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872 Commits

Author SHA1 Message Date
Efraim Flashner
2aab587f84
Merge remote-tracking branch 'origin/master' into core-updates 2021-03-24 20:50:44 +02:00
Kei Kebreau
b7c19f2850
gnu: wxmaxima: Update to 21.02.0. 
* gnu/packages/maths.scm (wxmaxima): Update to 21.02.0.
 2021-03-13 00:19:00 -05:00
Christopher Baines
a8448da0f4
Merge branch 'master' into core-updates 2021-03-06 00:18:30 +00:00
Efraim Flashner
0f8a646e03
gnu: octave: Update to 6.2.0. 
* gnu/packages/maths.scm (octave): Update to 6.2.0.
[source]: Download tar.xz tarball.
[native-inputs]: Remove lzip.
 2021-03-02 10:46:56 +02:00
Nicolas Goaziou
1ca4b76b52
gnu: slepc: Use HTTPS home page URI. 
* gnu/packages/maths.scm (slepc)[home-page]: Use HTTPS URI.
 2021-02-28 12:01:20 +01:00
Nicolas Goaziou
bebfe06776
gnu: elpa: Use HTTPS home page URI. 
* gnu/packages/maths.scm (elpa)[home-page]: Use HTTPS URI.
 2021-02-28 11:02:20 +01:00
Gerd Heber
f601cdc698
gnu: Add HDF5 1.12.0. 
* gnu/packages/maths.scm (hdf5-1.12): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-02-21 16:03:40 -05:00
Danny Milosavljevic
abd318ff4b
Merge branch 'master' into core-updates 2021-02-11 19:12:36 +01:00
Kei Kebreau
311e8d72f1
gnu: wxmaxima: Update to 21.01.0. 
* gnu/packages/maths.scm (wxmaxima): Update to 21.01.0.
[inputs]: Remove libomp.
 2021-02-09 16:28:58 -05:00
Eric Bavier
8effdd1969
gnu: hdf5: Update to 1.8.22. 
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.
 2021-02-08 13:25:34 -06:00
Christopher Baines
e740cc6140
Merge branch 'master' into core-updates 2021-02-03 09:57:35 +00:00
Maxim Cournoyer
d42245d401
gnu: Adjust package collection to Wrap using GUIX_PYTHONPATH. 
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.
 2021-02-01 11:54:01 -05:00
Maxim Cournoyer
82f5f6b14c
gnu: Replace all uses of texlive-union by texlive-updmap.cfg. 
* 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.
 2021-01-29 13:35:47 -05:00
Kei Kebreau
f5f642058a
gnu: wxmaxima: Update to 20.12.2. 
* 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.
 2021-01-17 18:07:29 -05:00
Kei Kebreau
9aa0a98ea0
gnu: gnuplot: Update to 5.4.1. 
* gnu/packages/maths.scm (gnuplot): Update to 5.4.1.
[arguments]: Set GNUTERM in #:make-flags.
 2021-01-17 18:07:29 -05:00
Maxim Cournoyer
01f0707207
Merge branch 'staging' into 'core-updates'. 
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
 2021-01-13 23:45:53 -05:00
Efraim Flashner
a2da6074d0
gnu: suitesparse: Install libraries into /lib. 
* gnu/packages/maths.scm (suitesparse)[arguments]: Add to
configure-flags to install programs built with cmake to use 'lib', not
'lib64.'
 2021-01-04 16:15:15 +02:00
Vincent Legoll
75166b29f2
gnu: matio: Update to 1.5.19. 
* gnu/packages/maths.scm (matio): Update to 1.5.19.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2020-12-31 14:50:34 +02:00
Greg Hogan
bbd2864272
gnu: openblas: Update to 0.3.13. 
* gnu/packages/maths.scm (openblas): Update to 0.3.13.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-12-27 15:50:08 +01:00
Ricardo Wurmus
6c7a0ffa1a
gnu: hypre: Remove obsolete build phase. 
* gnu/packages/maths.scm (hypre)[arguments]: Remove obsolete build phase
"set-HOME".
 2020-12-23 10:10:58 +01:00
Greg Hogan
20cf7f75ff
gnu: octave, octave-cli: Update to 6.1.0. 
* gnu/packages/maths.scm (octave, octave-cli): Update to 6.1.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-12-22 16:32:29 +01:00
Efraim Flashner
9a6cf550bd
gnu: glpk: Don't build static library. 
* gnu/packages/maths.scm (glpk)[arguments]: Add configure-flag to skip
static library.
 2020-12-17 22:26:30 +02:00
Efraim Flashner
885fe927e7
gnu: glpk: Update to 5.0. 
* 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.
 2020-12-17 22:26:30 +02:00
Vinicius Monego
0313617f65
gnu: veusz: Update to 3.3.1. 
* gnu/packages/maths.scm (veusz): Update to 3.3.1.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2020-12-13 00:26:53 +01:00
Vinicius Monego
5f40ad9ae2
gnu: sleef: Update to 3.5.1. 
* gnu/packages/maths.scm (sleef): Update to 3.5.1.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2020-12-12 21:43:39 +01:00
Eric Bavier
2a23e3f582
gnu: dealii: Update to 9.2.0. 
* gnu/packages/maths.scm (dealii): Update to 9.2.0.
 2020-12-09 13:42:05 -06:00
Ryan Prior
b5c51ae086
gnu: Add tiny-bignum. 
* gnu/packages/maths.scm (tiny-bignum): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2020-12-08 09:21:50 +00:00
Eric Bavier
705af5403b
gnu: superlu-dist: Update to 6.4.0. 
* 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.
 2020-12-05 11:14:56 -06:00
Eric Bavier
013cf93234
gnu: scotch: Update to 6.1.0 
* gnu/packages/maths.scm (scotch): Update to 6.1.0.
 2020-12-05 11:14:55 -06:00
Tobias Geerinckx-Rice
2368225019
gnu: metamath: Update to 0.193. 
* gnu/packages/maths.scm (metamath): Update to 0.193.
 2020-12-01 20:55:42 +01:00
Christopher Baines
ff01206345
Merge remote-tracking branch 'origin/master' into core-updates 2020-11-29 17:34:18 +00:00
Ludovic Courtès
03cb11400c
gnu: gsl: Build shared libraries only. 
* gnu/packages/maths.scm (gsl)[arguments]: Add #:configure-flags.
 2020-11-25 00:02:29 +01:00
Ludovic Courtès
4f6fbe7555
gnu: gsl: Demote conditional phase logic. 
* gnu/packages/maths.scm (gsl)[arguments]: Move 'cond' within
'modify-phases'.
 2020-11-25 00:02:29 +01:00
Martin Becze
62671027fb
gnu: z3: Update to 4.8.9. 
* gnu/packages/maths.scm (z3): Update to 4.8.9.

(cherry picked from commit dc2de508a3)

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2020-11-17 21:39:12 +00:00
Tobias Geerinckx-Rice
1b16727c18
gnu: units: Update to 2.21. 
* gnu/packages/maths.scm (units): Update to 2.21.
 2020-11-17 22:21:22 +01:00
Martin Becze
dc2de508a3
gnu: z3: Update to 4.8.9. 
* gnu/packages/maths.scm (z3): Update to 4.8.9.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2020-11-16 21:19:45 +00:00
Tobias Geerinckx-Rice
7ea957e2c5
gnu: superlu: Update to 5.2.2. 
* gnu/packages/maths.scm (superlu): Update to 5.2.2.
 2020-11-15 00:38:32 +01:00
Paul Garlick
c6843f1751
gnu: python-petsc4py: Fix build with python 3.8. 
* gnu/packages/maths.scm (python-petsc4py)[source]: Add snippet.
[native-inputs]: New field.
 2020-11-11 09:28:06 +00:00
Christopher Baines
d50ad6a7c6
gnu: netcdf-fortran: Update to 4.5.3. 
This allows the package to build with netcdf 4.7.4.

* gnu/packages/maths.scm (netcdf-fortran): Update to 4.5.3.
 2020-10-26 15:58:08 +00:00
Christopher Baines
a9291a28b2
gnu: netcdf: Update to 4.7.4. 
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.
 2020-10-26 15:57:27 +00:00
Ludovic Courtès
c5372cd488
gnu: hdf5: Default to 1.10. 
This is a followup to 5930963555.

* 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.
 2020-10-23 16:35:39 +02:00
Maxim Cournoyer
5e2140511c
Merge branch 'staging' 
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
 2020-10-19 13:11:40 -04:00
zimoun
229e04c66e
gnu: gmsh: Update to 4.6.0. 
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>
 2020-10-08 12:26:56 +02:00
Greg Hogan
786a04c9ae
gnu: SuiteSparse: Update to 5.8.1. 
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>
 2020-10-01 12:45:38 +02:00
Efraim Flashner
1628d57bb5
gnu: Fix package references. 
* 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.
 2020-09-30 09:28:26 +03:00
Greg Hogan
e364758d44
gnu: openblas: Update to 0.3.10. 
* gnu/packages/maths.scm (openblas): Update to 0.3.10.
[source]: Fetch from github.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2020-09-18 22:26:33 +02:00
Mathieu Othacehe
ade7638d84
Revert "gnu: openblas: Update to 0.3.10." 
This reverts commit c59e9f0a03 because it
triggers too many rebuilds.
 2020-09-18 14:05:51 +02:00
Greg Hogan
c59e9f0a03
gnu: openblas: Update to 0.3.10. 
* gnu/packages/maths.scm (openblas): Update to 0.3.10.
[source]: Fetch from github.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2020-09-18 08:57:48 +02:00
Eric Bavier
34d150dcb2
gnu: hdf5: Update to 1.10.7. 
Fixes CVE-2018-13870, CVE-2018-13869 and CVE-2018-17435.

* gnu/packages/maths.scm (hdf5-1.10): Update to 1.10.7.
 2020-09-17 11:37:02 -05:00
B. Wilson
0a7acf95db
gnu: metamath: Update to 0.192. 
* gnu/packages/maths.scm (metamath): Update to 0.192.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2020-09-08 12:12:36 +03:00