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2021-06-22gnu: 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". Ludovic Courtès
2021-06-20gnu: why3: Update to 1.3.3.•••* gnu/packages/maths.scm (why3): Update to 1.3.3. [arguments]: Adjust for newer ocaml-num. Julien Lepiller
2021-06-19Merge branch 'master' into core-updates•••Note: this merge actually changes the 'curl' and 'python-attrs' derivations, as part of solving caf4a7a2770ef4d05a6e18f40d602e51da749ddc and 12964df69a99de6190422c752fef65ef813f3b6b 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 Marius Bakke
2021-06-14gnu: wxmaxima: Update to 21.05.2.•••* gnu/packages/maths.scm (wxmaxima): Update to 21.05.2. Kei Kebreau
2021-06-14gnu: maxima: Update to 5.45.0.•••* gnu/packages/maths.scm (maxima): Update to 5.45.0. Kei Kebreau
2021-06-14gnu: 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. Maxim Cournoyer
2021-06-12gnu: 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> Jack Hill
2021-06-12gnu: libqalculate: Update to 3.19.0.•••* gnu/packages/maths (libqalculate): Update to 3.19.0. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Jack Hill
2021-06-06Merge 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 Marius Bakke
2021-06-06gnu: 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. Marius Bakke
2021-06-02gnu: Add frama-c.•••* gnu/packages/maths.scm (frama-c): New variable. Julien Lepiller
2021-06-02gnu: Add why3.•••* gnu/packages/maths.scm (why3): New variable. Julien Lepiller
2021-05-28gnu: 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> Eric Brown
2021-05-28gnu: Add cbc.•••* gnu/packages/maths.scm (cbc): New variable. Co-authored-by: Ludovic Courtès <ludo@gnu.org> Eric Brown
2021-05-25gnu: qhull: Build position independent.•••* gnu/packages/maths.scm (qhull)[arguments]: Add configure-flag to build code position independent. Efraim Flashner
2021-05-25gnu: 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. Efraim Flashner
2021-05-24gnu: HYPRE: Update source and home page URLs.•••* gnu/packages/maths.scm (hypre)[source]: Change to new repository home. [home-page]: Follow redirect. Marius Bakke
2021-05-23gnu: 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. Marius Bakke
2021-05-22Merge branch 'master' into core-updatesMarius Bakke
2021-05-22gnu: 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. Marius Bakke
2021-05-21gnu: Add numdiff.•••* gnu/packages/maths.scm (numdiff): New variable. Paul A. Patience
2021-05-18gnu: 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. Marius Bakke
2021-05-18gnu: qhull: Update to 2020.2.•••* gnu/packages/maths.scm (qhull): Update to 2020.2. Marius Bakke
2021-05-15gnu: 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. Marius Bakke
2021-05-15gnu: 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. Marius Bakke
2021-05-09Merge 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 Marius Bakke
2021-05-06gnu: Add cglm.•••* gnu/packages/maths.scm (cglm): New public variable. Tobias Geerinckx-Rice
2021-05-05gnu: Add libcerf.•••* gnu/packages/maths.scm (libcerf): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Vinicius Monego
2021-05-03gnu: octave, octave-cli: Explain difference.•••* gnu/packages/maths.scm (octave-cli, octave): Extended synopsis. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Konrad Hinsen
2021-04-29gnu: xaos: Update to 4.2.1.•••* gnu/packages/maths.scm (xaos): Update to 4.2.1. [arguments]: Patch call to "lrelease" in XaoS.pro. Kei Kebreau
2021-04-21gnu: wxmaxima: Update to 21.04.0.•••* gnu/packages/maths.scm (wxmaxima): Update to 21.04.0. Kei Kebreau
2021-04-16Merge 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 Efraim Flashner
2021-04-12gnu: 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. Ludovic Courtès
2021-04-12gnu: 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> Philip McGrath
2021-04-09gnu: 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. Brendan Tildesley
2021-04-06gnu: 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> Franck Pérignon
2021-04-05gnu: 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> Felix Gruber
2021-03-29gnu: metis: Add 'release-monitoring-url' property.•••* gnu/packages/maths.scm (metis)[properties]: New field. Ludovic Courtès
2021-03-24Merge remote-tracking branch 'origin/master' into core-updatesEfraim Flashner
2021-03-13gnu: wxmaxima: Update to 21.02.0.•••* gnu/packages/maths.scm (wxmaxima): Update to 21.02.0. Kei Kebreau
2021-03-06Merge branch 'master' into core-updatesChristopher Baines
2021-03-02gnu: 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. Efraim Flashner
2021-02-28gnu: slepc: Use HTTPS home page URI.•••* gnu/packages/maths.scm (slepc)[home-page]: Use HTTPS URI. Nicolas Goaziou
2021-02-28gnu: elpa: Use HTTPS home page URI.•••* gnu/packages/maths.scm (elpa)[home-page]: Use HTTPS URI. Nicolas Goaziou
2021-02-21gnu: Add HDF5 1.12.0.•••* gnu/packages/maths.scm (hdf5-1.12): New variable. Signed-off-by: Leo Famulari <leo@famulari.name> Gerd Heber
2021-02-11Merge branch 'master' into core-updatesDanny Milosavljevic
2021-02-09gnu: wxmaxima: Update to 21.01.0.•••* gnu/packages/maths.scm (wxmaxima): Update to 21.01.0. [inputs]: Remove libomp. Kei Kebreau
2021-02-08gnu: 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. Eric Bavier
2021-02-03Merge branch 'master' into core-updatesChristopher Baines
2021-02-01gnu: 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. Maxim Cournoyer
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