Merge branch 'master' into staging

2026-05-24 18:11:51 +02:00 · 2022-06-12 22:49:47 +02:00
parent 091eb323ba 9c036f2dfb
commit 622545de6c
59 changed files with 1748 additions and 1412 deletions
@@ -1127,6 +1127,77 @@ IPv6, proxies, and Unix sockets.")
    (license (list license:bsd-3
                   license:bsd-2))))  ; atomicio.*, socks.c

+(define-public nmon
+  (package
+    (name "nmon")
+    (version "16n")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://sourceforge/nmon/lmon" version ".c"))
+       (sha256
+        (base32 "1wpm2f30414b87kpbr9hbidblr5cmfby5skwqd0fkpi5v712q0f0"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list #:tests? #f                  ; no test suite
+           #:phases
+           #~(modify-phases %standard-phases
+               (replace 'unpack
+                 (lambda _
+                   (copy-file #$(package-source this-package) "lmon.c")))
+               (delete 'configure)      ; no build system
+               (replace 'build
+                 ;; There is an example ‘Makefile’ in the .c file.
+                 (lambda _
+                   ;; These #defines aren't well-documented and, e.g., POWER was
+                   ;; not actually tested on every possible TARGET-POWERPC?.
+                   (let* ((system #$(cond ((target-x86-32?) "X86")
+                                          ((target-x86-64?) "X86")
+                                          ((target-arm?) "ARM")
+                                          ((target-powerpc?) "POWER")
+                                          (else "CROSS_FINGERS"))))
+                     (format #t "Building for ~a~%" system)
+                     (invoke #$(cc-for-target) "-o" "nmon" "lmon.c"
+                             "-g" "-Wall" "-D" system
+                             "-lncurses" "-lm"))))
+               (replace 'install
+                 (lambda _
+                   (let ((bin (string-append #$output "/bin"))
+                         (man1 (string-append #$output "/share/man/man1")))
+                     (install-file "nmon" bin)
+                     (mkdir-p man1)
+                     (copy-file #$(this-package-native-input "man-page")
+                                (string-append man1 "/nmon.1"))))))))
+    (native-inputs
+     (list `("man-page"
+             ,(origin
+                ;; There is no man page upstream, so install Debian's.
+                (method url-fetch)
+                (uri (string-append "https://salsa.debian.org/carnil/nmon/"
+                                    "-/raw/debian/" version "+debian-1/"
+                                    "debian/nmon.1"))
+                (sha256
+                 (base32
+                  "1gpvd2kjyhs18sh6sga5bk9wj8s78blfd4c0m38r0wl92jx2yv1b"))))))
+    (inputs
+     (list ncurses))
+    (home-page "http://nmon.sourceforge.net/")
+    (synopsis
+     "Monitor system performance in a terminal or to a @file{.csv} log file")
+    (description
+     "@acronym{Nmon, Nigel's performance monitor} is yet another system monitor
+useful in systems administration, debugging, tuning, and benchmarking.
+
+The configurable ncurses interface displays all the classic resource usage
+statistics (CPU, memory, network, disk, ...) as real-time graphs or numbers.
+It can also list the processes responsible in a @command{top}-like table.
+
+A less common nmon feature is its ability to create highly detailed log files
+in @acronym{CSV, comma-separated values} format.  These can be imported into
+spreadsheets or fed straight into an @acronym{RRD, round-robin database} using
+@command{rrdtool} for further analyisis, or to create colourful graphs.")
+    (license license:gpl3+)))
+
 (define-public sipcalc
  (package
    (name "sipcalc")
@@ -1769,7 +1840,7 @@ system administrator.")
 (define-public sudo
  (package
    (name "sudo")
-    (version "1.9.11")
+    (version "1.9.11p1")
    (source (origin
              (method url-fetch)
              (uri
@@ -1779,7 +1850,7 @@ system administrator.")
                                    version ".tar.gz")))
              (sha256
               (base32
-                "1gjingc1h7d6p17m0nn87yiwh8gbdchg4w4kv8s4g89wv0q6wixm"))
+                "0jr52rmig9h367j0n6h3lp5xf54jsycnvdih42wg9bd9d4d6r2zb"))
              (modules '((guix build utils)))
              (snippet
               '(begin
@@ -2232,13 +2232,13 @@ targeted by a kinase.")
 (define-public r-deepsnv
  (package
    (name "r-deepsnv")
-    (version "1.42.0")
+    (version "1.42.1")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "deepSNV" version))
              (sha256
               (base32
-                "0si1x2bi5pff1dicpqg7hv4ziq46vm7lic72724ljsclpz9bfv6q"))))
+                "0bgj1grv3a5bqhcdsw445x49kl3pz367svy6fnrzfsk9bmj46kgn"))))
    (properties `((upstream-name . "deepSNV")))
    (build-system r-build-system)
    (propagated-inputs
@@ -3103,13 +3103,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biocparallel
  (package
    (name "r-biocparallel")
-    (version "1.30.2")
+    (version "1.30.3")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "BiocParallel" version))
              (sha256
               (base32
-                "0rqvwhs6d8ls1rq7j5ywl5k0qgblxpzimilyw335bi1yad5s10h3"))))
+                "1rs3wmasl9mx7f399iclvm0bnvggvjj2a88zbi294r5m8wxqlc92"))))
    (properties
     `((upstream-name . "BiocParallel")))
    (build-system r-build-system)
@@ -3142,7 +3142,7 @@ powerful online queries from gene annotation to database mining.")
                (string-append
                 m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
    (propagated-inputs
-     (list r-futile-logger r-snow r-bh))
+     (list r-bh r-codetools r-futile-logger r-snow))
    (native-inputs
     (list r-knitr))
    (home-page "https://bioconductor.org/packages/BiocParallel")
@@ -3934,13 +3934,13 @@ alignments.")
 (define-public r-genomicfeatures
  (package
    (name "r-genomicfeatures")
-    (version "1.48.1")
+    (version "1.48.3")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "GenomicFeatures" version))
              (sha256
               (base32
-                "18ain5s0ry6w0ki4c0czvwax2ncigrldyac30a6mlbzyaga6i54h"))))
+                "0f14p1ma2y8l60p9sxmh5j0axws9by1cznczb2jxipphpb4slpl1"))))
    (properties
     `((upstream-name . "GenomicFeatures")))
    (build-system r-build-system)
@@ -4193,14 +4193,14 @@ Shiny-based display methods for Bioconductor objects.")
 (define-public r-keggrest
  (package
    (name "r-keggrest")
-    (version "1.36.0")
+    (version "1.36.2")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "KEGGREST" version))
       (sha256
        (base32
-         "0hzlm6nzmx0iyjh063512a3ghc1xqb58g5z2bnd2wl4y42iww7bg"))))
+         "1rn03w8y80prbvzahkvf8275haiymnjj1ijcgn55p3d0sb54yzgw"))))
    (properties `((upstream-name . "KEGGREST")))
    (build-system r-build-system)
    (propagated-inputs
@@ -5909,13 +5909,13 @@ libraries for systems that do not have these available via other means.")
 (define-public r-zellkonverter
  (package
    (name "r-zellkonverter")
-    (version "1.6.1")
+    (version "1.6.2")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "zellkonverter" version))
       (sha256
-        (base32 "1w3qi35vk289cpky1pb0wgg1hr55s5kdw7np98i9c1vmwi3gvwr7"))))
+        (base32 "0s1n3impm4k55pac8mr18czylsc30yqcvdfdki4sawk74b2rkx8c"))))
    (properties `((upstream-name . "zellkonverter")))
    (build-system r-build-system)
    (propagated-inputs
@@ -6383,14 +6383,14 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
  (package
    (name "r-chippeakanno")
-    (version "3.30.0")
+    (version "3.30.1")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "ChIPpeakAnno" version))
       (sha256
        (base32
-         "1ch636j3zd6hcfnl455vjs36wffrdhwzyvkbikcwjg7idiknjdkf"))))
+         "0a26glldxczcfymjvd45gv5m4hympziivm6wwx4ab9wld7n43l8y"))))
    (properties `((upstream-name . "ChIPpeakAnno")))
    (build-system r-build-system)
    (propagated-inputs
@@ -7652,14 +7652,14 @@ single cell assay data.")
 (define-public r-monocle
  (package
    (name "r-monocle")
-    (version "2.24.0")
+    (version "2.24.1")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "monocle" version))
       (sha256
        (base32
-         "1fyqd7qhij2iyx9vdmgnx2qf0w3kwbkmg805539zrmxry8cwfldb"))))
+         "11g1wx0f1yzhg3x1aa3d5l7pqlzxj16s0gha21skxkgld8k2x8xn"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-biobase
@@ -8699,14 +8699,14 @@ All the visualization methods are developed based on ggplot2 graphics.")
 (define-public r-clusterprofiler
  (package
    (name "r-clusterprofiler")
-    (version "4.4.1")
+    (version "4.4.2")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "clusterProfiler" version))
       (sha256
        (base32
-         "03bg3agisrm4q10gg57dksvd1ws37if6a1gwcxaybb4c50zadm8p"))))
+         "07fbc3d06990qy1qcaqqgm5ma2l0h08bwfkqrnlfd9f2xcppdywd"))))
    (properties
     `((upstream-name . "clusterProfiler")))
    (build-system r-build-system)
@@ -10768,14 +10768,14 @@ annotations.")
 (define-public r-rsubread
  (package
    (name "r-rsubread")
-    (version "2.10.1")
+    (version "2.10.2")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "Rsubread" version))
       (sha256
        (base32
-         "1cf80gmzz4c1pvif3350ifsmsbfplyl2na39n8g3x0zkwpl6ijdc"))))
+         "1pvyx8nxv10s816hgxrnw60hp9rlqjdgjq3ajpzqxgxmmlhnk0v0"))))
    (properties `((upstream-name . "Rsubread")))
    (build-system r-build-system)
    (inputs (list zlib))
@@ -12235,14 +12235,14 @@ data.")
 (define-public r-universalmotif
  (package
    (name "r-universalmotif")
-    (version "1.14.0")
+    (version "1.14.1")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "universalmotif" version))
       (sha256
        (base32
-         "0n2msyyy1xhapkd66j4xwabg4qfd62l01p1nmafjwifnjsx45xvp"))))
+         "1sm54z8aq3534qjsa19wychhwcvwnjlkydmiqqvidiiwcxwqpjsr"))))
    (properties
     `((upstream-name . "universalmotif")))
    (build-system r-build-system)
@@ -13806,14 +13806,14 @@ provided.")
 (define-public r-hdf5array
  (package
    (name "r-hdf5array")
-    (version "1.24.0")
+    (version "1.24.1")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "HDF5Array" version))
       (sha256
        (base32
-         "0s9vj74359ckmwl8r951jxrzkidslwdl9qamkhz8ilw8b5awxyw4"))))
+         "1r1lg7k60qgb489xkypd4gvm1fmdlihvylb5va6xj58ipndbfday"))))
    (properties `((upstream-name . "HDF5Array")))
    (build-system r-build-system)
    (inputs
@@ -830,13 +830,13 @@ servers supporting the protocol.")
 (define-public python-pybedtools
  (package
    (name "python-pybedtools")
-    (version "0.8.2")
+    (version "0.9.0")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "pybedtools" version))
              (sha256
               (base32
-                "0wc7z8g8prgdx7n5chjva2fdq03wiwhqisjjxzkjg1j5k5ha7151"))))
+                "18rhzk08d3rpxhi5xh6pqg64x6v5q3daw6y3v54k85v4swncjrwj"))))
    (build-system python-build-system)
    (arguments
     `(#:modules ((srfi srfi-26)
@@ -896,11 +896,16 @@ servers supporting the protocol.")
    (home-page "https://pythonhosted.org/pybedtools/")
    (synopsis "Python wrapper for BEDtools programs")
    (description
-     "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs,
+     "This package is a Python wrapper for Aaron Quinlan's BEDtools programs,
 which are widely used for genomic interval manipulation or \"genome algebra\".
 pybedtools extends BEDTools by offering feature-level manipulations from with
 Python.")
-    (license license:gpl2+)))
+    ;; pypi lists GPLv2 in the PKG-INFO and website, but was relicensed in
+    ;; version 0.9.0 and the LICENSE.txt is consistant with the source code.
+    ;;
+    ;; pybedtools/include/gzstream.cpp and pybedtools/include/gzstream.h are
+    ;; licensed lgpl2.1+
+    (license (list license:expat license:lgpl2.1+))))

 (define-public python-biom-format
  (package
@@ -3,7 +3,7 @@
 ;;; Copyright © 2016, 2017, 2018, 2019, 2021 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018, 2020–2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018, 2019 Pierre Neidhardt <mail@ambrevar.xyz>
-;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2019, 2020, 2022 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2019, 2021 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
@@ -399,7 +399,7 @@ as dictionaries, skip lists, and memory pools.")
 (define-public packcc
  (package
    (name "packcc")
-    (version "1.5.0")
+    (version "1.7.2")
    (home-page "https://github.com/arithy/packcc")
    (source (origin
              (method git-fetch)
@@ -409,7 +409,7 @@ as dictionaries, skip lists, and memory pools.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "1n9ivsa6b9ps2jbh34bycjqjpbwbk85l4jjg46pfhqxzz96793wy"))))
+                "1mb6ys5ylvjz0xpq6769ir98s80p98s9ahd0c9k8p2ra1w20vz33"))))
    (build-system gnu-build-system)
    (arguments
     '(#:phases (modify-phases %standard-phases
@@ -433,8 +433,7 @@ as dictionaries, skip lists, and memory pools.")
                        (install-file "release/bin/packcc"
                                      (string-append out "/bin"))
                        (install-file "../../README.md"
-                                      (string-append out "/share/doc/packcc"))
-                        #t))))))
+                                      (string-append out "/share/doc/packcc"))))))))
    (native-inputs
     (list bats))
    (synopsis "Packrat parser generator for C")
@@ -390,7 +390,7 @@ features that are not supported by the standard @code{stdio} implementation.")
 (define-public universal-ctags
  (package
    (name "universal-ctags")
-    (version "5.9.20210509.0")
+    (version "5.9.20220605.0")
    (source
     (origin
       (method git-fetch)
@@ -400,14 +400,14 @@ features that are not supported by the standard @code{stdio} implementation.")
       (file-name (git-file-name name version))
       (sha256
        (base32
-         "1sq94bnbzr40zwihfnsna759bbak0lw27j0yn12iwpg4xgb4hhwp"))
+         "0mri7m2qsw5pyq1ajapawvxn2cdrzg1vi4w2bdq0z4ws4q03lj7k"))
       (modules '((guix build utils)))
       (snippet
        '(begin
           ;; Remove the bundled PackCC and associated build rules.
           (substitute* "Makefile.am"
             (("^PACKCC = .*")
-              "PACKCC = packcc")
+              "PACKCC = packcc\n")
             (("\\$\\(PACKCC_FILES\\)")
              "")
             (("\\$\\(PEG_SRCS\\) \\$\\(PEG_HEADS\\): \\$\\(PACKCC\\)")
@@ -437,7 +437,7 @@ features that are not supported by the standard @code{stdio} implementation.")
    (native-inputs
     (list autoconf automake packcc perl pkg-config))
    (inputs
-     (list jansson libseccomp libxml2 libyaml))
+     (list jansson libseccomp libxml2 libyaml pcre2))
    (home-page "https://ctags.io/")
    (synopsis "Generate tag files for source code")
    (description
@@ -2575,29 +2575,30 @@ chunks.")
 (define-public c-blosc
  (package
    (name "c-blosc")
-    (version "1.18.1")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/Blosc/c-blosc")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1ywq8j70149859vvs19wgjq89d6xsvvmvm2n1dmkzpchxgrvnw70"))))
+    (version "1.21.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Blosc/c-blosc")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0gy9a7wp7x71x5l3rprx8wpb3c5cn7wqc77gdiffq35hr34q88p9"))
+       (modules '((guix build utils)))
+       (snippet
+        ;; In a rare victory, we may delete all bundled libs to no ill effect.
+        '(delete-file-recursively "internal-complibs"))))
    (build-system cmake-build-system)
    (arguments
     `(#:configure-flags
-       '("-DDEACTIVATE_AVX2=ON"
+       '("-DBUILD_STATIC=OFF"
+         "-DDEACTIVATE_AVX2=ON"
         "-DPREFER_EXTERNAL_LZ4=ON"
-         "-DPREFER_EXTERNAL_SNAPPY=ON"
         "-DPREFER_EXTERNAL_ZLIB=ON"
         "-DPREFER_EXTERNAL_ZSTD=ON")))
    (inputs
-     `(("lz4" ,lz4)
-       ("snappy" ,snappy)
-       ("zlib" ,zlib)
-       ("zstd:lib" ,zstd "lib")))
+     (list lz4 snappy zlib `(,zstd "lib")))
    (home-page "https://blosc.org")
    (synopsis "Blocking, shuffling and lossless compression library")
    (description
@@ -886,7 +886,7 @@ and make @code{cpplint} usable in wider contexts.")
 (define-public reproc
  (package
    (name "reproc")
-    (version "14.1.0")
+    (version "14.2.4")
    (source
      (origin
        (method git-fetch)
@@ -895,13 +895,12 @@ and make @code{cpplint} usable in wider contexts.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-          (base32
-            "1n71wb50qv2dmhjgw7azx5gigbrp19l2n3d41g9p05l5l0y1qg0q"))))
+          (base32 "09xnf8hmld1fk8j33zwlz1qcxnjdx1ncbg62csic9va4m1wc2v1d"))))
   (build-system cmake-build-system)
   (arguments
      ;; No tests.
    `(#:tests? #f
-      ;; Enable building of shared library.
+      ;; Build the shared library instead of a static one.
      #:configure-flags `("-DBUILD_SHARED_LIBS=1")))
   (native-inputs
    (list pkg-config))
@@ -104,6 +104,7 @@
  #:use-module (gnu packages sqlite)
  #:use-module (gnu packages statistics)
  #:use-module (gnu packages tcl)
+  #:use-module (gnu packages tex)
  #:use-module (gnu packages textutils)
  #:use-module (gnu packages tls)
  #:use-module (gnu packages uglifyjs)
@@ -30466,7 +30467,26 @@ package online.")
    (properties `((upstream-name . "prereg")))
    (build-system r-build-system)
    (propagated-inputs
-      (list r-rmarkdown))
+      (list r-rmarkdown
+            ;; The package provides a custom LaTex template in
+            ;; inst/rmd/prereg_form.tex, which depends on these packages:
+            texlive-amsmath
+            texlive-booktabs
+            texlive-etoolbox
+            texlive-generic-iftex
+            texlive-latex-fancyhdr
+            texlive-latex-fancyvrb
+            texlive-latex-geometry
+            texlive-latex-graphics
+            texlive-latex-threeparttable
+            texlive-latex-titlesec
+            texlive-latex-upquote
+            texlive-listings
+            texlive-polyglossia
+            texlive-titling
+            texlive-tools
+            texlive-ulem
+            (texlive-updmap.cfg (list texlive-amsfonts texlive-lm))))
    (home-page "https://github.com/crsh/prereg")
    (synopsis
      "R Markdown Templates to preregister Scientific Studies")
@@ -1160,7 +1160,7 @@ developed in C/C++ to MariaDB and MySQL databases.")
 (define-public galera
  (package
    (name "galera")
-    (version "26.4.10")
+    (version "26.4.12")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -1169,7 +1169,7 @@ developed in C/C++ to MariaDB and MySQL databases.")
                    (recursive? #t)))
              (file-name (git-file-name name version))
              (sha256
-               (base32 "1n6zhzwj713ixyqvcjn4ldlq0y9fxqgvmqv3cj3h4207v9lwlxxz"))))
+               (base32 "0n4272mvr8a6h5prbhvl376asdp89ipix5yx5n6i1iiw9bs3v76l"))))
    (build-system cmake-build-system)
    (inputs
     (list check boost openssl))
@@ -1384,7 +1384,7 @@ pictures, sounds, or video.")
    (home-page "https://www.timescale.com/")
    (synopsis "Time-series extension for PostgreSQL")
    (description
-     "TimescaleDB is an database designed to make SQL scalable for
+     "TimescaleDB is a database designed to make SQL scalable for
 time-series data.  It is engineered up from PostgreSQL and packaged as a
 PostgreSQL extension, providing automatic partitioning across time and space
 (partitioning key), as well as full SQL support.")
@@ -1889,7 +1889,7 @@ extremely small.")
                "1yinx39960y241vf2sknxj0dfz82a5m9gvklq5rw78k0nlyrjawa"))))
    (build-system perl-build-system)
    (synopsis "Database independent interface for Perl")
-    (description "This package provides an database interface for Perl.")
+    (description "This package provides a database interface for Perl.")
    (home-page "https://metacpan.org/release/DBI")
    (license license:perl-license)))

@@ -3025,44 +3025,58 @@ development.")
 (define-public python-pyodbc-c
  (package
    (name "python-pyodbc-c")
-    (version "3.1.4")
+    (version "3.1.5")
    (source
     (origin
-       (method url-fetch)
-       (uri (string-append "https://gitlab.com/daym/pyodbc-c/repository/"
-                           "archive.tar.gz?ref=v" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.com/daym/pyodbc-c/")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
       (sha256
-        (base32
-         "05aq2297k779xidmxcwkrrxjvj1bh2q7d9a1rcjv6zr15y764ga9"))
-       (file-name (string-append name "-" version ".tar.gz"))))
+        (base32 "08y60c5sx0k953zfx0s2a155l8py968sb17ap9a9fg8bjnj783k8"))))
    (build-system python-build-system)
    (inputs
     (list unixodbc))
    (arguments
-     `(;; No unit tests exist.
+     `(;; The tests require a running SQL server that they don't help set up.
       #:tests? #f))
-    (home-page "https://github.com/mkleehammer/pyodbc")
-    (synopsis "Python ODBC Library")
+    (home-page "https://gitlab.com/daym/pyodbc-c")
+    (synopsis "Python ODBC Library written in C")
    (description "@code{python-pyodbc-c} provides a Python DB-API driver
-for ODBC.")
+for ODBC, similar to python-pyodbc but written in C.
+
+It's designed to stand alone and not have other dependencies on other packages
+or languages.  It uses only Python's built-in data types.")
    (license (license:x11-style "file://LICENSE.TXT"))))

 (define-public python-pyodbc
  (package
    (name "python-pyodbc")
-    (version "4.0.30")
+    (version "4.0.32")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "pyodbc" version))
       (sha256
-        (base32 "0skjpraar6hcwsy82612bpj8nw016ncyvvq88j5syrikxgp5saw5"))
-       (file-name (string-append name "-" version ".tar.gz"))))
+        (base32 "0sqs0x2l5mk3yv0wwz3ya8yh5f4babihyhc8hjbf2m86b71z1rcv"))
+       (modules '((guix build utils)))
+       (snippet
+        ;; Delete precompiled binaries.  The corresponding source is included.
+        #~(for-each delete-file (find-files "." "\\.pyc$")))))
    (build-system python-build-system)
    (inputs
     (list unixodbc))
    (arguments
-     `(#:tests? #f))                    ; no unit tests exist
+     ;; XXX Tests fail with ‘Can't open lib 'SQL Server Native Client 10.0' :
+     ;; file not found (0) (SQLDriverConnect)")’.
+     (list #:tests? #f
+           #:phases
+           #~(modify-phases %standard-phases
+               (replace 'check
+                 (lambda* (#:key tests? #:allow-other-keys)
+                   (when tests?
+                     (invoke "python3" "tests3/test.py")))))))
    (home-page "https://github.com/mkleehammer/pyodbc")
    (synopsis "Python ODBC Library")
    (description "@code{python-pyodbc} provides a Python DB-API driver
@@ -74,7 +74,7 @@
 (define-public diffoscope
  (package
    (name "diffoscope")
-    (version "215")
+    (version "216")
    (source
     (origin
       (method git-fetch)
@@ -83,7 +83,7 @@
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "16pyqbyrfsxjnpmr9913x2brz3mxplhz62rxwix1c0p7afwjw835"))
+        (base32 "066w4mcrjvymwii5j5hylcslpz18wgd5afl11z1n3588j8c1zw15"))
       (patches
        (search-patches "diffoscope-fix-llvm-test.patch"))))
    (build-system python-build-system)
@@ -93,6 +93,7 @@
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system glib-or-gtk)
  #:use-module (guix build-system go)
+  #:use-module (guix build-system meson)
  #:use-module (guix build-system python)
  #:use-module (guix build-system trivial)
  #:use-module (guix build-system scons)
@@ -883,7 +884,7 @@ passphrases.")
 (define-public ndctl
  (package
    (name "ndctl")
-    (version "72.1")
+    (version "73")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -892,12 +893,16 @@ passphrases.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "1lvrhlad5n43bal053ihgbwr1k4ka2kscrjwr9rs5xnf2vy7204v"))))
-    (build-system gnu-build-system)
+                "19kp1ly74bj7gavs03q7caci0lqr0rsi5y45zx5m8in4h19xk1kb"))))
+    (build-system meson-build-system)
    (arguments
     (list #:configure-flags
-           #~(list "--disable-asciidoctor" ; use docbook-xsl instead
-                   "--without-systemd")
+           #~(list (string-append "-Drootprefix=" #$output)
+                   (string-append "-Dbashcompletiondir=" #$output
+                                  "/share/bash-completion/completions")
+                   (string-append "-Dsysconfdir=" #$output "/etc")
+                   "-Dasciidoctor=disabled" ; use docbook-xsl instead
+                   "-Dsystemd=disabled")
           #:phases
           #~(modify-phases %standard-phases
               (add-after 'unpack 'fix-version
@@ -910,17 +915,11 @@ passphrases.")
                   (substitute* "git-version-gen"
                     (("/bin/sh") (which "sh")))
                   (substitute* "git-version"
-                     (("/bin/bash") (which "bash"))))))
-           #:make-flags
-           #~(list (string-append "BASH_COMPLETION_DIR=" #$output
-                                  "/share/bash-completion/completions"))))
+                     (("/bin/bash") (which "bash"))))))))
    (native-inputs
     (list asciidoc
-           automake
-           autoconf
           bash-completion
           docbook-xsl
-           libtool
           libxml2
           pkg-config
           xmlto
@@ -940,7 +939,7 @@ passphrases.")
 libnvdimm (non-volatile memory device) sub-system in the Linux kernel.")
    ;; COPYING says LGPL2.1, but many source files are GPL2 so that's
    ;; the effective license.  Note that some files under ccan/ are
-    ;; covered by BSD-3 or public domain, see the individual folders.
+    ;; covered by BSD-3 or public domain, see the individual directories.
    (license license:gpl2)))

 (define-public dmraid
@@ -1253,7 +1252,7 @@ that support this feature).")
 (define-public memkind
  (package
    (name "memkind")
-    (version "1.12.0")
+    (version "1.13.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -1261,7 +1260,7 @@ that support this feature).")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
-               (base32 "1s52vl2jlrdc8nxnvf993x9mcag56qxcaniiijhmsv42a26hvjk4"))))
+               (base32 "0zbil6xqmsrnh773ihxyfna6pvvxv3kczdb3g863ssflwwvv7h4w"))))
    (build-system gnu-build-system)
    (inputs
     (list ;; memkind patched jemalloc to add je_arenalookupx,
@@ -323,8 +323,8 @@ experience for your users, your family and yourself")
             vala                       ;for Vala bindings
             ;; For tests
             dbus
-             ;; python-wrapper
-             ;; python-pygobject
+             python-wrapper
+             python-pygobject
             which
             yelp-tools))
      ;; Required by liblightdm-gobject-1.pc.
@@ -113,6 +113,7 @@
 ;;; Copyright © 2022 Peter Polidoro <peter@polidoro.io>
 ;;; Copyright © 2022 Luis Felipe López Acevedo <luis.felipe.la@protonmail.com>
 ;;; Copyright © 2022 Thomas Albers Raviola <thomas@thomaslabs.org>
+;;; Copyright © 2022 Haider Mirza <haider@haider.gq>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -247,7 +248,7 @@
 (define-public emacs-geiser
  (package
    (name "emacs-geiser")
-    (version "0.23.1")
+    (version "0.23.2")
    (source
     (origin
       (method git-fetch)
@@ -256,7 +257,7 @@
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1lvnk71fb4qkh8a7h7spsdhmc9nnj1lwgp9wr3c2fgzjqsl62kgr"))))
+        (base32 "0p5cwx0xwva4ajgj8hnrk8bx6n3hv1z7aqs4zivp81crnq4077yw"))))
    (build-system emacs-build-system)
    (arguments
     '(#:phases
@@ -278,7 +279,7 @@
     (list texinfo))
    (propagated-inputs
     (list emacs-project emacs-transient))
-    (home-page "https://nongnu.org/geiser/")
+    (home-page "https://www.nongnu.org/geiser/")
    (synopsis "Collection of Emacs modes for Scheme hacking")
    (description
     "Geiser is a collection of Emacs major and minor modes that conspire with
@@ -296,7 +297,7 @@ e.g. emacs-geiser-guile for Guile.")
 (define-public emacs-geiser-guile
  (package
    (name "emacs-geiser-guile")
-    (version "0.23")
+    (version "0.23.2")
    (source
     (origin
       (method git-fetch)
@@ -305,13 +306,19 @@ e.g. emacs-geiser-guile for Guile.")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1v9f90smnk41nz1pjy5mwz199y8p4qar3llgaryzxr7s4wg2v9wi"))))
+        (base32 "18m5ldj4r4c2hxgvv5b4azl90r8az1kn5f3s913h971asyv4wx06"))))
    (build-system emacs-build-system)
    (arguments
     (list
      #:include #~(cons "^src/" %default-include)
      #:phases
      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-geiser-guile-binary
+            (lambda* (#:key inputs #:allow-other-keys)
+              (substitute* "geiser-guile.el"
+                (("\\(t \"guile\")")
+                 (format #f "(t ~s)"
+                         (search-input-file inputs "bin/guile"))))))
          (add-after 'make-autoloads 'patch-autoloads
            (lambda _
              (substitute* (string-append (elpa-directory #$output)
@@ -321,11 +328,9 @@ e.g. emacs-geiser-guile for Guile.")
                (("\\(geiser-activate-implementation .*\\)" all)
                 (string-append
                  "(eval-after-load 'geiser-impl '" all ")"))))))))
-    (inputs
-     (list guile-3.0))
-    (propagated-inputs
-     (list emacs-geiser))
-    (home-page "https://nongnu.org/geiser/")
+    (inputs (list guile-3.0))
+    (propagated-inputs (list emacs-geiser))
+    (home-page "https://www.nongnu.org/geiser/")
    (synopsis "Guile Scheme support for Geiser")
    (description
     "This package adds support for the Guile Scheme implementation to Geiser,
@@ -358,34 +363,57 @@ using geiser.")
      (home-page "https://github.com/xiaohanyu/ac-geiser"))))

 (define-public emacs-geiser-gauche
-  (package
-    (name "emacs-geiser-gauche")
-    (version "0.0.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://gitlab.com/emacs-geiser/gauche.git")
-             (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0rxncnzx7qgcpvc8nz0sd8r0hwrplazzraahdwhbpq0q6z8ywqgg"))))
-    (build-system emacs-build-system)
-    (arguments
-     `(#:include (cons "^geiser-gauche\\.scm$" %default-include)))
-    (native-inputs
-     (list emacs-geiser))
-    (home-page "https://gitlab.com/emacs-geiser/gauche")
-    (synopsis "Gauche Scheme support for Geiser")
-    (description
-     "This package adds support for the Gauche Scheme implementation to Geiser,
+  ;; The latest 0.14 release has an unbound variable (geiser-scheme-dir).
+  (let ((commit "96fa06aaeef18cc1b3b519e83dbb7be09eeb0d07")
+        (revision "0"))
+    (package
+      (name "emacs-geiser-gauche")
+      (version (git-version "0.14" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://gitlab.com/emacs-geiser/gauche.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1ppracwfl1snq0ifdlyxpdlv7fbn3pbxm1hd1ihgqivii5nbya9r"))))
+      (build-system emacs-build-system)
+      (arguments
+       (list
+        #:include '(cons "^geiser-gauche\\.scm$" %default-include)
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-after 'unpack 'patch-geiser-gauche-binary
+              (lambda* (#:key inputs #:allow-other-keys)
+                (emacs-substitute-sexps "geiser-gauche.el"
+                  ("geiser-custom--defcustom geiser-gauche-binary"
+                   (search-input-file inputs "bin/gosh")))))
+            (add-after 'make-autoloads 'patch-autoloads
+              (lambda _
+                (substitute* (string-append (elpa-directory #$output)
+                                            "/geiser-gauche-autoloads.el")
+                  ;; Activating implementations fails when Geiser is not yet
+                  ;; loaded, so let's defer that until it is.
+                  (("\\(geiser-activate-implementation .*\\)" all)
+                   (string-append
+                    "(eval-after-load 'geiser-impl '" all ")"))
+                  (("\\(geiser-implementation-extension .*\\)" all)
+                   (string-append
+                    "(eval-after-load 'geiser-impl '" all ")"))))))))
+      (inputs (list gauche))
+      (propagated-inputs (list emacs-geiser))
+      (home-page "https://gitlab.com/emacs-geiser/gauche")
+      (synopsis "Gauche Scheme support for Geiser")
+      (description
+       "This package adds support for the Gauche Scheme implementation to Geiser,
 a generic Scheme interaction mode for the GNU Emacs editor.")
-    (license license:expat)))
+      (license license:expat))))

 (define-public emacs-geiser-racket
  (package
    (name "emacs-geiser-racket")
-    (version "0.16")
+    (version "1.0")
    (source
     (origin
       (method git-fetch)
@@ -394,13 +422,19 @@ a generic Scheme interaction mode for the GNU Emacs editor.")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1aqsvmk1hi7kc3j4h8xlza7c6rwm71v98fv5wpw8kmyj9vsp49wx"))))
+        (base32 "04gwd9qa0785zfr6m9a5443ilgvyz05l06cb1waicf83sgp8xl32"))))
    (build-system emacs-build-system)
    (arguments
     (list
      #:include #~(cons "^src/" %default-include)
      #:phases
      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-geiser-racket-binary
+            (lambda* (#:key inputs #:allow-other-keys)
+              (substitute* "geiser-racket.el"
+                (("\\(t \"racket\")")
+                 (format #f "(t ~s)"
+                         (search-input-file inputs "bin/racket"))))))
          (add-after 'make-autoloads 'patch-autoloads
            (lambda _
              (substitute* (string-append (elpa-directory #$output)
@@ -410,14 +444,12 @@ a generic Scheme interaction mode for the GNU Emacs editor.")
                (("\\(geiser-activate-implementation .*\\)" all)
                 (string-append
                  "(eval-after-load 'geiser-impl '" all ")"))
-	        (("\\(geiser-implementation-extension .*\\)" all)
+                (("\\(geiser-implementation-extension .*\\)" all)
                 (string-append
                  "(eval-after-load 'geiser-impl '" all ")"))))))))
-    (inputs
-     (list racket))
-    (propagated-inputs
-     (list emacs-geiser))
-    (home-page "https://nongnu.org/geiser/")
+    (inputs (list racket))
+    (propagated-inputs (list emacs-geiser))
+    (home-page "https://www.nongnu.org/geiser/")
    (synopsis "Racket support for Geiser")
    (description
     "This package adds support for the Racket implementation to Geiser,
@@ -537,6 +569,27 @@ editing @file{.hgignore} files used by the Mercurial version control
 system.")
      (license license:gpl3+))))

+(define-public emacs-platformio-mode
+  (package
+    (name "emacs-platformio-mode")
+    (version "0.3.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ZachMassia/PlatformIO-Mode")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0ian50v9vaz7kqzn20bhqadq50h0l3zhjkmniinpz4q9klh7drh9"))))
+    (build-system emacs-build-system)
+    (propagated-inputs (list emacs-async emacs-projectile))
+    (home-page "https://github.com/zachmassia/platformio-mode")
+    (synopsis "Minor mode for building and uploading PlatformIO projects")
+    (description "This package provices an Emacs minor mode for building and
+uploading PlatformIO projects.")
+    (license license:gpl3+)))
+
 (define-public emacs-hyperbole
  (package
    (name "emacs-hyperbole")
@@ -1377,7 +1430,7 @@ organizing remote Go repository clones.")
 (define-public emacs-ghub
  (package
    (name "emacs-ghub")
-    (version "3.5.5")
+    (version "3.5.6")
    (source
     (origin
       (method git-fetch)
@@ -1386,7 +1439,7 @@ organizing remote Go repository clones.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1px27nh4cr3r16qmvig72jdirjzllvm2m4dzm59kfznhg3rf7vj0"))))
+        (base32 "1pw1rjrvvanlcxv3rb64s2p646zfaipp7h7v8djlrrnlgy6mwbqd"))))
    (build-system emacs-build-system)
    (arguments
     (list
@@ -3916,7 +3969,7 @@ evaluations.  The entry point is @code{M-x build-farm} command.")
 (define-public emacs-d-mode
  (package
    (name "emacs-d-mode")
-    (version "2.0.11")
+    (version "2.0.12")
    (source
     (origin
       (method git-fetch)
@@ -3925,7 +3978,7 @@ evaluations.  The entry point is @code{M-x build-farm} command.")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0vkl470vvmxap8ca773a0jvjvalmvdbbax3qvgjdclp54ml75al4"))))
+        (base32 "0mwd412d2kha8avkyhvvkh8r7an859xk18f7phgx7kj989pr3xkr"))))
    (build-system emacs-build-system)
    (propagated-inputs
     (list emacs-undercover))
@@ -4136,16 +4189,16 @@ in the center.")
 (define-public emacs-undo-tree
  (package
    (name "emacs-undo-tree")
-    (version "0.8.1")
+    (version "0.8.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://gitlab.com/tsc25/undo-tree")
-             (commit (string-append "release/" version))))
+             (commit "42aab056e37e033816b2d192f9121b89410b958e"))) ; no 0.8.2 tag
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1khkwrrbwaimspc013n4k9mpv8g302r0zkrsqnza2x1d3qznn08y"))))
+        (base32 "1xvkxc078b4z5zqwndz6jcv4ga8yd2ci32v7l8pdvqjmz7fq7bfz"))))
    (build-system emacs-build-system)
    (propagated-inputs
     (list emacs-queue))
@@ -11233,14 +11286,14 @@ of its name.")
 (define-public emacs-rainbow-mode
  (package
    (name "emacs-rainbow-mode")
-    (version "1.0.5")
+    (version "1.0.6")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://elpa.gnu.org/packages/"
-                           "rainbow-mode-" version ".el"))
+                           "rainbow-mode-" version ".tar"))
       (sha256
-        (base32 "159fps843k5pap9k04a7ll1k3gw6d9c6w08lq4bbc3lqg78aa2l9"))))
+        (base32 "04v73cm1cap19vwc8lqsw0rmfr9v7r3swc4wgxnk9dnzxi9j2527"))))
    (build-system emacs-build-system)
    (home-page "https://elpa.gnu.org/packages/rainbow-mode.html")
    (synopsis "Colorize color names in buffers")
@@ -12826,7 +12879,7 @@ passive voice.")
 (define-public emacs-org
  (package
    (name "emacs-org")
-    (version "9.5.3")
+    (version "9.5.4")
    (source
     (origin
       (method git-fetch)
@@ -12835,7 +12888,7 @@ passive voice.")
             (commit (string-append "release_" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0h1n6gqxv3kj3y98n5547rhpw4qnp03lfar79npb4paqgpxf76wb"))))
+        (base32 "1an866kkn5r84933s04agm1c3197kza2pvk8lqp2xzpjd09ba394"))))
    (build-system emacs-build-system)
    (arguments
     `(#:tests? #t
@@ -18587,6 +18640,28 @@ files, allowing for actions to be performed based on search criteria.")
 Chinese to English.")
    (license license:gpl3+)))

+(define-public emacs-org-auto-tangle
+  (package
+    (name "emacs-org-auto-tangle")
+    (version "0.4.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/yilkalargaw/org-auto-tangle")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1zb7vcmhmjiqpbbhqrqci689rnpn10p985cs5jk9sgg66xsbrgs3"))))
+    (build-system emacs-build-system)
+    (propagated-inputs (list emacs-async))
+    (home-page "https://github.com/yilkalargaw/org-auto-tangle")
+    (synopsis "Automatically tangle code blocks on save")
+    (description
+     "@code{org-auto-tangle} allows you to automatically tangle code blocks
+whenever saving an @code{org-mode} file.")
+    (license license:bsd-2)))
+
 (define-public emacs-org-auto-expand
  (let ((commit "4938d5f6460e2f8f051ba9ac000b291bfa43ef62")
        (revision "1"))
@@ -19494,16 +19569,14 @@ or expressions with SVG rounded box labels that are fully customizable.")
 (define-public emacs-kind-icon
  (package
    (name "emacs-kind-icon")
-    (version "0.1.4")
+    (version "0.1.5")
    (source
     (origin
       (method url-fetch)
-       (uri (string-append
-             "https://elpa.gnu.org/packages/kind-icon-"
-             version
-             ".tar"))
+       (uri (string-append "https://elpa.gnu.org/packages/kind-icon-"
+                           version ".tar"))
       (sha256
-        (base32 "00pyvnq4dx51l2wbhvm6k6cx5xmy32j4h1lkr5kr8s3j5w83ip25"))))
+        (base32 "0qajj89vkgc9gbgff6akzll53jy0kgkv6c9jvwpl32rbg8v0wp63"))))
    (build-system emacs-build-system)
    (propagated-inputs (list emacs-svg-lib))
    (home-page "https://github.com/jdtsmith/kind-icon")
@@ -27826,7 +27899,7 @@ Emacs that integrate with major modes like Org-mode.")
 (define-public emacs-modus-themes
  (package
    (name "emacs-modus-themes")
-    (version "2.4.0")
+    (version "2.4.1")
    (source
     (origin
       (method git-fetch)
@@ -27835,7 +27908,7 @@ Emacs that integrate with major modes like Org-mode.")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0ia6r68fqbv64r9jm92vmqypq15nl8yy07n18hqrfbp1fy47zds1"))))
+        (base32 "0b4y8dzyc9qwwaf2ngqiwyfcnhwlr49kxhc96laqk20lvjlfsrnx"))))
    (native-inputs (list texinfo))
    (build-system emacs-build-system)
    (arguments
@@ -27937,28 +28010,30 @@ and it should work well with 256 color terminals.")
    (license license:gpl3+)))

 (define-public emacs-dimmer
-  (package
-    (name "emacs-dimmer")
-    (version "0.4.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/gonewest818/dimmer.el")
-             (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "0dw0qh5hm1x76s5cqxvylvmjgy0jwy11xm258g6kmx6w1k6r1d2l"))))
-    (build-system emacs-build-system)
-    (home-page "https://github.com/gonewest818/dimmer.el")
-    (synopsis "Visually highlights the selected buffer in Emacs")
-    (description "Dimmer provides a minor mode that indicates which buffer is
+  (let ((commit "2f915b100044e09dd647b22085e1696249c4b115")
+        (revision "1"))
+    (package
+      (name "emacs-dimmer")
+      (version (git-version "0.4.2" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/gonewest818/dimmer.el")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "00y6645zjary1sz7517qy5pjwfm5ipsc46sypmdygin65hbbc8wg"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/gonewest818/dimmer.el")
+      (synopsis "Visually highlights the selected buffer in Emacs")
+      (description "Dimmer provides a minor mode that indicates which buffer is
 currently active by dimming the faces in the other buffers.  It does this
 nondestructively, and computes the dimmed faces dynamically such that your
 overall color scheme is shown in a muted form without requiring you to define
 what is a \"dim\" version of every face.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))

 (define-public emacs-minibuffer-line
  (package
@@ -31512,6 +31587,59 @@ zoomable and moveable map display, display of tracks and POIs from GPX files,
 parallel fetching of tiles with cURL, and more.")
    (license license:gpl3+)))

+(define-public emacs-corfu-terminal
+  ;; Upstream does not tag releases, version taken from package header.
+  (let ((commit "7c5a8a1c07b6c1a41b358b083d5bf7773701d26b")
+        (revision "0"))
+    (package
+      (name "emacs-corfu-terminal")
+      (version (git-version "0.4" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri
+          (git-reference
+           (url "https://codeberg.org/akib/emacs-corfu-terminal")
+           (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0pk5vfcz8w4hiqrwzwpxdjzlbhla0bw7a1h6v0mqxad0j9y7v3nw"))))
+      (build-system emacs-build-system)
+      (propagated-inputs (list emacs-corfu emacs-popon))
+      (home-page "https://codeberg.org/akib/emacs-corfu-terminal/")
+      (synopsis "Replace corfu child frames with popups")
+      (description
+       "This package replaces the child frames @code{emacs-corfu} uses
+with popups, which also work in the terminal.")
+      (license license:gpl3+))))
+
+(define-public emacs-corfu-doc-terminal
+  ;; Upstream does not tag releases, version taken from package header.
+  (let ((commit "d8945c64b52d76e864b767b3048674f222daf80b")
+        (revision "0"))
+    (package
+      (name "emacs-corfu-doc-terminal")
+      (version (git-version "0.5" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri
+          (git-reference
+           (url "https://codeberg.org/akib/emacs-corfu-doc-terminal")
+           (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0j0dd8np5x93wic22bc5i9h7bq2gj700n4fh11dzzgsj14lv2r5k"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       (list emacs-corfu emacs-corfu-doc emacs-corfu-terminal emacs-popon))
+      (home-page "https://codeberg.org/akib/emacs-corfu-doc-terminal/")
+      (synopsis "Replace corfu docmentation child frames with popups")
+      (description
+       "This package replaces the child frames @code{emacs-corfu-doc} uses
+with popups, which also work in the terminal.")
+      (license license:gpl3+))))
+
 (define-public emacs-popon
  ;; Upstream does not tag releases.  The commit below matches the version
  ;; bump.
@@ -1840,7 +1840,8 @@ an embedded event driven algorithm.")
    (arguments
     (substitute-keyword-arguments (package-arguments libngspice)
       ((#:configure-flags flags)
-        `(delete "--with-ngshared" ,flags))
+        `(cons "--with-readline=yes"
+               (delete "--with-ngshared" ,flags)))
       ((#:phases phases)
        `(modify-phases ,phases
           (add-after 'unpack 'delete-include-files
@@ -2740,21 +2741,19 @@ export filters.")
 (define-public meshlab
  (package
    (name "meshlab")
-    (version "2020.06")
+    (version "2022.02")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/cnr-isti-vclab/meshlab")
-                    (commit (string-append "Meshlab-" version))
+                    (commit (string-append "MeshLab-" version))
                    (recursive? #t)))
              (file-name (git-file-name name version))
              (sha256
-               (base32 "1cgx24wxh2ah5pff51rcrk6x8qcdjpkxcdak7s4cfzmxvjlshydd"))))
+               (base32 "0dkh9qw9z2160s6gjiv0a601kp6hvl66cplvi8rfc892zcykgiwd"))))
    (build-system cmake-build-system)
    (inputs
     (list qtbase-5
-           qtscript
-           qtxmlpatterns
           mesa
           glu
           glew
@@ -2764,34 +2763,29 @@ export filters.")
           libfreenect
           lib3ds
           openctm
-           ;; FIXME: Compilation fails with system qhull:
-           ;; https://github.com/cnr-isti-vclab/meshlab/issues/678
-           ;; ("qhull" ,qhull)
-           ))
+           qhull))
    (arguments
-     `(#:tests? #f                                ; Has no tests
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'go-to-source-dir
-           (lambda _ (chdir "src") #t))
-         (add-after 'install 'move-files
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((lib (string-append (assoc-ref outputs "out")
-                                       "/lib")))
-               (rename-file
-                (string-append lib "/meshlab/libmeshlab-common.so")
-                (string-append lib "/libmeshlab-common.so"))
-               #t))))))
+     (list #:tests? #f                  ; Has no tests
+           #:configure-flags
+           #~(list (string-append "-DCMAKE_MODULE_LINKER_FLAGS=-Wl,-rpath="
+                                  #$output "/lib/meshlab")
+                   (string-append "-DCMAKE_SHARED_LINKER_FLAGS=-Wl,-rpath="
+                                  #$output "/lib/meshlab")
+                   (string-append "-DCMAKE_EXE_LINKER_FLAGS=-Wl,-rpath="
+                                  #$output "/lib/meshlab"))
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'go-to-source-dir
+                 (lambda _ (chdir "src"))))))
    (synopsis "3D triangular mesh processing and editing software")
    (home-page "https://www.meshlab.net/")
-    (description "MeshLab is a system for the processing and
-editing of unstructured large 3D triangular meshes.  It is aimed to help the
-processing of the typical not-so-small unstructured models arising in 3D
-scanning, providing a set of tools for editing, cleaning, healing, inspecting,
-rendering and converting this kind of meshes.  These tools include MeshLab
-proper, a versatile program with a graphical user interface, and meshlabserver,
-a program that can perform mesh processing tasks in batch mode, without a
-GUI.")
+    (description "MeshLab is a system for the processing and editing of large,
+unstructured, 3D triangular meshes.  It is aimed to help the processing of the
+typical, not-so-small unstructured models arising in 3D scanning, providing a
+set of tools for editing, cleaning, healing, inspecting, rendering and
+converting this kind of meshes.  These tools include MeshLab proper, a
+versatile program with a graphical user interface, and @samp{meshlabserver}, a
+program that can perform mesh processing tasks in batch mode, without a GUI.")
    (license license:gpl3+)))

 (define-public poke
@@ -2200,7 +2200,7 @@ Every puzzle has a complete solution, although there may be more than one.")
   (license license:gpl2+)))

 (define-public retux
-  (let ((release "1.5")
+  (let ((release "1.6.1")
        (revision 0))
    (package
      (name "retux")
@@ -2216,7 +2216,7 @@ Every puzzle has a complete solution, although there may be more than one.")
                                    release "-src.zip"))
                (sha256
                 (base32
-                  "1yima7s36hn2kh5h08lczc5iid8jbdxk7x1g5ms6knaznzj7rll3"))))
+                  "1bkyfm0h4kys0x7c1340fnkhgnmcrf4j2xjm250r5w8q6l7v2wj4"))))
      (build-system python-build-system)
      (arguments
       `(#:tests? #f                    ; no check target
@@ -2237,12 +2237,11 @@ Every puzzle has a complete solution, although there may be more than one.")
                    (string-append "\"" data "\",")))

                 (copy-file "retux.py" (string-append bin "/retux"))
-                 (copy-recursively "data" data)
-                 #t))))))
+                 (copy-recursively "data" data)))))))
      (native-inputs
       (list unzip))
      (inputs
-       (list python-sge python-six python-xsge))
+       (list python-sge python-xsge))
      (home-page "https://retux-game.github.io/")
      (synopsis "Action platformer game")
      (description
@@ -9,7 +9,7 @@
 ;;; Copyright © 2017 Petter <petter@mykolab.ch>
 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
-;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019, 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;; Copyright © 2019, 2020, 2021 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
@@ -176,6 +176,23 @@ or through unencrypted TCP/IP suitable for use behind a firewall with
 shared NFS home directories.")
    (license license:gpl2+)))                     ; or Academic Free License 2.1

+;;; This variant is used for the Jami service: it provides an entry point to
+;;; further customize the configuration of the D-Bus instance run by the
+;;; jami-dbus-session service.
+(define-public dbus-for-jami
+  (hidden-package
+   (package/inherit dbus
+     (name "dbus-for-jami")
+     (arguments
+      (substitute-keyword-arguments (package-arguments dbus)
+        ((#:phases phases)
+         `(modify-phases ,phases
+            (add-after 'unpack 'customize-config
+              (lambda _
+                (substitute* "bus/session.conf.in"
+                  (("@SYSCONFDIR_FROM_PKGDATADIR@/dbus-1/session-local.conf")
+                   "/var/run/jami/session-local.conf")))))))))))
+
 (define glib
  (package
    (name "glib")
@@ -16,6 +16,7 @@
 ;;; Copyright © 2021, 2022 Justin Veilleux <terramorpha@cock.li>
 ;;; Copyright © 2021 Attila Lendvai <attila@lendvai.name>
 ;;; Copyright © 2021 Charles Jackson <charles.b.jackson@protonmail.com>
+;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -37,6 +38,7 @@
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system copy)
  #:use-module (guix build-system meson)
+  #:use-module (guix build-system python)
  #:use-module (guix gexp)
  #:use-module (guix git-download)
  #:use-module (guix packages)
@@ -50,6 +52,7 @@
  #:use-module (gnu packages base)
  #:use-module (gnu packages bash)
  #:use-module (gnu packages build-tools)
+  #:use-module (gnu packages check)
  #:use-module (gnu packages gettext)
  #:use-module (gnu packages glib)
  #:use-module (gnu packages gnome)
@@ -58,6 +61,7 @@
  #:use-module (gnu packages image)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
+  #:use-module (gnu packages python-science)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages ssh)
  #:use-module (gnu packages tls)
@@ -217,6 +221,86 @@ simple and consistent.")
 and a few extra features.")
    (license license:gpl3)))

+(define-public gnome-plots
+  (package
+    (name "gnome-plots")
+    (version "0.6.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/alexhuntley/Plots")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "168wcsrkmvq79xmwvbq615msd4q0rg7f57xqicidnr78jx4x37rd"))))
+    (build-system python-build-system)
+    (inputs
+     (list bash-minimal                 ; for wrap-program
+           gtk+
+           pango
+           python-freetype-py
+           python-jinja2
+           python-lark-parser
+           python-numpy
+           python-pycairo
+           python-pyglm
+           python-pygobject
+           python-pyopengl))
+    (native-inputs
+     (list python-pytest))
+    (arguments
+     (list
+      #:imported-modules `((guix build glib-or-gtk-build-system)
+                           ,@%python-build-system-modules)
+      #:modules '((guix build python-build-system)
+                  ((guix build glib-or-gtk-build-system) #:prefix glib-or-gtk:)
+                  (guix build utils)
+                  (ice-9 match))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'adjust-lark-requirement
+            (lambda _
+              (substitute* "setup.py"
+                (("lark") "lark-parser"))))
+          (add-after 'install 'install-more
+            (lambda _
+              (let* ((datadir (string-append #$output "/share"))
+                     (help (string-append datadir "/help"))
+                     (icons (string-append datadir "/icons/hicolor")))
+                (map (lambda (filename)
+                       (match (string-split filename #\/)
+                         ((_ lang dir ... name)
+                          (install-file filename
+                                        (string-join (cons* help lang "plots" dir)
+                                                     "/")))))
+                     (find-files "help"))
+                (install-file "res/com.github.alexhuntley.Plots.desktop"
+                              (string-append datadir "/applications/"))
+                (install-file "res/com.github.alexhuntley.Plots.svg"
+                              (string-append icons "/scalable/apps/"))
+                (install-file "res/com.github.alexhuntley.Plots-symbolic.svg"
+                              (string-append icons "/symbolic/apps/")))))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "pytest" "-vv"))))
+          (add-after 'wrap 'gi-wrap
+            (lambda _
+              (let ((prog (string-append #$output "/bin/plots")))
+                (wrap-program prog
+                  `("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH")))))))
+          (add-after 'wrap 'glib-or-gtk-wrap
+            (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))))
+    (home-page "https://apps.gnome.org/app/com.github.alexhuntley.Plots/")
+    (synopsis "Simple graph plotting")
+    (description "Plots makes it easy to visualise mathematical formulae.  In
+addition to basic arithmetic operations, it supports trigonometric,
+hyperbolic, exponential, and logarithmic functions, as well as arbitrary sums
+and products.  Plots is designed to integrate well with the GNOME desktop and
+takes advantage of modern hardware using OpenGL.")
+    (license license:gpl3+)))
+
 (define-public gnome-shell-extension-appindicator
  (package
    (name "gnome-shell-extension-appindicator")
@@ -6694,7 +6694,7 @@ a secret password store, an adblocker, and a modern UI.")
 (define-public epiphany
  (package
    (name "epiphany")
-    (version "41.2")
+    (version "42.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnome/sources/epiphany/"
@@ -6702,65 +6702,61 @@ a secret password store, an adblocker, and a modern UI.")
                                  "epiphany-" version ".tar.xz"))
              (sha256
               (base32
-                "0k7b22zq3z1kllzqxgwsvwb1lp0j6rjb3k1hvhna3i573wc4mpji"))
-              (patches
-               (search-patches "epiphany-update-libportal-usage.patch"))))
+                "0b8rhns3b58f8dnp83mm1g933aqf88d8wrfyyp7jq3fihvw2rh4j"))))
    (build-system meson-build-system)
    (arguments
-     `(#:glib-or-gtk? #t
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'skip-gtk-update-icon-cache
-           ;; Don't create 'icon-theme.cache'.
-           (lambda _
-             (substitute* "post_install.py"
-               (("gtk-update-icon-cache") "true"))))
-         (add-after 'unpack 'disable-failing-tests
-           (lambda _
-             (substitute* "tests/meson.build"
-               ;; embed_shell fails, because webkitgtk apparently no longer
-               ;; supports overriding the ftp schema web_app_utils fails due
-               ;; to missing network access.
-               (("(embed_shell|web_app_utils)_test,")
-                "find_program('sh'), args: ['-c', 'exit 77'],"))))
-         (add-before 'check 'pre-check
-           (lambda _
-             ;; Tests require a running X server.
-             (system "Xvfb :1 &")
-             (setenv "DISPLAY" ":1"))))
-       #:configure-flags
-       ;; Otherwise, the RUNPATH will lack the final 'epiphany' path component.
-       (list (string-append "-Dc_link_args=-Wl,-rpath="
-                            (assoc-ref %outputs "out") "/lib/epiphany"))))
-    (propagated-inputs
-     (list dconf))
-    (native-inputs
-     `(("desktop-file-utils" ,desktop-file-utils) ; for update-desktop-database
-       ("glib:bin" ,glib "bin") ; for glib-mkenums
-       ("intltool" ,intltool)
-       ("itstool" ,itstool)
-       ("pkg-config" ,pkg-config)
-       ("xmllint" ,libxml2)
-       ("xorg-server" ,xorg-server-for-tests)))
-    (inputs
-     `(("avahi" ,avahi)
-       ("gcr" ,gcr)
-       ("librsvg" ,librsvg) ; for loading SVG files
-       ("glib-networking" ,glib-networking)
-       ("gnome-desktop" ,gnome-desktop)
-       ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
-       ("json-glib" ,json-glib)
-       ("iso-codes" ,iso-codes)
-       ("libarchive" ,libarchive)
-       ("libdazzle" ,libdazzle)
-       ("libhandy" ,libhandy)
-       ("libnotify" ,libnotify)
-       ("libportal" ,libportal)
-       ("libsecret" ,libsecret)
-       ("libxslt" ,libxslt)
-       ("nettle" ,nettle) ; for hogweed
-       ("sqlite" ,sqlite)
-       ("webkitgtk" ,webkitgtk-with-libsoup2)))
+     (list
+      #:glib-or-gtk? #t
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'skip-gtk-update-icon-cache
+            ;; Don't create 'icon-theme.cache'.
+            (lambda _
+              (substitute* "post_install.py"
+                (("gtk-update-icon-cache") "true"))))
+          (add-after 'unpack 'disable-failing-tests
+            (lambda _
+              (substitute* "tests/meson.build"
+                ;; embed_shell fails, because webkitgtk apparently no longer
+                ;; supports overriding the ftp schema web_app_utils fails due
+                ;; to missing network access.
+                (("(embed_shell|web_app_utils)_test,")
+                 "find_program('sh'), args: ['-c', 'exit 77'],"))))
+          (add-before 'check 'pre-check
+            (lambda _
+              ;; Tests require a running X server.
+              (system "Xvfb :1 &")
+              (setenv "DISPLAY" ":1"))))
+      #:configure-flags
+      ;; Otherwise, the RUNPATH will lack the final 'epiphany' path component.
+      #~(list (string-append "-Dc_link_args=-Wl,-rpath="
+                             #$output "/lib/epiphany"))))
+    (propagated-inputs (list dconf))
+    (native-inputs (list desktop-file-utils ; for update-desktop-database
+                         `(,glib "bin") ; for glib-mkenums
+                         intltool
+                         itstool
+                         pkg-config
+                         libxml2
+                         xorg-server-for-tests))
+    (inputs (list avahi
+                  gcr
+                  librsvg ; for loading SVG files
+                  glib-networking
+                  gnome-desktop
+                  gsettings-desktop-schemas
+                  json-glib
+                  iso-codes
+                  libarchive
+                  libdazzle
+                  libhandy
+                  libnotify
+                  libportal
+                  libsecret
+                  libxslt
+                  nettle ; for hogweed
+                  sqlite
+                  webkitgtk-with-libsoup2))
    (home-page "https://wiki.gnome.org/Apps/Web")
    (synopsis "GNOME web browser")
    (description
@@ -9784,3 +9784,62 @@ Features:
     "@code{go-github-com-go-chi-chi-v5} is an HTTP router that lets the user
 decompose request handling into many smaller layers.")
    (license license:expat)))
+
+(define-public go-sigs-k8s-io-yaml
+  (package
+    (name "go-sigs-k8s-io-yaml")
+    (version "1.3.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/kubernetes-sigs/yaml")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0qxs0ppqwqrfqs4aywyn1h28xh1qlj5ds4drmygaz1plrxj02dqn"))))
+    (build-system go-build-system)
+    (arguments '(#:import-path "sigs.k8s.io/yaml"))
+    (propagated-inputs (list go-gopkg-in-yaml-v2 go-github-com-davecgh-go-spew))
+    (home-page "https://sigs.k8s.io/yaml")
+    (synopsis "YAML marshaling and unmarshaling support for Go")
+    (description
+     "This package provides a Go library that first converts YAML to JSON
+using @code{go-yaml} and then uses @code{json.Marshal} and
+@code{json.Unmarshal} to convert to or from the struct. This means that
+it effectively reuses the JSON struct tags as well as the custom JSON
+methods @code{MarshalJSON} and @code{UnmarshalJSON} unlike
+@code{go-yaml}.
+
+kubernetes-sigs/yaml is a permanent fork of
+@url{https://github.com/ghodss/yaml,ghodss/yaml}.")
+    (license (list license:expat license:bsd-3))))
+
+(define-public go-github-com-google-go-jsonnet
+  (package
+    (name "go-github-com-google-go-jsonnet")
+    (version "0.18.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/google/go-jsonnet")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1dghqygag123zkgh2vrnq82cdag5z0p03v3489pwhs06r5g27wm3"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/google/go-jsonnet/cmd/jsonnet"
+       #:unpack-path "github.com/google/go-jsonnet"))
+    (propagated-inputs (list go-sigs-k8s-io-yaml go-gopkg-in-yaml-v2
+                             go-github-com-sergi-go-diff
+                             go-github-com-fatih-color))
+    (home-page "https://github.com/google/go-jsonnet")
+    (synopsis "Go implementation of Jsonnet")
+    (description
+     "This package provides an implementation of the @url{http://jsonnet.org/,
+Jsonnet} data templating language in Go.  It is a feature-complete,
+production-ready implementation, compatible with the original Jsonnet C++
+implementation.")
+    (license license:asl2.0)))
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017, 2018, 2019, 2020, 2022 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
-;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2020, 2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2021, 2022 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2020 Alexander Krotov <krotov@iitp.ru>
@@ -143,7 +143,7 @@ more.")
  (package
    (inherit igraph)
    (name "python-igraph")
-    (version "0.9.10")
+    (version "0.9.11")
    (source (origin
              (method git-fetch)
              ;; The PyPI archive lacks tests.
@@ -153,7 +153,7 @@ more.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "06qvwmiw2klk3bg8g5af0ppjwrm9kzy4595w5d06qh2v3gq0svbk"))))
+                "1xlr0cnf3a1vs9n2psvgrmjhld4n1xr79kkjqzby4pxxyzk1bydn"))))
    (build-system python-build-system)
    (arguments
     (list
@@ -15,7 +15,7 @@
 ;;; Copyright © 2016 Patrick Hetu <patrick.hetu@auf.org>
 ;;; Copyright © 2016 Nikita <nikita@n0.is>
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017–2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017, 2019, 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2018, 2020 Arun Isaac <arunisaac@systemreboot.net>
@@ -1563,14 +1563,14 @@ guile-gnome-platform (GNOME developer libraries), and guile-gtksourceview.")
 (define-public cairomm
  (package
    (name "cairomm")
-    (version "1.16.0")
+    (version "1.16.1")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://www.cairographics.org/releases/"
                                  name "-" version ".tar.xz"))
              (sha256
               (base32
-                "1ya4y7qa000cjawqwswbqv26y5icfkmhs5iiiil4dxgrqn91923y"))))
+                "1im2yjzvjfx8s7cal9kwq23z936kppfmyag2zsnbim4dx7c60q3g"))))
    (build-system meson-build-system)
    (outputs '("out" "doc"))
    (arguments
@@ -1588,18 +1588,17 @@ guile-gnome-platform (GNOME developer libraries), and guile-gtksourceview.")
               (mkdir-p (string-append doc "/share"))
               (rename-file
                (string-append out "/share/doc")
-                (string-append doc "/share/doc"))
-               #t))))))
+                (string-append doc "/share/doc"))))))))
    (native-inputs
-     `(("boost" ,boost)
-       ("dot" ,graphviz)
-       ("doxygen" ,doxygen)
-       ("mm-common" ,mm-common)
-       ("perl" ,perl)
-       ("pkg-config" ,pkg-config)
-       ("xsltproc" ,libxslt)))
+     (list boost
+           doxygen
+           graphviz
+           mm-common
+           perl
+           pkg-config
+           libxslt))
    (inputs
-     `(("fontconfig" ,fontconfig)))
+     (list fontconfig))
    (propagated-inputs
     (list libsigc++ cairo))
    (home-page "https://cairographics.org/")
@@ -435,7 +435,16 @@ integrates with various databases on GUI toolkits such as Qt and Tk.")
       ((#:configure-flags flags)
        ;; Otherwise, the build would fail with: "error: invalid conversion
        ;; from ‘const char*’ to ‘char*’ [-fpermissive]".
-        `(cons "-DCMAKE_CXX_FLAGS=-fpermissive" ,flags))))))
+        `(cons "-DCMAKE_CXX_FLAGS=-fpermissive" ,flags))
+       ((#:phases phases)
+        #~(modify-phases #$phases
+            (add-after 'unpack 'remove-kernel-version
+              ;; Avoid embedding the kernel version for reproducible builds
+              (lambda _
+                (substitute*
+                    "ThirdParty/hdf5/vtkhdf5/config/cmake/libhdf5.settings.cmake.in"
+                  (("Host system: \\@CMAKE_HOST_SYSTEM\\@")
+                   "Host system: @CMAKE_SYSTEM_NAME@"))))))))))

 (define-public opencv
  (package
@@ -151,7 +151,7 @@ irssi, but graphical.")
 (define-public irssi
  (package
    (name "irssi")
-    (version "1.2.3")
+    (version "1.4.1")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/irssi/irssi/"
@@ -159,7 +159,7 @@ irssi, but graphical.")
                                  version ".tar.xz"))
              (sha256
               (base32
-                "17vninwcdfxw39xl2q55qircckckjk2xlvkvlwgj5lhlxppvyix6"))))
+                "00bmwkpzhqqnsajakk7dviap1i8s89375kwpdyxg65ms3ds94xka"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases
@@ -172,8 +172,7 @@ irssi, but graphical.")
                       (string-append "--prefix=" out)
                       (string-append "--enable-true-color")
                       (string-append "--with-proxy")
-                       (string-append "--with-socks")
-                       (string-append "--with-bot")))))
+                       (string-append "--with-socks")))))
         (add-before 'check 'set-home
           (lambda _
             (setenv "HOME" (getcwd)))))))
@@ -182,10 +181,14 @@ irssi, but graphical.")
    (native-inputs
     (list pkg-config))
    (home-page "https://irssi.org/")
-    (synopsis "Terminal-based IRC client")
+    (synopsis "Extensible terminal-based IRC client")
    (description
-     "Irssi is a terminal based IRC client for UNIX systems.  It also supports
-SILC and ICB protocols via plugins.")
+     "Irssi is a text terminal-based @acronym{IRC, Internet relay chat} client.
+It is completely themable and extensible through Perl scripts, of which many
+have already been written by the community.
+
+Plug-ins add support for other protocols like @acronym{SILC, Secure Internet Live
+Conferencing} and @acronym{ICB, Internet Citizen's Band}.")
    (license license:gpl2+)))

 (define-public weechat
@@ -3,7 +3,7 @@
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016, 2017 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017, 2019, 2021 Carlo Zancanaro <carlo@zancanaro.id.au>
-;;; Copyright © 2017-2021 Julien Lepiller <julien@lepiller.eu>
+;;; Copyright © 2017-2022 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
 ;;; Copyright © 2016, 2017, 2018 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2017, 2019, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -4371,6 +4371,14 @@ from source tags and class annotations.")))
             (copy-recursively "src/main/resources"
                               "build/classes/")
             #t))
+         (add-before 'build 'fix-jdom
+           (lambda _
+             ;; The newer version of jdom now sets multiple features by default
+             ;; that are not supported.
+             ;; Skip these features
+             (substitute* "src/main/java/org/codehaus/plexus/metadata/merge/MXParser.java"
+               (("throw new XmlPullParserException\\(\"unsupporte feature \"\\+name\\);")
+                "// skip"))))
         (add-before 'build 'reinstate-cli
           ;; The CLI was removed in 2.1.0, but we still need it to build some
           ;; maven dependencies, and some parts of maven itself. We can't use
@@ -4537,6 +4545,14 @@ from source tags and class annotations.")))
             (copy-recursively "src/main/resources"
                               "build/classes/")
             #t))
+         (add-before 'build 'fix-jdom
+           (lambda _
+             ;; The newer version of jdom now sets multiple features by default
+             ;; that are not supported.
+             ;; Skip these features
+             (substitute* "src/main/java/org/codehaus/plexus/metadata/merge/MXParser.java"
+               (("throw new XmlPullParserException\\(\"unsupporte feature \"\\+name\\);")
+                "// skip"))))
         (add-before 'check 'fix-test-location
           (lambda _
             (substitute* '("src/test/java/org/codehaus/plexus/metadata/DefaultComponentDescriptorWriterTest.java"
@@ -351,17 +351,17 @@ 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-5.17-version "5.17.12")
+(define-public linux-libre-5.17-version "5.17.14")
 (define-public linux-libre-5.17-gnu-revision "gnu")
 (define deblob-scripts-5.17
  (linux-libre-deblob-scripts
   linux-libre-5.17-version
   linux-libre-5.17-gnu-revision
   (base32 "08ip5g827f30qzb3j2l19zkbdqv00sij46nbrjg75h5kkasdbfgr")
-   (base32 "1zd4ds6ha4a2acqnalp234r2m9rz9p30qmy1aqri78i06aw7flwn")))
+   (base32 "1654fibbwnbcgnikn1qqa5igd2j90kslbb3pshph5wpj052cvgjy")))
 (define-public linux-libre-5.17-pristine-source
  (let ((version linux-libre-5.17-version)
-        (hash (base32 "0yr8xfds5l1s3lk8qk67mgy0l4yh2jfvjc7xwrfws3ci020ss9a2")))
+        (hash (base32 "0r2skbgxzw42cn29mr7i9w7fczzxhc1lx3xvri44ljjyfdqn7r0b")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-5.17)))
@@ -369,37 +369,37 @@ 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 "5.15.44")
+(define-public linux-libre-5.15-version "5.15.46")
 (define-public linux-libre-5.15-gnu-revision "gnu")
 (define deblob-scripts-5.15
  (linux-libre-deblob-scripts
   linux-libre-5.15-version
   linux-libre-5.15-gnu-revision
   (base32 "1n57mz5agvf1d0ggbg080d7hvx8p9y0iqxkq4ypg10a7n96zy7y5")
-   (base32 "0gs92qbpvirwd02rpwwnja7771z2azbiy9ppy9ynpr14lxmzxnnh")))
+   (base32 "17xsn91h0c2d8igpzgmjm1g58nfpihlhgg9wm8zbfyd5g4airs8f")))
 (define-public linux-libre-5.15-pristine-source
  (let ((version linux-libre-5.15-version)
-        (hash (base32 "1p1jz0lxmzyj0c51afqghylg9kblk8zmlw92zq6bsn37wlwbrylv")))
+        (hash (base32 "0srp0wypl24gf5yz91mpk1c2kllabq6wvby1wqrrbdwvfx35figb")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-5.15)))

-(define-public linux-libre-5.10-version "5.10.119")
+(define-public linux-libre-5.10-version "5.10.121")
 (define-public linux-libre-5.10-gnu-revision "gnu1")
 (define deblob-scripts-5.10
  (linux-libre-deblob-scripts
   linux-libre-5.10-version
   linux-libre-5.10-gnu-revision
   (base32 "0mw7qn77y9c6wrnw4rjvf75cpm1w6n1aqqhf8cnghcb97p2yxxrf")
-   (base32 "1xyhz0dyrkg2avz382ly3dzpa5v89x49gfzx80c1drpwsk7jg6gp")))
+   (base32 "1ryfc8fppigssrzz5lfbqgli49cgs3lmf0yh46lpi2k0j2x30qcc")))
 (define-public linux-libre-5.10-pristine-source
  (let ((version linux-libre-5.10-version)
-        (hash (base32 "04952zaz2kfwf7agy4laz50f9sl3mrnpqlbwbj84q1xpl9akwd9y")))
+        (hash (base32 "1iljaaiwqg30rqb9zxrxc4l1p56q75jf0zvsrmn67z2a12sffi4h")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-5.10)))

-(define-public linux-libre-5.4-version "5.4.196")
+(define-public linux-libre-5.4-version "5.4.197")
 (define-public linux-libre-5.4-gnu-revision "gnu1")
 (define deblob-scripts-5.4
  (linux-libre-deblob-scripts
@@ -409,12 +409,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "05i286d98fm2pdf9724x1dsmfcm7gsd7yyyvxqlpisyj1kx14hda")))
 (define-public linux-libre-5.4-pristine-source
  (let ((version linux-libre-5.4-version)
-        (hash (base32 "1x5irgki792f21hm5146xary0260cl9r475kvw8vm9w32vyx18ig")))
+        (hash (base32 "1a1nzrx873vwlpm018l6rk19yh59badvwsknw3chbkbhzjrigbf2")))
   (make-linux-libre-source version
                            (%upstream-linux-source version hash)
                            deblob-scripts-5.4)))

-(define-public linux-libre-4.19-version "4.19.245")
+(define-public linux-libre-4.19-version "4.19.246")
 (define-public linux-libre-4.19-gnu-revision "gnu1")
 (define deblob-scripts-4.19
  (linux-libre-deblob-scripts
@@ -424,12 +424,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "1dnjgx1nmawm9gm0yf15nl80nmg7hy7q2vl3jxjbwj6hlrfv5dmx")))
 (define-public linux-libre-4.19-pristine-source
  (let ((version linux-libre-4.19-version)
-        (hash (base32 "1s58qci6xhmss12glzkqk41kp60pqmzh4d84kyz4m4nf4xhdvzcr")))
+        (hash (base32 "0fmsglkvdgdmrkm53vyi9d4hvdl4py9qn1z0mni224n96rd2zb80")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-4.19)))

-(define-public linux-libre-4.14-version "4.14.281")
+(define-public linux-libre-4.14-version "4.14.282")
 (define-public linux-libre-4.14-gnu-revision "gnu1")
 (define deblob-scripts-4.14
  (linux-libre-deblob-scripts
@@ -439,12 +439,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "1dnjgx1nmawm9gm0yf15nl80nmg7hy7q2vl3jxjbwj6hlrfv5dmx")))
 (define-public linux-libre-4.14-pristine-source
  (let ((version linux-libre-4.14-version)
-        (hash (base32 "0pivb1m2cwqnlm8bhd4ccnlq9pwp2r5lmn77gp91k6vbjv3gkqis")))
+        (hash (base32 "18sp2qvk8dkjrlxwf4d470282m9wyvhajvyys9vs94rh1i3whdv6")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-4.14)))

-(define-public linux-libre-4.9-version "4.9.316")
+(define-public linux-libre-4.9-version "4.9.317")
 (define-public linux-libre-4.9-gnu-revision "gnu1")
 (define deblob-scripts-4.9
  (linux-libre-deblob-scripts
@@ -454,7 +454,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
   (base32 "14jyn2yrbm6ayp0bszs4f9jy3p1qkrj5p5gf5c42spr67aa2lv2v")))
 (define-public linux-libre-4.9-pristine-source
  (let ((version linux-libre-4.9-version)
-        (hash (base32 "05yd7djm6dcxv3vaylhmj3p0yml421azv8qabmhv4ric1f99idjp")))
+        (hash (base32 "06qdqcplslnp1ncaqvp5yjr294rz3x4qrxnv522v76awj6dkd8vy")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-4.9)))
@@ -3693,7 +3693,7 @@ for systems using the Linux kernel.  This includes commands such as
 (define-public inotify-tools
  (package
    (name "inotify-tools")
-    (version "3.20.11.0")
+    (version "3.22.6.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -3702,7 +3702,7 @@ for systems using the Linux kernel.  This includes commands such as
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "1m8avqccrhm38krlhp88a7v949f3hrzx060bbrr5dp5qw2nmw9j2"))))
+                "1j9j8k5zjp8m4cl53zjncnll9z4dnvzr4ygmfcjk0ci81i59b18i"))))
    (build-system gnu-build-system)
    (native-inputs
     (list autoconf automake libtool))
@@ -6362,8 +6362,7 @@ The collection contains a set of bandwidth and latency benchmark such as:
    (native-inputs
     (list autoconf automake pkg-config))
    (inputs
-     `(("libsysfs" ,sysfsutils)
-       ("openssl" ,openssl)))
+     (list sysfsutils openssl))
    (synopsis "Random number generator daemon")
    (description
     "Monitor a hardware random number generator, and supply entropy
@@ -7246,14 +7245,14 @@ re-use code and to avoid re-inventing the wheel.")
 (define-public libnftnl
  (package
    (name "libnftnl")
-    (version "1.2.1")
+    (version "1.2.2")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://netfilter.org/libnftnl/"
                           "libnftnl-" version ".tar.bz2"))
       (sha256
-        (base32 "0z4khm2mnys9mcl8ckwf19cw20jgrv8650nfncy3xcgs2k2aa23m"))))
+        (base32 "02kdxp4l1ds5lpkw6rxv6f7icc70am6ik3p9z5l8v48mkm7h1z4y"))))
    (build-system gnu-build-system)
    (native-inputs
     (list pkg-config))
@@ -7288,7 +7287,7 @@ used by nftables.")
 (define-public nftables
  (package
    (name "nftables")
-    (version "1.0.2")
+    (version "1.0.4")
    (source
     (origin
       (method url-fetch)
@@ -7297,9 +7296,7 @@ used by nftables.")
                  (string-append "https://www.nftables.org/projects/nftables"
                                 "/files/nftables-" version ".tar.bz2")))
       (sha256
-        (base32 "00jcjn1pl7qyqpg8pd4yhlkys7wbj4vkzgg73n27nmplzips6a0b"))
-       (patches
-        (search-patches "nftables-fix-makefile.patch"))))
+        (base32 "0ddsdj6zs78hndffl3iikpa1wzjxcpmr3xqcq4la71gnl7zb2zwj"))))
    (build-system gnu-build-system)
    (arguments `(#:configure-flags
                 '("--disable-static"
@@ -4457,7 +4457,7 @@ addition, removal, and random selection.")
 (define-public sbcl-quri
  (package
    (name "sbcl-quri")
-    (version "0.4.0")
+    (version "0.5.0")
    (source
     (origin
       (method git-fetch)
@@ -4466,7 +4466,7 @@ addition, removal, and random selection.")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0ka5haq3g72hvaz4hdv7y1d6df9ncmx029wwixn4r413gll5yxy7"))))
+        (base32 "0zpwjhs2zz9832wsjs00kbkjjl4bcs96krlnq9y75gi4f34fxj1x"))))
    (build-system asdf-build-system/sbcl)
    (arguments
     ;; Test system must be loaded before, otherwise tests fail with:
@@ -4481,7 +4481,7 @@ addition, removal, and random selection.")
    (synopsis "Yet another URI library for Common Lisp")
    (description
     "QURI (pronounced \"Q-ree\") is yet another URI library for Common
-Lisp. It is intended to be a replacement of PURI.")
+Lisp.  It is intended to be a replacement of PURI.")
    (license license:bsd-3)))

 (define-public cl-quri
@@ -577,9 +577,9 @@ output), and Binutils.")
         ;; These options are required for cross-compiling LLVM according
         ;; to <https://llvm.org/docs/HowToCrossCompileLLVM.html>.
         #$@(if (%current-target-system)
-                #~(,(string-append "-DLLVM_TABLEGEN="
-                                   #+(file-append this-package
-                                                  "/bin/llvm-tblgen"))
+                #~((string-append "-DLLVM_TABLEGEN="
+                                  #+(file-append this-package
+                                                 "/bin/llvm-tblgen"))
                   #$(string-append "-DLLVM_DEFAULT_TARGET_TRIPLE="
                                    (%current-target-system))
                   #$(string-append "-DLLVM_TARGET_ARCH="
@@ -3,7 +3,7 @@
 ;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
-;;; Copyright © 2018–2021 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018–2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Gábor Boskovits <boskovits@gmail.com>
 ;;; Copyright © 2019 Meiyo Peng <meiyo@riseup.net>
 ;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
@@ -164,29 +164,40 @@ commands, displaying the results via a web interface.")
 (define-public multitail
  (package
    (name "multitail")
-    (version "6.5.0")
+    (version "6.5.2")
    (source
     (origin
-      (method url-fetch)
-      (uri (string-append "https://vanheusden.com/multitail/multitail-"
-                          version ".tgz"))
+      (method git-fetch)
+      (uri (git-reference
+            (url "https://github.com/halturin/multitail")
+            (commit (string-append "v" version))))
+      (file-name (git-file-name name version))
      (sha256
-       (base32 "1vd9vdxyxsccl64ilx542ya5vlw2bpg6gnkq1x8cfqy6vxvmx7dj"))))
+       (base32 "17hg5qpangyx4m7hp2x4h56mp6w3wsaslg1il39qcpwsffh1rihc"))))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags
       (list (string-append "CC=" ,(cc-for-target))
-             (string-append "PREFIX="
-                            (assoc-ref %outputs "out")))
+             (string-append "PREFIX=" (assoc-ref %outputs "out"))
+             "SYSCONFDIR=$(PREFIX)/etc")
       #:phases
       (modify-phases %standard-phases
-         (add-after 'unpack 'patch-curses-lib
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (substitute* "mt.h"
-                 (("ncursesw\\/panel.h") "panel.h")
-                 (("ncursesw\\/ncurses.h") "ncurses.h")))
-             #t))
+         (add-after 'unpack 'fix-broken-build
+           ;; With some luck, you might be able to remove this when updating…
+           (lambda _
+             (substitute* "Makefile"
+               ((" \\*\\.txt") "")
+               ((".*CONFIG_DIR.*") "")
+               (("^install: .*" match)
+                (string-append match
+                               "\t$(INSTALL_DIR) $(DESTDIR)$(SYSCONFDIR)\n")))
+             (substitute* "version"
+               (("(VERSION=).*" _ assign)
+                (string-append assign ,version)))))
+         (add-after 'unpack 'patch-curses-headers
+           (lambda _
+             (substitute* "mt.h"
+               (("ncursesw/") ""))))
         (delete 'configure))           ; no configure script
       #:tests? #f)) ; no test suite (make check just runs cppcheck)
    (inputs (list ncurses))
@@ -229,7 +240,7 @@ library.")
 (define-public rsyslog
  (package
    (name "rsyslog")
-    (version "8.2112.0")
+    (version "8.2204.1")
    (source
     (origin
       (method git-fetch)
@@ -238,8 +249,7 @@ library.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32
-         "0bp124w2qv8hix5i0p04d8yvsipy18dhqm7zw8i6cwdgnhdadq96"))))
+        (base32 "0bsd1n3n4hvlkwf4g85g3fg37mnvkdmxsfdmg273gcachhyl5hbx"))))
    (build-system gnu-build-system)
    (arguments
     (list
@@ -253,9 +263,8 @@ library.")
      ;; them for a full-featured build.
      '(list "--enable-kmsg"
             "--enable-liblogging_stdlog"
-             "--enable-mmanon"
-             "--enable-mmcount"
             "--enable-unlimited_select"
+             "--enable-usertools"
         
             ;; Input plugins
             "--enable-imbatchreport"
@@ -297,7 +306,9 @@ library.")
             "--enable-pmsnare"

             ;; Message Modification Modules
+             "--enable-mmanon"
             "--enable-mmaudit"
+             "--enable-mmcount"
             "--enable-mmdarwin"
             "--enable-mmdblookup"
             "--enable-mmfields"
@@ -324,9 +335,18 @@ library.")
             "--enable-snmp"

             ;; Function modules
-             "--enable-fmhash_xxhash")))
+             "--enable-fmhash_xxhash"
+
+             ;; Needed to build rscryutil.1.gz.
+             "--enable-generate-man-pages")))
    (native-inputs
-     (list autoconf automake bison flex libtool pkg-config))
+     (list autoconf
+           automake
+           bison
+           flex
+           libtool
+           pkg-config
+           python-docutils))            ; rst2man for man pages
    (inputs
     (list curl
           cyrus-sasl
@@ -1333,14 +1333,14 @@ invoking @command{notifymuch} from the post-new hook.")
 (define-public notmuch
  (package
    (name "notmuch")
-    (version "0.35")
+    (version "0.36")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://notmuchmail.org/releases/notmuch-"
                           version ".tar.xz"))
       (sha256
-        (base32 "0fdc81m24xrbhfrhw00g12ak4b8hap4961sq7ap6q2pjqhac8cd8"))))
+        (base32 "0h6f6mh9m9vrijm638x5sbsl321b74a25cdasbxhx67x62w320hk"))))
    (build-system gnu-build-system)
    (arguments
     (list
@@ -1474,8 +1474,7 @@ useful for email address completion.")
             (let ((notmuch (assoc-ref inputs "notmuch")))
               (substitute* "notmuch/globals.py"
                 (("libnotmuch\\.so\\.")
-                  (string-append notmuch "/lib/libnotmuch.so.")))
-               #t))))))
+                  (string-append notmuch "/lib/libnotmuch.so.")))))))))
    (home-page (package-home-page notmuch))
    (synopsis "Python bindings of the Notmuch mail indexing library")
    (description
@@ -1632,7 +1631,7 @@ compresses it.")
 (define-public claws-mail
  (package
    (name "claws-mail")
-    (version "4.0.0")
+    (version "4.1.0")
    (source
     (origin
       (method url-fetch)
@@ -1640,7 +1639,7 @@ compresses it.")
        (string-append "https://www.claws-mail.org/releases/claws-mail-"
                       version ".tar.xz"))
       (sha256
-        (base32 "0xg41rxxq2q5vhjzbh8p12s248kcljk6g7y0m6raq7nrllkbvwja"))))
+        (base32 "13ksh4iwr23zi86fwmiwxha94xqrr5zxq373i82rwaldvfh9q6hf"))))
    (build-system glib-or-gtk-build-system)
    (arguments
     `(#:configure-flags
@@ -1670,7 +1669,7 @@ compresses it.")
                (search-input-file inputs "/share/mime/globs"))))))))
    (native-inputs
     (list bison
-           ;;("docbook-utils" ,docbook-utils)
+           ;;docbook-utils
           flex
           gettext-minimal
           gobject-introspection
@@ -3671,7 +3670,7 @@ operators and scripters.")
 (define-public alpine
  (package
    (name "alpine")
-    (version "2.25")
+    (version "2.26")
    (source
     (origin
       (method git-fetch)
@@ -3684,14 +3683,12 @@ operators and scripters.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0z6dp3cpz1dmbxw41ravsx1bxychafp0ij8gvj96mzz7rm9pdnq3"))
+        (base32 "1padh9kgn9blzjf0016i2f15c615fk17m8vg8kx301jhmc2r973h"))
       (modules '((guix build utils)))
       (snippet
        '(begin
           ;; Remove pre-built binaries scattered across the source repository.
-           (for-each delete-file (find-files "." "\\.(dll|exe)"))))
-       (patches
-        (search-patches "alpine-fix-privacy-policy-crash.patch"))))
+           (for-each delete-file (find-files "." "\\.(dll|exe)"))))))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags
@@ -1713,7 +1713,7 @@ instant messenger with audio and video chat capabilities.")
 (define-public qtox
  (package
    (name "qtox")
-    (version "1.17.4")
+    (version "1.17.6")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/qTox/qTox/releases"
@@ -1721,7 +1721,7 @@ instant messenger with audio and video chat capabilities.")
                                  "/v" version ".tar.gz"))
              (sha256
               (base32
-                "086hvm0q2vl2lq8zlp8s9sivlic6sg7ga5ixz01hbsyrashvil63"))
+                "1ml8z1xpp3qhip4vkr375jf7y5kc18g0apm91n5am6ricx37c01r"))
              (file-name (string-append name "-" version ".tar.gz"))))
    (build-system cmake-build-system)
    (arguments
@@ -2281,7 +2281,7 @@ perform creative live mixes with digital music files.")
 (define-public synthv1
  (package
    (name "synthv1")
-    (version "0.9.25")
+    (version "0.9.26")
    (source (origin
              (method url-fetch)
              (uri
@@ -2289,7 +2289,7 @@ perform creative live mixes with digital music files.")
                              "/synthv1-" version ".tar.gz"))
              (sha256
               (base32
-                "1i16036f9wm52c5pxkllq7ir749jcknbh35i9wcxd5n88p6mzw02"))))
+                "1asikh341f3vblrl8l07yakza80ybs8sid3n2qpsrvigaz3iymcd"))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #f))                    ; there are no tests
@@ -2299,7 +2299,8 @@ perform creative live mixes with digital music files.")
           alsa-lib
           new-session-manager
           liblo
-           qtbase-5))
+           qtbase-5
+           qtsvg))
    (native-inputs
     (list pkg-config qttools))
    (home-page "https://synthv1.sourceforge.io")
@@ -2312,7 +2313,7 @@ oscillators and stereo effects.")
 (define-public drumkv1
  (package
    (name "drumkv1")
-    (version "0.9.25")
+    (version "0.9.26")
    (source (origin
              (method url-fetch)
              (uri
@@ -2320,7 +2321,7 @@ oscillators and stereo effects.")
                              "/drumkv1-" version ".tar.gz"))
              (sha256
               (base32
-                "0p50b4k4zldagiwxs0micmdbqib46ysipdj8lkxqdv0pysmd72fc"))))
+                "0j05xqgcb7kwnnsgl6i7vbdsfq26chzs4zyq6pl0ipcmw4d82j8i"))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #f))                    ; there are no tests
@@ -2331,7 +2332,8 @@ oscillators and stereo effects.")
           alsa-lib
           new-session-manager
           liblo
-           qtbase-5))
+           qtbase-5
+           qtsvg))
    (native-inputs
     (list pkg-config qttools))
    (home-page "https://drumkv1.sourceforge.io")
@@ -2344,7 +2346,7 @@ effects.")
 (define-public samplv1
  (package
    (name "samplv1")
-    (version "0.9.25")
+    (version "0.9.26")
    (source (origin
              (method url-fetch)
              (uri
@@ -2352,7 +2354,7 @@ effects.")
                              "/samplv1-" version ".tar.gz"))
              (sha256
               (base32
-                "0d05b03knrwh1zr4p0kcyn58scy6a392f0xxm78cqf0gikd3bw5c"))))
+                "1rqz3hf39hk2m15ihrkn8f5cqgbkvz3rq6r2k35rvn7sgvcq1dli"))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #f))                    ; there are no tests
@@ -2363,7 +2365,8 @@ effects.")
           alsa-lib
           new-session-manager
           liblo
-           qtbase-5))
+           qtbase-5
+           qtsvg))
    (native-inputs
     (list pkg-config qttools))
    (home-page "https://samplv1.sourceforge.io")
@@ -2376,7 +2379,7 @@ effects.")
 (define-public padthv1
  (package
    (name "padthv1")
-    (version "0.9.25")
+    (version "0.9.26")
    (source (origin
              (method url-fetch)
              (uri
@@ -2384,7 +2387,7 @@ effects.")
                              "/padthv1-" version ".tar.gz"))
              (sha256
               (base32
-                "11fa2794g7dqsiw674wr2m4k0xdw89imqwa8mgms0igskxxbvjka"))))
+                "02pg0g4i65j46hirkc3xn7m2clm8krrafrkwjc1v8rkcdj6q2gw1"))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #f))                    ; there are no tests
@@ -2395,7 +2398,8 @@ effects.")
           new-session-manager
           liblo
           fftwf
-           qtbase-5))
+           qtbase-5
+           qtsvg))
    (native-inputs
     (list pkg-config qttools))
    (home-page "https://padthv1.sourceforge.io")
@@ -2772,6 +2772,12 @@ updates to the zebra daemon.")
         #:tests? #f ; No test suite.
         #:phases
         (modify-phases %standard-phases
+           (add-after 'unpack 'use-source-date-epoch-in-manpages
+             ;; For reproducible builds
+             (lambda _
+               (substitute* "Makefile"
+                 (("date --iso-8601")
+                  "date --iso-8601 --utc --date=@$(SOURCE_DATE_EPOCH)"))))
           (delete 'configure) ; No ./configure script.
           (add-before 'build 'patch-paths
             (lambda _
@@ -3359,7 +3365,7 @@ communication over HTTP.")
 (define-public restinio
  (package
    (name "restinio")
-    (version "0.6.14")
+    (version "0.6.15")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -3368,7 +3374,7 @@ communication over HTTP.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "0j44mglsljwkw49583hcsrl5ck2g56n9srnm10kpbsz2dx5apx98"))))
+                "1f8d5nfm8jqhspzsslwb1b7j4glipz31i9vszrcnkx3clc39nj2n"))))
    (build-system cmake-build-system)
    (inputs                             ; TODO: Need to force-keep references on some inputs, e.g. boost.
     (list zlib
@@ -1650,8 +1650,8 @@ in an isolated environment, in separate namespaces.")
    (license license:gpl3+)))

 (define-public nar-herder
-  (let ((commit "a24fbd108f75c8f27d2f68f2d1a051e2f3f3e191")
-        (revision "7"))
+  (let ((commit "042f49e5fb52ea844ed5d29c17b26fbc8ad49f0e")
+        (revision "8"))
    (package
      (name "nar-herder")
      (version (git-version "0" revision commit))
@@ -1662,7 +1662,7 @@ in an isolated environment, in separate namespaces.")
                      (commit commit)))
                (sha256
                 (base32
-                  "1jm6ks2sjcwih7j4wnp252qd73n8pydg7sd000ismpvg5p21l7fg"))
+                  "1i9vwjdvkchwndjikqq3j73x0mvp3ny63s62ixql70yhpdgz5l69"))
                (file-name (string-append name "-" version "-checkout"))))
      (build-system gnu-build-system)
      (arguments
@@ -4,7 +4,7 @@
 ;;; Copyright © 2015, 2016, 2017, 2018, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2016, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018–2022 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -327,7 +327,7 @@ by managing a queue of pending work.")
 (define-public slurm-drmaa
  (package
    (name "slurm-drmaa")
-    (version "1.1.2")
+    (version "1.1.3")
    (source (origin
              (method url-fetch)
              (uri (string-append
@@ -335,7 +335,7 @@ by managing a queue of pending work.")
                    version "/slurm-drmaa-" version ".tar.gz"))
              (sha256
               (base32
-                "0dn8ypqxdaq3k4jqwwx7msckxnmr6n2z5j68yffp50yy07ajbzjv"))))
+                "1fn3p4wjj0sgvx0isy3hiwi35vhxa2n2ksq5cn9sq2hg7yyb2phl"))))
    (build-system gnu-build-system)
    (arguments `(#:tests? #f)) ; The tests require "bats".
    (inputs
@@ -1,39 +0,0 @@
-X-Git-Url: https://repo.or.cz/alpine.git/blobdiff_plain/fb2217ac67706e4cbef69bea41041e2fb8b910e9..3ee981816abfb7d47ffc0ac522fff002b5749b72:/alpine/help.c
-
-diff --git a/alpine/help.c b/alpine/help.c
-index 4f1bf46..e9c7b34 100644
--- a/alpine/help.c
-+++ b/alpine/help.c
-@@ -36,6 +36,7 @@ static char rcsid[] = "$Id: help.c 1032 2008-04-11 00:30:04Z hubert@u.washington
- #include "../pith/detoken.h"
- #include "../pith/list.h"
- #include "../pith/margin.h"
-+#include "../pith/busy.h"
- 
- 
- typedef struct _help_scroll {
-@@ -135,10 +136,12 @@ helper_internal(HelpType text, char *frag, char *title, int flags)
-     is_external = 0;
- 
-     if(shown_text && *shown_text && !struncmp(*shown_text, "x-alpine-http:", 14)){
-	int status;
-+	int status, we_cancel = 0;
-+
-+	we_cancel = busy_cue(_("Retrieving help text"), NULL, 1);
- 	HTTPSTREAM *stream = http_open(*shown_text + 14);
- 	if(stream) help_text = http_get(stream, NULL);
-	status = stream->status ? stream->status->code : -1;
-+	status = stream && stream->status ? stream->status->code : -1;
- 	if(stream) http_close(stream);
- 	if(status != HTTP_OK){
- 	    shown_text = NO_HELP;
-@@ -165,7 +168,8 @@ helper_internal(HelpType text, char *frag, char *title, int flags)
- 		*rv = NULL;
- 	    }
- 	}
-
-+	if(we_cancel)
-+	   cancel_busy_cue(-1);
-     }
- 
-     if(F_ON(F_BLANK_KEYMENU,ps_global)){
@@ -1,53 +0,0 @@
-Fix for epiphany with libportal-0.5.
-
-This patch was adapted from upstream
-https://gitlab.gnome.org/GNOME/epiphany/-/commit/e4d259f614f75c26ad0d2094f4f569ffd1bc06d1
-
-diff --git a/lib/ephy-flatpak-utils.c b/lib/ephy-flatpak-utils.c
-index 6fc9a5dec17a63c0660cbc1d95103c8f77231d30..0fd90b3f178392930e812a8391fd81bf1371b8bf 100644
--- a/lib/ephy-flatpak-utils.c
-+++ b/lib/ephy-flatpak-utils.c
-@@ -29,7 +29,7 @@
- #include <gio/gio.h>
- #include <gio/gunixfdlist.h>
- #if USE_LIBPORTAL
-#include <libportal/portal-gtk3.h>
-+#include <libportal-gtk3/portal-gtk3.h>
- #endif
- #include <string.h>
- #include <sys/stat.h>
-diff --git a/lib/meson.build b/lib/meson.build
-index 264f9c5fb66268fc248f780b8d1c06c8291f856d..db0a0557f0ae634d7fb95e57aba0cd901ca4d6c1 100644
--- a/lib/meson.build
-+++ b/lib/meson.build
-@@ -66,6 +66,7 @@ libephymisc_deps = [
-   libxml_dep,
-   m_dep,
-   portal_dep,
-+  portal_gtk_dep,
-   sqlite3_dep,
-   webkit2gtk_dep
- ]
-diff --git a/meson.build b/meson.build
-index 0b9f862b22a23619289342ec39fa0a0274558c25..4285a975004e48366789a4e66f8b23f3af05a636 100644
--- a/meson.build
-+++ b/meson.build
-@@ -95,7 +95,8 @@ libhandy_dep = dependency('libhandy-1', version: '>= 1.5.0')
- libsecret_dep = dependency('libsecret-1', version: '>= 0.19.0')
- libxml_dep = dependency('libxml-2.0', version: '>= 2.6.12')
- nettle_dep = dependency('nettle', version: nettle_requirement)
-portal_dep = dependency('libportal', version: '>= 0.0.2', required: get_option('libportal'))
-+portal_dep = dependency('libportal', version: '>= 0.5', required: get_option('libportal'))
-+portal_gtk_dep = dependency('libportal-gtk3', version: '>= 0.5', required: get_option('libportal'))
- sqlite3_dep = dependency('sqlite3', version: '>= 3.22')
- 
- if get_option('soup2').enabled()
-@@ -108,7 +109,7 @@ else
-   webkit2gtk_web_extension_dep = dependency('webkit2gtk-web-extension-4.1', version: webkitgtk_requirement)
- endif
- 
-conf.set10('USE_LIBPORTAL', portal_dep.found())
-+conf.set10('USE_LIBPORTAL', portal_dep.found() and portal_gtk_dep.found())
- 
- webkit_revision = webkit2gtk_dep.get_variable(pkgconfig : 'revision', default_value : '')
- if webkit_revision == 'tarball'
@@ -1,34 +0,0 @@
-From 18a08fb7f0443f8bde83393bd6f69e23a04246b3 Mon Sep 17 00:00:00 2001
-From: Pablo Neira Ayuso <pablo@netfilter.org>
-Date: Tue, 22 Feb 2022 00:56:36 +0100
-Subject: examples: compile with `make check' and add AM_CPPFLAGS
-
-Compile examples via `make check' like libnftnl does. Use AM_CPPFLAGS to
-specify local headers via -I.
-
-Unfortunately, `make distcheck' did not catch this compile time error in
-my system, since it was using the nftables/libnftables.h file of the
-previous nftables release.
-
-Fixes: 5b364657a35f ("build: missing SUBIRS update")
-Fixes: caf2a6ad2d22 ("examples: add libnftables example program")
-Signed-off-by: Pablo Neira Ayuso <pablo@netfilter.org>
---
- examples/Makefile.am | 4 +++-
- 1 file changed, 3 insertions(+), 1 deletion(-)
-
-diff --git a/examples/Makefile.am b/examples/Makefile.am
-index c972170d..3b8b0b67 100644
--- a/examples/Makefile.am
-+++ b/examples/Makefile.am
-@@ -1,4 +1,6 @@
-noinst_PROGRAMS	= nft-buffer		\
-+check_PROGRAMS	= nft-buffer		\
- 		  nft-json-file
- 
-+AM_CPPFLAGS = -I$(top_srcdir)/include
-+
- LDADD = $(top_builddir)/src/libnftables.la
-- 
-cgit v1.2.3
-
@@ -5,7 +5,7 @@
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2017, 2021 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017, 2021, 2022 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
 ;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
@@ -42,8 +42,8 @@
   (version "8.45")
   (source (origin
            (method url-fetch)
-            (uri (string-append "https://ftp.pcre.org/pub/pcre/pcre-"
-                                version ".tar.bz2"))
+            (uri (string-append "mirror://sourceforge/pcre/pcre/"
+                                version "/pcre-" version ".tar.bz2"))
            (sha256
             (base32
              "1f7zichy6iimmkfrqdl575sdlm795cyc75szgg1vc2xvsbf6zbjd"))))
@@ -19,6 +19,7 @@
 ;;; Copyright © 2022 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2022 Paul A. Patience <paul@apatience.com>
 ;;; Copyright © 2022 Wiktor Żelazny <wzelazny@vurv.cz>
+;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -858,6 +859,32 @@ and more
@end itemize")
    (license license:gpl3)))

+(define-public python-pyglm
+  (package
+    (name "python-pyglm")
+    (version "2.5.7")
+    (source
+     (origin
+       ;; Test files are not included in the archive in pypi.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Zuzu-Typ/PyGLM")
+             (commit version)
+             ;; Checkout the bundled `glm` submodule.  PyGLM uses the
+             ;; currently unreleased GLM_EXT_matrix_integer feature.  Can
+             ;; maybe unbundle once glm@0.9.9.9 is released.
+             (recursive? #t)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "08v0cgkwsf8rxscx5g9c5p1dy38rvak2fy3q6hg985if1nj6d9ks"))))
+    (build-system python-build-system)
+    (home-page "https://github.com/Zuzu-Typ/PyGLM")
+    (synopsis "OpenGL Mathematics library for Python")
+    (description "PyGLM is a Python extension library which brings the OpenGL
+Mathematics (GLM) library to Python.")
+    (license license:zlib)))
+
 (define-public python-distributed
  (package
    (name "python-distributed")
@@ -3,7 +3,7 @@
 ;;; Copyright © 2013-2022 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013, 2014, 2015, 2016, 2019 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2014, 2017, 2021 Eric Bavier <bavier@posteo.net>
+;;; Copyright © 2014, 2017, 2021, 2022 Eric Bavier <bavier@posteo.net>
 ;;; Copyright © 2014, 2015 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2015 Omar Radwan <toxemicsquire4@gmail.com>
 ;;; Copyright © 2015 Pierre-Antoine Rault <par@rigelk.eu>
@@ -3086,7 +3086,13 @@ server.")
              (chdir "miniupnpc")
              (setenv "CC" #$(cc-for-target))
              (substitute* "Makefile"
-                (("/bin/sh") (search-input-file inputs "/bin/sh"))))))))
+                (("/bin/sh") (search-input-file inputs "/bin/sh")))))
+          (add-before 'subdir 'remove-kernel-version
+            ;; Avoid embedding the running kernel version for reproducible builds
+            (lambda _
+              (substitute*
+                  "miniupnpc/updateminiupnpcstrings.sh"
+                (("^OS_VERSION=`uname -r`") "OS_VERSION=Guix")))))))
    (inputs (list python))              ;we are building a Python extension
    (synopsis "UPnP client for Python")
    (description "Miniupnpc is a client library for Python programs to set up
@@ -12346,7 +12352,11 @@ libmagic.")))
                           ;; This test validates that 'pydevd' is not in the
                           ;; exception message, but it is due to being part
                           ;; of the build file name present in the message.
-                           "and not test_evaluate_exception_trace")))))
+                           "and not test_evaluate_exception_trace "
+                           ;; These fail on systems with YAMA LSM’s ptrace
+                           ;; scope > 0. Upstream issue:
+                           ;; https://github.com/fabioz/PyDev.Debugger/issues/218
+                           "and not test_attach_to_pid")))))
            (add-after 'install 'install-attach-binary
              (lambda _
                (install-file "attach.so"
@@ -12391,6 +12401,7 @@ and other @acronym{IDEs, Integrated Development Environments}.")
    (build-system python-build-system)
    (arguments
     (list
+      #:tests? #f ; Fail on systems with YAMA LSM’s ptrace scope > 0.
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'patch-sh-in-tests
@@ -12411,17 +12422,18 @@ and other @acronym{IDEs, Integrated Development Environments}.")
              (setenv "DEBUGPY_BUNDLING_DISABLED" "1")))
          (replace 'check
            (lambda* (#:key tests? #:allow-other-keys)
-              (invoke "pytest" "-vv"
-                      "-n" (number->string (parallel-job-count))
-                      "-k"
-                      (string-append
-                       ;; These tests cannot be run in parallel because their
-                       ;; test data would not be copied by xdist and lead to
-                       ;; import errors. (see:
-                       ;; https://github.com/microsoft/debugpy/issues/342 and
-                       ;; https://github.com/microsoft/debugpy/issues/880).
-                       "not test_custom_python_args "
-                       "and not test_autokill ")))))))
+              (when tests?
+                (invoke "pytest" "-vv"
+                        "-n" (number->string (parallel-job-count))
+                        "-k"
+                        (string-append
+                         ;; These tests cannot be run in parallel because their
+                         ;; test data would not be copied by xdist and lead to
+                         ;; import errors. (see:
+                         ;; https://github.com/microsoft/debugpy/issues/342 and
+                         ;; https://github.com/microsoft/debugpy/issues/880).
+                         "not test_custom_python_args "
+                         "and not test_autokill "))))))))
    (native-inputs
     ;; See: https://raw.githubusercontent.com/microsoft/debugpy/
     ;;      main/tests/requirements.txt.
@@ -19901,22 +19913,14 @@ design and layout.")
 (define-public python-pkginfo
  (package
    (name "python-pkginfo")
-    (version "1.8.2")
+    (version "1.8.3")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "pkginfo" version))
       (sha256
-        (base32 "1zrbn2gblb1q1rx0jlbd0vc9h1dm1bj0760p40ff5qjhcw5hsbjl"))))
+        (base32 "0z46w559hrl79gf7navgzimj21ma821wka27jh58fvyqilqs8kd8"))))
    (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-before 'check 'patch-tests
-           (lambda _
-             (substitute* "pkginfo/tests/test_installed.py"
-               (("test_ctor_w_package_no_PKG_INFO")
-                "_test_ctor_w_package_no_PKG_INFO")))))))
    (native-inputs
     (list python-wheel))
    (home-page "https://code.launchpad.net/~tseaver/pkginfo/trunk")
@@ -24363,7 +24367,7 @@ with features similar to the @command{wget} utility.")
 (define-public offlate
  (package
    (name "offlate")
-    (version "0.5")
+    (version "0.6.1")
    (source
      (origin
        (method git-fetch)
@@ -24373,33 +24377,37 @@ with features similar to the @command{wget} utility.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-          "13pqnbl05wcyldfvl75fp89vjgwsvxyc69vhnb17kkha2rc2k1h7"))))
+          "1sx5cv8pamyw1m089b6x8ykaxdkx26jk9cblhbzlf0m3ckz52jik"))))
    (build-system python-build-system)
    (arguments
     ;; No tests
     `(#:tests? #f
-       #:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'patch-for-pygit2
-                    (lambda _
-                      (substitute* "offlate/systems/git.py"
-                        (("pygit2.remote.RemoteCallbacks")
-                         "pygit2.RemoteCallbacks")))))))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'generate-fonts
+           (lambda _
+             (invoke "make" "fonts")))
+         (add-before 'build 'generate-translations
+           (lambda _
+             (invoke "make" "update-langs"))))))
    (propagated-inputs
      (list python-android-stringslib
            python-dateutil
            python-gitlab
            python-lxml
            python-polib
+            python-pycountry
            python-pyenchant
            python-pygit2
            python-pygithub
            python-pyqt
            python-requests
            python-ruamel.yaml
+            python-translate-toolkit
            python-translation-finder
            python-watchdog))
    (native-inputs
-     (list qttools))
+     (list qttools fontforge))
    (home-page "https://framagit.org/tyreunom/offlate")
    (synopsis "Offline translation interface for online translation tools")
    (description "Offlate offers a unified interface for different translation
@@ -24736,6 +24744,38 @@ usable as a configuration language.  This Python package implements parsing and
 dumping of JSON5 data structures.")
    (license license:asl2.0)))

+(define-public python-freetype-py
+  (package
+    (name "python-freetype-py")
+    (version "2.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "freetype-py" version ".zip"))
+       (sha256
+        (base32 "1l55wzy21jmdayjna29ahzxrf2fp68580978rs6kap1a4zilrdpr"))))
+    (build-system python-build-system)
+    (native-inputs
+     (list python-setuptools-scm
+           unzip))
+    (inputs (list freetype))
+    (arguments
+     `(#:phases
+       ;; Note: the pypi archive does not contain tests, but running the check
+       ;; phase will at least test whether the module loads correctly.
+       (modify-phases %standard-phases
+         (add-before 'build 'embed-library-reference
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "freetype/raw.py"
+               (("^(filename = ).*" _ >)
+                (string-append > "\"" (search-input-file inputs "/lib/libfreetype.so")
+                               "\"\n"))))))))
+    (home-page "https://github.com/rougier/freetype-py")
+    (synopsis "Freetype python bindings")
+    (description "Freetype Python provides bindings for the FreeType
+library.  Only the high-level API is bound.")
+    (license license:bsd-3)))
+
 (define-public python-frozendict
  (package
    (name "python-frozendict")
@@ -368,7 +368,7 @@ are already there.")
 (define-public direnv
  (package
    (name "direnv")
-    (version "2.28.0")
+    (version "2.31.0")
    (source
     (origin (method git-fetch)
             (uri (git-reference
@@ -377,7 +377,7 @@ are already there.")
             (file-name (git-file-name name version))
             (sha256
              (base32
-               "0yk53jn7wafklixclka17wyjjs2g5giigjr2bd0xzy10nrzwp7c9"))))
+               "1c52izjzkdhmyrfx1gmbp34n0qpxyxw0s94f0vy3ldlg8xr36wmk"))))
    (build-system go-build-system)
    (arguments
     '(#:import-path "github.com/direnv/direnv"
@@ -405,8 +405,7 @@ are already there.")
                 (invoke "go" "test" "./...")
                 ;; Clean up from the tests, especially so that the extra
                 ;; direnv executable that's generated is removed.
-                 (invoke "make" "clean")))
-             #t)))))
+                 (invoke "make" "clean"))))))))
    (native-inputs
     (list go-github-com-burntsushi-toml go-github-com-direnv-go-dotenv
           go-github-com-mattn-go-isatty go-golang-org-x-mod which))
@@ -6409,7 +6409,7 @@ files, including Rmarkdown files.")
 (define-public readstat
  (package
    (name "readstat")
-    (version "1.1.5")
+    (version "1.1.8")
    (source
     (origin
       (method git-fetch)
@@ -6418,7 +6418,7 @@ files, including Rmarkdown files.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "00sdmaq0qzp6kyv53fpfi6jf3iv4pd0ap0gmw3mbfip52bbnl55w"))))
+        (base32 "1r04lq45h1yn34v1mgfiqjfzyaqv4axqlby0nkandamcsqyhc7y4"))))
    (build-system gnu-build-system)
    (native-inputs
     (list autoconf automake gnu-gettext libtool))
@@ -835,7 +835,7 @@ eye-candy, customizable, and reasonably lightweight.")
 (define-public foot
  (package
    (name "foot")
-    (version "1.11.0")
+    (version "1.12.1")
    (home-page "https://codeberg.org/dnkl/foot")
    (source (origin
              (method git-fetch)
@@ -843,7 +843,7 @@ eye-candy, customizable, and reasonably lightweight.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "1d9bk8lhmw5lc8k0mw80g0vbwgxyh3gw5c7ppy3sir07s9y0y0fn"))))
+                "14jqs4sarxbrgi5pxz0afqa9jxq90cb5ayqd21qj2n65whqa5bpk"))))
    (build-system meson-build-system)
    (arguments
     `(;; Using a "release" build is recommended both for performance, and
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017, 2018, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2020–2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Jesse Gibbons <jgibbons2357+guix@gmail.com>
 ;;; Copyright © 2019, 2020, 2021 Timotej Lazar <timotej.lazar@araneo.si>
 ;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
@@ -57,8 +57,7 @@
           (for-each delete-file-recursively
                     (cons* "bitmaps/bsd" "bitmaps/sakura" "bitmaps/tomoyo"
                            "bitmasks/bsd" "bitmasks/sakura" "bitmasks/tomoyo"
-                            (find-files "cursors" "(bsd|card|petal).*\\.xbm")))
-           #t))))
+                            (find-files "cursors" "(bsd|card|petal).*\\.xbm")))))))
    (build-system gnu-build-system)
    (native-inputs
     (list imake))
@@ -73,8 +72,7 @@
             (invoke "xmkmf")
             ;; Fix incorrectly generated compiler flags.
             (substitute* "Makefile"
-               (("(CDEBUGFLAGS = ).*" _ front) (string-append front "-O2\n")))
-             #t))
+               (("(CDEBUGFLAGS = ).*" _ front) (string-append front "-O2\n")))))
         (replace 'install
           (lambda* (#:key outputs make-flags #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
@@ -89,12 +87,14 @@
               (copy-file "oneko.man" (string-append man6 "/oneko.6"))
               (copy-file "oneko.man.jp" (string-append man6-ja "/oneko.6"))
               (for-each (lambda (file) (install-file file doc))
-                         (find-files "." "README.*")))
-             #t)))))
+                         (find-files "." "README.*"))))))))
    (home-page "http://www.daidouji.com/oneko/")
    (synopsis "Cute cat chasing your mouse pointer")
-    (description "Displays a cat or another animated character that chases the
-mouse pointer around the screen while you work.")
+    (description
+     "Oneko displays an animated cat or dog that chases the mouse pointer---now
+an actual mouse or a bone---around the screen while you work.
+
+It was written for the X Window system and does not work well on Wayland.")
    (license license:public-domain))) ; see https://directory.fsf.org/wiki/Oneko

 (define-public sl
@@ -461,7 +461,7 @@ trouble using them, because you do not have to remember each snippet name.")
 (define-public vim-fugitive
  (package
    (name "vim-fugitive")
-    (version "3.6")
+    (version "3.7")
    (source
      (origin
        (method git-fetch)
@@ -470,7 +470,7 @@ trouble using them, because you do not have to remember each snippet name.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-         (base32 "17c3wzqkbzbf0nmlxpgk90yyv3d09209fqxqysand8bzb1cbfwzn"))))
+         (base32 "138290g2aph1jjhaza6biky5qi4ka6435s01bwxivllgb53g3irc"))))
    (build-system copy-build-system)
    (arguments
     '(#:install-plan
@@ -1590,16 +1590,16 @@ input from UTF-8 into the locale's encoding.")
 (define-public mkfontscale
  (package
    (name "mkfontscale")
-    (version "1.2.1")
+    (version "1.2.2")
    (source
      (origin
        (method url-fetch)
        (uri (string-append
               "mirror://xorg/individual/app/mkfontscale-"
               version
-               ".tar.bz2"))
+               ".tar.xz"))
        (sha256
-          (base32 "1ixsnsm2mn0zy9ksdid0lj6irnhvasfik9mz8bbrs5sajzmra16a"))))
+          (base32 "1i6mw97r2s1rb6spjj8fbdsgw6197smaqq2haqgnwhz73xdzpqwa"))))
    (build-system gnu-build-system)
    (inputs
      (list zlib xorgproto freetype libfontenc))
@@ -1991,14 +1991,14 @@ server.")
 (define-public xauth
  (package
    (name "xauth")
-    (version "1.1")
+    (version "1.1.2")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://xorg/individual/app/xauth-" version
-                           ".tar.bz2"))
+                           ".tar.xz"))
       (sha256
-        (base32 "032klzzw8r09z36x1272ssd79bcisz8j5p8gbdy111fiknvx27bd"))))
+        (base32 "0072ivzn4z59ysanz838nh8s4mcmdsx6q9xkvlfysv2k37ynmfkq"))))
    (build-system gnu-build-system)
    (inputs
     (list libxmu libxext libxau libx11))
@@ -2067,14 +2067,14 @@ legacy X clients.")
 (define-public xcalc
  (package
    (name "xcalc")
-    (version "1.1.0")
+    (version "1.1.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://xorg/individual/app/"
                           "xcalc-" version ".tar.gz"))
       (sha256
-        (base32 "0c768lh0nh28ram9ldldhaf51024fngc589v4pjmf3lxmzcihr58"))))
+        (base32 "0fwgnva716ymnrf8f4lvnqlyikf5c837054sxxlf3l5jpy4wh6cj"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases (modify-phases %standard-phases
@@ -2084,8 +2084,7 @@ legacy X clients.")
                     (substitute* "Makefile"
                       (("^appdefaultdir = .*$")
                        (string-append "appdefaultdir = " %output
-                                       ,%app-defaults-dir "\n")))
-                     #t)))))
+                                       ,%app-defaults-dir "\n"))))))))
    (inputs
     (list libxaw))
    (native-inputs
@@ -2299,17 +2298,17 @@ left-handed version of the cursors is also included.")
 (define-public xdpyinfo
  (package
    (name "xdpyinfo")
-    (version "1.3.2")
+    (version "1.3.3")
    (source
      (origin
        (method url-fetch)
        (uri (string-append
               "mirror://xorg/individual/app/xdpyinfo-"
               version
-               ".tar.bz2"))
+               ".tar.xz"))
        (sha256
          (base32
-            "0ldgrj4w2fa8jng4b3f3biaj0wyn8zvya88pnk70d7k12pcqw8rh"))))
+            "01n21ygbvzycjasv97rk33b14qdbshr1pkxysqvfx61y5zb5yv9m"))))
    (build-system gnu-build-system)
    (inputs
      (list xorgproto
@@ -2486,15 +2485,15 @@ including most mice, keyboards, tablets and touchscreens.")
 (define-public xf86-input-libinput
  (package
    (name "xf86-input-libinput")
-    (version "1.1.0")
+    (version "1.2.1")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "mirror://xorg/individual/driver/"
-                    name "-" version ".tar.bz2"))
+                    name "-" version ".tar.xz"))
              (sha256
               (base32
-                "05ldqr10f2rrnshyk3lc773rz0gp3ccdzwa8n7lsc94i850jl7g1"))))
+                "06wpgqga4kc5ph5bd5cabfg0gdcdkbd65jrdx467qcfvkmdxnlc1"))))
    (build-system gnu-build-system)
    (arguments
     '(#:configure-flags
@@ -2658,14 +2657,14 @@ as USB mice.")
 (define-public xf86-video-amdgpu
  (package
    (name "xf86-video-amdgpu")
-    (version "21.0.0")
+    (version "22.0.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://xorg/individual/driver/"
-                           "xf86-video-amdgpu-" version ".tar.bz2"))
+                           "xf86-video-amdgpu-" version ".tar.xz"))
       (sha256
-        (base32 "125dq85n46yqmnmr2hknxwcqicwlvz2b2phf0m963fpg9l1j6y30"))))
+        (base32 "0rl2fxhhgcjywn2z8h9gmvm58zjy93lx391ax76krp0m55hgn8wx"))))
    (build-system gnu-build-system)
    (inputs (list xorg-server))
    (native-inputs (list pkg-config))
@@ -2777,14 +2776,14 @@ X server.")
 (define-public xf86-video-dummy
  (package
    (name "xf86-video-dummy")
-    (version "0.3.8")
+    (version "0.4.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://xorg/individual/driver/"
-                           "xf86-video-dummy-" version ".tar.bz2"))
+                           "xf86-video-dummy-" version ".tar.xz"))
       (sha256
-        (base32 "1fcm9vwgv8wnffbvkzddk4yxrh3kc0np6w65wj8k88q7jf3bn4ip"))))
+        (base32 "0nhy9sd49ig9z00mp9sjbdkfzjgsm71szwjqnry8qn60r3jym377"))))
    (build-system gnu-build-system)
    (inputs (list xorg-server))
    (native-inputs (list pkg-config))
@@ -4091,17 +4090,17 @@ running on X server.")
 (define-public xlsfonts
  (package
    (name "xlsfonts")
-    (version "1.0.6")
+    (version "1.0.7")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "mirror://xorg/individual/app/xlsfonts-"
             version
-             ".tar.bz2"))
+             ".tar.xz"))
       (sha256
        (base32
-         "0s6kxgv78chkwsqmhw929f4pf91gq63f4yvixxnan1h00cx0pf49"))))
+         "0r84wp4352hbfcaybqp2khipm40293byvrfyrlslrd37m52njwkv"))))
    (build-system gnu-build-system)
    (inputs
     (list xorgproto libx11))
@@ -4217,7 +4216,7 @@ tastes.")
 (define-public xorg-sgml-doctools
  (package
    (name "xorg-sgml-doctools")
-    (version "1.11")
+    (version "1.12")
    (source
      (origin
        (method url-fetch)
@@ -4227,7 +4226,7 @@ tastes.")
               ".tar.bz2"))
        (sha256
          (base32
-            "0k5pffyi5bx8dmfn033cyhgd3gf6viqj3x769fqixifwhbgy2777"))))
+            "01n8zqlkqjcxk1c59pk279y08gzhc14r03dhq3lxayy1xpfzvab5"))))
    (build-system gnu-build-system)
    (native-inputs (list pkg-config))
    (home-page "https://www.x.org/wiki/")
@@ -5681,7 +5680,7 @@ Intrinsics (Xt) Library.")
 (define-public twm
  (package
    (name "twm")
-    (version "1.0.11")
+    (version "1.0.12")
    (source
     (origin
       (method url-fetch)
@@ -5689,7 +5688,7 @@ Intrinsics (Xt) Library.")
                           version ".tar.xz"))
       (sha256
        (base32
-         "1iv8kdb18n9vk3is5fyh6l40ipq9mkgx8ppj86byf464vr1ais7l"))))
+         "1r5gfv1gvcjn39v7n6znpnvifwhlw2zf8gfrxq8vph84vva03wma"))))
    (build-system gnu-build-system)
    (inputs
     (list libxt libxmu libxext xorgproto))
@@ -6486,8 +6485,6 @@ X11 servers, Windows, or macOS.")
                  (guix build emacs-utils))
       #:imported-modules (,@%gnu-build-system-modules
                           (guix build emacs-utils))
-       #:parallel-build? #f ; for reproducible generation of
-                            ; share/uim/installed-modules.scm
       #:configure-flags
       (list "--with-anthy-utf8"
             (string-append "--with-lispdir=" %output "/share/emacs")
@@ -2,6 +2,7 @@
 ;;; Copyright © 2021 Liliana Marie Prikler <liliana.prikler@gmail.com>
 ;;; Copyright © 2021 Sarah Morgensen <iskarian@mgsn.dev>
 ;;; Copyright © 2021 Calum Irwin <calumirwin1@gmail.com>
+;;; Copyright © 2022 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -99,4 +100,7 @@ toolchain.  Among other features it provides
@item concurrency via async functions.
@end itemize")
    (home-page "https://github.com/ziglang/zig")
+    ;; Currently building zig can take up to 10GB of RAM for linking stage1:
+    ;; https://github.com/ziglang/zig/issues/6485
+    (supported-systems %64bit-supported-systems)
    (license license:expat)))