "abtest")))
(build-system r-build-system)
(propagated-inputs
`(("r-matrix" ,r-matrix)
("r-mvtnorm" ,r-mvtnorm)
("r-plotrix" ,r-plotrix)
("r-qgam" ,r-qgam)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-rcpp" ,r-rcpp)
("r-sn" ,r-sn)
("r-truncnorm" ,r-truncnorm)
("r-vgam" ,r-vgam)))
("r-truncnorm" ,r-truncnorm)))
(home-page "https://cran.r-project.org/web/packages/abtest/")
(synopsis "Bayesian A/B testing")
(description
@ -18107,14 +18333,14 @@ (define-public r-actfrag
(define-public r-fda
(package
(name "r-fda")
(version "2.4.8.1")
(version "5.1.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "fda" version))
(sha256
(base32
"0g50kj1dx7zarjv0lgwyzd2c7bv6di7nkndmywday5vjywgl8m7a"))))
"0js4ggl3aiwsqk6npwz72yhcznkb63smddds24ngf6a0p8yp5p2x"))))
(properties `((upstream-name . "fda")))
(build-system r-build-system)
(propagated-inputs
@ -18569,14 +18795,14 @@ (define-public r-adagio
(define-public r-univoutl
(package
(name "r-univoutl")
(version "0.1-5")
(version "0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "univOutl" version))
(sha256
(base32
"193wrpkvgmlrx43nag8w3ivrlqm37nm6g86wcvd3bgw3hchs70gi"))))
"0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
(properties `((upstream-name . "univOutl")))
(build-system r-build-system)
(propagated-inputs
@ -19513,17 +19739,20 @@ (define-public r-isocodes
(define-public r-stopwords
(package
(name "r-stopwords")
(version "1.0")
(version "2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "stopwords" version))
(sha256
(base32
"1nmi0bpd0c238g5b8ch1v034m5ng9llhs519cgxdrj3sh9fplwlv"))))
"155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
(properties `((upstream-name . "stopwords")))
(build-system r-build-system)
(propagated-inputs `(("r-isocodes" ,r-isocodes)))
(propagated-inputs
`(("r-desc" ,r-desc)
("r-isocodes" ,r-isocodes)
("r-usethis" ,r-usethis)))
(home-page "https://github.com/quanteda/stopwords")
(synopsis "Multilingual stopword lists")
(description
@ -19627,14 +19856,14 @@ (define-public r-quanteda
(define-public r-topicmodels
(package
(name "r-topicmodels")
(version "0.2-9")
(version "0.2-11")
(source
(origin
(method url-fetch)
(uri (cran-uri "topicmodels" version))
(sha256
(base32
"1757r5x8bsl4dk106xg6481mvdkdz9vwg87n7rpbvdkavsvhyxs0"))))
"0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
(properties `((upstream-name . "topicmodels")))
(build-system r-build-system)
(native-inputs
@ -19990,19 +20219,18 @@ (define-public r-openmx
(define-public r-kutils
(package
(name "r-kutils")
(version "1.69")
(version "1.70")
(source
(origin
(method url-fetch)
(uri (cran-uri "kutils" version))
(sha256
(base32
"12pg26a85h0jxlfcyai68dbh4bq1gnq8v1ngi8k9qvafbrpc6gx8"))))
"06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
(properties `((upstream-name . "kutils")))
(build-system r-build-system)
(propagated-inputs
`(("r-foreign" ,r-foreign)
("r-lavaan" ,r-lavaan)
("r-openxlsx" ,r-openxlsx)
("r-plyr" ,r-plyr)
("r-runit" ,r-runit)
@ -21404,3 +21632,40 @@ (define-public r-rxnat
Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
download images.")
(license license:gpl2)))
(define-public r-rserve
(package
(name "r-rserve")
(version "1.8-6")
(source
(origin
(method url-fetch)
(uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
version ".tar.gz"))
(sha256
(base32
"017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-checkmate" ,r-checkmate)
("r-mime" ,r-mime)
("r-jsonlite" ,r-jsonlite)
("r-knitr" ,r-knitr)
("r-r6" ,r-r6)
("r-rcpp" ,r-rcpp)
("r-uuid" ,r-uuid)))
(inputs
`(("openssl" ,openssl)
("zlib" ,zlib)))
(home-page "https://github.com/s-u/Rserve")
(synopsis
"Server providing access to R from many languages and systems")
(description
"Rserve acts as a socket server (TCP/IP or local sockets) which allows
binary requests to be sent to R. Every connection has a separate workspace
and working directory. Client-side implementations are available for popular
languages such as C/C++ and Java, allowing any application to use facilities
of R without the need of linking to R code. Rserve supports remote
connection, user authentication and file transfer. A simple R client is
included in this package as well.")
(license license:gpl2)))

3771
gnu/packages/crates-io.scm
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File diff suppressed because it is too large Load diff

4
gnu/packages/cups.scm
View file

@ -673,14 +673,14 @@ (define-public foomatic-filters
(define-public foo2zjs
(package
(name "foo2zjs")
(version "20200207")
(version "20200426")
(source (origin
(method url-fetch)
;; XXX: This is an unversioned URL!
(uri "http://foo2zjs.rkkda.com/foo2zjs.tar.gz")
(sha256
(base32
"0pf1sm29gnrhhpyvq95jskvr874h5r4kls9w10gc24z23fjmr5zx"))))
"0wwh29ddd59q18r1jpi3166lgnwr8zn9lry82vahc2g96l97isp7"))))
(build-system gnu-build-system)
(arguments
'(#:phases (modify-phases %standard-phases

28
gnu/packages/databases.scm
View file

@ -2211,24 +2211,24 @@ (define-public python2-peewee
(define-public python-tortoise-orm
(package
(name "python-tortoise-orm")
(version "0.16.3")
(version "0.16.7")
(source
(origin
(method url-fetch)
(uri (pypi-uri "tortoise-orm" version))
(sha256
(base32
"01hbvfyxs2qd1mjc96aipwsdxxhydw8ww686r4gsf87bl6f98dvz"))))
"0wr7p4v0b16ypm9fcpwpl99kf491m6w3jkd13xcsgq13fy73fbqc"))))
(build-system python-build-system)
;; Disable tests for now. They pull in a lot of dependencies.
(arguments `(#:tests? #f))
(native-inputs
`(("python-ciso8601" ,python-ciso8601)
("python-asynctest" ,python-asynctest)
`(("python-asynctest" ,python-asynctest)
("python-nose2" ,python-nose2)))
(propagated-inputs
`(("python-aiosqlite" ,python-aiosqlite)
("python-pypika" ,python-pypika)
("python-ciso8601" ,python-ciso8601)
("python-typing-extensions"
,python-typing-extensions)))
(home-page
@ -2757,14 +2757,14 @@ (define-public python2-apsw
(define-public python-aiosqlite
(package
(name "python-aiosqlite")
(version "0.11.0")
(version "0.12.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "aiosqlite" version))
(sha256
(base32
"1f3zdldp9zgrw6qz5fsp3wa5zw73cjf139pj4vf24ryv895320jg"))))
"1w8248yz85xyzvvh4jaxnc59fqil45aka6h82kn1rcih4rjxbnn1"))))
(build-system python-build-system)
(native-inputs
`(("python-aiounittest" ,python-aiounittest)))
@ -3088,14 +3088,16 @@ (define-public python2-sql
(define-public python-pypika
(package
(name "python-pypika")
(version "0.36.0")
(version "0.37.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "PyPika" version))
(sha256
(base32
"0qzn5vygirg52dlizm6ayzdc5llq8p2krrx0kymr236lrz89wqp8"))))
(origin (method git-fetch)
(uri (git-reference
(url "https://github.com/kayak/pypika.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"089z1c778q1fwhzsc88ws8j5gm2hgxknibabn4wpax8rz2bfs3ck"))))
(build-system python-build-system)
(native-inputs
`(("python-parameterized" ,python-parameterized)))

11
gnu/packages/diffoscope.scm
View file

@ -57,6 +57,7 @@ (define-module (gnu packages diffoscope)
#:use-module (gnu packages ssh)
#:use-module (gnu packages statistics)
#:use-module (gnu packages textutils)
#:use-module (gnu packages tls)
#:use-module (gnu packages video)
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
@ -69,7 +70,7 @@ (define-module (gnu packages diffoscope)
#:use-module (ice-9 match))
(define-public diffoscope
(let ((version "141"))
(let ((version "143"))
(package
(name "diffoscope")
(version version)
@ -81,7 +82,7 @@ (define-public diffoscope
(file-name (git-file-name name version))
(sha256
(base32
"0pls2jryx394ysaz0g8h959lhrsdqak9bkxjd5r6sdckgiikplkj"))))
"0j58dqdk8ln8y0bcnfy37ljs37nkl56lzxqns396300ysln0qiwm"))))
(build-system python-build-system)
(arguments
`(#:phases (modify-phases %standard-phases
@ -96,8 +97,8 @@ (define-public diffoscope
(add-after 'unpack 'add-known-tools
(lambda _
(substitute* "diffoscope/external_tools.py"
(("'debian': 'hdf5-tools'")
"'debian': 'hdf5-tools', 'guix': 'hdf5'"))))
(("'debian': 'openssl'")
"'debian': 'openssl', 'guix': 'openssl'"))))
;; This test is broken because our `file` package has a
;; bug in berkeley-db file type detection.
(add-after 'unpack 'remove-berkeley-test
@ -161,6 +162,7 @@ (define-public diffoscope
(native-inputs `(("python-pytest" ,python-pytest)
("python-chardet" ,python-chardet)
("python-binwalk" ,python-binwalk)
("python-h5py" ,python-h5py)
("python-pypdf2" ,python-pypdf2)
("python-progressbar33" ,python-progressbar33)
;; test suite skips tests when tool is missing
@ -205,6 +207,7 @@ (define-public diffoscope
("ocaml" ,ocaml)
("odt2txt" ,odt2txt)
("openssh" ,openssh)
("openssl" ,openssl)
("pgpdump" ,pgpdump)
("poppler" ,poppler)
("python-jsbeautifier" ,python-jsbeautifier)

192
gnu/packages/emacs-xyz.scm
View file

@ -34,7 +34,7 @@
;;; Copyright © 2017, 2018, 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2018 Sohom Bhattacharjee <soham.bhattacharjee15@gmail.com>
;;; Copyright © 2018, 2019 Mathieu Lirzin <mthl@gnu.org>
;;; Copyright © 2018, 2019 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2018, 2019, 2020 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2018, 2019 Tim Gesthuizen <tim.gesthuizen@yahoo.de>
;;; Copyright © 2018, 2019 Jack Hill <jackhill@jackhill.us>
;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
@ -69,6 +69,7 @@
;;; Copyright © 2020 Jérémy Korwin-Zmijowski <jeremy@korwin-zmijowski.fr>
;;; Copyright © 2020 Alberto Eleuterio Flores Guerrero <barbanegra+guix@posteo.mx>
;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2020 pinoaffe <pinoaffe@airmail.cc>
;;;
;;; This file is part of GNU Guix.
;;;
@ -476,6 +477,31 @@ (define-public emacs-magit-popup
process, passing on the arguments as command line arguments.")
(license license:gpl3+)))
(define-public emacs-magit-annex
(let ((commit "ef5dce6267e9118a5eca82a22bcad0b67826c23a")
(revision "1"))
(package
(name "emacs-magit-annex")
(version (git-version "1.7.1" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/magit/magit-annex.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0vzkydgl889cq173zjl89g2vrddb9abc4a8gljiz3b4a7n5b1nrd"))))
(build-system emacs-build-system)
(propagated-inputs
`(("magit" ,emacs-magit)
("transient" ,emacs-transient)))
(home-page "https://github.com/magit/magit-annex/")
(synopsis "Git-annex support for Magit")
(description
"Magit-annex adds a few git-annex operations to the Magit interface.")
(license license:gpl3+))))
(define-public emacs-minions
(package
(name "emacs-minions")
@ -2462,6 +2488,37 @@ (define-public emacs-extempore-mode
running Extempore process, and more.")
(license license:bsd-2))))
(define-public emacs-kakoune
;; Package has no release. Version is extracted from "Version:" keyword in
;; main file.
(let ((commit "d73d14e69ea38076af50cc69f846808383ff539d")
(revision "0"))
(package
(name "emacs-kakoune")
(version (git-version "0.1" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/jmorag/kakoune.el.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0nk6jdy1y5mc3ryd0smiqghrk6iv34d5grc7f7migmshlbq0np92"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-expand-region" ,emacs-expand-region)
("emacs-multiple-cursors" ,emacs-multiple-cursors)
("emacs-ryo-modal" ,emacs-ryo-modal)))
(home-page "https://github.com/jmorag/kakoune.el")
(synopsis "Emacs simple simulation, but not emulation, of Kakoune")
(description "This package provides many, but not all of the editing
primitives in the Kakoune editor. Unlike Evil mode for Vim, this is a very
shallow emulation, which seeks to do as little work as possible, leveraging
Emacs native editing commmands and the work of other packages wherever
possible.")
(license license:expat))))
(define-public emacs-keyfreq
(package
(name "emacs-keyfreq")
@ -2567,9 +2624,9 @@ (define-public emacs-symon
(license license:gpl2+)))
(define-public emacs-sx
(let ((version "20180212")
(revision "1")
(commit "833435fbf90d1c9e927d165b155f3b1ef39271de"))
(let ((version "20191229")
(revision "0")
(commit "e9d1093c97507a6d7b4f4710ef65200dae725e5f"))
(package
(name "emacs-sx")
(version (git-version version revision commit))
@ -2581,8 +2638,7 @@ (define-public emacs-sx
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1369xaxq1vy3d9yh862ddnhddikdpg2d0wv1ly00pnvdp9v4cqgd"))))
(base32 "0m90ddwm8j0y6d1ppqhd2gil1107k202blw6mzm5bdambn4nfqkf"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-markdown-mode" ,emacs-markdown-mode)))
@ -2593,6 +2649,54 @@ (define-public emacs-sx
Stack Overflow, Super User, and other StackExchange sites.")
(license license:gpl3+))))
(define-public emacs-toml-mode
(let ((version "0.1.3")
(revision "0")
(commit "f6c61817b00f9c4a3cab1bae9c309e0fc45cdd06"))
(package
(name "emacs-toml-mode")
(version (git-version version revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/dryman/toml-mode.el.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "05b4ksay85c8y5ncax0qsvnmplwsfiw24z16a58gkarjz938hb57"))))
(build-system emacs-build-system)
(home-page "https://github.com/dryman/toml-mode.el")
(synopsis "Emacs major mode for editing TOML files")
(description
;; XXX: Ideally we'd use @acronym for "TOML", but Guile's Texinfo
;; parser does not currently support @comma{}, making it impossible
;; to use commas in the @acronym arguments.
"This package provides a major mode for editing files in @dfn{TOML}
(Tom's Obvious, Minimal Language) data format.")
(license license:gpl3+))))
(define-public emacs-twittering-mode
(package
(name "emacs-twittering-mode")
(version "3.1.0")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/twmode"
"/twittering-mode-" version
"/twittering-mode-" version ".tar.xz"))
(sha256
(base32 "02imis1gxz90lah0b5n37j2hlsaw5igss11d85vpsm5d1bgw8j28"))))
(build-system emacs-build-system)
(home-page "http://twmode.sourceforge.net")
(synopsis "Emacs major mode for Twitter")
(description
"Twittering mode is an Emacs major mode for Twitter.
You can check timelines, tweet, mark posts as favorites and so on with
Emacs.")
(license license:gpl2+)))
(define-public emacs-f
(package
(name "emacs-f")
@ -7252,6 +7356,30 @@ (define-public emacs-rainbow-mode
names, e.g. #0000ff is displayed in white with a blue background.")
(license license:gpl3+)))
(define-public emacs-ryo-modal
;; Package has no release. Version is extracted from "Version:" keyword in
;; main file.
(let ((commit "3a54312eea7023a86ca3f8eb3c03c872554bff2f")
(revision "0"))
(package
(name "emacs-ryo-modal")
(version (git-version "0.4" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Kungsgeten/ryo-modal.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1cyvp3bi6yhckbdnq98xvghmhdzghya5y9wd7hxjawibs75rza95"))))
(build-system emacs-build-system)
(home-page "http://github.com/Kungsgeten/ryo-modal")
(synopsis "Emacs minor mode for defining modal editing environments")
(description "RYO modal provides a convenient way of defining modal
keybindings in Emacs, and does not come with any predefined bindings.")
(license license:expat))))
(define-public emacs-visual-fill-column
(package
(name "emacs-visual-fill-column")
@ -14320,7 +14448,7 @@ (define-public emacs-org-reveal
(build-system emacs-build-system)
(home-page "https://github.com/yjwen/org-reveal")
(synopsis "Org and Reveal.js powered HTML presentation tool")
(description "Org-Reveal is a command@{org-mode} extension that allows
(description "Org-Reveal is a @command{org-mode} extension that allows
to create beautiful presentations (slides) with 3D effects from simple but
powerful Org contents.")
(license license:gpl3+))))
@ -15864,10 +15992,10 @@ (define-public emacs-evil-mc
(license license:expat))))
(define-public emacs-evil-org
(let ((commit "b6d652a9163d3430a9e0933a554bdbee5244bbf6"))
(let ((commit "9d4be14118bf27094a30dbff349b815f098aacbf"))
(package
(name "emacs-evil-org")
(version (git-version "0.1.1" "1" commit))
(version (git-version "1.0.2" "1" commit))
(source
(origin
(method git-fetch)
@ -15877,7 +16005,7 @@ (define-public emacs-evil-org
(file-name (git-file-name name version))
(sha256
(base32
"176hrw7y7nczffbyhsa167b8rvfacsmcafm2gpkrdjqlrikbmrhl"))))
"1fxxfkinb0gq4p5b686r7z4jrkv98zfgh5z889zkjacncv8ibswn"))))
(build-system emacs-build-system)
(propagated-inputs `(("emacs-evil" ,emacs-evil)))
(home-page
@ -18122,7 +18250,7 @@ (define-public emacs-mpdel
(define-public emacs-vterm
(let ((version "0")
(revision "1")
(commit "7d7381fa8104b55b70148cf147523d9ab7f01fcd"))
(commit "e63bd65eece7c5de3a534b7e2fdbe58256ec2da0"))
(package
(name "emacs-vterm")
(version (git-version version revision commit))
@ -18134,7 +18262,7 @@ (define-public emacs-vterm
(file-name (git-file-name name version))
(sha256
(base32
"04a2jlhmr20ipgzpnba3yryw3ly7qdxjgaw10dwn9wxy1yqmapz1"))))
"0iq857w54qmazxh23fipz85fb9i6dav3f63g0ghpmi6mybfp6i5v"))))
(build-system emacs-build-system)
(arguments
`(#:modules ((guix build emacs-build-system)
@ -18145,14 +18273,11 @@ (define-public emacs-vterm
(guix build cmake-build-system))
#:phases
(modify-phases %standard-phases
(add-before 'add-source-to-load-path 'remove-vterm-module-make
(add-before 'add-source-to-load-path 'substitute-vterm-module-path
(lambda* (#:key outputs #:allow-other-keys)
;; Remove the Emacs Lisp file.
(delete-file "vterm-module-make.el")
;; Remove references to the removed file.
(make-file-writable "vterm.el")
(chmod "vterm.el" #o644)
(emacs-substitute-sexps "vterm.el"
("(or (require 'vterm-module nil t)"
("(require 'vterm-module nil t)"
`(module-load
,(string-append (assoc-ref outputs "out")
"/lib/vterm-module.so"))))
@ -21334,6 +21459,7 @@ (define-public emacs-telega
(sha256
(base32
"0mv6i80958d9crzspzik5xh5g8326115bvg2frgv0dp9p6rm86m3"))
(patches (search-patches "emacs-telega-test-env.patch"))
(file-name (git-file-name name version))))
(build-system gnu-build-system)
(arguments
@ -21425,7 +21551,12 @@ (define-public emacs-telega
(native-inputs
`(("tdlib" ,tdlib)
("libtgvoip" ,libtgvoip) ; VoIP support.
("emacs" ,emacs)
;; Use Emacs with wide ints on 32-bit architectures.
("emacs" ,(match (%current-system)
((or "i686-linux" "armhf-linux")
emacs-wide-int)
(_
emacs)))
("python" ,python)))
(synopsis "GNU Emacs client for the Telegram messenger")
(description
@ -22591,3 +22722,26 @@ (define-public emacs-uml-mode
comments or emails.")
(license license:gpl3+))))
(define-public emacs-trashed
(package
(name "emacs-trashed")
(version "1.9.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/shingo256/trashed/")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "13grdi12iwlw4fiphdfmvclfpbr6ajlgfbfyi7v41z8k3rxz4ypz"))))
(build-system emacs-build-system)
(home-page "https://github.com/shingo256/trashed/")
(synopsis "View and edit system trash can in Emacs")
(description "Open, view, browse, restore or permanently delete trashed
files or directories in trash can with Dired-like look and feel. The trash
can has to be compliant with freedesktop.org. In Emacs, you can trash files by
deleting them with @code{(setq delete-by-moving-to-trash t)}. This package
provides a simple but convenient user interface to manage those trashed
files.")
(license license:gpl3+)))

11
gnu/packages/emacs.scm
View file

@ -401,6 +401,17 @@ (define-public emacs-no-x-toolkit
((#:configure-flags cf)
`(cons "--with-x-toolkit=no" ,cf)))))))
(define-public emacs-wide-int
(package
(inherit emacs)
(name "emacs-wide-int")
(synopsis "The extensible, customizable, self-documenting text
editor (with wide ints)" )
(arguments
(substitute-keyword-arguments (package-arguments emacs)
((#:configure-flags flags)
`(cons "--with-wide-int" ,flags))))))
(define-public guile-emacs
(let ((commit "41120e0f595b16387eebfbf731fff70481de1b4b")
(revision "0"))

2
gnu/packages/game-development.scm
View file

@ -1777,7 +1777,7 @@ (define-public guile-chickadee
(define-public guile3.0-chickadee
(package
(inherit guile-chickadee)
(name "guile-chickadee")
(name "guile3.0-chickadee")
(version "0.4.0")
(source (origin
(method url-fetch)

5
gnu/packages/gnome.scm
View file

@ -8073,13 +8073,14 @@ (define-public gnome-calendar
("glib-bin" ,glib "bin") ; For glib-compile-schemas
("pkg-config" ,pkg-config)))
(inputs
`(("evolution-data-server" ,evolution-data-server)
("gnome-online-accounts:lib" ,gnome-online-accounts "lib")
`(("gnome-online-accounts:lib" ,gnome-online-accounts "lib")
("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
("libdazzle" ,libdazzle)
("libedataserverui" ,evolution-data-server)
("libgweather" ,libgweather)
("geoclue" ,geoclue)))
(propagated-inputs
`(("evolution-data-server" ,evolution-data-server)))
(home-page "https://wiki.gnome.org/Apps/Calendar")
(synopsis "GNOME's calendar application")
(description

4
gnu/packages/gsasl.scm
View file

@ -35,14 +35,14 @@ (define-module (gnu packages gsasl)
(define-public libntlm
(package
(name "libntlm")
(version "1.5")
(version "1.6")
(source (origin
(method url-fetch)
(uri (string-append "https://www.nongnu.org/libntlm/releases/"
"libntlm-" version ".tar.gz"))
(sha256
(base32
"1gcvv7f9rggpxay81qv6kw5hr6gd4qiyzkbwhzz02fx9jvv9kmsk"))))
"08b83nss16jsn213j326yhn1vnrz10k15fwq6jm5b1vdn23nndzj"))))
(build-system gnu-build-system)
(synopsis "Library that implements NTLM authentication")
(description

37
gnu/packages/hardware.scm
View file

@ -79,6 +79,43 @@ (define-public ddcutil
(license (list license:bsd-3 ; FindDDCUtil.cmake
license:gpl2+)))) ; everything else
(define-public edid-decode
(let ((commit "74b64180d67bb009d8d9ea1b6f18ad41aaa16396") ; 2020-04-22
(revision "1"))
(package
(name "edid-decode")
(version (git-version "0.0.0" revision commit))
(source
(origin
(method git-fetch)
(file-name (git-file-name name version))
(uri (git-reference
(url "git://linuxtv.org/edid-decode.git")
(commit commit)))
(sha256
(base32 "0nirp5bza08zj5d8bjgcm0p869hdg3qg3mwa7999pjdrzmn7s2ah"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; No test suite
#:make-flags
(list (string-append "DESTDIR=" (assoc-ref %outputs "out"))
"bindir=/bin" "mandir=/share/man")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-cross-compilation
(lambda* (#:key native-inputs target #:allow-other-keys)
(when target
(substitute* "Makefile"
(("\\$\\(CXX\\)")
(string-append target "-g++"))))
#t))
(delete 'configure))))
(home-page "https://git.linuxtv.org/edid-decode.git/")
(synopsis "Decode @dfn{EDID} data in human-readable format")
(description "edid-decode decodes @dfn{EDID} monitor description data in
human-readable format and checks if it conforms to the standards.")
(license license:expat))))
;; Distinct from memtest86, which is obsolete.
(define-public memtest86+
(package

52
gnu/packages/linphone.scm
View file

@ -410,6 +410,7 @@ (define-public liblinphone
"/linphone-" version ".tar.gz"))
(sha256
(base32 "0phhkx55xdyg28d4wn8l8q4yvsmdgzmjiw584d4s190sq1azm91x"))))
(outputs '("out" "doc" "tester"))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ; No test target
@ -430,41 +431,60 @@ (define-public liblinphone
(guix build utils))
#:phases
(modify-phases %standard-phases
(add-after 'install 'glib-or-gtk-compile-schemas
(assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-compile-schemas))
(add-after 'install 'glib-or-gtk-wrap
(assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap))
(add-after 'unpack 'patch
(lambda _
(substitute* "gtk/main.c"
(("#include \"liblinphone_gitversion.h\"")
""))
#t)))))
#t))
(add-after 'install 'separate-outputs
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(doc (assoc-ref outputs "doc"))
(tester (assoc-ref outputs "tester"))
(tester-name (string-append ,name "_tester")))
;; Copy the tester executable.
(mkdir-p (string-append tester "/bin"))
(rename-file (string-append out "/bin/" tester-name)
(string-append tester "/bin/" tester-name))
;; Copy the tester data files.
(mkdir-p (string-append tester "/share/"))
(rename-file (string-append out "/share/" tester-name)
(string-append tester "/share/" tester-name))
;; Copy the HTML and XML documentation.
(copy-recursively
(string-append out "/share/doc/linphone-" ,version)
(string-append doc "/share/doc/" ,name "-" ,version))
(delete-file-recursively
(string-append out "/share/doc/linphone-" ,version))
#t)))
(add-after 'separate-outputs 'glib-or-gtk-compile-schemas
(assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-compile-schemas))
(add-after 'glib-or-gtk-compile-schemas 'glib-or-gtk-wrap
(assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))))
(native-inputs
`(("dot" ,graphviz)
`(("gettext" ,gettext-minimal)
("udev" ,eudev) ;for libudev.h
;; For generating the C++ wrappers.
("dot" ,graphviz)
("doxygen" ,doxygen)
("gettext" ,gettext-minimal)
("iconv" ,libiconv)
("python" ,python)
("xml2" ,libxml2)
("zlib" ,zlib)))
("pystache" ,python-pystache)
("six" ,python-six)))
(inputs
`(("bctoolbox" ,bctoolbox)
("belcard" ,belcard)
("bellesip" ,belle-sip)
("bzrtp", bzrtp)
("hicolor-icon-theme" ,hicolor-icon-theme) ; Hard-coded for GTK UI
("iconv" ,libiconv)
("glib" ,glib)
("gtk2" ,gtk+-2)
("mediastreamer2" ,mediastreamer2)
("notify" ,libnotify)
("ortp" ,ortp)
("pystache" ,python-pystache)
("six" ,python-six)
("sqlite" ,sqlite)
("udev" ,eudev)))
(propagated-inputs
`(("murrine" ,murrine))) ; Required for GTK UI
("xml2" ,libxml2)
("zlib" ,zlib)))
(synopsis "Belledonne Communications Softphone Library")
(description "Liblinphone is a high-level SIP library integrating
all calling and instant messaging features into an unified

12
gnu/packages/linux.scm
View file

@ -369,26 +369,26 @@ (define (%upstream-linux-source version hash)
(sha256 hash)))
(define-public linux-libre-5.6-version "5.6.7")
(define-public linux-libre-5.6-version "5.6.8")
(define-public linux-libre-5.6-pristine-source
(let ((version linux-libre-5.6-version)
(hash (base32 "1jljcva3gxg1yc2kw3jjgmhzzdm16nylzxl63zbndjza547l5813")))
(hash (base32 "1pw2q9509jzp84b6qasaais2ws25v2wrjh072q0x3j520zzl5q8r")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-5.6)))
(define-public linux-libre-5.4-version "5.4.35")
(define-public linux-libre-5.4-version "5.4.36")
(define-public linux-libre-5.4-pristine-source
(let ((version linux-libre-5.4-version)
(hash (base32 "1m06k19pbb3wz8z2dgf03jvzbbdh6q8jwwdz509s902a53vxasz1")))
(hash (base32 "13avfvimjyg4lhj9micgib9bb5qpx11cja5liypid0rf2acfmymr")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-5.4)))
(define-public linux-libre-4.19-version "4.19.118")
(define-public linux-libre-4.19-version "4.19.119")
(define-public linux-libre-4.19-pristine-source
(let ((version linux-libre-4.19-version)
(hash (base32 "15lcq3xky59v88vb8vvnmgcsmm1fadz0m4jyrii6rynsz5jr6x49")))
(hash (base32 "1klvdzz8sndg2zsr1anfy9p5fc1aapjqvc249myrbndyf55bk91b")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.19)))

140
gnu/packages/lisp-xyz.scm
View file

@ -2670,10 +2670,11 @@ (define-public cl-sqlite
(sbcl-package->cl-source-package sbcl-cl-sqlite))
(define-public sbcl-parenscript
(let ((commit "061d8e286c81c3f45c84fb2b11ee7d83f590a8f8"))
;; Source archives are overwritten on every release, we use the Git repo instead.
(let ((commit "7a1ac46353cecd144fc91915ba9f122aafcf4766"))
(package
(name "sbcl-parenscript")
(version (git-version "2.6" "1" commit))
(version (git-version "2.7.1" "1" commit))
(source
(origin
(method git-fetch)
@ -2683,7 +2684,7 @@ (define-public sbcl-parenscript
(file-name (git-file-name "parenscript" version))
(sha256
(base32
"1kbhgsjbikc73m5cwdp4d4fdafyqcr1b7b630qjrziql0nh6mi3k"))))
"0c22lqarrpbq82dg1sb3y6mp6w2faczp34ymzhnmff88yfq1xzsf"))))
(build-system asdf-build-system/sbcl)
(inputs
`(("cl-ppcre" ,sbcl-cl-ppcre)
@ -2916,7 +2917,20 @@ (define-public sbcl-cl-cffi-gtk-gobject
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "gobject/gobject.init.lisp"
(("libgobject" all) (string-append
(assoc-ref inputs "glib") "/lib/" all))))))))))
(assoc-ref inputs "glib") "/lib/" all)))))
(add-after 'install 'link-source
;; Since source is particularly heavy (16MiB+), let's reuse it
;; across the different components of cl-ffi-gtk.
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
"/share/common-lisp/sbcl-source/"
"cl-cffi-gtk-glib"))
(out-source (string-append (assoc-ref outputs "out")
"/share/common-lisp/sbcl-source/"
"cl-cffi-gtk-gobject")))
(delete-file-recursively out-source)
(symlink glib-source out-source)
#t))))))))
(define-public sbcl-cl-cffi-gtk-gio
(package
@ -2936,7 +2950,20 @@ (define-public sbcl-cl-cffi-gtk-gio
(substitute* "gio/gio.init.lisp"
(("libgio" all)
(string-append
(assoc-ref inputs "glib") "/lib/" all))))))))))
(assoc-ref inputs "glib") "/lib/" all)))))
(add-after 'install 'link-source
;; Since source is particularly heavy (16MiB+), let's reuse it
;; across the different components of cl-ffi-gtk.
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
"/share/common-lisp/sbcl-source/"
"cl-cffi-gtk-glib"))
(out-source (string-append (assoc-ref outputs "out")
"/share/common-lisp/sbcl-source/"
"cl-cffi-gtk-gio")))
(delete-file-recursively out-source)
(symlink glib-source out-source)
#t))))))))
(define-public sbcl-cl-cffi-gtk-cairo
(package
@ -2955,7 +2982,20 @@ (define-public sbcl-cl-cffi-gtk-cairo
(substitute* "cairo/cairo.init.lisp"
(("libcairo" all)
(string-append
(assoc-ref inputs "cairo") "/lib/" all))))))))))
(assoc-ref inputs "cairo") "/lib/" all)))))
(add-after 'install 'link-source
;; Since source is particularly heavy (16MiB+), let's reuse it
;; across the different components of cl-ffi-gtk.
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
"/share/common-lisp/sbcl-source/"
"cl-cffi-gtk-glib"))
(out-source (string-append (assoc-ref outputs "out")
"/share/common-lisp/sbcl-source/"
"cl-cffi-gtk-cairo")))
(delete-file-recursively out-source)
(symlink glib-source out-source)
#t))))))))
(define-public sbcl-cl-cffi-gtk-pango
(package
@ -2976,7 +3016,20 @@ (define-public sbcl-cl-cffi-gtk-pango
(substitute* "pango/pango.init.lisp"
(("libpango" all)
(string-append
(assoc-ref inputs "pango") "/lib/" all))))))))))
(assoc-ref inputs "pango") "/lib/" all)))))
(add-after 'install 'link-source
;; Since source is particularly heavy (16MiB+), let's reuse it
;; across the different components of cl-ffi-gtk.
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
"/share/common-lisp/sbcl-source/"
"cl-cffi-gtk-glib"))
(out-source (string-append (assoc-ref outputs "out")
"/share/common-lisp/sbcl-source/"
"cl-cffi-gtk-pango")))
(delete-file-recursively out-source)
(symlink glib-source out-source)
#t))))))))
(define-public sbcl-cl-cffi-gtk-gdk-pixbuf
(package
@ -2985,6 +3038,7 @@ (define-public sbcl-cl-cffi-gtk-gdk-pixbuf
(inputs
`(("gdk-pixbuf" ,gdk-pixbuf)
("cl-cffi-gtk-gobject" ,sbcl-cl-cffi-gtk-gobject)
("cl-cffi-gtk-glib" ,sbcl-cl-cffi-gtk-glib)
,@(package-inputs sbcl-cl-cffi-gtk-boot0)))
(arguments
`(#:asd-file "gdk-pixbuf/cl-cffi-gtk-gdk-pixbuf.asd"
@ -2995,7 +3049,20 @@ (define-public sbcl-cl-cffi-gtk-gdk-pixbuf
(substitute* "gdk-pixbuf/gdk-pixbuf.init.lisp"
(("libgdk_pixbuf" all)
(string-append
(assoc-ref inputs "gdk-pixbuf") "/lib/" all))))))))))
(assoc-ref inputs "gdk-pixbuf") "/lib/" all)))))
(add-after 'install 'link-source
;; Since source is particularly heavy (16MiB+), let's reuse it
;; across the different components of cl-ffi-gtk.
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
"/share/common-lisp/sbcl-source/"
"cl-cffi-gtk-glib"))
(out-source (string-append (assoc-ref outputs "out")
"/share/common-lisp/sbcl-source/"
"cl-cffi-gtk-gdk-pixbuf")))
(delete-file-recursively out-source)
(symlink glib-source out-source)
#t))))))))
(define-public sbcl-cl-cffi-gtk-gdk
(package
@ -3003,6 +3070,7 @@ (define-public sbcl-cl-cffi-gtk-gdk
(name "sbcl-cl-cffi-gtk-gdk")
(inputs
`(("gtk" ,gtk+)
("cl-cffi-gtk-glib" ,sbcl-cl-cffi-gtk-glib)
("cl-cffi-gtk-gobject" ,sbcl-cl-cffi-gtk-gobject)
("cl-cffi-gtk-gio" ,sbcl-cl-cffi-gtk-gio)
("cl-cffi-gtk-gdk-pixbuf" ,sbcl-cl-cffi-gtk-gdk-pixbuf)
@ -3022,7 +3090,20 @@ (define-public sbcl-cl-cffi-gtk-gdk
(substitute* "gdk/gdk.package.lisp"
(("libgtk" all)
(string-append
(assoc-ref inputs "gtk") "/lib/" all))))))))))
(assoc-ref inputs "gtk") "/lib/" all)))))
(add-after 'install 'link-source
;; Since source is particularly heavy (16MiB+), let's reuse it
;; across the different components of cl-ffi-gtk.
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
"/share/common-lisp/sbcl-source/"
"cl-cffi-gtk-glib"))
(out-source (string-append (assoc-ref outputs "out")
"/share/common-lisp/sbcl-source/"
"cl-cffi-gtk-gdk")))
(delete-file-recursively out-source)
(symlink glib-source out-source)
#t))))))))
(define-public sbcl-cl-cffi-gtk
(package
@ -3041,7 +3122,22 @@ (define-public sbcl-cl-cffi-gtk
#:test-asd-file "test/cl-cffi-gtk-test.asd"
;; TODO: Tests fail with memory fault.
;; See https://github.com/Ferada/cl-cffi-gtk/issues/24.
#:tests? #f))))
#:tests? #f
#:phases
(modify-phases %standard-phases
(add-after 'install 'link-source
;; Since source is particularly heavy (16MiB+), let's reuse it
;; across the different components of cl-ffi-gtk.
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
"/share/common-lisp/sbcl-source/"
"cl-cffi-gtk-glib"))
(out-source (string-append (assoc-ref outputs "out")
"/share/common-lisp/sbcl-source/"
"cl-cffi-gtk")))
(delete-file-recursively out-source)
(symlink glib-source out-source)
#t))))))))
(define-public cl-cffi-gtk
(sbcl-package->cl-source-package sbcl-cl-cffi-gtk))
@ -11443,21 +11539,19 @@ (define-public sbcl-osicat
(arguments
`(#:phases
(modify-phases %standard-phases
(add-before 'validate-runpath 'cleanup-files
;; The cleanup phase moves files around but we need to keep the
;; directory structure for the grovel-generated library.
(replace 'cleanup
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(lib (string-append out "/lib/sbcl")))
(for-each
delete-file
(filter (lambda (file)
(not (member (basename file)
'("basic-unixint__grovel"
"libosicat.so"
"osicat--system.fasl"
"osicat.asd"
"unixint__grovel"))))
(find-files lib ".*")))
#t))))))
(lib (string-append out "/lib/sbcl/")))
(delete-file-recursively (string-append lib "src"))
(delete-file-recursively (string-append lib "tests"))
(for-each delete-file
(filter (lambda (file)
(not (member (basename file) '("libosicat.so"))))
(find-files (string-append lib "posix") ".*"))))
#t)))))
(inputs
`(("alexandria" ,sbcl-alexandria)
("cffi" ,sbcl-cffi)

41
gnu/packages/lisp.scm
View file

@ -223,7 +223,7 @@ (define-public gcl
(define-public ecl
(package
(name "ecl")
(version "16.1.3")
(version "20.4.24")
(source
(origin
(method url-fetch)
@ -231,26 +231,22 @@ (define-public ecl
"https://common-lisp.net/project/ecl/static/files/release/"
name "-" version ".tgz"))
(sha256
(base32 "0m0j24w5d5a9dwwqyrg0d35c0nys16ijb4r0nyk87yp82v38b9bn"))
(modules '((guix build utils)))
(snippet
'(begin
;; Adjust for ABI change in LibFFI 3.3. See:
;; https://gitlab.com/embeddable-common-lisp/ecl/-/issues/302
;; https://gitlab.com/embeddable-common-lisp/ecl/-/merge_requests/171
(substitute* "src/c/ffi.d"
(("FFI_SYSV") "FFI_UNIX64"))
#t))))
(base32 "01qgdmr54wkj854f69qdm9sybrvd6gd21dpx4askdaaqybnkh237"))))
(build-system gnu-build-system)
;; src/configure uses 'which' to confirm the existence of 'gzip'.
(native-inputs `(("cl-asdf" ,cl-asdf)
("which" ,which)))
(inputs `(("gmp" ,gmp)
("libatomic-ops" ,libatomic-ops)
("libgc" ,libgc)
("libffi" ,libffi)))
(native-inputs
`(("cl-asdf" ,cl-asdf)
("which" ,which)
("texinfo" ,texinfo)))
(inputs
`(("gmp" ,gmp)
("libatomic-ops" ,libatomic-ops)
("libgc" ,libgc)
("libffi" ,libffi)))
(arguments
`(#:configure-flags '("--without-rt")
;; FIXME: As of version 20.4.24, we pass 17995 tests and fail 7.
;; 2-3 tests may be due to FHS assumptions.
#:tests? #t
#:parallel-tests? #f
#:phases
@ -311,9 +307,10 @@ (define-public ecl
C/C++ compiler, being able to build standalone executables and libraries, and
supporting ASDF, Sockets, Gray streams, MOP, and other useful components.")
;; Note that the file "Copyright" points to some files and directories
;; which aren't under the lgpl2.0+ and instead contain many different,
;; which aren't under the lgpl2.1+ and instead contain many different,
;; non-copyleft licenses.
(license license:lgpl2.0+)))
;; See https://common-lisp.net/project/ecl/posts/ECL-license.html.
(license license:lgpl2.1+)))
(define-public clisp
(package
@ -375,14 +372,14 @@ (define-public clisp
(define-public sbcl
(package
(name "sbcl")
(version "2.0.3")
(version "2.0.4")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/sbcl/sbcl/" version "/sbcl-"
version "-source.tar.bz2"))
(sha256
(base32 "001gckyw8hl842nk7nwf5kcspzkc1g8dycpwylzh5chl6893ym5m"))))
(base32 "1lc2i4qq1kfdybmxnj2zq2hn3hfx0vvlqim4gvlgvs3bfr0lcaqj"))))
(build-system gnu-build-system)
(outputs '("out" "doc"))
(native-inputs
@ -401,7 +398,7 @@ (define-public sbcl
;;
;; CCL is not bootstrappable so it won't do. CLISP 2.49 seems to work.
;; ECL too. ECL builds SBCL about 20% slower than CLISP. As of
;; 2019-09-05, ECL was last updated in 2016 while CLISP was last updated
;; 2019-09-05, ECL was last updated in 2020 while CLISP was last updated
;; in 2010.
;;
;; For now we stick to CLISP for all systems. We keep the `match' here to

75
gnu/packages/machine-learning.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2017, 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
@ -13,6 +13,7 @@
;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2020 Konrad Hinsen <konrad.hinsen@fastmail.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -835,13 +836,13 @@ (define-public python-scikit-learn
(inputs
`(("openblas" ,openblas)))
(native-inputs
`(("python-joblib" ,python-joblib)
("python-pytest" ,python-pytest)
`(("python-pytest" ,python-pytest)
("python-pandas" ,python-pandas) ;for tests
("python-cython" ,python-cython)))
(propagated-inputs
`(("python-numpy" ,python-numpy)
("python-scipy" ,python-scipy)))
("python-scipy" ,python-scipy)
("python-joblib" ,python-joblib)))
(home-page "https://scikit-learn.org/")
(synopsis "Machine Learning in Python")
(description
@ -867,6 +868,35 @@ (define-public python2-scikit-learn
(base32
"08zbzi8yx5wdlxfx9jap61vg1malc9ajf576w7a0liv6jvvrxlpj")))))))
(define-public python-scikit-rebate
(package
(name "python-scikit-rebate")
(version "0.6")
(source (origin
(method url-fetch)
(uri (pypi-uri "skrebate" version))
(sha256
(base32
"1h7qs9gjxpzqabzhb8rmpv3jpmi5iq41kqdibg48299h94iikiw7"))))
(build-system python-build-system)
;; Pandas is only needed to run the tests.
(native-inputs
`(("python-pandas" ,python-pandas)))
(propagated-inputs
`(("python-numpy" ,python-numpy)
("python-scipy" ,python-scipy)
("python-scikit-learn" ,python-scikit-learn)
("python-joblib" ,python-joblib)))
(home-page "https://epistasislab.github.io/scikit-rebate/")
(synopsis "Relief-based feature selection algorithms for Python")
(description "Scikit-rebate is a scikit-learn-compatible Python
implementation of ReBATE, a suite of Relief-based feature selection algorithms
for Machine Learning. These algorithms excel at identifying features that are
predictive of the outcome in supervised learning problems, and are especially
good at identifying feature interactions that are normally overlooked by
standard feature selection algorithms.")
(license license:expat)))
(define-public python-autograd
(let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
(revision "0")
@ -1027,8 +1057,8 @@ (define-public python2-fastlmm
;; There have been no proper releases yet.
(define-public kaldi
(let ((commit "2f95609f0bb085bd3a1dc5eb0a39f3edea59e606")
(revision "1"))
(let ((commit "d4791c0f3fc1a09c042dac365e120899ee2ad21e")
(revision "2"))
(package
(name "kaldi")
(version (git-version "0" revision commit))
@ -1040,7 +1070,7 @@ (define-public kaldi
(file-name (git-file-name name version))
(sha256
(base32
"082qh3pfi7hvncylp4xsmkfahbd7gb0whdfa4rwrx7fxk9rdh3kz"))))
"07k80my6f19mhrkwbzhjsnpf9871wmrwkl0ym468i830w67qyjrz"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
@ -1138,8 +1168,8 @@ (define-public kaldi
(license license:asl2.0))))
(define-public gst-kaldi-nnet2-online
(let ((commit "617e43e73c7cc45eb9119028c02bd4178f738c4a")
(revision "1"))
(let ((commit "cb227ef43b66a9835c14eb0ad39e08ee03c210ad")
(revision "2"))
(package
(name "gst-kaldi-nnet2-online")
(version (git-version "0" revision commit))
@ -1151,7 +1181,7 @@ (define-public gst-kaldi-nnet2-online
(file-name (git-file-name name version))
(sha256
(base32
"0xh3w67b69818s6ib02ara4lw7wamjdmh4jznvkpzrs4skbs9jx9"))))
"1i6ffwiavxx07ri0lxix6s8q0r31x7i4xxvhys5jxkixf5q34w8g"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are none
@ -1209,8 +1239,9 @@ (define-public gst-kaldi-nnet2-online
(license license:asl2.0))))
(define-public kaldi-gstreamer-server
(let ((commit "1735ba49c5dc0ebfc184e45105fc600cd9f1f508")
(revision "1"))
;; This is the tip of the py3 branch
(let ((commit "f68cab490be7eb0da2af1475fbc16655f50a60cb")
(revision "2"))
(package
(name "kaldi-gstreamer-server")
(version (git-version "0" revision commit))
@ -1222,7 +1253,7 @@ (define-public kaldi-gstreamer-server
(file-name (git-file-name name version))
(sha256
(base32
"0j701m7lbwmzqxsfanj882v7881hrbmpqybbczbxqpcbg8q34w0k"))))
"17lh1368vkg8ngrcbn2phvigzlmalrqg6djx2gg61qq1a0nj87dm"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are no tests that can be run automatically
@ -1238,6 +1269,14 @@ (define-public kaldi-gstreamer-server
;; are reproducible.
(setenv "PYTHONHASHSEED" "0")
(with-directory-excursion "kaldigstserver"
;; See https://github.com/alumae/kaldi-gstreamer-server/issues/232
(substitute* "master_server.py"
(("\\.replace\\('\\\\.*") ")"))
;; This is a Python 2 file
(delete-file "decoder_test.py")
(delete-file "test-buffer.py")
(for-each (lambda (file)
(apply invoke
`("python"
@ -1288,12 +1327,10 @@ (define-public kaldi-gstreamer-server
#t))))))
(inputs
`(("gst-kaldi-nnet2-online" ,gst-kaldi-nnet2-online)
("python2" ,python-2)
("python2-futures" ,python2-futures)
("python2-pygobject" ,python2-pygobject)
("python2-pyyaml" ,python2-pyyaml)
("python2-tornado" ,python2-tornado)
("python2-ws4py" ,python2-ws4py-for-kaldi-gstreamer-server)))
("python" ,python-wrapper)
("python-pygobject" ,python-pygobject)
("python-pyyaml" ,python-pyyaml)
("python-tornado" ,python-tornado-6)))
(home-page "https://github.com/alumae/kaldi-gstreamer-server")
(synopsis "Real-time full-duplex speech recognition server")
(description "This is a real-time full-duplex speech recognition server,

12
gnu/packages/magic-wormhole.scm
View file

@ -29,14 +29,14 @@ (define-module (gnu packages magic-wormhole)
(define-public magic-wormhole-mailbox-server
(package
(name "magic-wormhole-mailbox-server")
(version "0.3.1")
(version "0.4.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "magic-wormhole-mailbox-server" version))
(sha256
(base32
"1q6zhbx8fcpk7rchclm7yqcxdsc1x97hki2ji61sa544r5xvxv55"))))
"1yw8i8jv5iv1kkz1aqimskw7fpichjn6ww0fq0czbalwj290bw8s"))))
(build-system python-build-system)
(arguments
'(#:phases
@ -68,14 +68,14 @@ (define-public magic-wormhole-mailbox-server
(define-public magic-wormhole-transit-relay
(package
(name "magic-wormhole-transit-relay")
(version "0.1.2")
(version "0.2.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "magic-wormhole-transit-relay" version))
(sha256
(base32
"11w5gdc6am2ph5rns60x0694sx4zrlzxj540jljhn5cmnbx1ngxi"))))
"0ppsx2s1ysikns1h053x67z2zmficbn3y3kf52bzzslhd2s02j6b"))))
(build-system python-build-system)
(arguments
`(#:phases
@ -107,14 +107,14 @@ (define-public magic-wormhole-transit-relay
(define-public magic-wormhole
(package
(name "magic-wormhole")
(version "0.11.2")
(version "0.12.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "magic-wormhole" version))
(sha256
(base32
"01fr4bi6kc6fz9n3c4qq892inrc3nf6p2djy65yvm7xkvdxncydf"))))
"0q41j99718y7m95zg1vaybnsp31lp6lhyqkbv4yqz5ys6jixh3qv"))))
(build-system python-build-system)
(arguments
'(#:phases

41
gnu/packages/maths.scm
View file

@ -5,7 +5,7 @@
;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Eric Bavier <bavier@posteo.net>
;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
@ -1320,6 +1320,45 @@ (define-public hdf5-parallel-openmpi
#t))))))
(synopsis "Management suite for data with parallel IO support")))
(define-public hdf5-blosc
(package
(name "hdf5-blosc")
(version "1.0.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Blosc/hdf5-blosc.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1nj2bm1v6ymm3fmyvhbn6ih5fgdiapavlfghh1pvbmhw71cysyqs"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags
(list (string-append "-DBLOSC_INSTALL_DIR="
(assoc-ref %build-inputs "c-blosc"))
(string-append "-DPLUGIN_INSTALL_PATH="
(assoc-ref %outputs "out")
"/hdf5/lib/plugin"))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'do-not-build-blosc
(lambda _
(substitute* "CMakeLists.txt"
(("set\\(BLOSC_INSTALL_DIR.*") "")
(("ExternalProject_Add\\(project_blosc") "message("))
#t)))))
(inputs
`(("c-blosc" ,c-blosc)
("hdf5" ,hdf5-1.10)))
(home-page "https://github.com/Blosc/hdf5-blosc")
(synopsis "Filter for HDF5 using the Blosc compressor")
(description "This is a filter for HDF5 that uses the Blosc compressor; by
installing this filter, you can read and write HDF5 files with
Blosc-compressed datasets.")
(license license:expat)))
(define-public h5check
(package
(name "h5check")

4
gnu/packages/mpd.scm
View file

@ -92,7 +92,7 @@ (define-public libmpdclient
(define-public mpd
(package
(name "mpd")
(version "0.21.22")
(version "0.21.23")
(source (origin
(method url-fetch)
(uri
@ -101,7 +101,7 @@ (define-public mpd
"/mpd-" version ".tar.xz"))
(sha256
(base32
"18lvyv3crijki5nxjdhf1byayyavdvj07dk6rm856n4vi78qfmjn"))))
"18q72b9baj5cdpq0yn60qm7q4g8vwqqyqndl9xg3f3w0m4n557s3"))))
(build-system meson-build-system)
(arguments
`(#:configure-flags '("-Ddocumentation=true"))) ;the default is 'false'...

7
gnu/packages/music.scm
View file

@ -99,6 +99,7 @@ (define-module (gnu packages music)
#:use-module (gnu packages gnome)
#:use-module (gnu packages gpodder)
#:use-module (gnu packages graphics)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages gstreamer)
#:use-module (gnu packages gtk)
#:use-module (gnu packages guile)
@ -5158,7 +5159,7 @@ (define-public helm
(define-public zrythm
(package
(name "zrythm")
(version "0.8.200")
(version "0.8.333")
(source
(origin
(method url-fetch)
@ -5166,7 +5167,7 @@ (define-public zrythm
version ".tar.xz"))
(sha256
(base32
"13ivxbrd44qnhyh46dcr94dvqxg8cn4bbd8xm77ljw0p9b4ks4zs"))))
"0x2kxr5zz058jpy6k6ymj0fi2gqfcgrlv4qkwz9443hjy5345iwb"))))
(build-system meson-build-system)
(arguments
`(#:glib-or-gtk? #t
@ -5190,7 +5191,9 @@ (define-public zrythm
("fftwf" ,fftwf)
("gettext" ,gettext-minimal)
("glibc" ,glibc)
("graphviz" ,graphviz)
("gtk+" ,gtk+)
("gtksourceview" ,gtksourceview)
("guile" ,guile-2.2)
("libcyaml" ,libcyaml)
("libsamplerate" ,libsamplerate)

15
gnu/packages/openldap.scm
View file

@ -6,6 +6,7 @@
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@ -60,6 +61,7 @@ (define-module (gnu packages openldap)
(define-public openldap
(package
(name "openldap")
(replacement openldap-2.4.50)
(version "2.4.49")
(source (origin
(method url-fetch)
@ -125,6 +127,19 @@ (define-public openldap
(license openldap2.8)
(home-page "https://www.openldap.org/")))
(define openldap-2.4.50
(package
(inherit openldap)
(version "2.4.50")
(source (origin
(method url-fetch)
(uri (string-append "https://www.openldap.org/software/download/"
"OpenLDAP/openldap-release/openldap-" version
".tgz"))
(sha256
(base32
"1f46nlfwmys110j36sifm7ah8m8f3s10c3vaiikmmigmifapvdaw"))))))
(define-public nss-pam-ldapd
(package
(name "nss-pam-ldapd")

19
gnu/packages/openstack.scm
View file

@ -4,6 +4,7 @@
;;; Copyright © 2016, 2017, 2019 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2020 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -130,21 +131,31 @@ (define-public python2-debtcollector
(define-public python-hacking
(package
(name "python-hacking")
(version "1.0.0")
(version "1.1.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "hacking" version))
(sha256
(base32
"0s9l99s64jsyvm28fa4hzllbdi21sb7jn4gzdf1pd5ckvy7p4b0k"))))
"1vlgh81v4vsw3q3cf7qggsp043vq16knp203lrll82h7l7rhd8r3"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'delete-broken-test
(lambda _
;; TODO: Just one test fails:
;; hacking.tests.test_doctest.HackingTestCase.test_pycodestyle
;; (H403-hacking_docstring_multiline_end-line-5)
(delete-file "hacking/tests/test_doctest.py")
#t)))))
(propagated-inputs
`(("python-flake8" ,python-flake8-2.5)
`(("python-flake8" ,python-flake8-2.6)
("python-mccabe-0.2.1" ,python-mccabe-0.2.1)
("python-pbr" ,python-pbr)
("python-pep8-1.5.7" ,python-pep8-1.5.7)
("python-pyflakes-0.8.1" ,python-pyflakes-0.8.1)
("python-pyflakes-1.2" ,python-pyflakes-1.2)
("python-six" ,python-six)))
(native-inputs
`( ;; Tests

4
gnu/packages/package-management.scm
View file

@ -112,7 +112,7 @@ (define-public guix
;; Note: the 'update-guix-package.scm' script expects this definition to
;; start precisely like this.
(let ((version "1.1.0")
(commit "569c55bee2a74106b3ab8a07187ea9cd8cce410e")
(commit "619f9181a363576894a433206008b139255062dd")
(revision 2))
(package
(name "guix")
@ -129,7 +129,7 @@ (define-public guix
(commit commit)))
(sha256
(base32
"036lg8qj6hh2093lqwxdmwdir8frck8ap5king8sl4j29yc59jzc"))
"1lk0h9zgry7m78nv70gxwb57pw1d5yzay477gxsc43v1aa7zg8sp"))
(file-name (string-append "guix-" version "-checkout"))))
(build-system gnu-build-system)
(arguments

14
gnu/packages/patches/emacs-telega-test-env.patch Normal file
View file

@ -0,0 +1,14 @@
Test Emacs environment on startup.
Patch by Diego N. Barbato
--- a/telega.el 2020-02-07 17:07:18.549970090 +0100
+++ b/telega.el 2020-02-07 17:10:08.383499765 +0100
@@ -82,6 +82,7 @@
"Start telegramming.
If prefix ARG is given, then will not pop to telega root buffer."
(interactive "P")
+ (telega-test-env t)
(telega--create-hier)
(unless (telega-server-live-p)

35
gnu/packages/python-science.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
@ -162,6 +162,39 @@ (define-public python2-scipy
(base32
"1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))
(define-public python2-weave
(package
(name "python2-weave")
(version "0.16.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "weave" version))
(sha256
(base32 "0jnm3584mfichgwgrd1gk5i42ll9c08nkw9716n947n4338f6ghs"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _
(invoke "nosetests" "-v"
"--exclude"
"test_(user|incorrect_ownership|char_fail|obj_fail)"))))))
(propagated-inputs
`(("python-numpy" ,python2-numpy)))
(native-inputs
`(("python-nose" ,python2-nose)))
(home-page "https://www.scipy.org/")
(synopsis "Tools for including C/C++ code within Python code")
(description "Weave is the stand-alone version of the obsolete Scipy
submodule @code{scipy.weave}. It is Python 2.x only, and is provided for
users that need new versions of Scipy but have existing code that still
depends on @code{scipy.weave}. For new code, users are recommended to use
Cython.")
(license license:bsd-3)))
(define-public python-scikit-image
(package
(name "python-scikit-image")

112
gnu/packages/python-web.scm
View file

@ -879,6 +879,37 @@ (define-public python-tornado
(license license:asl2.0)
(properties `((python2-variant . ,(delay python2-tornado))))))
(define-public python-tornado-6
(package
(name "python-tornado")
(version "6.0.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "tornado" version))
(sha256
(base32
"1p5n7sw4580pkybywg93p8ddqdj9lhhy72rzswfa801vlidx9qhg"))))
(build-system python-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _
(invoke "python" "-m" "tornado.test.runtests")
#t)))))
(native-inputs
`(("python-certifi" ,python-certifi)))
(home-page "https://www.tornadoweb.org/")
(synopsis "Python web framework and asynchronous networking library")
(description
"Tornado is a Python web framework and asynchronous networking library,
originally developed at FriendFeed. By using non-blocking network I/O,
Tornado can scale to tens of thousands of open connections, making it ideal
for long polling, WebSockets, and other applications that require a long-lived
connection to each user.")
(license license:asl2.0)))
(define-public python2-tornado
(let ((tornado (package-with-python2 (strip-python2-variant python-tornado))))
(package (inherit tornado)
@ -3280,32 +3311,6 @@ (define-public python-ws4py
Python.")
(license license:bsd-3)))
;; kaldi-gstreamer-server does not yet work with python-ws4py > 0.3.2
(define-public python2-ws4py-for-kaldi-gstreamer-server
(package (inherit python-ws4py)
(name "python2-ws4py")
(version "0.3.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ws4py" version))
(sha256
(base32
"12ys3dv98awhrxd570vla3hqgzq3avjhq4yafhghhq3a942y1928"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:phases
(modify-phases %standard-phases
;; We don't have a package for cherrypy.
(add-after 'unpack 'remove-cherrypy-support
(lambda _
(delete-file "ws4py/server/cherrypyserver.py")
#t)))))
(propagated-inputs
`(("python-gevent" ,python2-gevent)
("python-tornado" ,python2-tornado)))))
(define-public python-slugify
(package
(name "python-slugify")
@ -3633,3 +3638,58 @@ (define-public grip
appear. Changes you make to the file will be instantly reflected in the browser
without requiring a page refresh.")
(license license:expat))))
(define-public python-port-for
(package
(name "python-port-for")
(version "0.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "port-for" version))
(sha256
(base32
"1pncxlj25ggw99r0ijfbkq70gd7cbhqdx5ivsxy4jdp0z14cpda7"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'use-urllib3
(lambda _
(substitute* "port_for/_download_ranges.py"
(("urllib2") "urllib3"))
#t)))))
(propagated-inputs
`(("python-urllib3" ,python-urllib3)))
(native-inputs
`(("python-mock" ,python-mock)))
(home-page "https://github.com/kmike/port-for/")
(synopsis "TCP localhost port finder and association manager")
(description
"This package provides a utility that helps with local TCP ports
management. It can find an unused TCP localhost port and remember the
association.")
(license license:expat)))
(define-public python-livereload
(package
(name "python-livereload")
(version "2.6.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "livereload" version))
(sha256
(base32
"0rhggz185bxc3zjnfpmhcvibyzi86i624za1lfh7x7ajsxw4y9c9"))))
(build-system python-build-system)
(propagated-inputs
`(("python-six" ,python-six)
("python-tornado" ,python-tornado)))
(home-page "https://github.com/lepture/python-livereload")
(synopsis "Python LiveReload")
(description
"Python LiveReload provides a command line utility, @command{livereload},
for starting a web server in a directory. It can trigger arbitrary commands
and serve updated contents upon changes to the directory.")
(license license:bsd-3)))

285
gnu/packages/python-xyz.scm
View file

@ -39,7 +39,7 @@
;;; Copyright © 2017 Ben Sturmfels <ben@sturm.com.au>
;;; Copyright © 2017, 2018, 2019 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2017 José Miguel Sánchez García <jmi2k@openmailbox.org>
;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019 Kei Kebreau <kkebreau@posteo.net>
;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2017 Muriithi Frederick Muriuki <fredmanglis@gmail.com>
@ -413,16 +413,17 @@ (define-public python-pymediainfo
(define-public python-psutil
(package
(name "python-psutil")
(version "5.6.5")
(version "5.7.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "psutil" version))
(sha256
(base32 "0isil5jxwwd8awz54qk28rpgjg43i5l6yl70g40vxwa4r4m56lfh"))))
(base32 "03jykdi3dgf1cdal9bv4fq9zjvzj9l9bs99gi5ar81sdl5nc2pk8"))))
(build-system python-build-system)
(arguments
;; FIXME: some tests does not return and times out.
;; FIXME: some tests do not return and time out. Some tests fail because
;; some processes survive kill().
'(#:tests? #f))
(home-page "https://www.github.com/giampaolo/psutil")
(synopsis "Library for retrieving information on running processes")
@ -641,6 +642,30 @@ (define-public python2-backport-ssl-match-hostname
and verifies that it matches the intended target hostname.")
(license license:psfl)))
(define-public python-bitarray
(package
(name "python-bitarray")
(version "1.2.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "bitarray" version))
(sha256
(base32
"1kxrlxfj9nrx512sfwifwl9z4v6ky3qschl0zmk3s3dvc3s7bmif"))))
(build-system python-build-system)
(home-page "https://github.com/ilanschnell/bitarray")
(synopsis "Efficient arrays of booleans")
(description "This package provides an object type which efficiently
represents an array of booleans. Bitarrays are sequence types and behave very
much like usual lists. Eight bits are represented by one byte in a contiguous
block of memory. The user can select between two representations:
little-endian and big-endian. All of the functionality is implemented in C.
Methods for accessing the machine representation are provided. This can be
useful when bit level access to binary files is required, such as portable
bitmap image files. Also, when dealing with compressed data which uses
variable bit length encoding, you may find this module useful.")
(license license:psfl)))
(define-public python-boolean.py
(package
(name "python-boolean.py")
@ -3208,6 +3233,77 @@ (define-public python2-docutils-0.14
(base32
"0x22fs3pdmr42kvz6c654756wja305qv6cx1zbhwlagvxgr4xrji"))))))
(define-public python-restructuredtext-lint
(package
(name "python-restructuredtext-lint")
(version "1.3.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "restructuredtext-lint" version))
(sha256
(base32
"026rdy5h82ng4vqxk8fnprii9d6qxf7hkygiv0a8afjvdlsxmcwp"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(delete 'check)
(add-after 'install 'check
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
(when tests?
(add-installed-pythonpath inputs outputs)
(invoke "nosetests" "-v"))
#t)))))
(propagated-inputs
`(("python-docutils" ,python-docutils)))
(native-inputs
`(("python-nose" ,python-nose)))
(home-page "https://github.com/twolfson/restructuredtext-lint")
(synopsis "reStructuredText linter")
(description "This package provides a linter for the reStructuredText
format.")
(license license:unlicense)))
(define-public python-doc8
(package
(name "python-doc8")
(version "0.8.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "doc8" version))
(sha256
(base32
"0hw5w8mpgsp51qg8nnq28p7y1jiksvz7a0axnn5bkgss3af9zy1d"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(delete 'check)
(add-after 'install 'check
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
(when tests?
(add-installed-pythonpath inputs outputs)
(invoke "pytest" "-v"))
#t)))))
(propagated-inputs
`(("python-chardet" ,python-chardet)
("python-docutils" ,python-docutils)
("python-restructuredtext-lint" ,python-restructuredtext-lint)
("python-six" ,python-six)
("python-stevedore" ,python-stevedore)))
(native-inputs
`(("python-testtools" ,python-testtools)
("python-pytest" ,python-pytest)))
(home-page "https://launchpad.net/doc8")
(synopsis
"Style checker for Sphinx (or other) RST documentation")
(description
"Doc8 is an opinionated style checker for reStructured Text and plain
text styles of documentation.")
(license license:asl2.0)))
(define-public python-pygments
(package
(name "python-pygments")
@ -4794,27 +4890,38 @@ (define-public python-matplotlib-venn
three-way Venn diagrams in @code{matplotlib}.")
(license license:expat)))
(define-public python2-pysnptools
(define-public python-pysnptools
(package
(name "python2-pysnptools")
(version "0.3.13")
(name "python-pysnptools")
(version "0.4.11")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pysnptools" version))
(sha256
(base32
"0lnis5xsl7bi0hz4f7gbicahzi5zlxkc21nk3g374xv8fb5hb3qm"))))
"0gxr0bjix307wvk0qh7vkafbxbzfpdmq0wlswpxyyaymy0fwcypv"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2 ; only Python 2.7 is supported
#:tests? #f)) ; test files (e.g. examples/toydata.bim) not included
`(#:tests? #f ; no test data are included
#:phases
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
(if tests?
(begin
(add-installed-pythonpath inputs outputs)
(invoke "python3" "pysnptools/test.py"))
#t))))))
(propagated-inputs
`(("python2-numpy" ,python2-numpy)
("python2-scipy" ,python2-scipy)
("python2-pandas" ,python2-pandas)))
`(("python-dill" ,python-dill)
("python-h5py" ,python-h5py)
("python-numpy" ,python-numpy)
("python-pandas" ,python-pandas)
("python-psutil" ,python-psutil)
("python-scipy" ,python-scipy)))
(native-inputs
`(("python2-cython" ,python2-cython)))
`(("python-cython" ,python-cython)))
(home-page "http://microsoftgenomics.github.io/PySnpTools/")
(synopsis "Library for reading and manipulating genetic data")
(description
@ -4824,6 +4931,9 @@ (define-public python2-pysnptools
operators such as union, intersection, and difference.")
(license license:asl2.0)))
(define-public python2-pysnptools
(package-with-python2 python-pysnptools))
(define-public python-socksipy-branch
(package
(name "python-socksipy-branch")
@ -7328,6 +7438,27 @@ (define-public python-pyflakes
(define-public python2-pyflakes
(package-with-python2 python-pyflakes))
;; Flake8 2.6 requires an older version of pyflakes.
;; This should be removed ASAP.
(define-public python-pyflakes-1.2
(package (inherit python-pyflakes)
(version "1.2.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyflakes" version))
(sha256
(base32
"17hkw8yd44cr8fz13phy4aih3r5j2p7ild4zlvqdh2c8dmiinjif"))))
(arguments
'(#:phases
(modify-phases %standard-phases
;; This one test fails.
(replace 'check
(lambda _ (invoke "pytest" "-vv" "-k" "not test_f_string"))))))
(native-inputs
`(("python-pytest" ,python-pytest)))))
(define-public python-mccabe
(package
(name "python-mccabe")
@ -7386,25 +7517,6 @@ (define-public python-pep8-1.5.7
(define-public python2-pep8-1.5.7
(package-with-python2 python-pep8-1.5.7))
;; Flake8 2.4.1 requires an older version of pyflakes.
;; This should be removed ASAP.
(define-public python-pyflakes-0.8.1
(package (inherit python-pyflakes)
(version "0.8.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyflakes" version))
(sha256
(base32
"0sbpq6pqm1i9wqi41mlfrsc5rk92jv4mskvlyxmnhlbdnc80ma1z"))))
(arguments
;; XXX Tests not compatible with Python 3.5.
'(#:tests? #f))))
(define-public python2-pyflakes-0.8.1
(package-with-python2 python-pyflakes-0.8.1))
(define-public python-flake8
(package
(name "python-flake8")
@ -7451,31 +7563,39 @@ (define-public python2-flake8
("python2-typing" ,python2-typing)
,@(package-propagated-inputs base))))))
;; python-hacking requires flake8 <2.6.0.
(define-public python-flake8-2.5
;; python-hacking requires flake8 <2.7.0.
(define-public python-flake8-2.6
(package
(inherit python-flake8)
(version "2.5.5")
(version "2.6.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "flake8" version))
(sha256
(base32
"1snylqwbmrylbx3r1wpz8ggk98f6bcag4441ag8mm2l7wyn58sij"))))
"0y57hzal0j84dh9i1g1g6dc4aywvrnhy2fjmmbglpv5ajihxh713"))))
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'use-later-pycodestyles
(lambda __
(substitute* '("flake8.egg-info/requires.txt"
"setup.py")
(("pycodestyle >= 2.0, < 2.1")
"pycodestyle >= 2.0"))
#t))
(delete 'check)
(add-after 'install 'check
(lambda* (#:key inputs outputs #:allow-other-keys)
(add-installed-pythonpath inputs outputs)
(invoke "pytest" "-v")
#t)))))
(propagated-inputs
`(("python-pep8" ,python-pep8)
,@(package-propagated-inputs python-flake8)))
(properties `((python2-variant . ,(delay python2-flake8-2.5))))))
(define-public python2-flake8-2.5
(package
(inherit python2-flake8)
(version (package-version python-flake8-2.5))
(source (origin
(inherit (package-source python-flake8-2.5))))
(propagated-inputs
`(("python2-pep8" ,python2-pep8)
,@(package-propagated-inputs python2-flake8)))))
("python-pycodestyle" ,python-pycodestyle)
("python-entrypoints" ,python-entrypoints)
("python-pyflakes" ,python-pyflakes-1.2)
("python-mccabe" ,python-mccabe)))))
(define-public python-flake8-polyfill
(package
@ -19695,3 +19815,70 @@ (define-public python-osc
dependencies. It implements the @uref{http://opensoundcontrol.org/spec-1_0,
Open Sound Control 1.0} specification.")
(license license:unlicense)))
(define-public python-voluptuous
(package
(name "python-voluptuous")
(version "0.11.7")
(source
(origin
(method url-fetch)
(uri (pypi-uri "voluptuous" version))
(sha256
(base32
"0mplkcpb5d8wjf8vk195fys4y6a3wbibiyf708imw33lphfk9g1a"))))
(build-system python-build-system)
(native-inputs
`(("python-nose" ,python-nose)))
(home-page "https://github.com/alecthomas/voluptuous")
(synopsis "Python data validation library")
(description
"Voluptuous is a Python data validation library. It is primarily
intended for validating data coming into Python as JSON, YAML, etc.")
(license license:bsd-3)))
(define-public python-cmd2
(package
(name "python-cmd2")
(version "1.0.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cmd2" version))
(sha256
(base32
"1f18plbc9yyvhn0js3d2bii9yld8zfl775gxsaw9jza5pmlg9ss2"))))
(build-system python-build-system)
(propagated-inputs
`(("python-attrs" ,python-attrs)
("python-colorama" ,python-colorama)
("python-pyperclip" ,python-pyperclip)
("python-wcwidth" ,python-wcwidth)))
(native-inputs
`(("python-codecov" ,python-codecov)
("python-coverage" ,python-coverage)
("python-doc8" ,python-doc8)
("python-flake8" ,python-flake8)
("python-invoke" ,python-invoke)
("python-mock" ,python-mock)
("python-pytest" ,python-pytest)
("python-pytest-cov" ,python-pytest-cov)
("python-pytest-mock" ,python-pytest-mock)
("python-setuptools-scm" ,python-setuptools-scm)
("python-sphinx" ,python-sphinx)
("python-sphinx-autobuild" ,python-sphinx-autobuild)
("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme)
("python-tox" ,python-tox)
("python-twine" ,python-twine)
("which" ,which)))
(home-page "https://github.com/python-cmd2/cmd2")
(synopsis "Tool for building interactive command line applications")
(description
"Cmd2 is a tool for building interactive command line applications in
Python. Its goal is to make it quick and easy for developers to build
feature-rich and user-friendly interactive command line applications. It
provides a simple API which is an extension of Python's built-in @code{cmd}
module. @code{cmd2} provides a wealth of features on top of @code{cmd} to
make your life easier and eliminates much of the boilerplate code which would
be necessary when using @code{cmd}.")
(license license:expat)))

138
gnu/packages/radio.scm
View file

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017, 2018, 2019 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2019 Christopher Howard <christopher@librehacker.com>
;;; Copyright © 2019, 2020 Christopher Howard <christopher@librehacker.com>
;;; Copyright © 2019, 2020 Evan Straw <evan.straw99@gmail.com>
;;; Copyright © 2020 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2020 Danny Milosavljevic <dannym@scratchpost.org>
@ -26,6 +26,7 @@ (define-module (gnu packages radio)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix utils)
#:use-module (gnu packages algebra)
#:use-module (gnu packages audio)
#:use-module (gnu packages autotools)
@ -266,7 +267,6 @@ (define-public gnuradio
("ghostscript" ,ghostscript)
("orc" ,orc)
("pkg-config" ,pkg-config)
("python" ,python)
("python-cheetah" ,python-cheetah)
("python-mako" ,python-mako)
("python-pyzmq" ,python-pyzmq)
@ -293,6 +293,7 @@ (define-public gnuradio
("log4cpp" ,log4cpp)
("pango" ,pango)
("portaudio" ,portaudio)
("python" ,python)
("python-click" ,python-click)
("python-click-plugins" ,python-click-plugins)
("python-lxml" ,python-lxml)
@ -363,6 +364,17 @@ (define-public gnuradio
(wrap-program (string-append out "/bin/gnuradio-companion")
`("GI_TYPELIB_PATH" ":" prefix ,(filter identity paths))))
#t)))))
(native-search-paths
;; Variables required to find third-party plugins at runtime.
(list (search-path-specification
(variable "GRC_BLOCKS_PATH")
(files '("share/gnuradio/grc/blocks")))
(search-path-specification
(variable "PYTHONPATH")
(files (list (string-append "lib/python"
(version-major+minor
(package-version python))
"/site-packages"))))))
(synopsis "Toolkit for software-defined radios")
(description
"GNU Radio is a development toolkit that provides signal processing blocks
@ -399,8 +411,8 @@ (define-public gnuradio-osmosdr
("fftwf" ,fftwf)
("gmp" ,gmp)
("gnuradio" ,gnuradio)
("hackrf" ,hackrf)
("log4cpp" ,log4cpp)
;; TODO: Add more drivers.
("rtl-sdr" ,rtl-sdr)
("volk" ,volk)))
(synopsis "GNU Radio block for interfacing with various radio hardware")
@ -537,14 +549,14 @@ (define-public gqrx
(define-public fldigi
(package
(name "fldigi")
(version "4.1.11")
(version "4.1.12")
(source
(origin
(method url-fetch)
(uri (string-append "http://www.w1hkj.com/files/fldigi/fldigi-"
version ".tar.gz"))
(sha256
(base32 "1y62xn1pim38ibaf2mbl8b7aq20jdaac6lgggb9r402w9bj5b196"))))
(base32 "1yjjv2ss84xfiaidypp476mhrbpnw4zf7mb5cdqwhdh604x0svr1"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))
@ -654,6 +666,73 @@ (define-public flwrap
(home-page "http://www.w1hkj.com/")
(license license:gpl3+)))
(define-public hackrf
;; Using a git commit because there have been many many commits
;; since the relase two years ago, but no sign of a promised
;; release for many months now.
(let ((commit "43e6f99fe8543094d18ff3a6550ed2066c398862")
(revision "0"))
(package
(name "hackrf")
(version (git-version "2018.01.1" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mossmann/hackrf.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0avnv693xi0zsnrvkbfn0ln1r3s1iyj0bz7sc3gxay909av0pvbc"))))
(build-system cmake-build-system)
(arguments
'(#:configure-flags
(list "-DUDEV_RULES_GROUP=dialout"
(string-append "-DUDEV_RULES_PATH="
(assoc-ref %outputs "out")
"/lib/udev/rules.d"))
#:phases
(modify-phases %standard-phases
(add-before 'configure 'enter-source-directory
(lambda _
(chdir "host")
#t))
(add-after 'install 'delete-static-library
(lambda* (#:key outputs #:allow-other-keys)
(delete-file (string-append (assoc-ref outputs "out")
"/lib/libhackrf.a"))
#t))
(add-before 'install-license-files 'leave-source-directory
(lambda _
(chdir "..")
#t)))
#:tests? #f)) ; no test suite
(native-inputs
`(("pkg-config" ,pkg-config)))
(inputs
`(("fftw" ,fftw)
("fftwf" ,fftwf)
("libusb" ,libusb)))
(home-page "https://greatscottgadgets.com/hackrf/")
(synopsis "User-space library and utilities for HackRF SDR")
(description
"Command line utilities and a C library for controlling the HackRF
Software Defined Radio (SDR) over USB. Installing this package installs
the userspace hackrf utilities and C library. To install the hackrf
udev rules, you must add this package as a system service via
modify-services. E.g.:
@lisp
(services
(modify-services
%desktop-services
(udev-service-type config =>
(udev-configuration (inherit config)
(rules (cons hackrf
(udev-configuration-rules config)))))))
@end lisp")
(license license:gpl2))))
(define-public hamlib
(package
(name "hamlib")
@ -762,3 +841,52 @@ (define-public wsjtx
weak-signal conditions.")
(home-page "https://www.physics.princeton.edu/pulsar/k1jt/wsjtx.html")
(license license:gpl3)))
(define-public xnec2c
(package
(name "xnec2c")
(version "4.1.1")
(source
(origin
(method url-fetch)
(uri (string-append "http://www.5b4az.org/pkg/nec2/xnec2c/xnec2c-"
version ".tar.bz2"))
(sha256
(base32 "1myvlkfybb2ha8l0h96ca3iz206zzy9z5iizm0sbab2zzp78n1r9"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))
(inputs
`(("gtk+" ,gtk+)))
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-makefile
(lambda* (#:key outputs #:allow-other-keys)
(substitute* '("Makefile.am" "Makefile.in")
;; The DESTDIR variable does not get replaced the prefix
;; in the final Makefile, so let's do here.
(("\\$\\(DESTDIR\\)/usr")
(assoc-ref outputs "out")))
#t))
(add-after 'fix-makefile 'fix-paths
(lambda* (#:key outputs #:allow-other-keys)
;; Increase the max length of the path to the glade file,
;; so that the '/gnu/store/...' path can fit in.
(substitute* '("src/shared.c" "src/shared.h")
(("char xnec2c_glade\\[64\\];")
"char xnec2c_glade[256];"))
;; Fix hard coded references to '/usr/...'.
(substitute* '("src/geom_edit.c" "src/main.c")
(("\"/usr")
(string-append "\"" (assoc-ref outputs "out"))))
#t)))))
(synopsis "Antenna modeling software")
(description
"Xnec2c is a GTK3-based graphical version of nec2c, a translation to the
C language of NEC2, the FORTRAN Numerical Electromagnetics Code commonly used
for antenna simulation and analysis. It can be used to define the geometry of
an antenna, and then plot the radiation pattern or frequency-related data like
gain and standing wave ratio.")
(home-page "http://www.5b4az.org/")
(license license:gpl3+)))

51
gnu/packages/rust-apps.scm
View file

@ -3,6 +3,7 @@
;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
;;; Copyright © 2020 Leo Famulari <leo@famulari.name>
;;;
;;; This file is part of GNU Guix.
;;;
@ -290,7 +291,7 @@ (define-public rust-cbindgen
("serde" ,rust-serde-1.0)
("serde-json" ,rust-serde-json-1.0)
("syn" ,rust-syn-1.0)
("tempfile" ,rust-tempfile-3.0)
("tempfile" ,rust-tempfile-3.1)
("toml" ,rust-toml-0.5))))
(home-page "https://github.com/eqrion/cbindgen/")
(synopsis "Tool for generating C bindings to Rust code")
@ -298,6 +299,21 @@ (define-public rust-cbindgen
"This package provides a tool for generating C/C++ bindings to Rust code.")
(license license:mpl2.0)))
(define-public rust-cbindgen-0.12
(package
(inherit rust-cbindgen)
(name "rust-cbindgen")
(version "0.12.2")
(source
(origin
(method url-fetch)
(uri (crate-uri "cbindgen" version))
(file-name
(string-append name "-" version ".tar.gz"))
(sha256
(base32
"13jzbmjz1bmmfr0i80hw6ar484mgabx3hbpb2ynhk0ddqi0yr58m"))))))
(define-public tokei
(package
(name "tokei")
@ -358,3 +374,36 @@ (define-public tokei
show number of files, total lines within those files and code, comments, and
blanks grouped by language.")
(license (list license:expat license:asl2.0))))
(define-public rust-cargo-c
(package
(name "rust-cargo-c")
(version "0.5.2")
(source
(origin
(method url-fetch)
(uri (crate-uri "cargo-c" version))
(file-name
(string-append name "-" version ".tar.gz"))
(sha256
(base32
"1is72jm0r73pqx2g3h1n6lvrcirwd91mmajsmb3jjg4jnayfkp0w"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
(("rust-cbindgen" ,rust-cbindgen-0.12)
("rust-pretty-env-logger" ,rust-pretty-env-logger-0.3)
("rust-structopt" ,rust-structopt-0.3)
("rust-log" ,rust-log-0.4)
("rust-toml" ,rust-toml-0.5)
("rust-cargo-metadata" ,rust-cargo-metadata-0.9)
("rust-serde" ,rust-serde-1.0)
("rust-serde-derive" ,rust-serde-derive-1.0)
("rust-regex" ,rust-regex-1.3))))
(home-page "https://github.com/lu-zero/cargo-c")
(synopsis "Build and install C-compatible libraries")
(description
"This package produces and installs a correct pkg-config file, a static
library and a dynamic library, and a C header to be used by any C (and
C-compatible) software.")
(license license:expat)))

48
gnu/packages/sphinx.scm
View file

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014 David Thompson <davet@gnu.org>
;;; Copyright © 2015, 2017, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2017, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016, 2017 Leo Famulari <leo@famulari.name>
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2016, 2017, 2018, 2019 Marius Bakke <mbakke@fastmail.com>
@ -597,3 +597,49 @@ (define-public python-sphinx-intl
"A utility tool that provides several features that make it easy to
translate and to apply translation to Sphinx generated document.")
(license license:bsd-2)))
(define-public python-sphinx-autobuild
(package
(name "python-sphinx-autobuild")
(version "0.7.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "sphinx-autobuild" version))
(sha256
(base32
"0kn753dyh3b1s0h77lbk704niyqc7bamvq6v3s1f6rj6i20qyf36"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
;; See https://github.com/GaretJax/sphinx-autobuild/pull/72
(add-after 'unpack 'use-later-port-for
(lambda _
(substitute* "requirements.txt"
(("port_for==.*") "port_for\n"))
#t))
(delete 'check)
(add-after 'install 'check
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
(when tests?
(add-installed-pythonpath inputs outputs)
(invoke "pytest" "-v"))
#t)))))
(propagated-inputs
`(("python-argh" ,python-argh)
("python-livereload" ,python-livereload)
("python-pathtools" ,python-pathtools)
("python-port-for" ,python-port-for)
("python-pyyaml" ,python-pyyaml)
("python-tornado" ,python-tornado)
("python-watchdog" ,python-watchdog)))
(native-inputs
`(("python-pytest" ,python-pytest)))
(home-page "https://github.com/GaretJax/sphinx-autobuild")
(synopsis "Rebuild Sphinx documentation when a change is detected")
(description
"This package lets you watch a Sphinx directory and rebuild the
documentation when a change is detected. It also includes a livereload
enabled web server.")
(license license:expat)))

87
gnu/packages/statistics.scm
View file

@ -183,7 +183,7 @@ (define-public libxls
(define r-with-tests
(package
(name "r-with-tests")
(version "3.6.3")
(version "4.0.0")
(source (origin
(method url-fetch)
(uri (string-append "mirror://cran/src/base/R-"
@ -191,7 +191,7 @@ (define r-with-tests
version ".tar.gz"))
(sha256
(base32
"13xaxwfbzj0bd6rn2n27z0n04lb93mcyq991w4vdbbg8v282jc49"))))
"0h1995smlyiyhx7gpg9paxsfqrcn6g9bbp5h9r47i6an3clv1gh6"))))
(build-system gnu-build-system)
(arguments
`(#:disallowed-references (,tzdata-for-tests)
@ -269,6 +269,11 @@ (define r-with-tests
(("my \\$date = strftime \"%B %Y\", localtime" line)
(string-append line " 1"))))
#t))
(add-before 'build 'set-locales
(lambda _
(setlocale LC_ALL "C")
(setenv "LC_ALL" "C")
#t))
(add-before 'configure 'set-default-pager
;; Set default pager to "cat", because otherwise it is "false",
;; making "help()" print nothing at all.
@ -322,7 +327,9 @@ (define r-with-tests
("perl" ,perl)
("pkg-config" ,pkg-config)
("texinfo" ,texinfo) ; for building HTML manuals
("texlive" ,(texlive-union (list texlive-fonts-ec
("texlive" ,(texlive-union (list texlive-ae
texlive-inconsolata
texlive-fonts-ec
texlive-amsfonts
texlive-latex-base
texlive-latex-fancyvrb
@ -331,7 +338,8 @@ (define r-with-tests
texlive-latex-oberdiek
texlive-latex-tools
texlive-latex-upquote
texlive-latex-url)))
texlive-latex-url
texlive-latex-xkeyval)))
("tzdata" ,tzdata-for-tests)
("xz" ,xz)))
(inputs
@ -347,7 +355,7 @@ (define r-with-tests
("libpng" ,libpng)
("libtiff" ,libtiff)
("libxt" ,libxt)
("pcre" ,pcre)
("pcre2" ,pcre2)
("readline" ,readline)
;; This avoids a reference to the ungraftable static bash. R uses the
;; detected shell for the "system" procedure.
@ -399,14 +407,14 @@ (define-public rmath-standalone
(define-public r-boot
(package
(name "r-boot")
(version "1.3-24")
(version "1.3-25")
(source
(origin
(method url-fetch)
(uri (cran-uri "boot" version))
(sha256
(base32
"0yv0l55kjmlfdx1xhgyjdi0bskxhfal74wr5jxaib1qj99nmkm49"))))
"1gpvi1h3nqhnnsfy96rlhakdpj84iqqsxr29rr3261sknky3aj26"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/boot")
(synopsis "Bootstrap functions for R")
@ -420,14 +428,14 @@ (define-public r-boot
(define-public r-mass
(package
(name "r-mass")
(version "7.3-51.5")
(version "7.3-51.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "MASS" version))
(sha256
(base32
"1k0m7pa4gb5apzrrkb5kx5d7bmkm2pl5g15vwb6j067hrqahck26"))))
"1viyxy22qp8abzzzlbck55b0i81rrdygim1dq2pm52s2v13mq0z2"))))
(properties `((upstream-name . "MASS")))
(build-system r-build-system)
(home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
@ -441,14 +449,14 @@ (define-public r-mass
(define-public r-class
(package
(name "r-class")
(version "7.3-16")
(version "7.3-17")
(source
(origin
(method url-fetch)
(uri (cran-uri "class" version))
(sha256
(base32
"1jpdgj0lsi60q0mqbhfw809w8d66whix27y6wpdzll6775g3j3ll"))))
"04qk8qia0qr8893fizmkbd5hsqn6m8383c0cyn9xnmkmvyv8a7xy"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mass" ,r-mass)))
@ -504,14 +512,14 @@ (define-public r-codetools
(define-public r-foreign
(package
(name "r-foreign")
(version "0.8-76")
(version "0.8-79")
(source
(origin
(method url-fetch)
(uri (cran-uri "foreign" version))
(sha256
(base32
"1z6x2x1z12wnv0z4p74d91r5wfaq30sdz4ynwx0lncz1q45mhbh5"))))
"1d5rk4k3khjrir1b4ciridd6vdpcgzi35r7p7ra4ky7vbaabcdmg"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/foreign")
(synopsis "Read data stored by other statistics software")
@ -524,14 +532,14 @@ (define-public r-foreign
(define-public r-kernsmooth
(package
(name "r-kernsmooth")
(version "2.23-16")
(version "2.23-17")
(source
(origin
(method url-fetch)
(uri (cran-uri "KernSmooth" version))
(sha256
(base32
"1acrkbdn3a74y4dndkcdl1njnpfqz7gk3bsz03g8lfj8l7z53hmq"))))
"11g6b0q67vasxag6v9m4px33qqxpmnx47c73yv1dninv2pz76g9b"))))
(properties `((upstream-name . "KernSmooth")))
(build-system r-build-system)
(native-inputs
@ -635,14 +643,14 @@ (define-public r-mgcv
(define-public r-nnet
(package
(name "r-nnet")
(version "7.3-13")
(version "7.3-14")
(source
(origin
(method url-fetch)
(uri (cran-uri "nnet" version))
(sha256
(base32
"1z0rj5cm4ycw1y0gd5wwwg8c2298v90iybgqdqh17967jbi2125f"))))
"1bzl62p5awva5kxcncs6lrdrkqp9ljd993zia731ckfpcjbrw6sx"))))
(build-system r-build-system)
(home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
(synopsis "Feed-forward neural networks and multinomial log-linear models")
@ -673,14 +681,14 @@ (define-public r-rpart
(define-public r-spatial
(package
(name "r-spatial")
(version "7.3-11")
(version "7.3-12")
(source
(origin
(method url-fetch)
(uri (cran-uri "spatial" version))
(sha256
(base32
"04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
"0qrdhzd5r78iwi46nk8jr56dzz5l5imkflxjw64d0ys0wyg06fbn"))))
(build-system r-build-system)
(home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
(synopsis "Functions for kriging and point pattern analysis")
@ -1624,14 +1632,14 @@ (define-public r-rlang
(define-public r-tibble
(package
(name "r-tibble")
(version "3.0.0")
(version "3.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "tibble" version))
(sha256
(base32
"0s84h8ls5qwixbs1n5safr3xqmg3p0llzdrd9sp4vs2572mwzqzi"))))
"17m7xvn423snq9dmr0bhx42j5rbc53w1viizxx4bvq37nz7m4i8m"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
@ -1694,25 +1702,28 @@ (define-public r-dplyr
(define-public r-dbplyr
(package
(name "r-dbplyr")
(version "1.4.2")
(version "1.4.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "dbplyr" version))
(sha256
(base32
"1q2dflr88s5a1amzfld3087q422vf70052qn84zyd8895kdg10xp"))))
"1si8sahr1kwq1xgjzi9klkahad07pyrsngy75y1f74f64907pb39"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
("r-dbi" ,r-dbi)
("r-dplyr" ,r-dplyr)
("r-glue" ,r-glue)
("r-lifecycle" ,r-lifecycle)
("r-purrr" ,r-purrr)
("r-r6" ,r-r6)
("r-rlang" ,r-rlang)
("r-tibble" ,r-tibble)
("r-tidyselect" ,r-tidyselect)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/tidyverse/dbplyr")
(synopsis "Dplyr back end for databases")
(description
@ -1989,14 +2000,14 @@ (define-public r-ade4
(define-public r-xml2
(package
(name "r-xml2")
(version "1.3.1")
(version "1.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "xml2" version))
(sha256
(base32
"0r7rxp922785dcryghbb3wxqgdav7mafwnmxjqfx8zaj3v1q2j3z"))))
"1kx400v62xkd5xal7rzz7jcarz94ac8g1sh4i2dqr78qwgkzj8nz"))))
(build-system r-build-system)
(inputs
`(("libxml2" ,libxml2)
@ -2446,14 +2457,16 @@ (define-public r-devtools
(define-public r-withr
(package
(name "r-withr")
(version "2.1.2")
(version "2.2.0")
(source (origin
(method url-fetch)
(uri (cran-uri "withr" version))
(sha256
(base32
"11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1"))))
"10mmfffjbnb2zq5x0kqhhb4z6va4micc6pjzvlfji34gyhffa8ac"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/jimhester/withr")
(synopsis "Run code with temporarily modified global state")
(description
@ -2514,13 +2527,13 @@ (define-public r-readr
(define-public r-plotrix
(package
(name "r-plotrix")
(version "3.7-7")
(version "3.7-8")
(source (origin
(method url-fetch)
(uri (cran-uri "plotrix" version))
(sha256
(base32
"1x92mmyfry127zzr6cmcj6kjsc4zhxrrdlr0jcxn3bb0hpdfps54"))))
"104llmr6dvlcnfpmd8zbdlv63k79djc4qqgadjavj4v4cmz1zkcc"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/plotrix")
(synopsis "Various plotting functions")
@ -2575,13 +2588,13 @@ (define-public r-latticeextra
(define-public r-rcpparmadillo
(package
(name "r-rcpparmadillo")
(version "0.9.860.2.0")
(version "0.9.870.2.0")
(source (origin
(method url-fetch)
(uri (cran-uri "RcppArmadillo" version))
(sha256
(base32
"1rg9ak0zbv8d9cyj10jq52nrcbk1pvfz28kbkhpx79mpjhrl7pb5"))))
"1r7iajxvbyvslsy16rqacc95azmjciw9lvcq31xl97fl09kmsq5v"))))
(properties `((upstream-name . "RcppArmadillo")))
(build-system r-build-system)
(propagated-inputs
@ -3743,18 +3756,20 @@ (define-public r-hexbin
(define-public r-purrr
(package
(name "r-purrr")
(version "0.3.3")
(version "0.3.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "purrr" version))
(sha256
(base32
"17lyys7dxjrwsfkq7a7hw65iy3qn3pp1sn70srdy64jf8adahc8g"))))
"1cj091rsjdj2xz16qhynyw72gh5cyhznifcfbrbygndfr4xwksr3"))))
(build-system r-build-system)
(propagated-inputs
`(("r-magrittr" ,r-magrittr)
("r-rlang" ,r-rlang)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/hadley/purrr")
(synopsis "Functional programming tools")
(description
@ -4942,16 +4957,16 @@ (define-public r-fpc
(define-public r-vgam
(package
(name "r-vgam")
(version "1.1-2")
(version "1.1-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "VGAM" version))
(sha256
(base32 "0kyan3a4ys2xbg9kf167cyf1gk7g963id62cjm2ij4i7y4wi61zq"))))
(base32 "1hwlrdx3nhdp83pvy1h23i16vbbhi4kizdhr58c8nvg7kqdzb7qc"))))
(properties `((upstream-name . "VGAM")))
(build-system r-build-system)
(inputs
(native-inputs
`(("gfortran" ,gfortran)))
(home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
(synopsis "Vector generalized linear and additive models")

26
gnu/packages/tex.scm
View file

@ -4757,6 +4757,32 @@ (define-public texlive-ae
via the CM-super, Latin Modern and (in a restricted way) CM-LGC font sets.")
(license license:lppl1.3+)))
(define-public texlive-inconsolata
(package
(inherit (simple-texlive-package
"texlive-inconsolata"
(list "/doc/fonts/inconsolata/"
"/fonts/enc/dvips/inconsolata/"
"/fonts/map/dvips/inconsolata/"
"/fonts/opentype/public/inconsolata/"
"/fonts/tfm/public/inconsolata/"
"/fonts/type1/public/inconsolata/"
"/tex/latex/inconsolata/")
(base32
"1a77w26m4c4j0202s1qkikz7ha6cxlv8zxhzi9s3l0x1l2pl7cr2")
#:trivial? #t))
(home-page "https://www.ctan.org/pkg/inconsolata")
(synopsis "Monospaced font with support files for use with TeX")
(description
"Inconsolata is a monospaced font designed by Raph Levien. This package
contains the font (in both Adobe Type 1 and OpenType formats) in regular and
bold weights, with additional glyphs and options to control slashed zero,
upright quotes and a shapelier lower-case L, plus metric files for use with
TeX, and LaTeX font definition and other relevant files.")
(license (list license:lppl1.3+
license:silofl1.1
license:asl2.0))))
(define-public texlive-times
(package
(inherit (simple-texlive-package

4
gnu/packages/text-editors.scm
View file

@ -123,7 +123,7 @@ (define-public vis
(define-public kakoune
(package
(name "kakoune")
(version "2019.12.10")
(version "2020.01.16")
(source
(origin
(method url-fetch)
@ -131,7 +131,7 @@ (define-public kakoune
"releases/download/v" version "/"
"kakoune-" version ".tar.bz2"))
(sha256
(base32 "1y1gzax2dl7flh676k0rl1vacv10j7p5krkmb67b0afbrql8vbb6"))))
(base32 "1bhd990gywdwdhxc5dn83wwj418c5cw1ndqycf7k0a02kxlg3550"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags

6
gnu/packages/valgrind.scm
View file

@ -2,7 +2,7 @@
;;; Copyright © 2013, 2014 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
@ -35,7 +35,7 @@ (define-public valgrind
(version "3.15.0")
(source (origin
(method url-fetch)
(uri (list (string-append "http://www.valgrind.org/downloads"
(uri (list (string-append "https://sourceware.org/pub/valgrind"
"/valgrind-" version ".tar.bz2")
(string-append "ftp://sourceware.org/pub/valgrind"
"/valgrind-" version ".tar.bz2")))
@ -71,7 +71,7 @@ (define-public valgrind
`(("gdb" ,gdb)))
(native-inputs
`(("perl" ,perl)))
(home-page "http://www.valgrind.org/")
(home-page "https://www.valgrind.org/")
(synopsis "Debugging and profiling tool suite")
(description
"Valgrind is an instrumentation framework for building dynamic analysis

155
gnu/packages/video.scm
View file

@ -5,7 +5,7 @@
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015 Andy Patterson <ajpatter@uwaterloo.ca>
;;; Copyright © 2015, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016, 2017, 2018, 2019 Alex Vong <alexvong1995@gmail.com>
;;; Copyright © 2016, 2017 Alex Griffin <a@ajgrf.com>
;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
@ -40,6 +40,7 @@
;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;; Copyright © 2020 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2020 Alex McGrath <amk@amk.ie>
;;;
;;; This file is part of GNU Guix.
;;;
@ -66,6 +67,7 @@ (define-module (gnu packages video)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix svn-download)
#:use-module (guix build-system cargo)
#:use-module (guix build-system cmake)
#:use-module (guix build-system copy)
#:use-module (guix build-system gnu)
@ -90,6 +92,7 @@ (define-module (gnu packages video)
#:use-module (gnu packages cmake)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpp)
#:use-module (gnu packages crates-io)
#:use-module (gnu packages curl)
#:use-module (gnu packages dejagnu)
#:use-module (gnu packages dns)
@ -140,6 +143,7 @@ (define-module (gnu packages video)
#:use-module (gnu packages qt)
#:use-module (gnu packages rdesktop)
#:use-module (gnu packages ruby)
#:use-module (gnu packages rust-apps)
#:use-module (gnu packages samba)
#:use-module (gnu packages sdl)
#:use-module (gnu packages serialization)
@ -3950,3 +3954,152 @@ (define-public w-scan
@end itemize\n")
(home-page "https://www.gen2vdr.de/wirbel/w_scan/index2.html")
(license license:gpl2+)))
(define-public rav1e
(package
(name "rav1e")
(version "0.3.0")
(source
(origin
(method url-fetch)
(uri (crate-uri "rav1e" version))
(file-name
(string-append name "-" version ".tar.gz"))
(sha256
(base32
"1bsmj8kqzs5pf8dl98rsl6a67cljj1gkj3b5hmd8hn8wdy4ya173"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
(("rust-simd-helpers" ,rust-simd-helpers-0.1)
("rust-ivf" ,rust-ivf-0.1)
("rust-cfg-if" ,rust-cfg-if-0.1)
("rust-paste" ,rust-paste-0.1)
("rust-signal-hook" ,rust-signal-hook-0.1)
("rust-aom-sys" ,rust-aom-sys-0.1)
("rust-nasm-rs" ,rust-nasm-rs-0.1)
("rust-arbitrary" ,rust-arbitrary-0.2)
("rust-better-panic" ,rust-better-panic-0.2)
("rust-noop-proc-macro"
,rust-noop-proc-macro-0.2)
("rust-num-traits" ,rust-num-traits-0.2)
("rust-rand-chacha" ,rust-rand-chacha-0.2)
("rust-err-derive" ,rust-err-derive-0.2)
("rust-interpolate-name"
,rust-interpolate-name-0.2)
("rust-rustc-version" ,rust-rustc-version-0.2)
("rust-scan-fmt" ,rust-scan-fmt-0.2)
("rust-libc" ,rust-libc-0.2)
("rust-image" ,rust-image-0.22)
("rust-arg-enum-proc-macro"
,rust-arg-enum-proc-macro-0.3)
("rust-num-derive" ,rust-num-derive-0.3)
("rust-dav1d-sys" ,rust-dav1d-sys-0.3)
("rust-backtrace" ,rust-backtrace-0.3)
("rust-log" ,rust-log-0.4)
("rust-y4m" ,rust-y4m-0.5)
("rust-arrayvec" ,rust-arrayvec-0.5)
("rust-toml" ,rust-toml-0.5)
("rust-fern" ,rust-fern-0.5)
("rust-rust-hawktracer"
,rust-rust-hawktracer-0.7)
("rust-rand" ,rust-rand-0.7)
("rust-itertools" ,rust-itertools-0.8)
("rust-bitstream-io" ,rust-bitstream-io-0.8)
("rust-console" ,rust-console-0.9)
("rust-serde" ,rust-serde-1.0)
("rust-cc" ,rust-cc-1.0)
("rust-rayon" ,rust-rayon-1.3)
("rust-byteorder" ,rust-byteorder-1.3)
("rust-clap" ,rust-clap-2)
("rust-vergen" ,rust-vergen-3.1))
#:cargo-development-inputs
(("rust-rand-chacha" ,rust-rand-chacha-0.2)
("rust-interpolate-name"
,rust-interpolate-name-0.2)
("rust-criterion" ,rust-criterion-0.3)
("rust-pretty-assertions"
,rust-pretty-assertions-0.6)
("rust-rand" ,rust-rand-0.7)
("rust-semver" ,rust-semver-0.9))
#:phases
(modify-phases %standard-phases
(replace 'build
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(invoke "cargo" "cinstall" "--release"
(string-append "--prefix=" out))))))))
(native-inputs
`(("cargo-c" ,rust-cargo-c)))
(inputs
`(("nasm" ,nasm)))
(home-page "https://github.com/xiph/rav1e/")
(synopsis "The fastest and safest AV1 encoder")
(description
"The fastest and safest AV1 encoder.")
(license license:bsd-2)))
(define-public peek
(package
(name "peek")
(version "1.5.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/phw/peek.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1xwlfizga6hvjqq127py8vabaphsny928ar7mwqj9cyqfl6fx41x"))))
(build-system meson-build-system)
(arguments '(#:glib-or-gtk? #t))
(inputs
`(("gtk+" ,gtk+)))
(native-inputs
`(("desktop-file-utils" ,desktop-file-utils) ; for update-desktop-database
("gettext" ,gettext-minimal)
("glib:bin" ,glib "bin") ; for glib-compile-resources
("gtk+-bin" ,gtk+ "bin") ; For gtk-update-icon-cache
("pkg-config" ,pkg-config)
("vala" ,vala)))
(home-page "https://github.com/phw/peek")
(synopsis "Simple animated GIF screen recorder")
(description
"Peek makes it easy to create short screencasts of a screen area. It was
built for the specific use case of recording screen areas, e.g. for easily
showing UI features of your own apps or for showing a bug in bug reports.
With Peek, you simply place the Peek window over the area you want to record
and press \"Record\". Peek is optimized for generating animated GIFs, but you
can also directly record to WebM or MP4 if you prefer.")
(license license:gpl3+)))
(define-public wf-recorder
(package
(name "wf-recorder")
(version "0.2.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ammen99/wf-recorder.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1cw6kpcbl33wh95pvy32xrsrm6kkk1awccr3phyh885xjs3b3iim"))))
(build-system meson-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))
(inputs
`(("ffmpeg" ,ffmpeg)
("pulseaudio" ,pulseaudio)
("wayland" ,wayland)
("wayland-protocols" ,wayland-protocols)
("libx264" ,libx264)))
(home-page "https://github.com/ammen99/wf-recorder")
(synopsis "Screen recorder for wlroots-based compositors")
(description
"@code{wf-recorder} is a utility program for screen recording of
wlroots-based compositors. More specifically, those that support
@code{wlr-screencopy-v1} and @code{xdg-output}.")
(license license:expat)))

31
gnu/packages/vpn.scm
View file

@ -11,6 +11,7 @@
;;; Copyright © 2019, 2020 Leo Famulari <leo@famulari.name>
;;; Copyright © 2019 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
;;;
;;; This file is part of GNU Guix.
;;;
@ -34,6 +35,7 @@ (define-module (gnu packages vpn)
#:use-module (guix git-download)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system linux-module)
#:use-module (guix build-system python)
#:use-module (gnu packages)
#:use-module (gnu packages admin)
@ -465,19 +467,24 @@ (define-public wireguard-linux-compat
(sha256
(base32
"0ymprz3h4b92wlcqm5k5vmcgap8pjv202bgkdx0axmp12n1lmyvx"))))
(build-system gnu-build-system)
(build-system linux-module-build-system)
(outputs '("out"
"kernel-patch"))
(arguments
`(#:tests? #f ; No test suite
#:modules ((guix build gnu-build-system)
#:modules ((guix build linux-module-build-system)
(guix build utils)
(ice-9 popen)
(ice-9 textual-ports))
#:phases
(modify-phases %standard-phases
(delete 'configure) ; No ./configure script
(replace 'build
(add-before 'build 'change-directory
(lambda _
(chdir "./src")
#t))
(add-after 'build 'build-patch
(lambda* (#:key outputs #:allow-other-keys)
(let* ((patch-builder "./kernel-tree-scripts/create-patch.sh")
(let* ((patch-builder "../kernel-tree-scripts/create-patch.sh")
(port (open-input-pipe patch-builder))
(str (get-string-all port)))
(close-pipe port)
@ -485,15 +492,21 @@ (define-public wireguard-linux-compat
(lambda (port)
(format port "~a" str))))
#t))
(replace 'install
(add-after 'install 'install-patch
(lambda* (#:key outputs #:allow-other-keys)
(install-file "wireguard.patch"
(assoc-ref %outputs "out"))
(assoc-ref %outputs "kernel-patch"))
#t))
;; So that 'install-license-files' works...
(add-before 'install-license-files 'reset-cwd
(lambda _
(chdir "..")
#t)))))
(home-page "https://git.zx2c4.com/wireguard-linux-compat/")
(synopsis "WireGuard kernel module for Linux 3.10 through 5.5")
(description "This is an out-of-tree Linux kernel patch adding WireGuard to
kernel versions 3.10 through 5.5. WireGuard was added to Linux 5.6.")
(description "This package contains an out-of-tree kernel patch and
a loadable module adding WireGuard to Linux kernel versions 3.10 through 5.5.
WireGuard was added to Linux 5.6.")
(license license:gpl2)))
(define-public wireguard-tools

58
gnu/packages/web.scm
View file

@ -4814,16 +4814,23 @@ (define-public hubbub
(define-public ikiwiki
(package
(name "ikiwiki")
(version "3.20190228")
(version "3.20200202.3")
(source
(origin
(method url-fetch)
(uri (string-append "http://snapshot.debian.org/archive/debian/"
"20190301T035241Z/pool/main/i/ikiwiki/ikiwiki_"
version ".orig.tar.xz"))
(method git-fetch)
(uri (git-reference
(url "git://git.ikiwiki.info/")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"17pyblaqhkb61lxl63bzndiffism8k859p54k3k4sghclq6lsynh"))))
"0fphyqzlk9y8v9s89ypsmrnbhyymzrpc2w0liy0n4knc7kk2pabq"))
(snippet
'(begin
;; The POT file requires write permission during the build
;; phase.
(chmod "po/ikiwiki.pot" #o644)
#t))))
(build-system perl-build-system)
(arguments
`(#:phases
@ -4837,10 +4844,21 @@ (define-public ikiwiki
" addenv(\"PERL5LIB\", \""
(getenv "PERL5LIB")
"\");")))))
(add-after 'patch-source-shebangs 'patch-Makefile
(add-after 'patch-source-shebangs 'patch-Makefiles
(lambda _
(substitute* "Makefile.PL"
(("SYSCONFDIR\\?=") "SYSCONFDIR?=$(PREFIX)"))
(("SYSCONFDIR\\?=") "SYSCONFDIR?=$(PREFIX)"))
(with-directory-excursion "po"
(substitute* "Makefile"
(("PERL5LIB=") "PERL5LIB=${PERL5LIB}:")))
#t))
(add-before 'build 'set-modification-times
;; The wiki '--refresh' steps, which are executed during
;; the check phase, require recent timestamps on files in
;; the 'doc' and 'underlays' directories.
(lambda _
(invoke "find" "doc" "underlays" "-type" "f" "-exec"
"touch" "{}" "+")
#t))
(add-after 'install 'wrap-programs
(lambda* (#:key outputs #:allow-other-keys)
@ -4854,10 +4872,6 @@ (define-public ikiwiki
#t))))))
(native-inputs
`(("which" ,which)
("perl-html-tagset" ,perl-html-tagset)
("perl-timedate" ,perl-timedate)
("perl-xml-sax" ,perl-xml-sax)
("perl-xml-simple" ,perl-xml-simple)
("gettext" ,gettext-minimal)
("subversion" ,subversion)
("git" ,git)
@ -4866,14 +4880,24 @@ (define-public ikiwiki
("mercurial" ,mercurial)))
(inputs
`(("python" ,python-wrapper)
("perl-authen-passphrase" ,perl-authen-passphrase)
("perl-cgi-formbuilder" ,perl-cgi-formbuilder)
("perl-cgi-session" ,perl-cgi-session)
("perl-cgi-simple" ,perl-cgi-simple)
("perl-db-file" ,perl-db-file)
("perl-html-parser" ,perl-html-parser)
("perl-file-mimeinfo" ,perl-file-mimeinfo)
("perl-html-tagset" ,perl-html-tagset)
("perl-image-magick" ,perl-image-magick)
("perl-mail-sendmail" ,perl-mail-sendmail)
("perl-timedate" ,perl-timedate)
("perl-xml-sax" ,perl-xml-sax)
("perl-xml-simple" ,perl-xml-simple)
("perl-xml-twig" ,perl-xml-twig)
("po4a" ,po4a)))
(propagated-inputs
`(("perl-html-parser" ,perl-html-parser)
("perl-html-scrubber" ,perl-html-scrubber)
("perl-html-template" ,perl-html-template)
("perl-image-magick" ,perl-image-magick)
("perl-json" ,perl-json)
("perl-text-markdown-discount" ,perl-text-markdown-discount)
("perl-uri" ,perl-uri)
@ -7143,8 +7167,8 @@ (define-public nghttp2
(license license:expat)))
(define-public hpcguix-web
(let ((commit "f39c90b35e99e4122b0866ec4337020d61c81508")
(revision "4"))
(let ((commit "9de63562b06b4aef3a3afe5ecb18d3c91e57ee74")
(revision "5"))
(package
(name "hpcguix-web")
(version (git-version "0.0.1" revision commit))
@ -7156,7 +7180,7 @@ (define-public hpcguix-web
(file-name (git-file-name name version))
(sha256
(base32
"0idzzlwnaymk6hm5q9nh146h5m6vd8acp32vlmzp6qq08mimfkq7"))))
"0wjgj2s7v2cyz6dx24c111rxs99i84sfvxl4ch8brnh02j2606jz"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((guix build gnu-build-system)

95
gnu/packages/wm.scm
View file

@ -33,6 +33,8 @@
;;; Copyright © 2019, 2020 Alexandru-Sergiu Marton <brown121407@member.fsf.org>
;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
;;; Copyright © 2020 Boris A. Dekshteyn <harlequin78@gmail.com>
;;; Copyright © 2020 Marcin Karpezo <sirmacik@wioo.waw.pl>
;;;
;;; This file is part of GNU Guix.
;;;
@ -149,7 +151,7 @@ (define-public bspwm
(define-public herbstluftwm
(package
(name "herbstluftwm")
(version "0.7.2")
(version "0.8.1")
(source
(origin
(method url-fetch)
@ -157,9 +159,9 @@ (define-public herbstluftwm
version ".tar.gz"))
(sha256
(base32
"1kc18aj9j3nfz6fj4qxg9s3gg4jvn6kzi3ii24hfm0vqdpy17xnz"))
"0c1lf82z6a56g8asin91cmqhzk3anw0xwc44b31bpjixadmns57y"))
(file-name (string-append "herbstluftwm-" version ".tar.gz"))))
(build-system gnu-build-system)
(build-system cmake-build-system)
(inputs
`(("dzen" ,dzen)
("dmenu" ,dmenu)
@ -169,13 +171,20 @@ (define-public herbstluftwm
("xsetroot" ,xsetroot)
("libx11" ,libx11)
("libxext" ,libxext)
("libxinerama" ,libxinerama)))
("libxinerama" ,libxinerama)
("libxrandr" ,libxrandr)))
(native-inputs
`(("pkg-config" ,pkg-config)))
`(("asciidoc" ,asciidoc)
("pkg-config" ,pkg-config)))
(arguments
'(#:phases
'(#:tests? #f
#:configure-flags
(let ((out (assoc-ref %outputs "out")))
(list "-DCC=gcc"
(string-append "-DCMAKE_INSTALL_SYSCONF_PREFIX=" out "/etc")
(string-append "-DBASHCOMPLETIONDIR=" out "/etc/bash_completion.d")))
#:phases
(modify-phases %standard-phases
(delete 'configure) ; no configure script
(add-after 'install 'install-xsession
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@ -190,17 +199,7 @@ (define-public herbstluftwm
Comment=Manual tiling window manager~@
Exec=~a/bin/herbstluftwm~@
Type=XSession~%" out)))
#t))))
#:tests? #f
#:make-flags
(let ((out (assoc-ref %outputs "out")))
(list "CC=gcc"
(string-append "PREFIX=''")
(string-append "DESTDIR=" out)
(string-append "FISHCOMPLETIONDIR="
"/share/fish/vendor_completions.d")
(string-append "BASHCOMPLETIONDIR=" out
"/etc/bash_completion.d")))))
#t))))))
(synopsis "Tiling window manager for X11")
(description "herbstluftwm is a manual tiling window manager for X11 using
Xlib and GLib. Its main features are:
@ -1732,6 +1731,36 @@ (define-public sbcl-stumpwm-ttf-fonts
rendering.")
(license (list license:gpl2+ license:gpl3+ license:bsd-2)))))
(define-public sbcl-stumpwm-pass
(let ((commit "dd5b037923ec7d3cc27c55806bcec5a1b8cf4e91")
(revision "1"))
(package
(name "sbcl-pass")
(version (git-version "0.0.1" revision commit)) ;no upstream release
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/stumpwm/stumpwm-contrib.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0ahxdj9f884afpzxczx6mx7l4nwg4kw6afqaq7lwhf7lxcwylldn"))))
(inputs
`(("stumpwm" ,stumpwm "lib")))
(build-system asdf-build-system/sbcl)
(arguments
'(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "util/pass"))))))
(home-page "https://github.com/stumpwm/stumpwm-contrib")
(synopsis "Integrate @code{pass} wih StumpWM")
(description "This package provides an interface which integrates
password-store into StumpWM.")
(license (list license:gpl2+ license:gpl3+ license:bsd-2)))))
(define-public sbcl-stumpwm-globalwindows
(let ((commit "dd5b037923ec7d3cc27c55806bcec5a1b8cf4e91")
(revision "1"))
@ -1762,6 +1791,36 @@ (define-public sbcl-stumpwm-globalwindows
windows in the current X session.")
(license (list license:gpl2+ license:gpl3+ license:bsd-2)))))
(define-public sbcl-stumpwm-swm-gaps
(let ((commit "dd5b037923ec7d3cc27c55806bcec5a1b8cf4e91")
(revision "1"))
(package
(name "sbcl-swm-gaps")
(version (git-version "0.0.1" revision commit)) ;no upstream release
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/stumpwm/stumpwm-contrib.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0ahxdj9f884afpzxczx6mx7l4nwg4kw6afqaq7lwhf7lxcwylldn"))))
(inputs
`(("stumpwm" ,stumpwm "lib")))
(build-system asdf-build-system/sbcl)
(arguments
'(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "util/swm-gaps"))))))
(home-page "https://github.com/stumpwm/stumpwm-contrib")
(synopsis "Gaps between windows for StumpWM")
(description "This package provides a StumpWM module which adds gaps
between windows.")
(license (list license:gpl2+ license:gpl3+ license:bsd-2)))))
(define-public lemonbar
(let ((commit "35183ab81d2128dbb7b6d8e119cc57846bcefdb4")
(revision "1"))

38
gnu/packages/xdisorg.scm
View file

@ -35,6 +35,7 @@
;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
;;; Copyright © 2020 Damien Cassou <damien@cassou.me>
;;; Copyright © 2020 John Soo <jsoo1@asu.edu>
;;; Copyright © 2020 Boris A. Dekshteyn <boris.dekshteyn@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -2288,3 +2289,40 @@ (define-public clipmenu
depending on the value of @code{CM_LAUNCHER}) to let the user select a clip.
After selection, the clip is put onto the PRIMARY and CLIPBOARD X selections.")
(license license:public-domain))))
(define-public kbdd
(package
(name "kbdd")
(version "0.7.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/qnikst/kbdd.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0qkq75grbd4wkx4nlvswgavpijk9ad0pzqyj89a0ayjsbsn36pqy"))))
(build-system gnu-build-system)
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("glib" ,glib "bin")
("pkg-config" ,pkg-config)))
(inputs
`(("dbus-glib", dbus-glib)
("glib" ,glib)
("libx11" ,libx11)))
(home-page "https://github.com/qnikst/kbdd")
(synopsis "Per-window keyboard layout switching daemon for X")
(description "@command{kbdd} is a simple keyboard layout switching
program, which is designed to run in an X11 session and remember
keyboard layouts on a per-window basis. That can be very handy for a
user of a non-US keyboard who does not want to jump through layouts back
and forth while typing in terminals (mostly in a latin alphabet) and
some kind of chat (in native language).
@command{kbdd} also supports D-Bus signals, which makes it possible to
create layout indicator widgets.")
(license license:bsd-2)))

62
gnu/packages/xorg.scm
View file

@ -24,6 +24,7 @@
;;; Copyright © 2020 Leo Prikler <leo.prikler@student.tugraz.at>
;;; Copyright © 2020 Florian Pelz <pelzflorian@pelzflorian.de>
;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -65,7 +66,9 @@ (define-module (gnu packages xorg)
#:use-module (gnu packages gnupg)
#:use-module (gnu packages gperf)
#:use-module (gnu packages gtk)
#:use-module (gnu packages inkscape)
#:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages libbsd)
#:use-module (gnu packages libedit)
#:use-module (gnu packages linux)
@ -2245,6 +2248,65 @@ (define-public xcursor-themes
(license license:x11)))
(define-public hackneyed-x11-cursors
;; The current release 0.8 suffers from non-deterministic build problems.
(let ((revision "1")
(commit "9423cef2e2e5ff6b1d65d61f7108c97bc7f5fdfb"))
(package
(name "hackneyed-x11-cursors")
(version (git-version "0.8.1" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://gitlab.com/Enthymeme/hackneyed-x11-cursors.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0f637i76sdwz3nm1g1iynamq6j0i6k3c70fpl0fmd0dlynm8ga96"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ;no test suite
#:make-flags (list (string-append "PREFIX=" %output))
#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-before 'build 'set-inkscape-environment-variable
(lambda* (#:key inputs #:allow-other-keys)
(let ((inkscape (string-append (assoc-ref inputs "inkscape")
"/bin/inkscape")))
(setenv "INKSCAPE" inkscape)
#t)))
(add-before 'build 'placate-inkscape-warnings
(lambda _
(setenv "HOME" (getcwd))
#t))
(add-after 'build 'generate-black-cursors
(lambda* (#:key make-flags parallel-build #:allow-other-keys)
(let ((build (assoc-ref %standard-phases 'build))
(make-flags/extended
`(,@make-flags
"THEME_NAME=Hackneyed-Dark"
"COMMON_SOURCE=theme/common-dark.svg"
"RSVG_SOURCE=theme/right-handed-dark.svg"
"LSVG_SOURCE=theme/left-handed-dark.svg")))
(build #:make-flags make-flags/extended
#:parallel-build parallel-build))))
(add-after 'install 'install-black-cursors
(lambda* (#:key make-flags #:allow-other-keys)
(apply invoke `("make" "install" ,@make-flags
"THEME_NAME=Hackneyed-Dark")))))))
(native-inputs `(("imagemagick" ,imagemagick)
("inkscape" ,inkscape)
("xcursorgen" ,xcursorgen)))
(home-page "https://gitlab.com/Enthymeme/hackneyed-x11-cursors")
(synopsis "Classic cursor theme for X11")
(description "Hackneyed is a scalable cursor theme mildly resembling old
Windows 3.x cursors. The cursors are available in white and black colors. A
left-handed version of the cursors is also included.")
(license license:x11))))
(define-public xcursorgen
(package
(name "xcursorgen")

13
gnu/services.scm
View file

@ -318,11 +318,10 @@ (define-syntax modify-services
;;; Core services.
;;;
(define (system-derivation mentries mextensions)
(define (system-derivation entries mextensions)
"Return as a monadic value the derivation of the 'system' directory
containing the given entries."
(mlet %store-monad ((entries mentries)
(extensions (mapm/accumulate-builds identity
(mlet %store-monad ((extensions (mapm/accumulate-builds identity
mextensions)))
(lower-object
(file-union "system"
@ -691,10 +690,10 @@ (define setuid-program-service-type
(define (packages->profile-entry packages)
"Return a system entry for the profile containing PACKAGES."
(mlet %store-monad ((profile (profile-derivation
(packages->manifest
(delete-duplicates packages eq?)))))
(return `(("profile" ,profile)))))
(with-monad %store-monad
(return `(("profile" ,(profile
(content (packages->manifest
(delete-duplicates packages eq?)))))))))
(define profile-service-type
;; The service that populates the system's profile---i.e.,

3
gnu/services/docker.scm
View file

@ -1,5 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2018 Danny Milosavljevic <dannym@scratchpost.org>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -94,7 +95,7 @@ (define (docker-shepherd-service config)
file-system-/sys/fs/cgroup/cpuset
file-system-/sys/fs/cgroup/devices
file-system-/sys/fs/cgroup/memory
; TODO: file-system-/sys/fs/cgroup/pids
file-system-/sys/fs/cgroup/pids
networking
udev))
(start #~(make-forkexec-constructor

41
gnu/system.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015, 2016 Alex Kost <alezost@gmail.com>
;;; Copyright © 2016 Chris Marusich <cmmarusich@gmail.com>
@ -491,26 +491,25 @@ (define (package-for-kernel target-kernel module-package)
(define* (operating-system-directory-base-entries os)
"Return the basic entries of the 'system' directory of OS for use as the
value of the SYSTEM-SERVICE-TYPE service."
(let ((locale (operating-system-locale-directory os)))
(mlet* %store-monad ((kernel -> (operating-system-kernel os))
(modules ->
(operating-system-kernel-loadable-modules os))
(kernel
(profile-derivation
(packages->manifest
(cons kernel
(map (lambda (module)
(if (package? module)
(package-for-kernel kernel module)
module))
modules)))
#:hooks (list linux-module-database)))
(initrd -> (operating-system-initrd-file os))
(params -> (operating-system-boot-parameters-file os)))
(return `(("kernel" ,kernel)
("parameters" ,params)
("initrd" ,initrd)
("locale" ,locale)))))) ;used by libc
(let* ((locale (operating-system-locale-directory os))
(kernel (operating-system-kernel os))
(modules (operating-system-kernel-loadable-modules os))
(kernel (profile
(content (packages->manifest
(cons kernel
(map (lambda (module)
(if (package? module)
(package-for-kernel kernel
module)
module))
modules))))
(hooks (list linux-module-database))))
(initrd (operating-system-initrd-file os))
(params (operating-system-boot-parameters-file os)))
`(("kernel" ,kernel)
("parameters" ,params)
("initrd" ,initrd)
("locale" ,locale)))) ;used by libc
(define (operating-system-default-essential-services os)
"Return the list of essential services for OS. These are special services

3
gnu/system/file-systems.scm
View file

@ -1,5 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -389,7 +390,7 @@ (define %control-groups
;; parent directory.
(dependencies (list parent))))
'("cpuset" "cpu" "cpuacct" "memory" "devices" "freezer"
"blkio" "perf_event")))))
"blkio" "perf_event" "pids")))))
(define %elogind-file-systems
;; We don't use systemd, but these file systems are needed for elogind,

6
gnu/system/linux-container.scm
View file

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015 David Thompson <davet@gnu.org>
;;; Copyright © 2016, 2017, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016, 2017, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2019 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
;;;
@ -53,9 +53,7 @@ (define base
(operating-system-default-essential-services os)))
(cons (service system-service-type
(let ((locale (operating-system-locale-directory os)))
(with-monad %store-monad
(return `(("locale" ,locale))))))
`(("locale" ,(operating-system-locale-directory os))))
;; If network is to be shared with the host, remove network
;; configuration files from etc-service.
(if shared-network?

9
gnu/tests/install.scm
View file

@ -254,7 +254,7 @@ (define marionette
(make-marionette
`(,(which #$(qemu-command system))
"-no-reboot"
"-m" "800"
"-m" "1200"
#$@(cond
((string=? "ext4" installation-disk-image-file-system-type)
#~("-drive"
@ -389,6 +389,7 @@ (define-os-with-source (%minimal-os-on-vda %minimal-os-on-vda-source)
(services (cons (service marionette-service-type
(marionette-configuration
(imported-modules '((gnu services herd)
(guix build utils)
(guix combinators)))))
%base-services))))
@ -1060,7 +1061,7 @@ (define installation-os-for-gui-tests
(define* (installation-target-os-for-gui-tests
#:key (encrypted? #f))
(operating-system
(inherit %minimal-os)
(inherit %minimal-os-on-vda)
(users (append (list (user-account
(name "alice")
(comment "Bob's sister")
@ -1076,9 +1077,9 @@ (define* (installation-target-os-for-gui-tests
%base-user-accounts))
;; The installer does not create a swap device in guided mode with
;; encryption support.
(swap-devices (if encrypted? '() '("/dev/vdb2")))
(swap-devices (if encrypted? '() '("/dev/vda2")))
(services (cons (service dhcp-client-service-type)
(operating-system-user-services %minimal-os)))))
(operating-system-user-services %minimal-os-on-vda)))))
(define* (installation-target-desktop-os-for-gui-tests
#:key (encrypted? #f))

16
gnu/tests/reconfigure.scm
View file

@ -136,14 +136,6 @@ (define dummy-service
(stop #~(const #t))
(respawn? #f)))
;; Return the Shepherd service file for SERVICE, after ensuring that it
;; exists in the store.
(define (ensure-service-file service)
(let ((file (shepherd-service-file service)))
(mlet* %store-monad ((store-object (lower-object file))
(_ (built-derivations (list store-object))))
(return file))))
(define (test enable-dummy disable-dummy)
(with-imported-modules '((gnu build marionette))
#~(begin
@ -187,10 +179,12 @@ (define (running-services marionette)
(test-end)
(exit (= (test-runner-fail-count (test-runner-current)) 0)))))
(mlet* %store-monad ((file (ensure-service-file dummy-service)))
(let ((enable (upgrade-services-program (list file) '(dummy) '() '()))
(gexp->derivation
"upgrade-services"
(let* ((file (shepherd-service-file dummy-service))
(enable (upgrade-services-program (list file) '(dummy) '() '()))
(disable (upgrade-services-program '() '() '(dummy) '())))
(gexp->derivation "upgrade-services" (test enable disable)))))
(test enable disable))))
(define* (run-install-bootloader-test)
"Run a test of an OS running INSTALL-BOOTLOADER-PROGRAM, which installs a

4
guix/channels.scm
View file

@ -568,9 +568,7 @@ (define (instance->entry instance drv)
(define (package-cache-file manifest)
"Build a package cache file for the instance in MANIFEST. This is meant to
be used as a profile hook."
(mlet %store-monad ((profile (profile-derivation manifest
#:hooks '())))
(let ((profile (profile (content manifest) (hooks '()))))
(define build
#~(begin
(use-modules (gnu packages))

14
guix/import/crate.scm
View file

@ -201,14 +201,16 @@ (define crate
(lookup-crate crate-name))
(define version-number
(or version
(crate-latest-version crate)))
(and crate
(or version
(crate-latest-version crate))))
(define version*
(find (lambda (version)
(string=? (crate-version-number version)
version-number))
(crate-versions crate)))
(and crate
(find (lambda (version)
(string=? (crate-version-number version)
version-number))
(crate-versions crate))))
(and crate version*
(let* ((dependencies (crate-version-dependencies version*))

36
guix/profiles.scm
View file

@ -125,6 +125,15 @@ (define-module (guix profiles)
profile-derivation
profile-search-paths
profile
profile?
profile-name
profile-content
profile-hooks
profile-locales?
profile-allow-collisions?
profile-relative-symlinks?
generation-number
generation-profile
generation-numbers
@ -1660,6 +1669,33 @@ (define search-paths
. ,(length
(manifest-entries manifest))))))))
;; Declarative profile.
(define-record-type* <profile> profile make-profile
profile?
(name profile-name (default "profile")) ;string
(content profile-content) ;<manifest>
(hooks profile-hooks ;list of procedures
(default %default-profile-hooks))
(locales? profile-locales? ;Boolean
(default #t))
(allow-collisions? profile-allow-collisions? ;Boolean
(default #f))
(relative-symlinks? profile-relative-symlinks? ;Boolean
(default #f)))
(define-gexp-compiler (profile-compiler (profile <profile>) system target)
"Compile PROFILE to a derivation."
(match profile
(($ <profile> name manifest hooks
locales? allow-collisions? relative-symlinks?)
(profile-derivation manifest
#:name name
#:hooks hooks
#:locales? locales?
#:allow-collisions? allow-collisions?
#:relative-symlinks? relative-symlinks?
#:system system #:target target))))
(define* (profile-search-paths profile
#:optional (manifest (profile-manifest profile))
#:key (getenv (const #f)))

7
guix/scripts/edit.scm
View file

@ -56,10 +56,9 @@ (define (show-help)
(show-bug-report-information))
(define %editor
;; XXX: It would be better to default to something more likely to be
;; pre-installed on an average GNU system. Since Nano is not suited for
;; editing Scheme, Emacs is used instead.
(make-parameter (or (getenv "VISUAL") (getenv "EDITOR") "emacs")))
;; Nano is sensible default, as it is installed by base system.
;; For development, user can set custom value for $EDITOR.
(make-parameter (or (getenv "VISUAL") (getenv "EDITOR") "nano")))
(define (search-path* path file)
"Like 'search-path' but exit if FILE is not found."

33
guix/scripts/pack.scm
View file

@ -1071,7 +1071,21 @@ (define with-provenance
(localstatedir? (assoc-ref opts 'localstatedir?))
(entry-point (assoc-ref opts 'entry-point))
(profile-name (assoc-ref opts 'profile-name))
(gc-root (assoc-ref opts 'gc-root)))
(gc-root (assoc-ref opts 'gc-root))
(profile (profile
(content manifest)
;; Always produce relative symlinks for
;; Singularity (see
;; <https://bugs.gnu.org/34913>).
(relative-symlinks?
(or relocatable?
(eq? 'squashfs pack-format)))
(hooks (if bootstrap?
'()
%default-profile-hooks))
(locales? (not bootstrap?)))))
(define (lookup-package package)
(manifest-lookup manifest (manifest-pattern (name package))))
@ -1085,22 +1099,7 @@ (define (lookup-package package)
to your package list.")))
(run-with-store store
(mlet* %store-monad ((profile (profile-derivation
manifest
;; Always produce relative
;; symlinks for Singularity (see
;; <https://bugs.gnu.org/34913>).
#:relative-symlinks?
(or relocatable?
(eq? 'squashfs pack-format))
#:hooks (if bootstrap?
'()
%default-profile-hooks)
#:locales? (not bootstrap?)
#:target target))
(drv (build-image name profile
(mlet* %store-monad ((drv (build-image name profile
#:target
target
#:compressor

8
guix/scripts/substitute.scm
View file

@ -494,7 +494,8 @@ (define (at-most max-length lst)
(loop (+ 1 len) tail (cons head result)))))))
(define* (http-multiple-get base-uri proc seed requests
#:key port (verify-certificate? #t))
#:key port (verify-certificate? #t)
(batch-size 1000))
"Send all of REQUESTS to the server at BASE-URI. Call PROC for each
response, passing it the request object, the response, a port from which to
read the response body, and the previous result, starting with SEED, à la
@ -504,7 +505,7 @@ (define* (http-multiple-get base-uri proc seed requests
(requests requests)
(result seed))
(define batch
(at-most 1000 requests))
(at-most batch-size requests))
;; (format (current-error-port) "connecting (~a requests left)..."
;; (length requests))
@ -536,9 +537,10 @@ (define batch
(()
(match (drop requests processed)
(()
(close-port p)
(reverse result))
(remainder
(connect port remainder result))))
(connect p remainder result))))
((head tail ...)
(let* ((resp (read-response p))
(body (response-body-port resp))

23
tests/crate.scm
View file

@ -55,7 +55,7 @@ (define test-foo-dependencies
\"dependencies\": [
{
\"crate_id\": \"bar\",
\"kind\": \"normal\",
\"kind\": \"normal\"
}
]
}")
@ -87,20 +87,20 @@ (define test-root-dependencies
\"dependencies\": [
{
\"crate_id\": \"intermediate-1\",
\"kind\": \"normal\",
\"kind\": \"normal\"
},
{
\"crate_id\": \"intermediate-2\",
\"kind\": \"normal\",
\"kind\": \"normal\"
}
{
\"crate_id\": \"leaf-alice\",
\"kind\": \"normal\",
\"kind\": \"normal\"
},
{
\"crate_id\": \"leaf-bob\",
\"kind\": \"normal\",
},
\"kind\": \"normal\"
}
]
}")
@ -131,15 +131,15 @@ (define test-intermediate-1-dependencies
\"dependencies\": [
{
\"crate_id\": \"intermediate-2\",
\"kind\": \"normal\",
\"kind\": \"normal\"
},
{
\"crate_id\": \"leaf-alice\",
\"kind\": \"normal\",
\"kind\": \"normal\"
},
{
\"crate_id\": \"leaf-bob\",
\"kind\": \"normal\",
\"kind\": \"normal\"
}
]
}")
@ -171,8 +171,8 @@ (define test-intermediate-2-dependencies
\"dependencies\": [
{
\"crate_id\": \"leaf-bob\",
\"kind\": \"normal\",
},
\"kind\": \"normal\"
}
]
}")
@ -233,6 +233,7 @@ (define test-leaf-bob-dependencies
(define test-source-hash
"")
(test-begin "crate")
(test-equal "guix-package->crate-name"

2
tests/gem.scm
View file

@ -52,7 +52,7 @@ (define test-bar-json
\"homepage_uri\": \"https://example.com\",
\"dependencies\": {
\"runtime\": [
{ \"name\": \"bundler\" },
{ \"name\": \"bundler\" }
]
},
\"licenses\": null

13
tests/profiles.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014 Alex Kost <alezost@gmail.com>
;;;
;;; This file is part of GNU Guix.
@ -223,6 +223,17 @@ (define glibc
(string=? (dirname (readlink bindir))
(derivation->output-path guile))))))
(test-assertm "<profile>"
(mlet* %store-monad
((entry -> (package->manifest-entry %bootstrap-guile))
(profile -> (profile (hooks '()) (locales? #f)
(content (manifest (list entry)))))
(drv (lower-object profile))
(profile -> (derivation->output-path drv))
(bindir -> (string-append profile "/bin"))
(_ (built-derivations (list drv))))
(return (file-exists? (string-append bindir "/guile")))))
(test-assertm "profile-derivation relative symlinks, one entry"
(mlet* %store-monad
((entry -> (package->manifest-entry %bootstrap-guile))

7
tests/pypi.scm
View file

@ -46,13 +46,13 @@ (define test-json
\"1.0.0\": [
{
\"url\": \"https://example.com/foo-1.0.0.egg\",
\"packagetype\": \"bdist_egg\",
\"packagetype\": \"bdist_egg\"
}, {
\"url\": \"https://example.com/foo-1.0.0.tar.gz\",
\"packagetype\": \"sdist\",
\"packagetype\": \"sdist\"
}, {
\"url\": \"https://example.com/foo-1.0.0-py2.py3-none-any.whl\",
\"packagetype\": \"bdist_wheel\",
\"packagetype\": \"bdist_wheel\"
}
]
}
@ -120,6 +120,7 @@ (define test-metadata-with-extras-jedi "\
Requires-Dist: pytest (>=3.1.0); extra == 'testing'
")
(test-begin "pypi")
(test-equal "guix-package->pypi-name, old URL style"