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2021-03-24Merge remote-tracking branch 'origin/master' into core-updatesEfraim Flashner
2021-03-13gnu: wxmaxima: Update to 21.02.0.Kei Kebreau
* gnu/packages/maths.scm (wxmaxima): Update to 21.02.0.
2021-03-06Merge branch 'master' into core-updatesChristopher Baines
2021-03-02gnu: octave: Update to 6.2.0.Efraim Flashner
* gnu/packages/maths.scm (octave): Update to 6.2.0. [source]: Download tar.xz tarball. [native-inputs]: Remove lzip.
2021-02-28gnu: slepc: Use HTTPS home page URI.Nicolas Goaziou
* gnu/packages/maths.scm (slepc)[home-page]: Use HTTPS URI.
2021-02-28gnu: elpa: Use HTTPS home page URI.Nicolas Goaziou
* gnu/packages/maths.scm (elpa)[home-page]: Use HTTPS URI.
2021-02-21gnu: Add HDF5 1.12.0.Gerd Heber
* gnu/packages/maths.scm (hdf5-1.12): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2021-02-11Merge branch 'master' into core-updatesDanny Milosavljevic
2021-02-09gnu: wxmaxima: Update to 21.01.0.Kei Kebreau
* gnu/packages/maths.scm (wxmaxima): Update to 21.01.0. [inputs]: Remove libomp.
2021-02-08gnu: hdf5: Update to 1.8.22.Eric Bavier
Fixes CVE-2018-14033, CVE-2018-11206, CVE-2018-13870, CVE-2018-13869, and CVE-2018-17435 * gnu/packages/maths.scm (hdf5-1.8): Update to 1.8.22. * gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch: Delete upstreamed patch. * gnu/local/mk (dist_patch_DATA): Remove it.
2021-02-03Merge branch 'master' into core-updatesChristopher Baines
2021-02-01gnu: Adjust package collection to Wrap using GUIX_PYTHONPATH.Maxim Cournoyer
This change was automated using: $ git ls-files | grep .scm | \ xargs sed 's/(getenv "PYTHONPATH")/(getenv "GUIX_PYTHONPATH")/' -i $ git ls-files | grep .scm | \ xargs sed 's/`("PYTHONPATH"/`("GUIX_PYTHONPATH"/' -i * gnu/packages/admin.scm (nmap): (dstat): Wrap using GUIX_PYTHONPATH. * gnu/packages/audio.scm (jack-2): (carla): Likewise. * gnu/packages/benchmark.scm (fio): Likewise. * gnu/packages/bioinformatics.scm (couger): Likewise. (gess, find-circ, filtlong, nanopolish): Likewise. * gnu/packages/cdrom.scm (cdemu-client): Likewise. * gnu/packages/chemistry.scm (avogadro): Likewise. * gnu/packages/connman.scm (econnman): Likewise. * gnu/packages/cups.scm (hplip): Likewise. * gnu/packages/debug.scm (scanmem): Likewise. * gnu/packages/display-managers.scm (lightdm): Likewise. * gnu/packages/ebook.scm (cozy): Likewise. * gnu/packages/education.scm (anki): Likewise. * gnu/packages/engineering.scm (kicad, volk, freecad): Likewise. * gnu/packages/game-development.scm (renpy): Likewise. * gnu/packages/games.scm (roguebox-adventures) (seahorse-adventures, kajongg): Likewise. * gnu/packages/gimp.scm (gimp, glimpse): Likewise. * gnu/packages/glib.scm (itstool): Likewise. * gnu/packages/gnome.scm (gnome-music, gtg, rhythmbox): Likewise. (eolie, d-feet, gedit, caribou, gnome-shell, authenticator) (gnome-todo, orca, passwordsafe, terminator, setzer) (libratbag, komikku): Likewise. * gnu/packages/gps.scm (gpsd): Likewise. * gnu/packages/gtk.scm (gtk-doc): Likewise. * gnu/packages/ibus.scm (ibus, ibus-libpinyin, ibus-anthy) (ibus-libhangul): Likewise. * gnu/packages/inkscape.scm (inkscape-1.0): Likewise. * gnu/packages/linux.scm (bcc): Likewise. * gnu/packages/mail.scm (notifymuch): Likewise. * gnu/packages/maths.scm (units): Likewise. * gnu/packages/music.scm (solfege): Likewise. * gnu/packages/networking.scm (blueman): Likewise. * gnu/packages/patchutils.scm (patchwork): Likewise. * gnu/packages/photo.scm (rapid-photo-downloader, entangle): Likewise. * gnu/packages/plotutils.scm (asymptote): Likewise. * gnu/packages/presentation.scm (presentty): Likewise. * gnu/packages/screen.scm (byobu): Likewise. * gnu/packages/storage.scm (ceph): Likewise. * gnu/packages/syndication.scm (liferea): Likewise. * gnu/packages/task-management.scm (blanket): Likewise. * gnu/packages/text-editors.scm (manuskript): Likewise. * gnu/packages/version-control.scm (gitless, cgit, git-when-merged) (git-imerge): Likewise. * gnu/packages/video.scm (pitivi): Likewise. * gnu/packages/virtualization.scm (criu): Likewise. * gnu/packages/xfce.scm (catfish): Likewise.
2021-01-29gnu: Replace all uses of texlive-union by texlive-updmap.cfg.Maxim Cournoyer
* doc/build.scm (pdf-manual) Replace texlive-union by texlive-updmap.cfg. * gnu/packages/algebra.scm (pari-gp): Likewise. * gnu/packages/bioinformatics.scm (discrover, velvet): Likewise. * gnu/packages/chez.scm (chez-scheme, chez-web, chez-sockets): Likewise. * gnu/packages/docbook.scm (dblatex): Likewise. * gnu/packages/emacs-xyz.scm (emacs-auctex): Likewise. * gnu/packages/engineering.scm (fastcap): Likewise. * gnu/packages/guile-xyz.scm (emacsy, guile-cv): Likewise. * gnu/packages/lisp.scm (sbcl): Likewise. * gnu/packages/maths.scm (octave, hypre): Likewise. * gnu/packages/music.scm (lilypond): Likewise. * gnu/packages/plotutils.scm (asymptote): Likewise. * gnu/packages/python-xyz.scm (python-numpy-documentation) (python-matplotlib-documentation, python-ipython-documentation) (python-pypandoc): Likewise. * gnu/packages/radio.scm (gnuradio, libosmo-dsp): Likewise. * gnu/packages/scheme.scm (mit-scheme): Likewise. * gnu/packages/statistics.scm (r-with-tests): Likewise. * gnu/packages/tex.scm (simple-texlive-package) (texlive-xmltex, texlive-tiny, texlive-jadetex, teximpatient, lyx): Likewise.
2021-01-17gnu: wxmaxima: Update to 20.12.2.Kei Kebreau
* gnu/packages/maths.scm (wxmaxima): Update to 20.12.2. [arguments]: Remove #:test-target and disable tests. Remove 'pre-check phase. [native-inputs]: Remove xorg-server-for-tests. [inputs]: Add libomp.
2021-01-17gnu: gnuplot: Update to 5.4.1.Kei Kebreau
* gnu/packages/maths.scm (gnuplot): Update to 5.4.1. [arguments]: Set GNUTERM in #:make-flags.
2021-01-13Merge branch 'staging' into 'core-updates'.Maxim Cournoyer
Conflicts: gnu/local.mk gnu/packages/cmake.scm gnu/packages/curl.scm gnu/packages/gl.scm gnu/packages/glib.scm gnu/packages/guile.scm gnu/packages/node.scm gnu/packages/openldap.scm gnu/packages/package-management.scm gnu/packages/python-xyz.scm gnu/packages/python.scm gnu/packages/tls.scm gnu/packages/vpn.scm gnu/packages/xorg.scm
2021-01-04gnu: suitesparse: Install libraries into /lib.Efraim Flashner
* gnu/packages/maths.scm (suitesparse)[arguments]: Add to configure-flags to install programs built with cmake to use 'lib', not 'lib64.'
2020-12-31gnu: matio: Update to 1.5.19.Vincent Legoll
* gnu/packages/maths.scm (matio): Update to 1.5.19. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-12-27gnu: openblas: Update to 0.3.13.Greg Hogan
* gnu/packages/maths.scm (openblas): Update to 0.3.13. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-12-23gnu: hypre: Remove obsolete build phase.Ricardo Wurmus
* gnu/packages/maths.scm (hypre)[arguments]: Remove obsolete build phase "set-HOME".
2020-12-22gnu: octave, octave-cli: Update to 6.1.0.Greg Hogan
* gnu/packages/maths.scm (octave, octave-cli): Update to 6.1.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-12-17gnu: glpk: Don't build static library.Efraim Flashner
* gnu/packages/maths.scm (glpk)[arguments]: Add configure-flag to skip static library.
2020-12-17gnu: glpk: Update to 5.0.Efraim Flashner
* gnu/packages/maths.scm (glpk): Update to 5.0. (glpk-4.65): New variable. * gnu/packages/algebra.scm (giac)[inputs]: Replace glpk with glpk-4.
2020-12-13gnu: veusz: Update to 3.3.1.Vinicius Monego
* gnu/packages/maths.scm (veusz): Update to 3.3.1. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2020-12-12gnu: sleef: Update to 3.5.1.Vinicius Monego
* gnu/packages/maths.scm (sleef): Update to 3.5.1. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2020-12-09gnu: dealii: Update to 9.2.0.Eric Bavier
* gnu/packages/maths.scm (dealii): Update to 9.2.0.
2020-12-08gnu: Add tiny-bignum.Ryan Prior
* gnu/packages/maths.scm (tiny-bignum): New variable. Signed-off-by: Christopher Baines <mail@cbaines.net>
2020-12-05gnu: superlu-dist: Update to 6.4.0.Eric Bavier
* gnu/packages/maths.scm (superlu-dist): Update to 6.4.0 [source]: Use git-fetch, as tarballs are no longer published. * gnu/packages/patches/superlu-dist-awpm-grid.patch: Remove all but the first hunk; they are unnecessary.
2020-12-05gnu: scotch: Update to 6.1.0Eric Bavier
* gnu/packages/maths.scm (scotch): Update to 6.1.0.
2020-12-01gnu: metamath: Update to 0.193.Tobias Geerinckx-Rice
* gnu/packages/maths.scm (metamath): Update to 0.193.
2020-11-29Merge remote-tracking branch 'origin/master' into core-updatesChristopher Baines
2020-11-25gnu: gsl: Build shared libraries only.Ludovic Courtès
* gnu/packages/maths.scm (gsl)[arguments]: Add #:configure-flags.
2020-11-25gnu: gsl: Demote conditional phase logic.Ludovic Courtès
* gnu/packages/maths.scm (gsl)[arguments]: Move 'cond' within 'modify-phases'.
2020-11-17gnu: z3: Update to 4.8.9.Martin Becze
* gnu/packages/maths.scm (z3): Update to 4.8.9. (cherry picked from commit dc2de508a38d8e0a3f93e8d6ded225d3a7e32548) Signed-off-by: Christopher Baines <mail@cbaines.net>
2020-11-17gnu: units: Update to 2.21.Tobias Geerinckx-Rice
* gnu/packages/maths.scm (units): Update to 2.21.
2020-11-16gnu: z3: Update to 4.8.9.Martin Becze
* gnu/packages/maths.scm (z3): Update to 4.8.9. Signed-off-by: Christopher Baines <mail@cbaines.net>
2020-11-15gnu: superlu: Update to 5.2.2.Tobias Geerinckx-Rice
* gnu/packages/maths.scm (superlu): Update to 5.2.2.
2020-11-11gnu: python-petsc4py: Fix build with python 3.8.Paul Garlick
* gnu/packages/maths.scm (python-petsc4py)[source]: Add snippet. [native-inputs]: New field.
2020-10-26gnu: netcdf-fortran: Update to 4.5.3.Christopher Baines
This allows the package to build with netcdf 4.7.4. * gnu/packages/maths.scm (netcdf-fortran): Update to 4.5.3.
2020-10-26gnu: netcdf: Update to 4.7.4.Christopher Baines
This will fix an issue building qgis. * gnu/packages/maths.scm (netcdf): Update to 4.7.4. [source]: Remove the netcdf-tst_h_par.patch, also change the naming of the source tarball, as the name seems to have changed for recent releases. [inputs]: Update hdf5 and add curl. * gnu/packages/patches/netcdf-tst_h_par.patch: Delete. * gnu/local.mk (dist_patch_DATA): Remove deleted patch.
2020-10-23gnu: hdf5: Default to 1.10.Ludovic Courtès
This is a followup to 593096355501dfd76c2e92b1fbd87f940ab1d1f2. * gnu/packages/maths.scm (hdf5): Change to HDF5-1.10. (hdf-java, hdf-eos5, h5check, netcdf, matio)[inputs]: Use HDF5-1.8. * gnu/packages/java.scm (java-cisd-jhdf5)[inputs]: Likewise.
2020-10-19Merge branch 'staging'Maxim Cournoyer
Conflicts: gnu/packages/admin.scm gnu/packages/commencement.scm gnu/packages/gdb.scm gnu/packages/llvm.scm gnu/packages/package-management.scm gnu/packages/tls.scm
2020-10-08gnu: gmsh: Update to 4.6.0.zimoun
Gmsh bundles METIS 5 released with Apache License 2.0 since upstream commit eaff7f6477fe876991615cfa4b5832bd5f12994b. Instead, Gmsh is linked with the package 'metis'. * gnu/packages/maths.scm (gmsh): Update to 4.6.0. (propagated-inputs): Replace 'opencascade-oce' by 'opencascade-occt', add 'metis'. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-10-01gnu: SuiteSparse: Update to 5.8.1.Greg Hogan
From 0d8692dfebc6ac4b515c06612ab8da4c898719eb Mon Sep 17 00:00:00 2001 From: Greg Hogan <code@greghogan.com> Date: Tue, 29 Sep 2020 11:54:38 +0000 Subject: [PATCH] gnu: SuiteSparse: Update to 5.8.1. * gnu/packages/maths.scm (suitesparse): Update to 5.8.1. [arguments]: Remove unnecessary flag and use default blas and lapack. [inputs]: Add new dependencies for SLIP_LU component. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-09-30gnu: Fix package references.Efraim Flashner
* gnu/packages/algebra.scm (iml)[inputs]: Correctly refer to package inputs. * gnu/packages/astronomy.scm (xplanet), * gnu/packages/audio.scm (redkite, libaudec, lv2lint, lv2toweb), * gnu/packages/bioconductor.scm (r-cummerbund), * gnu/packages/chicken.scm (chicken), * gnu/packages/conky.scm (conky), * gnu/packages/cran.scm (r-latex2exp), * gnu/packages/crates-io.scm (rust-rgb), * gnu/packages/databases.scm (mariadb), * gnu/packages/diffoscope.scm (reprotest), * gnu/packages/file-systems.scm (glusterfs), * gnu/packages/finance.scm (electron-cash), * gnu/packages/games.scm (rinutils, ksudoku, kdiamond, kigo), * gnu/packages/geo.scm (grass), * gnu/packages/gnome.scm (libmediaart, gnome-contacts, geoclue), * gnu/packages/gnucash.scm (aqbanking), * gnu/packages/image.scm (mtpaint), * gnu/packages/kde-internet.scm (kopete, ktorrent), * gnu/packages/kde-utils.scm (kmousetool, kmouth, kronometer), * gnu/packages/linphone.scm (liblinphone), * gnu/packages/maths.scm (ppl), * gnu/packages/mercury.scm (mercury-minimal), * gnu/packages/music.scm (bjumblr, bschaffl, lsp-plugins, spectacle-analyzer, helm, tap-lv2, wolf-shaper, shiru-lv2), * gnu/packages/networking.scm (restinio), * gnu/packages/prolog.scm (swi-prolog), * gnu/packages/python-web.scm (gunicorn), * gnu/packages/python-xyz.scm (python-docusign-esign), * gnu/packages/ruby.scm (ruby-cucumber, ruby_version, ruby-addressable), * gnu/packages/sagemath.scm (python-cypari2), * gnu/packages/skarnet.scm (s6-linux-init), * gnu/packages/vpn.scm (sshuttle), * gnu/packages/web.scm (libcyaml), * gnu/packages/xdisorg.scm (kbdd), * gnu/packages/xorg.scm (xpra): Same.
2020-09-18gnu: openblas: Update to 0.3.10.Greg Hogan
* gnu/packages/maths.scm (openblas): Update to 0.3.10. [source]: Fetch from github. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2020-09-18Revert "gnu: openblas: Update to 0.3.10."Mathieu Othacehe
This reverts commit c59e9f0a03241ef3c7b8042054fd54e327f7539a because it triggers too many rebuilds.
2020-09-18gnu: openblas: Update to 0.3.10.Greg Hogan
* gnu/packages/maths.scm (openblas): Update to 0.3.10. [source]: Fetch from github. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2020-09-17gnu: hdf5: Update to 1.10.7.Eric Bavier
Fixes CVE-2018-13870, CVE-2018-13869 and CVE-2018-17435. * gnu/packages/maths.scm (hdf5-1.10): Update to 1.10.7.
2020-09-08gnu: metamath: Update to 0.192.B. Wilson
* gnu/packages/maths.scm (metamath): Update to 0.192. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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