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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
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@ -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
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@ -152,24 +152,22 @@
(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
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@ -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 @@ dictionaries, including personal ones.")
(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
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@ -157,7 +157,7 @@ programs for the manipulation and analysis of astronomical data.")
(define-public stellarium
(package
(name "stellarium")
(version "0.19.3")
(version "0.20.1")
(source
(origin
(method url-fetch)
@ -165,7 +165,7 @@ programs for the manipulation and analysis of astronomical data.")
"/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
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@ -1979,14 +1979,14 @@ significantly faster and have minimal dependencies.")
(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
View file

@ -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 @@
#: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 @@
#: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 @@ precious backup space.
@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
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@ -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 @@ annotations for the genome of the model mouse Mus musculus.")
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 @@ annotations.")
"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 @@ performing parallel computations on multicore machines.")
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 @@ examples' of Affymetrix data, unlike the artificial examples included in the
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 @@ and regression inferences from RNA-sequencing data.")
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 @@ database (e.g. JASPAR). It can also be used to visualize motifs, motif
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 @@ and parameters of which are trained on a set of aligned reads and a reference
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 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
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 @@ files and writing bioinformatics applications.")
"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 @@ samples into a single report. It contains modules for a large number of
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 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
(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 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
("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 @@ provided.")
(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 @@ version does count multisplits.")
(define-public minimap2
(package
(name "minimap2")
(version "2.10")
(version "2.17")
(source
(origin
(method url-fetch)
@ -13161,7 +13266,7 @@ version does count multisplits.")
"minimap2-" version ".tar.bz2"))
(sha256
(base32
"080w9066irkbhbyr4nmf19pzkdd2s4v31hpzlajgq2y0drr6zcsj"))))
"0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are none
@ -13208,6 +13313,42 @@ cases include:
@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 @@ in RNA-seq data.")
(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 @@ in RNA-seq data.")
;; 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 @@ in RNA-seq data.")
("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 @@ in RNA-seq data.")
("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 @@ from forcing GEXP-PROMISE."
#: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 @@ from forcing GEXP-PROMISE."
%chromium-version ".tar.xz"))
(sha256
(base32
"0ahqh3vmzbpai4xwn7qybgw9phc8ssjdvfc7384mxqk9swqgv7qg"))))
"1ls663s1f74p912x42qp3zcvm17kmjiv1ij6yy1c14gdhcpmjx7z"))))
(define %ungoogled-origin
(origin
@ -275,7 +275,7 @@ from forcing GEXP-PROMISE."
(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 @@
#: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 @@ independent. Supported formats are 7z, ARJ, bzip2, gzip, LHA, lzma, lzop,
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 @@
#: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 @@
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 @@ legends.")
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 @@ small, reproducible, and runnable examples on code-oriented websites or email.
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 @@ application framework for R, making it easy to create attractive dashboards.")
(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 @@ processes. Most of its code is based on the @code{psutil} Python package.")
(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 @@ multi-dimensional data.")
(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 @@ any subsequent lookup as it keeps the hash table in memory.")
(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 @@ plot networks.")
(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 @@ quantile mixture from L-moments and trimmed L-moments.")
(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 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
;; 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 @@ by base R methods related to model fitting.")
(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 @@ by base R methods related to model fitting.")
("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 @@ timeout. It can also poll several processes at once.")
(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 @@ terminals.")
(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 @@ other add-on packages.")
(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 @@ bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
(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 @@ used to teach mathematics, statistics, computation and modeling.")
(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 @@ Hothorn, Westfall, 2010, CRC Press).")
(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 @@ Hothorn, Westfall, 2010, CRC Press).")
("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 @@ differentiation.")
(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 @@ effects models and Bayesian models.")
(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 @@ terminals that do not support Unicode.")
(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 @@ Bioconductor packages.")
(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 @@ features (e.g. local modes).")
(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 @@ library.")
(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 @@ JASA, 94:496-509.")
(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 @@ them in distributed compute environments.")
(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 @@ the local machine to, say, distributed processing on a remote compute cluster.")
(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 @@ tessellation.")
(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 @@ authoring books and technical documents with R Markdown.")
(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 @@ external dependencies. This package has is implemented purely in R.")
(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 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
;; 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 @@ includes data sets from oceanography.")
(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 @@ both R code and compiled C/C++/FORTRAN code.")
(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 @@ be used further by e.g. graphic devices.")
(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 @@ for original research. A variety of user defined options and formatting are
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 @@ actigraphy-measured activity counts data.")
(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 @@ functions.")
(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 @@ character codes as well as the UN M.49 area codes.")
(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 @@ machine learning, visually representing text and text analyses, and more.")
(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 @@ estimate parameters given observed data.")
(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 @@ infinite-precision rational arithmetic.")
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
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@ -673,14 +673,14 @@ printer/driver specific, but spooler-independent PPD file.")
(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 @@ can autogenerate peewee models using @code{pwiz}, a model generator.")
(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 @@ translate the complete SQLite API into Python.")
(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 @@ transforms idiomatic python function calls to well-formed SQL queries.")
(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 @@
#: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 @@
#:use-module (ice-9 match))
(define-public diffoscope
(let ((version "141"))
(let ((version "143"))
(package
(name "diffoscope")
(version version)
@ -81,7 +82,7 @@
(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 @@
(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 @@
(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 @@
("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 @@ these arguments. The prototypical use is for the command to call an external
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 @@ create an Extempore REPL, connect the current @code{extempore-mode} buffer to a
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 @@ strings.")
(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 @@ strings.")
(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 @@ strings.")
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 @@ of its name.")
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 @@ notes.")
(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 @@ provide an incremental search that moves all fake cursors in sync.")
(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 @@ provide an incremental search that moves all fake cursors in sync.")
(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 @@ stored playlists.")
(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 @@ stored playlists.")
(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 @@ stored playlists.")
(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 @@ fish-completion. It can be used in both Eshell and M-x shell.")
(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 @@ fish-completion. It can be used in both Eshell and M-x shell.")
(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 @@ ASCII UML sequence diagrams in Emacs, which can be embedded in source code,
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 @@ editor (without an 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 @@ that parenthetically inclined game developers need to make 2D (and eventually
(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 @@ desktop. It supports world clock, stop watch, alarms, and count down timer.")
("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-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 @@ calibrated, and restored when the calibration is applied.")
(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 @@ including media capture, encoding and decoding, and rendering.")
"/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 @@ including media capture, encoding and decoding, and rendering.")
(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 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(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 @@ relational database engine.")
(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 @@ relational database engine.")
(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 @@ is a library for creating graphical user interfaces.")
(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 @@ is a library for creating graphical user interfaces.")
(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 @@ is a library for creating graphical user interfaces.")
(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 @@ is a library for creating graphical user interfaces.")
(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 @@ is a library for creating graphical user interfaces.")
(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 @@ is a library for creating graphical user interfaces.")
(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 @@ is a library for creating graphical user interfaces.")
(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 @@ is a library for creating graphical user interfaces.")
(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 @@ is a library for creating graphical user interfaces.")
#: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 @@ MOP easier to use.")
(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 @@ interface to the Tk widget system.")
(define-public ecl
(package
(name "ecl")
(version "16.1.3")
(version "20.4.24")
(source
(origin
(method url-fetch)
@ -231,26 +231,22 @@ interface to the Tk widget system.")
"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 @@ bytecode compiler and interpreter, being able to compile Common Lisp with any
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 @@ an interpreter, a compiler, a debugger, and much more.")
(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 @@ an interpreter, a compiler, a debugger, and much more.")
;;
;; 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
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@ -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 @@ computing environments.")
(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 @@ data analysis.")
(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 @@ association studies (GWAS) on extremely large data sets.")
;; 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 @@ association studies (GWAS) on extremely large data sets.")
(file-name (git-file-name name version))
(sha256
(base32
"082qh3pfi7hvncylp4xsmkfahbd7gb0whdfa4rwrx7fxk9rdh3kz"))))
"07k80my6f19mhrkwbzhjsnpf9871wmrwkl0ym468i830w67qyjrz"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
@ -1138,8 +1168,8 @@ written in C++.")
(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 @@ written in C++.")
(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 @@ automatically.")
(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 @@ automatically.")
(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 @@ automatically.")
;; 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 @@ exec ~a ~a/~a \"$@\"~%"
#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
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@ -29,14 +29,14 @@
(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 @@ connection, or through a transit-relay.")
(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 @@ together, allowing them to pretend they have a direct connection.")
(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 @@ Swath).")
#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 @@ interfacing MPD in the C, C++ & Objective C languages.")
(define-public mpd
(package
(name "mpd")
(version "0.21.22")
(version "0.21.23")
(source (origin
(method url-fetch)
(uri
@ -101,7 +101,7 @@ interfacing MPD in the C, C++ & Objective C languages.")
"/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 @@
#: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 @@ and as an LV2 plugin.")
(define-public zrythm
(package
(name "zrythm")
(version "0.8.200")
(version "0.8.333")
(source
(origin
(method url-fetch)
@ -5166,7 +5167,7 @@ and as an LV2 plugin.")
version ".tar.xz"))
(sha256
(base32
"13ivxbrd44qnhyh46dcr94dvqxg8cn4bbd8xm77ljw0p9b4ks4zs"))))
"0x2kxr5zz058jpy6k6ymj0fi2gqfcgrlv4qkwz9443hjy5345iwb"))))
(build-system meson-build-system)
(arguments
`(#:glib-or-gtk? #t
@ -5190,7 +5191,9 @@ and as an LV2 plugin.")
("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-public openldap
(package
(name "openldap")
(replacement openldap-2.4.50)
(version "2.4.49")
(source (origin
(method url-fetch)
@ -125,6 +127,19 @@
(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 @@ manner.")
(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 @@
;; 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 @@
(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 @@ routines such as routines for numerical integration and optimization.")
(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 @@ connection to each user.")
(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 @@ such as IoT applications or multi-user database-driven business applications.")
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 @@ and rendering come directly from GitHub, so you'll know exactly how it will
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 @@ data for video and audio files.")
(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 @@ certificate returned by the server to which a connection has been established,
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 @@ reStructuredText.")
(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 @@ toolkits.")
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 @@ those files. It can also efficiently manipulate ranges of integers using set
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 @@ PEP 8.")
(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 @@ complexity of Python source code.")
(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 @@ complexity of Python source code.")
("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 @@ workspace...")
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 @@
#: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 @@ used by RDS Spy, and audio files containing @dfn{multiplex} signals (MPX).")
("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 @@ used by RDS Spy, and audio files containing @dfn{multiplex} signals (MPX).")
("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 @@ used by RDS Spy, and audio files containing @dfn{multiplex} signals (MPX).")
(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 @@ environment.")
("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 @@ using GNU Radio and the Qt GUI toolkit.")
(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 @@ for correctness.")
(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 @@ modes were all designed for making reliable, confirmed QSOs under extreme
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 @@ gitignore rules.")
("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 @@ gitignore rules.")
"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 @@ gitignore rules.")
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 @@ to be able to read and render the Doxygen xml output.")
"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 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
(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 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
version ".tar.gz"))
(sha256
(base32
"13xaxwfbzj0bd6rn2n27z0n04lb93mcyq991w4vdbbg8v282jc49"))))
"0h1995smlyiyhx7gpg9paxsfqrcn6g9bbp5h9r47i6an3clv1gh6"))))
(build-system gnu-build-system)
(arguments
`(#:disallowed-references (,tzdata-for-tests)
@ -269,6 +269,11 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
(("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 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
("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 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
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 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
("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 @@ available, greatly increasing its breadth and scope.")
(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 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
(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 @@ Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
(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 @@ code for possible problems.")
(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 @@ for reading and writing some dBase files.")
(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 @@ distributions beyond the exponential family.")
(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 @@ classification, regression and survival trees.")
(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 @@ like tidy evaluation.")
(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 @@ database.")
(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 @@ and environmental data in the framework of Euclidean exploratory methods.")
(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 @@ tools to simplify the devolpment of R packages.")
(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 @@ disk (or a connection).")
(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 @@ well as additional utilities such as panel and axis annotation functions.")
(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 @@ It uses and relies on grid graphics and formal (S4) classes and methods.")
(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 @@ groupings.")
(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 @@ fonts. Note that direct substitutes for the bitmapped EC fonts are available,
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 @@ based command language.")
(define-public kakoune
(package
(name "kakoune")
(version "2019.12.10")
(version "2020.01.16")
(source
(origin
(method url-fetch)
@ -131,7 +131,7 @@ based command language.")
"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 @@
(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 @@
`(("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 @@
#: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 @@
#: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 @@
#: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 @@ result in several formats:
@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 @@
#: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 @@ The peer-to-peer VPN implements a Layer 2 (Ethernet) network between the peers
(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 @@ The peer-to-peer VPN implements a Layer 2 (Ethernet) network between the peers
(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 @@ NetSurf project.")
(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 @@ NetSurf project.")
" 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 @@ NetSurf project.")
#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 @@ NetSurf project.")
("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 @@ compressed JSON header blocks.
(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 @@ compressed JSON header blocks.
(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 @@ the leaves of a full binary tree.")
(define-public herbstluftwm
(package
(name "herbstluftwm")
(version "0.7.2")
(version "0.8.1")
(source
(origin
(method url-fetch)
@ -157,9 +159,9 @@ the leaves of a full binary tree.")
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 @@ the leaves of a full binary tree.")
("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 @@ the leaves of a full binary tree.")
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 @@ productive, customizable lisp based systems.")
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 @@ rendering.")
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 @@ to find all available clips and launches @command{dmenu} (or @command{rofi},
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 @@
#: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 @@ X server: @code{handhelds}, @code{redglass} and @code{whiteglass}.")
(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 @@ This is a shorthand for (map (lambda (svc) ...) %base-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 @@ executables, making them setuid-root.")))
(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 @@ loop-back communications.")
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 @@ possible (that is if there's a LINUX keyword argument in the build system)."
(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 @@ TARGET in the other system."
;; 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 @@ from OS that are needed on the bare metal and not in a container."
(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 @@ packages defined in installation-os."
(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 @@ per %test-installed-os, this test is expensive in terms of CPU and storage.")
(services (cons (service marionette-service-type
(marionette-configuration
(imported-modules '((gnu services herd)
(guix build utils)
(guix combinators)))))
%base-services))))
@ -1060,7 +1061,7 @@ build (current-guix) and then store a couple of full system images.")
(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 @@ build (current-guix) and then store a couple of full system images.")
%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 @@ Shepherd (PID 1) by unloading obsolete services and loading new services."
(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 @@ Shepherd (PID 1) by unloading obsolete services and loading new services."
(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 @@ channel instances."
(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 @@ latest version of CRATE-NAME."
(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 @@
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 @@ are cross-built for TARGET."
. ,(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 @@ Start $VISUAL or $EDITOR to edit the definitions of PACKAGE...\n"))
(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 @@ Create a bundle of PACKAGE.\n"))
(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 @@ Create a bundle of PACKAGE.\n"))
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 @@ MAX-LENGTH first elements."
(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 @@ initial connection on which HTTP requests are sent."
(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 @@ initial connection on which HTTP requests are sent."
(()
(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 @@
\"dependencies\": [
{
\"crate_id\": \"bar\",
\"kind\": \"normal\",
\"kind\": \"normal\"
}
]
}")
@ -87,20 +87,20 @@
\"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 @@
\"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 @@
\"dependencies\": [
{
\"crate_id\": \"leaf-bob\",
\"kind\": \"normal\",
},
\"kind\": \"normal\"
}
]
}")
@ -233,6 +233,7 @@
(define test-source-hash
"")
(test-begin "crate")
(test-equal "guix-package->crate-name"

2
tests/gem.scm
View file

@ -52,7 +52,7 @@
\"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 @@
(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 @@
\"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 @@ Provides-Extra: testing
Requires-Dist: pytest (>=3.1.0); extra == 'testing'
")
(test-begin "pypi")
(test-equal "guix-package->pypi-name, old URL style"