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1061 Commits

Author SHA1 Message Date
Liliana Marie Prikler
95c88e381b
gnu: Add minizinc. 
* gnu/packages/maths.scm (minizinc): New variable.
 2021-09-25 14:18:02 +02:00
Liliana Marie Prikler
93cef6e768
gnu: Add gecode. 
* gnu/packages/maths.scm (gecode): New variable.
 2021-09-25 14:18:02 +02:00
Ludovic Courtès
3cdb16cb50
gnu: fp16: Install Python files in the site directory. 
* gnu/packages/maths.scm (fp16)[arguments]: New field.
 2021-09-24 13:48:49 +02:00
Marius Bakke
5c3cb22c9b
Merge branch 'master' into core-updates-frozen 
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
 2021-09-17 01:25:52 +02:00
Guillaume Le Vaillant
bad54e6384
gnu: aris: Fix build. 
* gnu/packages/maths.scm (aris)[arguments]: Pass '-fcommon' to CFLAGS.
 2021-09-16 10:18:19 +02:00
Ludovic Courtès
921595fa65
gnu: gsl: Comment out more tests that fail on i686-linux. 
* gnu/packages/maths.scm (gsl)[arguments]: In 'disable-failing-tests'
phase, comment out more tests.
 2021-09-14 15:49:56 +02:00
Nicolas Goaziou
e02984ac4e
gnu: nauty: Update to 2.7r3. 
* gnu/packages/maths.scm (nauty): Update to 2.7r3.
 2021-09-11 23:15:02 +02:00
Ludovic Courtès
7be2b83102
gnu: netcdf-parallel-openmpi: Allow compilation with GCC 10. 
* gnu/packages/maths.scm (netcdf)[source]: Add 'modules' and 'snippet'.
 2021-09-11 18:14:07 +02:00
Ludovic Courtès
d9dfbf886d
Merge branch 'master' into core-updates-frozen 2021-09-07 14:19:08 +02:00
Ludovic Courtès
b949f34f31
gnu: Use the non-deprecated TeX packages. 
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.
 2021-09-06 22:02:15 +02:00
Tobias Geerinckx-Rice
0eea6168c1
gnu: vc: Update to 1.4.2. 
* gnu/packages/maths.scm (vc): Update to 1.4.2.
 2021-09-04 22:09:01 +02:00
Nicolas Goaziou
1943f17f90
gnu: nauty: Update to 2.7r2. 
* gnu/packages/maths.scm (nauty): Update to 2.7r2.
 2021-09-04 08:03:55 +02:00
Guillaume Le Vaillant
e1b711b1f5
gnu: maxima: Fix build. 
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.
 2021-08-23 10:48:15 +02:00
Guillaume Le Vaillant
d130eaf13e
gnu: netcdf-fortran: Fix compiling with gfortran 10. 
* gnu/packages/maths.scm (netcdf-fortran)[arguments]: Add
  'allow-argument-mismatch' flag for gfortran in 'configure-flags'.
 2021-08-20 14:10:49 +02:00
Guillaume Le Vaillant
361d4627ab
gnu: netcdf: Fix build. 
* gnu/packages/maths.scm (netcdf)[arguments]: Fix regexp in 'patch-settings'
  phase.
 2021-08-20 14:10:49 +02:00
Guillaume Le Vaillant
979611d4dd
gnu: hdf4: Fix compiling with gfortran 10. 
* gnu/packages/maths.scm (hdf4)[arguments]: Add 'allow-argument-mismatch' flag
  for gfortran in 'configure-flags'. Fix regexp in 'patch-settings' phase.
 2021-08-20 14:10:49 +02:00
Marius Bakke
c4133c43c7
Merge branch 'master' into core-updates-frozen 
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
 2021-08-12 00:30:27 +02:00
Marius Bakke
d2e102d4e4
Merge branch 'master' into core-updates-frozen 2021-08-01 23:23:32 +02:00
Marius Bakke
b029be2ee0
Merge branch 'master' into core-updates-frozen 
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
 2021-07-29 22:34:57 +02:00
Jean-Baptiste Volatier
1978d716a9
gnu: openlibm: Fix cross-compiling. 
* gnu/packages/maths.scm (openlibm)[arguments]: Add configure-flag to
use cc-for-target.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-28 16:05:31 +03:00
Jean-Baptiste Volatier
4709b74bc8
gnu: openlibm: Update to 0.7.4. 
* gnu/packages/maths.scm (openlibm): Update to 0.7.4.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-28 16:05:31 +03:00
Ludovic Courtès
1daa662722
gnu: Add FP16. 
* gnu/packages/patches/fp16-system-libraries.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/maths.scm (fp16): New variable.
 2021-07-29 21:54:55 +02:00
Ludovic Courtès
a9bc8a25eb
gnu: Add FXDiv. 
* gnu/packages/maths.scm (fxdiv): New variable.
* gnu/packages/patches/fxdiv-system-libraries.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2021-07-29 21:54:54 +02:00
Paul A. Patience
06c11434c9
gnu: dealii-openmpi: Add Trilinos dependency. 
* 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>
 2021-08-10 17:32:18 +02:00
Paul Garlick
64d4bc089e
gnu: Add optizelle. 
* gnu/packages/maths.scm (optizelle): New variable.
 2021-08-05 09:29:59 +01:00
Guix Together
d3ede451cf
gnu: Add bitwise. 
* 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>
 2021-08-04 10:56:07 +03:00
Tobias Geerinckx-Rice
781a2befee
gnu: gsegrafix: Update to 1.0.7.2. 
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+.
 2021-07-26 09:47:22 +02:00
Efraim Flashner
b8894e8065
gnu: openblas: Use dynamic arch support for aarch64-linux. 
* gnu/packages/maths.scm (openblas)[arguments]: Adjust make-flags to
build multiple architecture optimized versions for aarch64-linux.
 2021-07-25 10:29:07 +03:00
Ludovic Courtès
828cfdc47e
gnu: Use 'search-input-file' when looking for .jar files. 
* 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.
 2021-07-24 16:23:23 +02:00
Ludovic Courtès
bc64d9554b
gnu: 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.
 2021-07-24 16:23:23 +02:00
Ludovic Courtès
ae112039ac
gnu: Use 'search-input-file' when searching for Automake files. 
* gnu/packages/audio.scm (libsbsms)[arguments]: Use 'search-input-file'
when searching for Automake file.
* gnu/packages/maths.scm (hdf-java): Likewise.
 2021-07-24 16:23:22 +02:00
Marius Bakke
b51bb5bcdc
gnu: gsl: Update to 2.7. 
* gnu/packages/maths.scm (gsl): Update to 2.7.
[arguments]: Remove trailing #t's.
 2021-07-23 17:26:43 +02:00
Paul A. Patience
4a136a3b7f
gnu: dealii: Update to 9.3.1 and clean up. 
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>
 2021-07-20 22:36:51 +02:00
Paul A. Patience
6bd1d4a18b
gnu: Add nomad-optimizer. 
* gnu/packages/maths.scm (nomad-optimizer): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-07-19 19:57:52 +02:00
Ludovic Courtès
0e47fcced4
Merge branch 'master' into core-updates 2021-07-18 19:50:01 +02:00
Ivan Gankevich
68ce40cad7
gnu: Add blitz. 
* gnu/packages/maths.scm (blitz): New variable.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2021-07-16 10:02:08 +05:30
Efraim Flashner
7a27129c82
gnu: gmsh: Sort inputs alphabetically. 
* gnu/packages/maths.scm (gmsh)[propagated-inputs]: Sort alphabetically.
 2021-07-13 15:44:02 +03:00
Efraim Flashner
c5cfa23b9c
gnu: gmsh: Simply downloading source logic. 
* gnu/packages/maths.scm (gmsh)[source]: Use string-replace-substring.
 2021-07-13 15:34:26 +03:00
Paul A. Patience
cb78595fe3
gnu: gmsh: Update to 4.8.4. 
* gnu/packages/maths.scm (gmsh): Update to 4.8.4.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-13 15:20:23 +03:00
Paul Garlick
b9fd7f9d5b
gnu: gmsh: Install Python API in standard directory. 
* gnu/packages/maths.scm (gmsh)[imported-modules]: New argument.
[modules]: New argument.
[phases]: New argument.
[inputs]: Add python.
 2021-07-12 16:19:46 +01:00
Jan (janneke) Nieuwenhuizen
9bd65f0583
gnu: mcrl2: Update to 202106.0. 
* gnu/packages/maths.scm (mcrl2): Update to 202106.0.
 2021-07-08 09:51:12 +02:00
Efraim Flashner
4b4d4d7bae
gnu: openblas: Fix building on powerpc64le-linux. 
* gnu/packages/maths.scm (openblas)[arguments]: Add make-flags to enable
building for powerpc64le-linux.
 2021-07-07 09:10:44 +03:00
Efraim Flashner
67ce43c0d3
gnu: openblas: Fix building on armhf-linux. 
* gnu/packages/maths.scm (openblas)[arguments]: Add make-flag to set
target architecture.
 2021-07-07 09:10:44 +03:00
Tobias Geerinckx-Rice
b9aab8e89c
gnu: atlas: Extend build time-out. 
* gnu/packages/maths.scm (atlas)[properties]: Quadruple the timeout.
 2021-07-02 20:51:43 +02:00
Tobias Geerinckx-Rice
25631d6fef
gnu: gnuplot: Update to 5.4.2. 
* gnu/packages/maths.scm (gnuplot): Update to 5.4.2.
 2021-07-02 16:56:12 +02:00
Ludovic Courtès
94bae22204
gnu: scotch: Update to 6.1.1. 
* gnu/packages/maths.scm (scotch): Update to 6.1.1.
[native-inputs]: Add GFORTRAN.
[arguments]: Set 'FC' in 'Makefile.in'.
(scotch32)[arguments]: Likewise.
(scotch-shared)[arguments]: Likewise.
 2021-06-29 12:37:31 +02:00
Ludovic Courtès
a09d69f68f
gnu: scotch: Add 'release-monitoring-url' property. 
* gnu/packages/maths.scm (scotch)[properties]: New field.
 2021-06-29 00:00:13 +02:00
Ludovic Courtès
9931d2779f
gnu: suitesparse: Update to 5.10.1. 
* gnu/packages/maths.scm (suitesparse): Update to 5.10.1.
 2021-06-25 15:12:05 +02:00
Ludovic Courtès
285f9d5e95
gnu: suitesparse: Link against OpenBLAS rather than LAPACK. 
* gnu/packages/maths.scm (suitesparse)[inputs]: Replace LAPACK with
OPENBLAS.
[arguments]: Add "BLAS"and "LAPACK" to #:make-flags.
 2021-06-25 15:12:05 +02:00
Kei Kebreau
6dafd60b33
gnu: maxima: Update to 5.45.1. 
* gnu/packages/maths.scm (maxima): Update to 5.45.1.
[home-page]: Follow redirect.
 2021-06-24 14:41:44 -04:00
Tobias Geerinckx-Rice
9dea3f101f
Merge branch 'master' into core-updates 
Conflicts:
	gnu/packages/cups.scm
	gnu/packages/python-web.scm
	gnu/packages/web.scm
	guix/build/maven/pom.scm
 2021-06-23 18:45:21 +02:00
Ludovic Courtès
c7a5c3e0bb
gnu: petsc: Link against OpenBLAS rather than LAPACK. 
OpenBLAS performs better than LAPACK, the reference implementation.
This is also consistent with the choice of BLAS/LAPACK implementations
made in most other packages.

* gnu/packages/maths.scm (petsc)[inputs]: Replace LAPACK by OPENBLAS.
[arguments]: Pass "--with-openblas=1".
 2021-06-22 17:55:05 +02:00
Julien Lepiller
6e6769dde0
gnu: why3: Update to 1.3.3. 
* gnu/packages/maths.scm (why3): Update to 1.3.3.
[arguments]: Adjust for newer ocaml-num.
 2021-06-20 13:13:56 +02:00
Marius Bakke
6f9a80b331
Merge branch 'master' into core-updates 
Note: this merge actually changes the 'curl' and 'python-attrs' derivations,
as part of solving caf4a7a277 and
12964df69a respectively.

4604d43c0e (gnu: gnutls@3.6.16: Fix cross-compilation.) was ignored because it
cannot currently be tested.

 Conflicts:
	gnu/local.mk
	gnu/packages/aidc.scm
	gnu/packages/boost.scm
	gnu/packages/curl.scm
	gnu/packages/nettle.scm
	gnu/packages/networking.scm
	gnu/packages/python-xyz.scm
	gnu/packages/tls.scm
 2021-06-19 17:38:47 +02:00
Kei Kebreau
e84a710b57
gnu: wxmaxima: Update to 21.05.2. 
* gnu/packages/maths.scm (wxmaxima): Update to 21.05.2.
 2021-06-14 13:02:50 -04:00
Kei Kebreau
a029cb5e5c
gnu: maxima: Update to 5.45.0. 
* gnu/packages/maths.scm (maxima): Update to 5.45.0.
 2021-06-14 13:02:50 -04:00
Maxim Cournoyer
ea0a51071e
gnu: 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.
 2021-06-14 00:24:42 -04:00
Jack Hill
b736334732
gnu: qalculate-gtk: Update to 3.19.0. 
* gnu/packages/maths.scm (qalculate-gtk): Update to 3.19.0.
[phases]: Remove 'add-pot-file.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-06-12 22:58:10 +02:00
Jack Hill
ea1778ebd4
gnu: libqalculate: Update to 3.19.0. 
* gnu/packages/maths (libqalculate): Update to 3.19.0.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-06-12 22:57:54 +02:00
Marius Bakke
8d59c262ad
Merge branch 'master' into core-updates 
Conflicts:
	gnu/local.mk
	gnu/packages/algebra.scm
	gnu/packages/bioinformatics.scm
	gnu/packages/curl.scm
	gnu/packages/docbook.scm
	gnu/packages/emacs-xyz.scm
	gnu/packages/maths.scm
	gnu/packages/plotutils.scm
	gnu/packages/python-web.scm
	gnu/packages/python-xyz.scm
	gnu/packages/radio.scm
	gnu/packages/readline.scm
	gnu/packages/tls.scm
	gnu/packages/xml.scm
	gnu/packages/xorg.scm
 2021-06-06 21:16:32 +02:00
Marius Bakke
f72a1253a1
gnu: hypre: Update to 2020.0. 
* gnu/packages/maths.scm (hypre): Update to 2020.0.
[source](modules, snippet): Remove.
[native-inputs]: Remove PERL, NETPBM and GHOSTSCRIPT.  Add PYTHON,
PYTHON-SPHINX and PYTHON-BREATHE.  Add TEXLIVE-ADJUSTBOX, TEXLIVE-AMSFONTS,
TEXLIVE-CAPTION, TEXLIVE-ETOOLBOX, TEXLIVE-JKNAPPEN, TEXLIVE-SECTSTY,
TEXLIVE-TEX-GYRE, TEXLIVE-WASY, TEXLIVE-XCOLOR, TEXLIVE-GENERIC-LISTOFITEMS,
TEXLIVE-GENERIC-ULEM, TEXLIVE-LATEX-CAPT-OF, TEXLIVE-LATEX-CMAP,
TEXLIVE-LATEX-COLORTBL, TEXLIVE-LATEX-ETOC, TEXLIVE-LATEX-FANCYHDR,
TEXLIVE-LATEX-FANCYVRB, TEXLIVE-LATEX-FLOAT, TEXLIVE-LATEX-FNCYCHAP,
TEXLIVE-LATEX-FRAMED, TEXLIVE-LATEX-GEOMETRY, TEXLIVE-LATEX-HANGING,
TEXLIVE-LATEX-MULTIROW, TEXLIVE-LATEX-NATBIB, TEXLIVE-LATEX-NEEDSPACE,
TEXLIVE-LATEX-NEWUNICODECHAR, TEXLIVE-LATEX-PARSKIP,
TEXLIVE-LATEX-STACKENGINE, TEXLIVE-LATEX-TABULARY, TEXLIVE-LATEX-TITLESEC,
TEXLIVE-LATEX-TOCLOFT, TEXLIVE-LATEX-UPQUOTE, TEXLIVE-LATEX-VARWIDTH,
TEXLIVE-LATEX-WASYSYM, and TEXLIVE-LATEX-WRAPFIG to TEXLIVE-UPDMAP.CFG.
[arguments]: Adjust doc build target and installation phase.  Remove trailing
 #t's.
 2021-06-06 00:12:53 +02:00
Julien Lepiller
b94bc3ea30
gnu: Add frama-c. 
* gnu/packages/maths.scm (frama-c): New variable.
 2021-06-02 03:10:12 +02:00
Julien Lepiller
c9b3627d56
gnu: Add why3. 
* gnu/packages/maths.scm (why3): New variable.
 2021-06-02 03:10:04 +02:00
Eric Brown
30713c2c2a
gnu: ipopt: Update to 3.13.4 
* gnu/packages/maths.scm (ipopt): Update to 3.13.4, update URL.
[license]: Change to LICENSE:EPL2.0.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2021-05-28 23:04:43 +02:00
Eric Brown
f5871b19cc
gnu: Add cbc. 
* gnu/packages/maths.scm (cbc): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2021-05-28 23:04:43 +02:00
Efraim Flashner
0ffac75ece
gnu: qhull: Build position independent. 
* gnu/packages/maths.scm (qhull)[arguments]: Add configure-flag to build
code position independent.
 2021-05-25 17:24:58 +03:00
Efraim Flashner
c942e17c29
gnu: qhull: Link binaries to shared library. 
This drops the package size by nearly 60%.

* gnu/packages/maths.scm (qhull)[arguments]: Add configure-flag to link
binaries to shared library.
 2021-05-25 15:50:57 +03:00
Marius Bakke
9b4f9039e8
gnu: HYPRE: Update source and home page URLs. 
* gnu/packages/maths.scm (hypre)[source]: Change to new repository home.
[home-page]: Follow redirect.
 2021-05-24 22:02:40 +02:00
Marius Bakke
dbcf2b61b1
gnu: Fix erroneous uses of 'package/inherit'. 
These packages use a different source/version from the inherited package, and
thus should not inherit replacements.

* gnu/packages/check.scm (googletest-1.8, python-pytest-runner-2): Use record
inheritance instead of PACKAGE/INHERIT.
* gnu/packages/crates-io.scm (rust-bindgen-0.49, rust-bytes-0.4,
rust-colored-1.9.1, rust-difference-1, rust-docopt-0.8, rust-html5ever-0.23,
rust-http-0.1, rust-http-body-0.1, rust-loom-0.2, rust-loom-0.1,
rust-pulldown-cmark-0.0.8, rust-ring-0.13, rust-rustls-0.12, rust-sct-0.3,
rust-term-0.2, rust-untrusted-0.6, rust-webpki-0.18, rust-webpki-roots-0.17,
rust-webpki-roots-0.14): Likewise.
* gnu/packages/emacs.scm (emacs-next, emacs-next-pgtk, guile-emacs): Likewise.
* gnu/packages/guile.scm (guile-2.2.4): Likewise.
* gnu/packages/maths.scm (hdf5-1.10, hdf5-1.12): Likewise.
* gnu/packages/protobuf.scm (protobuf-3.6, protobuf-3.5, python-protobuf-3.6):
Likewise.
* gnu/packages/python-web.scm (python2-html2text): Likewise.
* gnu/packages/python-xyz.scm (python-pygments/fixed, python2-numpy,
python2-urwid, python2-markdown, python2-fonttools): Likewise.
* gnu/packages/racket.scm (racket): Likewise.
* gnu/packages/sequoia.scm (sequoia4pEp): Likewise.
 2021-05-23 17:49:56 +02:00
Marius Bakke
4ea6852c5f
Merge branch 'master' into core-updates 2021-05-22 17:21:57 +02:00
Marius Bakke
f20de6161b
gnu: ATLAS: Fix build with GCC 10. 
* gnu/packages/patches/atlas-gfortran-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/maths.scm (atlas)[source](patches): New field.
 2021-05-22 17:08:13 +02:00
Paul A. Patience
d2e531fa43
gnu: Add numdiff. 
* gnu/packages/maths.scm (numdiff): New variable.
 2021-05-21 12:34:33 +02:00
Marius Bakke
b52f635e41
gnu: hdf5: Fix invalid regex range. 
* gnu/packages/maths.scm (hdf5-1.8)[arguments]: Use [a-zA-Z] instead of [a-Z]
as range in regular expression.
 2021-05-18 22:23:48 +02:00
Marius Bakke
c6f1e13aab
gnu: qhull: Update to 2020.2. 
* gnu/packages/maths.scm (qhull): Update to 2020.2.
 2021-05-18 22:23:48 +02:00
Marius Bakke
d6915cb8ae
gnu: arpack-ng@3.3: Don't use unstable source tarball. 
* gnu/packages/maths.scm (arpack-ng-3.3.0)[name, home-page]: Remove.
[source]: Switch to GIT-FETCH.  Inline uses of NAME and HOME-PAGE.
 2021-05-15 19:18:46 +02:00
Marius Bakke
6b496f7b32
gnu: arpack-ng: Update to 3.8.0. 
* gnu/packages/maths.scm (arpack-ng): Update to 3.8.0.
[native-inputs]: Add PKG-CONFIG.
[inputs]: Add EIGEN.
 2021-05-15 19:18:46 +02:00
Marius Bakke
f034264204
Merge branch 'master' into core-updates 
Conflicts:
	gnu/local.mk
	gnu/packages/bioinformatics.scm
	gnu/packages/django.scm
	gnu/packages/gtk.scm
	gnu/packages/llvm.scm
	gnu/packages/python-web.scm
	gnu/packages/python.scm
	gnu/packages/tex.scm
	guix/build-system/asdf.scm
	guix/build/emacs-build-system.scm
	guix/profiles.scm
 2021-05-09 21:29:46 +02:00
Tobias Geerinckx-Rice
72e2e8fa29
gnu: Add cglm. 
* gnu/packages/maths.scm (cglm): New public variable.
 2021-05-06 16:46:40 +02:00
Vinicius Monego
adc96e1db3
gnu: Add libcerf. 
* gnu/packages/maths.scm (libcerf): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-05-05 16:56:44 +02:00
Konrad Hinsen
36252dff9b
gnu: octave, octave-cli: Explain difference. 
* gnu/packages/maths.scm (octave-cli, octave): Extended synopsis.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-05-03 18:26:49 +02:00
Kei Kebreau
685e4733ad
gnu: xaos: Update to 4.2.1. 
* gnu/packages/maths.scm (xaos): Update to 4.2.1.
[arguments]: Patch call to "lrelease" in XaoS.pro.
 2021-04-29 00:44:03 -04:00
Kei Kebreau
235f2c98b9
gnu: wxmaxima: Update to 21.04.0. 
* gnu/packages/maths.scm (wxmaxima): Update to 21.04.0.
 2021-04-21 17:09:37 -04:00
Efraim Flashner
fcc39864db
Merge remote-tracking branch 'origin/master' into core-updates 
Conflicts:
	gnu/local.mk
	gnu/packages/boost.scm
	gnu/packages/chez.scm
	gnu/packages/compression.scm
	gnu/packages/crates-io.scm
	gnu/packages/docbook.scm
	gnu/packages/engineering.scm
	gnu/packages/gcc.scm
	gnu/packages/gl.scm
	gnu/packages/gtk.scm
	gnu/packages/nettle.scm
	gnu/packages/python-check.scm
	gnu/packages/python-xyz.scm
	gnu/packages/radio.scm
	gnu/packages/rust.scm
	gnu/packages/sqlite.scm
	guix/build-system/node.scm
 2021-04-16 14:39:48 +03:00
Ludovic Courtès
f67663d669
gnu: blis: Add deprecated aliases. 
Add deprecated aliases for packages removed in the parent commit.

* gnu/packages/maths.scm (blis-sandybridge, blis-haswell, blis-knl): New
variables.
 2021-04-12 12:38:01 +02:00
Philip McGrath
969adb235e
gnu: blis: Update to 0.8.1. 
* gnu/packages/maths.scm (make-blis): Remove internal function.
Inline into ...
(bliss): ... this variable. Update to 0.8.1.
[native-inputs]: Add "python" and "perl".
[arguments]: Adjust 'configure' phase to take advantage of new support
for "configuration families" with runtime hardware detection. Select
configuration automatically based on target systems, and allow
"--blis-config=" in #:configure-flags to override the default.
When building for x86_64, include all supported microarchetecture
specializations. Add "--enable-verbose-make" configure flag for better
build logs. Stop ignoring other flags from #:configure-flags.
Remove explicit #:substitutable? argument: the package is now always
substitutable. Add (srfi srfi-1) to #:modules.
(blis/x86_64): Remove internal macro.
(blis-sandybridge): Remove package: included in 'blis'.
(blis-haswell): Remove package: included in 'blis'.
(blis-knl): Remove package: included in 'blis'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-04-12 12:38:01 +02:00
Brendan Tildesley
c990604cb0
gnu: python-sip: Update to 5.5.0. Add python-sip-4 
* gnu/packages/qt.scm (python-sip): Update to 5.5.0.
(python-sip-4): New variable. Rename the old python-sip to python-sip-4.
(python2-sip): Inherit from python-sip-4.
* gnu/packages/maths.scm (veusz)[native-inputs]: Use python-sip-4.
* gnu/packages/pdf.scm (python-poppler-qt5): Use python-sip-4.
* gnu/packages/geo.scm (qgis)[arguments]: Fix build for python-sip@5.
 2021-04-09 16:09:23 -04:00
Franck Pérignon
5fd046cbfd
gnu: Add scotch and pt-scotch with shared libraries 
* gnu/packages/maths.scm (scotch-shared, pt-scotch-shared): New variables.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-04-06 13:54:09 -04:00
Felix Gruber
bab809cef0
gnu: suitesparse: Update to 5.9.0. 
* gnu/packages/maths.scm (suitesparse): Update to 5.9.0.
[arguments]: Use cc-for-target instead of hard-coding gcc.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-04-05 15:54:21 +03:00
Ludovic Courtès
de2e36411f
gnu: metis: Add 'release-monitoring-url' property. 
* gnu/packages/maths.scm (metis)[properties]: New field.
 2021-03-29 23:33:40 +02:00
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
Efraim Flashner
9bb7534a3d
gnu: Add libflame. 
* gnu/packages/maths.scm (libflame): New variable.
 2020-08-27 18:19:09 +03:00
Andreas Enge
f37e2388d0
gnu: lrslib: Update to 7.1. 
* gnu/packages/maths.scm (lrslib): Update to 7.1.
 2020-08-27 14:53:54 +02:00
Ludovic Courtès
253fcfe6fe
gnu: octave: Remove unneeded 'source' field. 
* gnu/packages/maths.scm (octave)[source]: Remove.  It had been
unnecessary since b66741edc9.
 2020-08-26 00:51:57 +02:00
Ludovic Courtès
51c55cedda
gnu: netcdf-parallel-openmpi: Allow MPI tests to pass. 
* gnu/packages/maths.scm (netcdf-parallel-openmpi)[arguments]: Add
'mip-setup' phase.
 2020-08-26 00:51:57 +02:00
Ludovic Courtès
5930963555
gnu: hdf5-parallel-openmpi: Update to 1.10.6. 
* gnu/packages/maths.scm (hdf5-parallel-openmpi): Inherit from HDF5-1.10.
 2020-08-26 00:51:57 +02:00
Ludovic Courtès
4788e55420
gnu: hdf5: Use 'package/inherit' for variants. 
* gnu/packages/maths.scm (hdf5-1.10, hdf5-parallel-openmpi): Use
'package/inherit'.
 2020-08-26 00:51:56 +02:00
Ludovic Courtès
3b8eea1c40
gnu: hdf5: Distinguish the default hdf5 version. 
* gnu/packages/maths.scm (hdf5): Rename to...
(hdf-1.8): ... this.
(hdf5-1.10): Adjust accordingly.
(hdf5): New variable.
 2020-08-26 00:51:56 +02:00
Kei Kebreau
e79fe4f675
gnu: wxmaxima: Update to 20.06.6. 
* gnu/packages/maths.scm (wxmaxima): Update to 20.06.6.
[arguments]: Add 'patch-doc-path phase.
 2020-08-16 17:30:55 -04:00
Vinicius Monego
7294cbecdd
gnu: Add veusz. 
* gnu/packages/maths.scm (veusz): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2020-08-16 09:36:21 +02:00
Ricardo Wurmus
698673699e
gnu: Add clapack. 
* gnu/packages/maths.scm (clapack): New variable.
 2020-08-10 21:58:38 +02:00
Jan (janneke) Nieuwenhuizen
abe3c5ed7d
gnu: mcrl2: Update to 202006.0. 
* gnu/packages/maths.scm (mcrl2): Update to 202006.0.
 2020-08-04 17:02:09 +02:00