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-rw-r--r--doc/guix.texi28
-rw-r--r--etc/release-manifest.scm5
-rw-r--r--etc/teams.scm.in5
-rw-r--r--gnu/local.mk1
-rw-r--r--gnu/packages/audio.scm56
-rw-r--r--gnu/packages/benchmark.scm2
-rw-r--r--gnu/packages/bioconductor.scm527
-rw-r--r--gnu/packages/bioinformatics.scm133
-rw-r--r--gnu/packages/check.scm7
-rw-r--r--gnu/packages/cran.scm446
-rw-r--r--gnu/packages/databases.scm155
-rw-r--r--gnu/packages/emacs-xyz.scm352
-rw-r--r--gnu/packages/emulators.scm40
-rw-r--r--gnu/packages/engineering.scm44
-rw-r--r--gnu/packages/games.scm12
-rw-r--r--gnu/packages/gnome.scm4
-rw-r--r--gnu/packages/gnuzilla.scm8
-rw-r--r--gnu/packages/hardware.scm21
-rw-r--r--gnu/packages/image-viewers.scm2
-rw-r--r--gnu/packages/linux.scm12
-rw-r--r--gnu/packages/lisp-xyz.scm281
-rw-r--r--gnu/packages/maths.scm203
-rw-r--r--gnu/packages/package-management.scm234
-rw-r--r--gnu/packages/python-crypto.scm17
-rw-r--r--gnu/packages/python-web.scm83
-rw-r--r--gnu/packages/python-xyz.scm18
-rw-r--r--gnu/packages/shellutils.scm55
-rw-r--r--gnu/packages/statistics.scm64
-rw-r--r--gnu/packages/tex.scm253
-rw-r--r--gnu/packages/tree-sitter.scm7
-rw-r--r--gnu/packages/wm.scm22
-rw-r--r--gnu/services/base.scm42
-rw-r--r--gnu/services/configuration.scm1
-rw-r--r--gnu/system.scm10
-rw-r--r--gnu/tests/pam.scm97
-rw-r--r--guix/import/texlive.scm55
36 files changed, 2849 insertions, 453 deletions
diff --git a/doc/guix.texi b/doc/guix.texi
index c49e51b72e..a58ea8f9ec 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -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
diff --git a/etc/release-manifest.scm b/etc/release-manifest.scm
index 83983c0738..773910ac80 100644
--- a/etc/release-manifest.scm
+++ b/etc/release-manifest.scm
@@ -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
diff --git a/etc/teams.scm.in b/etc/teams.scm.in
index 4c95c48543..a8957b4ea0 100644
--- a/etc/teams.scm.in
+++ b/etc/teams.scm.in
@@ -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")
diff --git a/gnu/local.mk b/gnu/local.mk
index 65662f8667..724cd3216a 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -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 \
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 4f4e7bc947..50ff678095 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -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")
diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm
index 52970f58fe..0cc8def918 100644
--- a/gnu/packages/benchmark.scm
+++ b/gnu/packages/benchmark.scm
@@ -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
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fe446df67a..2e529d4770 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -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
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fda01e00ca..f7adca0860 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -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
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index cfa604127b..631aac7db7 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -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
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index e88d893517..f2bdd750ca 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -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
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 3b8fefc122..d8c8499fdd 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -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)))
diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index da2856abc8..de4a7f301a 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -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
diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm
index 166c3b4ec6..7e73b217ea 100644
--- a/gnu/packages/emulators.scm
+++ b/gnu/packages/emulators.scm
@@ -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))))
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 65b0c0eab4..18f2d024b1 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -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")
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 5825b8d936..23b6c39c46 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -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
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 0efb98b97c..8c38b94a21 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -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
diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index 475c2b5a38..3e153ec55c 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -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
diff --git a/gnu/packages/hardware.scm b/gnu/packages/hardware.scm
index c00a6e2d91..299d7b96a1 100644
--- a/gnu/packages/hardware.scm
+++ b/gnu/packages/hardware.scm
@@ -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
diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm
index f7719600a7..d8d6304a85 100644
--- a/gnu/packages/image-viewers.scm
+++ b/gnu/packages/image-viewers.scm
@@ -254,7 +254,7 @@ actions.")
libarchive
libchamplain
libheif
- libjpeg
+ libjpeg-turbo
libpng
libraw
libtiff
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 2bd4650e52..69ed7bc710 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -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)))
diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index e0025b784c..ff6eebed25 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -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"))
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index a304d4befa..286532fa70 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -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
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 537d01e164..29cb481862 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -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
diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index c9071c4cf6..c3e36ff2e4 100644
--- a/gnu/packages/python-crypto.scm
+++ b/gnu/packages/python-crypto.scm
@@ -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
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index d186653544..d84b5efdf9 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -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")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index bf29f4d4b0..85105ce00a 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -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")
diff --git a/gnu/packages/shellutils.scm b/gnu/packages/shellutils.scm
index 277d2d2647..20d246be52 100644
--- a/gnu/packages/shellutils.scm
+++ b/gnu/packages/shellutils.scm
@@ -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")
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index a5ea61b5de..93459f8051 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -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
diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 40accf642d..b40e72c582 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -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
diff --git a/gnu/packages/tree-sitter.scm b/gnu/packages/tree-sitter.scm
index 8dda7737ca..b91345bb36 100644
--- a/gnu/packages/tree-sitter.scm
+++ b/gnu/packages/tree-sitter.scm
@@ -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"
diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index bcc68fbad2..4e52554b87 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -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")
diff --git a/gnu/services/base.scm b/gnu/services/base.scm
index 5b0b3bb0ab..e063828d3b 100644
--- a/gnu/services/base.scm
+++ b/gnu/services/base.scm
@@ -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
diff --git a/gnu/services/configuration.scm b/gnu/services/configuration.scm
index 174c2f20d2..ed9d95f906 100644
--- a/gnu/services/configuration.scm
+++ b/gnu/services/configuration.scm
@@ -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
diff --git a/gnu/system.scm b/gnu/system.scm
index 48cc68f449..c17c6e4e98 100644
--- a/gnu/system.scm
+++ b/gnu/system.scm
@@ -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))
diff --git a/gnu/tests/pam.scm b/gnu/tests/pam.scm
new file mode 100644
index 0000000000..5cf13d97d7
--- /dev/null
+++ b/gnu/tests/pam.scm
@@ -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))))))
diff --git a/guix/import/texlive.scm b/guix/import/texlive.scm
index 82014ee568..086cd363a9 100644
--- a/guix/import/texlive.scm
+++ b/guix/import/texlive.scm
@@ -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