guix-patches - Patches for guix

	Commit message (Collapse)	Author	Age
*	gnu: rdkit: Update to 2023.09.4.	David Elsing	2024-02-13
\| \| \| \| \| \| \| \| \| \| \|	* gnu/packages/chemistry.scm (rdkit): Update to 2023.09.4. [arguments]: Skip testConrec test in check phase. [native-inputs]: Replace catch2 with catch2-3. * gnu/packages/patches/rdkit-unbundle-external-dependencies.patch: Adjust patch. [supported-systems]: New field. Signed-off-by: Christopher Baines <mail@cbaines.net>
*	gnu: freesasa: Fix memerr tests.	David Elsing	2024-02-13
\| \| \| \| \| \| \|	* gnu/packages/chemistry.scm (freesasa)[arguments]: Add "CFLAGS=-fno-builtin-malloc" to #:configure-flags. Signed-off-by: Christopher Baines <mail@cbaines.net>
*	gnu: avalon-toolkit: Update to 2.0.5a.	David Elsing	2024-02-13
\| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \|	The bug freeing static memory and the makefile have been improved upstream, so we don't have to work around them anymore. Now, two static libraries are built instead. * gnu/packages/chemistry.scm (avalon-toolkit): Update to 2.0.5a. [source]: Switch to git reference from GitHub. Adjust snippet. Add patch from the RDKit fork. [arguments]: Remove 'dont-free-static-memory phase. Use provided makefile. Adjust 'install phase. * gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Christopher Baines <mail@cbaines.net>
*	gnu: yaehmop: Update to 2023.03.1.	David Elsing	2024-02-13
\| \| \| \| \| \|	* gnu/packages/chemistry.scm (yaehmop): Update to 2023.03.1. Signed-off-by: Christopher Baines <mail@cbaines.net>
*	gnu: coordgenlibs: Update to 3.0.2.	David Elsing	2024-02-13
\| \| \| \| \| \|	* gnu/packages/chemistry.scm (coordgenlibs): Update to 3.0.2. Signed-off-by: Christopher Baines <mail@cbaines.net>
*	gnu: maeparser: Update to 1.3.1.	David Elsing	2024-02-13
\| \| \| \| \| \|	* gnu/packages/chemistry.scm (maeparser): Update to 1.3.1. Signed-off-by: Christopher Baines <mail@cbaines.net>
*	gnu: gemmi: Update to 0.6.4.	David Elsing	2024-02-13
\| \| \| \| \| \| \| \|	* gnu/packages/chemistry.scm (gemmi): Update to 0.6.4. [arguments]: Adjust include/gemmi/sprintf.hpp -> src/sprintf.cpp. (freesasa)[arguments]: Link to gemmi_cpp explicitly. Signed-off-by: Christopher Baines <mail@cbaines.net>
*	gnu: msgpack: Deprecate with msgpack-c.	Maxim Cournoyer	2024-01-09
\| \| \| \| \| \| \| \| \| \| \| \| \| \| \|	* gnu/packages/serialization.scm (msgpack-c): New variable. (msgpack-cxx): New variable. (msgpack): Rename to... (msgpack-3): ... this, and inherit from msgpack-c. * gnu/packages/vim.scm (eovim) [arguments]: Add help-cmake-find-msgpack-c phase. [inputs]: Replace msgpack with msgpack-c. * gnu/packages/terminals.scm (tmate) [inputs]: Replace msgpack with msgpack-3. * gnu/packages/networking.scm (opendht) [propagated-inputs]: Replace msgpack with msgpack-cxx. * gnu/packages/chemistry.scm (mmtf-cpp) [propagated-inputs]: Likewise.
*	gnu: python-pymol: Remove msgpack from native-inputs.	Maxim Cournoyer	2023-08-21
\| \| \| \| \| \| \| \| \|	It's now propagated by mmtf-cpp. * gnu/packages/chemistry.scm (python-pymol) [native-inputs]: Remove msgpack. Reviewed-by: Andreas Enge <andreas@enge.fr>
*	gnu: avogadrolibs: Remove msgpack from native-inputs.	Maxim Cournoyer	2023-08-21
\| \| \| \| \| \| \| \| \|	It's now propagated by mmtf-cpp. * gnu/packages/chemistry.scm (avogadrolibs) [native-inputs]: Remove msgpack. Reviewed-by: Andreas Enge <andreas@enge.fr>
*	gnu: mmtf-cpp: Update to 1.1.0.	Maxim Cournoyer	2023-08-21
\| \| \| \| \| \| \|	* gnu/packages/chemistry.scm (mmtf-cpp): Update to 1.1.0. [propagated-inputs]: Add msgpack. Reviewed-by: Andreas Enge <andreas@enge.fr>
*	gnu: python-pymol: Fix launch script.	David Elsing	2023-07-26
\| \| \| \| \| \| \|	* gnu/packages/chemistry.scm (python-pymol)[#:phases]: Add 'disable-unchroot. [native-inputs]: Remove python-setuptools. Signed-off-by: Andreas Enge <andreas@enge.fr>
*	gnu: Rationalize texlive-updmap.cfg and texlive-tiny inputs.	Nicolas Goaziou	2023-07-18
\| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \|	TEXLIVE-UPDMAP.CFG and TEXLIVE-TINY should only be used as native inputs. Also remove texlive packages already provided by them. * doc/build.scm (pdf-manual): * gnu/packages/algebra.scm (pari-gp): * gnu/packages/bioinformatics.scm (discrover): (phyml): (velvet): * gnu/packages/chemistry.scm (yaehmop): * gnu/packages/chez.scm (stex-bootstrap): (chez-web): (chez-sockets): * gnu/packages/cran.scm (r-prereg): * gnu/packages/docbook.scm (dblatex): * gnu/packages/emacs-xyz.scm (emacs-auctex): * gnu/packages/engineering.scm (fastcap): * gnu/packages/fsf.scm (book-faif): * gnu/packages/graphviz.scm (dot2tex): * gnu/packages/maths.scm (hypre): * gnu/packages/ocaml.scm (unison): (ocaml-bibtex2html): * gnu/packages/plotutils.scm (asymptote): * gnu/packages/python-xyz.scm (python-nbconvert): (python-pypandoc): * gnu/packages/radio.scm (gnuradio): (libosmo-dsp): * gnu/packages/statistics.scm (r-with-tests): * gnu/packages/tex.scm (texlive-makecmds): (texlive-innerscript): (teximpatient): (texlive-xkeyval): Remove texlive packages already provided by TEXLIVE-UPDMAP.CFG. Don't add TEXLIVE-TINY or TEXLIVE-UPDMAP.CFG as inputs.
*	gnu: yaehmop: Fix build due to missing TeX Live scripts.	Nicolas Goaziou	2023-07-18
\| \| \| \| \|	* gnu/packages/chemistry.scm (yaehmop)[native-inputs]: Add missing "latexmk" and "repstopdf" scripts.
*	gnu: texlive-fonts-ec -> texlive-ec.	Nicolas Goaziou	2023-07-18
\| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \|	* gnu/packages/tex.scm (texlive-ec): New variable. (texlive-fonts-ec): Deprecate variable. (lyx): (biber): * gnu/packages/python-xyz.scm (python-pypandoc): * gnu/packages/statistics.scm (r-with-tests): * doc/build.scm (pdf-manual): * gnu/packages/bioinformatics.scm (discrover): (phyml): (velvet): * gnu/packages/chemistry.scm (yaehmop): * gnu/packages/chez.scm (stex-bootstrap): * gnu/packages/ocaml.scm (unison): (ocaml-bibtex2html): * gnu/packages/plotutils.scm (asymptote): Use new name.
*	gnu: texlive-latex-geometry -> texlive-geometry.	Nicolas Goaziou	2023-07-18
\| \| \| \| \| \| \| \| \| \| \| \| \|	* gnu/packages/tex.scm (texlive-geometry): New variable. (texlive-latex-geometry): Deprecate variable. (texlive-xindy): * gnu/packages/chemistry.scm (yaehmop): * gnu/packages/cran.scm (r-prereg): * gnu/packages/graphviz.scm (dot2tex): * gnu/packages/maths.scm (hypre): * gnu/packages/plotutils.scm (asymptote): * gnu/packages/python-xyz.scm (python-nbconvert): * gnu/packages/sphinx.scm (python-sphinx): Use new name.
*	Merge remote-tracking branch 'savannah/master' into core-updates	Christopher Baines	2023-03-02
\|\ \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \|	Conflicts: gnu/local.mk gnu/packages/autotools.scm gnu/packages/cmake.scm gnu/packages/gnuzilla.scm gnu/packages/haskell.scm gnu/packages/pdf.scm gnu/packages/python-xyz.scm gnu/packages/samba.scm gnu/packages/tex.scm gnu/packages/tls.scm gnu/packages/wxwidgets.scm
\| *	gnu: Use HTTPS package home pages wherever possible.	Tobias Geerinckx-Rice	2023-02-19
\| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \|	* gnu/packages/accessibility.scm (florence)[home-page]: Use HTTPS. * gnu/packages/admin.scm (netcat, nmon)[home-page]: Likewise. * gnu/packages/algebra.scm (mpfrcx, cm, flint, fftw, r-dtt)[home-page]: Likewise. * gnu/packages/apr.scm (apr, apr-util)[home-page]: Likewise. * gnu/packages/aspell.scm (aspell-dict-it)[home-page]: Likewise. * gnu/packages/astronomy.scm (casacore, sextractor, libnova) (xplanet)[home-page]: Likewise. * gnu/packages/audio.scm (libtimidity, alsa-modular-synth, azr3, tao) (freepats, rakarrack, liblo, libshout-idjc, timidity++, libsbsms) (libmodplug, libxmp, xmp, sox, drc, gsm, gnaural) (streamripper)[home-page]: Likewise. * gnu/packages/authentication.scm (pamtester)[home-page]: Likewise. * gnu/packages/backup.scm (grsync)[home-page]: Likewise. * gnu/packages/bioconductor.scm (r-nmf, r-edger, r-limma) (r-plgem)[home-page]: Likewise. * gnu/packages/bioinformatics.scm (python-biom-format, bowtie, bowtie1) (bwa, crossmap, java-htsjdk, java-htsjdk-latest, java-picard) (java-picard-2.10.3, kaiju, proteinortho, rsem, rseqc, seek, samtools) (snap-aligner, subread, stringtie, r-centipede, prinseq, emboss, phylip) (libsbml)[home-page]: Likewise. * gnu/packages/build-tools.scm (tup)[home-page]: Likewise. * gnu/packages/cdrom.scm (libcddb, cdrdao, cdrtools) (cd-discid)[home-page]: Likewise. * gnu/packages/check.scm (cunit, python-nose) (python-pyhamcrest)[home-page]: Likewise. * gnu/packages/chemistry.scm (gromacs)[home-page]: Likewise. * gnu/packages/chez.scm (chez-fmt)[home-page]: Likewise. * gnu/packages/code.scm (lcov, uncrustify, cscope)[home-page]: Likewise. * gnu/packages/compression.scm (p7zip)[home-page]: Likewise. * gnu/packages/cran.scm (r-emdist, r-proj4, r-zoo, r-ggalluvial) (r-orgmassspecr, r-polychrome, r-partykit, r-rcpp, r-ff, r-emdbook) (r-fitdistrplus, r-linprog, r-geometry, r-dtw, r-fst, r-rjags) (r-intergraph, r-qualv, r-labelled, r-survey, r-coin, r-fmsb, r-tm) (r-corpcor, r-rmpfr, r-spatialextremes, r-longitudinal, r-genenet) (r-bayesm, r-seqinr, r-mpm, r-text2vec, r-rgdal, r-seewave, r-hdrcde) (r-shapes, r-anytime, r-stm, r-d3network, r-tam, r-directlabels) (r-spatstat-utils, r-spatstat-sparse, r-spatstat-data, r-spatstat-geom) (r-spatstat-core, r-spatstat-linnet, r-spatstat-random, r-spatstat) (r-rcpptoml, r-mlecens, r-seurat, r-mlearning, r-zooimage)[home-page]: Likewise. * gnu/packages/crates-io.scm (rust-nickel-0.11, rust-thrift-0.13) (rust-trust-dns-https-0.20, rust-trust-dns-native-tls-0.20) (rust-trust-dns-openssl-0.20, rust-trust-dns-proto-0.20) (rust-trust-dns-resolver-0.20, rust-trust-dns-rustls-0.20) (rust-uint-0.9, rust-yaml-rust-0.4)[home-page]: Likewise. * gnu/packages/crypto.scm (libdecaf, ccrypt)[home-page]: Likewise. * gnu/packages/curl.scm (curlpp)[home-page]: Likewise. * gnu/packages/databases.scm (python-pylibmc, unixodbc, wiredtiger) (libpqxx, mdbtools, virtuoso-ose, libdbi, libdbi-drivers) (soci)[home-page]: Likewise. * gnu/packages/debian.scm (apt-mirror)[home-page]: Likewise. * gnu/packages/debug.scm (remake)[home-page]: Likewise. * gnu/packages/disk.scm (sdparm, idle3-tools, duc)[home-page]: Likewise. * gnu/packages/django.scm (python-django-haystack)[home-page]: Likewise. * gnu/packages/djvu.scm (djvulibre, djview)[home-page]: Likewise. * gnu/packages/dns.scm (dnsmasq)[home-page]: Likewise. * gnu/packages/docbook.scm (dblatex, docbook2x)[home-page]: Likewise. * gnu/packages/documentation.scm (scrollkeeper)[home-page]: Likewise. * gnu/packages/ebook.scm (liblinebreak)[home-page]: Likewise. * gnu/packages/electronics.scm (xoscope)[home-page]: Likewise. * gnu/packages/emacs-xyz.scm (emacs-bbdb, emacs-caps-lock, emacs-djvu) (emacs-pabbrev, emacs-twittering-mode, emacs-filladapt, emacs-rudel) (emacs-stream, emacspeak, emacs-cc-mode, emacs-eldoc, emacs-jsonrpc) (emacs-gtk-look, emacs-xclip, emacs-slime-volleyball, emacs-minimap) (emacs-auto-dictionary-mode, emacs-persist, emacs-shell-command+) (emacs-map, emacs-xref, emacs-dictionary)[home-page]: Likewise. * gnu/packages/embedded.scm (sdcc)[home-page]: Likewise. * gnu/packages/engineering.scm (asco, libngspice, libspnav) (openctm)[home-page]: Likewise. * gnu/packages/erlang.scm (erlang-erlware-commons)[home-page]: Likewise. * gnu/packages/file-systems.scm (jfsutils, curlftpfs)[home-page]: Likewise. * gnu/packages/finance.scm (gbonds)[home-page]: Likewise. * gnu/packages/flashing-tools.scm (dfu-util, srecord)[home-page]: Likewise. * gnu/packages/fltk.scm (ntk)[home-page]: Likewise. * gnu/packages/fonts.scm (font-terminus, font-tex-gyre) (font-comic-neue)[home-page]: Likewise. * gnu/packages/fontutils.scm (ttf2pt1, potrace, libspiro)[home-page]: Likewise. * gnu/packages/fpga.scm (icestorm, gtkwave, gtkwave) (python-myhdl)[home-page]: Likewise. * gnu/packages/freedesktop.scm (libatasmart)[home-page]: Likewise. * gnu/packages/ftp.scm (weex)[home-page]: Likewise. * gnu/packages/game-development.scm (dds, python-tmx, sfxr, quesoglc) (eureka, plib)[home-page]: Likewise. * gnu/packages/games.scm (abe, alex4, armagetronad, barony) (foobillard++, golly, ltris, pipewalker, prboom-plus, trigger-rally) (cmatrix, pinball, pioneers, tennix, chromium-bsu, freeciv, kiki) (quakespasm, frotz, frotz-dumb-terminal, frotz-sdl, btanks) (flare-engine, chessx, barrage, cgoban, passage)[home-page]: Likewise. * gnu/packages/geo.scm (python-geopandas, saga)[home-page]: Likewise. * gnu/packages/gl.scm (freeglut, gl2ps)[home-page]: Likewise. * gnu/packages/gnome.scm (cogl, clutter-gtk, clutter-gst, bluefish) (workrave)[home-page]: Likewise. * gnu/packages/gnustep.scm (wmnd, wmfire, wmfire)[home-page]: Likewise. * gnu/packages/graph.scm (mscgen)[home-page]: Likewise. * gnu/packages/graphics.scm (assimp, alembic, ctl, agg) (opencsg)[home-page]: Likewise. * gnu/packages/graphviz.scm (gts)[home-page]: Likewise. * gnu/packages/gtk.scm (gtkspell3)[home-page]: Likewise. * gnu/packages/guile-xyz.scm (guile-irregex)[home-page]: Likewise. * gnu/packages/haskell-apps.scm (cpphs)[home-page]: Likewise. * gnu/packages/haskell-check.scm (ghc-hunit)[home-page]: Likewise. * gnu/packages/haskell-web.scm (ghc-http-client-restricted) (ghc-blaze-html, ghc-happstack-server, ghc-sourcemap)[home-page]: Likewise. * gnu/packages/haskell-xyz.scm (ghc-assoc, ghc-cairo, ghc-cborg) (ghc-csv, ghc-glob, ghc-gtk2hs-buildtools, ghc-hmatrix-gsl-stats) (ghc-intervalmap, ghc-lens-family-core, ghc-managed, ghc-mountpoints) (ghc-network-multicast, ghc-optional-args, ghc-regex, ghc-spoon) (ghc-transformers, ghc-turtle, ghc-utf8-light, ghc-wizards) (ghc-template-haskell, ghc-boot-th, ghc-binary-orphans) (ghc-postgresql-simple)[home-page]: Likewise. * gnu/packages/hexedit.scm (ht, bvi)[home-page]: Likewise. * gnu/packages/hunspell.scm (hunspell-dict-hu)[home-page]: Likewise. * gnu/packages/image-processing.scm (mia)[home-page]: Likewise. * gnu/packages/image-viewers.scm (geeqie, gpicview, luminance-hdr) (qiv)[home-page]: Likewise. * gnu/packages/image.scm (libuemf, devil, steghide, optipng, niftilib) (sng, mtpaint)[home-page]: Likewise. * gnu/packages/java-xml.scm (java-simple-xml, java-jaxp) (java-apache-xml-commons-resolver)[home-page]: Likewise. * gnu/packages/java.scm (java-cisd-base, java-cisd-args4j) (java-hamcrest-core, java-jsr305, java-eclipse-osgi) (java-eclipse-equinox-common, java-eclipse-core-jobs) (java-eclipse-equinox-registry, java-eclipse-equinox-app) (java-eclipse-equinox-preferences, java-eclipse-core-contenttype) (java-eclipse-text, java-treelayout, java-aopalliance, java-jeromq) (java-cdi-api)[home-page]: Likewise. * gnu/packages/jemalloc.scm (jemalloc-4.5.0)[home-page]: Likewise. * gnu/packages/julia-xyz.scm (julia-recipespipeline)[home-page]: Likewise. * gnu/packages/kde-internet.scm (kget)[home-page]: Likewise. * gnu/packages/kde-systemtools.scm (dolphin-plugins) (konsole)[home-page]: Likewise. * gnu/packages/kodi.scm (fstrcmp)[home-page]: Likewise. * gnu/packages/language.scm (hime, libchewing)[home-page]: Likewise. * gnu/packages/lego.scm (nqc)[home-page]: Likewise. * gnu/packages/lesstif.scm (lesstif)[home-page]: Likewise. * gnu/packages/libcanberra.scm (libcanberra)[home-page]: Likewise. * gnu/packages/libdaemon.scm (libdaemon)[home-page]: Likewise. * gnu/packages/libffi.scm (libffi)[home-page]: Likewise. * gnu/packages/libreoffice.scm (libwpd, libwpg, libwps)[home-page]: Likewise. * gnu/packages/libusb.scm (libmtp, gmtp)[home-page]: Likewise. * gnu/packages/linux.scm (e2fsprogs, extundelete, lsscsi, net-tools) (kbd, sysfsutils, cpuid, libpfm4)[home-page]: Likewise. * gnu/packages/lisp-check.scm (sbcl-ptester, sbcl-xlunit)[home-page]: Likewise. * gnu/packages/lisp-xyz.scm (sbcl-html-encode, sbcl-py-configparser) (sbcl-cl-utilities, sbcl-series, sbcl-uffi, sbcl-clsql, sbcl-sycamore) (sbcl-osicat, sbcl-hu.dwim.common, sbcl-caveman, sbcl-trivial-shell) (sbcl-trivial-benchmark, sbcl-screamer, sbcl-smug)[home-page]: Likewise. * gnu/packages/lisp.scm (lush2)[home-page]: Likewise. * gnu/packages/logging.scm (log4cpp)[home-page]: Likewise. * gnu/packages/lua.scm (lua-ldoc)[home-page]: Likewise. * gnu/packages/machine-learning.scm (mcl, openfst, rxcpp)[home-page]: Likewise. * gnu/packages/mail.scm (muchsync, procmail, sendmail) (opensmtpd-filter-dkimsign, crm114)[home-page]: Likewise. * gnu/packages/man.scm (libpipeline, man-db)[home-page]: Likewise. * gnu/packages/maths.scm (lapack, scalapack, hdf-eos5, itpp, gmsh) (metamath, p4est, armadillo, suitesparse, atlas, lpsolve, wcalc, why3) (frama-c)[home-page]: Likewise. * gnu/packages/mcrypt.scm (mcrypt, libmcrypt, libmhash)[home-page]: Likewise. * gnu/packages/minetest.scm (minetest-advtrains)[home-page]: Likewise. * gnu/packages/monitoring.scm (python-whisper, python-carbon) (hostscope)[home-page]: Likewise. * gnu/packages/mp3.scm (id3lib, libmp3splt, mp3splt, mpg321) (lame)[home-page]: Likewise. * gnu/packages/multiprecision.scm (mpc)[home-page]: Likewise. * gnu/packages/music.scm (aria-maestosa, lingot, setbfree, bristol) (portmidi, python-pyportmidi, zynaddsubfx, yoshimi, aj-snapshot) (schismtracker, midicsv, midicsv, qmidiarp, qmidiroute, dssi, tap-lv2) (shiru-lv2)[home-page]: Likewise. * gnu/packages/ncurses.scm (stfl)[home-page]: Likewise. * gnu/packages/networking.scm (lksctp-tools, mbuffer, ifstatus, bird) (tunctl, traceroute)[home-page]: Likewise. * gnu/packages/node-xyz.scm (node-mersenne)[home-page]: Likewise. * gnu/packages/ntp.scm (openntpd)[home-page]: Likewise. * gnu/packages/ocaml.scm (opam, hevea, ocaml-menhir, ocaml-piqilib) (ocaml-graph, cubicle)[home-page]: Likewise. * gnu/packages/opencl.scm (python-pyopencl)[home-page]: Likewise. * gnu/packages/package-management.scm (xstow, modules)[home-page]: Likewise. * gnu/packages/parallel.scm (xjobs)[home-page]: Likewise. * gnu/packages/pdf.scm (podofo, qpdf, xournal, impressive)[home-page]: Likewise. * gnu/packages/perl.scm (perl-math-vecstat, perltidy)[home-page]: Likewise. * gnu/packages/photo.scm (libpano13, enblend-enfuse, hugin)[home-page]: Likewise. * gnu/packages/plan9.scm (drawterm)[home-page]: Likewise. * gnu/packages/plotutils.scm (guile-charting, ploticus)[home-page]: Likewise. * gnu/packages/popt.scm (argtable, popt)[home-page]: Likewise. * gnu/packages/profiling.scm (otf2)[home-page]: Likewise. * gnu/packages/pulseaudio.scm (pulseaudio)[home-page]: Likewise. * gnu/packages/python-check.scm (python-mypy)[home-page]: Likewise. * gnu/packages/python-web.scm (python-cssutils) (python-translationstring)[home-page]: Likewise. * gnu/packages/python-xyz.scm (python-diskcache, python-doxyqml) (python-docutils, python-pexpect, python-importlib-resources) (python-simplegeneric, python-urwid, python-xlrd, python-xlwt) (python-pyasn1, python-pythondialog, python-tftpy, python-random2) (python-arcp, python-pyopengl, python-sortedcollections) (python-sortedcontainers, python-yapsy, python-pydispatcher) (python-posix-ipc)[home-page]: Likewise. * gnu/packages/qt.scm (qwt, libqglviewer, signond)[home-page]: Likewise. * gnu/packages/radio.scm (unixcw, gnuais)[home-page]: Likewise. * gnu/packages/raspberry-pi.scm (bcm2835)[home-page]: Likewise. * gnu/packages/rdf.scm (clucene, rasqal, redland)[home-page]: Likewise. * gnu/packages/regex.scm (tre)[home-page]: Likewise. * gnu/packages/rsync.scm (librsync)[home-page]: Likewise. * gnu/packages/ruby.scm (ruby-packnga, ruby-nokogiri, ruby-oj, ruby-ox) (ruby-sinatra, ruby-citrus, ruby-cbor, ruby-roda)[home-page]: Likewise. * gnu/packages/scheme.scm (scheme48, tinyscheme)[home-page]: Likewise. * gnu/packages/screen.scm (dtach)[home-page]: Likewise. * gnu/packages/scsi.scm (sg3-utils)[home-page]: Likewise. * gnu/packages/sdl.scm (libmikmod, sdl-pango)[home-page]: Likewise. * gnu/packages/shellutils.scm (hstr, rig)[home-page]: Likewise. * gnu/packages/simulation.scm (python-dolfin-adjoint)[home-page]: Likewise. * gnu/packages/smalltalk.scm (smalltalk)[home-page]: Likewise. * gnu/packages/speech.scm (espeak)[home-page]: Likewise. * gnu/packages/stalonetray.scm (stalonetray)[home-page]: Likewise. * gnu/packages/statistics.scm (jags, r-mass, r-class, r-lattice) (r-matrix, r-nnet, r-spatial, r-bit, r-bit64, r-digest, r-xtable) (python-statsmodels, r-ade4, r-latticeextra, r-rcurl, r-xml, r-mvtnorm) (r-robustbase, r-minqa, r-fdrtool, java-jdistlib, xlispstat)[home-page]: Likewise. * gnu/packages/swig.scm (swig)[home-page]: Likewise. * gnu/packages/task-management.scm (wtime)[home-page]: Likewise. * gnu/packages/tcl.scm (itcl, tclxml, tclx)[home-page]: Likewise. * gnu/packages/terminals.scm (libtermkey, mlterm, libvterm) (libvterm)[home-page]: Likewise. * gnu/packages/tex.scm (texlive-lm, texlive-lm-math, texlive-cs) (texlive-csplain, biber, texmaker)[home-page]: Likewise. * gnu/packages/text-editors.scm (joe)[home-page]: Likewise. * gnu/packages/textutils.scm (drm-tools, docx2txt)[home-page]: Likewise. * gnu/packages/tv.scm (tvtime)[home-page]: Likewise. * gnu/packages/unicode.scm (libunibreak)[home-page]: Likewise. * gnu/packages/upnp.scm (libupnp)[home-page]: Likewise. * gnu/packages/version-control.scm (cvs)[home-page]: Likewise. * gnu/packages/video.scm (transcode, libquicktime, mjpegtools, aalib) (liba52, libmpeg2, x265, libdv, dvdauthor, aegisub, pitivi, gavl) (dvdbackup, guvcview, video-contact-sheet)[home-page]: Likewise. * gnu/packages/virtualization.scm (bochs)[home-page]: Likewise. * gnu/packages/w3m.scm (w3m)[home-page]: Likewise. * gnu/packages/web.scm (qjson, libquvi-scripts, libquvi, quvi) (tidy-html, htmlcxx)[home-page]: Likewise. * gnu/packages/wm.scm (evilwm, menumaker)[home-page]: Likewise. * gnu/packages/wv.scm (wv)[home-page]: Likewise. * gnu/packages/wxwidgets.scm (wxsvg)[home-page]: Likewise. * gnu/packages/xdisorg.scm (mtdev, xsel)[home-page]: Likewise. * gnu/packages/xfig.scm (xfig, transfig)[home-page]: Likewise. * gnu/packages/xml.scm (openjade, python-pyxb, xmlstarlet, xmlrpc-c) (opensp)[home-page]: Likewise. * gnu/packages/xorg.scm (xf86-video-qxl)[home-page]: Likewise.
\| *	gnu: Remove unneeded module imports.	Efraim Flashner	2023-02-16
\| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \|	* gnu/packages/abiword.scm, * gnu/packages/ada.scm, * gnu/packages/agda.scm, * gnu/packages/backup.scm, * gnu/packages/barrier.scm, * gnu/packages/bioinformatics.scm, * gnu/packages/bootstrap.scm, * gnu/packages/bqn.scm, * gnu/packages/c.scm, * gnu/packages/chemistry.scm, * gnu/packages/coq.scm, * gnu/packages/cross-base.scm, * gnu/packages/databases.scm, * gnu/packages/emacs-xyz.scm, * gnu/packages/enlightenment.scm, * gnu/packages/games.scm, * gnu/packages/geo.scm, * gnu/packages/ghostscript.scm, * gnu/packages/gl.scm, * gnu/packages/golang.scm, * gnu/packages/jami.scm, * gnu/packages/java-maths.scm, * gnu/packages/kde-frameworks.scm, * gnu/packages/kde-plasma.scm, * gnu/packages/language.scm, * gnu/packages/libreoffice.scm, * gnu/packages/linphone.scm, * gnu/packages/lisp.scm, * gnu/packages/llvm.scm, * gnu/packages/machine-learning.scm, * gnu/packages/minetest.scm, * gnu/packages/monitoring.scm, * gnu/packages/nfs.scm, * gnu/packages/ocr.scm, * gnu/packages/opencl.scm, * gnu/packages/pdf.scm, * gnu/packages/python-xyz.scm, * gnu/packages/racket.scm, * gnu/packages/rust.scm, * gnu/packages/syncthing.scm, * gnu/packages/syndication.scm, * gnu/packages/telegram.scm, * gnu/packages/vulkan.scm, * gnu/packages/web-browsers.scm, * gnu/packages/web.scm, * gnu/packages/webkit.scm: Remove some unecessary module imports.
* \|	gnu: texlive-graphics: Use over deprecated texlive-latex-graphics.	Efraim Flashner	2023-01-30
\|/ \| \| \| \| \| \| \| \| \|	* gnu/packages/bioinformatics.scm (phyml)[native-inputs], * gnu/packages/chemistry.scm (yaehmop)[native-inputs], * gnu/packages/graphviz.scm (dot2tex)[propagated-inputs], * gnu/packages/maths.scm (cddlib)[native-inputs], * gnu/packages/statistics.scm (r-with-tests)[native-inputs], * gnu/packages/tex.scm (texlive-apa6)[propagated-inputs]: Replace texlive-latex-graphics with texlive-graphics.
*	gnu: gromacs: Mark as tunable.	Ludovic Courtès	2023-01-12
\| \| \| \|	* gnu/packages/chemistry.scm (gromacs)[properties]: New field.
*	gnu: gromacs: Remove input labels and use gexps.	Ludovic Courtès	2023-01-10
\| \| \| \| \|	* gnu/packages/chemistry.scm (gromacs)[arguments]: Turn into gexps. [native-inputs]: Remove labels. Remove (package-source googletest).
*	gnu: gromacs: Update to 2022.4.	Ludovic Courtès	2023-01-10
\| \| \| \| \|	* gnu/packages/chemistry.scm (gromacs): Update to 2022.4. * gnu/packages/patches/gromacs-tinyxml2.patch: Adjust accordingly.
*	gnu: python-setuptools: Move to python-build.	Lars-Dominik Braun	2022-10-27
\| \| \| \| \| \| \| \| \| \| \|	* gnu/packages/python-xyz.scm (python-setuptools): Move… * gnu/packages/python-build.scm: …here. * gnu/packages/chemistry.scm, gnu/packages/messaging.scm, gnu/packages/sequoia.scm, tests/lint.scm: Adjust module imports accordingly. Co-authored-by: Marius Bakke <marius@gnu.org>
*	gnu: Add rdkit.	David Elsing	2022-10-15
\| \| \| \| \| \|	* gnu/packages/chemistry.scm (rdkit): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
*	gnu: Add ringdecomposerlib.	David Elsing	2022-10-15
\| \| \| \| \| \|	* gnu/packages/chemistry.scm (ringdecomposerlib): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
*	gnu: Add avalon-toolkit.	David Elsing	2022-10-15
\| \| \| \| \| \|	* gnu/packages/chemistry.scm (avalon-toolkit): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
*	gnu: Add yaehmop.	David Elsing	2022-10-15
\| \| \| \| \| \|	* gnu/packages/chemistry.scm (yaehmop): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
*	gnu: Add coordgenlibs.	David Elsing	2022-10-15
\| \| \| \| \| \|	* gnu/packages/chemistry.scm (coordgenlibs): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
*	gnu: Add maeparser.	David Elsing	2022-10-15
\| \| \| \| \| \|	* gnu/packages/chemistry.scm (maeparser): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
*	gnu: Add freesasa.	David Elsing	2022-10-15
\| \| \| \| \| \|	* gnu/packages/chemistry.scm (freesasa): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
*	gnu: Add gemmi.	David Elsing	2022-10-15
\| \| \| \| \| \| \| \| \|	* gnu/packages/patches/gemmi-fix-pegtl-usage.patch: New file. * gnu/packages/patches/gemmi-fix-sajson-types.patch: New file. * gnu/local.mk (dist_patch_DATA): Register them here. * gnu/packages/chemistry.scm (gemmi): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
*	gnu: Add sajson-for-gemmi.	David Elsing	2022-10-15
\| \| \| \| \| \|	* gnu/packages/cpp.scm (sajson-for-gemmi): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
*	gnu: catch-framework2: Rename variable to catch2.	Maxim Cournoyer	2022-09-15
\| \| \| \| \| \|	Automated with: git grep -l catch-framework2 \| xargs sed 's/catch-framework2/catch2/g' -i
*	gnu: Remove python2-numpy.	Maxim Cournoyer	2022-05-31
\| \| \| \| \| \| \| \|	* gnu/packages/python-xyz.scm (python2-numpy): Delete variable. (python2-numpy-1.8): Likewise. (python-numpy)[properties]: Delete field. * gnu/packages/maths.scm (flann): Delete comment. * gnu/packages/chemistry.scm (with-numpy-1.8): Delete procedure.
*	gnu: Remove nmoldyn.	Maxim Cournoyer	2022-05-31
\| \| \| \|	* gnu/packages/chemistry.scm (nmoldyn): Delete variable.
*	gnu: Remove domainfinder.	Maxim Cournoyer	2022-05-31
\| \| \| \|	* gnu/packages/chemistry.scm (domainfinder): Delete variable.
*	gnu: Simplify package inputs.	Ludovic Courtès	2021-12-13
\| \| \| \| \| \| \| \|	This commit was obtained by running: ./pre-inst-env guix style without any additional argument.
*	Merge remote-tracking branch 'origin/master' into core-updates-frozen.	Mathieu Othacehe	2021-10-12
\|\
\| *	gnu: Add python-pymol.	Ricardo Wurmus	2021-09-20
\| \| \| \| \| \| \| \|	* gnu/packages/chemistry.scm (python-pymol): New variable.
* \|	gnu: Use 'search-input-file' when looking for executables.	Ludovic Courtès	2021-07-24
\|/ \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \|	* gnu/packages/admin.scm (isc-dhcp): Use 'search-input-file' when looking for executables. * gnu/packages/audio.scm (ableton-link): Likewise. * gnu/packages/benchmark.scm (fio): Likewise. * gnu/packages/bioinformatics.scm (roary): Likewise. (ngless): Likewise. * gnu/packages/boost.scm (boost-for-irods): Likewise. * gnu/packages/bootloaders.scm (grub): Likewise. (grub-efi): Likewise. * gnu/packages/chemistry.scm (inchi): Likewise. * gnu/packages/dictionaries.scm (ding): Likewise. * gnu/packages/dlang.scm (ldc): Likewise. * gnu/packages/education.scm (childsplay): Likewise. * gnu/packages/emacs-xyz.scm (emacs-hyperbole): Likewise. (emacs-haskell-mode): Likewise. (emacs-auctex): Likewise. (emacs-ggtags): Likewise. (emacs-graphviz-dot-mode): Likewise. (emacs-flycheck-grammalecte): Likewise. (emacs-counsel-notmuch): Likewise. (emacspeak): Likewise. (emacs-exwm): Likewise. (emacs-exwm-x): Likewise. (emacs-treemacs): Likewise. (emacs-telega): Likewise. (emacs-exiftool): Likewise. * gnu/packages/emulators.scm (higan): Likewise. * gnu/packages/engineering.scm (freehdl): Likewise. (librepcb): Likewise. * gnu/packages/entr.scm (entr): Likewise. * gnu/packages/file-systems.scm (libeatmydata): Likewise. (xfstests): Likewise. (mergerfs): Likewise. (mergerfs-tools): Likewise. * gnu/packages/finance.scm (monero-gui): Likewise. * gnu/packages/flashing-tools.scm (flashrom): Likewise. * gnu/packages/fontutils.scm (fontforge): Likewise. * gnu/packages/game-development.scm (python2-renpy): Likewise. * gnu/packages/games.scm (opensurge): Likewise. (xboard): Likewise. (hyperrogue): Likewise. (flare-game): Likewise. (chessx): Likewise. * gnu/packages/geo.scm (grass): Likewise. * gnu/packages/glib.scm (glib): Likewise. * gnu/packages/gnome.scm (mm-common): Likewise. (network-manager-openvpn): Likewise. (network-manager-vpnc): Likewise. (network-manager-openconnect): Likewise. (apostrophe): Likewise. * gnu/packages/gnupg.scm (pius): Likewise. (jetring): Likewise. * gnu/packages/gnuzilla.scm (icedove): Likewise. * gnu/packages/golang.scm (go-1.4): Likewise. * gnu/packages/graphviz.scm (xdot): Likewise. * gnu/packages/guile-xyz.scm (jupyter-guile-kernel): Likewise. * gnu/packages/haskell-xyz.scm (ghc-hindent): Likewise. * gnu/packages/ibus.scm (ibus): Likewise. * gnu/packages/image.scm (phockup): Likewise. * gnu/packages/irc.scm (quassel): Likewise. * gnu/packages/java.scm (drip): Likewise. (ant-bootstrap): Likewise. (tla2tools): Likewise. * gnu/packages/julia.scm (julia): Likewise. * gnu/packages/less.scm (lesspipe): Likewise. * gnu/packages/libreoffice.scm (libreoffice): Likewise. * gnu/packages/linux.scm (fuse): Likewise. (lm-sensors): Likewise. (bluez): Likewise. (fakeroot): Likewise. (inputattach): Likewise. * gnu/packages/lisp-xyz.scm (sbcl-cl-diskspace): Likewise. * gnu/packages/lisp.scm (lisp-repl-core-dumper): Likewise. * gnu/packages/lua.scm (fennel): Likewise. * gnu/packages/lxde.scm (spacefm): Likewise. * gnu/packages/mail.scm (public-inbox): Likewise. * gnu/packages/maths.scm (hdf-java): Likewise. (maxima): Likewise. (frama-c): Likewise. * gnu/packages/messaging.scm (libgadu): Likewise. * gnu/packages/music.scm (denemo): Likewise. (curseradio): Likewise. * gnu/packages/netpbm.scm (netpbm): Likewise. * gnu/packages/networking.scm (blueman): Likewise. (squid): Likewise. (aircrack-ng): Likewise. * gnu/packages/node.scm (node): Likewise. (node-llparse-frontend-bootstrap): Likewise. (node-llparse-bootstrap): Likewise. (llhttp-bootstrap): Likewise. (node-lts): Likewise. * gnu/packages/ocaml.scm (ocaml-4.11): Likewise. (opam): Likewise. (ocaml-graph): Likewise. * gnu/packages/orpheus.scm (orpheus): Likewise. * gnu/packages/password-utils.scm (password-store): Likewise. * gnu/packages/python.scm (pypy3): Likewise. * gnu/packages/qt.scm (qt5ct): Likewise. * gnu/packages/radio.scm (libosmo-dsp): Likewise. * gnu/packages/ruby.scm (ruby-pandoc-ruby): Likewise. * gnu/packages/rust.scm (rust-1.30): Likewise. * gnu/packages/screen.scm (byobu): Likewise. * gnu/packages/statistics.scm (r-with-tests): Likewise. * gnu/packages/suckless.scm (surf): Likewise. * gnu/packages/syndication.scm (gfeeds): Likewise. * gnu/packages/telephony.scm (mumble): Likewise. * gnu/packages/terminals.scm (alacritty): Likewise. * gnu/packages/tex.scm (texlive-bin): Likewise. * gnu/packages/uml.scm (plantuml): Likewise. * gnu/packages/version-control.scm (python-git-multimail): Likewise. (gitolite): Likewise. (hg-commitsigs): Likewise. (git-when-merged): Likewise. (git-imerge): Likewise. (gita): Likewise. * gnu/packages/video.scm (you-get): Likewise. * gnu/packages/vim.scm (eovim): Likewise. * gnu/packages/virtualization.scm (qemu): Likewise. (virt-manager): Likewise. (criu): Likewise. * gnu/packages/vpn.scm (strongswan): Likewise. (xl2tpd): Likewise. * gnu/packages/wm.scm (i3lock-fancy): Likewise. * gnu/packages/wxwidgets.scm (python-wxpython): Likewise. (python2-wxpython): Likewise. * gnu/packages/xdisorg.scm (autorandr): Likewise. * gnu/packages/xorg.scm (hackneyed-x11-cursors): Likewise. (v86d): Likewise. (mkfontdir): Likewise. (xpra): Likewise.
*	gnu: Rename qtbase to qtbase-5.	Maxim Cournoyer	2021-06-14
\| \| \| \| \| \| \| \| \| \| \| \|	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.
*	gnu: openbabel: Update to 3.1.1.	Kei Kebreau	2021-02-01
\| \| \| \| \| \|	* gnu/packages/chemistry.scm (openbabel): Update to 3.1.1. [source]: Update URI. [arguments]: Temporarily skip tests on i686-linux.
*	gnu: inchi: Update to 1.06.	Kei Kebreau	2021-02-01
\| \| \| \| \| \|	* gnu/packages/chemistry.scm (inchi): Update to 1.06. [source]: Use HTTPS. [native-inputs]: Update inchi-doc hash.
*	gnu: Remove avogadro.	Leo Famulari	2021-01-29
\| \| \| \| \| \| \| \| \| \|	This package fails to build and has been superseded by avogadro2. * gnu/packages/chemistry.scm (avogadro): Remove variable. * gnu/packages/patches/avogadro-boost148.patch, gnu/packages/patches/avogadro-eigen3-update.patch, gnu/packages/patches/avogadro-python-eigen-lib.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Remove them.
*	gnu: Add avogadro2.	Kei Kebreau	2021-01-25
\| \| \| \|	* gnu/packages/chemistry.scm (avogadro2): New variable.
*	gnu: Add avogadrolibs.	Kei Kebreau	2021-01-25
\| \| \| \|	* gnu/packages/chemistry.scm (avogadrolibs): New variable.
*	gnu: Add libmsym.	Kei Kebreau	2021-01-25
\| \| \| \|	* gnu/packages/chemistry.scm (libmsym): New variable.
*	gnu: Add molequeue.	Kei Kebreau	2021-01-25
\| \| \| \|	* gnu/packages/chemistry.scm (molequeue): New variable.
*	gnu: Add mmtf-cpp.	Kei Kebreau	2021-01-25
\| \| \| \|	* gnu/packages/chemistry.scm (mmtf-cpp): New variable.