me
/
guix
Archived
1
0
Fork 0
Code

Merge branch 'master' into staging

master
Maxim Cournoyer 2023-03-31 10:48:54 -04:00
parent 3d9a57e128 47ea688fd2
commit 99b25b1313
No known key found for this signature in database
GPG Key ID: 1260E46482E63562
36 changed files with 2849 additions and 453 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

28
doc/guix.texi
View File

@ -18959,7 +18959,6 @@ will fail if @var{device} does not exist.
@end table
@end deftp
@anchor{pam-limits-service}
@cindex session limits
@cindex ulimit
@cindex priority
@ -18967,22 +18966,23 @@ will fail if @var{device} does not exist.
@cindex jackd
@cindex nofile
@cindex open file descriptors
@deffn {Scheme Procedure} pam-limits-service [#:limits @code{'()}]
Return a service that installs a configuration file for the
@anchor{pam-limits-service-type}
@defvar pam-limits-service-type
Type of the service that installs a configuration file for the
@uref{http://linux-pam.org/Linux-PAM-html/sag-pam_limits.html,
@code{pam_limits} module}. The procedure optionally takes a list of
@code{pam-limits-entry} values, which can be used to specify
@code{pam_limits} module}. The value for this service type is
a list of @code{pam-limits-entry} values, which can be used to specify
@code{ulimit} limits and @code{nice} priority limits to user sessions.
By default, the value is the empty list.
The following limits definition sets two hard and soft limits for all
login sessions of users in the @code{realtime} group:
@lisp
(pam-limits-service
(list
(pam-limits-entry "@@realtime" 'both 'rtprio 99)
(pam-limits-entry "@@realtime" 'both 'memlock 'unlimited)))
(service pam-limits-service-type
(list
(pam-limits-entry "@@realtime" 'both 'rtprio 99)
(pam-limits-entry "@@realtime" 'both 'memlock 'unlimited)))
@end lisp
The first entry increases the maximum realtime priority for
@ -18994,9 +18994,9 @@ Another useful example is raising the maximum number of open file
descriptors that can be used:
@lisp
(pam-limits-service
(list
(pam-limits-entry "*" 'both 'nofile 100000)))
(service pam-limits-service-type
(list
(pam-limits-entry "*" 'both 'nofile 100000)))
@end lisp
In the above example, the asterisk means the limit should apply to any
@ -19005,7 +19005,7 @@ maximum system value visible in the @file{/proc/sys/fs/file-max} file,
else the users would be prevented from login in. For more information
about the Pluggable Authentication Module (PAM) limits, refer to the
@samp{pam_limits} man page from the @code{linux-pam} package.
@end deffn
@end defvar
@defvar greetd-service-type
@uref{https://git.sr.ht/~kennylevinsen/greetd, @code{greetd}} is a minimal and

5
etc/release-manifest.scm
View File

@ -1,6 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2020-2022 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
;;; Copyright © 2023 Andreas Enge <andreas@enge.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@ -73,9 +74,7 @@ TARGET."
"connman" "network-manager" "network-manager-applet"
"openssh" "ntp" "tor"
"linux-libre" "grub-hybrid"
;; FIXME: Add IceCat when Rust is available on i686.
;;"icecat"
))
"icecat"))
%default-xorg-modules))
(define %packages-to-cross-build

5
etc/teams.scm.in
View File

@ -461,7 +461,8 @@ GLib/GIO, GTK, GStreamer and Webkit."
(team 'lxqt
#:name "LXQt team"
#:description "LXQt desktop environment."
#:scope (list "gnu/packages/lxqt.scm")))
#:scope (list "gnu/packages/lxqt.scm"
"gnu/packages/qt.scm")))
(define-member (person "Eric Bavier"
@ -482,7 +483,7 @@ GLib/GIO, GTK, GStreamer and Webkit."
(define-member (person "Andreas Enge"
"andreas@enge.fr")
science)
lxqt science)
(define-member (person "Tobias Geerinckx-Rice"
"me@tobias.gr")

1
gnu/local.mk
View File

@ -782,6 +782,7 @@ GNU_SYSTEM_MODULES = \
%D%/tests/messaging.scm \
%D%/tests/networking.scm \
%D%/tests/package-management.scm \
%D%/tests/pam.scm \
%D%/tests/reconfigure.scm \
%D%/tests/rsync.scm \
%D%/tests/samba.scm \

56
gnu/packages/audio.scm
View File

@ -42,6 +42,7 @@
;;; Copyright © 2022 Andy Tai <atai@atai.org>
;;; Copyright © 2023 Sergiu Ivanov <sivanov@colimite.fr>
;;; Copyright © 2023 David Thompson <dthompson2@worcester.edu>
;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -66,8 +67,8 @@
#:use-module (gnu packages backup)
#:use-module (gnu packages base)
#:use-module (gnu packages bison)
#:use-module (gnu packages build-tools)
#:use-module (gnu packages boost)
#:use-module (gnu packages build-tools)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages curl)
@ -86,6 +87,7 @@
#:use-module (gnu packages gnome)
#:use-module (gnu packages gnunet) ; libmicrohttpd
#:use-module (gnu packages gperf)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages groff)
#:use-module (gnu packages gstreamer)
#:use-module (gnu packages gtk)
@ -95,6 +97,7 @@
#:use-module (gnu packages libbsd)
#:use-module (gnu packages libffi)
#:use-module (gnu packages libusb)
#:use-module (gnu packages linphone)
#:use-module (gnu packages linux)
#:use-module (gnu packages llvm)
#:use-module (gnu packages machine-learning)
@ -120,8 +123,6 @@
#:use-module (gnu packages serialization)
#:use-module (gnu packages sqlite)
#:use-module (gnu packages telephony)
#:use-module (gnu packages linphone)
#:use-module (gnu packages linux)
#:use-module (gnu packages tls)
#:use-module (gnu packages valgrind)
#:use-module (gnu packages video)
@ -3964,6 +3965,55 @@ compression modes. This package contains command-line programs and library to
encode and decode wavpack files.")
(license license:bsd-3)))
(define-public libmixed
;; Release is much outdated.
(let ((commit "91e6b9f2438bca41205fade02c9d8f4f938838b6")
(revision "0"))
(package
(name "libmixed")
(version (git-version "2.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Shirakumo/libmixed")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "01vwgv8ivpg7a4y95krkgh656mmklsn1k3fmhwp474aj82grd3m4"))))
(build-system cmake-build-system)
(arguments
(list
;; FIXME: (Sharlatan-20230326T121542+0100): Tests failed 1/34, 1 failed,
;; 33 passed. There is not simple way to disable just one test.
;; https://github.com/Shirakumo/libmixed/issues/13
#:tests? #f
#:configure-flags
#~(list "-DBUILD_STATIC=OFF"
"-DCMAKE_CXX_FLAGS=-O3 -fPIC"
"-DCMAKE_C_FLAGS=-O3 -fPIC")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'fix-paths
(lambda _
(substitute* "CMakeLists.txt"
(("/usr/local") #$output))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "./tester")))))))
(native-inputs (list doxygen graphviz))
(inputs (list mpg123 ncurses))
(home-page "https://github.com/Shirakumo/libmixed")
(synopsis "Low-level audio mixer pipeline library")
(description
"Libmixed is a library for real-time audio processing pipelines for use
in audio/video/games. It can serve as a base architecture for complex DSP
systems.")
(license (list license:bsd-2 ; libsamplerate
license:gpl2 ; spiralfft
license:zlib)))))
(define-public libmodplug
(package
(name "libmodplug")

2
gnu/packages/benchmark.scm
View File

@ -473,7 +473,7 @@ test any system or protocol.
Note: Locust will complain if the available open file descriptors limit for
the user is too low. To raise such limit on a Guix System, refer to
@samp{info guix --index-search=pam-limits-service}.")
@samp{info guix --index-search=pam-limits-service-type}.")
(license license:expat)))
(define-public interbench

527
gnu/packages/bioconductor.scm
View File

@ -640,6 +640,50 @@ from several related annotation packages.")
data.")
(license license:artistic2.0)))
(define-public r-illuminahumanmethylation450kmanifest
(package
(name "r-illuminahumanmethylation450kmanifest")
(version "0.4.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri
"IlluminaHumanMethylation450kmanifest"
version 'annotation))
(sha256
(base32
"0qx75xwifrbkqmbkd8dhf44c34ibmbivqh7y8rvgrsizmi5ybcj1"))))
(properties `((upstream-name . "IlluminaHumanMethylation450kmanifest")))
(build-system r-build-system)
(propagated-inputs (list r-minfi))
(home-page
"https://bioconductor.org/packages/IlluminaHumanMethylation450kmanifest")
(synopsis "Annotation for Illumina's 450k methylation arrays")
(description "This package provides a manifest for Illumina's 450k array
data.")
(license license:artistic2.0)))
(define-public r-illuminahumanmethylationepicanno-ilm10b4-hg19
(package
(name "r-illuminahumanmethylationepicanno-ilm10b4-hg19")
(version "0.6.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri
"IlluminaHumanMethylationEPICanno.ilm10b4.hg19"
version 'annotation))
(sha256
(base32
"0687b4k8hwfc18qgdd9ypv1skp37jd204fszba0gmrv3dc92i09c"))))
(properties `((upstream-name . "IlluminaHumanMethylationEPICanno.ilm10b4.hg19")))
(build-system r-build-system)
(propagated-inputs (list r-minfi))
(home-page
"https://doi.org/doi:10.18129/B9.bioc.IlluminaHumanMethylationEPICanno.ilm10b4.hg19")
(synopsis "Annotation for Illumina's EPIC methylation arrays")
(description
"This is an annotation package for Illumina's EPIC methylation arrays.")
(license license:artistic2.0)))
(define-public r-org-ce-eg-db
(package
(name "r-org-ce-eg-db")
@ -1392,6 +1436,26 @@ curated cell type labels, for use in procedures like automated annotation of
single-cell data or deconvolution of bulk RNA-seq.")
(license license:gpl3)))
(define-public r-champdata
(package
(name "r-champdata")
(version "2.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ChAMPdata" version 'experiment))
(sha256
(base32
"0rz762szfl02h4d3dj7ckd41ji9mdsja8nxqw6fl086z337041zw"))))
(properties `((upstream-name . "ChAMPdata")))
(build-system r-build-system)
(propagated-inputs (list r-biocgenerics r-genomicranges))
(home-page "https://bioconductor.org/packages/ChAMPdata")
(synopsis "Data packages for ChAMP package")
(description
"This package provides datasets needed for ChAMP including a test dataset
and blood controls for CNA analysis.")
(license license:gpl3)))
(define-public r-chromstardata
(package
(name "r-chromstardata")
@ -1434,6 +1498,63 @@ display copy number variation. Files are stored as GRanges objects from the
GenomicRanges Bioconductor package.")
(license license:gpl2)))
(define-public r-flowsorted-blood-450k
(package
(name "r-flowsorted-blood-450k")
(version "1.36.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "FlowSorted.Blood.450k"
version 'experiment))
(sha256
(base32
"1ha9qsp5g3g2yhnk574x6xhg95bb29ywvmg3ns1c50z69v6wbraq"))))
(properties `((upstream-name . "FlowSorted.Blood.450k")))
(build-system r-build-system)
(propagated-inputs (list r-minfi))
(home-page "https://bioconductor.org/packages/FlowSorted.Blood.450k")
(synopsis
"Illumina HumanMethylation data on sorted blood cell populations")
(description
"This package provides raw data objects for the Illumina 450k DNA
methylation microarrays, and an object depicting which CpGs on the array are
associated with cell type.")
(license license:artistic2.0)))
(define-public r-flowsorted-blood-epic
(package
(name "r-flowsorted-blood-epic")
(version "2.2.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "FlowSorted.Blood.EPIC" version
'experiment))
(sha256
(base32
"1vybj69jxnirqg6ik03q3pb1vv23z8mir7wpi2ys7iljf5ixzgl1"))))
(properties `((upstream-name . "FlowSorted.Blood.EPIC")))
(build-system r-build-system)
(propagated-inputs
(list r-annotationhub
r-experimenthub
r-genefilter
r-minfi
r-nlme
r-quadprog
r-s4vectors
r-summarizedexperiment))
(native-inputs (list r-knitr))
(home-page "https://github.com/immunomethylomics/FlowSorted.Blood.EPIC")
(synopsis
"Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells")
(description
"This package provides raw data objects to be used for blood cell
proportion estimation in minfi and similar packages. The
@code{FlowSorted.Blood.EPIC} object is based in samples assayed by Brock
Christensen and colleagues; for details see Salas et al. 2018.
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554.")
(license license:gpl3)))
(define-public r-genelendatabase
(package
(name "r-genelendatabase")
@ -1523,6 +1644,28 @@ cluster labels and labels identifying spiked in cells. Column metadata
includes channel names, protein marker names, and protein marker classes.")
(license license:expat)))
(define-public r-illumina450probevariants-db
(package
(name "r-illumina450probevariants-db")
(version "1.34.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Illumina450ProbeVariants.db"
version 'experiment))
(sha256
(base32
"1c1iqxi17s1a1sa1vab2ma7pjq1dxal7ibsiahj66ys0pa4sm42p"))))
(properties `((upstream-name . "Illumina450ProbeVariants.db")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/Illumina450ProbeVariants.db")
(synopsis
"Variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes")
(description
"This package includes details on variants for each probe on the 450k
bead chip for each of the four populations (Asian, American, African and
European).")
(license license:gpl3)))
(define-public r-italicsdata
(package
(name "r-italicsdata")
@ -1565,6 +1708,79 @@ gene expression indicate a role for enhancer priming in immune response\", publi
in Nature Genetics, January 2018.")
(license license:gpl2+)))
(define-public r-minfidata
(package
(name "r-minfidata")
(version "0.44.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "minfiData" version 'experiment))
(sha256
(base32
"15s3kc629m2c78vkidmp6kcc28sn1wzjzrxazmd8z7x8cdad3q4g"))))
(properties `((upstream-name . "minfiData")))
(build-system r-build-system)
(propagated-inputs
(list r-illuminahumanmethylation450kanno-ilmn12-hg19
r-illuminahumanmethylation450kmanifest
r-minfi))
(home-page "https://bioconductor.org/packages/minfiData")
(synopsis "Example data for the Illumina Methylation 450k array")
(description
"This package provides data from 6 samples across 2 groups from 450k
methylation arrays.")
(license license:artistic2.0)))
(define-public r-missmethyl
(package
(name "r-missmethyl")
(version "1.32.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "missMethyl" version))
(sha256
(base32
"1rrm8m68kgjkrw1wdli5lrwqlavhbm490zgnj5vafzpvx7xajfma"))))
(properties `((upstream-name . "missMethyl")))
(build-system r-build-system)
(propagated-inputs
(list r-annotationdbi
r-biasedurn
r-biobase
r-biocgenerics
r-genomicranges
r-go-db
r-illuminahumanmethylation450kanno-ilmn12-hg19
r-illuminahumanmethylation450kmanifest
r-illuminahumanmethylationepicanno-ilm10b4-hg19
r-illuminahumanmethylationepicmanifest
r-iranges
r-limma
r-methylumi
r-minfi
r-org-hs-eg-db
r-ruv
r-s4vectors
r-statmod
r-stringr
r-summarizedexperiment))
(native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/missMethyl")
(synopsis "Analyzing Illumina HumanMethylation BeadChip data")
(description
"This is a package for normalization, testing for differential
variability and differential methylation and gene set testing for data from
Illumina's Infinium HumanMethylation arrays. The normalization procedure is
subset-quantile within-array normalization (SWAN), which allows Infinium I and
II type probes on a single array to be normalized together. The test for
differential variability is based on an empirical Bayes version of Levene's
test. Differential methylation testing is performed using RUV, which can
adjust for systematic errors of unknown origin in high-dimensional data by
using negative control probes. Gene ontology analysis is performed by taking
into account the number of probes per gene on the array, as well as taking
into account multi-gene associated probes.")
(license license:gpl2)))
(define-public r-msdata
(package
(name "r-msdata")
@ -2516,13 +2732,13 @@ problems.")
(define-public r-amaretto
(package
(name "r-amaretto")
(version "1.13.0")
(version "1.14.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AMARETTO" version))
(sha256
(base32
"18w65sf3h4yzw9v5xgkalxnkmgzgsx100v7qc7z4ifx10lgpji5n"))))
"06j75c4j71fkkw5s52nbzb3k084y2f4v4h3js9dgsxxrd6jkzfz9"))))
(properties `((upstream-name . "AMARETTO")))
(build-system r-build-system)
(propagated-inputs
@ -2761,13 +2977,13 @@ for use in Bioconductor’s AnnotationHub.")
(define-public r-anvil
(package
(name "r-anvil")
(version "1.10.1")
(version "1.10.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnVIL" version))
(sha256
(base32
"0iqsffkrxv28g9cddx2w05f2dbscwxhh6bpizwa8xaxhvn5bcpsv"))))
"1j7n8c47j3njd5rnlrj8bkn4q5z7jpm0c9rdq1mlwd2i1yy9fz9b"))))
(properties `((upstream-name . "AnVIL")))
(build-system r-build-system)
(propagated-inputs
@ -4533,6 +4749,46 @@ spent loading the full derfinder package when running the F-statistics
calculation in parallel.")
(license license:artistic2.0)))
(define-public r-dmrcate
(package
(name "r-dmrcate")
(version "2.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DMRcate" version))
(sha256
(base32
"0iphlsbam5fcxbj5j0cmqk3wz5ykwz0mvk3qbrhzxbpf2h4w2qib"))))
(properties `((upstream-name . "DMRcate")))
(build-system r-build-system)
(propagated-inputs
(list r-bsseq
r-dss
r-edger
r-experimenthub
r-genomeinfodb
r-genomicranges
r-gviz
r-iranges
r-limma
r-minfi
r-missmethyl
r-plyr
r-s4vectors
r-summarizedexperiment))
(native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/DMRcate")
(synopsis "Methylation array and sequencing spatial analysis methods")
(description
"This is a package for de novo identification and extraction of
@dfn{differentially methylated regions} (DMRs) from the human genome using
@dfn{Whole Genome Bisulfite Sequencing} (WGBS) and Illumina Infinium
Array (450K and EPIC) data. It provides functionality for filtering probes
possibly confounded by SNPs and cross-hybridisation. It includes
@code{GRanges} generation and plotting functions.")
;; GPLv3 with additional liability disclaimer.
(license license:gpl3)))
(define-public r-drimseq
(package
(name "r-drimseq")
@ -4568,6 +4824,32 @@ makes available functions for visualization and exploration of the data and
results.")
(license license:gpl3+)))
(define-public r-dss
(package
(name "r-dss")
(version "2.46.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DSS" version))
(sha256
(base32
"1qm0pq6495fn2zrbddaadb1w01ry76rg8mmbmxf3zws9pww48jgf"))))
(properties `((upstream-name . "DSS")))
(build-system r-build-system)
(propagated-inputs (list r-biobase r-biocparallel r-bsseq))
(native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/DSS")
(synopsis "Dispersion shrinkage for sequencing data")
(description
"DSS is an R library performing differential analysis for count-based
sequencing data. It detects @dfn{differentially expressed genes} (DEGs) from
RNA-seq, and differentially methylated loci or regions (DML/DMRs) from
@dfn{bisulfite sequencing} (BS-seq). The core of DSS is a dispersion
shrinkage method for estimating the dispersion parameter from Gamma-Poisson or
Beta-Binomial distributions.")
;; Any version of the GPL
(license (list license:gpl2+ license:gpl3+))))
(define-public r-bluster
(package
(name "r-bluster")
@ -4763,6 +5045,28 @@ domains etc.) from quantification of all types of RNASeq by tools such as
Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.")
(license license:gpl2+)))
;; This is a CRAN package, but it depends on qvalue from Bioconductor.
(define-public r-isva
(package
(name "r-isva")
(version "1.9")
(source (origin
(method url-fetch)
(uri (cran-uri "isva" version))
(sha256
(base32
"05qx9q0kg4ma23v4abhihw0vz017nq6hv2jzsiqx4d20ngh1dl4z"))))
(properties `((upstream-name . "isva")))
(build-system r-build-system)
(propagated-inputs (list r-fastica r-jade r-qvalue))
(home-page "https://cran.r-project.org/package=isva")
(synopsis "Independent surrogate variable analysis")
(description
"Independent Surrogate Variable Analysis is an algorithm for feature
selection in the presence of potential confounding factors (see Teschendorff
AE et al 2011, <doi: 10.1093/bioinformatics/btr171>).")
(license license:gpl2)))
(define-public r-italics
(package
(name "r-italics")
@ -5239,14 +5543,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
(define-public r-annotationforge
(package
(name "r-annotationforge")
(version "1.40.1")
(version "1.40.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationForge" version))
(sha256
(base32
"16wdcl56d5i8wrmin610kzs9ldy7h9w5fbnysjb1crkcgbikq1yy"))))
"1ab7nl9zrlhlkwjrjr69zqq5hy9a8rp457hcr075n8qm5r5lf6wd"))))
(properties
`((upstream-name . "AnnotationForge")))
(build-system r-build-system)
@ -5388,13 +5692,13 @@ on Bioconductor or which replace R functions.")
(define-public r-biomart
(package
(name "r-biomart")
(version "2.54.0")
(version "2.54.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
"0c6agi652kbffqwd1r3c22ncisqaiy3gqbc9fz13767rr71im6lq"))))
"13nhp97cklaimc3cd931hz584nc58szk2gyxrkfhp7knfli6jbpi"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
@ -5653,6 +5957,68 @@ genome data packages and support for efficient SNP representation.")
analysis.")
(license license:artistic2.0)))
(define-public r-champ
(package
(name "r-champ")
(version "2.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ChAMP" version))
(sha256
(base32
"10ss0a3miqrx92vy1r1h5rv3mnjn4iyl32q86s0x59d3fvqp2cx1"))))
(properties `((upstream-name . "ChAMP")))
(build-system r-build-system)
(propagated-inputs
(list r-bumphunter
r-champdata
r-combinat
r-dendextend
r-dmrcate
r-dnacopy
r-doparallel
r-dt
r-genomicranges
r-ggplot2
r-globaltest
r-goseq
r-hmisc
r-illumina450probevariants-db
r-illuminahumanmethylation450kmanifest
r-illuminahumanmethylationepicanno-ilm10b4-hg19
r-illuminahumanmethylationepicmanifest
r-illuminaio
r-impute
r-isva
r-kpmt
r-limma
r-marray
r-matrixstats
r-minfi
r-missmethyl
r-plotly
r-plyr
r-preprocesscore
r-prettydoc
r-quadprog
r-qvalue
r-rcolorbrewer
r-rmarkdown
r-rpmm
r-shiny
r-shinythemes
r-sva
r-watermelon))
(native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/ChAMP")
(synopsis
"Chip analysis methylation pipeline for Illumina HumanMethylation450 and EPIC")
(description
"The package includes quality control metrics, a selection of
normalization methods and novel methods to identify differentially methylated
regions and to highlight copy number alterations.")
(license license:gpl3)))
(define-public r-chipseeker
(package
(name "r-chipseeker")
@ -6145,6 +6511,48 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and
CAGE.")
(license license:gpl2+)))
(define-public r-enmix
(package
(name "r-enmix")
(version "1.34.02")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ENmix" version))
(sha256
(base32
"0rn541xfsxfdyzy3dn727bwrfpkgp12282lax7xg1j8584mk4pcf"))))
(properties `((upstream-name . "ENmix")))
(build-system r-build-system)
(propagated-inputs
(list r-annotationhub
r-biobase
r-doparallel
r-dynamictreecut
r-experimenthub
r-foreach
r-genefilter
r-geneplotter
r-gplots
r-gtools
r-illuminaio
r-impute
r-iranges
r-matrixstats
r-minfi
r-preprocesscore
r-quadprog
r-rpmm
r-s4vectors
r-summarizedexperiment))
(native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/release/bioc/html/ENmix.html")
(synopsis
"Quality control and analysis tools for Illumina DNA methylation BeadChip")
(description
"This package provides tools for quality control, analysis and
visualization of Illumina DNA methylation array data.")
(license license:artistic2.0)))
(define-public r-ensembldb
(package
(name "r-ensembldb")
@ -6524,6 +6932,30 @@ profiles and assignment of a status (gain, normal or loss) to each chromosomal
regions identified.")
(license license:gpl2)))
(define-public r-globaltest
(package
(name "r-globaltest")
(version "5.52.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "globaltest" version))
(sha256
(base32
"1g5dv3bw0fj8sq0hsr8c7nh6n1rzvx1bisqlyqjqq3f8lsyb51kb"))))
(properties `((upstream-name . "globaltest")))
(build-system r-build-system)
(propagated-inputs
(list r-annotate r-annotationdbi r-biobase r-survival))
(home-page "https://bioconductor.org/packages/globaltest")
(synopsis
"Test groups of covariates for association with a response variable")
(description
"The global test tests groups of covariates (or features) for association
with a response variable. This package implements the test with diagnostic
plots and multiple testing utilities, along with several functions to
facilitate the use of this test for gene set testing of GO and KEGG terms.")
(license license:gpl2+)))
(define-public r-gostats
(package
(name "r-gostats")
@ -7962,14 +8394,14 @@ the available RAM.")
(define-public r-rhdf5filters
(package
(name "r-rhdf5filters")
(version "1.10.0")
(version "1.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "rhdf5filters" version))
(sha256
(base32
"17x2a3122mm3z9qnalw25am2x08cfpm17nwhigabid3ha3d2mgz1"))))
"14rkr0fisy7qrvjikpnwxwag79205hdxy6nkpwz501li4fr1rbnp"))))
(properties `((upstream-name . "rhdf5filters")))
(build-system r-build-system)
(propagated-inputs
@ -8368,6 +8800,33 @@ sequence motif occurrences across a large set of sequences centred at a common
reference point and sorted by a user defined feature.")
(license license:gpl3+)))
(define-public r-shinymethyl
(package
(name "r-shinymethyl")
(version "1.34.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "shinyMethyl" version))
(sha256
(base32
"1xbadc4xszcqh211r8z0wp417f17aczz834icli17mcsl996ln3a"))))
(properties `((upstream-name . "shinyMethyl")))
(build-system r-build-system)
(propagated-inputs
(list r-biocgenerics
r-illuminahumanmethylation450kmanifest
r-matrixstats
r-minfi
r-rcolorbrewer
r-shiny))
(native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/shinyMethyl")
(synopsis "Interactive visualization for Illumina methylation arrays")
(description
"This package provides an interactive tool for visualizing Illumina
methylation array data. Both the 450k and EPIC array are supported.")
(license license:artistic2.0)))
(define-public r-shortread
(package
(name "r-shortread")
@ -14341,6 +14800,46 @@ gene fusion discovery. It can be applied to all major sequencing techologies
and to both short and long sequence reads.")
(license license:gpl3)))
(define-public r-flowai
(package
(name "r-flowai")
(version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "flowAI" version))
(sha256
(base32
"18zrlnjw89iglxhw65ys8x4r44pdzp5chrgwx7w44sh7yd8576g9"))))
(properties `((upstream-name . "flowAI")))
(build-system r-build-system)
(propagated-inputs
(list r-changepoint
r-flowcore
r-ggplot2
r-knitr
r-plyr
r-rcolorbrewer
r-reshape2
r-rmarkdown
r-scales))
(native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/flowAI")
(synopsis
"Automatic and interactive quality control for flow cytometry data")
(description
"This package is able to perform an automatic or interactive quality
control on FCS data acquired using flow cytometry instruments. By evaluating
three different properties:
@enumerate
@item flow rate
@item signal acquisition, and
@item dynamic range,
@end enumerate
the quality control enables the detection and removal of anomalies.")
(license license:gpl2+)))
(define-public r-flowutils
(package
(name "r-flowutils")
@ -14616,14 +15115,14 @@ statistics to the plot.")
(define-public r-flowclust
(package
(name "r-flowclust")
(version "3.36.0")
(version "3.36.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowClust" version))
(sha256
(base32
"1l1lfgm6x06gyzda36m6gvqmb91zbrz8m83b1fnfzpxkhqha20yq"))))
"1r27nm5dxlhl5rk96dkjfx8326bvdgx55xg4w2zji3m49x9db2gs"))))
(properties `((upstream-name . "flowClust")))
(build-system r-build-system)
(arguments
@ -19518,14 +20017,14 @@ using aCGH or sequencing.")
(define-public r-bionero
(package
(name "r-bionero")
(version "1.6.0")
(version "1.6.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioNERO" version))
(sha256
(base32
"10nwgp8a9chn33p5k7cdp920rraiw187xfrylyd9bq010c7vp7xh"))))
"0ijdnl43cgzywgsz80jd6q0irixh6367qm1ll5ww1rcr4xas2nsl"))))
(properties `((upstream-name . "BioNERO")))
(build-system r-build-system)
(propagated-inputs

133
gnu/packages/bioinformatics.scm
View File

@ -13991,6 +13991,85 @@ cells with similar identification cards in the different cytometric profiles
is then merged.")
(license license:gpl2))))
(define-public r-cytoexplorer
(let ((commit "0efb1cc19fc701ae03905cf1b8484c1dfeb387df")
(revision "1"))
(package
(name "r-cytoexplorer")
(version (git-version "1.1.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/DillonHammill/CytoExploreR")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1y7dadsy15i47rjmdq6ns80jzm6p0zmixll37q68ba2c7xn5pq3v"))
(snippet
'(delete-file
"docs/articles/CytoExploreR_files/vis-4.20.1/vis.min.js"))))
(properties `((upstream-name . "CytoExploreR")))
(build-system r-build-system)
(arguments
(list
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'process-javascript
(lambda* (#:key inputs #:allow-other-keys)
(with-directory-excursion "docs/articles/CytoExploreR_files/"
(let ((source (search-input-file inputs "/dist/vis.js"))
(target "vis-4.20.1/vis.min.js"))
(invoke "esbuild" source "--minify"
(string-append "--outfile=" target)))))))))
(propagated-inputs
(list r-biocgenerics
r-bslib
r-data-table
r-dplyr
r-embedsom
r-flowai
r-flowcore
r-flowworkspace
r-gtools
r-magrittr
r-mass
r-opencyto
r-purrr
r-rhandsontable
r-robustbase
r-rsvd
r-rtsne
r-shiny
r-superheat
r-tibble
r-tidyr
r-umap
r-visnetwork))
(native-inputs
`(("esbuild" ,esbuild)
("r-knitr" ,r-knitr)
("js-vis"
,(let ((version "4.20.1"))
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/almende/vis")
(commit (string-append "v" version))))
(file-name (git-file-name "js-vis" version))
(sha256
(base32
"09ldcqzzki5c0jlwas5992qjffqxnx6j5sl703qccfw7rg1hn469")))))))
(home-page "https://github.com/DillonHammill/CytoExploreR")
(synopsis "Interactive analysis of cytometry data")
(description
"This package has been developed under ROpenSci gudelines to integrate
conventional and cutting edge cytometry analysis tools under a unified
framework. It aims to represent an intuitive and interactive approach to
analysing cytometry data in R.")
(license license:gpl2))))
(define-public r-giotto
(let ((commit "3c8067cedbf6e3112edcac2ae796de05fd9d6fe4")
(revision "1"))
@ -14049,6 +14128,60 @@ is then merged.")
spatial single-cell expression data.")
(license license:expat))))
(define-public r-illuminahumanmethylationepicanno-ilm10b5-hg38
(let ((commit "3db06910e27f626e0cc8b335ff45cf9a4050a36a")
(revision "1"))
(package
(name "r-illuminahumanmethylationepicanno-ilm10b5-hg38")
(version (git-version "0.0.1" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url
"https://github.com/achilleasNP/IlluminaHumanMethylationEPICanno.ilm10b5.hg38")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0y8fhiwmkldi57f8nq64njfgljw68cm6pb1vh44hjwcc12k48sqr"))))
(properties `((upstream-name . "IlluminaHumanMethylationEPICanno.ilm10b5.hg38")))
(build-system r-build-system)
(propagated-inputs (list r-minfi))
(home-page
"https://github.com/achilleasNP/IlluminaHumanMethylationEPICanno.ilm10b5.hg38")
(synopsis "Illumina Human Methylation EPIC Annotation version 1.0B5")
(description
"This package provides a companion annotation file to the
@code{IlluminaHumanMethylationEPICmanifest} package based on the same
annotation 1.0B5.")
(license license:artistic2.0))))
(define-public r-maxprobes
(let ((commit "c2120dba972e12115280ef274ff80550cee5b264")
(revision "1"))
(package
(name "r-maxprobes")
(version (git-version "0.0.2" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/markgene/maxprobes")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1kij9bds2l9mwm519bzyd2608563qjlmbrayhva1s0vgml5iq9wh"))))
(properties `((upstream-name . "maxprobes")))
(build-system r-build-system)
(propagated-inputs (list r-minfi r-minfidata))
(native-inputs (list r-knitr))
(home-page "https://github.com/markgene/maxprobes")
(synopsis "Methylation array cross-reactive probes")
(description
"The Maxprobes package collects cross-reactive probes of Illumina
methylation array 450K and EPIC/850K.")
(license license:gpl2+))))
(define-public gffread
;; We cannot use the tagged release because it is not in sync with gclib.
;; See https://github.com/gpertea/gffread/issues/26

7
gnu/packages/check.scm
View File

@ -1322,11 +1322,14 @@ and many external plugins.")
"0f8c31v5r2kgjixvy267n0nhc4xsy65g3n9lz1i1377z5pn5ydjg"))))
(arguments
(substitute-keyword-arguments (package-arguments python-pytest)
((#:phases phases #~%standard-phases)
((#:phases phases #~%standard-phases)
#~(modify-phases #$phases
(add-before 'build 'pretend-version
(lambda _
(setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))))))))
(setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))))))
(propagated-inputs
(modify-inputs (package-propagated-inputs python-pytest)
(replace "python-pluggy" python-pluggy-next)))))
(define-public python-pytest-bootstrap
(package

446
gnu/packages/cran.scm
View File

@ -428,14 +428,14 @@ etc.")
(define-public r-datawizard
(package
(name "r-datawizard")
(version "0.6.5")
(version "0.7.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "datawizard" version))
(sha256
(base32
"0il98vmy8l4wrisqz9xli7iki2ajdlsxyhh4k4grrd28gzkj8lgb"))))
"19bihl1nxd11gxwz3m71dprs3ykwp96pz24b38w6i6azin82apy0"))))
(properties `((upstream-name . "datawizard")))
(build-system r-build-system)
(propagated-inputs
@ -592,6 +592,35 @@ edition of the book \"Data Mining with R, learning with case studies\"
by Luis Torgo, published by CRC Press.")
(license license:gpl2+)))
(define-public r-embedsom
(package
(name "r-embedsom")
(version "2.1.2")
(source (origin
(method url-fetch)
(uri (cran-uri "EmbedSOM" version))
(sha256
(base32
"0k4hja5y7qd0n3gfaxzxrz4wpxc1w9d4d4xbb63rq2nfk3lj7a42"))))
(properties `((upstream-name . "EmbedSOM")))
(build-system r-build-system)
(propagated-inputs
(list r-fnn
r-ggplot2
r-igraph
r-matrix
r-rtsne
r-umap
r-uwot))
(native-inputs (list r-knitr))
(home-page "https://github.com/exaexa/EmbedSOM")
(synopsis "Fast embedding guided by self-organizing map")
(description
"This package provides a smooth mapping of multidimensional points into
low-dimensional space defined by a self-organizing map. It is designed to
work with FlowSOM and flow-cytometry use-cases.")
(license license:gpl3+)))
(define-public r-emdist
(package
(name "r-emdist")
@ -708,14 +737,14 @@ such as counts or binary matrices.")
(define-public r-googledrive
(package
(name "r-googledrive")
(version "2.0.0")
(version "2.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "googledrive" version))
(sha256
(base32
"09jsiknzyfgxd0nzdr3wrrjw24allch2x74h96qg8vh8dad4cp30"))))
"0x2biilbphh77p7cxp2cvinjx45hnb5xksw775nwksqvpwxkaw0d"))))
(properties `((upstream-name . "googledrive")))
(build-system r-build-system)
(propagated-inputs
@ -943,14 +972,14 @@ pronounceable identifiers.")
(define-public r-googlesheets4
(package
(name "r-googlesheets4")
(version "1.0.1")
(version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "googlesheets4" version))
(sha256
(base32
"14b5lzn6vjn72mw7vf3lzm2ppbjf0wr0n6sw0v5r6h4lk37cnki8"))))
"1jcfih6f62phj7fdvknkkj46s9cvsnhshvkglg6xif7mpr1mbqah"))))
(properties `((upstream-name . "googlesheets4")))
(build-system r-build-system)
(propagated-inputs
@ -962,12 +991,14 @@ pronounceable identifiers.")
r-googledrive
r-httr
r-ids
r-lifecycle
r-magrittr
r-purrr
r-rematch2
r-rlang
r-tibble
r-vctrs))
r-vctrs
r-withr))
(home-page "https://github.com/tidyverse/googlesheets4")
(synopsis "Access Google Sheets using the Sheets API V4")
(description
@ -996,6 +1027,71 @@ matrix decomposition, sparse principal components analysis, and sparse
canonical correlation analysis.")
(license license:gpl2+)))
(define-public r-prettydoc
(package
(name "r-prettydoc")
(version "0.4.1")
(source (origin
(method url-fetch)
(uri (cran-uri "prettydoc" version))
(sha256
(base32
"0aa89jnqhz0l69inrgm1f1riq5bm3ksb8wjl8d4x2f320adsd50h"))
(snippet
'(for-each delete-file
'("inst/resources/js/auto-render.min.js"
"inst/resources/js/katex.min.js")))))
(properties `((upstream-name . "prettydoc")))
(build-system r-build-system)
(arguments
`(#:modules ((guix build utils)
(guix build r-build-system)
(srfi srfi-1))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'process-javascript
(lambda* (#:key inputs #:allow-other-keys)
(with-directory-excursion "inst/resources/js/"
(call-with-values
(lambda ()
(unzip2
`((,(search-input-file inputs "dist/katex.js")
"katex.min.js")
(,(search-input-file inputs "dist/contrib/auto-render.js")
"auto-render.min.js"))))
(lambda (sources targets)
(for-each (lambda (source target)
(format #true "Processing ~a --> ~a~%"
source target)
(invoke "esbuild" source "--minify"
(string-append "--outfile=" target)))
sources targets)))))))))
(inputs (list pandoc))
(propagated-inputs (list r-rmarkdown))
(native-inputs
(list esbuild
r-knitr
r-rmarkdown
(let ((version "0.12.0"))
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/KaTeX/KaTeX")
(commit (string-append "v" version))))
(file-name (git-file-name "js-katex" version))
(sha256
(base32
"0pdfw28affnfpqpnf244acf5rkxdy2gk63669myy7ysg4z0i1n8j"))))))
(home-page "https://github.com/yixuan/prettydoc")
(synopsis "Create pretty documents from R markdown")
(description
"This is a package for creating tiny yet beautiful documents and
vignettes from R Markdown. The package provides the @code{html_pretty} output
format as an alternative to the @code{html_document} and @code{html_vignette}
engines that convert R Markdown into HTML pages. Various themes and syntax
highlight styles are supported.")
(license license:asl2.0)))
(define-public r-proj4
(package
(name "r-proj4")
@ -1046,6 +1142,33 @@ Functions include searching for people, searching by DOI, or searching by
Orcid ID.")
(license license:expat)))
(define-public r-ruv
(package
(name "r-ruv")
(version "0.9.7.1")
(source (origin
(method url-fetch)
(uri (cran-uri "ruv" version))
(sha256
(base32
"1n4q9mrp9f644spbns6bbnzmlabrg90hwkdfg3hnm3rxp9b4xid0"))))
(properties `((upstream-name . "ruv")))
(build-system r-build-system)
(propagated-inputs (list r-ggplot2 r-gridextra r-scales))
(home-page "https://cran.r-project.org/web/packages/ruv/index.html")
(synopsis "Detect and remove unwanted variation using negative controls")
(description
"This package implements the RUV (Remove Unwanted Variation) algorithms.
These algorithms attempt to adjust for systematic errors of unknown origin in
high-dimensional data. The algorithms were originally developed for use with
genomic data, especially microarray data, but may be useful with other types
of high-dimensional data as well. The algorithms require the user to specify
a set of negative control variables, as described in the references. The
algorithms included in this package are RUV-2, RUV-4, RUV-inv, RUV-rinv,
RUV-I, and RUV-III, along with various supporting algorithms.")
;; Any version of the GPL.
(license (list license:gpl2+ license:gpl3+))))
(define-public r-waldo
(package
(name "r-waldo")
@ -3075,14 +3198,14 @@ model fitting and error handling.")
(define-public r-modelr
(package
(name "r-modelr")
(version "0.1.10")
(version "0.1.11")
(source
(origin
(method url-fetch)
(uri (cran-uri "modelr" version))
(sha256
(base32
"0qqgdb7gpb1h9lf5zijg51gd0qmbzj8f37aykhv1w633cglacick"))))
"1lvv6gac3g4x1d58chbvlxlkd77qz21a3rlb64jvzwycx43dbswl"))))
(build-system r-build-system)
(propagated-inputs
(list r-broom
@ -3246,6 +3369,29 @@ re-imagining of @code{httr} that uses a pipe-based interface and solves more
of the problems that API wrapping packages face.")
(license license:expat)))
(define-public r-jade
(package
(name "r-jade")
(version "2.0-3")
(source (origin
(method url-fetch)
(uri (cran-uri "JADE" version))
(sha256
(base32
"1fj2wawx5ac1fvlp28naqha0i17f1sb47j2qqzgccvx17ycqmmjn"))))
(properties `((upstream-name . "JADE")))
(build-system r-build-system)
(propagated-inputs (list r-clue))
(home-page "https://cran.r-project.org/package=JADE")
(synopsis "Blind source separation methods")
(description
"In this package Cardoso's JADE algorithm as well as his functions for
joint diagonalization are ported to R. Also several other @dfn{blind source
separation} (BSS) methods, like AMUSE and SOBI, and some criteria for
performance evaluation of BSS algorithms, are given. The package is described
in Miettinen, Nordhausen and Taskinen (2017) <doi:10.18637/jss.v076.i02>.")
(license license:gpl2+)))
(define-public r-jsonify
(package
(name "r-jsonify")
@ -3341,13 +3487,13 @@ a list of p-values.")
(define-public r-htmltools
(package
(name "r-htmltools")
(version "0.5.4")
(version "0.5.5")
(source (origin
(method url-fetch)
(uri (cran-uri "htmltools" version))
(sha256
(base32
"0zij9zrgsi82q5c65sf4pbidnzrkfr763g0n4ypdhf8dd6l2i0h0"))))
"0nb6y99ffgj482clgnqbkhraxigr1ynpqv3d1znwd2ashnmkzcn8"))))
(build-system r-build-system)
(propagated-inputs
(list r-base64enc r-digest r-ellipsis r-fastmap r-rlang))
@ -4478,14 +4624,14 @@ contained in the navigation bar.")
(define-public r-spelling
(package
(name "r-spelling")
(version "2.2")
(version "2.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "spelling" version))
(sha256
(base32
"179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
"0vr5mgw9grnsnzsc29al72p05z786hnd6b9c6wq0c0dabk5szm2g"))))
(properties `((upstream-name . "spelling")))
(build-system r-build-system)
(propagated-inputs
@ -5119,13 +5265,13 @@ print, summary, plot, update, etc.
(define-public r-ps
(package
(name "r-ps")
(version "1.7.2")
(version "1.7.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "ps" version))
(sha256
(base32 "06mjwsn074195vd4yv7zzkmcf3sc124cw0cbnddj86swvggfn9cj"))))
(base32 "15wnn0wi253d3pmz0d98l4i6cn59d1h229g8valhh5arabn45b1v"))))
(build-system r-build-system)
(home-page "https://ps.r-lib.org")
(synopsis "List, query, and manipulate system processes")
@ -5523,13 +5669,13 @@ multi-dimensional data.")
(define-public r-ctrdata
(package
(name "r-ctrdata")
(version "1.11.1")
(version "1.12.1")
(source (origin
(method url-fetch)
(uri (cran-uri "ctrdata" version))
(sha256
(base32
"076v3bll8s6m61wcbwgrgrm34g0wa7gsc90mbwxwap1xfxyzjjsg"))))
"1m12vjwvzrwwb4d513vk171r25ww92qqv7rd2c3srmwzfi9ngy74"))))
(properties `((upstream-name . "ctrdata")))
(build-system r-build-system)
(propagated-inputs
@ -5537,6 +5683,7 @@ multi-dimensional data.")
r-curl
r-dplyr
r-httr
r-jqr
r-jsonlite
r-lubridate
r-nodbi
@ -5672,14 +5819,14 @@ rows, dropping names) to see if the modified versions are identical.")
(define-public r-dendextend
(package
(name "r-dendextend")
(version "1.16.0")
(version "1.17.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "dendextend" version))
(sha256
(base32
"0rl4f0b73s1gdjfxgpnz87lhv131qazxb6vsv2935ad266fd0bzc"))))
"08g5z5qyrn2nkw1jw5520sval4jf9l6invqwvzsv8dkjkq8nxsc7"))))
(build-system r-build-system)
(propagated-inputs
(list r-ggplot2 r-magrittr r-viridis))
@ -6631,6 +6778,26 @@ hypergeometric distributions. In addition two random number generators of
George Marsaglia are included.")
(license license:gpl2+)))
(define-public r-kpmt
(package
(name "r-kpmt")
(version "0.1.0")
(source (origin
(method url-fetch)
(uri (cran-uri "kpmt" version))
(sha256
(base32
"15d26khc0v3kc1c7l1avqp48pfqmc6xj32029mv7myivr41ashk3"))))
(properties `((upstream-name . "kpmt")))
(build-system r-build-system)
(propagated-inputs (list r-matrixstats))
(home-page "https://cran.r-project.org/package=kpmt")
(synopsis "Known population median test")
(description
"This package provides functions that implement the known population
median test.")
(license license:expat)))
(define-public r-ksamples
(package
(name "r-ksamples")
@ -6985,6 +7152,28 @@ is being phased out. A modern MySQL client based on Rcpp is available from
the RMariaDB package.")
(license license:gpl2)))
(define-public r-rpmm
(package
(name "r-rpmm")
(version "1.25")
(source (origin
(method url-fetch)
(uri (cran-uri "RPMM" version))
(sha256
(base32
"1j48dh434wfhfzka0l21w6f73qlwfm70r9gdddhn504i2d5m4jph"))))
(properties `((upstream-name . "RPMM")))
(build-system r-build-system)
(propagated-inputs (list r-cluster))
(home-page "https://cran.r-project.org/package=RPMM")
(synopsis "Recursively partitioned mixture model")
(description
"This package provides a recursively partitioned mixture model for Beta
and Gaussian mixtures. This is a model-based clustering algorithm that
returns a hierarchy of classes, similar to hierarchical clustering, but also
similar to finite mixture models.")
(license license:gpl2+)))
(define-public r-rpostgresql
(package
(name "r-rpostgresql")
@ -7611,14 +7800,14 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.")
(define-public r-jomo
(package
(name "r-jomo")
(version "2.7-4")
(version "2.7-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "jomo" version))
(sha256
(base32
"1zck7p872k080hyfs0hibq7v13zmsry1jdlnq7k33ff1iljbq99d"))))
"05xfkj65nqd987pp5bhl4jy46qxwjll5mxnjii6qrmfmjld177q5"))))
(build-system r-build-system)
(propagated-inputs
(list r-lme4 r-mass r-ordinal r-survival r-tibble))
@ -7814,13 +8003,13 @@ and density estimation")
(define-public r-smurf
(package
(name "r-smurf")
(version "1.1.4")
(version "1.1.5")
(source (origin
(method url-fetch)
(uri (cran-uri "smurf" version))
(sha256
(base32
"09a56ayqnnal1h5xxnh4pcn0zyi1kg2fj40y872n4jcnbl8xcvbi"))))
"1gpzzj67x0i70vw1x4rv56mhk2b74ynvdsy93rzmdk6b2h3dvv46"))))
(properties `((upstream-name . "smurf")))
(build-system r-build-system)
(propagated-inputs
@ -7831,8 +8020,7 @@ and density estimation")
r-mgcv
r-rcolorbrewer
r-rcpp
r-rcpparmadillo
r-speedglm))
r-rcpparmadillo))
(native-inputs (list r-knitr))
(home-page "https://gitlab.com/TReynkens/smurf")
(synopsis "Sparse multi-type regularized feature modeling")
@ -8230,14 +8418,14 @@ multivariate function estimation using smoothing splines.")
(define-public r-cli
(package
(name "r-cli")
(version "3.6.0")
(version "3.6.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "cli" version))
(sha256
(base32
"15mqi8cacj7x588f1a7x805lwqbga2ha62k79qyxahrhh0qq21xn"))))
"0djyl08k7nhlbzgnfx7gq8w00s7c9f66bd11bvi9lzz6qz70cc5y"))))
(build-system r-build-system)
(home-page "https://github.com/r-lib/cli#readme")
(synopsis "Helpers for developing command line interfaces")
@ -8504,13 +8692,13 @@ iVAT).")
(define-public r-xfun
(package
(name "r-xfun")
(version "0.37")
(version "0.38")
(source
(origin
(method url-fetch)
(uri (cran-uri "xfun" version))
(sha256
(base32 "1yg1b21nwpnggb498z0j3lp11w6fwni7q7rd88fnm8xfnbq9yq9v"))))
(base32 "12n60c18rgg65qxnlp4sv6q9zryiz146844ayd28kipnjpwc4457"))))
(build-system r-build-system)
;; knitr itself depends on xfun
#;
@ -8591,14 +8779,14 @@ estimated from a given sample.")
(define-public r-vctrs
(package
(name "r-vctrs")
(version "0.6.0")
(version "0.6.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "vctrs" version))
(sha256
(base32
"0mwp56s87bdrg5xr4mnjr0qrdsq18dmfs3d640qkbbka9qn722xy"))))
"10qjirgdq0bn2s84vqx5c78i85mdp5mxwdfn30kayh3wpmij8mbp"))))
(build-system r-build-system)
(propagated-inputs
(list r-cli r-glue r-lifecycle r-rlang))
@ -8630,14 +8818,14 @@ estimated from a given sample.")
(define-public r-pillar
(package
(name "r-pillar")
(version "1.8.1")
(version "1.9.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "pillar" version))
(sha256
(base32
"1v47dm2v4nlswd1gmgcx5c7yrgn1ksdfr9lqkc63jf2nkv6af1ig"))))
"1k3sp37dpn46d2xbq621alpvzgnm06x5qb87nk169y47q23b8gpj"))))
(build-system r-build-system)
(propagated-inputs
(list r-cli
@ -9549,14 +9737,14 @@ interface.")
(define-public r-trend
(package
(name "r-trend")
(version "1.1.4")
(version "1.1.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "trend" version))
(sha256
(base32
"1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
"12xswr925jjbkdccjiigkr6a44jmgvzwvnizciv6rr3mnklv6n66"))))
(build-system r-build-system)
(propagated-inputs
(list r-extradistr))
@ -10170,13 +10358,13 @@ It also includes interpolation functions.")
(define-public r-simplermarkdown
(package
(name "r-simplermarkdown")
(version "0.0.4")
(version "0.0.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "simplermarkdown" version))
(sha256
(base32 "069pgx5m22rdqa21lyn5zqm9ym3g7w6z1d2wjwms8b1f2cp6266g"))))
(base32 "0lffwsrhsdqcqhklh24v0y0x6w4vq9jch93m330kfdv2amab1l06"))))
(properties `((upstream-name . "simplermarkdown")))
(build-system r-build-system)
(propagated-inputs
@ -10552,14 +10740,14 @@ used.")
(define-public r-arules
(package
(name "r-arules")
(version "1.7-5")
(version "1.7-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "arules" version))
(sha256
(base32
"0d04w28hl9gcrvkj0v0q77x4a89jhvzf1imw58xfgncap8mc6555"))))
"0syrbh85vzhp9plm95dhq6pfanzbxqm4wcahw3y2d26gvi2nmzwm"))))
(build-system r-build-system)
(propagated-inputs
(list r-generics r-matrix))
@ -11028,19 +11216,18 @@ finance, conversion from and to JSON, and many other applications.")
(define-public r-dtplyr
(package
(name "r-dtplyr")
(version "1.3.0")
(version "1.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "dtplyr" version))
(sha256
(base32
"1y40yrfdw1wbx7jqmql69yi3q52lzjpqgr4jwnhjr33hw6kxvg0v"))))
"1rfnr1f3dzzivzmw9jjaclckkany6c625bqr8lkx32qbcjd6iad5"))))
(properties `((upstream-name . "dtplyr")))
(build-system r-build-system)
(propagated-inputs
(list r-cli
r-crayon
r-data-table
r-dplyr
r-glue
@ -11606,14 +11793,14 @@ publication-ready plots.")
(define-public r-ellipse
(package
(name "r-ellipse")
(version "0.4.3")
(version "0.4.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "ellipse" version))
(sha256
(base32
"0im9d36dixpksms52v6nsb3l0z2c7wc25r9j0f08naj6qc8jpvq2"))))
"1r4srqgpzh4r0cryc74gjcfwj0j54ibzh325bi31aa9dwi9dw03z"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/ellipse/")
(synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
@ -11650,14 +11837,14 @@ clustering.")
(define-public r-factominer
(package
(name "r-factominer")
(version "2.7")
(version "2.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "FactoMineR" version))
(sha256
(base32
"03952kcnwrm61kn5im55ky1j91nm5x4i4f5gs115li6gck63xf17"))))
"0lgqbw7534wadkdv7zh1y5nanl72jys070qydznmaj2cmvvqd460"))))
(properties `((upstream-name . "FactoMineR")))
(build-system r-build-system)
(propagated-inputs
@ -11995,14 +12182,14 @@ references and Rd files.")
(define-public r-officer
(package
(name "r-officer")
(version "0.6.1")
(version "0.6.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "officer" version))
(sha256
(base32
"19sn36aaxr2bmxm8lrs1vqmc4fc1gfwarp418pn09jk105ckykh8"))))
"0dfk1didy5lfh07chqfwlrdlrib7a5na65rb71ipnxlhbiwbaj09"))))
(build-system r-build-system)
(propagated-inputs
(list r-openssl r-r6 r-ragg r-uuid r-xml2 r-zip))
@ -12317,13 +12504,13 @@ tidyverse workflow.")
(define-public r-nodbi
(package
(name "r-nodbi")
(version "0.9.1")
(version "0.9.2")
(source (origin
(method url-fetch)
(uri (cran-uri "nodbi" version))
(sha256
(base32
"1hn0wy2ry9l3wwqrshmf82cxigkm16wycwprv458bcvb5k6ayy5m"))))
"167zhlyl0crn24zyw9rz9spa5xh8nxpzl94vqsk02r849n4qvzx9"))))
(properties `((upstream-name . "nodbi")))
(build-system r-build-system)
(propagated-inputs
@ -13189,13 +13376,13 @@ ABC algorithms.")
(define-public r-abctools
(package
(name "r-abctools")
(version "1.1.4")
(version "1.1.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "abctools" version))
(sha256
(base32 "02c473fqj7yd27flma2x7flqzqbrnba2xfcjy466nww0sm1vvhjg"))))
(base32 "0yxmj28ym8919l27m04yjyc7mya1iy5ap4p980grsh7m4cgpx3bh"))))
(build-system r-build-system)
(propagated-inputs
(list r-abc r-abind r-hmisc r-plyr))
@ -13283,14 +13470,14 @@ repeated measures data, respectively.")
(define-public r-gam
(package
(name "r-gam")
(version "1.22-1")
(version "1.22-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "gam" version))
(sha256
(base32
"1h84klxs7wbksn9hsqdspmska9q5pmy6q71fmwm4bcmdrqixr8gv"))))
"1yh2rahcbi2fbsi1yps1l51xxljc7lcs7h729y5vjj4l492pywzy"))))
(properties `((upstream-name . "gam")))
(build-system r-build-system)
(propagated-inputs
@ -13358,14 +13545,14 @@ both to consistency and asymptotic normality.")
(define-public r-dofuture
(package
(name "r-dofuture")
(version "0.12.2")
(version "1.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "doFuture" version))
(sha256
(base32
"0w07pmzpsfq4kvfc745s1i9b6dfn1df1wrfi4s9ys4ir3g2s8nk1"))))
"1pxwpfmxswbsd1f2ifj9kdq9hi9q0x2wwv2kv0xq178ymmywi2sz"))))
(properties `((upstream-name . "doFuture")))
(build-system r-build-system)
(arguments
@ -13374,7 +13561,7 @@ both to consistency and asymptotic normality.")
(add-after 'unpack 'set-HOME
(lambda _ (setenv "HOME" "/tmp"))))))
(propagated-inputs
(list r-foreach r-future r-globals r-iterators))
(list r-foreach r-future r-future-apply r-globals r-iterators))
(native-inputs
(list r-r-rsp)) ; vignette builder
(home-page "https://github.com/HenrikBengtsson/doFuture")
@ -14754,14 +14941,14 @@ Bayesian modeling.")
(define-public r-tmb
(package
(name "r-tmb")
(version "1.9.2")
(version "1.9.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "TMB" version))
(sha256
(base32
"0kz5a3y6xcqz2ycxq6ff3jasc2hkvq2rxnpr618nng7k9gljc504"))))
"10cl88v3jdjv0sacfvk1g9y7sl918rxlyk9ddy2d1y7055j8y0qg"))))
(properties `((upstream-name . "TMB")))
(build-system r-build-system)
(propagated-inputs
@ -16009,22 +16196,39 @@ netCDF files.")
Bioconductor packages.")
(license license:artistic2.0)))
;; TODO: one more minified JavaScript files is included that should be built
;; from the included .src.js files, but it is not entirely clear how. The
;; file is inst/htmlwidgets/lib/rglClass/rglClass.min.js.
(define-public r-rgl
(package
(name "r-rgl")
(version "1.0.1")
(version "1.1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "rgl" version))
(sha256
(base32
"1j1g1b1j6azhg944ddzzrxgynb2bfl14l5qz58n4mhvxrbx018w9"))))
"1blasg60x38z57ds6x7yb4rvjx21yf4s99q93sl1w9h6mg14d8jg"))
(snippet
'(delete-file "inst/htmlwidgets/lib/CanvasMatrix/CanvasMatrix.min.js"))))
(build-system r-build-system)
(arguments
(list
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'process-javascript
(lambda* (#:key inputs #:allow-other-keys)
(with-directory-excursion "inst/htmlwidgets/lib/"
(let ((source "CanvasMatrix/CanvasMatrix.src.js")
(target "CanvasMatrix/CanvasMatrix.min.js"))
(invoke "esbuild" source "--minify"
(string-append "--outfile=" target)))))))))
(native-inputs
(list pkg-config
(list esbuild
pkg-config
r-knitr
r-rmarkdown)) ;for vignettes
r-rmarkdown)) ;for vignettes
(inputs
(list freetype
libpng
@ -16077,13 +16281,13 @@ to colexicographical order.")
(define-public r-multidplyr
(package
(name "r-multidplyr")
(version "0.1.2")
(version "0.1.3")
(source (origin
(method url-fetch)
(uri (cran-uri "multidplyr" version))
(sha256
(base32
"081x9n46dl6vpp5q6pilw3w5wpdi3r9kwi9n6h4k2p2iqg1s96lb"))))
"18yl24s1g8wf3xi6f0k7jhs99ka4dslxf5p9ax9m5l1rbva5xdwj"))))
(properties `((upstream-name . "multidplyr")))
(build-system r-build-system)
(propagated-inputs
@ -18972,14 +19176,14 @@ them in distributed compute environments.")
(define-public r-parallelly
(package
(name "r-parallelly")
(version "1.34.0")
(version "1.35.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "parallelly" version))
(sha256
(base32
"1x5gk008813i9c2i7qdhpmlbq2xdgv5q47xcmc6lb8p475q9sqqi"))))
"1kaxmmkwjxnympxsyphwfdba6nmp4jszhrsy5h2snshr0xjrnpiz"))))
(properties `((upstream-name . "parallelly")))
(build-system r-build-system)
(home-page "https://github.com/HenrikBengtsson/parallelly")
@ -24342,15 +24546,48 @@ function and interfaces to external frameworks.")
(define-public r-covr
(package
(name "r-covr")
(version "3.6.1")
(version "3.6.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "covr" version))
(sha256
(base32 "0mqiqmbwq5f083lda208nqd4ya0f912bkkya2i62fkqsii1ibgpz"))))
(base32 "0ns8xbq1l21mg8p2aiqv5h306a3vpn64j6jrgzbv8iv1a7kqrrmc"))
(modules '((guix build utils)))
(snippet
'(with-directory-excursion "inst/www/shared"
(for-each delete-file
'("bootstrap/js/bootstrap.min.js"
"bootstrap/shim/html5shiv.min.js"
"bootstrap/shim/respond.min.js"))))))
(properties `((upstream-name . "covr")))
(build-system r-build-system)
(arguments
(list
#:modules '((guix build utils)
(guix build r-build-system)
(srfi srfi-1))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'process-javascript
(lambda* (#:key inputs #:allow-other-keys)
(with-directory-excursion "inst/www/shared"
(call-with-values
(lambda ()
(unzip2
`((,(search-input-file inputs "/dist/js/bootstrap.js")
"bootstrap/js/bootstrap.min.js")
(,(search-input-file inputs "/dist/html5shiv.js")
"bootstrap/shim/html5shiv.min.js")
(,(search-input-file inputs "/dest/respond.src.js")
"bootstrap/shim/respond.min.js"))))
(lambda (sources targets)
(for-each (lambda (source target)
(format #true "Processing ~a --> ~a~%"
source target)
(invoke "esbuild" source "--minify"
(string-append "--outfile=" target)))
sources targets)))))))))
(propagated-inputs
(list r-crayon
r-digest
@ -24360,7 +24597,38 @@ function and interfaces to external frameworks.")
r-withr
r-yaml))
(native-inputs
(list r-knitr)) ; for vignettes
(list esbuild
r-knitr ;for vignettes
(let ((version "3.3.5"))
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/twbs/bootstrap")
(commit (string-append "v" version))))
(file-name (git-file-name "js-bootstrap" version))
(sha256
(base32
"1zxrjhnnd594rflnwzqhbx3rx0gjlh6hgx9v2nppgkmrkqb7y1a4"))))
(let ((version "3.7.2"))
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/aFarkas/html5shiv")
(commit version)))
(file-name (git-file-name "js-html5shiv" version))
(sha256
(base32
"0mw4bbl9a9d1ibywscjgmbky0jkj4081l1yd4x3ss0flwaa3fwsk"))))
(let ((version "1.4.2"))
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/scottjehl/Respond")
(commit version)))
(file-name (git-file-name "js-respond" version))
(sha256
(base32
"00xid731rirc7sdy1gc8qal3v9g0agr2qx15hm4x97l1lcbylyn2"))))))
(home-page "https://github.com/r-lib/covr")
(synopsis "Test coverage for R packages")
(description
@ -27212,14 +27480,14 @@ number embedded in the file rather than the file extension.")
(define-public r-imager
(package
(name "r-imager")
(version "0.42.18")
(version "0.42.19")
(source
(origin
(method url-fetch)
(uri (cran-uri "imager" version))
(sha256
(base32
"0ljkcvs91sjddndwdbaqg0nf9sksm0284s6kg05k027wnvbkc5f1"))))
"1qp1190cb7pssl22vakd8z8zvj6mmhrn7jk6wkjyrv28lv5vqyhq"))))
(properties `((upstream-name . "imager")))
(build-system r-build-system)
(inputs
@ -27272,14 +27540,14 @@ it may be seen by an animal with less acute vision.")
(define-public r-caret
(package
(name "r-caret")
(version "6.0-93")
(version "6.0-94")
(source
(origin
(method url-fetch)
(uri (cran-uri "caret" version))
(sha256
(base32
"01sa1h9pc3a062pwm0rxadvg9qxszwcylya7llv08fcxhy46n5ac"))))
"1a191n9qswvf8ri6id8picqgdqx15l6mp996v6f77fv0l8yfh597"))))
(build-system r-build-system)
(propagated-inputs
(list r-e1071
@ -29608,14 +29876,14 @@ using the @code{rstan} and @code{rstanarm} packages).")
(define-public r-rstantools
(package
(name "r-rstantools")
(version "2.3.0")
(version "2.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "rstantools" version))
(sha256
(base32
"0bc22fxpw4xvdxx8716wbasw8rpkpipb428cv764s8c0mkk2szlk"))))
"0xb9rb6nlqsqxi08hx9iwqpfz6ssdmh6axyk7d399j7zhklg5m42"))))
(properties `((upstream-name . "rstantools")))
(build-system r-build-system)
(inputs (list pandoc))
@ -29817,14 +30085,14 @@ Additional storage back-ends can be added easily.")
(define-public r-zyp
(package
(name "r-zyp")
(version "0.11")
(version "0.11-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "zyp" version))
(sha256
(base32
"0jmddxg88qb9f38ywdy4min7w5qadnkhqxd46b0j0gjsq95vw85q"))))
"0gqds43ivbsi4770nxj5sf4mp51m410svnap0v1rh8vlk3gkb3l9"))))
(properties `((upstream-name . "zyp")))
(build-system r-build-system)
(propagated-inputs
@ -29841,13 +30109,13 @@ climate data.")
(define-public r-rlecuyer
(package
(name "r-rlecuyer")
(version "0.3-5")
(version "0.3-7")
(source (origin
(method url-fetch)
(uri (cran-uri "rlecuyer" version))
(sha256
(base32
"09mniai7v8gapr6hd3zm8sm3vi1zcyhgym389904ykb2yx7l68s7"))))
"0g5z26wsbv3wzrc3gl1z97qxdk5m2pvfg3f5zqkz98wzh1z49b35"))))
(properties `((upstream-name . "rlecuyer")))
(build-system r-build-system)
(home-page
@ -30693,14 +30961,14 @@ vignette for more information and examples.")
(define-public r-distributional
(package
(name "r-distributional")
(version "0.3.1")
(version "0.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "distributional" version))
(sha256
(base32
"0pr34yq6igb7ciqss2ldwa7gc55xvla040x8rkd8m2hcrz5mczkj"))))
"1y08s301mxz7c54lxa1j0zzbsrgphxv5hsyam3jswcw274rxd0y8"))))
(properties
`((upstream-name . "distributional")))
(build-system r-build-system)
@ -31027,18 +31295,18 @@ counting and recursive k-means partitioning.")
(define-public r-hardhat
(package
(name "r-hardhat")
(version "1.2.0")
(version "1.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "hardhat" version))
(sha256
(base32
"0y5dxpd4gsrs365x1v4qf2vq7hq2qb6f6x50dyj29xmmn760wcpr"))))
"0bp83yw7j34iwir2f73ainic11cdz0q18m5v1kbx8vdsw84z17zy"))))
(properties `((upstream-name . "hardhat")))
(build-system r-build-system)
(propagated-inputs
(list r-glue r-rlang r-tibble r-vctrs))
(list r-cli r-glue r-rlang r-tibble r-vctrs))
(native-inputs
(list r-knitr))
(home-page "https://github.com/tidymodels/hardhat")
@ -34256,13 +34524,13 @@ package also supersedes the package @code{BBmisc}.")
(define-public r-mlr3pipelines
(package
(name "r-mlr3pipelines")
(version "0.4.2")
(version "0.4.3")
(source (origin
(method url-fetch)
(uri (cran-uri "mlr3pipelines" version))
(sha256
(base32
"09pk3dwjcg5rbpwa1k21srdpvf2dlxq4b5p71cvkha85jx2gdgh6"))))
"1ycrm4i0k38mkw1r1a5sxp761wdz3p0q72xz6qqg3qsyva4ba0wz"))))
(build-system r-build-system)
(propagated-inputs
(list r-backports
@ -38068,13 +38336,13 @@ supports @command{sf} and @command{stars}.")
(define-public r-automap
(package
(name "r-automap")
(version "1.1-1")
(version "1.1-9")
(source (origin
(method url-fetch)
(uri (cran-uri "automap" version))
(sha256
(base32
"11l6iygq66jg11lilwjmf7l250dcvhilx6zv2lm746rjzchwga0s"))))
"0hrsdynjxv0n5n1pbdk05rgrcwfd0g5p9pgdbicx4ljk73nhl1zk"))))
(properties `((upstream-name . "automap")))
(build-system r-build-system)
(propagated-inputs (list r-ggplot2

155
gnu/packages/databases.scm
View File

@ -59,6 +59,7 @@
;;; Copyright © 2022 muradm <mail@muradm.net>
;;; Copyright © 2022 Thomas Albers Raviola <thomas@thomaslabs.org>
;;; Copyright © 2021, 2022 jgart <jgart@dismail.de>
;;; Copyright © 2023 Felix Gruber <felgru@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -3573,6 +3574,79 @@ this library provides functions to facilitate such comparisons.")
SQLAlchemy Database Toolkit for Python.")
(license license:expat)))
(define-public python-sqlite-fts4
(package
(name "python-sqlite-fts4")
(version "1.0.3")
(source (origin
(method url-fetch)
(uri (pypi-uri "sqlite-fts4" version))
(sha256
(base32
"034kx0ac556sywy1p4qcrc36l24w3q0xwswqv2z9s3k8yvm5xc3q"))))
(build-system python-build-system)
(native-inputs (list python-pytest))
(home-page "https://github.com/simonw/sqlite-fts4")
(synopsis "Python functions for working with SQLite FTS4 search")
(description "This package provides custom SQLite functions written
in Python for ranking documents indexed using the SQLite's FTS4 full
text search extension.")
(license license:asl2.0)))
(define-public python-sqlite-utils
(package
(name "python-sqlite-utils")
(version "3.30")
(source (origin
(method git-fetch) ;for tests
(uri (git-reference
(url "https://github.com/simonw/sqlite-utils")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1a58syvh5jp40vi5libsxkqy99z75kj4ckxqmylbhd342ppfy1wp"))))
(build-system pyproject-build-system)
(arguments
(list #:phases #~(modify-phases %standard-phases
(add-after 'unpack 'relax-requirements
(lambda _
(substitute* "setup.py"
;; This is a variant designed to have a binary
;; wheel made available on PyPI, which is not a
;; concern to Guix.
(("click-default-group-wheel")
"click-default-group")))))))
(propagated-inputs (list python-click python-click-default-group
python-dateutil python-sqlite-fts4
python-tabulate))
(native-inputs (list python-pytest))
(home-page "https://github.com/simonw/sqlite-utils")
(synopsis
"CLI tool and Python utility functions for manipulating SQLite databases")
(description
"This package provides a CLI tool and Python utility functions for
manipulating SQLite databases. It's main features are:
@itemize
@item
Pipe JSON (or CSV or TSV) directly into a new SQLite database file,
automatically creating a table with the appropriate schema.
@item
Run in-memory SQL queries, including joins, directly against data in
CSV, TSV or JSON files and view the results.
@item
Configure SQLite full-text search against your database tables and run
search queries against them, ordered by relevance.
@item
Run transformations against your tables to make schema changes that
SQLite ALTER TABLE does not directly support, such as changing the type
of a column.
@item
Extract columns into separate tables to better normalize your existing
data.
@end itemize")
(license license:asl2.0)))
(define-public python-pickleshare
(package
(name "python-pickleshare")
@ -5031,3 +5105,84 @@ generic interface to caching backends of any variety, and additionally
provides API hooks which integrate these cache backends with the locking
mechanism of @code{dogpile}.")
(license license:expat)))
(define-public datasette
(package
(name "datasette")
(version "0.64.2")
(source (origin
(method git-fetch) ;for tests
(uri (git-reference
(url "https://github.com/simonw/datasette")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1c8ajdaraynrjvsb8xxxnkb7zgm5fwq60qczaz00n465ki80j4h3"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
;; There are multiple unexplained test failures (see:
;; https://github.com/simonw/datasette/issues/2048).
#~(list "-k" (string-append
"not (test_database_page_for_database_with_dot_in_name"
" or test_row_strange_table_name"
" or test_database_with_space_in_name"
" or test_tilde_encoded_database_names"
" or test_weird_database_names"
" or test_css_classes_on_body"
" or test_templates_considered"
" or test_row_html_compound_primary_key"
" or test_edit_sql_link_on_canned_queries"
" or test_alternate_url_json"
" or test_table_with_slashes_in_name"
" or test_searchable"
" or test_custom_query_with_unicode_characters"
" or test_searchmode)")
"-n" (number->string (parallel-job-count))
"-m" "not serial") ;cannot run in parallel
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'relax-requirements
(lambda _
;; The package needlessly specifies exact versions
;; of dependencies, when it works fine with others.
(substitute* "setup.py"
(("(black)==[0-9\\.]+" _ package)
package)
(("click-default-group-wheel")
"click-default-group")))))))
(propagated-inputs
(list python-aiofiles
python-asgi-csrf
python-asgiref
python-click
python-click-default-group
python-httpx
python-hupper
python-itsdangerous
python-janus
python-jinja2
python-mergedeep
python-pint
python-pluggy-next
python-pyyaml
python-uvicorn))
(native-inputs
(list python-beautifulsoup4
python-black
python-cogapp
python-pytest-7.1
python-pytest-asyncio
python-pytest-runner
python-pytest-timeout
python-pytest-xdist-next
python-setuptools
python-trustme))
(home-page "https://datasette.io/")
(synopsis "Multi-tool for exploring and publishing data")
(description "Datasette is a tool for exploring and publishing data.
It helps people take data of any shape or size and publish that as an
interactive, explorable website and accompanying API.")
(license license:asl2.0)))

352
gnu/packages/emacs-xyz.scm
View File

@ -49,7 +49,7 @@
;;; Copyright © 2019, 2020, 2021 Joseph LaFreniere <joseph@lafreniere.xyz>
;;; Copyright © 2019 Todor Kondić <tk.code@protonmail.com>15669
;;; Copyright © 2019 Amar Singh <nly@disroot.org>
;;; Copyright © 2019, 2022 Baptiste Strazzulla <bstrazzull@hotmail.fr>
;;; Copyright © 2019, 2022, 2023 Baptiste Strazzulla <bstrazzull@hotmail.fr>
;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
;;; Copyright © 2019 Jens Mølgaard <jens@zete.tk>
;;; Copyright © 2019, 2020 Amin Bandali <bandali@gnu.org>
@ -2686,14 +2686,14 @@ project root.")
(define-public emacs-relint
(package
(name "emacs-relint")
(version "1.21")
(version "1.22")
(source
(origin
(method url-fetch)
(uri (string-append "https://elpa.gnu.org/packages/"
"relint-" version ".tar"))
(sha256
(base32 "12453agy7y3ayqn32fi11ljlnk8ck3i1aljw5wzm0yyqp00m73x3"))))
(base32 "1525hk961q4af06c5a60m7ryp5g8yvfxjp5nmmgkci7vl3ing8zi"))))
(build-system emacs-build-system)
(propagated-inputs (list emacs-xr))
(home-page "https://github.com/mattiase/relint")
@ -3894,7 +3894,7 @@ of bibliographic references.")
(define-public emacs-corfu
(package
(name "emacs-corfu")
(version "0.35")
(version "0.36")
(source
(origin
(method git-fetch)
@ -3903,7 +3903,7 @@ of bibliographic references.")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1xqg796844wk6kvn3xw4bqlxn9ra6jlwk7rsc5gy4j77l0gwl441"))))
(base32 "02glwnny9b4pwhq5inrakfz03zrq0zq1vr4npv88yla6pg8v87xx"))))
(build-system emacs-build-system)
(arguments
(list
@ -5363,33 +5363,42 @@ environments.")
(license license:gpl2+)))
(define-public emacs-lemon
(let ((commit "37a6e6d6ef0900ca19c820a2dbc122c7fe6d86cf")
(revision "0"))
(package
(name "emacs-lemon")
(version (git-version "2.0.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://codeberg.org/emacs-weirdware/lemon")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0bc77vzi4p6mlzmhgybbldlpcsiiv4xqrd5lnc7wzvmxv8byhqpm"))))
(build-system emacs-build-system)
(native-inputs
(list emacs-blight emacs-emms))
(propagated-inputs
(list emacs-s))
(home-page "https://codeberg.org/emacs-weirdware/lemon")
(synopsis "System monitors in the echo area")
(description
"Lemon is a tiny system monitor which displays system information in
(package
(name "emacs-lemon")
(version "2.1.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://codeberg.org/emacs-weirdware/lemon")
(commit "b10e992a25757a91723c7d554a5fa8e14291e702")))
(file-name (git-file-name name version))
(sha256
(base32 "18yclk2zzqcahzhz2kq8g9gy1xnnxiy6rxs2lwhskj475kvwy2f9"))))
(build-system emacs-build-system)
(arguments
(list
#:tests? #true
;; Only one test out of the four passes
#:test-command #~(list "emacs" "-Q" "--batch" "-L" "."
;; "-l" "lemon--test.el"
;; "-l" "lemon-monitor--test.el"
;; "-l" "lemon-sparkline--test.el"
"-l" "lemon-time--test.el"
"-f" "ert-run-tests-batch-and-exit")))
(native-inputs
(list emacs-blight emacs-emms))
(propagated-inputs
(list emacs-s))
(home-page "https://codeberg.org/emacs-weirdware/lemon")
(synopsis "System monitors in the echo area")
(description
"Lemon is a tiny system monitor which displays system information in
the echo area when Emacs is has been idle for a few seconds. This is a fork
of zk_phi’s Symon, which has been largely rewritten. It works nicely with
EXWM.")
(license license:gpl3+))))
(license license:gpl3+)))
(define-public emacs-sx
(let ((version "20191229")
@ -6171,7 +6180,7 @@ result.")
(define-public emacs-rg
(package
(name "emacs-rg")
(version "2.2.1")
(version "2.3.0")
(source
(origin
(method git-fetch)
@ -6180,7 +6189,7 @@ result.")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1nxzplpk5cf6hhr2v85bmg68i6am96shi2zq7m83fs96bilhwsp5"))))
(base32 "1adici6hs4ivz7lqhrgdm9g1rz0mgvrsa7pkr2pcx6mg1f0qnlmr"))))
(build-system emacs-build-system)
(arguments
(list
@ -7144,7 +7153,7 @@ snippets for yasnippet.")
;; Package has no release. Version is extracted from "Version:" keyword in
;; main file.
(let ((commit "02b1da6278e43cc9cc0356110cc6bfbb37eb8241")
(revision "1"))
(revision "1"))
(package
(name "emacs-mode-line-idle")
(version (git-version "0.1" revision commit))
@ -7228,7 +7237,7 @@ truncation.")
(define-public emacs-sqlite
;; XXX: There is no tagged commit.
(let ((commit "dad42b8bbca4994be1871343dd18fd6528ee5797")
(revision "0"))
(revision "0"))
(package
(name "emacs-sqlite")
(build-system emacs-build-system)
@ -7237,8 +7246,8 @@ truncation.")
(origin
(method git-fetch)
(uri (git-reference
(url "https://gitlab.com/cnngimenez/sqlite.el")
(commit commit)))
(url "https://gitlab.com/cnngimenez/sqlite.el")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "06ln4vijl8kii3nzc5cscgsadx1fqgxksflijd3ain83bn8g4wrd"))))
@ -8239,14 +8248,14 @@ variables, and so on. The mode also allows you to execute Tup commands.")
(define-public emacs-compat
(package
(name "emacs-compat")
(version "29.1.4.0")
(version "29.1.4.1")
(source (origin
(method url-fetch)
(uri (string-append "https://elpa.gnu.org/packages/"
"compat-" version ".tar"))
(sha256
(base32
"1y1x50r4ai4k8sa5qi5zbjz8216lpk9vjd0k681l1ha2aqn8l3pr"))))
"1r8laxmdyrpz4nmzjrndd668bks4fgmbya04m0bfzwvhlrsca940"))))
(build-system emacs-build-system)
(home-page "https://git.sr.ht/~pkal/compat")
(synopsis "Emacs Lisp Compatibility Library")
@ -9023,7 +9032,7 @@ SuperCollider is a platform for audio synthesis and algorithmic composition.")
(define-public emacs-soothe-theme
;; There is no named branch.
(let ((commit "0786fe70c6c1b4ddcfb932fdc6862b9611cfc09b")
(revision "0"))
(revision "0"))
(package
(name "emacs-soothe-theme")
(version (git-version "20141027.2233" revision commit))
@ -9031,11 +9040,11 @@ SuperCollider is a platform for audio synthesis and algorithmic composition.")
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/emacsfodder/emacs-soothe-theme")
(commit commit)))
(url "https://github.com/emacsfodder/emacs-soothe-theme")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "10gh1hvxq9gm29r6qzlnva7vjidd7n4kih4z2ihyvbvy9za20xqw"))))
(base32 "10gh1hvxq9gm29r6qzlnva7vjidd7n4kih4z2ihyvbvy9za20xqw"))))
(build-system emacs-build-system)
(home-page "https://github.com/emacsfodder/emacs-soothe-theme")
(synopsis "Colorful, but muted theme for Emacs, dark background with light text")
@ -12487,6 +12496,38 @@ for SPARQL. It can also execute queries against a SPARQL HTTP endpoint, such
as Fuseki or DBPedia.")
(license license:gpl3+)))
(define-public emacs-sphinx-doc
(let ((commit "1eda612a44ef027e5229895daa77db99a21b8801")
(revision "1"))
(package
(name "emacs-sphinx-doc")
(version (git-version "0.3.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/naiquevin/sphinx-doc.el")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0q72i95yx3xa57jlgr7dik6prf20hi8bp8xf3f5c6ificv7i5378"))))
(build-system emacs-build-system)
(arguments
(list
#:tests? #true
#:test-command #~(list "emacs" "-Q" "--batch"
"-l" "sphinx-doc-tests.el"
"-f" "ert-run-tests-batch-and-exit")))
(propagated-inputs (list emacs-dash emacs-s))
(home-page "https://github.com/naiquevin/sphinx-doc.el")
(synopsis
"Generate Sphinx friendly docstrings for Python functions in Emacs")
(description
"Sphinx Doc is an Emacs minor mode for inserting docstring skeletons
for Python functions and methods. The structure of the docstring is as per
the equirement of the Sphinx documentation generator.")
(license license:expat))))
(define-public emacs-better-defaults
(package
(name "emacs-better-defaults")
@ -12495,8 +12536,8 @@ as Fuseki or DBPedia.")
(origin
(method git-fetch)
(uri (git-reference
(url "https://git.sr.ht/~technomancy/better-defaults")
(commit version)))
(url "https://git.sr.ht/~technomancy/better-defaults")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
@ -13420,6 +13461,27 @@ Python, together offering features such as navigation, documentation,
completion, interactive development and more.")
(license license:gpl3+))))
(define-public emacs-railscasts-theme
(let ((commit "1340c3f6c2717761cab95617cf8dcbd962b1095b")
(revision "0"))
(package
(name "emacs-railscasts-theme")
(version (git-version "0.1" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mikenichols/railscasts-theme")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"021x1l5kzsbm0qj5a3bngxa7ickm4lbwsdz81a2ks9pi1ivmw205"))))
(build-system emacs-build-system)
(home-page "https://github.com/mikenichols/railscasts-theme")
(synopsis "Railscasts is a color theme for Emacs")
(description "Railscasts is a color theme for Emacs.")
(license license:expat))))
(define-public emacs-rainbow-delimiters
(package
(name "emacs-rainbow-delimiters")
@ -14541,7 +14603,7 @@ Lua programming language}.")
(define-public emacs-ebuild-mode
(package
(name "emacs-ebuild-mode")
(version "1.62")
(version "1.63")
(source
(origin
(method url-fetch)
@ -14550,7 +14612,7 @@ Lua programming language}.")
"ebuild-mode-" version ".tar.xz"))
(file-name (string-append name "-" version ".tar.xz"))
(sha256
(base32 "1l547d2q9l62zn53cwnjkxzqsblx72jh9a1vl753qlnyy689zvfp"))))
(base32 "1pkdyxiprj94z062y6nlm5w34gxyazbkg3yzhfscnm087p7pbg82"))))
(build-system emacs-build-system)
(arguments
(list
@ -15208,7 +15270,7 @@ passive voice.")
(define-public emacs-org
(package
(name "emacs-org")
(version "9.6.1")
(version "9.6.2")
(source
(origin
(method git-fetch)
@ -15217,7 +15279,7 @@ passive voice.")
(commit (string-append "release_" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0iycj54ksanx6n3s06xhf0ax1cqjdcxynmz6cby27bcsj0sqflnp"))))
(base32 "0z1251fb9zn09cpv6ici3rqnfwjhm1rp5q36n17z7snd0dkh0x7h"))))
(build-system emacs-build-system)
(arguments
(list
@ -15650,11 +15712,10 @@ extensibility.")
(license license:gpl3+)))
(define-public emacs-autocrypt
(let ((commit "5b55f8d37545e9c441788627c17e350d7edf4055")
(revision "0"))
(let ((commit "a90aa6b644fe8cf72af9e1615a7c50b36b739e7c")) ;version bump
(package
(name "emacs-autocrypt")
(version (git-version "0.4.0" revision commit))
(version "0.4.1")
(source (origin
(method git-fetch)
(uri (git-reference
@ -15663,19 +15724,15 @@ extensibility.")
(file-name (git-file-name name version))
(sha256
(base32
"0b06xnjkgwjpxl96mdi674pmvdaiwncifi1a30wxhl1dwr7kr084"))))
"124qf96g2xbz3wz0ihix4l1g4prpa023hx0klf72clx92dhjjgjj"))))
(build-system emacs-build-system)
(home-page "https://git.sr.ht/~pkal/autocrypt")
(synopsis "Autocrypt implementation for Emacs")
(description "@code{emacs-autocrypt} is an implementation of
Autocrypt (@url{https://autocrypt.org/}) for various Emacs MUAs. Autocrypt is
(description "Autocrypt package is an implementation of
Autocrypt (@url{https://autocrypt.org/}) for various Emacs MUAs,
a cryptographic protocol for email clients aiming to simplify key exchange and
encryption.
Run @code{M-x autocrypt-create-account} to initialize an autocrypt key, and
add @code{autocrypt-mode} to your MUA's hooks (@code{gnus-mode-hook},
@code{message-mode-hook}, ...) to activate its usage.")
(license license:cc0))))
encryption.")
(license license:gpl3+))))
(define-public emacs-nginx-mode
(package
@ -15931,6 +15988,47 @@ using a convenient notation.")
(license (list license:gpl3+
license:fdl1.3+)))) ;GFDLv1.3+ for the manual
(define-public emacs-beframe
(let ((commit "edfab6eefe4ac35cd8d1ed87fc7f670496d25e40")) ;version bump
(package
(name "emacs-beframe")
(version "0.2.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://git.sr.ht/~protesilaos/beframe")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0sd8r3icaj2gl7f62fyzlwkkb05mc3cwsqgicw0n1x07s5ir3129"))))
(build-system emacs-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'install 'makeinfo
(lambda _
(invoke "emacs"
"--batch"
"--eval=(require 'ox-texinfo)"
"--eval=(find-file \"README.org\")"
"--eval=(org-texinfo-export-to-info)")
(install-file "beframe.info"
(string-append #$output "/share/info")))))))
(native-inputs
(list texinfo))
(home-page "https://protesilaos.com/emacs/beframe")
(synopsis "Isolate Emacs buffers per frame")
(description
"Beframe enables a frame-oriented Emacs workflow where each frame has
access to the list of buffers visited therein. In the interest of brevity, we
call buffers that belong to frames ``beframed''. Producing multiple frames
does not generate multiple buffer lists. There still is only one global list
of buffers. Beframing them simply filters the list.")
(license (list license:gpl3+
license:fdl1.3+))))) ; GFDLv1.3+ for the manual
(define-public emacs-gn-mode
(package
(name "emacs-gn-mode")
@ -17288,6 +17386,48 @@ guidelines. It also includes a couple handy IDE-type features such as
documentation search and a source and class browser.")
(license license:gpl3+)))
(define-public emacs-pippel
(let ((commit "cb194952ee150e77601d3233dabdb521b976ee79")
(revision "0"))
(package
(name "emacs-pippel")
(version (git-version "0.1" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/arifer612/pippel")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"17606l24yyrjxa4rc0p2zj50lfbayqldw4phhi59yqf61289d520"))))
(build-system emacs-build-system)
(arguments
(list
#:include #~(cons "^pippel\\.py$" %default-include)
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'substitute-pippel-package-path
(lambda _
(emacs-substitute-variables "pippel.el"
("pippel-package-path" (elpa-directory #$output)))))
(add-after 'unpack 'substitute-python-path
(lambda* (#:key inputs #:allow-other-keys)
(emacs-substitute-variables "pippel.el"
("pippel-python-command"
(search-input-file inputs "/bin/python"))))))))
(inputs
(list python-wrapper))
(propagated-inputs
(list emacs-dash emacs-s))
(home-page "https://github.com/arifer612/pippel")
(synopsis "Emacs frontend to Python package manager Pip")
(description
"Pippel is an Emacs frontend for the Python package manager Pip. As
Pippel also uses Tabulated List mode, it provides a similar package menu like
@code{package-list-packages}.")
(license license:gpl3+))))
(define-public emacs-pos-tip
(package
(name "emacs-pos-tip")
@ -18141,12 +18281,12 @@ variable instead, to remind you of that variable's meaning.")
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/rejeep/ert-runner.el")
(commit (string-append "v" version))))
(url "https://github.com/rejeep/ert-runner.el")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"08gygn9fjank5gpi4v6ynrkn0jbknxbwsn7md4p9ndygdbmnkf98"))))
(base32
"08gygn9fjank5gpi4v6ynrkn0jbknxbwsn7md4p9ndygdbmnkf98"))))
(build-system emacs-build-system)
(inputs
(list emacs-ansi
@ -18158,22 +18298,22 @@ variable instead, to remind you of that variable's meaning.")
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'install 'install-executable
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(source-directory (string-append
(getenv "TMPDIR") "/source")))
(substitute* "bin/ert-runner"
(("ERT_RUNNER=\"\\$\\(dirname \\$\\(dirname \\$0\\)\\)")
(string-append "ERT_RUNNER=\"" (elpa-directory out))))
(install-file "bin/ert-runner" (string-append out "/bin"))
(wrap-program (string-append out "/bin/ert-runner")
(list "EMACSLOADPATH" ":" 'prefix
;; Do not capture the transient source directory in
;; the wrapper.
(delete source-directory
(string-split (getenv "EMACSLOADPATH") #\:))))
#t))))
(add-after 'install 'install-executable
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(source-directory (string-append
(getenv "TMPDIR") "/source")))
(substitute* "bin/ert-runner"
(("ERT_RUNNER=\"\\$\\(dirname \\$\\(dirname \\$0\\)\\)")
(string-append "ERT_RUNNER=\"" (elpa-directory out))))
(install-file "bin/ert-runner" (string-append out "/bin"))
(wrap-program (string-append out "/bin/ert-runner")
(list "EMACSLOADPATH" ":" 'prefix
;; Do not capture the transient source directory in
;; the wrapper.
(delete source-directory
(string-split (getenv "EMACSLOADPATH") #\:))))
#t))))
#:include (cons* "^reporters/.*\\.el$" %default-include)))
(home-page "https://github.com/rejeep/ert-runner.el")
(synopsis "Opinionated Ert testing workflow")
@ -19966,8 +20106,8 @@ files.")
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/jschaf/powershell.el")
(commit commit)))
(url "https://github.com/jschaf/powershell.el")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1cxhzaaig88zhylyycvb3849r85j1ijqklnh9zbqsfl2zhpb0g5c"))))
@ -29603,6 +29743,27 @@ generating a temp buffer in which any useful Emacs utilities and modes can be
invoked.")
(license license:gpl3+))))
(define-public emacs-exwm-modeline
(package
(name "emacs-exwm-modeline")
(version "0.1.3")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/SqrtMinusOne/exwm-modeline")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0b84wa8n5740p7wyia3skc8683inypha51w85mxn62wz6vfpjfp4"))))
(build-system emacs-build-system)
(propagated-inputs (list emacs-exwm))
(home-page "https://github.com/SqrtMinusOne/exwm-modeline")
(synopsis "Modeline segment for EXWM")
(description "This package provides a modeline segment to display EXWM
workspaces.")
(license license:gpl3+)))
(define-public emacs-ert-async
(package
(name "emacs-ert-async")
@ -30392,14 +30553,14 @@ well as an option for visually flashing evaluated s-expressions.")
(define-public emacs-tramp
(package
(name "emacs-tramp")
(version "2.6.0.2")
(version "2.6.0.3")
(source
(origin
(method url-fetch)
(uri (string-append "https://elpa.gnu.org/packages/"
"tramp-" version ".tar"))
(sha256
(base32 "0pfrsgci1rqrykkfyxm9wsn7f0l3rzc2vj1fas27w925l0k0lrci"))))
(base32 "0hcm20qk62k9irqdfcb44js9jkff43fji07la33arnjqvswrqs6n"))))
(build-system emacs-build-system)
(arguments
(list
@ -33210,8 +33371,8 @@ Wordnet.")
(define-public emacs-metal-mercury-mode
(let ((commit "99e2d8fb7177cae3bfa2dec2910fc28216d5f5a8")
(revision "1")
(version "0.0.0"))
(revision "1")
(version "0.0.0"))
(package
(name "emacs-metal-mercury-mode")
(version (git-version version revision commit))
@ -36514,6 +36675,27 @@ a Vertico extension which provides a way to pop up a frame at point to show
a vertical completion UI.")
(license license:gpl3+)))
(define-public emacs-tintin-mode
(let ((commit "82e71e1db92ee3d94c7d0208bafc5de337193de8")
(revision "1"))
(package
(name "emacs-tintin-mode")
(version (git-version "1.0.1" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/sunwayforever/tintin-mode")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1p6ryqb8m30cp0zyawb6bs8wy3ga7gm60lcan0xx1fy3wx8qip33"))))
(build-system emacs-build-system)
(home-page "https://github.com/sunwayforever/tintin-mode")
(synopsis "Emacs major mode for highlighting and indenting TinTin++ scripts.")
(description "This major mode focuses on highlighting as many aspects of the TinTin++ scripting language as possible, organizing commands into functional categories and highlighting specific modes that many commands use to accomplish different tasks.")
(license license:asl2.0))))
;;;
;;; Avoid adding new packages to the end of this file. To reduce the chances
;;; of a merge conflict, place them above by existing packages with similar

40
gnu/packages/emulators.scm
View File

@ -17,6 +17,7 @@
;;; Copyright © 2021 Felix Gruber <felgru@posteo.net>
;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2023 c4droid <c4droid@foxmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -2580,3 +2581,42 @@ on a Commodore C64, C128 etc.")
"This package provides an assembler and emulator for the Uxn
stack-machine, written in ANSI C. Graphical output is implemented using SDL2.")
(license license:expat))))
(define-public emu8051
(let ((commit "5dc681275151c4a5d7b85ec9ff4ceb1b25abd5a8")
(revision "1"))
(package
(name "emu8051")
(version (git-version "0.1" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/jarikomppa/emu8051")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1xxmkcwvd5fjnhwbricafg4xvxvr8dxhfanyfp4rbksw37dgk2fx"))
(modules '((guix build utils)))
(snippet #~(begin
;; Replace LDFLAGS -lcurses to -lncurses
(substitute* "Makefile"
(("-lcurses") "-lncurses"))))))
(build-system gnu-build-system)
(arguments
(list #:tests? #f ;No test suite
#:make-flags #~(list (string-append "CC="
#$(cc-for-target)))
#:phases
#~(modify-phases %standard-phases
(delete 'configure) ;No ./configure script
(replace 'install
;; No installation procedure
(lambda _
(install-file "emu"
(string-append #$output "/bin")))))))
(inputs (list ncurses))
(home-page "https://github.com/jarikomppa/emu8051")
(synopsis "8051/8052 emulator with curses-based UI")
(description "emu8051 is a simulator of the 8051/8052 microcontrollers.")
(license license:expat))))

44
gnu/packages/engineering.scm
View File

@ -132,6 +132,7 @@
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages pretty-print)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages pulseaudio)
#:use-module (gnu packages python)
#:use-module (gnu packages python-check)
#:use-module (gnu packages python-crypto)
@ -1619,6 +1620,49 @@ the API of spice simulators. Based on transformations specified in XML
language, ADMS transforms Verilog-AMS code into other target languages.")
(license license:gpl3)))
(define-public audmes
(package
(name "audmes")
(version "20220420")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/audmes/audmes%20sources/"
"audmes-source-" version ".zip"))
(sha256
(base32 "0yxjq2p1ca2wy2idwrlxr3b4vbp0d9268jll90y7l55fbid8vkp2"))))
(build-system cmake-build-system)
(arguments
(list
#:tests? #false ;there are none
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'prepare-csv.h
(lambda* (#:key inputs #:allow-other-keys)
(mkdir "libfccp")
(install-file (search-input-file inputs "csv.h") "libfccp"))))))
(inputs
(list alsa-lib pulseaudio wxwidgets))
(native-inputs
(list unzip
(let ((commit "4ade42d5f8c454c6c57b3dce9c51c6dd02182a66"))
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ben-strasser/fast-cpp-csv-parser")
(commit commit)))
(file-name (git-file-name "csv.h" (git-version "0" "0" commit)))
(sha256
(base32
"1y7ads97gkrjg1jc532n8gmjry0qhqxginw1gq7b4lk9s0pyl540"))))))
(home-page "https://sourceforge.net/projects/audmes/")
(synopsis "Oscilloscope and spectrum analyzer using sound card")
(description
"The audio measurement system is a system for audio measurement through
sound card. It contains: generator, oscilloscope, audio spectrum
analyzer (FFT) and frequency sweep plot.")
(license license:gpl2+)))
(define-public capstone
(package
(name "capstone")

12
gnu/packages/games.scm
View File

@ -6920,7 +6920,7 @@ at their peak of economic growth and military prowess.
(define-public open-adventure
(package
(name "open-adventure")
(version "1.12")
(version "1.14")
(source
(origin
(method git-fetch)
@ -6929,7 +6929,7 @@ at their peak of economic growth and military prowess.
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "07mg7cp12g27dw8sya17jqz6qp93q7c8zadsvym3w602z87g40in"))))
(base32 "1fb1fw1mq7czd90q1mf22g5nqvv7g1mfhhgs6slba7yzx2kbv4d0"))))
(build-system gnu-build-system)
(arguments
(list
@ -9094,7 +9094,7 @@ levels to unlock.")
(define simgear
(package
(name "simgear")
(version "2020.3.17")
(version "2020.3.18")
(source
(origin
(method url-fetch)
@ -9102,7 +9102,7 @@ levels to unlock.")
(version-major+minor version) "/"
"simgear-" version ".tar.bz2"))
(sha256
(base32 "0z1pkxs4fw8xkiainxgcpayhmn0b4c0sc2j6q88x66zzvk89qpjc"))
(base32 "1jin6rbz4s83x4k91lbdw5gb0vrc8frbmwpc55wl0wmiaqjwzhbc"))
(modules '((guix build utils)))
(snippet
'(begin
@ -9147,7 +9147,7 @@ and also provides the base for the FlightGear Flight Simulator.")
(version-major+minor version) "/"
"flightgear-" version ".tar.bz2"))
(sha256
(base32 "0m0qbyf9i84avkfmjm1a5bijl1nqs7wnpw7rfz53ls52mkgdww36"))
(base32 "0dyyi1v97w3mdwsv9kdd194inz1461wqv3zy3wyai0n17wdf7a1r"))
(modules '((guix build utils)))
(snippet
'(begin
@ -9219,7 +9219,7 @@ and also provides the base for the FlightGear Flight Simulator.")
"FlightGear-" version "-data.txz"))
(sha256
(base32
"1s6qahfia3llghfqgx990brg7gbb7z7accsq528kcyp6k8mvlpia"))))))
"0f2jn2br27ahf5gggx70zcp80wrylahw7nbqdcx7ml9qphg6rjak"))))))
(home-page "https://www.flightgear.org/")
(synopsis "Flight simulator")
(description "The goal of the FlightGear project is to create a

4
gnu/packages/gnome.scm
View File

@ -8498,7 +8498,7 @@ users.")
(define-public network-manager
(package
(name "network-manager")
(version "1.43.4")
(version "1.41.2")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/NetworkManager/"
@ -8508,7 +8508,7 @@ users.")
"network-manager-meson.patch"))
(sha256
(base32
"03sq59hb99farkn2z2kiidcmq86jc13ppjvm6s0k8cdxkcpivals"))))
"0v5a5fw1zwa94ksz6d7hyj14wwdxzmswgm81ryhxmyn3nrcf1akg"))))
(build-system meson-build-system)
(outputs '("out"
"doc")) ; 8 MiB of gtk-doc HTML

8
gnu/packages/gnuzilla.scm
View File

@ -1119,8 +1119,8 @@ standards of the IceCat project.")
"ru" "sco" "si" "sk" "sl" "son" "sq" "sr" "sv-SE" "szl" "ta" "te" "th" "tl"
"tr" "trs" "uk" "ur" "uz" "vi" "xh" "zh-CN" "zh-TW"))
(define %icedove-build-id "20230314000000") ;must be of the form YYYYMMDDhhmmss
(define %icedove-version "102.9.0")
(define %icedove-build-id "20230328000000") ;must be of the form YYYYMMDDhhmmss
(define %icedove-version "102.9.1")
;; Provides the "comm" folder which is inserted into the icecat source.
;; Avoids the duplication of Icecat's source tarball.
@ -1129,11 +1129,11 @@ standards of the IceCat project.")
(method hg-fetch)
(uri (hg-reference
(url "https://hg.mozilla.org/releases/comm-esr102")
(changeset "db735c436e680abf21cc67f9a29b42fdf30d416d")))
(changeset "a8965ef0b30705f497df3df718db60d9dc2c304f")))
(file-name (string-append "thunderbird-" %icedove-version "-checkout"))
(sha256
(base32
"114vvwlrmjilczwsg9nfcg08560vijlydw1pdrbkvxjbfgsxny71"))))
"14lj30a9hmiwxpriyfls245y1wj2j3hfwrsbf7s5d9ligjqldjag"))))
(define (comm-source->locales+changeset source)
"Given SOURCE, a checkout of the Thunderbird 'comm' component, return the

21
gnu/packages/hardware.scm
View File

@ -15,6 +15,7 @@
;;; Copyright © 2022 Marcel Kupiec <formbi@protonmail.com>
;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2022 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2023 Spencer Skylar Chan <schan12@umd.edu>
;;;
;;; This file is part of GNU Guix.
;;;
@ -482,31 +483,15 @@ RGB animations.")
(define-public ddcutil
(package
(name "ddcutil")
(version "1.3.2")
(version "1.4.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://www.ddcutil.com/tarballs/"
"ddcutil-" version ".tar.gz"))
(sha256
(base32 "0hm0cm4m4hk1jjy7kddg613mynvwlii3kp8al0j9v3c6mcx3p4mx"))))
(base32 "14svdjpw9xn1czl4vff4jg2i9bp83lxcbzxj7hxn63z3gzacaj4k"))))
(build-system gnu-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'install 'install-udev-rules
(lambda* (#:key outputs #:allow-other-keys)
;; Move the udev rules to their expected location in Guix
;; System, so they can be more easily used.
(let ((rules.d (string-append #$output "/lib/udev/rules.d")))
(mkdir-p (dirname rules.d))
(rename-file (string-append #$output "/share/ddcutil/data")
rules.d)
;; Patch a reference to the ddcutil command.
(substitute* (string-append rules.d "/45-ddcutil-usb.rules")
(("/usr/bin/ddcutil")
(search-input-file outputs "bin/ddcutil")))))))))
(native-inputs
(list pkg-config))
(inputs

2
gnu/packages/image-viewers.scm
View File

@ -254,7 +254,7 @@ actions.")
libarchive
libchamplain
libheif
libjpeg
libjpeg-turbo
libpng
libraw
libtiff

12
gnu/packages/linux.scm
View File

@ -483,7 +483,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
;; The current "stable" kernels. That is, the most recently released major
;; versions that are still supported upstream.
(define-public linux-libre-6.2-version "6.2.8")
(define-public linux-libre-6.2-version "6.2.9")
(define-public linux-libre-6.2-gnu-revision "gnu")
(define deblob-scripts-6.2
(linux-libre-deblob-scripts
@ -493,12 +493,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(base32 "0ir5vvbdh6dly5ld8mfp7285g8k88w5bb32hj4wmgyqsbfqc6rf2")))
(define-public linux-libre-6.2-pristine-source
(let ((version linux-libre-6.2-version)
(hash (base32 "0rgn8k9rhk819bazcaz7fbk5ba1hph02izqrw06ag0rgsj3svl7y")))
(hash (base32 "1xa3znandhyn1ygbfv4cl83mwn33hphj1jdc59s0wgy0ck0ljd4h")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-6.2)))
(define-public linux-libre-6.1-version "6.1.21")
(define-public linux-libre-6.1-version "6.1.22")
(define-public linux-libre-6.1-gnu-revision "gnu")
(define deblob-scripts-6.1
(linux-libre-deblob-scripts
@ -508,7 +508,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(base32 "0cchdhjra74zanyk14brv2l2dvxpg8dn58rn477lgfb44mcnhq33")))
(define-public linux-libre-6.1-pristine-source
(let ((version linux-libre-6.1-version)
(hash (base32 "0fnr2pw4pi0vnkpv8hfipya09cgdz6ghks7p6vdl2d71dawb2g5k")))
(hash (base32 "1a7xkjqj13q5dgk1gml27kdzs381p0z203alamd0wkgprr0r3s1b")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-6.1)))
@ -516,7 +516,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
;; The "longterm" kernels — the older releases with long-term upstream support.
;; Here are the support timelines:
;; <https://www.kernel.org/category/releases.html>
(define-public linux-libre-5.15-version "5.15.104")
(define-public linux-libre-5.15-version "5.15.105")
(define-public linux-libre-5.15-gnu-revision "gnu")
(define deblob-scripts-5.15
(linux-libre-deblob-scripts
@ -526,7 +526,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(base32 "03hwhwbcicwyx5i30d6m715kwgrxz4h21xhk55wnawlk8zhx3r35")))
(define-public linux-libre-5.15-pristine-source
(let ((version linux-libre-5.15-version)
(hash (base32 "0m3bscml2mvafbj5k9a3qa8akfxms8wfpzsr687lfblr17735ibi")))
(hash (base32 "0kz4ymaqb1kpniqq2mwv3z8rirz5yyf1c9m648kqblij0djkgd81")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-5.15)))

281
gnu/packages/lisp-xyz.scm
View File

@ -119,6 +119,7 @@
#:use-module (gnu packages web)
#:use-module (gnu packages webkit)
#:use-module (gnu packages xdisorg)
#:use-module (gnu packages xiph)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
#:use-module (ice-9 match)
@ -2427,6 +2428,43 @@ consistent across multiple Common Lisp implementations.")
(define-public ecl-trivial-features
(sbcl-package->ecl-package sbcl-trivial-features))
(define-public sbcl-harmony
(let ((commit "0b57483cc0341936c201b620f82a8542c606991f")
(revision "0"))
(package
(name "sbcl-harmony")
(version (git-version "2.0.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Shirakumo/harmony")
(commit commit)))
(file-name (git-file-name "cl-harmony" version))
(sha256
(base32 "0pqmfi3yi3gi7b7dyayrb621hp60rn7hasq0cl0fis3vg0fp5dja"))))
(build-system asdf-build-system/sbcl)
(inputs
(list sbcl-atomics
sbcl-bordeaux-threads
sbcl-cl-mixed
sbcl-stealth-mixin
sbcl-trivial-features))
(home-page "https://shirakumo.github.io/harmony/")
(synopsis "Common Lisp sound server and sound processing library")
(description
"HARMONY is a library that provides you with audio processing tools as
well as an audio server to play back music, sfx, and so forth. It is most
suited for use in a game engine, but may feasibly also be used for more
advanced things such as a DAW")
(license license:zlib))))
(define-public ecl-harmony
(sbcl-package->ecl-package sbcl-harmony))
(define-public cl-harmony
(sbcl-package->cl-source-package sbcl-harmony))
(define-public sbcl-hu.dwim.asdf
(let ((commit "67cdf84390e530af4303cc4bc815fdf2a5e48f59"))
(package
@ -6924,6 +6962,53 @@ mostly Common Lisp implementation.")
(define-public ecl-cl-fastcgi
(sbcl-package->ecl-package sbcl-cl-fastcgi))
(define-public sbcl-cl-flac
(let ((commit "d094d33d3cc2cf263263b917798d338eded3c532")
(revision "0"))
(package
(name "sbcl-cl-flac")
(version (git-version "1.0.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Shirakumo/cl-flac")
(commit commit)))
(file-name (git-file-name "cl-flac" version))
(sha256
(base32 "1dgr5xqf175hzq3sxpbixxia2k2g3rz0pn6msch4dnvk7a1naqlc"))
(modules '((guix build utils)))
(snippet
;; Delete bundled libraries.
`(begin
(delete-file-recursively "static")))))
(build-system asdf-build-system/sbcl)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-paths
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "low-level.lisp"
(("libflac.so")
(search-input-file inputs "/lib/libFLAC.so"))))))))
(inputs
(list flac
sbcl-cffi
sbcl-documentation-utils
sbcl-trivial-features
sbcl-trivial-garbage))
(home-page "https://shirakumo.github.io/cl-flac")
(synopsis "CFFI bindings to libflac for Common Lisp")
(description "This package provides CFFI bindings to the @code{libflac}
audio library for Common Lisp.")
(license license:zlib))))
(define-public ecl-cl-flac
(sbcl-package->ecl-package sbcl-cl-flac))
(define-public cl-flac
(sbcl-package->cl-source-package sbcl-cl-flac))
(define-public sbcl-clack
(let ((commit "6fd0279424f7ba5fd4f92d69a1970846b0b11222")
(revision "2"))
@ -19129,6 +19214,86 @@ encodings.")
(define-public cl-mime
(sbcl-package->cl-source-package sbcl-cl-mime))
(define-public sbcl-cl-mixed
(let ((commit "4aaff134d3902d93a2a8605c10de4bcfc62d7afa")
(revision "0"))
(package
(name "sbcl-cl-mixed")
(version (git-version "2.1.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Shirakumo/cl-mixed")
(commit commit)))
(file-name (git-file-name "cl-mixed" version))
(sha256
(base32 "1mrj95lxb1gbxxm89x8gy1ifw2ic1p5wwpapkxcd2jr8abw7zny0"))
(modules '((guix build utils)))
(snippet
;; Delete bundled libraries.
`(begin
(delete-file-recursively "static")))))
(build-system asdf-build-system/sbcl)
(arguments
'(#:asd-systems '("cl-mixed"
"cl-mixed-examples"
"cl-mixed-flac"
"cl-mixed-vorbis"
"cl-mixed-alsa"
"cl-mixed-jack"
"cl-mixed-mpg123"
"cl-mixed-mpt"
"cl-mixed-out123"
"cl-mixed-pulse"
"cl-mixed-sdl2"
"cl-mixed-wav")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-paths
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "low-level.lisp"
(("libmixed.so.2")
(search-input-file inputs "/lib/libmixed.so.2"))))))))
(inputs
(list libmixed
sbcl-alexandria
sbcl-cffi
sbcl-cl-flac
sbcl-cl-mpg123
sbcl-cl-out123
sbcl-cl-vorbis
sbcl-documentation-utils
sbcl-sdl2
sbcl-static-vectors
sbcl-trivial-features))
(home-page "https://shirakumo.github.io/cl-mixed/")
(synopsis "Extended audio library for Common Lisp")
(description
"This package provides CFFI binding to @code{libmixed} audio library for
Common Lisp with support of other audio formats available on GNU/Linux systems:
@itemize
@item @acronym{Alsa, Advanced Linux Sound Architecture}
@item @acronym{Jack, JackAudio toolkit}
@item @acronym{Openmpt, Libopenmpt playback drain for tracker files}
@item @acronym{PulseAudio, PulseAudio based playback drain}
@item Flac (via CL-FLAC)
@item Mpg123 (via CL-MPG123)
@item Ogg/vorbis (via CL-VORBIS)
@item Out123 (via CL-OUT123)
@item WAV
@end itemize")
(license license:zlib))))
(define-public ecl-cl-mixed
(sbcl-package->ecl-package sbcl-cl-mixed))
(define-public cl-mixed
(sbcl-package->cl-source-package sbcl-cl-mixed))
(define-public sbcl-lispbuilder-sdl
(let ((commit "589b3c6d552bbec4b520f61388117d6c7b3de5ab"))
(package
@ -21283,8 +21448,7 @@ joysticks, and other such HID devices.")
;; ...
;; "trial-glop"
"trial-gltf"
;; TODO: It requires a long packaging journey.
;; "trial-harmony"
"trial-harmony"
"trial-jpeg"
"trial-notify"
"trial-png"
@ -21330,6 +21494,7 @@ joysticks, and other such HID devices.")
sbcl-form-fiddle
sbcl-glop
sbcl-glsl-toolkit
sbcl-harmony
sbcl-ieee-floats
sbcl-jzon
sbcl-lambda-fiddle
@ -23959,6 +24124,67 @@ Vernacular builds on Overlord and is inspired by Racket.")
(define-public cl-vernacular
(sbcl-package->cl-source-package sbcl-vernacular))
(define-public sbcl-cl-collider
(let ((commit "a46908896982868955b29bfb3a5337a0af489b0b")
(revision "0"))
(package
(name "sbcl-cl-collider")
(version (git-version "2018.7.15" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/byulparan/cl-collider")
(commit commit)))
(file-name (git-file-name "cl-collider" version))
(sha256
(base32 "10wvjbwvbgr0b57hpfxycg90yjmb29pirygr1sxrdaqxll328sz1"))))
(build-system asdf-build-system/sbcl)
(arguments
(list #:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'patch-executables-and-paths
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "server.lisp"
(("/usr/local/lib/SuperCollider/plugins")
(search-input-directory
inputs "/lib/SuperCollider/plugins"))
(("/usr/local/share/SuperCollider/Extensions")
(search-input-directory
inputs "/share/SuperCollider/Extensions"))
(("which scsynth")
(string-append
"which "
(search-input-file inputs "/bin/scsynth")))
(("jack_connect")
(search-input-file inputs "/bin/jack_connect"))))))))
(inputs
(list jack-1
supercollider
sbcl-alexandria
sbcl-bordeaux-threads
sbcl-cffi
sbcl-cl-ppcre
sbcl-flexi-streams
sbcl-ieee-floats ; sc-osc dependencies.
sbcl-named-readtables
sbcl-osc
sbcl-pileup
sbcl-simple-inferiors ; For ecl.
sbcl-split-sequence
sbcl-usocket))
(synopsis "SuperCollider client for CommonLisp")
(description "This package provides a SuperCollider client for
Common Lisp.")
(home-page "https://github.com/byulparan/cl-collider/")
(license license:public-domain))))
(define-public cl-collider
(sbcl-package->cl-source-package sbcl-cl-collider))
(define-public ecl-cl-collider
(sbcl-package->ecl-package sbcl-cl-collider))
(define-public sbcl-osc
(let ((commit "9f0a9d3da310a3a0f654f48af0203816f3f371ad")
(revision "0"))
@ -28033,6 +28259,57 @@ generation as well as numerous distributions.")
(define-public ecl-cl-variates
(sbcl-package->ecl-package sbcl-cl-variates))
(define-public sbcl-cl-vorbis
(let ((commit "c5835cd7091aea9e2e389ad359d244542d637758")
(revision "0"))
(package
(name "sbcl-cl-vorbis")
(version (git-version "1.0.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Shirakumo/cl-vorbis")
(commit commit)))
(file-name (git-file-name "cl-vorbis" version))
(sha256
(base32 "0713pl5c2khfpf8m3h1l2y0ilack7akf580h70jq6qcrnq3h4b40"))
(modules '((guix build utils)))
(snippet
;; Delete bundled libraries, GlibC and Vorbis sources.
`(begin
(delete-file-recursively "static")
(for-each delete-file '("glibc-2.13.h"
"stb_vorbis.c"
"stb_vorbis_patch.c"))))))
(build-system asdf-build-system/sbcl)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-paths
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "low-level.lisp"
(("libvorbis-lin-amd64.so")
(search-input-file inputs "/lib/libvorbis.so"))))))))
(inputs
(list libvorbis
sbcl-cffi
sbcl-documentation-utils
sbcl-static-vectors
sbcl-trivial-features
sbcl-trivial-garbage))
(home-page "https://shirakumo.github.io/cl-vorbis/")
(synopsis "OGG/Vorbis decoding using stb_vorbis for Common Lisp")
(description "This package provides CFFI bindings for the
@code{stb_vorbis} audio library to Common Lisp.")
(license license:zlib))))
(define-public ecl-cl-vorbis
(sbcl-package->ecl-package sbcl-cl-vorbis))
(define-public cl-vorbis
(sbcl-package->cl-source-package sbcl-cl-vorbis))
(define-public sbcl-cephes
(let ((commit "d87146fa38c8425ffb5fe425eee5eb3e818bacd4")
(revision "0"))

203
gnu/packages/maths.scm
View File

@ -5218,6 +5218,95 @@ packages.")
;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
(license (list license:gpl2+ license:lgpl2.1+))))
;; This outdated version is used to build the scilab package.
(define-public suitesparse-3
(package
(inherit suitesparse)
(name "suitesparse")
(version "3.1.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/DrTimothyAldenDavis/SuiteSparse")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0wxk755nzps0c9la24zqknqkzjp6rcj5q9jhd973mff1pqja3clz"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ;no "check" target
#:make-flags
,#~(list
(string-append "CC=gcc")
"AR=gcc -shared -o"
"RANLIB=touch"
"CFLAGS=-O3 -fPIC -I../Include"
"TBB=-ltbb"
;; Disable metis@4 (nonfree) support.
"CHOLMOD_CONFIG=-DNPARTITION"
"METIS="
"METIS_PATH="
;; The default is to link against netlib lapack. Use OpenBLAS
;; instead.
"BLAS=-lopenblas" "LAPACK=-lopenblas"
(string-append "INSTALL_LIB="
(assoc-ref %outputs "out") "/lib")
(string-append "INSTALL_INCLUDE="
(assoc-ref %outputs "out") "/include")
"library")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'correct-build-configuration
(lambda _
;; Invert build order: CHOLMOD before KLU.
(substitute* "Makefile"
(("\t\\( cd CHOLMOD ; \\$\\(MAKE\\) \\)\n$")
"")
(("\\( cd KLU ; \\$\\(MAKE\\) \\)")
(string-append "( cd CHOLMOD ; $(MAKE) )\n\t"
"( cd KLU ; $(MAKE) )")))
;; Build shared libraries.
(substitute* (find-files "." "akefile$")
(("lib([a-z]+)\\.a" all libname)
(string-append "lib" libname ".so")))
;; Delete broken KLU Demo step.
(substitute* "KLU/Makefile"
(("\\( cd Demo ; \\$\\(MAKE\\) \\)")
""))))
(replace 'install
(lambda _
;; Install libraries.
(for-each
(lambda (x)
(install-file
x
(string-append (assoc-ref %outputs "out") "/lib")))
(find-files "." "\\.so$"))
;; Install header files.
(for-each
(lambda (x)
(install-file
x
(string-append (assoc-ref %outputs "out") "/include")))
(find-files "." "\\.h$"))))
,@(if (target-riscv64?)
;; GraphBLAS FTBFS on riscv64-linux
`((add-after 'unpack 'skip-graphblas
(lambda _
(substitute* "Makefile"
((".*cd GraphBLAS.*") "")
(("metisinstall gbinstall moninstall")
"moninstall")))))
'())
(delete 'configure)))) ;no configure script
(inputs
(list tbb openblas gmp mpfr))))
(define-public atlas
(package
(name "atlas")
@ -6072,6 +6161,14 @@ structured and unstructured grid problems.")))
(base32
"0vr8c1mz1k6mz0sgh6n3scl5c3a71iqmy5fnydrgq504icj4vym4"))))
(build-system gnu-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-before 'install 'install-matioConfig.h
(lambda _
(install-file "src/matioConfig.h"
(string-append #$output "/include")))))))
(inputs
(list zlib hdf5-1.8))
(home-page "http://matio.sourceforge.net/")
@ -8569,3 +8666,109 @@ primal-dual interior-point method are made available. Interfaces are
provided for applications written in C++ and Python. Parallel
computation is supported via MPI.")
(license license:bsd-2))))
(define-public scilab
(package
(name "scilab")
(version "5.5.0")
(source
(origin
(method url-fetch)
(uri
(string-append "https://oos.eu-west-2.outscale.com/scilab-releases/"
version "/scilab-" version "-src.tar.gz"))
(sha256
(base32 "1hx57aji5d78brwqcf8a34i1hasm3h4nw46xjg7cgxj09s8yz5kq"))))
(build-system gnu-build-system)
(native-inputs (list pkg-config gfortran))
(inputs (list libxml2
`(,pcre "bin")
`(,pcre "out")
readline
hdf5-1.8
curl
openblas
lapack
arpack-ng
fftw
gettext-minimal
suitesparse-3
tcl
tk
libx11
matio))
(arguments
`(#:tests? #f
#:configure-flags
,#~(list
"--enable-relocatable"
"--disable-static-system-lib"
;; Disable all java code.
"--without-gui"
"--without-javasci"
"--disable-build-help"
"--with-external-scirenderer"
;; Tcl and Tk library locations.
(string-append "--with-tcl-include="
(string-drop-right
(search-input-file %build-inputs "include/tcl.h")
(string-length "/tcl.h")))
(string-append "--with-tcl-library="
(string-drop-right
(search-input-directory %build-inputs "lib/tcl8")
(string-length "/tcl8")))
(string-append "--with-tk-include="
(string-drop-right
(search-input-file %build-inputs "include/tk.h")
(string-length "/tk.h")))
(string-append "--with-tk-library="
(string-drop-right
(search-input-directory %build-inputs "lib/tk8.6")
(string-length "/tk8.6")))
;; There are some 2018-fortran errors that are ignored
;; with this fortran compiler flag.
"FFLAGS=-fallow-argument-mismatch")
#:phases
,#~(modify-phases %standard-phases
(add-before 'build 'pre-build
(lambda _
;; Fix scilab script.
(substitute* "bin/scilab"
(("\\/bin\\/ls")
(which "ls")))
;; Fix core.start.
(substitute* "modules/core/etc/core.start"
(("'SCI/modules")
"SCI+'/modules"))
;; Fix fortran compilation error.
(substitute*
"modules/differential_equations/src/fortran/twodq.f"
(("node\\(10\\),node1\\(10\\),node2\\(10\\),coef")
"node(9),node1(9),node2(9),coef"))
;; Fix C compilation errors.
;; remove &
(substitute* "modules/hdf5/src/c/h5_readDataFromFile_v1.c"
(("(H5Rdereference\\(_iDatasetId, H5R_OBJECT, )&(.*)\\);$"
all common ref)
(string-append common ref)))
;; fix multiple definitions
(substitute* "modules/tclsci/src/c/TCL_Command.h"
(("^__thread")
"extern __thread"))
(substitute* "modules/tclsci/src/c/InitTclTk.c"
(("BOOL TK_Started = FALSE;" all)
(string-append all "\n"
"__threadId TclThread;" "\n"
"__threadSignal InterpReady;" "\n"
"__threadSignalLock InterpReadyLock;"
"\n")))
;; Set SCIHOME to /tmp before macros compilation.
(setenv "SCIHOME" "/tmp"))))))
(home-page "https://scilab.org")
(synopsis "Software for engineers and scientists")
(description "This package provides the non-graphical version of the Scilab
software for engineers and scientists. Scilab is used for signal processing,
statistical analysis, image enhancement, fluid dynamics simulations, numerical
optimization, and modeling, simulation of explicit and implicit dynamical
systems and symbolic manipulations.")
(license license:cecill))) ;CeCILL v2.1

234
gnu/packages/package-management.scm
View File

@ -1137,7 +1137,7 @@ written entirely in Python.")
(define-public conan
(package
(name "conan")
(version "1.50.0")
(version "2.0.2")
(source
(origin
(method git-fetch) ;no tests in PyPI archive
@ -1147,104 +1147,113 @@ written entirely in Python.")
(file-name (git-file-name name version))
(sha256
(base32
"1jjrinz5wkcxfvwdpldrv4h7vacdyz88cc4af5vi3sdnjra0i0m5"))))
"1y4qmqnw3s8xv64lgp388qpj9vqharyfqi5s8dxvgsns6cafv7lf"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'relax-requirements
(lambda _
(substitute* "conans/requirements.txt"
(("node-semver==0.6.1")
"node-semver>=0.6.1")
(("Jinja2>=2.9, <3")
"Jinja2>=2.9")
(("PyYAML>=3.11, <6.0")
"PyYAML"))))
(add-after 'unpack 'patch-paths
(lambda* (#:key inputs #:allow-other-keys)
(let ((coreutils (assoc-ref inputs "coreutils")))
;; It seems that PATH is manipulated, as printenv is not found
;; during tests. Patch in its exact location.
(substitute* "conan/tools/env/environment.py"
(("printenv")
(string-append coreutils "/bin/printenv")))
(substitute* "conans/client/envvars/environment.py"
(("#!/usr/bin/env")
(string-append "#!" coreutils "/bin/env"))))))
(add-before 'check 'set-home
(lambda _
(setenv "HOME" "/tmp")))
(replace 'check
(lambda* (#:key tests? outputs #:allow-other-keys)
(define system ,(or (%current-target-system)
(%current-system)))
(when tests?
(setenv "PATH" (string-append (getenv "PATH") ":"
(assoc-ref outputs "out") "/bin"))
(invoke "python" "-m" "pytest"
"-n" "auto" ;parallelize tests
"-m" "not slow and not tool_svn"
;; Disable problematic tests.
"-k"
(string-append
;; These tests rely on networking.
"not shallow_clone_remote "
"and not remote_build "
"and not download_retries_errors "
"and not ftp "
"and not build_local_different_folders "
;; These expect CMake available at fixed versions.
"and not custom_cmake "
"and not default_cmake "
"and not bazel " ;bazel is not packaged
;; Guix sets PKG_CONFIG_PATH itself, which is not
;; expected by the following test.
"and not pkg_config_path "
"and not compare " ;caused by newer node-semver?
;; Guix is not currently a supported package manager.
"and not system_package_tool "
;; These expect GCC 5 to be available.
"and not test_reuse "
"and not test_install "
;; The installed configure script trips on the /bin/sh
;; shebang. We'd have to patch it in the Python code.
"and not test_autotools "
"and not test_use_build_virtualenv "
;; This test is architecture-dependent.
"and not test_toolchain_linux "
;; This one fails for unknown reasons (see:
;; https://github.com/conan-io/conan/issues/9671).
"and not test_build "
;; These tests expect the 'apt' command to be available.
"and not test_apt_check "
"and not test_apt_install_substitutes "
(if (not (string-prefix? "x86_64" system))
;; These tests either assume the machine is
;; x86_64, or require a cross-compiler to target
;; it.
(string-append
"and not cpp_package "
"and not exclude_code_analysis "
"and not cmakedeps_multi "
"and not locally_build_linux "
"and not custom_configuration "
"and not package_from_system "
"and not cross_build_command "
"and not test_package "
"and not test_deleted_os "
"and not test_same ")
"")
(if (not (or (string-prefix? "x86_64" system)
(string-prefix? "i686" system)))
;; These tests either assume the machine is i686,
;; or require a cross-compiler to target it.
(string-append
"and not vcvars_raises_when_not_found "
"and not conditional_generators "
"and not test_folders "
"and not settings_as_a_dict_conanfile ")
"")))))))))
(list
#:modules '((guix build python-build-system)
(guix build utils)
(ice-9 format))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'patch-paths
(lambda* (#:key inputs #:allow-other-keys)
;; It seems that PATH is manipulated, as printenv is not found
;; during tests. Patch in its exact location.
(substitute* "conan/tools/env/environment.py"
(("printenv")
(search-input-file inputs "bin/printenv")))))
(add-after 'unpack 'patch-hard-coded-GCC-references
(lambda _
;; The test suite expects GCC 9 to be used (see:
;; https://github.com/conan-io/conan/issues/13575). Render the
;; check version agnostic.
(substitute* "conans/test/functional/toolchains/meson/_base.py"
(("__GNUC__9")
"__GNUC__"))))
(add-after 'unpack 'use-current-cmake-for-tests
(lambda _
(substitute* (find-files "conans/test" "\\.py$")
(("@pytest.mark.tool\\(\"cmake\", \"3.23\")")
"@pytest.mark.tool(\"cmake\")"))))
(add-before 'check 'configure-tests
(lambda _
(let* ((cmake-version #$(version-major+minor
(package-version cmake)))
(pkg-config-version #$(version-major+minor
(package-version pkg-config))))
(call-with-output-file "conans/test/conftest_user.py"
(lambda (port)
(format port "\
tools_locations = {
'apt_get': {'disabled': True},
'bazel': {'disabled': True},
'cmake': {'default': '~a',
'3.15': {'disabled': True},
'3.16': {'disabled': True},
'3.17': {'disabled': True},
'3.19': {'disabled': True},
'~:*~a': {}},
'pkg_config': {'exe': 'pkg-config',
'default': '~a',
'~:*~a': {}},
'svn': {'disabled': True}}~%" cmake-version pkg-config-version))))))
(add-before 'check 'set-home
(lambda _
(setenv "HOME" "/tmp")))
(replace 'check
(lambda* (#:key tests? outputs #:allow-other-keys)
(define system #$(or (%current-target-system)
(%current-system)))
(when tests?
(setenv "CONFIG_SHELL" (which "sh"))
(setenv "PATH" (string-append (getenv "PATH") ":"
#$output "/bin"))
(invoke "python" "-m" "pytest" "-vv"
"-n" (number->string (parallel-job-count))
"-m" "not slow"
;; Disable problematic tests.
"-k"
(string-append
;; These tests rely on networking.
"not download_retries_errors "
"and not ftp "
;; Guix sets PKG_CONFIG_PATH itself, which is not
;; expected by the following test.
"and not pkg_config_path "
"and not compare " ;caused by newer node-semver?
;; This test hard-codes a compiler version.
"and not test_toolchain "
;; The 'test_list' tests may fail
;; non-deterministically (see:
;; https://github.com/conan-io/conan/issues/13583).
"and not test_list "
;; These tests fail when Autoconf attempt to load a
;; shared library in the same directory (see:
;; https://github.com/conan-io/conan/issues/13577).
"and not test_other_client_can_link_autotools "
"and not test_autotools_lib_template "
(if (not (string-prefix? "x86_64" system))
;; These tests either assume the machine is
;; x86_64, or require a cross-compiler to target
;; it.
(string-append
"and not cpp_package "
"and not exclude_code_analysis "
"and not cmakedeps_multi "
"and not locally_build_linux "
"and not custom_configuration "
"and not package_from_system "
"and not cross_build_command "
"and not test_package "
"and not test_same ")
"")
(if (not (or (string-prefix? "x86_64" system)
(string-prefix? "i686" system)))
;; This test only works with default arch "x86",
;; "x86_64", "sparc" or "sparcv9".
"and not settings_as_a_dict_conanfile "
"")))))))))
(propagated-inputs
(list python-bottle
python-colorama
@ -1264,22 +1273,23 @@ written entirely in Python.")
python-tqdm
python-urllib3))
(inputs
(list coreutils)) ;for printenv
(list coreutils)) ;for printenv
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("cmake" ,cmake)
("git" ,git-minimal)
("meson" ,meson)
("ninja",ninja)
("pkg-config" ,pkg-config)
("python-bottle" ,python-bottle)
("python-mock" ,python-mock)
("python-parameterized" ,python-parameterized)
("python-pytest" ,python-pytest)
("python-pytest-xdist" ,python-pytest-xdist)
("python-webtest" ,python-webtest)
("which" ,which)))
(list autoconf-wrapper
automake
cmake
git-minimal
libtool
meson
ninja
pkg-config
python-bottle
python-mock
python-parameterized
python-pytest
python-pytest-xdist
python-webtest
which))
(home-page "https://conan.io")
(synopsis "Decentralized C/C++ package manager")
(description "Conan is a package manager for C and C++ developers that

17
gnu/packages/python-crypto.scm
View File

@ -1503,21 +1503,14 @@ items and collections, editing items, locking and unlocking collections
(define-public python-trustme
(package
(name "python-trustme")
(version "0.6.0")
(version "0.9.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "trustme" version))
(sha256
(base32 "0v3vr5z6apnfmklf07m45kv5kaqvm6hxrkaqywch57bjd2siiywx"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key inputs outputs #:allow-other-keys)
(add-installed-pythonpath inputs outputs)
(invoke "pytest" "-vv"))))))
(base32 "0v2qzszmyazfgc1snicdr4b4qdajpjd4pbinpgrn9vfff0yv41sy"))))
(build-system pyproject-build-system)
(native-inputs
(list python-more-itertools
python-pyopenssl
@ -1526,7 +1519,9 @@ items and collections, editing items, locking and unlocking collections
python-service-identity
python-zipp))
(propagated-inputs
(list python-cryptography))
(list python-cryptography
python-idna
python-ipaddress))
(home-page "https://github.com/python-trio/trustme")
(synopsis "Fake a certificate authority for tests")
(description

83
gnu/packages/python-web.scm
View File

@ -49,7 +49,7 @@
;;; Copyright © 2021 Alice Brenon <alice.brenon@ens-lyon.fr>
;;; Copyright © 2022 John Kehayias <john.kehayias@protonmail.com>
;;; Copyright © 2022 Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org>
;;; Copyright © 2022 Felix Gruber <felgru@posteo.net>
;;; Copyright © 2022, 2023 Felix Gruber <felgru@posteo.net>
;;; Copyright © 2022 Peter Polidoro <peter@polidoro.io>
;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
;;; Copyright © 2022 Luis Henrique Gomes Higino <luishenriquegh2701@gmail.com>
@ -570,6 +570,87 @@ communicate with each other, and positioned as an asynchronous successor to
WSGI. This package includes libraries for implementing ASGI servers.")
(license license:bsd-3)))
(define-public python-asgi-csrf
(package
(name "python-asgi-csrf")
(version "0.9")
(source (origin
(method git-fetch) ;for tests
(uri (git-reference
(url "https://github.com/simonw/asgi-csrf")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1j134mjh0ff61rvkm3q67m463j1bhyxc9dwsdany3scnd4vsqqws"))))
(build-system pyproject-build-system)
(arguments
(list #:test-flags
;; Provide a null config to avoid the extraneous dependency on
;; python-pytest-coverage.
#~(list "-c" "/dev/null"
;; Disable two failing tests (see:
;; https://github.com/simonw/asgi-csrf/issues/24).
"-k" (string-append
"not (test_multipart "
"or test_multipart_failure_wrong_token)"))))
(propagated-inputs (list python-itsdangerous python-multipart))
(native-inputs (list python-asgi-lifespan
python-httpx
python-pytest
python-pytest-asyncio
python-starlette))
(home-page "https://github.com/simonw/asgi-csrf")
(synopsis "ASGI middleware for protecting against CSRF attacks")
(description "This Asynchronous Server Gateway Interface (ASGI)
middleware protects against Cross-site request forgery (CSRF) attacks.
It implements the Double Submit Cookie pattern, where a cookie is set
that is then compared to a @code{csrftoken} hidden form field or a
@code{x-csrftoken} HTTP header.")
(license license:asl2.0)))
(define-public python-asgi-lifespan
(package
(name "python-asgi-lifespan")
(version "1.0.1")
(source (origin
(method git-fetch) ;for tests
(uri (git-reference
(url "https://github.com/florimondmanca/asgi-lifespan")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"10a5ci9ddr8wnjf3wai7xifbbplirhyrgvw4p28q0ha63cvhb2j2"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
'(list "-c" "/dev/null" ;ignore coverage-related options
"-k"
(string-append
;; XXX: Some tests fail because of a 'lifespan.shutdown.failed'
;; extra event, perhaps because our version of trio is older.
"not (test_lifespan_manager[asyncio-None-ValueError-None]"
" or test_lifespan_manager[asyncio-ValueError-None-None]"
" or test_lifespan_manager[asyncio-ValueError-ValueError-None]"
" or test_lifespan_manager[trio-None-ValueError-None]"
" or test_lifespan_manager[trio-ValueError-None-None]"
" or test_lifespan_manager[trio-ValueError-ValueError-None])"))))
(native-inputs (list python-pytest
python-pytest-asyncio
python-pytest-trio
python-starlette))
(propagated-inputs (list python-sniffio))
(home-page "https://github.com/florimondmanca/asgi-lifespan")
(synopsis "Programmatic startup/shutdown of ASGI apps")
(description "Programmatically send startup/shutdown lifespan events
into Asynchronous Server Gateway Interface (ASGI) applications. When
used in combination with an ASGI-capable HTTP client such as HTTPX, this
allows mocking or testing ASGI applications without having to spin up an
ASGI server.")
(license license:expat)))
(define-public python-css-html-js-minify
(package
(name "python-css-html-js-minify")

18
gnu/packages/python-xyz.scm
View File

@ -31635,6 +31635,24 @@ GeoJSON to WKT/WKB (Well-Known Text/Binary) or GeoPackage Binary, and vice
versa. Extended WKB/WKT are also supported.")
(license license:asl2.0)))
(define-public python-cogapp
(package
(name "python-cogapp")
(version "3.3.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "cogapp" version))
(sha256
(base32
"1c0xx3p3lzrlyqhmccyq9c50f8v9pqk2992gb4nl50h2yy1m3s8v"))))
(build-system pyproject-build-system)
(native-inputs (list python-pytest))
(home-page "https://nedbatchelder.com/code/cog")
(synopsis "Content generation tool that leverages Python")
(description "Cog is a file generation tool. It allows using pieces of
Python code as generators in your source files to generate arbitrary text.")
(license license:expat)))
(define-public python-bsdiff4
(package
(name "python-bsdiff4")

55
gnu/packages/shellutils.scm
View File

@ -15,6 +15,7 @@
;;; Copyright © 2021 Foo Chuan Wei <chuanwei.foo@hotmail.com>
;;; Copyright © 2021 Wiktor Żelazny <wzelazny@vurv.cz>
;;; Copyright © 2022 Jose G Perez Taveras <josegpt27@gmail.com>
;;; Copyright © 2023 Timo Wilken <guix@twilken.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -221,6 +222,60 @@ in Zsh intelligently.")
as you type.")
(license license:expat)))
(define-public zsh-completions
(package
(name "zsh-completions")
(version "0.34.0")
(home-page "https://github.com/zsh-users/zsh-completions")
(source (origin
(method git-fetch)
(uri (git-reference
(url home-page)
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0jjgvzj3v31yibjmq50s80s3sqi4d91yin45pvn3fpnihcrinam9"))))
(build-system copy-build-system)
(arguments
'(#:install-plan '(("src/" "share/zsh/site-functions/")
("README.md" "share/doc/zsh-completions/"))))
(synopsis "Additional completion definitions for Zsh")
(description
"This projects aims at gathering/developing new completion scripts that
are not available in Zsh yet. The scripts may be contributed to the Zsh
project when stable enough.")
(license (license:non-copyleft "file://LICENSE"
"Custom BSD-like, permissive, non-copyleft license."))))
(define-public zsh-history-substring-search
(package
(name "zsh-history-substring-search")
(version "1.0.2")
(home-page "https://github.com/zsh-users/zsh-history-substring-search")
(source (origin
(method git-fetch)
(uri (git-reference
(url home-page)
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0y8va5kc2ram38hbk2cibkk64ffrabfv1sh4xm7pjspsba9n5p1y"))))
(build-system copy-build-system)
(arguments
'(#:install-plan '(("zsh-history-substring-search.plugin.zsh"
"share/zsh/plugins/zsh-history-substring-search/")
("zsh-history-substring-search.zsh"
"share/zsh/plugins/zsh-history-substring-search/")
("README.md" "share/doc/zsh-history-substring-search/"))))
(synopsis "ZSH port of Fish history search (up arrow)")
(description
"This is a clean-room implementation of the Fish shell's history search
feature, where you can type in any part of any command from history and then
press chosen keys, such as the UP and DOWN arrows, to cycle through matches.")
(license license:bsd-3)))
(define-public zsh-syntax-highlighting
(package
(name "zsh-syntax-highlighting")

64
gnu/packages/statistics.scm
View File

@ -1299,14 +1299,14 @@ agnes cluster diagrams.")
(define-public r-gdtools
(package
(name "r-gdtools")
(version "0.3.2")
(version "0.3.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "gdtools" version))
(sha256
(base32
"0dji1iyf6x9vg6gjklzkb3x9vfydfi95idkvckj6208b1rwgwsj4"))))
"10rlx1ciyvh0ayic03kckv360idl9s1zyc2ar5lisns786c1hnns"))))
(build-system r-build-system)
(native-inputs
(list pkg-config))
@ -1317,7 +1317,6 @@ agnes cluster diagrams.")
r-fontquiver
r-gfonts
r-htmltools
r-memoise
r-rcpp
r-systemfonts))
(home-page "https://cran.r-project.org/web/packages/gdtools")
@ -1816,13 +1815,13 @@ and printing capabilities than traditional data frames.")
(define-public r-dplyr
(package
(name "r-dplyr")
(version "1.1.0")
(version "1.1.1")
(source (origin
(method url-fetch)
(uri (cran-uri "dplyr" version))
(sha256
(base32
"1msfp29lbddwdv8ibc2nkan0g1g4y4w5fws6802v6h6x95g57c4c"))))
"1xxvspk1nyns39dp2fqvxbvvnkkz4rcgmhrcrznr3h1qpayj9p6z"))))
(build-system r-build-system)
(propagated-inputs
(list r-cli
@ -1853,14 +1852,14 @@ database.")
(define-public r-dbplyr
(package
(name "r-dbplyr")
(version "2.3.1")
(version "2.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "dbplyr" version))
(sha256
(base32
"0a5cnh0fr81mak9ccqr91nsjqlxsnf6a2lmwrsgv7g1sjag0b4p1"))))
"1b3zf2ai4kp96wd6i4jg9b3n37bwbw7lfvxvs1i1kcn6brch1p0d"))))
(build-system r-build-system)
(propagated-inputs
(list r-blob
@ -2649,17 +2648,17 @@ were originally a part of the r-devtools package.")
(define-public r-hms
(package
(name "r-hms")
(version "1.1.2")
(version "1.1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "hms" version))
(sha256
(base32
"1vdx08irnh8q5232hriv47hh88hc55nbbrff7y6zbainff2akrhy"))))
"10h2k5j97fggq3hc0qzxv1q9821y21m326v3x99zsvpl1b3g89p6"))))
(build-system r-build-system)
(propagated-inputs
(list r-ellipsis r-lifecycle r-pkgconfig r-rlang r-vctrs))
(list r-lifecycle r-pkgconfig r-rlang r-vctrs))
(home-page "https://github.com/rstats-db/hms")
(synopsis "Pretty time of day")
(description
@ -2857,18 +2856,19 @@ certain criterion, e.g., it contains a certain regular file.")
(define-public r-rmarkdown
(package
(name "r-rmarkdown")
(version "2.20")
(version "2.21")
(source
(origin
(method url-fetch)
(uri (cran-uri "rmarkdown" version))
(sha256
(base32 "178mc3dqm11y58k8jdhm1yi11bbl1h7bls9d8f94ngmlzjdhbxyp"))))
(base32 "0a5czn18clfnw0a9nd5v98ah4h47i32423s6jdf126ni4aj20ny2"))))
(properties `((upstream-name . "rmarkdown")))
(build-system r-build-system)
(propagated-inputs
(list r-bslib
r-evaluate
r-fontawesome
r-htmltools
r-jquerylib
r-jsonlite
@ -2890,13 +2890,13 @@ variety of formats.")
(define-public r-gtable
(package
(name "r-gtable")
(version "0.3.2")
(version "0.3.3")
(source (origin
(method url-fetch)
(uri (cran-uri "gtable" version))
(sha256
(base32
"1j162vkyvkyyz61smw36crgmd76jic17n9qfmn0cyvafzdyqyiwd"))))
"0fkv19h64cyxsadplvyzbpjliy9wlfg56hc8znvqg972g3cmi6ig"))))
(properties `((upstream-name . "gtable")))
(build-system r-build-system)
(propagated-inputs
@ -3009,13 +3009,13 @@ engine (version 3.8.8.2) is included.")
(define-public r-rcurl
(package
(name "r-rcurl")
(version "1.98-1.10")
(version "1.98-1.12")
(source (origin
(method url-fetch)
(uri (cran-uri "RCurl" version))
(sha256
(base32
"1m7i0q9scrh2bfr0nqs029052kznhlv3siz9055pzdvgig7jnqjs"))))
"1ci6lsxm0f13yzw712gcbq23syl54x5llvhs2w1b8wwm9vqgx0qs"))))
(properties `((upstream-name . "RCurl")))
(build-system r-build-system)
(arguments
@ -3032,7 +3032,7 @@ if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
(native-inputs
(list libxml2))
(inputs
(list curl zlib))
(list curl))
(propagated-inputs
(list r-bitops))
(home-page "https://www.omegahat.net/RCurl")
@ -3172,14 +3172,14 @@ statements.")
(define-public r-segmented
(package
(name "r-segmented")
(version "1.6-2")
(version "1.6-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "segmented" version))
(sha256
(base32
"0livckkhci3w1x9xai2m0a30fj06qsks2qds7y5jr9vwx03jqg21"))))
"0x7k5ycbvnfqsygrcyaaxnl0060x6869b345xc697hhr9sfxb4ai"))))
(build-system r-build-system)
(propagated-inputs (list r-mass r-nlme))
(home-page "https://cran.r-project.org/web/packages/segmented")
@ -3801,13 +3801,13 @@ analysis of large sparse or dense matrices.")
(define-public r-glmnet
(package
(name "r-glmnet")
(version "4.1-6")
(version "4.1-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "glmnet" version))
(sha256
(base32 "0c3y9g3k0f0yclcffxzgfhfylb3py0iydhyspcjdrl44lb7cdi5y"))))
(base32 "1a7af2658z9fmx0rcdx401lj86q73qkvsvlfnrp2bw4xv43bd85k"))))
(build-system r-build-system)
(native-inputs
(list gfortran r-knitr))
@ -4307,14 +4307,14 @@ and tidyr provides no margins or aggregation.")
(define-public r-hexbin
(package
(name "r-hexbin")
(version "1.28.2")
(version "1.28.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "hexbin" version))
(sha256
(base32
"0bbhs5pwxh474w62sq6gqvih7habancxng9wd4f2rgn6lv9zhhb2"))))
"0pyy97bh9xf9hijg3iw1z4ri01571r1fx7xqm3fjkzx4q48kbcqf"))))
(build-system r-build-system)
(propagated-inputs
(list r-lattice))
@ -5392,14 +5392,14 @@ can be efficiently implemented directly in the R language.")
(define-public r-robustbase
(package
(name "r-robustbase")
(version "0.95-0")
(version "0.95-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "robustbase" version))
(sha256
(base32
"094pxwp78bmqyn6vncyzrazqxnn8abqsbzhlcq44avfz8qffmyjw"))))
"1sm37gqs35cvkacigsla8kzvpzjzsrgkabf58ymk9pzcndnx4b46"))))
(build-system r-build-system)
(native-inputs
(list gfortran))
@ -5840,13 +5840,13 @@ Companion to Applied Regression, Third Edition, Sage.")
(define-public r-car
(package
(name "r-car")
(version "3.1-1")
(version "3.1-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "car" version))
(sha256
(base32 "1g6jdcxl2aig6zirdn3k5l48sjmpljzy1aadnlr6mr6pxqamiicg"))))
(base32 "1j3l8r3j05769gdfrqz0n38xviq6pww1cjrgdd0fkj3sjy8k89l9"))))
(build-system r-build-system)
(propagated-inputs
(list r-abind
@ -5988,14 +5988,14 @@ multivariate case.")
(define-public r-tclust
(package
(name "r-tclust")
(version "1.5-2")
(version "1.5-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "tclust" version))
(sha256
(base32
"12vg9q35srddjidrn3q955xybn6ldraya35s4955ypj61arp89j9"))))
"1a3i6kvfzc2d6rdf75w03n5172jihhqa8mvzcb4m8l0w6mgdlm9b"))))
(build-system r-build-system)
;; These are all suggested packages, not build dependencies.
(propagated-inputs
@ -7356,16 +7356,16 @@ Neyman, 1936; cf. Spiller et al., 2012), etc.")
(define-public r-mumin
(package
(name "r-mumin")
(version "1.47.1")
(version "1.47.5")
(source (origin
(method url-fetch)
(uri (cran-uri "MuMIn" version))
(sha256
(base32
"1xhsc9hmx2b3zqyvpjs64rs90ccrfcsglrq2mhh85mgplsnva8qj"))))
"0xqasb79lmdhff25zalzrpjwv6qs9qnxr54ypnqjjgshi96mbwvg"))))
(properties `((upstream-name . "MuMIn")))
(build-system r-build-system)
(propagated-inputs (list r-matrix r-nlme))
(propagated-inputs (list r-insight r-matrix r-nlme))
(home-page "https://cran.r-project.org/package=MuMIn")
(synopsis "Multi-Model Inference")
(description

253
gnu/packages/tex.scm
View File

@ -6,7 +6,7 @@
;;; Copyright © 2016, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2016 Thomas Danckaert <post@thomasdanckaert.be>
;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016-2023 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
;;; Copyright © 2017, 2020, 2021 Marius Bakke <marius@gnu.org>
;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
@ -24,6 +24,7 @@
;;; Copyright © 2022 Fabio Natali <me@fabionatali.com>
;;; Copyright © 2022 Philip McGrath <philip@philipmcgrath.com>
;;; Copyright © 2023 Thomas Albers Raviola <thomas@thomaslabs.org>
;;; Copyright © 2023 John Kehayias <john.kehayias@protonmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -740,6 +741,37 @@ the autogenerated files @file{language.dat} and @file{language.def} (and
default versions of those), etc.")
(license license:knuth)))
(define-public texlive-dvipdfmx
(let ((template (simple-texlive-package
"texlive-dvipdfmx"
(list "doc/dvipdfm/"
"doc/dvipdfmx/"
"doc/man/man1/"
"dvipdfmx/"
"fonts/cmap/dvipdfmx/"
"fonts/map/dvipdfmx/")
(base32
"04x93w777l9qzdzglwanb14k8cmq74kjcsgyanvp3bsmnn5zfrgz")
#:trivial? #t)))
(package
(inherit template)
(source
(origin
(inherit (package-source template))
;; This map file is supposed to be generated in a profile hook.
(snippet '(delete-file "fonts/map/dvipdfmx/updmap/kanjix.map"))))
(propagated-inputs (list texlive-glyphlist))
(home-page "https://www.tug.org/texlive/")
(synopsis "Extended version of dvipdfm")
(description
"Dvipdfmx (formerly dvipdfm-cjk) is a development of dvipdfm created to
support multi-byte character encodings and large character sets for East Asian
languages. Dvipdfmx, if \"called\" with the name dvipdfm, operates in a
\"dvipdfm compatibility\" mode, so that users of the both packages need only
keep one executable. A secondary design goal is to support as many \"PDF\"
features as does pdfTeX.")
(license license:gpl3+))))
(define-public texlive-dvips
(package
(inherit (simple-texlive-package
@ -1623,6 +1655,60 @@ described in the TeXbook, together with various supporting files (some also
discussed in the book).")
(license license:knuth)))
(define-public texlive-halloweenmath
(let ((template (simple-texlive-package
"texlive-halloweenmath"
(list "doc/latex/halloweenmath/"
"source/latex/halloweenmath/"
"tex/latex/halloweenmath/")
(base32
"1xq72k1p820b5q3haxf936g69p6gv34hr30870l96jnxa3ad7y05"))))
(package
(inherit template)
(outputs '("out" "doc"))
(arguments
(substitute-keyword-arguments (package-arguments template)
((#:tex-directory _ #t) "latex/halloweenmath")
((#:build-targets _ '()) '(list "halloweenmath.ins"))
((#:phases phases)
#~(modify-phases #$phases
(add-after 'unpack 'chdir
(lambda _ (chdir "source/latex/halloweenmath/")))
(add-after 'chdir 'non-interactive-build
;; When it realizes it cannot employ the usedir directive, the
;; build process stops and waits for an input before inserting
;; generated files in the working directory. Do not ask for
;; an input.
(lambda _
(substitute* "halloweenmath.ins"
(("\\Ask.*") "")
(("\\(your .*? will be ignored\\).*") ""))))
(replace 'copy-files
(lambda* (#:key inputs #:allow-other-keys)
(let ((origin (assoc-ref inputs "source"))
(source (string-append #$output
"/share/texmf-dist/source"))
(doc (string-append #$output:doc
"/share/texmf-dist/doc")))
(copy-recursively (string-append origin "/source") source)
(copy-recursively (string-append origin "/doc") doc))))))))
(native-inputs
(list texlive-bin
texlive-kpathsea
(texlive-updmap.cfg))) ;for psfonts.map
(propagated-inputs
(list texlive-amsmath texlive-pict2e))
(home-page "https://ctan.org/pkg/halloweenmath")
(synopsis "Scary and creepy math symbols with AMS-LaTeX integration")
(description
"The package defines a handful of commands for typesetting mathematical
symbols of various kinds, ranging from large operators to extensible
arrow-like relations and growing arrow-like math accents that all draw from
the classic Halloween-related iconography (pumpkins, witches, ghosts, cats,
and so on) while being, at the same time, seamlessly integrated within the
rest of the mathematics produced by (AmS-)LaTeX.")
(license license:lppl1.3+))))
(define-public texlive-hardwrap
(package
(inherit (simple-texlive-package
@ -3212,6 +3298,22 @@ verbatim mode; build \"example\" environments (showing both result and
verbatim source).")
(license license:lppl1.0+)))
(define-public texlive-glyphlist
(package
(inherit (simple-texlive-package
"texlive-glyphlist"
(list "fonts/map/glyphlist/")
(base32
"12nmmyh77vr2622lzi11nm1z1k2bxs7jz018yl4rwjlpg0sxg1ja")
#:trivial? #t))
(home-page "https://www.tug.org/texlive/")
(synopsis "Adobe glyph list and TeX extensions")
(description
"This package provides a map between traditional Adobe glyph names and
Unicode points; it is maintained by Adobe. The additional
@file{texglyphlist.txt} is maintained as part of lcdf-typetools.")
(license license:asl2.0)))
(define-public texlive-graphics-def
(package
(inherit (simple-texlive-package
@ -4391,6 +4493,55 @@ T2* and X2 encodings. These encodings cover (between them) pretty much every
language that is written in a Cyrillic alphabet.")
(license license:lppl1.3c+)))
(define-public texlive-pict2e
(let ((template (simple-texlive-package
"texlive-pict2e"
(list "doc/latex/pict2e/"
"source/latex/pict2e/"
"tex/latex/pict2e/")
(base32
"0pazv1khsgjhxc673qrhjrbzlkgmcj53qccb9hw7ygdajxrjc2ba"))))
(package
(inherit template)
(arguments
(substitute-keyword-arguments (package-arguments template)
((#:tex-directory _ #t) "latex/pict2e")
((#:build-targets _ '()) '(list "pict2e.ins"))
((#:phases phases)
#~(modify-phases #$phases
(add-after 'unpack 'chdir
(lambda _ (chdir "source/latex/pict2e/")))
(add-after 'build 'build-doc
(lambda _
(copy-file "p2e-drivers.dtx" "build/p2e-drivers.dtx")
(with-directory-excursion "build"
(invoke "pdflatex" "p2e-drivers.dtx")
(delete-file "p2e-drivers.dtx")
;; texlive.tlpbd expects a "pict2e.cfg" configuration file
;; instead of "pict2e-example.cfg". Please it.
(rename-file "pict2e-example.cfg" "pict2e.cfg"))))
(replace 'copy-files
(lambda* (#:key inputs #:allow-other-keys)
(let ((origin (assoc-ref inputs "source"))
(source (string-append #$output
"/share/texmf-dist/source"))
(doc (string-append #$output:doc
"/share/texmf-dist/doc")))
(copy-recursively (string-append origin "/source") source)
(copy-recursively (string-append origin "/doc") doc))))))))
(home-page "https://ctan.org/pkg/pict2e")
(native-inputs
(list (texlive-updmap.cfg)))
(synopsis "New implementation of picture commands")
(description
"This package extends the existing LaTeX @code{picture} environment,
using the familiar technique (the @code{graphics} and @code{color} packages)
of driver files (at present, drivers for dvips, pdfTeX, LuaTeX, XeTeX, VTeX,
dvipdfm, and dvipdfmx are available). The package documentation has a fair
number of examples of use, showing where things are improved by comparison
with the LaTeX @code{picture} environment.")
(license license:lppl1.3+))))
(define-public texlive-psnfss
(let ((template (simple-texlive-package
"texlive-psnfss"
@ -5016,6 +5167,44 @@ corresponding italics: light, regular, medium, bold, ...")
(license (list license:lppl
license:silofl1.1))))
(define-public texlive-firstaid
(let ((template (simple-texlive-package
"texlive-firstaid"
(list "/doc/latex/firstaid/"
"/source/latex/firstaid/"
"/tex/latex/firstaid/")
(base32
"1ahn47kz8a2qdmzdfdgjanf6h5bn8f2rzp1zvwgjpk1plcix8k90"))))
(package
(inherit template)
(arguments
(substitute-keyword-arguments (package-arguments template)
((#:tex-directory _ #t) "tex/latex/firstaid")
((#:build-targets _ '()) '(list "firstaid.ins"))
((#:phases phases)
#~(modify-phases #$phases
(add-after 'unpack 'chdir
(lambda _ (chdir "source/latex/firstaid/")))
(replace 'copy-files
(lambda* (#:key inputs #:allow-other-keys)
(let ((origin (assoc-ref inputs "source"))
(source (string-append #$output
"/share/texmf-dist/source"))
(doc (string-append #$output:doc
"/share/texmf-dist/doc")))
(copy-recursively (string-append origin "/source") source)
(copy-recursively (string-append origin "/doc") doc))))))))
(home-page "https://ctan.org/macros/latex/required/firstaid")
(synopsis
"First aid for external LaTeX files and packages that need updating")
(description
"This package contains some first aid for LaTeX packages or classes
that require updates because of internal changes to the LaTeX kernel that are
not yet reflected in the package's or class's code. The file
@file{latex2e-first-aid-for-external-files.ltx} provided by this package is
meant to be loaded during format generation and not by the user.")
(license license:lppl1.3c))))
(define-public texlive-latex-ifplatform
(package
(name "texlive-latex-ifplatform")
@ -11269,6 +11458,24 @@ family and SGML-based languages. Xindy is highly configurable, both in markup
terms and in terms of the collating order of the text being processed.")
(license license:gpl2+)))
(define-public texlive-nth
(package
(inherit (simple-texlive-package
"texlive-nth"
(list "tex/generic/nth/")
(base32
"0716sd99xjdkplm7jdmg4lx8lpfnnx6mxjp1l1sp2bfqcg73p4hm")
#:trivial? #t))
(home-page "https://ctan.org/macros/generic/misc/nth.sty")
(synopsis "Generate English ordinal numbers")
(description
"The command @code{\\nth{<number>}} generates English ordinal numbers of
the form 1st, 2nd, 3rd, 4th, etc. LaTeX package options may specify that the
ordinal mark be superscripted, and that negative numbers may be treated; Plain
TeX users have no access to package options, so need to redefine macros for
these changes.")
(license license:public-domain)))
(define-public texlive-fmtcount
(package
(inherit (simple-texlive-package
@ -12307,6 +12514,50 @@ interest. Since most such counters are simply incremented when they are
changed, the recorded value will usually be the maximum value.")
(license license:lppl1.3c+)))
(define-public texlive-xetex
(package
(inherit (simple-texlive-package
"texlive-xetex"
(list "/doc/man/man1/xetex.1"
"/doc/man/man1/xelatex.1"
"/doc/xetex/base/"
"/fonts/misc/xetex/fontmapping/base/"
"/tex/xelatex/xetexconfig/")
(base32
"1gmgagvsv2qknrjzjk840ca3wging8wfc20rgq7bnhphm9n87m6q")
#:trivial? #t))
(propagated-inputs
(list texlive-generic-atbegshi
texlive-latex-atveryend
texlive-babel
texlive-cm
texlive-dvipdfmx
texlive-etex
texlive-everyshi
texlive-firstaid
texlive-hyphen-base
texlive-latex-base
texlive-fonts-latex
texlive-latex-l3backend
texlive-latex-l3kernel
texlive-latex-l3packages
texlive-lm
texlive-tex-ini-files
texlive-tex-plain
texlive-unicode-data))
(home-page "https://www.tug.org/texlive/")
(synopsis "Extended variant of TeX for use with Unicode sources")
(description
"XeTeX is a TeX typesetting engine using Unicode and supporting modern font
technologies such as OpenType, TrueType or Apple Advanced Typography (AAT),
including OpenType mathematics fonts. XeTeX supports many extensions that
reflect its origins in linguistic research; it also supports micro-typography
(as available in pdfTeX). XeTeX was developed by the SIL (the first version
was specifically developed for those studying linguistics, and using Macintosh
computers). XeTeX's immediate output is an extended variant of DVI format,
which is ordinarily processed by a tightly bound processor (called
@code{xdvipdfmx}), that produces PDF.")
(license license:x11)))
;;;
;;; Avoid adding new packages to the end of this file. To reduce the chances
;;; of a merge conflict, place them above by existing packages with similar

7
gnu/packages/tree-sitter.scm
View File

@ -301,6 +301,13 @@ will be used in description and synopsis."
#:commit commit
#:license (list license:asl2.0 license:expat))))
(define-public tree-sitter-heex
(tree-sitter-grammar
"heex" "Heex"
"00330rgg67fq0d9gk1yswj78d9mn1jvvjmmy1k7cxpvm5993p3sw"
"0.6.0"
#:repository-url "https://github.com/phoenixframework/tree-sitter-heex"))
(define-public tree-sitter-bash
(tree-sitter-grammar
"bash" "Bash"

22
gnu/packages/wm.scm
View File

@ -1061,6 +1061,28 @@ experience.")
(home-page "http://fluxbox.org/")
(license license:expat)))
(define-public fbautostart
(package
(name "fbautostart")
(version "2.718281828")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/paultag/fbautostart.git")
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"13h6j5khi5axqhflzhayzgvyhxylmk5vsgin235ji440mzd516gz"))))
(build-system gnu-build-system)
(native-inputs
(list autoconf automake))
(synopsis "XDG autostarter for Fluxbox window manager")
(description "This package provides an autostarter complaint with
the XDG Autostart specification.")
(home-page "https://github.com/paultag/fbautostart")
(license license:expat)))
(define-public fnott
(package
(name "fnott")

42
gnu/services/base.scm
View File

@ -40,7 +40,7 @@
(define-module (gnu services base)
#:use-module (guix store)
#:use-module (guix deprecation)
#:autoload (guix diagnostics) (warning &fix-hint)
#:autoload (guix diagnostics) (warning formatted-message &fix-hint)
#:autoload (guix i18n) (G_)
#:use-module (guix combinators)
#:use-module (gnu services)
@ -246,7 +246,7 @@
kmscon-service-type
pam-limits-service-type
pam-limits-service
pam-limits-service ; deprecated
greetd-service-type
greetd-configuration
@ -1588,17 +1588,13 @@ information on the configuration file syntax."
(define pam-limits-service-type
(let ((security-limits
;; Create /etc/security containing the provided "limits.conf" file.
(lambda (limits-file)
`(("security/limits.conf"
,limits-file))))
(pam-extension
(let ((pam-extension
(lambda (pam)
(let ((pam-limits (pam-entry
(control "required")
(module "pam_limits.so")
(arguments '("conf=/etc/security/limits.conf")))))
(arguments
'("conf=/etc/security/limits.conf")))))
(if (member (pam-service-name pam)
'("login" "greetd" "su" "slim" "gdm-password" "sddm"
"sudo" "sshd"))
@ -1606,7 +1602,27 @@ information on the configuration file syntax."
(inherit pam)
(session (cons pam-limits
(pam-service-session pam))))
pam)))))
pam))))
;; XXX: Using file-like objects is deprecated, use lists instead.
;; This is to be reduced into the list? case when the deprecated
;; code gets removed.
;; Create /etc/security containing the provided "limits.conf" file.
(security-limits
(match-lambda
((? file-like? obj)
(warning (G_ "Using file-like value for \
'pam-limits-service-type' is deprecated~%"))
`(("security/limits.conf" ,obj)))
((? list? lst)
`(("security/limits.conf"
,(plain-file "limits.conf"
(string-join (map pam-limits-entry->string lst)
"\n" 'suffix)))))
(_ (raise
(formatted-message
(G_ "invalid input for 'pam-limits-service-type'~%")))))))
(service-type
(name 'limits)
(extensions
@ -1616,9 +1632,11 @@ information on the configuration file syntax."
(description
"Install the specified resource usage limits by populating
@file{/etc/security/limits.conf} and using the @code{pam_limits}
authentication module."))))
authentication module.")
(default-value '()))))
(define* (pam-limits-service #:optional (limits '()))
(define-deprecated (pam-limits-service #:optional (limits '()))
pam-limits-service-type
"Return a service that makes selected programs respect the list of
pam-limits-entry specified in LIMITS via pam_limits.so."
(service pam-limits-service-type

1
gnu/services/configuration.scm
View File

@ -264,7 +264,6 @@ does not have a default value" field kind)))
(serializer field-serializer)
(default-value-thunk
(lambda ()
(display '#,(id #'stem #'% #'stem))
(if (maybe-value-set? (syntax->datum field-default))
field-default
(configuration-missing-default-value

10
gnu/system.scm
View File

@ -1201,15 +1201,7 @@ use 'plain-file' instead~%")
;; By default, applications that use D-Bus, such as Emacs, abort at startup
;; when /etc/machine-id is missing. Make sure these warnings are non-fatal.
("DBUS_FATAL_WARNINGS" . "0")
;; XXX: Normally we wouldn't need to do this, but our glibc@2.23 package
;; used to look things up in 'PREFIX/lib/locale' instead of
;; '/run/current-system/locale' as was intended. Keep this hack around so
;; that people who still have glibc@2.23-using packages in their profiles
;; can use them correctly.
;; TODO: Remove when glibc@2.23 is long gone.
("GUIX_LOCPATH" . "/run/current-system/locale")))
("DBUS_FATAL_WARNINGS" . "0")))
;; Ensure LST is a list of <setuid-program> records and warn otherwise.
(define-with-syntax-properties (ensure-setuid-program-list (lst properties))

97
gnu/tests/pam.scm 100644
View File

@ -0,0 +1,97 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2023 Bruno Victal <mirai@makinata.eu>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu tests pam)
#:use-module (gnu tests)
#:use-module (gnu services)
#:use-module (gnu services base)
#:use-module (gnu system)
#:use-module (gnu system pam)
#:use-module (gnu system vm)
#:use-module (guix gexp)
#:use-module (ice-9 format)
#:export (%test-pam-limits
%test-pam-limits-deprecated))
;;;
;;; pam-limits-service-type
;;;
(define pam-limit-entries
(list
(pam-limits-entry "@realtime" 'both 'rtprio 99)
(pam-limits-entry "@realtime" 'both 'memlock 'unlimited)))
(define (run-test-pam-limits config)
"Run tests in a os with pam-limits-service-type configured."
(define os
(marionette-operating-system
(simple-operating-system
(service pam-limits-service-type config))))
(define vm
(virtual-machine os))
(define name (format #f "pam-limit-service~:[~;-deprecated~]"
(file-like? config)))
(define test
(with-imported-modules '((gnu build marionette))
#~(begin
(use-modules (gnu build marionette)
(srfi srfi-64))
(let ((marionette (make-marionette (list #$vm))))
(test-runner-current (system-test-runner #$output))
(test-begin #$name)
(test-assert "/etc/security/limits.conf ready"
(wait-for-file "/etc/security/limits.conf" marionette))
(test-equal "/etc/security/limits.conf content matches"
#$(string-join (map pam-limits-entry->string pam-limit-entries)
"\n" 'suffix)
(marionette-eval
'(call-with-input-file "/etc/security/limits.conf"
get-string-all)
marionette))
(test-end)))))
(gexp->derivation (string-append name "-test") test))
(define %test-pam-limits
(system-test
(name "pam-limits-service")
(description "Test that pam-limits-service can serialize its config
(as a list) to @file{limits.conf}.")
(value (run-test-pam-limits pam-limit-entries))))
(define %test-pam-limits-deprecated
(system-test
(name "pam-limits-service-deprecated")
(description "Test that pam-limits-service can serialize its config
(as a file-like object) to @file{limits.conf}.")
(value (run-test-pam-limits
(plain-file "limits.conf"
(string-join (map pam-limits-entry->string
pam-limit-entries)
"\n" 'suffix))))))

55
guix/import/texlive.scm
View File

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017, 2021, 2022, 2023 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;;
;;; This file is part of GNU Guix.
@ -246,11 +246,15 @@ of those files are returned that are unexpectedly installed."
(define (tlpdb->package name version package-database)
(and-let* ((data (assoc-ref package-database name))
(dirs (files->directories
(map (lambda (dir)
(string-drop dir (string-length "texmf-dist/")))
(append (or (assoc-ref data 'docfiles) (list))
(or (assoc-ref data 'runfiles) (list))
(or (assoc-ref data 'srcfiles) (list))))))
(filter-map (lambda (dir)
;; Ignore any file not starting with the
;; expected prefix. Nothing good can come
;; from this.
(and (string-prefix? "texmf-dist/" dir)
(string-drop dir (string-length "texmf-dist/"))))
(append (or (assoc-ref data 'docfiles) (list))
(or (assoc-ref data 'runfiles) (list))
(or (assoc-ref data 'srcfiles) (list))))))
(name (guix-name name))
;; TODO: we're ignoring the VERSION argument because that
;; information is distributed across %texlive-tag and
@ -260,6 +264,12 @@ of those files are returned that are unexpectedly installed."
%texlive-tag "/Master/texmf-dist"))
(locations dirs)
(revision %texlive-revision)))
;; Ignore arch-dependent packages.
(filtered-depends
(or (and=> (assoc-ref data 'depend)
(lambda (inputs)
(remove (cut string-suffix? ".ARCH" <>) inputs)))
'()))
(source (with-store store
(download-multi-svn-to-store
store ref (string-append name "-svn-multi-checkout")))))
@ -278,24 +288,25 @@ of those files are returned that are unexpectedly installed."
;; package->definition in (guix import utils) expects to see a
;; version field.
(version ,version)
,@(or (and=> (assoc-ref data 'depend)
(lambda (inputs)
`((propagated-inputs
(list ,@(map (lambda (tex-name)
(let ((name (guix-name tex-name)))
(string->symbol name)))
inputs))))))
'())
,@(or (and=> (assoc-ref data 'catalogue-ctan)
(lambda (url)
`((home-page ,(string-append "https://ctan.org" url)))))
,@(match filtered-depends
(() '())
(inputs
`((propagated-inputs
(list ,@(map
(lambda (tex-name)
(let ((name (guix-name tex-name)))
(string->symbol name)))
inputs))))))
,@(or (and=> (assoc-ref data 'name)
(lambda (name)
`((home-page ,(string-append "https://ctan.org/pkg/"
name)))))
'((home-page "https://www.tug.org/texlive/")))
(synopsis ,(assoc-ref data 'shortdesc))
(description ,(beautify-description
(assoc-ref data 'longdesc)))
(license ,(string->license
(assoc-ref data 'catalogue-license))))
(or (assoc-ref data 'depend) (list)))))
(description ,(and=> (assoc-ref data 'longdesc) beautify-description))
(license ,(and=> (assoc-ref data 'catalogue-license)
string->license)))
filtered-depends)))
(define texlive->guix-package
(memoize