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539 Commits

Author SHA1 Message Date
Efraim Flashner 5c0b6d1b1d
gnu: elemental: Don't use unstable tarball. 
* gnu/packages/maths.scm (elemental)[source]: Download source using
git-fetch.
 2018-12-17 12:08:06 +02:00
Efraim Flashner 3b42e2be92
gnu: elemental: Fix indentation. 
* gnu/packages/maths.scm (elemental): Fix indentation of the package
definition.
 2018-12-17 12:08:06 +02:00
Efraim Flashner ad6c6a5be5
gnu: z3: Fix building on non-Intel machines. 
* gnu/packages/maths.scm (z3)[arguments]: Add phase to remove
unnecessary include statement.
 2018-12-17 12:08:06 +02:00
Efraim Flashner 2d7b99b3c6
gnu: z3: Declare source-file-name. 
* gnu/packages/maths.scm (z3)[source]: Add missing 'file-name.
 2018-12-17 12:08:05 +02:00
Pierre Neidhardt 9b405aeaa2
gnu: hypre: Replace texlive input with minimal texlive-union. 
* gnu/packages/maths.scm (hypre)[native-inputs]: Replace texlive with minimal
  texlive-union.
 2018-12-14 23:32:39 +01:00
Paul Garlick 72f95783f1
gnu: petsc-openmpi: Ensure compatibility of SCOTCH dependency. 
* 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>
 2018-12-10 00:28:11 +01:00
Kei Kebreau e0ae7e7374
gnu: Rename "qtoctave" to "octave". 
* gnu/packages/maths.scm (qtoctave): Define in terms of 'deprectated-package'.
(octave): New variable, formerly known as "qtoctave".
 2018-12-08 13:18:24 -05:00
Kei Kebreau 5537603fbf
gnu: Rename "octave" to "octave-cli". 
* 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.
 2018-12-08 13:17:31 -05:00
Paul Garlick af5236739e
gnu: petsc-openmpi: Configure with support for HYPRE preconditioner. 
* gnu/packages/maths.scm (petsc-openmpi)[inputs]: Add hypre-openmpi.
[arguments]: Add 'with-hypre=1' flag.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-12-04 10:58:50 +01:00
Marius Bakke 25ca46985c
Merge branch 'master' into core-updates 2018-11-29 15:56:49 +01:00
Kei Kebreau a5d474d798
gnu: maxima: Update to 5.42.1. 
* gnu/packages/maths.scm (maxima): Update to 5.42.1.
 2018-11-28 11:42:08 -05:00
Kei Kebreau c93b77ad37
gnu: wxmaxima: Update to 18.11.4. 
* gnu/packages/maths.scm (wxmaxima): Update to 18.11.4.
[source]: Switch to git-fetch.
 2018-11-27 22:11:48 -05:00
Marius Bakke 4d8f4a3f00
Merge branch 'master' into core-updates 2018-11-24 01:58:18 +01:00
Paul Garlick 57d30004e5
gnu: python-slepc4py: Update to 3.10.0. 
* gnu/packages/maths.scm (python-slepc4py): Update to 3.10.0.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-11-23 20:27:15 +01:00
Paul Garlick cd3681a237
gnu: python-petsc4py: Update to 3.10.0. 
* gnu/packages/maths.scm (python-petsc4py): Update to 3.10.0.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-11-23 20:27:15 +01:00
Paul Garlick e93da160ca
gnu: slepc: Update to 3.10.1. 
* gnu/packages/maths.scm (slepc): Update to 3.10.1.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-11-23 20:27:15 +01:00
Paul Garlick e6951e4ee0
gnu: petsc: Update to 3.10.2 
* gnu/packages/maths.scm (petsc): Update to 3.10.2.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-11-23 20:27:15 +01:00
Ludovic Courtès c491f7f8de
gnu: pt-scotch, pt-scotch32: Add Open MPI setup phase. 
* gnu/packages/maths.scm (pt-scotch)[arguments]: Use 'invoke' instead of
'system*'.  Add 'mpi-setup' phase.
(pt-scotch32)[arguments]: Likewise.
 2018-11-23 18:44:47 +01:00
Marius Bakke 4f70db97a0
Merge branch 'master' into core-updates 2018-11-20 01:14:12 +01:00
Marius Bakke 4a4f3e771b
gnu: z3: Update to 4.8.1. 
* gnu/packages/maths.scm (z3): Update to 4.8.1.
 2018-11-20 00:57:48 +01:00
Marius Bakke fb525bfd83
gnu: z3: Fetch source using git. 
* gnu/packages/maths.scm (z3)[source]: Change to GIT-FETCH.
 2018-11-20 00:57:48 +01:00
Julien Lepiller 564cf93f2a
gnu: ocaml: Update to 4.7.0. 
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.
 2018-11-18 18:51:08 +01:00
Kei Kebreau 1472d19abf
gnu: maxima: Fix tests on i686 and x86_64. 
* gnu/packages/maths.scm (maxima)[arguments]: Replace check phase.
 2018-11-18 11:58:38 -05:00
Paul Garlick 6b5687d053
gnu: Add python-slepc4py. 
* gnu/packages/maths.scm (python-slepc4py): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-14 21:34:08 +01:00
Paul Garlick 90ff287401
gnu: Add python-petsc4py. 
* gnu/packages/maths.scm (python-petsc4py): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-11-14 21:34:08 +01:00
Marius Bakke 64461ba20a
Merge branch 'master' into core-updates 2018-11-09 17:02:08 +01:00
Kei Kebreau e4b62e229e
gnu: wxmaxima: Update to 18.10.1. 
* 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.
 2018-11-09 01:09:06 -05:00
Marius Bakke 55174e668f
Merge branch 'master' into core-updates 2018-11-07 21:09:57 +01:00
Ricardo Wurmus bb47aca5e7
gnu: Add hdf5-1.10. 
* gnu/packages/maths.scm (hdf5-1.10): New variable.
 2018-11-07 12:26:33 +01:00
Marius Bakke f4a5faa9dc
Merge branch 'master' into core-updates 2018-11-05 23:56:22 +01:00
Marius Bakke 66044a3698
gnu: glm: Update to 0.9.9.3. 
* gnu/packages/maths.scm (glm): Update to 0.9.9.3.
 2018-11-05 23:46:38 +01:00
Ricardo Wurmus 39528a5ee9
gnu: r-pracma: Update to 2.1.8. 
* gnu/packages/maths.scm (r-pracma): Update to 2.1.8.
[propagated-inputs]: Remove r-quadprog.
 2018-10-30 21:48:10 +01:00
Tobias Geerinckx-Rice 4795e5e177
gnu: units: Update to 2.18. 
* gnu/packages/maths.scm (units): Update to 2.18.
 2018-10-27 04:47:56 +02:00
Marius Bakke ffddb42d6c
Merge branch 'master' into core-updates 2018-10-21 18:06:02 +02:00
Kei Kebreau 82cbe4e046
gnu: maxima: Update to 5.42.0. 
* gnu/packages/maths.scm (maxima): Update to 5.42.0.
 2018-10-20 14:38:45 -04:00
Marius Bakke d02bb02f7d
Merge branch 'master' into core-updates 2018-10-17 20:47:11 +02:00
Ricardo Wurmus a8fa86c477
gnu: Add python-cvxopt. 
* gnu/packages/maths.scm (python-cvxopt, python2-cvxopt): New variables.
 2018-10-11 10:30:30 +02:00
Marius Bakke cf6db76d2a
Merge branch 'master' into core-updates 2018-10-05 19:15:39 +02:00
Paul Garlick 9e2aa70bad
gnu: petsc-openmpi: Configure with support for MUMPS solver. 
* 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>
 2018-10-04 18:21:17 -04:00
Marius Bakke 6a0427af6c
Merge branch 'master' into core-updates 2018-09-26 01:11:32 +02:00
Kei Kebreau 116af86f14
gnu: octave: Add a search path for CURLOPT_CAPATH. 
* gnu/packages/maths.scm (octave)[native-search-paths]: New field.
 2018-09-24 21:42:12 -04:00
Paul Garlick 45201bf245
gnu: hdf5-parallel-openmpi: Really enable parallel build. 
This fix ensures that the H5_HAVE_PARALLEL identifier is correctly set
in the file H5pubconf.h.

* gnu/packages/maths.scm (hdf5-parallel-openmpi)[arguments]: Add
the "--enable-parallel" flag to the list of configure flags.  Remove
the incompatible "--enable-cxx" flag.  Add 'mpi-setup' phase.

Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr>
 2018-09-21 17:04:37 +02:00
Paul Garlick b0d1e60fff
gnu: hdf5: Allow for absence of utility script. 
* gnu/packages/maths.scm (hdf5)[arguments]: Add condition to 'split'
phase to check for existence of h5fc script.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-21 17:04:37 +02:00
Marius Bakke 2817ac3c18
Merge branch 'master' into core-updates 2018-09-20 13:37:58 +02:00
Tobias Geerinckx-Rice 9923d5a40f
gnu: Use INVOKE & return #t from Ruby package phases. 
* gnu/packages/maths.scm (ruby-asciimath)[arguments]: Return #t from
all phases.
* gnu/packages/rails.scm (ruby-debug-inspector)[arguments]: Substitute
INVOKE for SYSTEM*.
* gnu/packages/ruby.scm (ruby-permutation, ruby-blankslate)
(ruby-minitest-pretty-diff, ruby-guard, ruby-rb-inotify, ruby-tins)
(ruby-gem-hadar, ruby-term-ansicolor, ruby-json-pure)
(ruby-activesupport, ruby-redcloth, ruby-netrc, ruby-unf-ext, ruby-yard)
(ruby-turn, ruby-sqlite3, ruby-shoulda-context, ruby-shoulda-matchers)
(ruby-shoulda, ruby-httpclient, ruby-ansi, ruby-bio-commandeer)
(ruby-rubytest, ruby-brass, ruby-qed, ruby-ae, ruby-lemon, ruby-hashery)
(ruby-rc4, ruby-concurrent)[arguments]: Likewise.
 2018-09-20 04:17:04 +02:00
Marius Bakke 4d679255da
gnu: glm: Update to 0.9.9.2. 
* gnu/packages/maths.scm (glm): Update to 0.9.9.2.
 2018-09-19 15:20:21 +02:00
Marius Bakke f03c4ec649
gnu: arpack-ng: Update to 3.6.3. 
* gnu/packages/maths.scm (arpack-ng): Update to 3.6.3.
 2018-09-19 15:20:21 +02:00
Marius Bakke 622ef2b90a
gnu: arpack-ng: Don't use unstable tarball. 
* gnu/packages/maths.scm (arpack-ng)[source]: Use GIT-FETCH.
 2018-09-19 15:20:21 +02:00
Eric Brown daa6036fda
gnu: Add openblas-ilp64. 
* gnu/packages/maths.scm (openblas-ilp64): New variable.

Co-authored-by: Ludovic Courtès <ludovic.courtes@inria.fr>
 2018-09-14 11:23:07 +02:00
Leo Famulari d763940711
Merge branch 'master' into core-updates 2018-09-13 13:32:39 -04:00