code:
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012, 2013, 2017 Ludovic Courtès <ludo@gnu.org>
;;;
;;; 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 gperf)
  #:use-module (guix licenses)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix build-system gnu))

(define-public gperf
  (package
    (name "gperf")
    (version "3.1")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "mirror://gnu/gperf/gperf-"
                          version ".tar.gz"))
      (sha256
       (base32
        "1qispg6i508rq8pkajh26cznwimbnj06wq9sd85vg95v8nwld1aq"))))
    (build-system gnu-build-system)
    (arguments '(#:parallel-tests? #f))
    (home-page "https://www.gnu.org/software/gperf/")
    (synopsis "Perfect hash function generator")
    (description
     "gperf is a perfect hash function generator.  For a given list of
strings, it produces a hash function and hash table in C or C++ code.  That
the hash function is perfect means that no collisions can exist and that
look-ups can be made by single string comparisons.")
    (license gpl3+)))

(define-public gperf-3.0
  ;; This older version would use 'unsigned int' in its generated lookup
  ;; functions whereas 3.1 uses 'size_t', which causes breakage such as
  ;; <https://github.com/wingo/elogind/issues/8>.
  (package
    (inherit gperf)
    (version "3.0.4")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/gperf/gperf-"
                                  version ".tar.gz"))
              (sha256
               (base32
                "0gnnm8iqcl52m8iha3sxrzrl9mcyhg7lfrhhqgdn4zj00ji14wbn"))))))

license: mit


code:
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019, 2020 Pierre Langlois <pierre.langlois@gmx.com>
;;; Copyright © 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; 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 gpodder)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix packages)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system python)
  #:use-module (gnu packages)
  #:use-module (gnu packages check)
  #:use-module (gnu packages freedesktop)
  #:use-module (gnu packages glib)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python-web)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages qt)
  #:use-module (gnu packages video))

(define-public gpodder
  (package
    (name "gpodder")
    (version "3.10.16")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/gpodder/gpodder")
             (commit version)))
       (sha256
        (base32
         "0pbpaasd7kj6y25nm45y1qyb9sxd4570f7g6zkfcpf6pa3nx7qkq"))
       (file-name (git-file-name name version))
       (patches (search-patches "gpodder-disable-updater.patch"))))
    (build-system python-build-system)
    (native-inputs
     `(("intltool" ,intltool)
       ("python-coverage" ,python-coverage)
       ("python-minimock" ,python-minimock)))
    (inputs
     `(("gtk+" ,gtk+)
       ("python-pygobject" ,python-pygobject)
       ("python-pycairo" ,python-pycairo)
       ("python-dbus" ,python-dbus)
       ("python-html5lib" ,python-html5lib)
       ("python-mygpoclient" ,python-mygpoclient)
       ("python-podcastparser" ,python-podcastparser)
       ("youtube-dl" ,youtube-dl)
       ("xdg-utils" ,xdg-utils)))
    (arguments
     '(#:phases
       (modify-phases %standard-phases
         ;; Avoid needing xdg-utils as a propagated input.
         (add-after 'unpack 'patch-xdg-open
           (lambda* (#:key inputs #:allow-other-keys)
             (let ((xdg-utils (assoc-ref inputs "xdg-utils")))
               (substitute* "src/gpodder/util.py"
                 (("xdg-open") (string-append xdg-utils "/bin/xdg-open")))
               #t)))
         (replace 'check
           (lambda _
             ; The `unittest' target overrides the PYTHONPATH variable.
             (substitute* "makefile"
               (("PYTHONPATH=src/") "PYTHONPATH=${PYTHONPATH}:src/"))
             (invoke "make" "unittest")))
         ;; 'msgmerge' introduces non-determinism by resetting the
         ;; POT-Creation-Date in .po files.
         (add-before 'install 'do-not-run-msgmerge
           (lambda _
             (substitute* "makefile"
               (("msgmerge") "true"))
             #t))
         (add-before 'install 'make-po-files-writable
           (lambda _
             (for-each
               (lambda (f)
                 (chmod f #o664))
               (find-files "po"))
             #t))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (setenv "PREFIX" (assoc-ref outputs "out"))
             (invoke "make" "install")))
         (add-after 'install 'wrap-gpodder
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out"))
                   (gi-typelib-path (getenv "GI_TYPELIB_PATH")))
               (wrap-program (string-append out "/bin/gpodder")
                 `("GI_TYPELIB_PATH" ":" prefix (,gi-typelib-path)))
               #t))))))
    (home-page "https://gpodder.github.io")
    (synopsis "Simple podcast client")
    (description "gPodder is a podcatcher, i.e. an application that allows
podcast feeds (RSS, Atom, Youtube, Soundcloud, Vimeo and XSPF) to be
subscribed to, checks for new episodes and allows the podcast to be saved
locally for later listening.")
    (license license:gpl3+)))

(define-public libmygpo-qt
  (package
    (name "libmygpo-qt")
    (version "1.1.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://stefan.derkits.at/files/"
                                  "libmygpo-qt/libmygpo-qt." version ".tar.gz"))
              (sha256
               (base32
                "1kg18qrq2rsswgzhl65r3mlyx7kpqg4wwnbp4yiv6svvmadmlxl2"))
              (patches (search-patches "libmygpo-qt-fix-qt-5.11.patch"
                                       "libmygpo-qt-missing-qt5-modules.patch"))))
    (build-system cmake-build-system)
    (native-inputs
     `(("pkg-config" ,pkg-config)))
    (inputs
     `(("qt" ,qtbase)))
    (arguments
     `(#:configure-flags '("-DMYGPO_BUILD_TESTS=ON")
       ;; TODO: Enable tests when https://github.com/gpodder/gpodder/issues/446
       ;; is fixed.
       #:tests? #f))
    (home-page "https://gpodder.github.io")
    (synopsis "Qt/C++ library wrapping the gpodder web service")
    (description "@code{libmygpo-qt} is a Qt/C++ library wrapping the
@url{https://gpodder.net} APIs.  It allows applications to discover, manage
and track podcasts.")
    (license license:lgpl2.1+)))

(define-public python-mygpoclient
  (package
    (name "python-mygpoclient")
    (version "1.8")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "mygpoclient" version))
       (sha256
        (base32
         "1fi5x6k1mngr0iviw2s4n1f3y2x7pwqy5ivkcrjdprzvwr37f0mh"))))
    (build-system python-build-system)
    (native-inputs
     `(("python-coverage" ,python-coverage)
       ("python-minimock" ,python-minimock)
       ("python-nose" ,python-nose)))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (replace 'check
           (lambda _
             (invoke "make" "test"))))))
    (home-page "https://mygpoclient.readthedocs.io")
    (synopsis "Python library for the gPodder web service")
    (description "@code{mygpoclient} provides an easy and structured way to
access the @url{https://gpodder.net} web services.  In addition to
subscription list synchronization and storage, the API supports uploading and
downloading episode status changes.")
    (license license:gpl3+)))

(define-public python-podcastparser
  (package
    (name "python-podcastparser")
    (version "0.6.5")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "podcastparser" version))
       (sha256
        (base32 "0k62ppg20i41gcc5x8ddjn7zbpy47hqpxzrq9257g2c71m4qw07b"))))
    (native-inputs
     `(("python-coverage" ,python-coverage)
       ("python-nose" ,python-nose)))
    (arguments
     '(#:phases
       (modify-phases %standard-phases
         (replace 'check
           (lambda _ (invoke "nosetests"))))))
    (build-system python-build-system)
    (home-page "http://gpodder.org/podcastparser")
    (synopsis "Simplified and fast RSS parser Python library")
    (description "@code{podcastparser} is a library for the gPodder project to
provide an easy and reliable way of parsing RSS and Atom-based podcast feeds
in Python.")
    (license license:isc)))


code:
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2020 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;; Copyright © 2020 Marius Bakke <marius@gnu.org>
;;;
;;; 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 gps)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system scons)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix utils)
  #:use-module (gnu packages)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages base)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages docbook)
  #:use-module (gnu packages glib)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages image)
  #:use-module (gnu packages libusb)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages qt)
  #:use-module (gnu packages sqlite)
  #:use-module (gnu packages xml))

(define-public gpsbabel
  (package
    (name "gpsbabel")
    (version "1.5.4")
    (source (origin
              (method url-fetch)
              ;; XXX: Downloads from gpsbabel.org are hidden behind a POST, so
              ;; get it from elsewhere.
              (uri (string-append
                    "mirror://debian/pool/main/g/gpsbabel/gpsbabel_"
                    version ".orig.tar.gz"))
              (sha256
               (base32
                "19hykxhyl567gf8qcrl33qhv95w0g4vxw9r3h9b8d8plx9bnaf8l"))
              (patches (search-patches
                        "gpsbabel-minizip.patch"
                        ;; XXX: Remove this patch on the next release.
                        "gpsbabel-qstring.patch"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  ;; Delete files under GPL-compatible licences but never used
                  ;; on GNU systems, rather than bloating the LICENSE field.
                  (delete-file "gui/serial_mac.cc")           ; Apple MIT
                  (delete-file "mingw/include/ddk/hidsdi.h") ; public domain
                  #t))))
    (build-system gnu-build-system)
    ;; TODO: "make doc" requires Docbook & co.
    (arguments
     `(#:configure-flags
       '("--with-zlib=system")
       ;; On i686, 'raymarine.test' fails because of a rounding error:
       ;; <http://hydra.gnu.org/build/133040>.  As a workaround, disable tests
       ;; on these platforms.
       ;; FIXME: On x86_64 with -std=gnu++11 tests also fail due to rounding
       ;; error.
       #:tests? #f))
    (inputs
     `(("expat" ,expat)
       ("zlib" ,zlib)
       ("qtbase" ,qtbase)))
    (native-inputs
     `(("which" ,which)
       ("qttools" ,qttools)
       ("libxml2" ,libxml2)))              ;'xmllint' needed for the KML tests
    (home-page "https://www.gpsbabel.org/")
    (synopsis "Convert and exchange data with GPS and map programs")
    (description
     "GPSBabel converts waypoints, tracks, and routes between hundreds of
popular GPS receivers and mapping programs.  It contains extensive data
manipulation abilities making it a convenient for server-side processing or as
the back-end for other tools.  It does not convert, transfer, send, or
manipulate maps.")
    (license (list license:expat        ; shapelib/*.[ch]
                   license:gpl2+))))    ; everything else

(define-public gpscorrelate
  (package
    (name "gpscorrelate")
    (version "2.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/dfandrich/gpscorrelate")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1kvybhfnygz79q3pgwc1q2x4ccmnsfscx2hzxnmzjbnc6arnqari"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (replace 'configure
           (lambda* (#:key inputs outputs #:allow-other-keys)
             ;; This is a rudimentary build system.
             (substitute* "Makefile"
               (("prefix[[:blank:]]*=.*$")
                (string-append "prefix = " (assoc-ref outputs "out")
                               "\n")))
             #t)))))
    (inputs
     `(("gtk+" ,gtk+)
       ("libxml2" ,libxml2)
       ("exiv2" ,exiv2)))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("docbook-xml" ,docbook-xml)
       ("docbook-xsl" ,docbook-xsl)
       ("libxslt" ,libxslt)))
    (home-page "https://dfandrich.github.io/gpscorrelate/")
    (synopsis "GPS photo correlation tool to geo-localize images")
    (description
     "GPS Correlate is a program to match a recorded GPS track with the EXIF
tags in digital camera photos, and update the EXIF tags with the location that
the photo was taken.  It does this by using the timestamp in the photo and
finding a data point in the GPS track that matches, or interpolating a point
between two other data points.")
    (license license:gpl2+)))

(define-public gama
  (package
    (name "gama")
    (version "2.09")
    (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://gnu/gama/gama-"
                            version ".tar.gz"))
        (sha256
         (base32
          "0c1b28frl6109arj09v4zr1xs859krn8871mkvis517g5pb55dc9"))))
    (build-system gnu-build-system)
    (arguments '(#:parallel-tests? #f)) ; race condition
    (native-inputs
     `(("libxml2" ,libxml2)))
    (inputs
     `(("expat" ,expat)
       ("sqlite" ,sqlite)))
    (home-page "https://www.gnu.org/software/gama")
    (synopsis "Adjustment of geodetic networks")
    (description
     "GNU Gama is a program for the adjustment of geodetic networks.  It is
useful in measurements where Global Positioning System (GPS) is not available,
such as underground.  It features the ability to adjust in local Cartesian
coordinates as well as partial support for adjustments in global coordinate systems.")
    (license license:gpl3+)))

(define-public gpxsee
  (package
    (name "gpxsee")
    (version "7.30")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/tumic0/GPXSee")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "09gajwqc30r9a2sn972qdx3gx0gki9n0zafq986hn6zsr3z43mfs"))))
    (build-system gnu-build-system)
    (arguments
     '(#:phases
       (modify-phases %standard-phases
         (replace 'configure
           ;; Use lrelease to convert TS translation files into QM files.
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (for-each (lambda (file)
                         (invoke "lrelease" file))
                       (find-files "lang" "\\.ts"))
             (invoke "qmake"
                     (string-append "PREFIX="
                                    (assoc-ref outputs "out"))))))))
    (inputs
     `(("qtbase" ,qtbase)))
    (native-inputs
     `(("qttools" ,qttools)))
    (home-page "https://www.gpxsee.org")
    (synopsis "GPS log file viewer and analyzer")
    (description
     "GPXSee is a Qt-based GPS log file viewer and analyzer that supports all
common GPS log file formats.  It can display multiple tracks on various on-
and off-line maps.  You can easily add more maps and graph other captured data
such as elevation, speed, heart rate, power, temperature, and gear shifts.")
    (license license:gpl3)))

(define-public gpsd
  (package
    (name "gpsd")
    (version "3.21")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://download-mirror.savannah.gnu.org"
                           "/releases/gpsd/gpsd-" version ".tar.gz"))
       (sha256
        (base32 "14gyqrbrq6jz4y6x59rdpv9d4c3pbn0vh1blq3iwrc6kz0x4ql35"))))
    (build-system scons-build-system)
    (native-inputs
     `(("bc" ,bc)
       ("pkg-config" ,pkg-config)))
    (inputs
     `(("bluez" ,bluez)
       ("dbus" ,dbus)
       ("gtk+" ,gtk+)
       ("libcap" ,libcap)
       ("libusb" ,libusb)
       ("ncurses" ,ncurses)
       ("python" ,python)
       ("python-pycairo" ,python-pycairo)
       ("python-pygobject" ,python-pygobject)
       ("python-pyserial" ,python-pyserial)
       ("python-wrapper" ,python-wrapper)
       ("qtbase" ,qtbase)))
    (arguments
     `(#:scons-flags
       (list (string-append "prefix=" %output)
             (let ((version ,(version-major+minor (package-version python))))
               (string-append "python_libdir=" %output
                              "/lib/python" version
                              "/site-packages"))
             "qt_versioned=5")
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'fix-build
           (lambda* (#:key outputs #:allow-other-keys)
             (substitute* "SConstruct"
               (("envs = \\{\\}")
                "envs = os.environ"))
             #t))
         (add-after 'install 'wrap-python-scripts
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (pycairo (assoc-ref inputs "python-pycairo"))
                    (pygobject (assoc-ref inputs "python-pygobject"))
                    (pyserial (assoc-ref inputs "python-pyserial"))
                    (sitedir (lambda (package)
                               (string-append package
                                              "/lib/python"
                                              ,(version-major+minor
                                                (package-version python))
                                              "/site-packages")))
                    (pythonpath (string-join (map sitedir
                                                  (list out pycairo pygobject
                                                        pyserial))
                                             ":")))
               (for-each (lambda (script)
                           (wrap-program (string-append out "/bin/" script)
                             `("PYTHONPATH" ":" prefix (,pythonpath))))
                         '("gegps" "gpscat" "gpsfake" "gpsprof"
                           "ubxtool" "xgps" "xgpsspeed" "zerk")))
             #t)))))
    (synopsis "GPS service daemon")
    (description
     "@code{gpsd} is a service daemon that monitors one or more GPSes or AIS
receivers attached to a host computer through serial or USB ports, making all
data on the location/course/velocity of the sensors available to be queried on
TCP port 2947 of the host computer.")
    (home-page "https://gpsd.gitlab.io/gpsd/")
    (license license:bsd-2)))


code:
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2020 Alexander Krotov <krotov@iitp.ru>
;;; Copyright © 2020 Pierre Langlois <pierre.langlos@gmx.com>
;;;
;;; 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 graph)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix packages)
  #:use-module (guix utils)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system python)
  #:use-module (guix build-system r)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (gnu packages)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages bioconductor)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages cran)
  #:use-module (gnu packages gd)
  #:use-module (gnu packages graphviz)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-science)
  #:use-module (gnu packages python-web)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages statistics)
  #:use-module (gnu packages swig)
  #:use-module (gnu packages time)
  #:use-module (gnu packages xml))

(define-public igraph
  (package
    (name "igraph")
    (version "0.8.2")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://github.com/igraph/igraph/releases/"
                           "download/" version "/igraph-" version ".tar.gz"))
       (sha256
        (base32 "158flvl80qh1l1ikfa04p1dzh8kapsvm6q80x3ih5gwcgcg4g2ki"))))
    (build-system gnu-build-system)
    (arguments
     `(#:configure-flags
       (list "--with-external-glpk"
             "--with-external-blas"
             "--with-external-lapack")))
    (inputs
     `(("gmp" ,gmp)
       ("glpk" ,glpk)
       ("libxml2" ,libxml2)
       ("lapack" ,lapack)
       ("openblas" ,openblas)
       ("zlib" ,zlib)))
    (home-page "https://igraph.org")
    (synopsis "Network analysis and visualization")
    (description
     "This package provides a library for the analysis of networks and graphs.
It can handle large graphs very well and provides functions for generating
random and regular graphs, graph visualization, centrality methods and much
more.")
    (license license:gpl2+)))

(define-public python-igraph
  (package (inherit igraph)
    (name "python-igraph")
    (version "0.8.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "python-igraph" version))
       (sha256
        (base32 "0wkxrs28qdvnrz7d4jzcf2bh6v2yqzx3wyfziihfgsi2gn6n60a6"))))
    (build-system python-build-system)
    (arguments
     '(#:configure-flags
       (list "--use-pkg-config")
       #:phases
       (modify-phases %standard-phases
         (replace 'build
           (lambda _
             (invoke "python" "./setup.py" "build" "--use-pkg-config")))
         (delete 'check)
         (add-after 'install 'check
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (add-installed-pythonpath inputs outputs)
             (invoke "pytest" "-v"))))))
    (inputs
     `(("igraph" ,igraph)))
    (propagated-inputs
     `(("python-texttable" ,python-texttable)))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("python-pytest" ,python-pytest)))
    (home-page "https://pypi.org/project/python-igraph/")
    (synopsis "Python bindings for the igraph network analysis library")))

(define-public r-rgraphviz
  (package
    (name "r-rgraphviz")
    (version "2.32.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "Rgraphviz" version))
       (sha256
        (base32
         "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y"))))
    (properties `((upstream-name . "Rgraphviz")))
    (build-system r-build-system)
    ;; FIXME: Rgraphviz bundles the sources of an older variant of
    ;; graphviz.  It does not build with the latest version of graphviz, so
    ;; we do not add graphviz to the inputs.
    (inputs `(("zlib" ,zlib)))
    (propagated-inputs
     `(("r-graph" ,r-graph)))
    (native-inputs
     `(("pkg-config" ,pkg-config)))
    (home-page "https://bioconductor.org/packages/Rgraphviz")
    (synopsis "Plotting capabilities for R graph objects")
    (description
     "This package interfaces R with the graphviz library for plotting R graph
objects from the @code{graph} package.")
    (license license:epl1.0)))

(define-public r-rbiofabric
  (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
        (revision "1"))
    (package
      (name "r-rbiofabric")
      (version (string-append "0.3-" revision "." (string-take commit 7)))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/wjrl/RBioFabric")
                      (commit commit)))
                (file-name (string-append name "-" version "-checkout"))
                (sha256
                 (base32
                  "1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
      (build-system r-build-system)
      (propagated-inputs
       `(("r-igraph" ,r-igraph)))
      (home-page "http://www.biofabric.org/")
      (synopsis "BioFabric network visualization")
      (description "This package provides an implementation of the function
@code{bioFabric} for creating scalable network digrams where nodes are
represented by horizontal lines, and edges are represented by vertical
lines.")
      (license license:expat))))

(define-public python-plotly
  (package
    (name "python-plotly")
    (version "4.8.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/plotly/plotly.py")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "08ab677gr85m10zhixr6dnmlfws8q6sra7nhyb8nf3r8dx1ffqhz"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'chdir
           (lambda _
             (chdir "packages/python/plotly")
             #t))
         (replace 'check
           (lambda _
             (invoke "pytest" "-x" "plotly/tests/test_core")
             (invoke "pytest" "-x" "plotly/tests/test_io")
             ;; FIXME: Add optional dependencies and enable their tests.
             ;; (invoke "pytest" "-x" "plotly/tests/test_optional")
             (invoke "pytest" "_plotly_utils/tests")))
         (add-before 'reset-gzip-timestamps 'make-files-writable
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out")))
               (for-each (lambda (file) (chmod file #o644))
                 (find-files out "\\.gz"))
               #t))))))
    (native-inputs
     `(("python-pytest" ,python-pytest)))
    (propagated-inputs
     `(("python-decorator" ,python-decorator)
       ("python-ipywidgets" ,python-ipywidgets)
       ("python-pandas" ,python-pandas)
       ("python-requests" ,python-requests)
       ("python-retrying" ,python-retrying)
       ("python-six" ,python-six)
       ("python-statsmodels" ,python-statsmodels)
       ("python-xarray" ,python-xarray)))
    (home-page "https://plotly.com/python/")
    (synopsis "Interactive plotting library for Python")
    (description "Plotly's Python graphing library makes interactive,
publication-quality graphs online.  Examples of how to make line plots, scatter
plots, area charts, bar charts, error bars, box plots, histograms, heatmaps,
subplots, multiple-axes, polar charts, and bubble charts. ")
    (license license:expat)))

(define-public python-plotly-2.4.1
  (package (inherit python-plotly)
    (version "2.4.1")
    (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "plotly" version))
        (sha256
         (base32
          "0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
   (native-inputs '())
   (propagated-inputs
    `(("python-decorator" ,python-decorator)
      ("python-nbformat" ,python-nbformat)
      ("python-pandas" ,python-pandas)
      ("python-pytz" ,python-pytz)
      ("python-requests" ,python-requests)
      ("python-six" ,python-six)))
    (arguments
     '(#:tests? #f)))) ; The tests are not distributed in the release

(define-public python2-plotly
  (package-with-python2 python-plotly-2.4.1))

(define-public python-louvain
  (package
    (name "python-louvain")
    (version "0.6.1")
    ;; The tarball on Pypi does not include the tests.
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/vtraag/louvain-igraph")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0w31537sifkf65sck1iaip5i6d8g64pa3wdwad83d6p9jwkck57k"))))
    (build-system python-build-system)
    (propagated-inputs
     `(("python-ddt" ,python-ddt)
       ("python-igraph" ,python-igraph)))
    (inputs
     `(("igraph" ,igraph)))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("python-pytest" ,python-pytest)))
    (home-page "https://github.com/vtraag/louvain-igraph")
    (synopsis "Algorithm for methods of community detection in large networks")
    (description
     "This package provides an implementation of the Louvain algorithm for use
with igraph.  Louvain is a general algorithm for methods of community
detection in large networks.

This package has been superseded by the @code{leidenalg} package and should
not be used for new projects.")
    (license license:gpl3+)))

(define-public faiss
  (package
    (name "faiss")
    (version "1.5.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/facebookresearch/faiss")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0pk15jfa775cy2pqmzq62nhd6zfjxmpvz5h731197c28aq3zw39w"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  (substitute* "utils.cpp"
                    (("#include <immintrin.h>")
                     "#ifdef __SSE__\n#include <immintrin.h>\n#endif"))
                  #t))))
    (build-system cmake-build-system)
    (arguments
     `(#:configure-flags
       (list "-DBUILD_WITH_GPU=OFF"  ; thanks, but no thanks, CUDA.
             "-DBUILD_TUTORIAL=OFF") ; we don't need those
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'prepare-build
           (lambda _
             (let ((features (list ,@(let ((system (or (%current-target-system)
                                                       (%current-system))))
                                       (cond
                                        ((string-prefix? "x86_64" system)
                                         '("-mavx" "-msse2" "-mpopcnt"))
                                        ((string-prefix? "i686" system)
                                         '("-msse2" "-mpopcnt"))
                                        (else
                                         '()))))))
               (substitute* "CMakeLists.txt"
                 (("-m64") "")
                 (("-mpopcnt") "") ; only some architectures
                 (("-msse4")
                  (string-append
                   (string-join features)
                   " -I" (getcwd)))
                 ;; Build also the shared library
                 (("ARCHIVE DESTINATION lib")
                  "LIBRARY DESTINATION lib")
                 (("add_library.*" m)
                  "\
add_library(objlib OBJECT ${faiss_cpu_headers} ${faiss_cpu_cpp})
set_property(TARGET objlib PROPERTY POSITION_INDEPENDENT_CODE 1)
add_library(${faiss_lib}_static STATIC $<TARGET_OBJECTS:objlib>)
add_library(${faiss_lib} SHARED $<TARGET_OBJECTS:objlib>)
install(TARGETS ${faiss_lib}_static ARCHIVE DESTINATION lib)
\n")))

             ;; See https://github.com/facebookresearch/faiss/issues/520
             (substitute* "IndexScalarQuantizer.cpp"
               (("#define USE_AVX") ""))

             ;; Make header files available for compiling tests.
             (mkdir-p "faiss")
             (for-each (lambda (file)
                         (mkdir-p (string-append "faiss/" (dirname file)))
                         (copy-file file (string-append "faiss/" file)))
                       (find-files "." "\\.h$"))
             #t))
         (replace 'check
           (lambda _
             (invoke "make" "-C" "tests"
                     (format #f "-j~a" (parallel-job-count)))))
         (add-after 'install 'remove-tests
           (lambda* (#:key outputs #:allow-other-keys)
             (delete-file-recursively
              (string-append (assoc-ref outputs "out")
                             "/test"))
             #t)))))
    (inputs
     `(("openblas" ,openblas)))
    (native-inputs
     `(("googletest" ,googletest)))
    (home-page "https://github.com/facebookresearch/faiss")
    (synopsis "Efficient similarity search and clustering of dense vectors")
    (description "Faiss is a library for efficient similarity search and
clustering of dense vectors.  It contains algorithms that search in sets of
vectors of any size, up to ones that possibly do not fit in RAM.  It also
contains supporting code for evaluation and parameter tuning.")
    (license license:bsd-3)))

(define-public python-faiss
  (package (inherit faiss)
    (name "python-faiss")
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'chdir
           (lambda _ (chdir "python") #t))
         (add-after 'chdir 'build-swig
           (lambda* (#:key inputs #:allow-other-keys)
             (with-output-to-file "../makefile.inc"
               (lambda ()
                 (let ((python-version ,(version-major+minor (package-version python))))
                   (format #t "\
PYTHONCFLAGS =-I~a/include/python~am/ -I~a/lib/python~a/site-packages/numpy/core/include
LIBS = -lpython~am -lfaiss
SHAREDFLAGS = -shared -fopenmp
CXXFLAGS = -fpermissive -fopenmp -fPIC
CPUFLAGS = ~{~a ~}~%"
                           (assoc-ref inputs "python*") python-version
                           (assoc-ref inputs "python-numpy") python-version
                           python-version
                           (list ,@(let ((system (or (%current-target-system)
                                                     (%current-system))))
                                     (cond
                                       ((string-prefix? "x86_64" system)
                                        '("-mavx" "-msse2" "-mpopcnt"))
                                       ((string-prefix? "i686" system)
                                        '("-msse2" "-mpopcnt"))
                                       (else
                                         '()))))))))
             (substitute* "Makefile"
               (("../libfaiss.a") ""))
             (invoke "make" "cpu"))))))
    (inputs
     `(("faiss" ,faiss)
       ("openblas" ,openblas)
       ("python*" ,python)
       ("swig" ,swig)))
    (propagated-inputs
     `(("python-matplotlib" ,python-matplotlib)
       ("python-numpy" ,python-numpy)))
    (description "Faiss is a library for efficient similarity search and
clustering of dense vectors.  This package provides Python bindings to the
Faiss library.")))

(define-public python-leidenalg
  (package
    (name "python-leidenalg")
    (version "0.7.0")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "leidenalg" version))
       (sha256
        (base32
         "15fwld9hdw357rd026mzcwpah5liy4f33vc9x9kwy37g71b2rjf1"))))
    (build-system python-build-system)
    (arguments '(#:tests? #f)) ; tests are not included
    (native-inputs
     `(("pkg-config" ,pkg-config)))
    (inputs
     `(("igraph" ,igraph)))
    (propagated-inputs
     `(("python-igraph" ,python-igraph)))
    (home-page "https://github.com/vtraag/leidenalg")
    (synopsis "Community detection in large networks")
    (description
     "Leiden is a general algorithm for methods of community detection in
large networks.  This package implements the Leiden algorithm in C++ and
exposes it to Python.  Besides the relative flexibility of the implementation,
it also scales well, and can be run on graphs of millions of nodes (as long as
they can fit in memory).  The core function is @code{find_partition} which
finds the optimal partition using the Leiden algorithm, which is an extension
of the Louvain algorithm, for a number of different methods.")
    (license license:gpl3+)))

(define-public edge-addition-planarity-suite
  (package
    (name "edge-addition-planarity-suite")
    (version "3.0.0.5")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url (string-append "https://github.com/graph-algorithms/"
                                  name))
              (commit (string-append "Version_" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "01cm7ay1njkfsdnmnvh5zwc7wg7x189hq1vbfhh9p3ihrbnmqzh8"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
       ("libtool" ,libtool)))
    (synopsis "Embedding of planar graphs")
    (description "The package provides a reference implementation of the
linear time edge addition algorithm for embedding planar graphs and
isolating planarity obstructions.")
    (license license:bsd-3)
    (home-page
      "https://github.com/graph-algorithms/edge-addition-planarity-suite")))

(define-public rw
  (package
    (name "rw")
    ;; There is a version 0.8, but the tarball is broken with symlinks
    ;; to /usr/share.
    (version "0.7")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/rankwidth/"
                                  "rw-" version ".tar.gz"))
       (sha256
        (base32
         "1rv2v42x2506x7f10349m1wpmmfxrv9l032bkminni2gbip9cjg0"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("pkg-config" ,pkg-config)))
    (inputs
     `(("igraph" ,igraph)))
    (home-page "https://sourceforge.net/projects/rankwidth/")
    (synopsis "Rank-width and rank-decomposition of graphs")
    (description "rw computes rank-width and rank-decompositions
of graphs.")
    (license license:gpl2+)))

(define-public mscgen
  (package
    (name "mscgen")
    (version "0.20")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "http://www.mcternan.me.uk/mscgen/software/mscgen-src-"
                           version ".tar.gz"))
       (sha256
        (base32
         "08yw3maxhn5fl1lff81gmcrpa4j9aas4mmby1g9w5qcr0np82d1w"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("pkg-config" ,pkg-config)))
    (inputs
     `(("gd" ,gd)))
    (home-page "http://www.mcternan.me.uk/mscgen/")
    (synopsis "Message Sequence Chart Generator")
    (description "Mscgen is a small program that parses Message Sequence Chart
descriptions and produces PNG, SVG, EPS or server side image maps (ismaps) as
the output.  Message Sequence Charts (MSCs) are a way of representing entities
and interactions over some time period and are often used in combination with
SDL.  MSCs are popular in Telecoms to specify how protocols operate although
MSCs need not be complicated to create or use.  Mscgen aims to provide a simple
text language that is clear to create, edit and understand, which can also be
transformed into common image formats for display or printing.")
    (license license:gpl2+)))