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2019-02-13gnu: dealii: Upgrade to 9.0.1.Eric Bavier
* gnu/packages/patches/dealii-mpi-deprecations.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/maths.scm (dealii)[source]: Upgrade to 9.0.1. Use patch. [arguments]: Use new MPI configuration flags.
2019-02-13gnu: Add ELPA.Eric Bavier
* gnu/packages/maths.scm (elpa, elpa-openmpi): New variables.
2019-02-13gnu: petsc: Upgrade to 3.10.3.Eric Bavier
* gnu/packages/maths.scm (petsc): Upgrade to 3.10.3.
2019-02-13gnu: scalapack: Remove use of deprecated MPI1 symbols.Eric Bavier
* gnu/packages/patches/scalapack-blacs-mpi-deprecations.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/maths.scm (scalapack)[source]: Use it.
2019-02-09Merge branch 'staging'Ludovic Courtès
2019-02-08gnu: Add dune-pdelab.Ricardo Wurmus
* gnu/packages/maths.scm (dune-pdelab): New variable.
2019-02-08gnu: Add dune-functions.Ricardo Wurmus
* gnu/packages/maths.scm (dune-functions): New variable.
2019-02-08gnu: Add dune-typetree.Ricardo Wurmus
* gnu/packages/maths.scm (dune-typetree): New variable.
2019-02-08gnu: Add dune-alugrid.Ricardo Wurmus
* gnu/packages/maths.scm (dune-alugrid): New variable.
2019-02-08gnu: Add dune-localfunctions.Ricardo Wurmus
* gnu/packages/maths.scm (dune-localfunctions): New variable.
2019-02-08gnu: Add dune-istl.Ricardo Wurmus
* gnu/packages/maths.scm (dune-istl): New variable.
2019-02-08gnu: Add dune-grid.Ricardo Wurmus
* gnu/packages/maths.scm (dune-grid): New variable.
2019-02-07gnu: hdf5: Upgrade to 1.8.21.Eric Bavier
* gnu/packages/maths.scm (hdf5): Upgrade to 1.8.21. [source]: Make version manipulations more readable using match.
2019-02-07gnu: hdf5: Remove use of deprecated MPI1 symbols.Eric Bavier
* gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch, gnu/packages/patches/hdf5-mpi-deprecations.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/maths.scm (hdf5, hdf5-1.10)[source]: Use them.
2019-02-07gnu: superlu-dist: Remove use of deprecated MPI1 symbols.Eric Bavier
* gnu/packages/patches/superlu-dist-fix-mpi-deprecations.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/maths.scm (superlu-dist)[source]: Use it.
2019-02-07gnu: Add dune-geometry.Ricardo Wurmus
* gnu/packages/maths.scm (dune-geometry): New variable.
2019-02-07gnu: Add dune-common.Ricardo Wurmus
* gnu/packages/maths.scm (dune-common): New variable.
2019-02-06gnu: wxmaxima: Update to 19.01.3.Kei Kebreau
* gnu/packages/maths.scm (wxmaxima): Update to 19.01.3.
2019-02-06gnu: maxima: Update to 5.42.2.Kei Kebreau
* gnu/packages/maths.scm (maxima): Update to 5.42.2.
2019-01-31Merge branch 'master' into stagingMarius Bakke
2019-01-26gnu: maxima: Patch hardcoded paths.Kei Kebreau
* gnu/packages/maths.scm: (maxima): Patch hardcoded paths. [arguments]: Add the phase 'patch-paths' to replace references to sed, dirname, and head with direct references to the store. [inputs]: Add sed.
2019-01-25gnu: dealii-openmpi: Setup MPI for tests.Eric Bavier
* gnu/packages/maths.scm (dealii-openmpi)[arguments]: Add 'mpi-setup' phase.
2019-01-25superlu-dist: Upgrade to 6.1.0.Eric Bavier
* gnu/packages/patches/superlu-dist-awpm-grid.patch: New file. * gnu/packages/maths.scm (superlu-dist)[source]: Upgrade to 6.0.0. Remove extraneous 'use-modules' in snippet. [build-system]: Change to cmake-build-system. [propagated-inputs]: Replace pt-scotch with pt-scotch32 to match integer sizes. Add "parmetis" input, from pt-scotch32. Move lapack to ... [inputs]: ...here. Add openblas and combinatorial-blas. [arguments]: Replace 'configure' phase with #:configure-flags. Add 'set-c++-standard' and 'omp-setup' phases. Remove 'create-install-directories, 'check', and 'install' phases, which are now handled by cmake. * gnu/local.mk (dist_patch_DATA): Add patch.
2019-01-25scotch: Upgrade to 6.0.6.Eric Bavier
* gnu/packages/maths.scm (scotch): Upgrade to 6.0.6. [source]: Remove patches that have been fixed upstream. [arguments]: Add 'install-metis' phase. [outputs]: New field. (pt-scotch, pt-scotch32)[arguments]: Add 'mpi-setup' phase. Use 'invoke'. * gnu/packages/patches/scotch-graph-diam-64.patch, gnu/packages/patches/scotch-graph-induce-type-64.patch, gnu/packages/patches/scotch-test-threading.patch: Delete files. * gnu/packages/patches/scotch-integer-declarations.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust as necessary.
2019-01-25gnu: Add Combinatorial BLAS.Eric Bavier
* gnu/packages/maths.scm (combinatorial-blas): New variable. * gnu/packages/patches/combinatorial-blas-awpm.patch, gnu/packages/patches/combinatorial-blas-io-fix.patch: New files * gnu/local.mk(dist_patch_DATA): Add them.
2019-01-20Merge branch 'master' into stagingLudovic Courtès
2019-01-18gnu: z3: Update to 4.8.4.Amin Bandali
* gnu/packages/maths.scm (z3): Update to 4.8.4. Signed-off-by: Leo Famulari <leo@famulari.name>
2019-01-15gnu: Separate Python core packages from the rest.Ricardo Wurmus
* gnu/packages/python.scm: Move hundreds of package definitions from here... * gnu/packages/python-xyz.scm: ...to this new module. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/ada.scm, gnu/packages/admin.scm, gnu/packages/android.scm, gnu/packages/audio.scm, gnu/packages/backup.scm, gnu/packages/benchmark.scm, gnu/packages/bioinformatics.scm, gnu/packages/bittorrent.scm, gnu/packages/calendar.scm, gnu/packages/check.scm, gnu/packages/chemistry.scm, gnu/packages/cluster.scm, gnu/packages/compression.scm, gnu/packages/connman.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm, gnu/packages/databases.scm, gnu/packages/dav.scm, gnu/packages/direct-connect.scm, gnu/packages/disk.scm, gnu/packages/django.scm, gnu/packages/dlang.scm, gnu/packages/docker.scm, gnu/packages/ebook.scm, gnu/packages/elf.scm, gnu/packages/emacs.scm, gnu/packages/emulators.scm, gnu/packages/engineering.scm, gnu/packages/enlightenment.scm, gnu/packages/finance.scm, gnu/packages/fltk.scm, gnu/packages/fontutils.scm, gnu/packages/freedesktop.scm, gnu/packages/game-development.scm, gnu/packages/games.scm, gnu/packages/geo.scm, gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm, gnu/packages/gnupg.scm, gnu/packages/gnuzilla.scm, gnu/packages/graph.scm, gnu/packages/graphics.scm, gnu/packages/graphviz.scm, gnu/packages/gtk.scm, gnu/packages/ham-radio.scm, gnu/packages/image-processing.scm, gnu/packages/image-viewers.scm, gnu/packages/image.scm, gnu/packages/irc.scm, gnu/packages/jrnl.scm, gnu/packages/julia.scm, gnu/packages/kde-frameworks.scm, gnu/packages/key-mon.scm, gnu/packages/libffi.scm, gnu/packages/libreoffice.scm, gnu/packages/libusb.scm, gnu/packages/lirc.scm, gnu/packages/logging.scm, gnu/packages/machine-learning.scm, gnu/packages/mail.scm, gnu/packages/mate.scm, gnu/packages/maths.scm, gnu/packages/medical.scm, gnu/packages/messaging.scm, gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/networking.scm, gnu/packages/nutrition.scm, gnu/packages/openldap.scm, gnu/packages/openstack.scm, gnu/packages/package-management.scm, gnu/packages/password-utils.scm, gnu/packages/patchutils.scm, gnu/packages/pdf.scm, gnu/packages/photo.scm, gnu/packages/polkit.scm, gnu/packages/protobuf.scm, gnu/packages/python-crypto.scm, gnu/packages/python-web.scm, gnu/packages/qt.scm, gnu/packages/rdf.scm, gnu/packages/ruby.scm, gnu/packages/search.scm, gnu/packages/selinux.scm, gnu/packages/serialization.scm, gnu/packages/shells.scm, gnu/packages/simulation.scm, gnu/packages/ssh.scm, gnu/packages/statistics.scm, gnu/packages/storage.scm, gnu/packages/sync.scm, gnu/packages/terminals.scm, gnu/packages/textutils.scm, gnu/packages/time.scm, gnu/packages/tls.scm, gnu/packages/tor.scm, gnu/packages/tryton.scm, gnu/packages/version-control.scm, gnu/packages/video.scm, gnu/packages/virtualization.scm, gnu/packages/vpn.scm, gnu/packages/web-browsers.scm, gnu/packages/web.scm, gnu/packages/wicd.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm: Update module references.
2019-01-13Merge branch 'master' into stagingMarius Bakke
2019-01-12gnu: r-pracma: Update to 2.2.2.Ricardo Wurmus
* gnu/packages/maths.scm (r-pracma): Update to 2.2.2.
2019-01-09Merge remote-tracking branch 'origin/master' into stagingEfraim Flashner
2019-01-07gnu: Move OCaml packages away from maths.scm.Ludovic Courtès
This removes (gnu packages ocaml) and related build system modules from the closure of (gnu packages maths). * gnu/packages/maths.scm (ocaml-gsl, ocaml4.01-gsl, cubicle): Move to... * gnu/packages/ocaml.scm: ... here.
2019-01-05gnu: octave: Fix makeinfo path configuration.Arun Isaac
* gnu/packages/maths.scm (octave-cli)[arguments]: Fix makeinfo path configuration in configure-makeinfo phase.
2018-12-23Merge branch 'master' into stagingMarius Bakke
2018-12-23gnu: z3: Update to 4.8.3 and provide python3 bindingsAmin Bandali
* gnu/packages/maths.scm (z3): Update to 4.8.3. [build-system]: Switch from cmake to make, and use the current scripts/mk_make.py build script instead of the now-deprecated contrib/cmake/bootstrap.py. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-12-22Merge branch 'master' into stagingMarius Bakke
2018-12-17gnu: elemental: Don't use unstable tarball.Efraim Flashner
* gnu/packages/maths.scm (elemental)[source]: Download source using git-fetch.
2018-12-17gnu: elemental: Fix indentation.Efraim Flashner
* gnu/packages/maths.scm (elemental): Fix indentation of the package definition.
2018-12-17gnu: z3: Fix building on non-Intel machines.Efraim Flashner
* gnu/packages/maths.scm (z3)[arguments]: Add phase to remove unnecessary include statement.
2018-12-17gnu: z3: Declare source-file-name.Efraim Flashner
* gnu/packages/maths.scm (z3)[source]: Add missing 'file-name.
2018-12-14gnu: hypre: Replace texlive input with minimal texlive-union.Pierre Neidhardt
* gnu/packages/maths.scm (hypre)[native-inputs]: Replace texlive with minimal texlive-union.
2018-12-12Merge branch 'master' into stagingMarius Bakke
2018-12-10gnu: petsc-openmpi: Ensure compatibility of SCOTCH dependency.Paul Garlick
* gnu/packages/maths.scm (petsc-openmpi)[inputs]: Replace pt-scotch with pt-scotch32 in order to prevent 'incompatible pointer' warnings being generated in the 'build' phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-12-09Merge branch 'master' into stagingMarius Bakke
2018-12-08gnu: Rename "qtoctave" to "octave".Kei Kebreau
* gnu/packages/maths.scm (qtoctave): Define in terms of 'deprectated-package'. (octave): New variable, formerly known as "qtoctave".
2018-12-08gnu: Rename "octave" to "octave-cli".Kei Kebreau
* gnu/packages/maths.scm (octave): Rename to... (octave-cli): ...this. [name]: Change to "octave-cli". (qtoctave): Inherit from octave-cli. (flann)[inputs]: Adjust accordingly. * gnu/packages/engineering.scm (qucs)[inputs]: Likewise. (qucs-s)[inputs]: Likewise. * gnu/packages/machine-learning.scm (shogun)[inputs]: Likewise.
2018-12-04gnu: OpenBLAS: Update to 0.3.4.Marius Bakke
* gnu/packages/maths.scm (openblas): Update to 0.3.4.
2018-12-04gnu: petsc-openmpi: Configure with support for HYPRE preconditioner.Paul Garlick
* gnu/packages/maths.scm (petsc-openmpi)[inputs]: Add hypre-openmpi. [arguments]: Add 'with-hypre=1' flag. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-29Merge branch 'master' into core-updatesMarius Bakke
2018-11-28gnu: maxima: Update to 5.42.1.Kei Kebreau
* gnu/packages/maths.scm (maxima): Update to 5.42.1.
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