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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
;;; Copyright © 2013 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2020 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2021, 2024 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be>
;;; Copyright © 2024 jgart <jgart@dismail.de>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages prolog)
  #:use-module (guix download)
  #:use-module (guix gexp)
  #:use-module (guix git-download)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system gnu)
  #:use-module (guix utils)
  #:use-module (gnu packages backup)
  #:use-module (gnu packages bash)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages crypto)
  #:use-module (gnu packages fontutils)
  #:use-module (gnu packages image)
  #:use-module (gnu packages libffi)
  #:use-module (gnu packages libunwind)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages readline)
  #:use-module (gnu packages texinfo)
  #:use-module (gnu packages tls)
  #:use-module (gnu packages valgrind)
  #:use-module (gnu packages version-control)
  #:use-module (gnu packages vim)
  #:use-module (gnu packages xorg)
  #:use-module (srfi srfi-1))

(define-public gprolog
  (package
    (name "gprolog")
    (version "1.5.0")
    (source
      (origin
        (method url-fetch)
        ;; Recent versions are not hosted on the GNU mirrors.
        (uri (list (string-append "http://gprolog.org/gprolog-" version
                                  ".tar.gz")
                   (string-append "mirror://gnu/gprolog/gprolog-" version
                                  ".tar.gz")))
        (sha256
         (base32
          "009ca4wn2q6xdmb0js0vz647cw5ygsqyyqc9svmjgahg7js441k7"))))
    (build-system gnu-build-system)
    (arguments
     `(#:configure-flags
       (list (string-append
              "--with-install-dir=" %output "/share/gprolog"))
       #:phases
       (modify-phases %standard-phases
         (add-before 'configure 'change-dir
           (lambda _
             (chdir "src"))))))
    (home-page "https://www.gnu.org/software/gprolog/")
    (synopsis "Prolog compiler")
    (description
     "GNU Prolog is a standards-compliant Prolog compiler with constraint
solving over finite domains.  It accepts Prolog+ constraint programs and
produces a compiled, native binary which can function in a stand-alone
manner.  It also features an interactive interpreter.")
    (license (list license:gpl2+
                   license:lgpl3+))

    ;; See 'configure' for the list of supported architectures.
    (supported-systems (fold delete
                             %supported-systems
                             '("armhf-linux" "mips64el-linux")))))

(define-public swi-prolog
  (package
    (name "swi-prolog")
    (version "9.3.8")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/SWI-Prolog/swipl-devel")
                    (recursive? #t) ; TODO: Determine if this can be split out.
                    (commit (string-append "V" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1q2dg7n3vf0qc9nxppbcqgbzj4rcjw8sv2vbg9s6i4ixxlsxr5y3"))))
    (build-system cmake-build-system)
    (arguments
     `(#:parallel-build? #t
       #:configure-flags
       ,#~(list
           #$@(if (%current-target-system)
                  ;; Set this manually, otherwise CMake would need to
                  ;; run a cross-compiled binary, which it can't do.
                  ;; These values were found on a Linux system.
                  #~("-DBSD_SIGNALS=1" "-DQSORT_R_GNU=1"
                     ;; If absent, the non-existent 'cc' is used.
                     "-DCMAKE_HOST_CC=gcc"
                     ;; swi-prolog needs a native copy of itself for
                     ;; cross-compilation.
                     "-DSWIPL_NATIVE_FRIEND=/nowhere"
                     (string-append "-DPROG_SWIPL="
                                    #+(this-package-native-input "swi-prolog")
                                    "/bin/swipl"))
                  #~())
           "-DINSTALL_DOCUMENTATION=ON"
           "-DSWIPL_INSTALL_IN_LIB=OFF") ; FIXME: Breaks RUNPATH validation.
       #:phases
       ,#~(modify-phases %standard-phases
            ;; XXX: Delete the test phase that attempts to write to the
            ;; immutable store.
            (add-after 'unpack 'delete-failing-tests
              (lambda _
                (substitute* "src/CMakeLists.txt"
                  ((" save") ""))
                (substitute* "src/test.pl"
                  (("testdir\\('Tests/save'\\).") ""))
                (delete-file-recursively "src/Tests/save")))
            #$@(if (%current-target-system)
                   ;; Prevent man_server.pl and swipl-lfr.pl from keeping a
                   ;; reference to the native swi-prolog.
                   ;; FIXME: libswipl.so and swipl-ld keep a reference to the
                   ;; cross-compiler.
                   #~((add-after 'install 'fix-cross-references
                        (lambda _
                          (define bin `(,(string-append #$output "/bin")))
                          (for-each (lambda (file) (patch-shebang file bin))
                                    (find-files #$output ".pl$")))))
                   #~()))))
    (native-inputs
     `(,@(if (%current-target-system)
             (begin
               (unless (equal? (target-64bit?)
                               (target-64bit? (%current-system)))
                 (error "swi-prolog requires --system and --target to have \
the same word size"))
               `(("swi-prolog" ,this-package)))
             '())
       ("texinfo" ,texinfo)
       ("perl" ,perl)
       ("pkg-config" ,pkg-config)))
    (inputs
     `(("bash-minimal" ,bash-minimal)   ;for some scripts in 'lib'
       ("zlib" ,zlib)
       ("gmp" ,gmp)
       ("readline" ,readline)
       ("libarchive" ,libarchive)
       ("libunwind" ,libunwind)
       ("libjpeg" ,libjpeg-turbo)
       ("libxcrypt" ,libxcrypt)
       ("libxft" ,libxft)
       ("fontconfig" ,fontconfig)
       ("openssl" ,openssl)))
    (home-page "https://www.swi-prolog.org/")
    (synopsis "ISO/Edinburgh-style Prolog interpreter")
    (description "SWI-Prolog is a fast and powerful ISO/Edinburgh-style Prolog
compiler with a rich set of built-in predicates.  It offers a fast, robust and
small environment which enables substantial applications to be developed with
it.")
    (license license:bsd-2)))

(define-public trealla
  (package
    (name "trealla")
    (version "2.63.9")
    (source
     (origin
       (method git-fetch)
       (uri
        (git-reference
         (url "https://github.com/trealla-prolog/trealla")
         (commit (string-append "v" version))))
       (sha256
        (base32 "1jab7s8dnass47lpb21kmq054n13szw65crq2759akli4bnsfi39"))
       (file-name (git-file-name name version))))
    (build-system gnu-build-system)
    (native-inputs
     (append
       (if (supported-package? valgrind)
           (list valgrind)
           '())
       (list xxd)))
    (inputs
     (list libffi openssl readline))
    (arguments
     (list
      #:make-flags #~(list (string-append "CC=" #$(cc-for-target)))
      #:test-target (if (this-package-native-input "valgrind")
                        "check"
                        "test")
      #:phases
      #~(modify-phases %standard-phases
          ;; Upstream does not use a configure script.
          (delete 'configure)
          (add-before 'build 'patch-package-version
            (lambda _
              (substitute* "Makefile"
                (("\\$\\(shell git describe --abbrev=4 --dirty --always --tags\\)")
                 (string-append "v" #$version)))))
          (replace 'install
            ;; Upstream does not provide an install target.
            (lambda _
              (install-file "tpl" (string-append #$output "/bin")))))))
    (home-page "https://trealla-prolog.org/")
    (synopsis "Compact and efficient Prolog interpreter")
    (description "This package provides a compact and efficient Prolog
interpreter with ISO Prolog aspirations.")
    (license
     (list license:expat
           ;; The tiny-regex-c library uses the Unlicense license.
           license:unlicense))))

(define-public logtalk
  (package
    (name "logtalk")
    (version "3.80.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://logtalk.org/files/logtalk-"
                           version ".tar.bz2"))
       (sha256 (base32 "0g4cc0qv921234548k3rkv1sdayicaa6zzh15vgn82ri9apwm3nh"))))
    (build-system gnu-build-system)
    (arguments
     (list #:tests? #f                  ;no tests
           #:phases
           #~(modify-phases %standard-phases
               (delete 'configure)      ;no configure script and Makefile
               (delete 'build)
               (replace 'install
                 (lambda* (#:key outputs #:allow-other-keys)
                   (mkdir #$output)
                   (invoke "./scripts/install.sh" "-p" #$output))))))
    (native-search-paths
     (list (search-path-specification
            (variable "LOGTALKHOME")
            (separator #f)              ;single valued
            (files '("share/logtalk")))))
    (home-page "https://logtalk.org/")
    (synopsis "Object-oriented logic programming language")
    (description "Logtalk is a declarative object-oriented logic programming language
that extends and leverages the Prolog language with a feature set suitable for
programming in the large.  As a multi-paradigm language, Logtalk includes support for
both prototypes and classes, protocols (interfaces), categories (components and
hot-patching), event-driven programming, coinduction, lambda expressions, and
high-level multi-threading programming.")
    ;; Most are under Apache License 2.0, some contributed libraries and ports are
    ;; under other licenses.
    (license (list license:asl2.0
                   license:artistic2.0
                   license:bsd-2
                   license:bsd-3
                   license:cc0
                   license:expat
                   license:gpl2+
                   license:osl2.1))))
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. Tobias Geerinckx-Rice 2023-02-16gnu: Remove unneeded module imports....* 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. Efraim Flashner 2023-01-30gnu: texlive-graphics: Use over deprecated texlive-latex-graphics....* 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. Efraim Flashner 2023-01-12gnu: gromacs: Mark as tunable....* gnu/packages/chemistry.scm (gromacs)[properties]: New field. Ludovic Courtès 2023-01-10gnu: gromacs: Remove input labels and use gexps....* gnu/packages/chemistry.scm (gromacs)[arguments]: Turn into gexps. [native-inputs]: Remove labels. Remove (package-source googletest). Ludovic Courtès 2023-01-10gnu: gromacs: Update to 2022.4....* gnu/packages/chemistry.scm (gromacs): Update to 2022.4. * gnu/packages/patches/gromacs-tinyxml2.patch: Adjust accordingly. Ludovic Courtès 2022-10-27gnu: python-setuptools: Move to python-build....* 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> Lars-Dominik Braun 2022-10-15gnu: Add rdkit....* gnu/packages/chemistry.scm (rdkit): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> David Elsing 2022-10-15gnu: Add ringdecomposerlib....* gnu/packages/chemistry.scm (ringdecomposerlib): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> David Elsing 2022-10-15gnu: Add avalon-toolkit....* gnu/packages/chemistry.scm (avalon-toolkit): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> David Elsing 2022-10-15gnu: Add yaehmop....* gnu/packages/chemistry.scm (yaehmop): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> David Elsing 2022-10-15gnu: Add coordgenlibs....* gnu/packages/chemistry.scm (coordgenlibs): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> David Elsing 2022-10-15gnu: Add maeparser....* gnu/packages/chemistry.scm (maeparser): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> David Elsing 2022-10-15gnu: Add freesasa....* gnu/packages/chemistry.scm (freesasa): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> David Elsing 2022-10-15gnu: Add gemmi....* 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> David Elsing 2022-10-15gnu: Add sajson-for-gemmi....* gnu/packages/cpp.scm (sajson-for-gemmi): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> David Elsing 2022-09-15gnu: catch-framework2: Rename variable to catch2....Automated with: git grep -l catch-framework2 | xargs sed 's/catch-framework2/catch2/g' -i Maxim Cournoyer 2022-05-31gnu: Remove python2-numpy....* 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. Maxim Cournoyer 2022-05-31gnu: Remove nmoldyn....* gnu/packages/chemistry.scm (nmoldyn): Delete variable. Maxim Cournoyer 2022-05-31gnu: Remove domainfinder....* gnu/packages/chemistry.scm (domainfinder): Delete variable. Maxim Cournoyer 2021-12-13gnu: Simplify package inputs....This commit was obtained by running: ./pre-inst-env guix style without any additional argument. Ludovic Courtès 2021-10-12Merge remote-tracking branch 'origin/master' into core-updates-frozen.Mathieu Othacehe 2021-09-20gnu: Add python-pymol....* gnu/packages/chemistry.scm (python-pymol): New variable. Ricardo Wurmus 2021-07-24gnu: Use 'search-input-file' when looking for executables....* 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. Ludovic Courtès 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 2021-02-01gnu: openbabel: Update to 3.1.1....* gnu/packages/chemistry.scm (openbabel): Update to 3.1.1. [source]: Update URI. [arguments]: Temporarily skip tests on i686-linux. Kei Kebreau 2021-02-01gnu: inchi: Update to 1.06....* gnu/packages/chemistry.scm (inchi): Update to 1.06. [source]: Use HTTPS. [native-inputs]: Update inchi-doc hash. Kei Kebreau 2021-01-29gnu: Remove avogadro....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. Leo Famulari 2021-01-25gnu: Add avogadro2....* gnu/packages/chemistry.scm (avogadro2): New variable. Kei Kebreau 2021-01-25gnu: Add avogadrolibs....* gnu/packages/chemistry.scm (avogadrolibs): New variable. Kei Kebreau 2021-01-25gnu: Add libmsym....* gnu/packages/chemistry.scm (libmsym): New variable. Kei Kebreau 2021-01-25gnu: Add molequeue....* gnu/packages/chemistry.scm (molequeue): New variable. Kei Kebreau 2021-01-25gnu: Add mmtf-cpp....* gnu/packages/chemistry.scm (mmtf-cpp): New variable. Kei Kebreau 2021-01-25gnu: Add spglib....* gnu/packages/chemistry.scm (spglib): New variable. Kei Kebreau 2020-07-12gnu: Remove ".git" from "https://github/…/….git"....Until now, 'lookup-origin' and thus 'lookup-origin-revision' in (guix swh) would sometimes return #f for these because the ".git" URLs are redirects to the non-".git" URLs. Consequently, 'guix lint -c archival' would keep saying "scheduled Software Heritage archival"; likewise, the fallback download code would fail. * gnu/packages/ada.scm, gnu/packages/admin.scm, gnu/packages/aidc.scm, gnu/packages/algebra.scm, gnu/packages/android.scm, gnu/packages/animation.scm, gnu/packages/arcan.scm, gnu/packages/assembly.scm, gnu/packages/audio.scm, gnu/packages/authentication.scm, gnu/packages/avr.scm, gnu/packages/axoloti.scm, gnu/packages/backup.scm, gnu/packages/bash.scm, gnu/packages/benchmark.scm, gnu/packages/bioconductor.scm, gnu/packages/bioinformatics.scm, gnu/packages/bittorrent.scm, gnu/packages/boost.scm, gnu/packages/build-tools.scm, gnu/packages/c.scm, gnu/packages/calendar.scm, gnu/packages/cdrom.scm, gnu/packages/check.scm, gnu/packages/chemistry.scm, gnu/packages/chez.scm, gnu/packages/clojure.scm, gnu/packages/code.scm, gnu/packages/compression.scm, gnu/packages/compton.scm, gnu/packages/coq.scm, gnu/packages/cpp.scm, gnu/packages/cran.scm, gnu/packages/crypto.scm, gnu/packages/curl.scm, gnu/packages/databases.scm, gnu/packages/datastructures.scm, gnu/packages/debug.scm, gnu/packages/disk.scm, gnu/packages/distributed.scm, gnu/packages/django.scm, gnu/packages/dlang.scm, gnu/packages/dns.scm, gnu/packages/docker.scm, gnu/packages/education.scm, gnu/packages/efi.scm, gnu/packages/elixir.scm, gnu/packages/emacs-xyz.scm, gnu/packages/embedded.scm, gnu/packages/emulators.scm, gnu/packages/engineering.scm, gnu/packages/erlang.scm, gnu/packages/fabric-management.scm, gnu/packages/file-systems.scm, gnu/packages/finance.scm, gnu/packages/firmware.scm, gnu/packages/flashing-tools.scm, gnu/packages/fonts.scm, gnu/packages/fontutils.scm, gnu/packages/fpga.scm, gnu/packages/game-development.scm, gnu/packages/games.scm, gnu/packages/genealogy.scm, gnu/packages/genimage.scm, gnu/packages/geo.scm, gnu/packages/gimp.scm, gnu/packages/gl.scm, gnu/packages/gnome-xyz.scm, gnu/packages/gnome.scm, gnu/packages/gnuzilla.scm, gnu/packages/golang.scm, gnu/packages/gpodder.scm, gnu/packages/graph.scm, gnu/packages/graphics.scm, gnu/packages/graphviz.scm, gnu/packages/groff.scm, gnu/packages/groovy.scm, gnu/packages/gtk.scm, gnu/packages/guile-xyz.scm, gnu/packages/guile.scm, gnu/packages/hardware.scm, gnu/packages/haskell-apps.scm, gnu/packages/haskell-xyz.scm, gnu/packages/hexedit.scm, gnu/packages/i2p.scm, gnu/packages/ibus.scm, gnu/packages/image-processing.scm, gnu/packages/image-viewers.scm, gnu/packages/image.scm, gnu/packages/ipfs.scm, gnu/packages/java-graphics.scm, gnu/packages/java-maths.scm, gnu/packages/java.scm, gnu/packages/javascript.scm, gnu/packages/jrnl.scm, gnu/packages/julia.scm, gnu/packages/jupyter.scm, gnu/packages/kodi.scm, gnu/packages/language.scm, gnu/packages/lego.scm, gnu/packages/less.scm, gnu/packages/libusb.scm, gnu/packages/linux.scm, gnu/packages/lirc.scm, gnu/packages/lisp-xyz.scm, gnu/packages/llvm.scm, gnu/packages/logging.scm, gnu/packages/lolcode.scm, gnu/packages/lua.scm, gnu/packages/lxde.scm, gnu/packages/lxqt.scm, gnu/packages/machine-learning.scm, gnu/packages/mail.scm, gnu/packages/markup.scm, gnu/packages/maths.scm, gnu/packages/maven.scm, gnu/packages/mes.scm, gnu/packages/messaging.scm, gnu/packages/monitoring.scm, gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/networking.scm, gnu/packages/node-xyz.scm, gnu/packages/ocaml.scm, gnu/packages/ocr.scm, gnu/packages/onc-rpc.scm, gnu/packages/opencl.scm, gnu/packages/opencog.scm, gnu/packages/pantheon.scm, gnu/packages/password-utils.scm, gnu/packages/patchutils.scm, gnu/packages/pdf.scm, gnu/packages/perl6.scm, gnu/packages/phabricator.scm, gnu/packages/popt.scm, gnu/packages/printers.scm, gnu/packages/prolog.scm, gnu/packages/protobuf.scm, gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm, gnu/packages/python-web.scm, gnu/packages/python-xyz.scm, gnu/packages/qt.scm, gnu/packages/radio.scm, gnu/packages/rails.scm, gnu/packages/rdf.scm, gnu/packages/rednotebook.scm, gnu/packages/rpc.scm, gnu/packages/rsync.scm, gnu/packages/ruby.scm, gnu/packages/rust.scm, gnu/packages/scheme.scm, gnu/packages/screen.scm, gnu/packages/security-token.scm, gnu/packages/selinux.scm, gnu/packages/serialization.scm, gnu/packages/shells.scm, gnu/packages/shellutils.scm, gnu/packages/simh.scm, gnu/packages/sml.scm, gnu/packages/ssh.scm, gnu/packages/statistics.scm, gnu/packages/stenography.scm, gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/synergy.scm, gnu/packages/telephony.scm, gnu/packages/terminals.scm, gnu/packages/tex.scm, gnu/packages/texinfo.scm, gnu/packages/text-editors.scm, gnu/packages/textutils.scm, gnu/packages/time.scm, gnu/packages/tmux.scm, gnu/packages/tor.scm, gnu/packages/toys.scm, gnu/packages/version-control.scm, gnu/packages/video.scm, gnu/packages/vim.scm, gnu/packages/virtualization.scm, gnu/packages/vlang.scm, gnu/packages/vnc.scm, gnu/packages/vpn.scm, gnu/packages/web-browsers.scm, gnu/packages/web.scm, gnu/packages/wireservice.scm, gnu/packages/wm.scm, gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xml.scm, gnu/packages/xorg.scm, tests/lint.scm: Remove trailing ".git" from 'git-reference' URL. Ludovic Courtès 2020-05-04gnu: Add gromacs....* gnu/packages/chemistry.scm (gromacs): New variable. * gnu/packages/patches/gromacs-tinyxml2.patch: New file... * gnu/local.mk (dist_patch_DATA): ...add it here. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Vincent Legoll 2020-05-04gnu: Add tng....* gnu/packages/chemistry.scm (tng): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Vincent Legoll 2020-04-26gnu: nmoldyn: Adjust for Guile 3.0....* gnu/packages/chemistry.scm (nmoldyn)[arguments]: Provide explicit destination in calls to FORMAT. Marius Bakke 2020-03-05gnu: domainfinder: Update home page URI....* gnu/packages/chemistry.scm (domainfinder)[home-page]: Update URI. Björn Höfling 2020-03-05gnu: nmoldyn: Upate home page URI....* gnu/packages/chemistry.scm (nmoldyn)[home-page]: Update URI. Björn Höfling 2019-11-21gnu: nmoldyn: New source code location....* gnu/packages/chemistry.scm (nmoldyn): New source code location. Following the annoucement of Bitbucket to delete all Mercurial repositories in June 2020, the source code has been migrated to GitHub. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Konrad Hinsen