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* Merge branch 'master' into core-updatesMarius Bakke2021-06-06
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
| * gnu: Add frama-c.Julien Lepiller2021-06-02
| | | | | | | | * gnu/packages/maths.scm (frama-c): New variable.
| * gnu: Add why3.Julien Lepiller2021-06-02
| | | | | | | | * gnu/packages/maths.scm (why3): New variable.
| * gnu: ipopt: Update to 3.13.4Eric Brown2021-05-28
| | | | | | | | | | | | | | * 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>
| * gnu: Add cbc.Eric Brown2021-05-28
| | | | | | | | | | | | * gnu/packages/maths.scm (cbc): New variable. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
| * gnu: qhull: Build position independent.Efraim Flashner2021-05-25
| | | | | | | | | | * gnu/packages/maths.scm (qhull)[arguments]: Add configure-flag to build code position independent.
| * gnu: qhull: Link binaries to shared library.Efraim Flashner2021-05-25
| | | | | | | | | | | | | | This drops the package size by nearly 60%. * gnu/packages/maths.scm (qhull)[arguments]: Add configure-flag to link binaries to shared library.
| * gnu: HYPRE: Update source and home page URLs.Marius Bakke2021-05-24
| | | | | | | | | | * gnu/packages/maths.scm (hypre)[source]: Change to new repository home. [home-page]: Follow redirect.
| * gnu: Fix erroneous uses of 'package/inherit'.Marius Bakke2021-05-23
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* | gnu: hypre: Update to 2020.0.Marius Bakke2021-06-06
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
* | Merge branch 'master' into core-updatesMarius Bakke2021-05-22
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| * gnu: Add numdiff.Paul A. Patience2021-05-21
| | | | | | | | * gnu/packages/maths.scm (numdiff): New variable.
| * gnu: hdf5: Fix invalid regex range.Marius Bakke2021-05-18
| | | | | | | | | | * gnu/packages/maths.scm (hdf5-1.8)[arguments]: Use [a-zA-Z] instead of [a-Z] as range in regular expression.
| * gnu: qhull: Update to 2020.2.Marius Bakke2021-05-18
| | | | | | | | * gnu/packages/maths.scm (qhull): Update to 2020.2.
| * gnu: arpack-ng@3.3: Don't use unstable source tarball.Marius Bakke2021-05-15
| | | | | | | | | | * 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.
| * gnu: arpack-ng: Update to 3.8.0.Marius Bakke2021-05-15
| | | | | | | | | | | | * gnu/packages/maths.scm (arpack-ng): Update to 3.8.0. [native-inputs]: Add PKG-CONFIG. [inputs]: Add EIGEN.
* | gnu: ATLAS: Fix build with GCC 10.Marius Bakke2021-05-22
| | | | | | | | | | | | * 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.
* | Merge branch 'master' into core-updatesMarius Bakke2021-05-09
|\| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
| * gnu: Add cglm.Tobias Geerinckx-Rice2021-05-06
| | | | | | | | * gnu/packages/maths.scm (cglm): New public variable.
| * gnu: Add libcerf.Vinicius Monego2021-05-05
| | | | | | | | | | | | * gnu/packages/maths.scm (libcerf): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| * gnu: octave, octave-cli: Explain difference.Konrad Hinsen2021-05-03
| | | | | | | | | | | | * gnu/packages/maths.scm (octave-cli, octave): Extended synopsis. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| * gnu: xaos: Update to 4.2.1.Kei Kebreau2021-04-29
| | | | | | | | | | * gnu/packages/maths.scm (xaos): Update to 4.2.1. [arguments]: Patch call to "lrelease" in XaoS.pro.
| * gnu: wxmaxima: Update to 21.04.0.Kei Kebreau2021-04-21
| | | | | | | | * gnu/packages/maths.scm (wxmaxima): Update to 21.04.0.
* | Merge remote-tracking branch 'origin/master' into core-updatesEfraim Flashner2021-04-16
|\| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
| * gnu: blis: Add deprecated aliases.Ludovic Courtès2021-04-12
| | | | | | | | | | | | | | Add deprecated aliases for packages removed in the parent commit. * gnu/packages/maths.scm (blis-sandybridge, blis-haswell, blis-knl): New variables.
| * gnu: blis: Update to 0.8.1.Philip McGrath2021-04-12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
| * gnu: python-sip: Update to 5.5.0. Add python-sip-4Brendan Tildesley2021-04-09
| | | | | | | | | | | | | | | | | | * 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.
| * gnu: Add scotch and pt-scotch with shared librariesFranck Pérignon2021-04-06
| | | | | | | | | | | | * gnu/packages/maths.scm (scotch-shared, pt-scotch-shared): New variables. Signed-off-by: Leo Famulari <leo@famulari.name>
| * gnu: suitesparse: Update to 5.9.0.Felix Gruber2021-04-05
| | | | | | | | | | | | | | * 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>
| * gnu: metis: Add 'release-monitoring-url' property.Ludovic Courtès2021-03-29
| | | | | | | | * gnu/packages/maths.scm (metis)[properties]: New field.
* | Merge remote-tracking branch 'origin/master' into core-updatesEfraim Flashner2021-03-24
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| * gnu: wxmaxima: Update to 21.02.0.Kei Kebreau2021-03-13
| | | | | | | | * gnu/packages/maths.scm (wxmaxima): Update to 21.02.0.
* | Merge branch 'master' into core-updatesChristopher Baines2021-03-06
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| * gnu: octave: Update to 6.2.0.Efraim Flashner2021-03-02
| | | | | | | | | | | | * gnu/packages/maths.scm (octave): Update to 6.2.0. [source]: Download tar.xz tarball. [native-inputs]: Remove lzip.
| * gnu: slepc: Use HTTPS home page URI.Nicolas Goaziou2021-02-28
| | | | | | | | * gnu/packages/maths.scm (slepc)[home-page]: Use HTTPS URI.
| * gnu: elpa: Use HTTPS home page URI.Nicolas Goaziou2021-02-28
| | | | | | | | * gnu/packages/maths.scm (elpa)[home-page]: Use HTTPS URI.
| * gnu: Add HDF5 1.12.0.Gerd Heber2021-02-21
| | | | | | | | | | | | * gnu/packages/maths.scm (hdf5-1.12): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
* | Merge branch 'master' into core-updatesDanny Milosavljevic2021-02-11
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| * gnu: wxmaxima: Update to 21.01.0.Kei Kebreau2021-02-09
| | | | | | | | | | * gnu/packages/maths.scm (wxmaxima): Update to 21.01.0. [inputs]: Remove libomp.
| * gnu: hdf5: Update to 1.8.22.Eric Bavier2021-02-08
| | | | | | | | | | | | | | | | | | | | 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.
* | Merge branch 'master' into core-updatesChristopher Baines2021-02-03
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| * gnu: wxmaxima: Update to 20.12.2.Kei Kebreau2021-01-17
| | | | | | | | | | | | | | | | * 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.
| * gnu: gnuplot: Update to 5.4.1.Kei Kebreau2021-01-17
| | | | | | | | | | * gnu/packages/maths.scm (gnuplot): Update to 5.4.1. [arguments]: Set GNUTERM in #:make-flags.
* | gnu: Adjust package collection to Wrap using GUIX_PYTHONPATH.Maxim Cournoyer2021-02-01
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* | gnu: Replace all uses of texlive-union by texlive-updmap.cfg.Maxim Cournoyer2021-01-29
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
* | Merge branch 'staging' into 'core-updates'.Maxim Cournoyer2021-01-13
|\| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
| * gnu: suitesparse: Install libraries into /lib.Efraim Flashner2021-01-04
| | | | | | | | | | | | * gnu/packages/maths.scm (suitesparse)[arguments]: Add to configure-flags to install programs built with cmake to use 'lib', not 'lib64.'
| * gnu: matio: Update to 1.5.19.Vincent Legoll2020-12-31
| | | | | | | | | | | | * gnu/packages/maths.scm (matio): Update to 1.5.19. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| * gnu: octave, octave-cli: Update to 6.1.0.Greg Hogan2020-12-22
| | | | | | | | | | | | * gnu/packages/maths.scm (octave, octave-cli): Update to 6.1.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| * gnu: glpk: Don't build static library.Efraim Flashner2020-12-17
| | | | | | | | | | * gnu/packages/maths.scm (glpk)[arguments]: Add configure-flag to skip static library.
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