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-rw-r--r--gnu/local.mk1
-rw-r--r--gnu/packages/astronomy.scm29
-rw-r--r--gnu/packages/bioconductor.scm30
-rw-r--r--gnu/packages/bioinformatics.scm57
-rw-r--r--gnu/packages/certs.scm4
-rw-r--r--gnu/packages/cran.scm99
-rw-r--r--gnu/packages/datastructures.scm4
-rw-r--r--gnu/packages/emacs-xyz.scm67
-rw-r--r--gnu/packages/games.scm4
-rw-r--r--gnu/packages/gcc.scm49
-rw-r--r--gnu/packages/geo.scm127
-rw-r--r--gnu/packages/gimp.scm6
-rw-r--r--gnu/packages/gl.scm91
-rw-r--r--gnu/packages/guile-xyz.scm10
-rw-r--r--gnu/packages/nss.scm5
-rw-r--r--gnu/packages/patches/mesa-fix-sporadic-test-failures.patch27
-rw-r--r--gnu/packages/python-check.scm116
-rw-r--r--gnu/packages/python-science.scm13
-rw-r--r--gnu/packages/python-xyz.scm44
-rw-r--r--gnu/packages/terminals.scm14
-rw-r--r--gnu/packages/time.scm37
-rw-r--r--gnu/packages/video.scm14
22 files changed, 640 insertions, 208 deletions
diff --git a/gnu/local.mk b/gnu/local.mk
index dfb8930771..77abf61d3c 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1558,7 +1558,6 @@ dist_patch_DATA = \
%D%/packages/patches/mercurial-hg-extension-path.patch \
%D%/packages/patches/mercurial-openssl-compat.patch \
%D%/packages/patches/mesa-opencl-all-targets.patch \
- %D%/packages/patches/mesa-fix-sporadic-test-failures.patch \
%D%/packages/patches/mhash-keygen-test-segfault.patch \
%D%/packages/patches/mia-fix-boost-headers.patch \
%D%/packages/patches/mia-vtk9.patch \
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 6133b19e6b..9bc790ef4b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -41,6 +41,7 @@
#:use-module (gnu packages flex)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gcc)
+ #:use-module (gnu packages geo)
#:use-module (gnu packages gettext)
#:use-module (gnu packages gl)
#:use-module (gnu packages glib)
@@ -1131,13 +1132,13 @@ accurately in real time at any rate desired.")
(define-public python-astropy
(package
(name "python-astropy")
- (version "5.2.1")
+ (version "5.2.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "astropy" version))
(sha256
- (base32 "08xc6brs7xwiqchhsjq8l10p6qc5p68cfxps7s889spqfyh2gbpn"))
+ (base32 "170ddflli35mvhf6pla7aizfw8a7ckq66g1mi1br99dx2r3y7ag6"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -1187,21 +1188,33 @@ accurately in real time at any rate desired.")
(invoke "python" "setup.py" "build_ext" "--inplace")
(invoke "python" "-m" "pytest" "--pyargs" "astropy"
;; Skip tests that need remote data.
- "-m" "not remote_data")))))))
+ "-k" (string-append
+ "not remote_data"
+ ;; XXX: Check why this tests failing.
+ " and not test_ignore_sigint"
+ " and not test_parquet_filter"))))))))
(native-inputs
(list pkg-config
+ python-colorlog
python-coverage
python-cython
python-extension-helpers
+ python-h5py
python-ipython
python-jplephem
python-objgraph
+ python-pandas
+ python-pyarrow
python-pytest
python-pytest-astropy
+ python-pytest-astropy-header
python-pytest-xdist
+ python-scikit-image
+ python-scipy
python-setuptools-scm
python-sgp4
- python-skyfield))
+ python-skyfield
+ python-timezonefinder))
(inputs
(list cfitsio expat wcslib))
(propagated-inputs
@@ -2549,13 +2562,13 @@ Moon position, etc.")
(define-public python-jplephem
(package
(name "python-jplephem")
- (version "2.17")
+ (version "2.18")
(source
(origin
(method url-fetch)
(uri (pypi-uri "jplephem" version))
(sha256
- (base32 "09xaibxnwbzzs3x9g3ibqa2la17z3r6in93321glh02dbibfbip1"))))
+ (base32 "1rgswy52ismij0bkmfqwbml5zikzvzzs1f833dwk0y64lkl12aa9"))))
(build-system python-build-system)
(arguments
`(#:phases
@@ -3095,13 +3108,13 @@ astronomical images, especially when there is no WCS information available.")
(define-public python-skyfield
(package
(name "python-skyfield")
- (version "1.39")
+ (version "1.46")
(source
(origin
(method url-fetch)
(uri (pypi-uri "skyfield" version))
(sha256
- (base32 "1qh3k7g9dm6idppk87hnwxpx9a22xx98vav0zk31p6291drak3as"))))
+ (base32 "1r4kpsh1pa4h3diyxy3gyapp0rykfjdqmn5w348a2ck2qkdlx997"))))
(build-system python-build-system)
(arguments
;; NOTE: (Sharlatan-20210207T163305+0000): tests depend on custom test
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 768b55b25e..72bf40cc41 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10101,6 +10101,36 @@ processing to visualization and annotation.")
large datasets, including support for on-disk data representation.")
(license license:expat)))
+(define-public r-multibac
+ (package
+ (name "r-multibac")
+ (version "1.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MultiBaC" version))
+ (sha256
+ (base32 "1qwf1mvw81hb929xpnx5x910f7qnax9lkylhwzcdw1814s4zj25i"))))
+ (properties `((upstream-name . "MultiBaC")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-ggplot2
+ r-matrix
+ r-multiassayexperiment
+ r-pcamethods
+ r-plotrix
+ r-ropls))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/MultiBaC")
+ (synopsis "Multiomic batch effect correction")
+ (description
+ "MultiBaC is a strategy to correct batch effects from multiomic datasets
+distributed across different labs or data acquisition events. MultiBaC is
+able to remove batch effects across different omics generated within separate
+batches provided that at least one common omic data type is included in all
+the batches considered.")
+ (license license:gpl3)))
+
(define-public r-multtest
(package
(name "r-multtest")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e48b340a3a..afca5ab93b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5169,6 +5169,63 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).")
;; GPLv3 or later.
(license license:gpl3+)))
+(define-public homer
+ (package
+ (name "homer")
+ (version "4.11.1")
+ (source
+ (origin
+ (method url-fetch/zipbomb)
+ (uri (string-append "http://homer.ucsd.edu/homer/data/software/homer.v"
+ version ".zip"))
+ (sha256
+ (base32
+ "0ay802swzq6ix9d8fkinpplcvyc1xyi3cjmj2x08jab7c40cvlc0"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'configure
+ (lambda _
+ (let ((share (string-append #$output "/share/homer")))
+ (mkdir-p share)
+ (substitute* "configureHomer.pl"
+ (("my \\$homeDir = \\$1;")
+ (string-append "my $homeDir = \"" share "\";"))))))
+ (replace 'build
+ (lambda _
+ (let ((share (string-append #$output "/share/homer")))
+ (copy-recursively "." share))
+ (invoke "perl" "configureHomer.pl" "-local")))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke (string-append #$output "/share/homer/bin/homer2")))))
+ (replace 'install
+ (lambda _
+ (mkdir-p (string-append #$output "/bin"))
+ (symlink (string-append #$output "/share/homer/bin/homer2")
+ (string-append #$output "/bin/homer2"))
+ (for-each patch-shebang
+ (find-files (string-append #$output "/share/homer/bin")
+ "\\.pl$")))))))
+ (inputs
+ (list perl))
+ (native-inputs
+ (list perl unzip))
+ (home-page "http://homer.ucsd.edu/homer")
+ (synopsis "Motif discovery and next generation sequencing analysis")
+ (description
+ "HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of
+tools for Motif Discovery and next-gen sequencing analysis. It is a
+collection of command line programs written in Perl and C++. HOMER was
+primarily written as a de novo motif discovery algorithm and is well suited
+for finding 8-20 bp motifs in large scale genomics data. HOMER contains many
+useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and
+numerous other types of functional genomics sequencing data sets.")
+ (license license:gpl3+)))
+
(define-public hmmer
(package
(name "hmmer")
diff --git a/gnu/packages/certs.scm b/gnu/packages/certs.scm
index 122882980b..58b4d50ec8 100644
--- a/gnu/packages/certs.scm
+++ b/gnu/packages/certs.scm
@@ -131,7 +131,7 @@ that was originally contributed to Debian.")
;; XXX We used to refer to the nss package here, but that eventually caused
;; module cycles. The below is a quick copy-paste job that must be kept in
;; sync manually. Surely there's a better way…?
- (version "3.85")
+ (version "3.88.1")
(source (origin
(method url-fetch)
(uri (let ((version-with-underscores
@@ -142,7 +142,7 @@ that was originally contributed to Debian.")
"nss-" version ".tar.gz")))
(sha256
(base32
- "15yj2gddlp68wj1k9q4q70vs6r7zx5qkbavcppmls5di212xdndg"))
+ "15il9fsmixa1r4446zq1wl627sg0hz9h67w6kjxz273xz3nl7li7"))
;; Create nss.pc and nss-config.
(patches (search-patches "nss-3.56-pkgconfig.patch"
"nss-getcwd-nonnull.patch"
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 3c7236581b..e5a6c806b4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -34316,6 +34316,37 @@ access methods and R-native hooks to ensure the Seurat object is familiar to
other R users.")
(license license:gpl3)))
+;; This is for r-seurat5
+(define-public r-seurat5object
+ (let ((commit "185884ae527d6ce71cb51d2e84a630030e8439a3")
+ (revision "1"))
+ (package
+ (inherit r-seuratobject)
+ (name "r-seurat5object")
+ (version (git-version "4.9.9.9084" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mojaveazure/seurat-object")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1nbai31gjsgiaazb4jhpqw8h04nm8xd131fng7zcw11kspj54n9z"))
+ ;; This file triggers renv, which we don't want to use.
+ (snippet '(delete-file ".Rprofile"))))
+ (propagated-inputs (list r-future
+ r-future-apply
+ r-generics
+ r-lifecycle
+ r-matrix
+ r-progressr
+ r-rcpp
+ r-rcppeigen
+ r-rlang
+ r-sp
+ r-spam)))))
+
(define-public r-seurat
(package
(name "r-seurat")
@@ -34384,6 +34415,74 @@ algorithms; density clustering, hierarchical clustering, k-means, and the
discovery of differentially expressed genes and markers.")
(license license:gpl3)))
+;; Seurat5 is only available via the seurat5 branch. It will replace r-seurat
+;; eventually once it has been released to CRAN.
+(define-public r-seurat5
+ (let ((commit "9d59c02042b9ae4f182fbde84cc8b18c0873ef4d")
+ (revision "1"))
+ (package
+ (inherit r-seurat)
+ (name "r-seurat5")
+ (version (git-version "4.9.9.9044" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/satijalab/seurat")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0y4wl6aanq9scn2clazlxsar35g64v4sfy561j43fq1i85na7m4i"))))
+ (propagated-inputs (list r-cluster
+ r-cowplot
+ r-fastdummies
+ r-fitdistrplus
+ r-future
+ r-future-apply
+ r-generics
+ r-ggplot2
+ r-ggrepel
+ r-ggridges
+ r-httr
+ r-ica
+ r-igraph
+ r-irlba
+ r-jsonlite
+ r-kernsmooth
+ r-leiden
+ r-lifecycle
+ r-lmtest
+ r-mass
+ r-matrix
+ r-matrixstats
+ r-miniui
+ r-patchwork
+ r-pbapply
+ r-plotly
+ r-png
+ r-progressr
+ r-rann
+ r-rcolorbrewer
+ r-rcpp
+ r-rcppannoy
+ r-rcppeigen
+ r-rcpphnsw
+ r-rcppprogress
+ r-reticulate
+ r-rlang
+ r-rocr
+ r-rspectra
+ r-rtsne
+ r-scales
+ r-scattermore
+ r-sctransform
+ r-seurat5object
+ r-shiny
+ r-spatstat-explore
+ r-spatstat-geom
+ r-tibble
+ r-uwot)))))
+
(define-public r-seuratdisk
(let ((commit "163f1aade5bac38ed1e9e9c912283a7e74781610")
(revision "1"))
diff --git a/gnu/packages/datastructures.scm b/gnu/packages/datastructures.scm
index bd6044e1d0..e9c9df1bf1 100644
--- a/gnu/packages/datastructures.scm
+++ b/gnu/packages/datastructures.scm
@@ -359,7 +359,7 @@ equivalent succinct data structure are (most of the time) identical.")
(define-public tllist
(package
(name "tllist")
- (version "1.0.5")
+ (version "1.1.0")
(home-page "https://codeberg.org/dnkl/tllist")
(source (origin
(method git-fetch)
@@ -367,7 +367,7 @@ equivalent succinct data structure are (most of the time) identical.")
(file-name (git-file-name name version))
(sha256
(base32
- "061mkg6hc9x89zya3bw18ymxlzd8fbhjipxpva8x01lh2vp1d4f0"))))
+ "03296h1w0rnsj87490cgy007axngyg1v8w3z5nvm6x5gcs6b8rg1"))))
(build-system meson-build-system)
(synopsis "Typed link list for C")
(description
diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 050e6377a3..4ddd9a36dd 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -128,6 +128,7 @@
;;; Copyright © 2023 Juliana Sims <juli@incana.org>
;;; Copyright © 2023 Evgeny Pisemsky <evgeny@pisemsky.com>
;;; Copyright © 2023 Gabriel Wicki <gabriel@erlikon.ch>
+;;; Copyright © 2022-2023 Simon Josefsson <simon@josefsson.org>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -3359,6 +3360,69 @@ defined in RFC 2425 and RFC 2426 to/from The Insidious Big Brother Database
(BBDB). Version 2.1 vCards are converted into version 3.0 on import.")
(license license:gpl2+))))
+(define-public emacs-eweouz
+ (package
+ (name "emacs-eweouz")
+ (version "0.12")
+ (source
+ (origin
+ (method url-fetch)
+ ;; README's git://git.err.no/eweouz is gone
+ (uri (string-append "mirror://debian/pool/main/e/eweouz/"
+ "eweouz_" version ".tar.xz"))
+ (file-name (string-append name "-" version ".tar.xz"))
+ (sha256
+ (base32
+ "192zl3dyphhvcrvn65bqsrc4h6zks8b747lp6pqbpbmsqy4g4mr8"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:modules '((guix build gnu-build-system)
+ ((guix build emacs-build-system) #:prefix emacs:)
+ (guix build utils)
+ (guix build emacs-utils))
+ #:imported-modules `(,@%gnu-build-system-modules
+ (guix build emacs-build-system)
+ (guix build emacs-utils))
+ #:configure-flags
+ #~(list (string-append "--with-lispdir="
+ (emacs:elpa-directory #$output)))
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'bootstrap
+ (lambda _ (invoke "autoreconf" "-vif")))
+ (add-after 'compress-documentation 'enter-lisp-dir
+ (lambda _ (chdir "lisp/")))
+ (add-after 'enter-lisp-dir 'emacs-patch-variables
+ (lambda _
+ (emacs-substitute-sexps "eweouz.el"
+ ("eweouz-helper-dirs"
+ `(list ,(string-append #$output "/libexec/eweouz"))))))
+ (add-after 'emacs-patch-variables 'emacs-expand-load-path
+ (assoc-ref emacs:%standard-phases 'expand-load-path))
+ (add-after 'emacs-expand-load-path 'emacs-add-install-to-native-load-path
+ (assoc-ref emacs:%standard-phases 'add-install-to-native-load-path))
+ (add-after 'emacs-add-install-to-native-load-path 'emacs-install
+ (assoc-ref emacs:%standard-phases 'install))
+ (add-after 'emacs-install 'emacs-build
+ (assoc-ref emacs:%standard-phases 'build))
+ (add-after 'emacs-install 'emacs-make-autoloads
+ (assoc-ref emacs:%standard-phases 'make-autoloads)))))
+ (native-inputs
+ (list autoconf
+ automake
+ emacs-minimal
+ pkg-config))
+ (inputs
+ (list evolution-data-server))
+ (home-page "https://tracker.debian.org/pkg/eweouz")
+ (synopsis "Emacs interface to Evolution Data Server")
+ (description
+ "Eweouz is an tool for looking up contacts from Evolution Data Server
+from Emacs. It is similar to BBDB, except much, much simpler.")
+ ;; Most things are GPLv2-only although lisp/vcard.el is GPLv2+.
+ (license (list license:gpl2 license:gpl2+))))
+
(define-public emacs-beacon
(package
(name "emacs-beacon")
@@ -16068,8 +16132,7 @@ structure, or any other pattern.")
(lambda* (#:key inputs #:allow-other-keys)
(let ((ffplay (search-input-file inputs "/bin/ffplay")))
(substitute* "tmr.el"
- (("\"ffplay ")
- (string-append "\"" ffplay " "))))
+ (("\"ffplay") (string-append "\"" ffplay))))
(emacs-substitute-variables "tmr.el"
("tmr-sound-file"
(search-input-file
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 4fb9775e8d..2e3994543a 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -4531,14 +4531,14 @@ world}, @uref{http://evolonline.org, Evol Online} and
(define openttd-engine
(package
(name "openttd-engine")
- (version "13.0")
+ (version "13.1")
(source
(origin (method url-fetch)
(uri (string-append "https://cdn.openttd.org/openttd-releases/"
version "/openttd-" version "-source.tar.xz"))
(sha256
(base32
- "0rxbsymfirkw2d9hn2lmi8yhlfx7qvpzhy7y7b48fw42w3hgi79k"))))
+ "1fsq1azddk1l11w89r93mgmhna34kvarfak7xy2q48rmf39j5psy"))))
(build-system cmake-build-system)
(inputs
(list allegro
diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm
index bdcc3f0508..47fb443155 100644
--- a/gnu/packages/gcc.scm
+++ b/gnu/packages/gcc.scm
@@ -556,17 +556,17 @@ Go. It also includes runtime support libraries for these languages.")
,@(package-inputs gcc-4.7)))))
(define %gcc-7.5-aarch64-micro-architectures
- ;; Suitable '-march' values for GCC 7.5.
+ ;; Suitable '-march' values for GCC 7.5 (info "(gcc) AArch64 Options").
;; TODO: Allow dynamically adding feature flags.
'("armv8-a" "armv8.1-a" "armv8.2-a" "armv8.3-a"))
(define %gcc-7.5-armhf-micro-architectures
- ;; Suitable '-march' values for GCC 7.5.
+ ;; Suitable '-march' values for GCC 7.5 (info "(gcc) ARM Options").
;; TODO: Allow dynamically adding feature flags.
'("armv7" "armv7-a" "armv7-m" "armv7-r" "armv7e-m" "armv7ve"
"armv8-a" "armv8-a+crc" "armv8.1-a" "armv8.1-a+crc"
"armv8-m.base" "armv8-m.main" "armv8-m.main+dsp"
- "iwmmxt" "iwmmxt2"))
+ "iwmmxt" "iwmmxt2" "armv8.2-a"))
(define %gcc-7.5-x86_64-micro-architectures
;; Suitable '-march' values for GCC 7.5 (info "(gcc) x86 Options").
@@ -589,7 +589,7 @@ Go. It also includes runtime support libraries for these languages.")
;; Suitable '-march' values for GCC 10.
;; TODO: Allow dynamically adding feature flags.
(append %gcc-7.5-armhf-micro-architectures
- '("armv8.2-a" "armv8.3-a" "armv8.4-a" "armv8.5-a" "armv8.6-a"
+ '("armv8.3-a" "armv8.4-a" "armv8.5-a" "armv8.6-a"
"armv8-r" "armv8.1-m.main")))
(define %gcc-10-x86_64-micro-architectures
@@ -603,7 +603,8 @@ Go. It also includes runtime support libraries for these languages.")
(define %gcc-11-aarch64-micro-architectures
;; Suitable '-march' values for GCC 11.
- %gcc-10-aarch64-micro-architectures) ;unchanged
+ (append %gcc-10-aarch64-micro-architectures
+ '("armv8-r")))
(define %gcc-11-armhf-micro-architectures
%gcc-10-armhf-micro-architectures)
@@ -615,6 +616,31 @@ Go. It also includes runtime support libraries for these languages.")
"btver1" "btver2"))) ;AMD
+;; Suitable '-march' values for GCC 12.
+(define %gcc-12-aarch64-micro-architectures
+ (append %gcc-11-aarch64-micro-architectures
+ '("armv8.7-a" "armv8.8-a" "armv9-a")))
+
+(define %gcc-12-armhf-micro-architectures
+ (append %gcc-11-armhf-micro-architectures
+ '("armv9-a")))
+
+(define %gcc-12-x86_64-micro-architectures
+ (append %gcc-11-x86_64-micro-architectures
+ '("znver4"))) ;AMD
+
+;; Suitable '-march' values for GCC 13.
+(define %gcc-13-aarch64-micro-architectures
+ (append %gcc-12-aarch64-micro-architectures
+ '("armv9.1-a" "armv9.2-a" "armv9.3-a")))
+
+(define %gcc-13-armhf-micro-architectures
+ %gcc-12-armhf-micro-architectures)
+
+(define %gcc-13-x86_64-micro-architectures
+ (append %gcc-12-x86_64-micro-architectures
+ '("graniterapids"))) ;Intel
+
(define-public gcc-7
(package
(inherit gcc-6)
@@ -735,19 +761,24 @@ It also includes runtime support libraries for these languages.")
(define-public gcc-12
(package
(inherit gcc-11)
- ;; Note: 'compiler-cpu-architectures' is unchanged compared to GCC 11.
- (version "12.2.0")
+ (version "12.3.0")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/gcc/gcc-"
version "/gcc-" version ".tar.xz"))
(sha256
(base32
- "1zrhca90c7hqnjz3jgr1vl675q3h5lrd92b5ggi00jjryffcyjg5"))
+ "0fwcvbgpmjdfj5drfs8k6bkqsmxmz8pv4cmmjcd451p7k57mv6ll"))
(patches (search-patches "gcc-12-strmov-store-file-names.patch"
"gcc-5.0-libvtv-runpath.patch"))
(modules '((guix build utils)))
- (snippet gcc-canadian-cross-objdump-snippet)))))
+ (snippet gcc-canadian-cross-objdump-snippet)))
+ (properties
+ `((compiler-cpu-architectures
+ ("aarch64" ,@%gcc-12-aarch64-micro-architectures)
+ ("armhf" ,@%gcc-12-armhf-micro-architectures)
+ ("x86_64" ,@%gcc-12-x86_64-micro-architectures))
+ ,@(package-properties gcc-11)))))
;; Note: When changing the default gcc version, update
diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index cd56f50bf0..1337e8f20b 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -14,7 +14,7 @@
;;; Copyright © 2020, 2022 Marius Bakke <marius@gnu.org>
;;; Copyright © 2020 Christopher Baines <mail@cbaines.net>
;;; Copyright © 2020, 2021, 2022, 2023 Felix Gruber <felgru@posteo.net>
-;;; Copyright © 2021 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2021, 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
;;; Copyright © 2021, 2023 Vinicius Monego <monego@posteo.net>
;;; Copyright © 2021 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2021, 2022 Nikolay Korotkiy <sikmir@disroot.org>
@@ -38,6 +38,7 @@
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages geo)
+ #:use-module ((guix licenses) #:prefix license:)
#:use-module (guix build-system ant)
#:use-module (guix build-system cmake)
#:use-module (guix build-system glib-or-gtk)
@@ -47,12 +48,11 @@
#:use-module (guix build-system pyproject)
#:use-module (guix build-system python)
#:use-module (guix build-system qt)
- #:use-module (guix gexp)
#:use-module (guix download)
+ #:use-module (guix gexp)
#:use-module (guix git-download)
- #:use-module (guix svn-download)
- #:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
+ #:use-module (guix svn-download)
#:use-module (guix utils)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
@@ -89,9 +89,9 @@
#:use-module (gnu packages gtk)
#:use-module (gnu packages haskell-apps)
#:use-module (gnu packages haskell-xyz)
+ #:use-module (gnu packages icu4c)
#:use-module (gnu packages image)
#:use-module (gnu packages image-processing)
- #:use-module (gnu packages icu4c)
#:use-module (gnu packages java)
#:use-module (gnu packages kde)
#:use-module (gnu packages libusb)
@@ -118,8 +118,8 @@
#:use-module (gnu packages readline)
#:use-module (gnu packages sdl)
#:use-module (gnu packages speech)
- #:use-module (gnu packages swig)
#:use-module (gnu packages sqlite)
+ #:use-module (gnu packages swig)
#:use-module (gnu packages textutils)
#:use-module (gnu packages time)
#:use-module (gnu packages tls)
@@ -227,6 +227,121 @@ data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more
than 600 operators available.")
(license license:bsd-3)))
+(define-public h3
+ (package
+ (name "h3")
+ (version "4.1.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/uber/h3")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0x764xzna8ka6yhgv2y4hb158a61y3g9a6835qckqp7wfkpqvb7f"))))
+ (build-system cmake-build-system)
+ (arguments
+ (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON")))
+ (home-page "https://h3geo.org/")
+ (synopsis "Hexagonal hierarchical geospatial indexing system")
+ (description "H3 is a geospatial indexing system using a hexagonal grid
+that can be (approximately) subdivided into finer and finer hexagonal grids,
+combining the benefits of a hexagonal grid with S2's hierarchical
+subdivisions.")
+ (license license:asl2.0)))
+
+;; For python-timezonefinder, remove it when it starts supporting newer
+;; version.
+(define-public h3-3
+ (package
+ (inherit h3)
+ (name "h3")
+ (version "3.7.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/uber/h3")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0bvsljfxmjvl23v9gxykc4aynjzh5xfy3wg02bxad7cknr1amx9j"))))))
+
+(define-public python-h3
+ (package
+ (name "python-h3")
+ (version "4.0.0b2")
+ (source
+ (origin
+ (method git-fetch) ; no tests data in PyPi package
+ (uri (git-reference
+ (url "https://github.com/uber/h3-py")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1k1n256hhlh05gjcj64pqh08zlaz6962jkb6nk1aazsgg8p41zs0"))
+ (modules '((guix build utils)))
+ ;; Remove bundeled H3 lib.
+ (snippet #~(begin (delete-file-recursively "src/h3lib")))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ ;; FIXME: Check why these tests are failing.
+ ;; test_versions - assert (4, 1) == (4, 0)
+ ;; test_resolution - h3._cy.error_system.H3Failed
+ #:test-flags #~(list "-k" (string-append
+ "not test_versions"
+ " and not test_resolution"))
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; Use packaged in Guix h3 source.
+ (add-after 'unpack 'patch-cmakelists
+ (lambda _
+ (substitute* "CMakeLists.txt"
+ (("add_subdirectory\\(src/h3lib\\)")
+ (string-append
+ "include_directories(" #$(this-package-input "h3")
+ "/include/h3)\n"
+ "link_directories(" #$(this-package-input "h3")
+ "/lib)\n"))
+ ((".*CMAKE_CURRENT_BINARY_DIR.*")
+ (string-append #$(this-package-input "h3")
+ "/include/h3/h3api.h\n"))))))))
+ (native-inputs
+ (list cmake-minimal
+ python-cython
+ python-numpy
+ python-pytest
+ python-scikit-build
+ python-setuptools-scm))
+ (inputs (list h3))
+ (home-page "https://uber.github.io/h3-py")
+ (synopsis "Python bindings for H3")
+ (description "This package provides a Python bindings for H3, a
+hierarchical hexagonal geospatial indexing system")
+ (license license:asl2.0)))
+
+;; For python-timezonefinder, remove it when it starts supporting newer
+;; version.
+(define-public python-h3-3
+ (package
+ (inherit python-h3)
+ (name "python-h3")
+ (version "3.7.6")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/uber/h3-py")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "16gxa1sivghxw179rik87r918mjasars2qkzidlwq83qfa4axn20"))))
+ (inputs
+ (modify-inputs (package-inputs python-h3)
+ (replace "h3" h3-3)))))
+
(define-public memphis
(package
(name "memphis")
diff --git a/gnu/packages/gimp.scm b/gnu/packages/gimp.scm
index 73102e30cf..b1ff08d652 100644
--- a/gnu/packages/gimp.scm
+++ b/gnu/packages/gimp.scm
@@ -1,7 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015, 2021 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016, 2018 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016, 2017, 2018, 2020 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016-2018, 2020, 2023 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
;;; Copyright © 2018 Thorsten Wilms <t_w_@freenet.de>
@@ -261,7 +261,7 @@ provided, as well as a framework to add new color models and data types.")
("libnsgif" ,libnsgif)
("libpng" ,libpng)
("libraw" ,libraw)
- ("librsvg" ,librsvg)
+ ("librsvg" ,(librsvg-for-system))
("libspiro" ,libspiro)
("libtiff" ,libtiff)
("libwebp" ,libwebp)
@@ -350,7 +350,7 @@ buffers.")
lcms ;optional, color management
libheif ;optional, HEIF + AVIF support
libmng ;optional, MNG support
- librsvg ;optional, SVG support
+ (librsvg-for-system) ;optional, SVG support
libxcursor ;optional, Mouse Cursor support
openexr-2 ;optional, EXR support
openjpeg ;optional, JPEG 2000 support
diff --git a/gnu/packages/gl.scm b/gnu/packages/gl.scm
index 3a63d70c7a..235b386dad 100644
--- a/gnu/packages/gl.scm
+++ b/gnu/packages/gl.scm
@@ -17,6 +17,7 @@
;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru>
;;; Copyright © 2021, 2022 John Kehayias <john.kehayias@protonmail.com>
;;; Copyright © 2022 Petr Hodina <phodina@protonmail.com>
+;;; Copyright © 2023 Kaelyn Takata <kaelyn.alexi@protonmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -266,21 +267,17 @@ also known as DXTn or DXTC) for Mesa.")
(define-public mesa
(package
(name "mesa")
- (version "22.2.4")
+ (version "23.0.3")
(source
(origin
(method url-fetch)
- (uri (list (string-append "https://mesa.freedesktop.org/archive/"
+ (uri (list (string-append "https://archive.mesa3d.org/"
"mesa-" version ".tar.xz")
(string-append "ftp://ftp.freedesktop.org/pub/mesa/"
- "mesa-" version ".tar.xz")
- (string-append "ftp://ftp.freedesktop.org/pub/mesa/"
- version "/mesa-" version ".tar.xz")))
+ "mesa-" version ".tar.xz")))
(sha256
(base32
- "1azpr68pdg63yq3igmzwsgn2ypg49m0mp3hfkq0lcyswr99npmv5"))
- (patches
- (list (search-patch "mesa-fix-sporadic-test-failures.patch")))))
+ "1mcjf41x2bhxs6yxars7nh2vfryfw50g6rvbcfbb1wqdv2jn4qrq"))))
(build-system meson-build-system)
(propagated-inputs
;; The following are in the Requires.private field of gl.pc.
@@ -314,8 +311,10 @@ also known as DXTn or DXTC) for Mesa.")
(@ (gnu packages base) which)))
(outputs '("out" "bin"))
(arguments
- `(#:configure-flags
- '(,@(match (%current-system)
+ (list
+ #:configure-flags
+ #~(list
+ #$@(match (%current-system)
("aarch64-linux"
;; TODO: Fix svga driver for non-Intel architectures.
'("-Dgallium-drivers=etnaviv,freedreno,kmsro,lima,nouveau,\
@@ -327,7 +326,7 @@ r300,r600,swrast,tegra,v3d,vc4,virgl"))
((or "powerpc64le-linux" "powerpc-linux" "riscv64-linux")
'("-Dgallium-drivers=nouveau,r300,r600,radeonsi,swrast,virgl"))
(_
- '("-Dgallium-drivers=iris,nouveau,r300,r600,radeonsi,\
+ '("-Dgallium-drivers=crocus,iris,nouveau,r300,r600,radeonsi,\
svga,swrast,virgl")))
;; Enable various optional features. TODO: opencl requires libclc,
;; omx requires libomxil-bellagio
@@ -344,7 +343,7 @@ svga,swrast,virgl")))
"-Dshared-glapi=enabled"
;; Explicitly enable Vulkan on some architectures.
- ,@(match (%current-system)
+ #$@(match (%current-system)
((or "i686-linux" "x86_64-linux")
'("-Dvulkan-drivers=intel,amd"))
((or "powerpc64le-linux" "powerpc-linux")
@@ -359,6 +358,10 @@ svga,swrast,virgl")))
;; Enable the Vulkan overlay layer on all architectures.
"-Dvulkan-layers=device-select,overlay"
+ ;; Enable the codecs that were built by default as part of the
+ ;; 21.3.x releases to avoid functionality regressions.
+ "-Dvideo-codecs=vc1dec,h264dec,h264enc,h265dec,h265enc"
+
;; Also enable the tests.
"-Dbuild-tests=true"
@@ -368,12 +371,12 @@ svga,swrast,virgl")))
;; documentation recommends using 'release' for performance anyway.
#:build-type "release"
- #:modules ((ice-9 match)
- (srfi srfi-1)
- (guix build utils)
- (guix build meson-build-system))
+ #:modules '((ice-9 match)
+ (srfi srfi-1)
+ (guix build utils)
+ (guix build meson-build-system))
#:phases
- (modify-phases %standard-phases
+ #~(modify-phases %standard-phases
(add-after 'unpack 'disable-failing-test
(lambda _
;; Disable the intel vulkan (anv_state_pool) tests, as they may
@@ -382,7 +385,7 @@ svga,swrast,virgl")))
(substitute* "src/intel/vulkan/meson.build"
(("if with_tests")
"if false"))
- ,@(match (%current-system)
+ #$@(match (%current-system)
("riscv64-linux"
;; According to the test logs the llvm JIT is not designed
;; for this architecture and the llvmpipe tests all segfault.
@@ -427,8 +430,8 @@ svga,swrast,virgl")))
(_
'((display "No tests to disable on this architecture.\n"))))))
(add-before 'configure 'fix-dlopen-libnames
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
+ (lambda _
+ (let ((out #$output))
;; Remain agnostic to .so.X.Y.Z versions while doing
;; the substitutions so we're future-safe.
(substitute* "src/glx/meson.build"
@@ -445,9 +448,9 @@ svga,swrast,virgl")))
(("\"gbm_dri\\.so")
(string-append "\"" out "/lib/dri/gbm_dri.so"))))))
(add-after 'install 'split-outputs
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out"))
- (bin (assoc-ref outputs "bin")))
+ (lambda _
+ (let ((out #$output)
+ (bin #$output:bin))
;; Not all architectures have the Vulkan overlay control script.
(mkdir-p (string-append out "/bin"))
(call-with-output-file (string-append out "/bin/.empty")
@@ -456,13 +459,13 @@ svga,swrast,virgl")))
(string-append bin "/bin"))
(delete-file-recursively (string-append out "/bin")))))
(add-after 'install 'symlinks-instead-of-hard-links
- (lambda* (#:key outputs #:allow-other-keys)
+ (lambda _
;; All the drivers and gallium targets create hard links upon
;; installation (search for "hardlink each megadriver instance"
;; in the makefiles). This is no good for us since we'd produce
;; nars that contain several copies of these files. Thus, turn
;; them into symlinks, which saves ~124 MiB.
- (let* ((out (assoc-ref outputs "out"))
+ (let* ((out #$output)
(lib (string-append out "/lib"))
(files (find-files lib
(lambda (file stat)
@@ -488,7 +491,33 @@ svga,swrast,virgl")))
file)
(symlink reference file)))
others))))
- (delete-duplicates inodes))))))))
+ (delete-duplicates inodes)))))
+ (add-after 'install 'set-layer-path-in-manifests
+ (lambda _
+ (let* ((out #$output)
+ (implicit-path (string-append
+ out
+ "/share/vulkan/implicit_layer.d/"))
+ (explicit-path (string-append
+ out
+ "/share/vulkan/explicit_layer.d/"))
+ (fix-layer-path
+ (lambda (layer-name)
+ (let* ((explicit (string-append explicit-path layer-name ".json"))
+ (implicit (string-append implicit-path layer-name ".json"))
+ (manifest (if (file-exists? explicit)
+ explicit
+ implicit)))
+ (substitute* manifest
+ (((string-append "\"lib" layer-name ".so\""))
+ (string-append "\"" out "/lib/lib" layer-name ".so\"")))))))
+ (for-each fix-layer-path '("VkLayer_MESA_device_select"
+ "VkLayer_MESA_overlay"))))))))
+ (native-search-paths
+ (list (search-path-specification
+ ;; Ensure the Mesa VDPAU drivers can be found.
+ (variable "VDPAU_DRIVER_PATH")
+ (files '("lib/vdpau")))))
(home-page "https://mesa3d.org/")
(synopsis "OpenGL and Vulkan implementations")
(description "Mesa is a free implementation of the OpenGL and Vulkan
@@ -507,7 +536,7 @@ from software emulation to complete hardware acceleration for modern GPUs.")
(arguments
(substitute-keyword-arguments (package-arguments mesa)
((#:configure-flags flags)
- `(cons "-Dgallium-opencl=standalone" ,flags))))
+ #~(cons "-Dgallium-opencl=standalone" #$flags))))
(inputs
(modify-inputs (package-inputs mesa)
(prepend libclc)))
@@ -521,10 +550,10 @@ from software emulation to complete hardware acceleration for modern GPUs.")
(arguments
(substitute-keyword-arguments (package-arguments mesa)
((#:configure-flags flags)
- `(cons "-Dgallium-opencl=icd"
- ,(delete "-Dgallium-opencl=standalone" flags)))
+ #~(cons "-Dgallium-opencl=icd"
+ (delete "-Dgallium-opencl=standalone" #$flags)))
((#:phases phases)
- `(modify-phases ,phases
+ #~(modify-phases #$phases
(add-after 'install 'mesa-icd-absolute-path
(lambda _
;; Use absolute path for OpenCL platform library.
@@ -532,7 +561,7 @@ from software emulation to complete hardware acceleration for modern GPUs.")
;; for ICD in our applications to find OpenCL platform.
(use-modules (guix build utils)
(ice-9 textual-ports))
- (let* ((out (assoc-ref %outputs "out"))
+ (let* ((out #$output)
(mesa-icd (string-append out "/etc/OpenCL/vendors/mesa.icd"))
(old-path (call-with-input-file mesa-icd get-string-all))
(new-path (string-append out "/lib/" (string-trim-both old-path))))
diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm
index 6462ee7963..540e5d71c0 100644
--- a/gnu/packages/guile-xyz.scm
+++ b/gnu/packages/guile-xyz.scm
@@ -311,8 +311,8 @@ currently does not do much, but it might in the future.")
(license license:gpl3+)))
(define-public guile-openai
- (let ((commit "252f2d5660bb546015d18c60be96d3cf60c4dcfa")
- (revision "1"))
+ (let ((commit "9265b641dea0246609b7bd5031f3f6780ef6a167")
+ (revision "2"))
(package
(name "guile-openai")
(version (git-version "0.1" revision commit))
@@ -324,7 +324,7 @@ currently does not do much, but it might in the future.")
(file-name (git-file-name name version))
(sha256
(base32
- "1qv0kr30d1x7ap1b0h03gl5pzp20xw4qd6b3l5v4iz4ka8qna9gi"))))
+ "0sydjsgdr6xxk1w5f8pf14wgimfy4fb1hpi8yml0nv83p7bfr1w3"))))
(build-system guile-build-system)
(arguments
(list
@@ -5593,7 +5593,7 @@ This module implements this interface by use of Guile's dynamic FFI.")
(define-public guile-goblins
(package
(name "guile-goblins")
- (version "0.10")
+ (version "0.11.0")
(source
(origin
(method url-fetch)
@@ -5602,7 +5602,7 @@ This module implements this interface by use of Guile's dynamic FFI.")
version ".tar.gz"))
(sha256
(base32
- "13nzmwi4m0j27rmn2ks0p3k620npnhx736q25n8llj2ivkn2vxd2"))))
+ "1ic4f65kbziszi5cz1b7ypl6acph6kdq5pc3wasa1jns3gkzfl6l"))))
(build-system gnu-build-system)
(arguments
(list #:make-flags
diff --git a/gnu/packages/nss.scm b/gnu/packages/nss.scm
index 7bb239dd27..8088f23aa6 100644
--- a/gnu/packages/nss.scm
+++ b/gnu/packages/nss.scm
@@ -103,8 +103,9 @@ in the Mozilla clients.")
(define-public nss
(package
(name "nss")
- ;; Also update and test the nss-certs package, which duplicates version and
- ;; source to avoid a top-level variable reference & module cycle.
+ ;; IMPORTANT: Also update and test the nss-certs package, which duplicates
+ ;; version and source to avoid a top-level variable reference & module
+ ;; cycle.
(version "3.88.1")
(source (origin
(method url-fetch)
diff --git a/gnu/packages/patches/mesa-fix-sporadic-test-failures.patch b/gnu/packages/patches/mesa-fix-sporadic-test-failures.patch
deleted file mode 100644
index 50ac5530a2..0000000000
--- a/gnu/packages/patches/mesa-fix-sporadic-test-failures.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-commit 7749599d737d205a88bbb6fa755ba095d9b581fa
-Author: Gert Wollny <gert.wollny@collabora.com>
-Date: Mon Aug 15 17:15:43 2022 +0200
-
- r600/sfn: Initialize out buffer when printing op
-
- 79ca456b4837b3bc21cf9ef3c03c505c4b4909f6
- r600/sfn: rewrite NIR backend
-
- Closes: #7021
-
- Signed-off-by: Gert Wollny <gert.wollny@collabora.com>
- Part-of: <https://gitlab.freedesktop.org/mesa/mesa/-/merge_requests/18130>
-
-diff --git a/src/gallium/drivers/r600/sfn/sfn_instr_export.cpp b/src/gallium/drivers/r600/sfn/sfn_instr_export.cpp
-index 3d40ea1796a..00826ed6457 100644
---- a/src/gallium/drivers/r600/sfn/sfn_instr_export.cpp
-+++ b/src/gallium/drivers/r600/sfn/sfn_instr_export.cpp
-@@ -206,7 +206,7 @@ bool WriteScratchInstr::do_ready() const
-
- void WriteScratchInstr::do_print(std::ostream& os) const
- {
-- char buf[6];
-+ char buf[6] = {0};
-
- os << "WRITE_SCRATCH ";
- if (m_address)
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 91a01df2ce..f272a252fc 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -518,16 +518,7 @@ Astropy project, but is optimized for use with astropy-related projects.")
(sha256
(base32 "04g2rh261s3s6ym8mwi4iv2a6anbgwvwzcvkyilfck6yxrncdqw5"))))
(build-system python-build-system)
- (arguments
- `(#:tests? #f ; there are no tests
- #:phases
- (modify-phases %standard-phases
- ;; There is a bug somewhere that makes pytest-filter-subpackage appear
- ;; as version 0.0.0 to setup.py. Remove it from the requirements.
- (add-after 'unpack 'remove-requirement
- (lambda _
- (substitute* "setup.cfg"
- ((".*pytest-filter-subpackage.*") "")))))))
+ (arguments (list #:tests? #f)) ; there are no tests
(native-inputs
(list python-attrs python-pytest-mock python-setuptools-scm))
(propagated-inputs
@@ -550,22 +541,22 @@ astropy related packages.")
(define-public python-pytest-arraydiff
(package
(name "python-pytest-arraydiff")
- (version "0.3")
+ (version "0.5.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pytest-arraydiff" version))
(sha256
- (base32 "05bcvhh2ycxa35znl8b3l9vkcmx7vwm5c3fpakbpw46c7vsn4bfy"))))
+ (base32 "1livzfbi7ag17hskd5845dh1kdir24f7jrbw8y2s1pyhzyz4jhbi"))))
(build-system python-build-system)
(arguments
;; Tests require python-astropy, which itself requires this package.
;; Disable tests to avoid the circular dependency problem.
'(#:tests? #f))
(native-inputs
- (list python-pytest)) ; for sanity-check
+ (list python-pytest python-setuptools-scm)) ; for sanity-check
(propagated-inputs
- (list python-numpy python-six))
+ (list python-numpy))
(home-page "https://github.com/astropy/pytest-arraydiff")
(synopsis "Pytest plugin to help with comparing array output from tests")
(description
@@ -577,32 +568,25 @@ are too large to conveniently hard-code them in the tests.")
(define-public python-pytest-doctestplus
(package
(name "python-pytest-doctestplus")
- (version "0.11.2")
+ (version "0.12.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pytest-doctestplus" version))
(sha256
- (base32 "0j1lvlj3ps975q9hmg8i6rpqm0313j3r18bc3l8mz6khb7vav4zk"))))
- (build-system python-build-system)
+ (base32 "10ciqylgziihxwxryxvxgmkqgws51pqcarn0gbh1d4cxx55rx5vs"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key inputs outputs tests? #:allow-other-keys)
- ;; Make the installed plugin discoverable by Pytest.
- (when tests?
- (add-installed-pythonpath inputs outputs)
- (invoke "python" "-m" "pytest" "-k"
- (string-append ; skip tests that require remote data
- "not test_remote_data_url"
- " and not test_remote_data_float_cmp"
- " and not test_remote_data_ignore_whitespace"
- " and not test_remote_data_ellipsis"
- " and not test_remote_data_requires"
- " and not test_remote_data_ignore_warnings"))))))))
+ (list #:test-flags
+ #~(list "-k" (string-append
+ "not test_remote_data_url"
+ " and not test_remote_data_float_cmp"
+ " and not test_remote_data_ignore_whitespace"
+ " and not test_remote_data_ellipsis"
+ " and not test_remote_data_requires"
+ " and not test_remote_data_ignore_warnings"))))
(native-inputs
- (list python-pytest python-setuptools-scm))
+ (list python-numpy python-pytest python-setuptools-scm))
(home-page "https://github.com/astropy/pytest-doctestplus")
(synopsis "Pytest plugin with advanced doctest features")
(description
@@ -640,27 +624,19 @@ for interactively selecting and running Pytest tests.")
(define-public python-pytest-filter-subpackage
(package
(name "python-pytest-filter-subpackage")
- (version "0.1.1")
+ (version "0.1.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pytest-filter-subpackage" version))
(sha256
- (base32 "1s4s2kd31yc65rfvl4xhy8xx806xhy59kc7668h6b6wq88xgrn5p"))))
- (build-system python-build-system)
- (arguments
- '(;; One test is failing. There's an issue reported upstream. See
- ;; https://github.com/astropy/pytest-filter-subpackage/issues/3.
- ;; Disable it for now.
- #:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key inputs outputs #:allow-other-keys)
- ;; Make the installed plugin discoverable by Pytest.
- (add-installed-pythonpath inputs outputs)
- (invoke "pytest" "-vv" "-k" "not test_with_rst"))))))
+ (base32 "10hpl3f7g2bm29lakmp8492b7lr0dp90khfni12m4gl02xks7bhz"))))
+ (build-system pyproject-build-system)
(native-inputs
- (list python-pytest python-pytest-cov python-pytest-doctestplus))
+ (list python-pytest
+ python-pytest-cov
+ python-pytest-doctestplus
+ python-setuptools-scm))
(home-page "https://github.com/astropy/pytest-filter-subpackage")
(synopsis "Pytest plugin for filtering based on sub-packages")
(description
@@ -759,30 +735,23 @@ were inadvertently left open at the end of a unit test.")
(define-public python-pytest-remotedata
(package
(name "python-pytest-remotedata")
- (version "0.3.2")
+ (version "0.4.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pytest-remotedata" version))
(sha256
- (base32 "1h6g6shib6z07azf12rnsa053470ggbd7hy3bnbw8nf3nza5h372"))))
- (build-system python-build-system)
+ (base32 "1j5106j331cfdyfcwzrbs3yby84mq1b0kddfysq12z2dwdcca8dy"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key inputs outputs #:allow-other-keys)
- ;; Make the installed plugin discoverable by Pytest.
- (add-installed-pythonpath inputs outputs)
- (invoke "pytest" "-vv" "-k"
- (string-append
- ;; These tests require internet access. Disable them.
- "not test_default_behavior"
- " and not test_strict_with_decorator")))))))
+ (list
+ #:test-flags #~(list "-k" (string-append
+ "not test_default_behavior"
+ " and not test_strict_with_decorator"))))
(native-inputs
- (list python-pytest))
+ (list python-pytest python-setuptools-scm))
(propagated-inputs
- (list python-six))
+ (list python-packaging))
(home-page "https://github.com/astropy/pytest-remotedata")
(synopsis "Pytest plugin for controlling remote data access")
(description
@@ -862,24 +831,25 @@ framework and makes it easy to undo any monkey patching. The fixtures are:
(define-public python-pytest-mpl
(package
(name "python-pytest-mpl")
- (version "0.11")
+ (version "0.16.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pytest-mpl" version))
(sha256
- (base32 "1km202c1s5kcn52fx0266p06qb34va3warcby594dh6vixxa9i96"))))
- (build-system python-build-system)
+ (base32 "0sa4229xkkah3fdg9wnqnvb9j13xsd3x1h5rwbsgb3sf2a0icmrd"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda _
- (invoke "pytest" "-vv"))))))
+ (list
+ #:test-flags #~(list "-m" "mpl_image_compare")))
(native-inputs
(list python-pytest))
(propagated-inputs
- (list python-matplotlib python-nose python-pillow))
+ (list python-jinja2
+ python-matplotlib
+ python-nose
+ python-packaging
+ python-pillow))
(home-page "https://github.com/matplotlib/pytest-mpl")
(synopsis "Pytest plugin to help with testing figures output from Matplotlib")
(description
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index e3f3b05ccd..c9f122c5c9 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -3,7 +3,7 @@
;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
-;;; Copyright © 2016, 2022 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2022, 2023 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016-2020, 2022 Marius Bakke <marius@gnu.org>
;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019, 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
@@ -568,20 +568,21 @@ Python module with the same interface, but (hopefully) faster.")
(define-public python-bottleneck
(package
(name "python-bottleneck")
- (version "1.3.2")
+ (version "1.3.7")
(source
(origin
(method url-fetch)
(uri (pypi-uri "Bottleneck" version))
(sha256
- (base32 "0wz5320jx3n4q2nsvwvc7cpi66b46qbals9v53m955rmcq5ry5r0"))))
+ (base32 "1y410r3scfhs6s1j1jpxig01qlyn2hr2izyh1qsdlsfl78vpwip1"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
- (lambda _
- (invoke "python" "setup.py" "pytest"))))))
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "python" "setup.py" "pytest")))))))
(native-inputs
(list python-hypothesis python-pytest python-pytest-runner))
(propagated-inputs
@@ -1762,7 +1763,7 @@ NeuroML2 models.")
"This package provides a Python library for working with NeuroML descriptions of
neuronal models")
(license license:bsd-3)))
-
+
;;;
;;; 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/python-xyz.scm b/gnu/packages/python-xyz.scm
index 3780cca062..4f48d80eb6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3785,23 +3785,30 @@ and is not compatible with JSON.")
(define-public python-extension-helpers
(package
(name "python-extension-helpers")
- (version "0.1")
+ (version "1.0.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "extension-helpers" version))
(sha256
- (base32 "10iqjzmya2h4sk765dlm1pbqypwlqyh8rw59a5m9i63d3klnz2mc"))))
- (build-system python-build-system)
+ (base32 "1rjha07ds633fb81hn3i2yzk3v2flbi6qa091ix4mkvrgk3gl6ya"))))
+ (build-system pyproject-build-system)
+ ;; FIXME: pytest failed to load test suit, find out why.
+ ;; - _pytest.pathlib.ImportPathMismatchError: ('extension_helpers.conftes
+ (arguments (list #:tests? #f))
(native-inputs
- (list python-coverage python-pytest-astropy python-pytest-cov
+ (list python-coverage
+ python-pytest
+ python-pytest-astropy
+ python-pytest-cov
python-setuptools-scm))
- (home-page "https://github.com/astropy/astropy-helpers")
- (synopsis
- "Utilities for building and installing packages in the Astropy ecosystem")
+ (home-page "https://extension-helpers.readthedocs.io")
+ (synopsis "Astropy ecosystem utilities for building and installing packages")
(description
- "The extension-helpers package includes many build, installation, and
-documentation-related tools used by the Astropy project.")
+ "The extension-helpers package includes convenience helpers to assist with
+building Python packages with compiled C/Cython extensions. It is developed by
+the Astropy project but is intended to be general and usable by any Python
+package.")
(license license:bsd-3)))
(define-public python-extras
@@ -14364,20 +14371,21 @@ systems, as a command line tool, and as a Python library.")
(define-public python-bleach
(package
(name "python-bleach")
- (version "5.0.0")
+ (version "5.0.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "bleach" version))
(sha256
- (base32 "0rc5avysbsl3w3i2qvb6522263zhwlvf50w0ifs8776w9c2wrmn6"))))
- (build-system python-build-system)
- (arguments
- '(#:phases (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests? (invoke "pytest" "-vv")))))))
- (propagated-inputs (list python-tinycss2 python-webencodings))
+ (base32 "0p089853pkwzf1j2zjlmw67pwbkk0whpzfx9dbrd56zb8xf2a0qd"))
+ (snippet
+ #~(begin
+ (use-modules (guix build utils))
+ (substitute* (find-files "." "\\.py$")
+ (("bleach\\._vendor\\.html5lib") "html5lib"))
+ (delete-file-recursively "bleach/_vendor/html5lib")))))
+ (build-system pyproject-build-system)
+ (propagated-inputs (list python-html5lib python-tinycss2 python-webencodings))
(native-inputs (list python-pytest))
(home-page "https://github.com/mozilla/bleach")
(synopsis "Whitelist-based HTML-sanitizing tool")
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index d6bcb8d093..570de2259e 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -842,7 +842,7 @@ eye-candy, customizable, and reasonably lightweight.")
(define-public foot
(package
(name "foot")
- (version "1.13.1")
+ (version "1.14.0")
(home-page "https://codeberg.org/dnkl/foot")
(source (origin
(method git-fetch)
@@ -850,7 +850,7 @@ eye-candy, customizable, and reasonably lightweight.")
(file-name (git-file-name name version))
(sha256
(base32
- "0k0zbh6adwr99y9aazlyvp6s1k8zaq2j6x8kqb8q9a5qjjg56lay"))))
+ "1187805pxygyl547w75i4cl37kaw8y8ng11r5qqldv6fm74k31mk"))))
(build-system meson-build-system)
(arguments
`(;; Using a "release" build is recommended both for performance, and
@@ -861,6 +861,12 @@ eye-candy, customizable, and reasonably lightweight.")
(native-inputs
(list ncurses ;for 'tic'
pkg-config scdoc wayland-protocols))
+ (native-search-paths
+ ;; FIXME: This should only be located in 'ncurses'. Nonetheless it is
+ ;; provided for usability reasons. See <https://bugs.gnu.org/22138>.
+ (list (search-path-specification
+ (variable "TERMINFO_DIRS")
+ (files '("share/terminfo")))))
(inputs
(list fcft libxkbcommon wayland))
(synopsis "Wayland-native terminal emulator")
@@ -1378,7 +1384,7 @@ terminal are replicated to the others.
(define-public tio
(package
(name "tio")
- (version "1.36")
+ (version "2.5")
(source
(origin
(method url-fetch)
@@ -1386,7 +1392,7 @@ terminal are replicated to the others.
"https://github.com/tio/tio/releases/download/v"
version "/tio-" version ".tar.xz"))
(sha256
- (base32 "0z27ghxjiw7y587l49jsb0anylm08m7imqjiwr21k1frxvydswsa"))))
+ (base32 "19s41i8f3kxchlaibp7wkq8gqgbpfdn0srkf1wcfx357j3p54f86"))))
(build-system meson-build-system)
(native-inputs (list pkg-config))
(inputs (list libinih))
diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm
index c0bcb848b3..36b561b041 100644
--- a/gnu/packages/time.scm
+++ b/gnu/packages/time.scm
@@ -21,6 +21,7 @@
;;; Copyright © 2021 Ryan Prior <rprior@protonmail.com>
;;; Copyright © 2021 Foo Chuan Wei <chuanwei.foo@hotmail.com>
;;; Copyright © 2022 Pradana AUMARS <paumars@courrier.dev>
+;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -40,7 +41,9 @@
(define-module (gnu packages time)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages geo)
#:use-module (gnu packages golang)
+ #:use-module (gnu packages libffi)
#:use-module (gnu packages perl)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
@@ -50,8 +53,10 @@
#:use-module (gnu packages)
#:use-module (guix build-system gnu)
#:use-module (guix build-system go)
+ #:use-module (guix build-system pyproject)
#:use-module (guix build-system python)
#:use-module (guix download)
+ #:use-module (guix gexp)
#:use-module (guix git-download)
#:use-module (guix licenses)
#:use-module (guix packages))
@@ -278,6 +283,38 @@ datetime module, available in Python 2.3+.")
Python datetime objects.")
(license expat)))
+(define-public python-timezonefinder
+ (package
+ (name "python-timezonefinder")
+ (version "6.2.0")
+ (source
+ (origin
+ (method git-fetch)
+ ;; The PyPi distribution doesn't include the tests.
+ (uri (git-reference
+ (url "https://github.com/jannikmi/timezonefinder")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0qv9rh6j8c1cqwh4sxrfl1m1ah4aqrf0w2kyrf5cgrpfxi6xr94z"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ ;; TODO: Guix has lower python-pytz than required in the latest
+ ;; version: pytz.exceptions.UnknownTimeZoneError:
+ ;; 'America/Ciudad_Juarez'
+ ;; It's optional, remove this constrain where python-pytz is updated.
+ #:test-flags #~(list "-k" "not test_with_pytz")))
+ (native-inputs
+ (list python-poetry-core python-pytest))
+ (propagated-inputs
+ (list python-cffi python-h3-3 python-numba python-numpy python-pytz))
+ (home-page "https://timezonefinder.michelfe.it/gui")
+ (synopsis "Finding the timezone of any coordinates on Earth offline")
+ (description "This is a python package for looking up the corresponding
+timezone for given coordinates on earth entirely offline.")
+ (license expat)))
+
(define-public python-tzlocal
(package
(name "python-tzlocal")
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 31fa687e87..23c06b33ba 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -1502,14 +1502,14 @@ quality and performance.")
(define-public libva
(package
(name "libva")
- (version "2.17.0")
+ (version "2.18.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/intel/libva/releases/download/"
version "/libva-" version ".tar.bz2"))
(sha256
- (base32 "1b2f1hik4x3n4n8217sg1k602wqjba8x20r7nsdmmq05qckyprgk"))))
+ (base32 "10j9rm6ajgp3fda7pwl058lchdip0wq20bvydil28ff2l3mpwmx3"))))
(build-system gnu-build-system)
(native-inputs
(list config pkg-config))
@@ -1558,14 +1558,14 @@ standards (MPEG-2, MPEG-4 ASP/H.263, MPEG-4 AVC/H.264, and VC-1/VMW3).")
(define-public libva-utils
(package
(name "libva-utils")
- (version "2.5.0")
+ (version "2.18.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/intel/libva-utils/releases/download/"
version "/libva-utils-" version ".tar.bz2"))
(sha256
- (base32 "05rasyqnsg522zqxak1q8rrm1hys7wwbi41kd0szjq0d27awjf4j"))))
+ (base32 "06n123kvzk51bx5cbhf34i3cfxc8vxmksgh5azycz9fwwcz3n7rm"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
@@ -1575,7 +1575,7 @@ standards (MPEG-2, MPEG-4 ASP/H.263, MPEG-4 AVC/H.264, and VC-1/VMW3).")
(list pkg-config))
(inputs
(list libdrm libva libx11 mesa wayland))
- (home-page "https://01.org/linuxmedia/vaapi")
+ (home-page "https://github.com/intel/libva-utils")
(synopsis "Collection of testing utilities for VA-API")
(description
"This is a collection of utilities to query and test the @acronym{VA-API,
@@ -3625,7 +3625,7 @@ present in modern GPUs.")
(define-public vdpauinfo
(package
(name "vdpauinfo")
- (version "1.4")
+ (version "1.5")
(source
(origin
(method git-fetch)
@@ -3634,7 +3634,7 @@ present in modern GPUs.")
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "0s84bavxr39w0r7zfaac7kpbfsg88hgymqyzcr0yvbj1yry3liz2"))))
+ (base32 "01nkk8rixzvicrg0cr90mbxyd4vdyd0739ipywn0mx56xddambmx"))))
(build-system gnu-build-system)
(arguments
`(#:phases
generated by cgit v1.2.3 (git 2.50.1) at 2025-08-03 00:59:21 +0000