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dnl -*- Autoconf -*- fragment for the C++ daemon.

AC_MSG_CHECKING([whether to build daemon])
AC_MSG_RESULT([$guix_build_daemon])

dnl C++ environment.  This macro must be used unconditionnaly.
AC_PROG_CXX
AM_PROG_AR
AC_LANG([C++])

if test "x$guix_build_daemon" = "xyes"; then

  GUIX_ASSERT_CXX11

  AC_PROG_RANLIB
  AC_CONFIG_HEADERS([nix/config.h])

  dnl Use 64-bit file system calls so that we can support files > 2 GiB.
  AC_SYS_LARGEFILE

  dnl Look for zlib, a required dependency.
  AC_CHECK_LIB([z], [gzdopen], [true],
    [AC_MSG_ERROR([Guix requires zlib.  See http://www.zlib.net/.])])
  AC_CHECK_HEADERS([zlib.h], [true],
    [AC_MSG_ERROR([Guix requires zlib.  See http://www.zlib.net/.])])

  dnl Look for libbz2, an optional dependency.
  AC_CHECK_LIB([bz2], [BZ2_bzWriteOpen], [HAVE_LIBBZ2=yes], [HAVE_LIBBZ2=no])
  if test "x$HAVE_LIBBZ2" = xyes; then
    AC_CHECK_HEADERS([bzlib.h])
    HAVE_LIBBZ2="$ac_cv_header_bzlib_h"
  fi

  dnl Look for SQLite, a required dependency.
  PKG_CHECK_MODULES([SQLITE3], [sqlite3 >= 3.6.19])

  AC_DEFINE_UNQUOTED([SYSTEM], ["$guix_system"],
    [Guix host system type--i.e., platform and OS kernel tuple.])

  case "$LIBGCRYPT_PREFIX" in
    no)
      LIBGCRYPT_CFLAGS=""
      ;;
    *)
      LIBGCRYPT_CFLAGS="-I$LIBGCRYPT_PREFIX/include"
      ;;
  esac

  case "$LIBGCRYPT_LIBDIR" in
    no | "")
      LIBGCRYPT_LIBS="-lgcrypt"
      ;;
    *)
      LIBGCRYPT_LIBS="-L$LIBGCRYPT_LIBDIR -lgcrypt"
      ;;
  esac

  AC_SUBST([LIBGCRYPT_CFLAGS])
  AC_SUBST([LIBGCRYPT_LIBS])

  save_CFLAGS="$CFLAGS"
  save_LDFLAGS="$LDFLAGS"
  CFLAGS="$CFLAGS $LIBGCRYPT_CFLAGS"
  LDFLAGS="$LDFLAGS $LIBGCRYPT_LDFLAGS"

  have_gcrypt=yes
  AC_CHECK_LIB([gcrypt], [gcry_md_open], [:], [have_gcrypt=no])
  AC_CHECK_HEADER([gcrypt.h], [:], [have_gcrypt=no])
  if test "x$have_gcrypt" != "xyes"; then
    AC_MSG_ERROR([GNU libgcrypt not found; please install it.])
  fi

  CFLAGS="$save_CFLAGS"
  LDFLAGS="$save_LDFLAGS"

  dnl Chroot support.
  AC_CHECK_FUNCS([chroot unshare])
  AC_CHECK_HEADERS([sched.h sys/param.h sys/mount.h sys/syscall.h])

  if test "x$ac_cv_func_chroot" != "xyes"; then
    AC_MSG_ERROR(['chroot' function missing, bailing out])
  fi

  dnl lutimes and lchown: used when canonicalizing store items.
  dnl posix_fallocate: used when extracting archives.
  dnl vfork: to speed up spawning of helper programs.
  dnl   `--> now disabled because of unpredictable behavior:
  dnl        see <http://lists.gnu.org/archive/html/guix-devel/2014-05/msg00036.html>
  dnl        and Nix commit f794465c (Nov. 2012).
  dnl sched_setaffinity: to improve RPC locality.
  dnl statvfs: to detect disk-full conditions.
  dnl strsignal: for error reporting.
  dnl statx: fine-grain 'stat' call, new in glibc 2.28.
  AC_CHECK_FUNCS([lutimes lchown posix_fallocate sched_setaffinity \
     statvfs nanosleep strsignal statx])

  dnl Check for <locale>.
  AC_LANG_PUSH(C++)
  AC_CHECK_HEADERS([locale])
  AC_LANG_POP(C++)


  dnl Check whether we have the `personality' syscall, which allows us
  dnl to do i686-linux builds on x86_64-linux machines.
  AC_CHECK_HEADERS([sys/personality.h])

  dnl Determine the appropriate default list of substitute URLs (GnuTLS
  dnl is required so we can default to 'https'.)
  guix_substitute_urls="https://ci.guix.gnu.org https://bordeaux.guix.gnu.org"

  AC_MSG_CHECKING([for default substitute URLs])
  AC_MSG_RESULT([$guix_substitute_urls])

  AC_DEFINE_UNQUOTED([GUIX_SUBSTITUTE_URLS], ["$guix_substitute_urls"],
    [Default list of substitute URLs used by 'guix-daemon'.])

  dnl Check for Guile-SSH, which is required by 'guix offload'.
  GUIX_CHECK_GUILE_SSH

  case "x$guix_cv_have_recent_guile_ssh" in
    xyes)
      guix_build_daemon_offload="yes"
      AC_DEFINE([HAVE_DAEMON_OFFLOAD_HOOK], [1],
	[Define if the daemon's 'offload' build hook is being built (requires Guile-SSH).])
      ;;
    *)
      guix_build_daemon_offload="no"
      ;;
  esac

  dnl Temporary directory used to store the daemon's data.
  GUIX_TEST_ROOT_DIRECTORY
  GUIX_TEST_ROOT="$ac_cv_guix_test_root"
  AC_SUBST([GUIX_TEST_ROOT])

  GUIX_CHECK_LOCALSTATEDIR
fi

AM_CONDITIONAL([HAVE_LIBBZ2], [test "x$HAVE_LIBBZ2" = "xyes"])
AM_CONDITIONAL([BUILD_DAEMON], [test "x$guix_build_daemon" = "xyes"])
AM_CONDITIONAL([BUILD_DAEMON_OFFLOAD],			\
  [test "x$guix_build_daemon" = "xyes"			\
   && test "x$guix_build_daemon_offload" = "xyes"])
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Efraim Flashner 2023-01-30gnu: texlive-graphics: Use over deprecated texlive-latex-graphics....* gnu/packages/bioinformatics.scm (phyml)[native-inputs], * gnu/packages/chemistry.scm (yaehmop)[native-inputs], * gnu/packages/graphviz.scm (dot2tex)[propagated-inputs], * gnu/packages/maths.scm (cddlib)[native-inputs], * gnu/packages/statistics.scm (r-with-tests)[native-inputs], * gnu/packages/tex.scm (texlive-apa6)[propagated-inputs]: Replace texlive-latex-graphics with texlive-graphics. Efraim Flashner 2023-01-12gnu: gromacs: Mark as tunable....* gnu/packages/chemistry.scm (gromacs)[properties]: New field. Ludovic Courtès 2023-01-10gnu: gromacs: Remove input labels and use gexps....* gnu/packages/chemistry.scm (gromacs)[arguments]: Turn into gexps. [native-inputs]: Remove labels. Remove (package-source googletest). Ludovic Courtès 2023-01-10gnu: gromacs: Update to 2022.4....* gnu/packages/chemistry.scm (gromacs): Update to 2022.4. * gnu/packages/patches/gromacs-tinyxml2.patch: Adjust accordingly. Ludovic Courtès 2022-10-27gnu: python-setuptools: Move to python-build....* gnu/packages/python-xyz.scm (python-setuptools): Move… * gnu/packages/python-build.scm: …here. * gnu/packages/chemistry.scm, gnu/packages/messaging.scm, gnu/packages/sequoia.scm, tests/lint.scm: Adjust module imports accordingly. Co-authored-by: Marius Bakke <marius@gnu.org> Lars-Dominik Braun 2022-10-15gnu: Add rdkit....* gnu/packages/chemistry.scm (rdkit): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> David Elsing 2022-10-15gnu: Add ringdecomposerlib....* gnu/packages/chemistry.scm (ringdecomposerlib): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> David Elsing 2022-10-15gnu: Add avalon-toolkit....* gnu/packages/chemistry.scm (avalon-toolkit): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> David Elsing 2022-10-15gnu: Add yaehmop....* gnu/packages/chemistry.scm (yaehmop): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> David Elsing 2022-10-15gnu: Add coordgenlibs....* gnu/packages/chemistry.scm (coordgenlibs): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> David Elsing 2022-10-15gnu: Add maeparser....* gnu/packages/chemistry.scm (maeparser): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> David Elsing 2022-10-15gnu: Add freesasa....* gnu/packages/chemistry.scm (freesasa): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> David Elsing 2022-10-15gnu: Add gemmi....* gnu/packages/patches/gemmi-fix-pegtl-usage.patch: New file. * gnu/packages/patches/gemmi-fix-sajson-types.patch: New file. * gnu/local.mk (dist_patch_DATA): Register them here. * gnu/packages/chemistry.scm (gemmi): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> David Elsing 2022-10-15gnu: Add sajson-for-gemmi....* gnu/packages/cpp.scm (sajson-for-gemmi): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> David Elsing 2022-09-15gnu: catch-framework2: Rename variable to catch2....Automated with: git grep -l catch-framework2 | xargs sed 's/catch-framework2/catch2/g' -i Maxim Cournoyer 2022-05-31gnu: Remove python2-numpy....* gnu/packages/python-xyz.scm (python2-numpy): Delete variable. (python2-numpy-1.8): Likewise. (python-numpy)[properties]: Delete field. * gnu/packages/maths.scm (flann): Delete comment. * gnu/packages/chemistry.scm (with-numpy-1.8): Delete procedure. Maxim Cournoyer 2022-05-31gnu: Remove nmoldyn....* gnu/packages/chemistry.scm (nmoldyn): Delete variable. Maxim Cournoyer 2022-05-31gnu: Remove domainfinder....* gnu/packages/chemistry.scm (domainfinder): Delete variable. Maxim Cournoyer 2021-12-13gnu: Simplify package inputs....This commit was obtained by running: ./pre-inst-env guix style without any additional argument. Ludovic Courtès 2021-10-12Merge remote-tracking branch 'origin/master' into core-updates-frozen.Mathieu Othacehe 2021-09-20gnu: Add python-pymol....* gnu/packages/chemistry.scm (python-pymol): New variable. Ricardo Wurmus 2021-07-24gnu: Use 'search-input-file' when looking for executables....* gnu/packages/admin.scm (isc-dhcp): Use 'search-input-file' when looking for executables. * gnu/packages/audio.scm (ableton-link): Likewise. * gnu/packages/benchmark.scm (fio): Likewise. * gnu/packages/bioinformatics.scm (roary): Likewise. (ngless): Likewise. * gnu/packages/boost.scm (boost-for-irods): Likewise. * gnu/packages/bootloaders.scm (grub): Likewise. (grub-efi): Likewise. * gnu/packages/chemistry.scm (inchi): Likewise. * gnu/packages/dictionaries.scm (ding): Likewise. * gnu/packages/dlang.scm (ldc): Likewise. * gnu/packages/education.scm (childsplay): Likewise. * gnu/packages/emacs-xyz.scm (emacs-hyperbole): Likewise. (emacs-haskell-mode): Likewise. (emacs-auctex): Likewise. (emacs-ggtags): Likewise. (emacs-graphviz-dot-mode): Likewise. (emacs-flycheck-grammalecte): Likewise. (emacs-counsel-notmuch): Likewise. (emacspeak): Likewise. (emacs-exwm): Likewise. (emacs-exwm-x): Likewise. (emacs-treemacs): Likewise. (emacs-telega): Likewise. (emacs-exiftool): Likewise. * gnu/packages/emulators.scm (higan): Likewise. * gnu/packages/engineering.scm (freehdl): Likewise. (librepcb): Likewise. * gnu/packages/entr.scm (entr): Likewise. * gnu/packages/file-systems.scm (libeatmydata): Likewise. (xfstests): Likewise. (mergerfs): Likewise. (mergerfs-tools): Likewise. * gnu/packages/finance.scm (monero-gui): Likewise. * gnu/packages/flashing-tools.scm (flashrom): Likewise. * gnu/packages/fontutils.scm (fontforge): Likewise. * gnu/packages/game-development.scm (python2-renpy): Likewise. * gnu/packages/games.scm (opensurge): Likewise. (xboard): Likewise. (hyperrogue): Likewise. (flare-game): Likewise. (chessx): Likewise. * gnu/packages/geo.scm (grass): Likewise. * gnu/packages/glib.scm (glib): Likewise. * gnu/packages/gnome.scm (mm-common): Likewise. (network-manager-openvpn): Likewise. (network-manager-vpnc): Likewise. (network-manager-openconnect): Likewise. (apostrophe): Likewise. * gnu/packages/gnupg.scm (pius): Likewise. (jetring): Likewise. * gnu/packages/gnuzilla.scm (icedove): Likewise. * gnu/packages/golang.scm (go-1.4): Likewise. * gnu/packages/graphviz.scm (xdot): Likewise. * gnu/packages/guile-xyz.scm (jupyter-guile-kernel): Likewise. * gnu/packages/haskell-xyz.scm (ghc-hindent): Likewise. * gnu/packages/ibus.scm (ibus): Likewise. * gnu/packages/image.scm (phockup): Likewise. * gnu/packages/irc.scm (quassel): Likewise. * gnu/packages/java.scm (drip): Likewise. (ant-bootstrap): Likewise. (tla2tools): Likewise. * gnu/packages/julia.scm (julia): Likewise. * gnu/packages/less.scm (lesspipe): Likewise. * gnu/packages/libreoffice.scm (libreoffice): Likewise. * gnu/packages/linux.scm (fuse): Likewise. (lm-sensors): Likewise. (bluez): Likewise. (fakeroot): Likewise. (inputattach): Likewise. * gnu/packages/lisp-xyz.scm (sbcl-cl-diskspace): Likewise. * gnu/packages/lisp.scm (lisp-repl-core-dumper): Likewise. * gnu/packages/lua.scm (fennel): Likewise. * gnu/packages/lxde.scm (spacefm): Likewise. * gnu/packages/mail.scm (public-inbox): Likewise. * gnu/packages/maths.scm (hdf-java): Likewise. (maxima): Likewise. (frama-c): Likewise. * gnu/packages/messaging.scm (libgadu): Likewise. * gnu/packages/music.scm (denemo): Likewise. (curseradio): Likewise. * gnu/packages/netpbm.scm (netpbm): Likewise. * gnu/packages/networking.scm (blueman): Likewise. (squid): Likewise. (aircrack-ng): Likewise. * gnu/packages/node.scm (node): Likewise. (node-llparse-frontend-bootstrap): Likewise. (node-llparse-bootstrap): Likewise. (llhttp-bootstrap): Likewise. (node-lts): Likewise. * gnu/packages/ocaml.scm (ocaml-4.11): Likewise. (opam): Likewise. (ocaml-graph): Likewise. * gnu/packages/orpheus.scm (orpheus): Likewise. * gnu/packages/password-utils.scm (password-store): Likewise. * gnu/packages/python.scm (pypy3): Likewise. * gnu/packages/qt.scm (qt5ct): Likewise. * gnu/packages/radio.scm (libosmo-dsp): Likewise. * gnu/packages/ruby.scm (ruby-pandoc-ruby): Likewise. * gnu/packages/rust.scm (rust-1.30): Likewise. * gnu/packages/screen.scm (byobu): Likewise. * gnu/packages/statistics.scm (r-with-tests): Likewise. * gnu/packages/suckless.scm (surf): Likewise. * gnu/packages/syndication.scm (gfeeds): Likewise. * gnu/packages/telephony.scm (mumble): Likewise. * gnu/packages/terminals.scm (alacritty): Likewise. * gnu/packages/tex.scm (texlive-bin): Likewise. * gnu/packages/uml.scm (plantuml): Likewise. * gnu/packages/version-control.scm (python-git-multimail): Likewise. (gitolite): Likewise. (hg-commitsigs): Likewise. (git-when-merged): Likewise. (git-imerge): Likewise. (gita): Likewise. * gnu/packages/video.scm (you-get): Likewise. * gnu/packages/vim.scm (eovim): Likewise. * gnu/packages/virtualization.scm (qemu): Likewise. (virt-manager): Likewise. (criu): Likewise. * gnu/packages/vpn.scm (strongswan): Likewise. (xl2tpd): Likewise. * gnu/packages/wm.scm (i3lock-fancy): Likewise. * gnu/packages/wxwidgets.scm (python-wxpython): Likewise. (python2-wxpython): Likewise. * gnu/packages/xdisorg.scm (autorandr): Likewise. * gnu/packages/xorg.scm (hackneyed-x11-cursors): Likewise. (v86d): Likewise. (mkfontdir): Likewise. (xpra): Likewise. Ludovic Courtès 2021-06-14gnu: Rename qtbase to qtbase-5....This change was automated via the following command: $ git ls-files | xargs sed -i 's/,qtbase)/,qtbase-5)/g' $ git ls-files | xargs sed -i 's/inherit qtbase)/inherit qtbase-5)/g' $ git ls-files | xargs sed -i 's/package-version qtbase)/package-version qtbase-5)/g' $ git checkout etc # to clear some spurious changes This is done so the qtbase package can be upgraded to version 6 in the following commit. Maxim Cournoyer 2021-02-01gnu: openbabel: Update to 3.1.1....* gnu/packages/chemistry.scm (openbabel): Update to 3.1.1. [source]: Update URI. [arguments]: Temporarily skip tests on i686-linux. Kei Kebreau 2021-02-01gnu: inchi: Update to 1.06....* gnu/packages/chemistry.scm (inchi): Update to 1.06. [source]: Use HTTPS. [native-inputs]: Update inchi-doc hash. Kei Kebreau 2021-01-29gnu: Remove avogadro....This package fails to build and has been superseded by avogadro2. * gnu/packages/chemistry.scm (avogadro): Remove variable. * gnu/packages/patches/avogadro-boost148.patch, gnu/packages/patches/avogadro-eigen3-update.patch, gnu/packages/patches/avogadro-python-eigen-lib.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Remove them. Leo Famulari 2021-01-25gnu: Add avogadro2....* gnu/packages/chemistry.scm (avogadro2): New variable. Kei Kebreau 2021-01-25gnu: Add avogadrolibs....* gnu/packages/chemistry.scm (avogadrolibs): New variable. Kei Kebreau 2021-01-25gnu: Add libmsym....* gnu/packages/chemistry.scm (libmsym): New variable. Kei Kebreau 2021-01-25gnu: Add molequeue....* gnu/packages/chemistry.scm (molequeue): New variable. Kei Kebreau 2021-01-25gnu: Add mmtf-cpp....* gnu/packages/chemistry.scm (mmtf-cpp): New variable. Kei Kebreau 2021-01-25gnu: Add spglib....* gnu/packages/chemistry.scm (spglib): New variable. Kei Kebreau 2020-07-12gnu: Remove ".git" from "https://github/…/….git"....Until now, 'lookup-origin' and thus 'lookup-origin-revision' in (guix swh) would sometimes return #f for these because the ".git" URLs are redirects to the non-".git" URLs. Consequently, 'guix lint -c archival' would keep saying "scheduled Software Heritage archival"; likewise, the fallback download code would fail. * gnu/packages/ada.scm, gnu/packages/admin.scm, gnu/packages/aidc.scm, gnu/packages/algebra.scm, gnu/packages/android.scm, gnu/packages/animation.scm, gnu/packages/arcan.scm, gnu/packages/assembly.scm, gnu/packages/audio.scm, gnu/packages/authentication.scm, gnu/packages/avr.scm, gnu/packages/axoloti.scm, gnu/packages/backup.scm, gnu/packages/bash.scm, gnu/packages/benchmark.scm, gnu/packages/bioconductor.scm, gnu/packages/bioinformatics.scm, gnu/packages/bittorrent.scm, gnu/packages/boost.scm, gnu/packages/build-tools.scm, gnu/packages/c.scm, gnu/packages/calendar.scm, gnu/packages/cdrom.scm, gnu/packages/check.scm, gnu/packages/chemistry.scm, gnu/packages/chez.scm, gnu/packages/clojure.scm, gnu/packages/code.scm, gnu/packages/compression.scm, gnu/packages/compton.scm, gnu/packages/coq.scm, gnu/packages/cpp.scm, gnu/packages/cran.scm, gnu/packages/crypto.scm, gnu/packages/curl.scm, gnu/packages/databases.scm, gnu/packages/datastructures.scm, gnu/packages/debug.scm, gnu/packages/disk.scm, gnu/packages/distributed.scm, gnu/packages/django.scm, gnu/packages/dlang.scm, gnu/packages/dns.scm, gnu/packages/docker.scm, gnu/packages/education.scm, gnu/packages/efi.scm, gnu/packages/elixir.scm, gnu/packages/emacs-xyz.scm, gnu/packages/embedded.scm, gnu/packages/emulators.scm, gnu/packages/engineering.scm, gnu/packages/erlang.scm, gnu/packages/fabric-management.scm, gnu/packages/file-systems.scm, gnu/packages/finance.scm, gnu/packages/firmware.scm, gnu/packages/flashing-tools.scm, gnu/packages/fonts.scm, gnu/packages/fontutils.scm, gnu/packages/fpga.scm, gnu/packages/game-development.scm, gnu/packages/games.scm, gnu/packages/genealogy.scm, gnu/packages/genimage.scm, gnu/packages/geo.scm, gnu/packages/gimp.scm, gnu/packages/gl.scm, gnu/packages/gnome-xyz.scm, gnu/packages/gnome.scm, gnu/packages/gnuzilla.scm, gnu/packages/golang.scm, gnu/packages/gpodder.scm, gnu/packages/graph.scm, gnu/packages/graphics.scm, gnu/packages/graphviz.scm, gnu/packages/groff.scm, gnu/packages/groovy.scm, gnu/packages/gtk.scm, gnu/packages/guile-xyz.scm, gnu/packages/guile.scm, gnu/packages/hardware.scm, gnu/packages/haskell-apps.scm, gnu/packages/haskell-xyz.scm, gnu/packages/hexedit.scm, gnu/packages/i2p.scm, gnu/packages/ibus.scm, gnu/packages/image-processing.scm, gnu/packages/image-viewers.scm, gnu/packages/image.scm, gnu/packages/ipfs.scm, gnu/packages/java-graphics.scm, gnu/packages/java-maths.scm, gnu/packages/java.scm, gnu/packages/javascript.scm, gnu/packages/jrnl.scm, gnu/packages/julia.scm, gnu/packages/jupyter.scm, gnu/packages/kodi.scm, gnu/packages/language.scm, gnu/packages/lego.scm, gnu/packages/less.scm, gnu/packages/libusb.scm, gnu/packages/linux.scm, gnu/packages/lirc.scm, gnu/packages/lisp-xyz.scm, gnu/packages/llvm.scm, gnu/packages/logging.scm, gnu/packages/lolcode.scm, gnu/packages/lua.scm, gnu/packages/lxde.scm, gnu/packages/lxqt.scm, gnu/packages/machine-learning.scm, gnu/packages/mail.scm, gnu/packages/markup.scm, gnu/packages/maths.scm, gnu/packages/maven.scm, gnu/packages/mes.scm, gnu/packages/messaging.scm, gnu/packages/monitoring.scm, gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/networking.scm, gnu/packages/node-xyz.scm, gnu/packages/ocaml.scm, gnu/packages/ocr.scm, gnu/packages/onc-rpc.scm, gnu/packages/opencl.scm, gnu/packages/opencog.scm, gnu/packages/pantheon.scm, gnu/packages/password-utils.scm, gnu/packages/patchutils.scm, gnu/packages/pdf.scm, gnu/packages/perl6.scm, gnu/packages/phabricator.scm, gnu/packages/popt.scm, gnu/packages/printers.scm, gnu/packages/prolog.scm, gnu/packages/protobuf.scm, gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm, gnu/packages/python-web.scm, gnu/packages/python-xyz.scm, gnu/packages/qt.scm, gnu/packages/radio.scm, gnu/packages/rails.scm, gnu/packages/rdf.scm, gnu/packages/rednotebook.scm, gnu/packages/rpc.scm, gnu/packages/rsync.scm, gnu/packages/ruby.scm, gnu/packages/rust.scm, gnu/packages/scheme.scm, gnu/packages/screen.scm, gnu/packages/security-token.scm, gnu/packages/selinux.scm, gnu/packages/serialization.scm, gnu/packages/shells.scm, gnu/packages/shellutils.scm, gnu/packages/simh.scm, gnu/packages/sml.scm, gnu/packages/ssh.scm, gnu/packages/statistics.scm, gnu/packages/stenography.scm, gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/synergy.scm, gnu/packages/telephony.scm, gnu/packages/terminals.scm, gnu/packages/tex.scm, gnu/packages/texinfo.scm, gnu/packages/text-editors.scm, gnu/packages/textutils.scm, gnu/packages/time.scm, gnu/packages/tmux.scm, gnu/packages/tor.scm, gnu/packages/toys.scm, gnu/packages/version-control.scm, gnu/packages/video.scm, gnu/packages/vim.scm, gnu/packages/virtualization.scm, gnu/packages/vlang.scm, gnu/packages/vnc.scm, gnu/packages/vpn.scm, gnu/packages/web-browsers.scm, gnu/packages/web.scm, gnu/packages/wireservice.scm, gnu/packages/wm.scm, gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xml.scm, gnu/packages/xorg.scm, tests/lint.scm: Remove trailing ".git" from 'git-reference' URL. Ludovic Courtès 2020-05-04gnu: Add gromacs....* gnu/packages/chemistry.scm (gromacs): New variable. * gnu/packages/patches/gromacs-tinyxml2.patch: New file... * gnu/local.mk (dist_patch_DATA): ...add it here. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Vincent Legoll 2020-05-04gnu: Add tng....* gnu/packages/chemistry.scm (tng): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Vincent Legoll 2020-04-26gnu: nmoldyn: Adjust for Guile 3.0....* gnu/packages/chemistry.scm (nmoldyn)[arguments]: Provide explicit destination in calls to FORMAT. Marius Bakke 2020-03-05gnu: domainfinder: Update home page URI....* gnu/packages/chemistry.scm (domainfinder)[home-page]: Update URI. Björn Höfling 2020-03-05gnu: nmoldyn: Upate home page URI....* gnu/packages/chemistry.scm (nmoldyn)[home-page]: Update URI. Björn Höfling 2019-11-21gnu: nmoldyn: New source code location....* gnu/packages/chemistry.scm (nmoldyn): New source code location. Following the annoucement of Bitbucket to delete all Mercurial repositories in June 2020, the source code has been migrated to GitHub. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Konrad Hinsen