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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.
2019-01-18gnu: 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.
2019-01-12gnu: r-pracma: Update to 2.2.2.Ricardo Wurmus
* gnu/packages/maths.scm (r-pracma): Update to 2.2.2.
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.
2018-12-23gnu: 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>
2018-12-17gnu: 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.
2018-12-10gnu: 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>
2018-12-08gnu: 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: 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.
2018-11-27gnu: wxmaxima: Update to 18.11.4.Kei Kebreau
* gnu/packages/maths.scm (wxmaxima): Update to 18.11.4. [source]: Switch to git-fetch.
2018-11-24Merge branch 'master' into core-updatesMarius Bakke
2018-11-23gnu: python-slepc4py: Update to 3.10.0.Paul Garlick
* gnu/packages/maths.scm (python-slepc4py): Update to 3.10.0. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2018-11-23gnu: python-petsc4py: Update to 3.10.0.Paul Garlick
* gnu/packages/maths.scm (python-petsc4py): Update to 3.10.0. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2018-11-23gnu: slepc: Update to 3.10.1.Paul Garlick
* gnu/packages/maths.scm (slepc): Update to 3.10.1. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2018-11-23gnu: petsc: Update to 3.10.2Paul Garlick
* gnu/packages/maths.scm (petsc): Update to 3.10.2. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2018-11-23gnu: pt-scotch, pt-scotch32: Add Open MPI setup phase.Ludovic Courtès
* gnu/packages/maths.scm (pt-scotch)[arguments]: Use 'invoke' instead of 'system*'. Add 'mpi-setup' phase. (pt-scotch32)[arguments]: Likewise.
2018-11-20Merge branch 'master' into core-updatesMarius Bakke
2018-11-20gnu: z3: Update to 4.8.1.Marius Bakke
* gnu/packages/maths.scm (z3): Update to 4.8.1.
2018-11-20gnu: z3: Fetch source using git.Marius Bakke
* gnu/packages/maths.scm (z3)[source]: Change to GIT-FETCH.
2018-11-18gnu: ocaml: Update to 4.7.0.Julien Lepiller
Update ocaml to the latest version and fixes dependent packages by updating them or by adding new inputs, such as ocaml-num and ocamlbuild, that were removed from the core ocaml package. Rename packages that cannot be built with the new compiler with an ocaml4.02 prefix. Add ocaml4.02 dependencies. * gnu/packages/ocaml.scm (ocaml): Update to 4.7.0. (ocaml-4.02, ocamlbuild, camlp4-4.02, ocaml-num, ocaml4.02-menhir) (ocaml4.02-lablgtk, ocaml4.02-findlib, ocaml4.02-ounit, ocaml4.02-camlzip) (ocaml4.02-ocamlmod, ocaml4.02-zarith, ocaml4.02-qcheck, ocaml4.02-qtest) (ocaml4.02-stringext, ocaml4.02-bisect, dune, ocaml-migrate-parsetree) (ocaml-ppx-tools-versioned, ocaml-ppx-tools-versioned) (ocaml4.02-bitstring, ocaml4.02-result, ocaml4.02-topkg, ocaml4.02-rresult) (ocaml4.02-sqlite3, ocaml4.02-csv, ocaml4.02-mtime, ocaml4.02-cmdliner) (ocaml4.02-fmt, ocaml4.02-astring, ocaml4.02-alcotest, ocaml4.02-ppx-tools) (ocaml4.02-react, ocaml4.02-ssl, ocaml4.02-lwt, ocaml-lwt-log) (ocaml4.02-lwt-log, ocaml4.02-logs, ocaml4.02-fpath, ocaml4.02-bos) (ocaml4.02-xmlm, ocaml4.02-ulex, ocaml4.02-uchar, ocaml4.02-uutf) (ocaml4.02-jsonm, ocaml4.02-ocurl, ocaml4.02-base64, ocaml4.02-omake) (ocaml4.02-batteries, ocaml4.02-pcre, ocaml4.02-oasis) (ocaml4.02-js-build-tools, ocaml4.02-cppo, ocaml-seq, ocaml4.02-seq) (ocaml4.02-re, ocaml4.02-ocplib-endian, ocaml4.02-easy-format) (ocaml4.02-piqilib, ocaml4.02-uuidm, ocaml4.02-graph, ocaml4.02-piqi) (ocaml4.02-camomile, ocaml4.02-zed, ocaml4.02-lambda-term): New packages. (opam): Update to 2.0.0. (camlp4): Update to 4.07+1. (camlp5): Update to 7.06. (hevea): Update to 2.32. (coq)[inputs]: Add ocaml-num. (emacs-tuareg): Update to 2.2.0. (ocaml-menhir)[native-inputs]: Add ocamlbuild. (ocaml-lablgtk): Update to 2.18.6. (unison)[inputs]: Use ocaml-4.02. (ocaml-findlib): Update to 1.8.0. (ocaml-ounit)[native-inputs]: Add ocamlbuild. (ocamlmod): Update to 0.0.9. (ocaml-frontc)[arguments]: Use ocaml-4.02. (ocaml-qcheck)[native-inputs]: Add ocamlbuild. (ocaml-qtest)[native-inputs]: Remove ocaml-findlib and add ocamlbuild. (ocaml-stringext)[native-inputs]: Add ocamlbuild. (ocaml-bisect): Update to 1.3.1. (ocaml4.01-bisect): Downgrade to 1.3. (ocaml-bitstring): Update to 3.1.0. (ocaml-topkg)[native-inputs]: Add ocamlbuild. (ocaml-rresult)[native-inputs]: Add ocamlbuild. (ocaml-sqlite3)[native-inputs]: Add ocamlbuild. (ocaml-csv)[native-inputs]: Add ocamlbuild. (ocaml-mtime)[native-inputs]: Add ocamlbuild. (ocaml-cmdliner)[native-inputs]: Add ocamlbuild. (ocaml-fmt)[native-inputs]: Add ocamlbuild. (ocaml-astring)[native-inputs]: Add ocamlbuild. (ocaml-alcotest)[native-inputs]: Add ocamlbuild. (ocaml-ppx-tools)[native-inputs]: Add ocamlbuild. (ocaml-react)[native-inputs]: Add ocamlbuild. (ocaml-ssl)[arguments]: Return #t in phases. (ocaml-lwt): Update to 4.1.0. (ocaml-logs)[native-inputs]: Add ocamlbuild. (ocaml-fpath)[native-inputs]: Add ocamlbuild. (ocaml-bos)[native-inputs]: Add ocamlbuild. (ocaml-xmlm): Update to 1.3.0. (ocaml-ulex): Update to 1.2.0. (ocaml-uchar)[native-inputs]: Add ocamlbuild. (ocaml-uutf): Update to 1.0.1. (ocaml-jsonm): Update to 1.0.1. (ocaml-ocurl): Update to 0.8.2. (ocaml-base64)[native-inputs]: Add ocamlbuild. (ocamlify)[native-inputs]: Use ocaml-4.02. (omake): Update to 0.10.3. (ocaml-batteries): Update to 2.9.0. (ocaml-pcre)[native-inputs]: Add ocamlbuild. (ocaml-expect): Update 0.0.6. (ocaml4.02-fileutils): Update to 0.5.3. (ocaml-oasis): Update 0.4.11. (ocaml-js-build-tools)[native-inputs]: Add ocamlbuild. (ocaml-bin-prot): Rename to ocaml4.02-bin-prot. (ocaml-fieldslib): Rename to ocaml4.02-fieldslib. (ocaml-ppx-core): Rename to ocaml4.02-ppx-core. (ocaml-ppx-optcomp): Rename to ocaml4.02-ppx-optcomp. (ocaml-ppx-driver): Rename to ocaml4.02-ppx-driver. (ocaml-cppo): Update to 1.6.5. (ocaml-ppx-deriving): Rename to ocaml4.02-ppx-deriving. (ocaml-ppx-type-conv): Rename to ocaml4.02-ppx-type-conv. (ocaml-ppx-inline-test): Rename to ocaml4.02-ppx-inline-test. (ocaml-ppx-bench): Rename to ocaml4.02-ppx-bench. (ocaml-ppx-compare): Rename to ocaml4.02-ppx-compare. (ocaml-sexplib): Rename to ocaml4.02-sexplib. (ocaml-typerep): Rename to ocaml4.02-typerep. (ocaml-variantslib): Rename to ocaml4.02-variantslib. (ocaml-ppx-sexp-conv): Rename to ocaml4.02-ppx-sexp-conv. (ocaml-ppx-variants-conv): Rename to ocaml4.02-ppx-variants-conv. (ocaml-ppx-here): Rename to ocaml4.02-ppx-here. (ocaml-ppx-assert): Rename to ocaml4.02-ppx-assert. (ocaml-ppx-enumerate): Rename to ocaml4.02-ppx-enumerate. (ocaml-ppx-let): Rename to ocaml4.02-ppx-let. (ocaml-ppx-typerep-conv): Rename to ocaml4.02-ppx-typerep-conv. (ocaml-ppx-sexp-value): Rename to ocaml4.02-ppx-sexp-value. (ocaml-ppx-pipebang): Rename to ocaml4.02-ppx-pipebang. (ocaml-ppx-bin-prot): Rename to ocaml4.02-ppx-bin-prot. (ocaml-ppx-fail): Rename to ocaml4.02-ppx-fail. (ocaml-ppx-custom-printf): Rename to ocaml4.02-ppx-custom-printf. (ocaml-ppx-sexp-message): Rename to ocaml4.02-ppx-sexp-message. (ocaml-ppx-fields-conv): Rename to ocaml4.02-ppx-fields-conv. (ocaml-re): Update to 1.8.0. (ocaml-ppx-expect): Rename to ocaml4.02-ppx-expect. (ocaml-ppx-jane): Rename to ocaml4.02-ppx-jane. (ocaml-core-kernel): Rename to ocaml4.02-core-kernel. (ocaml-async-kernel): Rename to ocaml4.02-async-kernel. (ocaml-async-rpc-kernel): Rename to ocaml4.02-async-rpc-kernel. (ocaml-core): Rename to ocaml4.02-core. (ocaml-async-unix): Rename to ocaml4.02-async-unix. (ocaml-async-extra): Rename to ocaml4.02-async-extra. (ocaml-async): Rename to ocaml4.02-async. (ocaml-ocplib-endian)[native-inputs]: Update to 1.0. (ocaml-cstruct): Rename to ocaml4.02-cstruct. (ocaml-hex): Rename to ocaml4.02-hex. (ocaml-ezjsonm): Rename to ocaml4.02-ezjsonm. (ocaml-uri): Rename to ocaml4.02-uri. (optcomp): Use ocaml-4.02. (ocaml-piqilib): Update to 0.6.14. (ocaml-uuidm)[native-inputs]: Add ocamlbuild. (ocaml-graph): Update to 1.8.8. (ocaml-piqi): Update to 0.7.6. (bap): Update to 1.3.0. (ocaml-camomile): Update to 1.0.1. (ocaml-jbuilder): Use ocaml-4.02. (ocaml-lambda-term): Update to 1.13. (ocaml-utop): Update to 2.2.0. (ocaml-integers)[native-inputs]: Add ocamlbuild. (ocaml-ctypes): Update to 0.14.0. (ocaml-ocb-stubblr)[native-inputs]: Add ocamlbuild. (ocaml-tsdl)[native-inputs]: Add ocamlbuild. * gnu/packages/machine-learning.scm (ocaml-mcl): Use ocaml-4.02. * gnu/packages/maths.scm (cubicle): Update to 1.1.2. * gnu/packages/patches/ocaml-bisect-fix-camlp4-in-another-directory.patch: Update patch. * guix/build-system/ocaml.scm: (default-ocaml4.02, default-ocaml4.02-findlib) (package-with-ocaml4.02, strip-ocaml4.02-variant): New variables.
2018-11-18gnu: maxima: Fix tests on i686 and x86_64.Kei Kebreau
* gnu/packages/maths.scm (maxima)[arguments]: Replace check phase.
2018-11-14gnu: Add python-slepc4py.Paul Garlick
* gnu/packages/maths.scm (python-slepc4py): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-14gnu: Add python-petsc4py.Paul Garlick
* gnu/packages/maths.scm (python-petsc4py): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-09Merge branch 'master' into core-updatesMarius Bakke
2018-11-09gnu: wxmaxima: Update to 18.10.1.Kei Kebreau
* gnu/packages/maths.scm (wxmaxima): Update to 18.10.1. [source]: Update URL and remove patch. * gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove patch.
2018-11-07Merge branch 'master' into core-updatesMarius Bakke
2018-11-07gnu: Add hdf5-1.10.Ricardo Wurmus
* gnu/packages/maths.scm (hdf5-1.10): New variable.
2018-11-05Merge branch 'master' into core-updatesMarius Bakke
2018-11-05gnu: glm: Update to 0.9.9.3.Marius Bakke
* gnu/packages/maths.scm (glm): Update to 0.9.9.3.
2018-10-30gnu: r-pracma: Update to 2.1.8.Ricardo Wurmus
* gnu/packages/maths.scm (r-pracma): Update to 2.1.8. [propagated-inputs]: Remove r-quadprog.
2018-10-27gnu: units: Update to 2.18.Tobias Geerinckx-Rice
* gnu/packages/maths.scm (units): Update to 2.18.
2018-10-21Merge branch 'master' into core-updatesMarius Bakke
2018-10-20gnu: maxima: Update to 5.42.0.Kei Kebreau
* gnu/packages/maths.scm (maxima): Update to 5.42.0.
2018-10-17Merge branch 'master' into core-updatesMarius Bakke
2018-10-11gnu: Add python-cvxopt.Ricardo Wurmus
* gnu/packages/maths.scm (python-cvxopt, python2-cvxopt): New variables.
2018-10-05Merge branch 'master' into core-updatesMarius Bakke
2018-10-04gnu: petsc-openmpi: Configure with support for MUMPS solver.Paul Garlick
* gnu/packages/maths.scm (petsc-openmpi)[inputs]: Add metis, mumps-openmpi, scalapack and pt-scotch. [arguments]: Add "--with-PACKAGENAME=1" flags. Move 'mpi-setup' phase ahead of 'configure' phase. Signed-off-by: Leo Famulari <leo@famulari.name>
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