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2021-10-31Merge remote-tracking branch 'origin/master' into core-updates-frozenEfraim Flashner
2021-10-28gnu: Add ocaml-z3.Julien Lepiller
* gnu/packages/maths.scm (ocaml-z3): New variable.
2021-10-24gnu: Add clingo.Liliana Marie Prikler
* gnu/packages/maths.scm (clingo): New variable.
2021-10-24gnu: Add clasp.Liliana Marie Prikler
* gnu/packages/maths.scm (clasp): New variable.
2021-10-24gnu: Add libpotassco.Liliana Marie Prikler
* gnu/packages/maths.scm (libpotassco): New variable.
2021-10-23gnu: hdf-java: Look for jars in the right place.Ludovic Courtès
* gnu/packages/maths.scm (hdf-java)[arguments]: Look for slf4j .jar files in the right place rather than share/java.
2021-10-23gnu: Use 'search-input-file' some more.Ludovic Courtès
This patch replaces occurrences of: (string-append (assoc-ref %build-inputs "…") "/…") by: (search-input-file %build-inputs "/…") * doc/guix.texi (Miscellaneous Services): Use 'search-input-file' in R Shiny example. * gnu/packages/admin.scm (screenfetch): Use 'search-input-file'. (ufetch): Likewise. (hosts): Likewise. * gnu/packages/backup.scm (dirvish): Likewise. * gnu/packages/code.scm (colormake): Likewise. * gnu/packages/compression.scm (makeself-safeextract): Likewise. * gnu/packages/debug.scm (scanmem): Likewise. * gnu/packages/education.scm (snap): Likewise. (omnitux): Likewise. * gnu/packages/emacs-xyz.scm (epipe): Likewise. * gnu/packages/games.scm (openttd-opensfx): Likewise. (openttd-openmsx): Likewise. (openrct2-title-sequences): Likewise. (openrct2-objects): Likewise. (mrrescue): Likewise. (0ad-data): Likewise. (xonotic-data): Likewise. (drascula): Likewise. (make-lure-package): Likewise. (make-queen-package): Likewise. (sky): Likewise. * gnu/packages/gnome.scm (network-manager): Likewise. * gnu/packages/gnuzilla.scm (icedove): Likewise. * gnu/packages/guile-xyz.scm (guile-shapefile): Likewise. * gnu/packages/hurd.scm (netdde): Likewise. * gnu/packages/javascript.scm (js-context-menu): Likewise. (js-commander): Likewise. (js-xmldom-sre): Likewise. * gnu/packages/kde-frameworks.scm (krunner): Likewise. * gnu/packages/kodi.scm (kodi-cli): Likewise. * gnu/packages/libreoffice.scm (hunspell-dict-pl): Likewise. * gnu/packages/linux.scm (e2fsck/static): Likewise. * gnu/packages/markup.scm (markdown): Likewise. * gnu/packages/maths.scm (hdf-java): Likewise. * gnu/packages/multiprecision.scm (libtomcrypt): Likewise. * gnu/packages/networking.scm (batctl): Likewise. * gnu/packages/python-xyz.scm (python-pymediainfo): Likewise. * gnu/packages/shells.scm (fish-foreign-env): Likewise. * gnu/packages/tex.scm (texlive-fonts-iwona): Likewise. * gnu/packages/upnp.scm (miniupnpc): Likewise. * gnu/packages/version-control.scm (git-annex-remote-rclone): Likewise. * gnu/packages/virtualization.scm (qemu): Likewise. * gnu/packages/web.scm (icedtea-web): Likewise. * gnu/packages/wm.scm (stumpish): Likewise.
2021-10-18gnu: hdf5@1.12: Update to 1.12.1.Tobias Geerinckx-Rice
* gnu/packages/maths.scm (hdf5-1.12): Update to 1.12.1.
2021-10-12Merge remote-tracking branch 'origin/master' into core-updates-frozen.Mathieu Othacehe
2021-10-08gnu: frama-c: Update to 23.1.Julien Lepiller
* gnu/packages/maths.scm (frama-c): Update to 23.1.
2021-10-08gnu: why3: Update to 1.4.0.Julien Lepiller
* gnu/packages/maths.scm (why3): Update to 1.4.0.
2021-10-07gnu: mcrl2: Update hash of modified-in-place tarball.Ludovic Courtès
Fixes <https://issues.guix.gnu.org/51074>. * gnu/packages/maths.scm (mcrl2)[source]: Update hash.
2021-09-25gnu: Add minizinc.Liliana Marie Prikler
* gnu/packages/maths.scm (minizinc): New variable.
2021-09-25gnu: Add gecode.Liliana Marie Prikler
* gnu/packages/maths.scm (gecode): New variable.
2021-09-24gnu: fp16: Install Python files in the site directory.Ludovic Courtès
* gnu/packages/maths.scm (fp16)[arguments]: New field.
2021-09-17Merge branch 'master' into core-updates-frozenMarius Bakke
Conflicts: gnu/packages/bioinformatics.scm gnu/packages/chez.scm gnu/packages/docbook.scm gnu/packages/ebook.scm gnu/packages/gnome.scm gnu/packages/linux.scm gnu/packages/networking.scm gnu/packages/python-web.scm gnu/packages/python-xyz.scm gnu/packages/tex.scm gnu/packages/version-control.scm gnu/packages/xml.scm guix/build-system/dune.scm guix/build-system/go.scm guix/build-system/linux-module.scm guix/packages.scm
2021-09-16gnu: aris: Fix build.Guillaume Le Vaillant
* gnu/packages/maths.scm (aris)[arguments]: Pass '-fcommon' to CFLAGS.
2021-09-14gnu: gsl: Comment out more tests that fail on i686-linux.Ludovic Courtès
* gnu/packages/maths.scm (gsl)[arguments]: In 'disable-failing-tests' phase, comment out more tests.
2021-09-11gnu: nauty: Update to 2.7r3.Nicolas Goaziou
* gnu/packages/maths.scm (nauty): Update to 2.7r3.
2021-09-11gnu: netcdf-parallel-openmpi: Allow compilation with GCC 10.Ludovic Courtès
* gnu/packages/maths.scm (netcdf)[source]: Add 'modules' and 'snippet'.
2021-09-07Merge branch 'master' into core-updates-frozenLudovic Courtès
2021-09-06gnu: Use the non-deprecated TeX packages.Ludovic Courtès
This commit leaves 'dblatex' and 'texlive-hyperref' as users of deprecated packages, but these have many dependents. * gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Use non-deprecated TeX Live packages. (velvet)[native-inputs]: Likewise. * gnu/packages/chez.scm (chez-scheme)[native-inputs]: Likewise. (chez-web)[native-inputs]: Likewise. * gnu/packages/engineering.scm (fastcap)[native-inputs]: Likewise. * gnu/packages/guile-xyz.scm (emacsy)[native-inputs]: Likewise. * gnu/packages/maths.scm (hypre)[native-inputs]: Likewise. * gnu/packages/music.scm (lilypond)[native-inputs]: Likewise. * gnu/packages/ocaml.scm (ocaml-bibtex2html)[native-inputs]: Likewise. * gnu/packages/plotutils.scm (asymptote)[native-inputs]: Likewise. * gnu/packages/python-xyz.scm (python-numpy-documentation)[native-inputs]: Likewise. (python-matplotlib-documentation)[native-inputs]: Likewise. (python-ipython-documentation)[native-inputs]: Likewise. (python-nbconvert)[native-inputs]: Likewise. (python-pypandoc)[native-inputs]: Likewise. * gnu/packages/statistics.scm (r-with-tests)[native-inputs]: Likewise. * gnu/packages/tex.scm (texlive-pstool)[propagated-inputs]: Likewise. (teximpatient)[native-inputs]: Likewise. (texlive-latex-pgf)[propagated-inputs]: Likewise. (texlive-beamer)[propagated-inputs]: Likewise.
2021-09-04gnu: vc: Update to 1.4.2.Tobias Geerinckx-Rice
* gnu/packages/maths.scm (vc): Update to 1.4.2.
2021-09-04gnu: nauty: Update to 2.7r2.Nicolas Goaziou
* gnu/packages/maths.scm (nauty): Update to 2.7r2.
2021-08-23gnu: maxima: Fix build.Guillaume Le Vaillant
Building with GCL is failing; build with SBCL instead. * gnu/packages/maths.scm (maxima)[inputs]: Replace gcl by sbcl. Add bash-minimal. [arguments]: Update 'configure-flags' and 'check' phase.
2021-08-20gnu: netcdf-fortran: Fix compiling with gfortran 10.Guillaume Le Vaillant
* gnu/packages/maths.scm (netcdf-fortran)[arguments]: Add 'allow-argument-mismatch' flag for gfortran in 'configure-flags'.
2021-08-20gnu: netcdf: Fix build.Guillaume Le Vaillant
* gnu/packages/maths.scm (netcdf)[arguments]: Fix regexp in 'patch-settings' phase.
2021-08-20gnu: hdf4: Fix compiling with gfortran 10.Guillaume Le Vaillant
* gnu/packages/maths.scm (hdf4)[arguments]: Add 'allow-argument-mismatch' flag for gfortran in 'configure-flags'. Fix regexp in 'patch-settings' phase.
2021-08-12Merge branch 'master' into core-updates-frozenMarius Bakke
Conflicts: gnu/packages/algebra.scm gnu/packages/games.scm gnu/packages/golang.scm gnu/packages/kerberos.scm gnu/packages/mail.scm gnu/packages/python.scm gnu/packages/ruby.scm gnu/packages/scheme.scm gnu/packages/tex.scm gnu/packages/tls.scm gnu/packages/version-control.scm
2021-08-01Merge branch 'master' into core-updates-frozenMarius Bakke
2021-07-29Merge branch 'master' into core-updates-frozenMarius Bakke
Conflicts: gnu/packages/bioinformatics.scm gnu/packages/cmake.scm gnu/packages/curl.scm gnu/packages/emacs-xyz.scm gnu/packages/gpodder.scm gnu/packages/music.scm gnu/packages/patches/glibc-bootstrap-system.patch gnu/packages/python-xyz.scm gnu/packages/shells.scm gnu/packages/statistics.scm
2021-07-28gnu: openlibm: Fix cross-compiling.Jean-Baptiste Volatier
* gnu/packages/maths.scm (openlibm)[arguments]: Add configure-flag to use cc-for-target. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-07-28gnu: openlibm: Update to 0.7.4.Jean-Baptiste Volatier
* gnu/packages/maths.scm (openlibm): Update to 0.7.4. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-07-29gnu: Add FP16.Ludovic Courtès
* gnu/packages/patches/fp16-system-libraries.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/maths.scm (fp16): New variable.
2021-07-29gnu: Add FXDiv.Ludovic Courtès
* gnu/packages/maths.scm (fxdiv): New variable. * gnu/packages/patches/fxdiv-system-libraries.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
2021-08-10gnu: dealii-openmpi: Add Trilinos dependency.Paul A. Patience
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi): New variable. (dealii-openmpi)[propagated-inputs]: Add trilinos-for-dealii-openmpi. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-08-05gnu: Add optizelle.Paul Garlick
* gnu/packages/maths.scm (optizelle): New variable.
2021-08-04gnu: Add bitwise.Guix Together
* gnu/packages/maths.scm (bitwise): New variable. Co-authored-by: jgart <jgart@dismail.de> Co-authored-by: Julien Lepiller <julien@lepiller.eu> Co-authored-by: Ryan Prior <rprior@protonmail.com> Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-07-26gnu: gsegrafix: Update to 1.0.7.2.Tobias Geerinckx-Rice
This keeps this ancient package on life support for now. * gnu/packages/maths.scm (gsegrafix): Update to 1.0.7.2. [source]: Download from gsegrafix-experimental's Savannah. [arguments]: Drop obsolete LDFLAGS. Disable static library build. [inputs]: Remove libgnomecanvas, libbonoboui, libgnomeui, libgnomeprintui, and popt. Add glib and gtk+.
2021-07-25gnu: openblas: Use dynamic arch support for aarch64-linux.Efraim Flashner
* gnu/packages/maths.scm (openblas)[arguments]: Adjust make-flags to build multiple architecture optimized versions for aarch64-linux.
2021-07-24gnu: Use 'search-input-file' when looking for .jar files.Ludovic Courtès
* gnu/packages/bioinformatics.scm (java-picard-1.113): Use 'search-input-file' when looking for *.jar. (fastqc): Likewise. * gnu/packages/groovy.scm (groovy): Likewise. * gnu/packages/java.scm (ant-bootstrap): Likewise. (ecj-bootstrap): Likewise. (java-cisd-base): Likewise. (java-cisd-args4j): Likewise. (java-cisd-jhdf5): Likewise. (java-native-access): Likewise. (java-native-access-platform): Likewise. * gnu/packages/maths.scm (hdf-java): Likewise.
2021-07-24gnu: Use 'search-input-file' when looking for executables.Ludovic Courtès
* 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.
2021-07-24gnu: Use 'search-input-file' when searching for Automake files.Ludovic Courtès
* gnu/packages/audio.scm (libsbsms)[arguments]: Use 'search-input-file' when searching for Automake file. * gnu/packages/maths.scm (hdf-java): Likewise.
2021-07-23gnu: gsl: Update to 2.7.Marius Bakke
* gnu/packages/maths.scm (gsl): Update to 2.7. [arguments]: Remove trailing #t's.
2021-07-20gnu: dealii: Update to 9.3.1 and clean up.Paul A. Patience
The cleanup notably: * Builds and installs the documentation into a separate doc output (in the process moving around some files erroneously installed into the root directory); and * Removes unnecessary inputs and moves some inputs into propagated-inputs (the candidates of which were determined with a search for "include.*LIBNAME" in include/deal.II). * gnu/packages/maths.scm (dealii): Reword comments. [version]: Update to 9.3.1. [outputs]: New field including doc output. [native-inputs]: New field. [inputs]: Sort them. Remove p4est (deal.II interfaces with it only when MPI is enabled). Move boost, suitesparse and tbb to... [propagated-inputs]: ...here. New field including hdf5, which is actually supported in deal.II without MPI. [arguments]<#:tests?>: New argument. The tests were not being run before anyway. <#:configure-flags>[-DDEAL_II_COMPONENT_DOCUMENTATION]: New flag. [-DDEAL_II_DOCREADME_RELDIR]: New flag. Prevents the LICENSE.md, README.md, detailed.log and summary.log files from being installed in the root directory (though note that the logs are removed in the new remove-build-logs phase). [-DDEAL_II_DOCHTML_RELDIR]: New flag. [-DDEAL_II_COMPILE_EXAMPLES]: New flag. [-DDEAL_II_EXAMPLES_RELDIR]: New flag. Prevents the examples directory from being installed in the root directory. [-DCMAKE_POSITION_INDEPENDENT_CODE]: Remove flag. The issue has been resolved. <#:phases>{remove-build-logs}: New phase. [home-page]: Add trailing slash. (dealii-openmpi): Use package/inherit. [inputs]: Sort them. Remove mumps-metis-openmpi (deal.II no longer interfaces with MUMPS). Move hdf5-parallel-openmpi, openmpi, p4est-openmpi, petsc-openmpi and slepc-openmpi to... [propagated-inputs]: ...here. New field. [arguments]<#:configure-flags>: Rename cf variable to flags. <#:phases>{mpi-setup}: Remove phase which is unused because the tests are disabled. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-07-19gnu: Add nomad-optimizer.Paul A. Patience
* gnu/packages/maths.scm (nomad-optimizer): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-07-18Merge branch 'master' into core-updatesLudovic Courtès
2021-07-16gnu: Add blitz.Ivan Gankevich
* gnu/packages/maths.scm (blitz): New variable. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2021-07-13gnu: gmsh: Sort inputs alphabetically.Efraim Flashner
* gnu/packages/maths.scm (gmsh)[propagated-inputs]: Sort alphabetically.
2021-07-13gnu: gmsh: Simply downloading source logic.Efraim Flashner
* gnu/packages/maths.scm (gmsh)[source]: Use string-replace-substring.
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