This change allows users to just do "guix shell asymptote"
or put asymptote into their manifest.scm and everything
to generate PDFs just works.  Importantly, users can still modify
which ghostscript is used by setting either the `ASYMPTOTE_GS`
environment variable or the `-gs` command-line flag.

* gnu/packages/plotutils.scm (asymptote)[native-inputs]:
  Move ghostscript to [inputs].
  [phases]{patch-pdf-viewer}: Rename to...
  {change-default-settings}: ...this.
  Set default gs to point at Guix's.

Merges: https://codeberg.org/guix/guix/pulls/9653
Reviewed-by: Cayetano Santos <csantosb@inventati.org>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>

* gnu/packages/plotutils.scm (guile-charting): Update to 72c148f.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Merges: #9507

* gnu/packages/plotutils.scm (matplotplusplus): New variable.

Signed-off-by: Andreas Enge <andreas@enge.fr>

* gnu/packages/plotutils.scm (guile-plotutils)[arguments]: Use gexps.

Change-Id: I0e66032a665c12a8495d32e7ea6a28a1c1e5558c
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Merges: #9103

* gnu/packages/plotutils.scm (guile-plotutils): Update to 1.0.2.
[arguments]: Add #:configure-flags.  In ‘set-library-file-name’ phase,
add “-C src”.
[native-inputs]: Change ‘autoconf’ to ‘autoconf-2.71’.

Change-Id: I14a1242e443718662a3d36516d81c2137bde5511
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

* gnu/packages/plotutils.scm (guile-plotutils)[home-page]: Change.
[source]: Use ‘git-fetch’.
[native-inputs]: Add ‘autoconf’, ‘automake’, and ‘libtool’.

Change-Id: I0d0ec587ca94ba211791627de6d677672b959568
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

* gnu/packages/plotutils.scm (asymptote): Update to 3.12.
[native-inputs]: Add libtool, vulkan-headers.
[inputs]: Add glfw, glslang, libglvnd, ncurses, spirv-tools,
vulkan-loader. Remove libgc.
[arguments]: Install LaTeX and ConTeXt ".sty" files at the proper location.
Change bootstrap process through phases.  Remove workaround for tiprc library.

Merges: !9114

Change-Id: Ie372268b4db001d9faac2f631674f188c1e95bd7

* gnu/packages/c.scm:  Remove references to (gnu packages flex).
* gnu/packages/video.scm: Likewise.
* gnu/packages/web.scm: Likewise.
* gnu/packages/admin.scm: Change (gnu packages flex)
  to (gnu packages compiler-tools).
* gnu/packages/algebra.scm: Likewise.
* gnu/packages/apparmor.scm: Likewise.
* gnu/packages/assembly.scm: Likewise.
* gnu/packages/astronomy.scm: Likewise.
* gnu/packages/audio.scm: Likewise.
* gnu/packages/bioinformatics.scm: Likewise.
* gnu/packages/bison.scm: Likewise.
* gnu/packages/bootloaders.scm: Likewise.
* gnu/packages/cdrom.scm: Likewise.
* gnu/packages/chemistry.scm: Likewise.
* gnu/packages/cluster.scm: Likewise.
* gnu/packages/cobol.scm: Likewise.
* gnu/packages/code.scm: Likewise.
* gnu/packages/commencement.scm: Likewise.
* gnu/packages/coq.scm: Likewise.
* gnu/packages/coreboot.scm: Likewise.
* gnu/packages/databases.scm: Likewise.
* gnu/packages/datalog.scm: Likewise.
* gnu/packages/debug.scm: Likewise.
* gnu/packages/dictionaries.scm: Likewise.
* gnu/packages/dns.scm: Likewise.
* gnu/packages/documentation.scm: Likewise.
* gnu/packages/dotnet.scm: Likewise.
* gnu/packages/education.scm: Likewise.
* gnu/packages/electronics.scm: Likewise.
* gnu/packages/embedded.scm: Likewise.
* gnu/packages/emulators.scm: Likewise.
* gnu/packages/engineering.scm: Likewise.
* gnu/packages/esolangs.scm: Likewise.
* gnu/packages/fabric-management.scm: Likewise.
* gnu/packages/file-systems.scm: Likewise.
* gnu/packages/finance.scm: Likewise.
* gnu/packages/firmware.scm: Likewise.
* gnu/packages/flashing-tools.scm: Likewise.
* gnu/packages/fontutils.scm: Likewise.
* gnu/packages/games.scm: Likewise.
* gnu/packages/gcc.scm: Likewise.
* gnu/packages/gdb.scm: Likewise.
* gnu/packages/geo.scm: Likewise.
* gnu/packages/gl.scm: Likewise.
* gnu/packages/glib.scm: Likewise.
* gnu/packages/gnome.scm: Likewise.
* gnu/packages/graph.scm: Likewise.
* gnu/packages/graphics.scm: Likewise.
* gnu/packages/groff.scm: Likewise.
* gnu/packages/gstreamer.scm: Likewise.
* gnu/packages/guile.scm: Likewise.
* gnu/packages/hardware.scm: Likewise.
* gnu/packages/haskell.scm: Likewise.
* gnu/packages/heads.scm: Likewise.
* gnu/packages/hurd.scm: Likewise.
* gnu/packages/image-processing.scm: Likewise.
* gnu/packages/instrumentation.scm: Likewise.
* gnu/packages/kde-frameworks.scm: Likewise.
* gnu/packages/kde-graphics.scm: Likewise.
* gnu/packages/kde-pim.scm: Likewise.
* gnu/packages/kde-sdk.scm: Likewise.
* gnu/packages/kerberos.scm: Likewise.
* gnu/packages/lego.scm: Likewise.
* gnu/packages/lesstif.scm: Likewise.
* gnu/packages/libreoffice.scm: Likewise.
* gnu/packages/lighting.scm: Likewise.
* gnu/packages/linux.scm: Likewise.
* gnu/packages/logging.scm: Likewise.
* gnu/packages/mail.scm: Likewise.
* gnu/packages/man.scm: Likewise.
* gnu/packages/maths.scm: Likewise.
* gnu/packages/mpi.scm: Likewise.
* gnu/packages/multiprecision.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/netpbm.scm: Likewise.
* gnu/packages/networking.scm: Likewise.
* gnu/packages/nickle.scm: Likewise.
* gnu/packages/ocaml.scm: Likewise.
* gnu/packages/package-management.scm: Likewise.
* gnu/packages/parallel.scm: Likewise.
* gnu/packages/plotutils.scm: Likewise.
* gnu/packages/pretty-print.scm: Likewise.
* gnu/packages/profiling.scm: Likewise.
* gnu/packages/qt.scm: Likewise.
* gnu/packages/radio.scm: Likewise.
* gnu/packages/rdesktop.scm: Likewise.
* gnu/packages/rpc.scm: Likewise.
* gnu/packages/rust.scm: Likewise.
* gnu/packages/security-token.scm: Likewise.
* gnu/packages/selinux.scm: Likewise.
* gnu/packages/shellutils.scm: Likewise.
* gnu/packages/simulation.scm: Likewise.
* gnu/packages/statistics.scm: Likewise.
* gnu/packages/telephony.scm: Likewise.
* gnu/packages/toys.scm: Likewise.
* gnu/packages/version-control.scm: Likewise.
* gnu/packages/virtualization.scm: Likewise.
* gnu/packages/vpn.scm: Likewise.
* gnu/packages/vulkan.scm: Likewise.
* gnu/packages/webkit.scm: Likewise.
* gnu/packages/wine.scm: Likewise.
* gnu/packages/wm.scm: Likewise.
* gnu/packages/xdisorg.scm: Likewise.
* gnu/packages/xorg.scm: Likewise.

Merges: https://codeberg.org/guix/guix/pulls/8483
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>

* gnu/packages/boost.scm (boost-for-source-highlight): Rename this ...
(boost-1.83): ... to this.
(boost-numpy): Inherit from boost-1.83.
* gnu/packages/pretty-print.scm (source-highlight): Update accordingly.

* gnu/packages/boost.scm (boost): Update to 1.89.0.
[source]: Remove patches.

* gnu/packages/boost.scm (mdds)
[propagated-inputs]: Replace boost with boost-1.83.

* gnu/packages/astronomy.scm (aoflagger),
* gnu/packages/embedded.scm (cc-tool),
* gnu/packages/games.scm (0ad, vcmi),
* gnu/packages/image.scm (gpick),
* gnu/packages/maths.scm (highfive),
* gnu/packages/plotutils.scm (asymptote)
[native-inputs]: Replace boost with boost-1.83.

* gnu/packages/audio.scm (guitarix, supercollider),
* gnu/packages/bioconductor.scm (r-mzr),
* gnu/packages/bioinformatics.scm (ataqv, bless, express, isolator,
metabat, r-velocytom, rsem, sailfish, salmon),
* gnu/packages/bittorrent.scm (libtorrent-rasterbar),
* gnu/packages/code.scm (sourcetrail),
* gnu/packages/compression.scm (innoextract),
* gnu/packages/cpp.scm (lager),
* gnu/packages/crypto.scm (cryfs),
* gnu/packages/electronics.scm (nextpnr, prjpeppercorn, prjtrellis,
pulseview),
* gnu/packages/emulators.scm (mupen64plus-video-glide64mk2),
* gnu/packages/engineering.scm (cadabra2, freecad, libigl,
openscad, prusa-slicer),
* gnu/packages/file-systems.scm (snapper),
* gnu/packages/finance.scm (ledger),
* gnu/packages/game-development.scm (dds),
* gnu/packages/games.scm (colobot, fifengine, knightsgame, leela-zero,
pokerth, supertux, wesnoth, wesnoth-server),
* gnu/packages/geo.scm (gplates),
* gnu/packages/gnucash.scm (gnucash),
* gnu/packages/graph.scm (python-graph-tool),
* gnu/packages/graphics.scma (openshadinglanguage),
* gnu/packages/i2p.scm (i2pd),
* gnu/packages/image-viewers.scm (luminance-hdr),
* gnu/packages/kde-graphics.scm (krita),
* gnu/packages/mail.scm (astroid),
* gnu/packages/medical.scm (orthanc, orthanc-mysql,
orthanc-postgresql),
* gnu/packages/messaging.scm (libphonenumber),
* gnu/packages/mpd.scm (ncmpcpp),
* gnu/packages/networking.scm (kismet),
* gnu/packages/opencog.scm (cogutil),
* gnu/packages/photo.scm (hugin),
* gnu/packages/poedit.scm (poedit),
* gnu/packages/radio.scm (gnuradio),
* gnu/packages/rdf.scm (lucene++),
* gnu/packages/serialization.scm (avro-cpp),
* gnu/packages/simulation.scm (fenics-dolfin),
* gnu/packages/version-control.scm (gource),
* gnu/packages/video.scm (aegisub, mkvtoolnix),
* gnu/packages/web.scm (websocketpp)
[inputs]: Replace boost with boost-1.83.

* gnu/packages/libreoffice.scm (libcmis): Update to 0.6.2-00a85bf6.
(librevenge): Update to 0.0.5.
[arguments]<#:configure-flags>: Remove reference to boost system
component for which the compatibility stub has been removed.
* gnu/packages/serialization.scm (msgpack-cxx): Update to 7.0.0.

Change-Id: I247f3eaecde3de3fe227586b840f0312b4797ee1

This reverts commit a7db92d9b389cbe565395523882c34c6eff2c21a, this time with
the more careful command, to avoid a world rebuild:

grep -rl --exclude-dir=build --exclude-dir=patches --exclude=ld-wrapper.in \
  --exclude=sitecustomize.py --exclude=guix-emacs.el maxim.cournoyer@gmail.com |
  xargs sed -i 's/maxim.cournoyer@gmail.com/maxim@guixotic.coop/g'

Change-Id: I0871f5cf9ace79e34e78e24154d0da6ea95a3a91