code:
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012, 2013 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2018 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 lout)
  #:use-module (guix licenses)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix build-system gnu)
  #:use-module (gnu packages ghostscript))

(define-public lout
  (package
    (name "lout")
    (version "3.40")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://savannah/lout/lout-"
                                  version ".tar.gz"))
              (sha256
               (base32
                "1gb8vb1wl7ikn269dd1c7ihqhkyrwk19jwx5kd0rdvbk6g7g25ix"))))
    (build-system gnu-build-system)     ; actually, just a makefile
    (outputs '("out" "doc"))
    (native-inputs
     `(("ghostscript" ,ghostscript)))
    (arguments
     `(#:modules ((guix build utils)
                  (guix build gnu-build-system)
                  (srfi srfi-1))        ; we need SRFI-1
       #:tests? #f                      ; no "check" target
       #:phases
       (modify-phases %standard-phases
         ;; This package is a bit tricky, because it doesn't follow the GNU
         ;; Build System rules.  Instead, it has a makefile that has to be
         ;; patched to set the prefix, etc., and it has no makefile rules to
         ;; build its documentation.
         (replace 'configure
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out"))
                   (doc (assoc-ref outputs "doc")))
               (substitute* "makefile"
                 (("^PREFIX[[:blank:]]*=.*$")
                  (string-append "PREFIX = " out "\n"))
                 (("^LOUTLIBDIR[[:blank:]]*=.*$")
                  (string-append "LOUTLIBDIR = " out "/lib/lout\n"))
                 (("^LOUTDOCDIR[[:blank:]]*=.*$")
                  (string-append "LOUTDOCDIR = " doc "/share/doc/lout\n"))
                 (("^MANDIR[[:blank:]]*=.*$")
                  (string-append "MANDIR = " out "/man\n")))
               (mkdir out)
               (mkdir (string-append out "/bin"))
               (mkdir (string-append out "/lib"))
               (mkdir (string-append out "/man"))
               (mkdir-p (string-append doc "/share/doc/lout"))
               #t)))
         (add-after 'install 'install-man-pages
           (lambda* (#:key outputs #:allow-other-keys)
             (invoke "make" "installman")
             #t))
         (add-after 'install 'install-doc
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "doc")))
               (setenv "PATH"
                       (string-append (assoc-ref outputs "out")
                                      "/bin:" (getenv "PATH")))
               (with-directory-excursion "doc"
                 (every (lambda (doc)
                          (format #t "doc: building `~a'...~%" doc)
                          (with-directory-excursion doc
                            (let ((file (string-append out "/share/doc/lout/"
                                                       doc ".ps")))
                              (unless (file-exists? "outfile.ps")
                                (invoke "lout" "-r4" "-o"
                                        "outfile.ps" "all"))
                              (copy-file "outfile.ps" file)
                              (invoke "ps2pdf"
                                      "-dPDFSETTINGS=/prepress"
                                      "-sPAPERSIZE=a4"
                                      file
                                      (string-append out "/share/doc/lout/"
                                                     doc ".pdf")))))
                        '("design" "expert" "slides" "user")))
               #t))))))
    (synopsis "Document layout system")
    (description
     "The Lout document formatting system reads a high-level description of
a document similar in style to LaTeX and produces a PostScript or plain text
output file.

Lout offers an unprecedented range of advanced features, including optimal
paragraph and page breaking, automatic hyphenation, PostScript EPS file
inclusion and generation, equation formatting, tables, diagrams, rotation and
scaling, sorted indexes, bibliographic databases, running headers and
odd-even pages, automatic cross referencing, multilingual documents including
hyphenation (most European languages are supported), formatting of computer
programs, and much more, all ready to use.  Furthermore, Lout is easily
extended with definitions which are very much easier to write than troff of
TeX macros because Lout is a high-level, purely functional language, the
outcome of an eight-year research project that went back to the
beginning.")
    (license gpl3+)
    (home-page "https://savannah.nongnu.org/projects/lout/")))


code:
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018 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 lsof)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix build-system gnu)
  #:use-module (gnu packages perl))

(define-public lsof
  (package
   (name "lsof")
   (version "4.91")
   (source
    (origin
      (method url-fetch)
      (uri
       (apply append
              (map
               (lambda (mirror-uri)
                 (let ((tarball (string-append name "_" version ".tar.bz2")))
                   (list
                    (string-append mirror-uri "/" tarball)
                    ;; Upon every new release, the previous one is moved here:
                    (string-append mirror-uri "/OLD/" tarball))))
               (list
                "ftp://lsof.itap.purdue.edu/pub/tools/unix/lsof/"

                ;; Add mirrors because the canonical FTP server at purdue.edu
                ;; bails out when it cannot do a reverse DNS lookup, as noted
                ;; at <http://people.freebsd.org/~abe/>.
                "ftp://ftp.fu-berlin.de/pub/unix/tools/lsof/"
                (string-append "http://www.mirrorservice.org/sites/"
                               "lsof.itap.purdue.edu/pub/tools/unix/lsof")
                (string-append "ftp://ftp.mirrorservice.org/sites/"
                               "lsof.itap.purdue.edu/pub/tools/unix/lsof")))))
      (sha256
       (base32 "18sh4hbl9jw2szkf0gvgan8g13f3g4c6s2q9h3zq5gsza9m99nn9"))))
   (build-system gnu-build-system)
   (native-inputs `(("perl" ,perl)))
   (arguments
    `(#:phases
      (modify-phases %standard-phases
        (replace 'unpack
          (lambda* (#:key source #:allow-other-keys)
            (let ((unpack (assoc-ref %standard-phases 'unpack)))
              (unpack #:source source)
              (unpack #:source (car (find-files "." "\\.tar$"))))))
        (replace 'configure
          (lambda _
            (setenv "LSOF_CC" "gcc")
            (setenv "LSOF_MAKE" "make")
            (invoke "./Configure" "linux")
            #t))
        (add-after 'configure 'patch-timestamps
          (lambda _
            (substitute* "Makefile"
              (("`date`") "`date --date=@1`"))
            #t))
        (add-before 'check 'disable-failing-tests
          (lambda _
            (substitute* "tests/Makefile"
              ;; Fails with ‘ERROR!!! client gethostbyaddr() failure’.
              (("(STDTST=.*) LTsock" _ prefix) prefix)
              ;; Fails without access to a remote NFS server.
              (("(OPTTST=.*) LTnfs"  _ prefix) prefix))
            #t))
        (replace 'check
          (lambda _
            (with-directory-excursion "tests"
              ;; Tests refuse to run on ‘unvalidated’ platforms.
              (make-file-writable "TestDB")
              (invoke "./Add2TestDB")

              ;; The ‘standard’ tests suggest running ‘optional’ ones as well.
              (invoke "make" "standard" "optional")
              #t)))
        (replace 'install
          (lambda* (#:key outputs #:allow-other-keys)
            (let ((out (assoc-ref outputs "out")))
              (install-file "lsof" (string-append out "/bin"))
              (install-file "lsof.8" (string-append out "/share/man/man8")))
            #t)))))
   (synopsis "Display information about open files")
   (description
    "Lsof stands for LiSt Open Files, and it does just that.
It lists information about files that are open by the processes running
on the system.")
   (license (license:fsf-free
             "file://00FAQ"
             "License inspired by zlib, see point 1.9 of 00FAQ in the distribution."))
   (home-page "http://people.freebsd.org/~abe/")))

license: mit


code:
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com>
;;; Copyright © 2014 Raimon Grau <raimonster@gmail.com>
;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2014 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 doncatnip <gnopap@gmail.com>
;;; Copyright © 2016, 2017 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2016 José Miguel Sánchez García <jmi2k@openmailbox.org>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.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 lua)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix utils)
  #:use-module (guix build utils)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system cmake)
  #:use-module (gnu packages)
  #:use-module (gnu packages readline)
  #:use-module (gnu packages tls)
  #:use-module (gnu packages xml)
  #:use-module (gnu packages glib)
  #:use-module (gnu packages libffi)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages xorg)
  #:use-module (gnu packages gtk))

(define-public lua
  (package
    (name "lua")
    (version "5.3.5")
    (source (origin
             (method url-fetch)
             (uri (string-append "https://www.lua.org/ftp/lua-"
                                 version ".tar.gz"))
             (sha256
              (base32 "1b2qn2rv96nmbm6zab4l877bd4zq7wpwm8drwjiy2ih4jqzysbhc"))
             (patches (search-patches "lua-pkgconfig.patch"
                                      "lua-liblua-so.patch"))))
    (build-system gnu-build-system)
    (inputs `(("readline" ,readline)))
    (arguments
     '(#:modules ((guix build gnu-build-system)
                  (guix build utils)
                  (srfi srfi-1))
       #:test-target "test"
       #:make-flags
       '("MYCFLAGS=-fPIC -DLUA_DL_DLOPEN"
         "linux")
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out")))
               (invoke "make" "install"
                       (string-append "INSTALL_TOP=" out)
                       (string-append "INSTALL_MAN=" out
                                      "/share/man/man1"))))))))
    (home-page "https://www.lua.org/")
    (synopsis "Embeddable scripting language")
    (description
     "Lua is a powerful, fast, lightweight, embeddable scripting language.  Lua
combines simple procedural syntax with powerful data description constructs
based on associative arrays and extensible semantics.  Lua is dynamically typed,
runs by interpreting bytecode for a register-based virtual machine, and has
automatic memory management with incremental garbage collection, making it ideal
for configuration, scripting, and rapid prototyping.")
    (license license:x11)))

(define-public lua-5.2
  (package (inherit lua)
           (version "5.2.4")
           (source
            (origin
              (method url-fetch)
              (uri (string-append "https://www.lua.org/ftp/lua-"
                                  version ".tar.gz"))
              (sha256
               (base32 "0jwznq0l8qg9wh5grwg07b5cy3lzngvl5m2nl1ikp6vqssmf9qmr"))
              (patches (search-patches "lua-pkgconfig.patch"
                                       "lua-liblua-so.patch"))))))

(define-public lua-5.1
  (package (inherit lua)
    (version "5.1.5")
    (source (origin
             (method url-fetch)
             (uri (string-append "https://www.lua.org/ftp/lua-"
                                 version ".tar.gz"))
             (sha256
              (base32 "0cskd4w0g6rdm2q8q3i4n1h3j8kylhs3rq8mxwl9vwlmlxbgqh16"))
             (patches (search-patches "lua51-liblua-so.patch"
                                      "lua-CVE-2014-5461.patch"
                                      "lua51-pkgconfig.patch"))))))

(define-public luajit
  (package
    (name "luajit")
    (version "2.1.0-beta3")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://luajit.org/download/LuaJIT-"
                                  version ".tar.gz"))
              (sha256
               (base32 "1hyrhpkwjqsv54hnnx4cl8vk44h9d6c9w0fz1jfjz00w255y7lhs"))
              (patches (search-patches "luajit-no_ldconfig.patch"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f                      ; luajit is distributed without tests
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)            ; no configure script
         (add-after 'install 'create-luajit-symlink
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin")))
               (with-directory-excursion bin
                 (symlink ,(string-append name "-" version)
                          ,name)
                 #t)))))
         #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")))))
    (home-page "https://www.luajit.org/")
    (synopsis "Just in time compiler for Lua programming language version 5.1")
    (description
     "LuaJIT is a Just-In-Time Compiler (JIT) for the Lua
programming language.  Lua is a powerful, dynamic and light-weight programming
language.  It may be embedded or used as a general-purpose, stand-alone
language.")
    (license license:x11)))

(define-public lua5.1-expat
  (package
    (name "lua5.1-expat")
    (version "1.3.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://matthewwild.co.uk/projects/"
                                  "luaexpat/luaexpat-" version ".tar.gz"))
              (sha256
               (base32
                "1hvxqngn0wf5642i5p3vcyhg3pmp102k63s9ry4jqyyqc1wkjq6h"))))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags
       (let ((out (assoc-ref %outputs "out")))
         (list "CC=gcc"
               (string-append "LUA_LDIR=" out "/share/lua/$(LUA_V)")
               (string-append "LUA_CDIR=" out "/lib/lua/$(LUA_V)")))
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (replace 'check
           (lambda _
             (setenv "LUA_CPATH" "src/?.so;;")
             (setenv "LUA_PATH"  "src/?.lua;;")
             (invoke "lua" "tests/test.lua")
             (invoke "lua" "tests/test-lom.lua"))))))
    (inputs
     `(("lua" ,lua-5.1)
       ("expat" ,expat)))
    (home-page "http://matthewwild.co.uk/projects/luaexpat/")
    (synopsis "SAX XML parser based on the Expat library")
    (description "LuaExpat is a SAX XML parser based on the Expat library.")
    (license (package-license lua-5.1))))

(define-public lua5.1-socket
  (package
    (name "lua5.1-socket")
    (version "3.0-rc1")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/diegonehab/luasocket/archive/v"
                    version ".tar.gz"))
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
                "0j8jx8bjicvp9khs26xjya8c495wrpb7parxfnabdqa5nnsxjrwb"))))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags
       (let ((out (assoc-ref %outputs "out")))
         (list (string-append "INSTALL_TOP=" out)))
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (replace 'check
           (lambda _
             (setenv "LUA_CPATH" (string-append "src/?.so." ,version ";;"))
             (setenv "LUA_PATH"  "src/?.lua;;")
             (when (zero? (primitive-fork))
               (invoke "lua" "test/testsrvr.lua"))
             (invoke "lua" "test/testclnt.lua"))))))
    (inputs
     `(("lua" ,lua-5.1)))
    (home-page "http://www.tecgraf.puc-rio.br/~diego/professional/luasocket/")
    (synopsis "Socket library for Lua")
    (description "LuaSocket is a Lua extension library that is composed by two
parts: a C core that provides support for the TCP and UDP transport layers,
and a set of Lua modules that add support for functionality commonly needed by
applications that deal with the Internet.

Among the supported modules, the most commonly used implement the
SMTP (sending e-mails), HTTP (WWW access) and FTP (uploading and downloading
files) client protocols.  These provide a very natural and generic interface
to the functionality defined by each protocol.  In addition, you will find
that the MIME (common encodings), URL (anything you could possible want to do
with one) and LTN12 (filters, sinks, sources and pumps) modules can be very
handy.")
    (license (package-license lua-5.1))))

(define-public lua5.1-filesystem
  (package
    (name "lua5.1-filesystem")
    (version "1.6.3")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/keplerproject/"
                                  "luafilesystem/archive/v_"
                                  "1_6_3" ".tar.gz"))
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
                "0s10ckxin0bysd6gaywqhxkpw3ybjhprr8m655b8cx3pxjwd49am"))))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags
       (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
       #:test-target "test"
       #:phases
       (modify-phases %standard-phases
         (delete 'configure))))
    (inputs
     `(("lua" ,lua-5.1)))
    (home-page "https://keplerproject.github.io/luafilesystem/index.html")
    (synopsis "File system library for Lua")
    (description "LuaFileSystem is a Lua library developed to complement the
set of functions related to file systems offered by the standard Lua
distribution.  LuaFileSystem offers a portable way to access the underlying
directory structure and file attributes.")
    (license (package-license lua-5.1))))

(define-public lua5.1-sec
  (package
    (name "lua5.1-sec")
    (version "0.6")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/brunoos/luasec/archive/"
                                  "luasec-" version ".tar.gz"))
              (sha256
               (base32
                "0pgd1anzznl4s0h16wg8dlw9mgdb9h52drlcki6sbf5y31fa7wyf"))))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags
       (let ((out (assoc-ref %outputs "out")))
         (list "linux"
               "CC=gcc"
               "LD=gcc"
               (string-append "LUAPATH=" out "/share/lua/5.1")
               (string-append "LUACPATH=" out "/lib/lua/5.1")))
       #:tests? #f ; no tests included
       #:phases
       (modify-phases %standard-phases
         (delete 'configure))))
    (inputs
     `(("lua" ,lua-5.1)
       ("openssl" ,openssl)))
    (propagated-inputs
     `(("lua-socket" ,lua5.1-socket)))
    (home-page "https://github.com/brunoos/luasec/wiki")
    (synopsis "OpenSSL bindings for Lua")
    (description "LuaSec is a binding for OpenSSL library to provide TLS/SSL
communication.  It takes an already established TCP connection and creates a
secure session between the peers.")
    (license (package-license lua-5.1))))

(define-public lua-lgi
  (package
    (name "lua-lgi")
    (version "0.9.2")
    (source
      (origin
        (method url-fetch)
        (uri (string-append
              "https://github.com/pavouk/lgi/archive/"
              version ".tar.gz"))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
          (base32
            "0kwcaj3ahi9gxfyp0lr5zgr6vi1mgsg9sz0980x0nwxlh9a11i6g"))))
    (build-system gnu-build-system)
    (arguments
     '(#:make-flags (list "CC=gcc"
                          (string-append "PREFIX=" (assoc-ref %outputs "out")))
       #:phases
       (modify-phases %standard-phases
         (delete 'configure) ; no configure script
         (add-before 'build 'set-env
           (lambda* (#:key inputs #:allow-other-keys)
             ;; we need to load cairo dynamically
             (let* ((cairo (string-append
                             (assoc-ref inputs "cairo") "/lib" )))
               (setenv "LD_LIBRARY_PATH" cairo)
               #t)))
         (add-before 'build 'set-lua-version
           (lambda _
             ;; lua version and therefore install directories are hardcoded
             ;; FIXME: This breaks when we update lua to >=5.3
             (substitute* "./lgi/Makefile"
               (("LUA_VERSION=5.1") "LUA_VERSION=5.2"))
             #t))
         (add-before 'check 'skip-test-gtk
           (lambda _
             ;; FIXME: Skip GTK tests:
             ;;   gtk3 - can't get it to run with the xorg-server config below
             ;;          and some non-gtk tests will also fail
             ;;   gtk2 - lots of functions aren't implemented
             ;; We choose gtk2 as the lesser evil and simply skip the test.
             ;; Currently, awesome is the only package that uses lua-lgi but
             ;; it doesn't need or interact with GTK using lua-lgi.
             (substitute* "./tests/test.lua"
               (("'gtk.lua',") "-- 'gtk.lua',"))
             #t))
         (add-before 'check 'start-xserver-instance
           (lambda* (#:key inputs #:allow-other-keys)
             ;; There must be a running X server during tests.
             (system (format #f "~a/bin/Xvfb :1 &"
                             (assoc-ref inputs "xorg-server")))
             (setenv "DISPLAY" ":1")
             #t)))))
    (inputs
     `(("gobject-introspection" ,gobject-introspection)
       ("glib" ,glib)
       ("pango" ,pango)
       ("gtk" ,gtk+-2)
       ("lua" ,lua)
       ("cairo" ,cairo)
       ("libffi" ,libffi)
       ("xorg-server" ,xorg-server)))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("dbus" ,dbus)))                          ;tests use 'dbus-run-session'
    (home-page "https://github.com/pavouk/lgi/")
    (synopsis "Lua bridge to GObject based libraries")
    (description
     "LGI is gobject-introspection based dynamic Lua binding to GObject
based libraries.  It allows using GObject-based libraries directly from Lua.
Notable examples are GTK+, GStreamer and Webkit.")
    (license license:expat)))

(define (make-lua-lpeg name lua)
  (package
    (name name)
    (version "1.0.1")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://www.inf.puc-rio.br/~roberto/lpeg/lpeg-"
                                  version ".tar.gz"))
              (sha256
               (base32 "0sq25z3r324a324ky73izgq9mbf66j2xvjp0fxf227rwxalzgnb2"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (delete 'configure)
         ;; `make install` isn't available, so we have to do it manually
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out"))
                   (lua-version ,(version-major+minor (package-version lua))))
               (install-file "lpeg.so"
                             (string-append out "/lib/lua/" lua-version))
               (install-file "re.lua"
                             (string-append out "/share/lua/" lua-version))
               #t))))
       #:test-target "test"))
    (inputs `(("lua" ,lua)))
    (synopsis "Pattern-matching library for Lua")
    (description
     "LPeg is a pattern-matching library for Lua, based on Parsing Expression
Grammars (PEGs).")
    (home-page "http://www.inf.puc-rio.br/~roberto/lpeg")
    (license license:expat)))

(define-public lua-lpeg
  (make-lua-lpeg "lua-lpeg" lua))

(define-public lua5.2-lpeg
  (make-lua-lpeg "lua5.2-lpeg" lua-5.2))

;; Lua 5.3 is not supported.
(define (make-lua-bitop name lua)
  (package
    (name name)
    (version "1.0.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://bitop.luajit.org/download/"
                                  "LuaBitOp-" version ".tar.gz"))
              (sha256
               (base32
                "16fffbrgfcw40kskh2bn9q7m3gajffwd2f35rafynlnd7llwj1qj"))))
    (build-system gnu-build-system)
    (arguments
     `(#:test-target "test"
       #:make-flags
       (list "INSTALL=install -pD"
             (string-append "INSTALLPATH=printf "
                            (assoc-ref %outputs "out")
                            "/lib/lua/"
                            ,(version-major+minor (package-version lua))
                            "/bit/bit.so"))
       #:phases
       (modify-phases %standard-phases
         (delete 'configure))))
    (inputs `(("lua" ,lua)))
    (home-page "https://bitop.luajit.org/index.html")
    (synopsis "Bitwise operations on numbers for Lua")
    (description
     "Lua BitOp is a C extension module for Lua which adds bitwise operations
on numbers.")
    (license license:expat)))

(define-public lua5.2-bitop
  (make-lua-bitop "lua5.2-bitop" lua-5.2))

(define-public lua5.1-bitop
  (make-lua-bitop "lua5.1-bitop" lua-5.1))

(define-public selene
  (package
    (name "selene")
    (version "2017.08.25")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/jeremyong/Selene.git")
                    ;; The release is quite old.
                    (commit "ffe1ade2568d4cff5894552be8f43e63e379a4c9")))
              (file-name "Selene")
              (sha256
               (base32
                "1axrgv3rxxdsaf807lwvklfzicn6x6gpf35narllrnz9lg6hn508"))))
    (build-system cmake-build-system)
    (arguments
     `(#:configure-flags
       ;; lua pc file in CMakeLists.txt is lua5.3.pc
       '("-DLUA_PC_CFG=lua;lua-5.3;lua-5.1")
       #:test-target "all"
       #:phases
       ;; This is a header only library
       (modify-phases %standard-phases
         (delete 'build)
         (replace 'install
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let* ((output (assoc-ref outputs "out"))
                    (source (assoc-ref inputs "source"))
                    (includedir (string-append output "/include")))
               (copy-recursively
                (string-append source "/include")
                includedir))
             #t))
         ;; The path of test files are hard coded.
         (replace 'check
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let* ((output (assoc-ref outputs "out"))
                    (source (assoc-ref inputs "source"))
                    (builddir (getcwd))
                    (testdir  (string-append builddir "/test")))
               (copy-recursively (string-append source "/test") testdir)
               (invoke "make")
               (mkdir-p "runner")
               (copy-file "./test_runner" "./runner/test_runner")
               (chdir "./runner")
               (invoke "./test_runner")))))))
    (native-inputs
     `(("lua" ,lua)
       ("pkg-config" ,pkg-config)))
    (home-page "https://github.com/jeremyong/Selene")
    (synopsis "Lua C++11 bindings")
    (description
     "Selene is a simple C++11 header-only library enabling seamless
 interoperability between C++ and Lua programming language.")
    (license license:zlib)))


code:
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015 Mathieu Lirzin <mthl@openmailbox.org>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2017 Brendan Tildesley <brendan.tildesley@openmailbox.org>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Ison111 <ison111@protonmail.com>
;;; Copyright © 2018 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 lxde)
  #:use-module (gnu packages)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages bash)
  #:use-module (gnu packages docbook)
  #:use-module (gnu packages freedesktop)
  #:use-module (gnu packages gettext)
  #:use-module (gnu packages glib)
  #:use-module (gnu packages gnome)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages image-viewers)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages lsof)
  #:use-module (gnu packages openbox)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages polkit)
  #:use-module (gnu packages text-editors)
  #:use-module (gnu packages video)
  #:use-module (gnu packages wm)
  #:use-module (gnu packages xml)
  #:use-module (gnu packages xorg)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system trivial)
  #:use-module (guix download)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix utils))

(define-public libfm
  (package
    (name "libfm")
    (version "1.3.0.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/pcmanfm/"
                                  "PCManFM%20%2B%20Libfm%20%28tarball%20release"
                                  "%29/LibFM/" name "-" version ".tar.xz"))
              (sha256
               (base32
                "0wkwbi1nyvqza3r1dhrq846axiiq0fy0dqgngnagh76fjrwnzl0q"))))
    (build-system gnu-build-system)
    (inputs `(("glib" ,glib)
              ("gtk+" ,gtk+-2)))
    (native-inputs `(("intltool"   ,intltool)
                     ("glib"       ,glib "bin") ; for gtester
                     ("libtool"    ,libtool)
                     ("menu-cache" ,menu-cache)
                     ("pkg-config" ,pkg-config)
                     ("vala"       ,vala)))
    (synopsis "File management support (core library)")
    (description "LibFM provides file management functions built on top of
Glib/GIO giving a higher-level API.")
    (home-page "https://lxde.org")
    (license license:gpl2+)))

(define-public libfm-extra
  (package (inherit libfm)
    (name "libfm-extra")
    (arguments '(#:configure-flags '("--with-extra-only")))
    (inputs `(("glib" ,glib)))
    (native-inputs `(("intltool"   ,intltool)
                     ("libtool"    ,libtool)
                     ("pkg-config" ,pkg-config)))
    (synopsis "File management support (extra library)")
    (description "This package contains standalone library which extends the
libFM file management library.")))

(define-public lxappearance
  (package
    (name "lxappearance")
    (version "0.6.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/lxde/"
                                  "LXAppearance/" name "-" version ".tar.xz"))
              (sha256
               (base32
                "07r0xbi6504zjnbpan7zrn7gi4j0kbsqqfpj8v2x94gr05p16qj4"))))
    (build-system gnu-build-system)
    (inputs `(("gtk+" ,gtk+-2)))
    (native-inputs `(("intltool"   ,intltool)
                     ("pkg-config" ,pkg-config)))
    (synopsis "LXDE GTK+ theme switcher")
    (description "LXAppearance is a desktop-independent GTK+ theme switcher
able to change themes, icons, and fonts used by GTK+ applications.")
    (home-page "https://lxde.org")
    (license license:gpl2+)))

(define-public lxrandr
  (package
    (name "lxrandr")
    (version "0.3.1")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/lxde/LXRandR"
                                  "%20%28monitor%20config%20tool%29/LXRandR%20"
                                  (version-major+minor version) ".x/"
                                  name "-" version ".tar.xz"))
              (sha256
               (base32
                "0khqi42paqg82jllb2kza4arf3fafzgq90fhyr3rw3d9hn23763d"))))
    (build-system gnu-build-system)
    (inputs `(("gtk+" ,gtk+-2)))
    (native-inputs `(("intltool"   ,intltool)
                     ("pkg-config" ,pkg-config)))
    (synopsis "LXDE monitor configuration tool")
    (description "LXRandR is a very basic monitor configuration tool.  It
relies on the X11 resize-and-rotate (RandR) extension but doesn't aim to be a
full frontend of it.  LXRandR only gives you some easy and quick options which
are intuitive.  It's suitable for laptop users who frequently uses projectors
or external monitor.")
    (home-page "https://lxde.org")
    (license license:gpl2+)))

(define-public lxtask
  (package
    (name "lxtask")
    (version "0.1.7")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/lxde/LXTask"
                                  "%20%28task%20manager%29/LXTask%20"
                                  (version-major+minor version) ".x/"
                                  name "-" version ".tar.xz"))
              (sha256
               (base32
                "1zihhvzsg9bl6k0gv7jwx6cgsi3rmcagvnmshc1h0mjq2immmdph"))))
    (build-system gnu-build-system)
    (inputs `(("gtk+" ,gtk+-2)))
    (native-inputs `(("intltool"   ,intltool)
                     ("pkg-config" ,pkg-config)))
    (synopsis "LXDE task manager")
    (description "LXTask is a lightweight task manager derived from Xfce task
manager with all dependencies on Xfce removed.  LXTask is based on the GTK+
toolkit.  It allows users to monitor and control of running processes.")
    (home-page "https://lxde.org")
    (license license:gpl2+)))

(define-public lxterminal
  (package
    (name "lxterminal")
    (version "0.3.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/lxde/LXTerminal"
                                  "%20%28terminal%20emulator%29/LXTerminal%20"
                                  version "/" name "-" version ".tar.xz"))
              (sha256
               (base32
                "1124pghrhnx6q4391ri8nvi6bsmvbj1dx81an08mird8jf2b2rii"))))
    (build-system gnu-build-system)
    (inputs `(("gtk+" ,gtk+-2)
              ("vte"  ,vte/gtk+-2)))
    (native-inputs `(("intltool"   ,intltool)
                     ("pkg-config" ,pkg-config)))
    (synopsis "LXDE terminal emulator")
    (description "LXTerminal is a VTE-based terminal emulator.  It supports
multiple tabs and has only minimal dependencies thus being completely
desktop-independent.  In order to reduce memory usage and increase the
performance, all instances of the terminal are sharing a single process.")
    (home-page "https://lxde.org")
    (license license:gpl2+)))

(define-public menu-cache
  (package
    (name "menu-cache")
    (version "1.0.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/lxde/" name "/"
                                  (version-major+minor version) "/"
                                  name "-" version ".tar.xz"))
              (sha256
               (base32
                "1m8j40npykfcfqs43kc0fmksal2jfmfi8lnb3mq3xy1lvvrfv0vg"))))
    (build-system gnu-build-system)
    (inputs `(("glib"  ,glib)
              ("libfm" ,libfm-extra)))
    (native-inputs `(("pkg-config" ,pkg-config)))
    (synopsis "LXDE implementation of the freedesktop menu's cache")
    (description "Menu-cache is a library creating and utilizing caches to
speed up the access to freedesktop.org defined application menus.")
    (home-page "https://lxde.org")
    (license license:lgpl2.1+)))

(define-public pcmanfm
  (package
    (name "pcmanfm")
    (version "1.3.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/" name "/"
                                  "PCManFM%20%2B%20Libfm%20%28tarball%20release"
                                  "%29/PCManFM/" name "-" version ".tar.xz"))
              (sha256
               (base32
                "1ywgfyklms5hqkapsbjps4kyx20ac0d1qk16ww74yagkyfdkwsas"))))
    (build-system gnu-build-system)
    (inputs `(("gtk+"   ,gtk+-2)
              ("gvfs"   ,gvfs)          ; for trash and mount support
              ("libfm"  ,libfm)
              ("libx11" ,libx11)))
    (native-inputs `(("intltool"   ,intltool)
                     ("libtool"    ,libtool)
                     ("pkg-config" ,pkg-config)))
    (propagated-inputs
     `(("lxmenu-data" ,lxmenu-data)))   ; for "Open With..." application list
    (synopsis "LXDE file manager")
    (description "PCMan is a lightweight GTK+ based file manager, compliant
with freedesktop.org standard.")
    (home-page "https://lxde.org")
    (license license:gpl2+)))

(define-public spacefm
  ;; SpaceFM is based on PCManFM.
  (package
    (name "spacefm")
    (version "1.0.6")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/IgnorantGuru/spacefm/archive/"
                    version ".tar.gz"))
              (sha256
                (base32
                  "1jg7xfyr7kihjnalxp8wxyb9qjk8hqf5l36rp3s0lvkpmpyakppy"))
              (file-name (string-append name "-" version ".tar.gz"))))
    (build-system gnu-build-system)
    (native-inputs `(("pkg-config" ,pkg-config)
                     ("intltool" ,intltool)))
    (inputs `(("bash" ,bash)
              ("gtk+" ,gtk+)
              ("eudev" ,eudev)
              ("desktop-file-utils" ,desktop-file-utils)
              ("shared-mime-info" ,shared-mime-info)
              ("ffmpegthumbnailer" ,ffmpegthumbnailer)
              ("jmtpfs" ,jmtpfs)
              ("lsof" ,lsof)
              ("udisks" ,udisks)))
    (arguments
     `(#:configure-flags (list (string-append "--with-bash-path="
                                              (assoc-ref %build-inputs "bash")
                                              "/bin/bash")
                               (string-append "--sysconfdir="
                                              (assoc-ref %outputs "out")
                                              "/etc"))))
    (home-page "http://ignorantguru.github.io/spacefm/")
    (synopsis "Multi-panel tabbed file manager")
    (description "SpaceFM is a graphical, multi-panel, tabbed file manager
based on PCManFM with built-in virtual file system, udev-based device manager,
customizable menu system, and Bash integration.")

    ;; The combination is GPLv3+ but src/exo is under LGPLv3+.
    (license license:gpl3+)))

(define-public lxmenu-data
  (package
    (name "lxmenu-data")
    (version "0.1.5")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://downloads.sourceforge.net/lxde/"
                           name "-" version ".tar.xz"))
       (sha256
        (base32
         "1f5sh2dvb3pdnjlcsyzq9543ck2jsqizkx3204cr22zm5s6j3qwz"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("intltool" ,intltool)))
    (synopsis "Freedesktop.org desktop menus for LXDE")
    (description
     "Lxmenu-data provides files required to build freedesktop.org
menu spec-compliant desktop menus for LXDE.")
    (home-page "https://lxde.org")
    (license license:lgpl2.1+)))

(define-public lxde-icon-theme
  (package
    (name "lxde-icon-theme")
    (version "0.5.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://downloads.sourceforge.net/lxde/"
                           name "-" version ".tar.xz"))
       (sha256
        (base32
         "0v4i6x86fr2hbx4fb2si7y2qzmj7h6hcjwaifnin18r8kwwvgl73"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("pkg-config" ,pkg-config)))
    (synopsis "LXDE default icon theme based on nuoveXT2")
    (description
     "Lxde-icon-theme provides an default icon theme for LXDE.")
    (home-page "https://lxde.org")
    (license license:lgpl3)))

(define-public lxde-common
  (package
    (name "lxde-common")
    (version "0.99.2")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://downloads.sourceforge.net/lxde/"
                           name "-" version ".tar.xz"))
       (sha256
        (base32
         "0mj84fa3f4ak1jjslrwc2q3ci9zxrxpciggviza9bjb0168brn8w"))))
    (build-system gnu-build-system)
    (arguments
     '(#:phases (modify-phases %standard-phases
                  (add-before 'configure 'set-lxsession
                    (lambda* (#:key inputs #:allow-other-keys)
                      ;; Set the right file name for 'lxsession'.
                      (let ((lxsession (assoc-ref inputs "lxsession")))
                        (substitute* "startlxde.in"
                          (("^exec .*/bin/lxsession")
                           (string-append "exec " lxsession
                                          "/bin/lxsession")))
                        #t))))))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("intltool" ,intltool)
       ("lxmenu-data" ,lxmenu-data)
       ("lxde-icon-theme" ,lxde-icon-theme)))
    (inputs
     `(("lxsession" ,lxsession)
       ;; ("lxlock" ,lxlock) ;for 'lxde-screenlock.desktop'
       ))
    (synopsis "Common files of the LXDE Desktop")
    (description
     "Lxde-common provides common files of the LXDE Desktop.")
    (home-page "https://lxde.org")
    (license license:gpl2+)))

(define-public lxinput
  (package
    (name "lxinput")
    (version "0.3.5")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://downloads.sourceforge.net/lxde/"
                           name "-" version ".tar.xz"))
       (sha256
        (base32
         "123f3yn4rp1w5b3n5aj3ad9snkxab29qkrs7bcvf5bx4cn57g3sf"))))
    (build-system gnu-build-system)
    (inputs
     `(("gtk+-2" ,gtk+-2)))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("intltool" ,intltool)))
    (synopsis "Tool for mouse and keyboard configuration in LXDE")
    (description
     "Lxinput provides a small program to configure keyboard and mouse
in LXDE.")
    (home-page "https://lxde.org")
    (license license:gpl2+)))

(define-public lxsession
  (package
    (name "lxsession")
    (version "0.5.3")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://downloads.sourceforge.net/lxde/"
                           name "-" version ".tar.xz"))
       (patches (search-patches "lxsession-use-gapplication.patch"))
       (sha256
        (base32
         "1a0zmyywwzdh59nc0l94cir18vhp633z4q2xfhn5zx11ajj45gwh"))
       (modules '((guix build utils)))
       (snippet
        ;; Remove C files generated by Vala so we can build from source.
        '(let* ((c->vala
                 (lambda (file)
                   (string-append (string-drop-right file 2)
                                  ".vala")))
                (generated-c-file?
                 (lambda (file stat)
                   (and (string-suffix? ".c" file)
                        (file-exists? (c->vala file))))))
           (for-each delete-file
                     (find-files "." generated-c-file?))
           #t))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'rm-stamp
           (lambda _
             (for-each delete-file (find-files "." "\\.stamp$"))))
         (add-after 'rm-stamp 'autoreconf
           (lambda _
             (zero? (system* "autoreconf" "-vfi")))))))
    (inputs
     `(("gtk+-2" ,gtk+-2)
       ("polkit" ,polkit)))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("intltool" ,intltool)
       ("docbook-xsl" ,docbook-xsl)
       ("vala" ,vala)
       ("autoconf" ,autoconf)
       ("automake" ,automake)))
    (synopsis "Lightweight X11 session manager")
    (description
     "Lxsession provides an lightweight X11 session manager.")
    (home-page "https://lxde.org")
    (license license:gpl2+)))

(define-public lxpanel
  (package
    (name "lxpanel")
    (version "0.9.3")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://downloads.sourceforge.net/lxde/"
                           name "-" version ".tar.xz"))
       (sha256
        (base32
         "1ccgv7jgl3y865cpb6w7baaz7468fxncm83bqxlwyni5bwhglb1l"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'install 'wrap
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out"))
                   (menu (assoc-ref inputs "lxmenu-data")))
               (wrap-program (string-append out "/bin/lxpanel")
                 `("XDG_DATA_DIRS" ":" prefix
                   (,(string-append menu "/share"))))
               #t))))))
    (inputs
     ;; TODO: libindicator-0.3.0
     `(("gtk+-2" ,gtk+-2)
       ("alsa-lib" ,alsa-lib)
       ("libwnck-2" ,libwnck-2)
       ("keybinder" ,keybinder)
       ("libxmu" ,libxmu)
       ("libxpm" ,libxpm)
       ("libxml2" ,libxml2)
       ("cairo" ,cairo)
       ("libx11" ,libx11)
       ("wireless-tools" ,wireless-tools)))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("intltool" ,intltool)
       ("docbook-xml" ,docbook-xml)
       ("gettext-minimal" ,gettext-minimal)))
    (propagated-inputs
     `(("lxmenu-data" ,lxmenu-data)
       ("libfm" ,libfm)
       ("menu-cache" ,menu-cache)))
    (synopsis "X11 Desktop panel for LXDE")
    (description
     "Lxpanel provides an X11 desktop panel for LXDE.")
    (home-page "https://lxde.org")
    (license license:gpl2+)))

(define-public lxde
  (package
    (name "lxde")
    (version (package-version lxde-common))
    (source #f)
    (build-system trivial-build-system)
    (arguments '(#:builder (begin (mkdir %output) #t)))
    (propagated-inputs
     ;; TODO:
     ;; lxshortcut, lxsession-edit
     ;; lxappearance-obconf
     `(("menu-cache" ,menu-cache)
       ("gpicview" ,gpicview)
       ("leafpad" ,leafpad)
       ("lxappearance" ,lxappearance)
       ("lxde-icon-theme" ,lxde-icon-theme)
       ("lxde-common" ,lxde-common)
       ("lxmenu-data" ,lxmenu-data)
       ("lxpanel" ,lxpanel)
       ("lxrandr" ,lxrandr)
       ("lxsession" ,lxsession)
       ("libfm" ,libfm)
       ("libfm-extra" ,libfm-extra)
       ("lxtask" ,lxtask)
       ("lxterminal" ,lxterminal)
       ("pcmanfm" ,pcmanfm)
       ("openbox" ,openbox)
       ("obconf" ,obconf)))
    (synopsis "Lightweight X11 Desktop Environment")
    (description
     "LXDE, which stands for Lightweight X11 Desktop Environment, is a
desktop environment which is lightweight and fast.  It is designed to be
user friendly and slim, while keeping the resource usage low.  LXDE uses
less RAM and less CPU while being a feature rich desktop environment.  Unlike
other tightly integrated desktops LXDE strives to be modular, so each
component can be used independently with few dependencies.")
    (home-page "https://lxde.org")
    (license license:gpl2+))) ; And others.

;;; lxde.scm ends here


code:
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
;;; Copyright © 2016 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
;;; Copyright © 2018 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 lxqt)
  #:use-module (guix download)
  #:use-module ((guix licenses) #:select (lgpl2.1+))
  #:use-module (guix packages)
  #:use-module (guix utils)
  #:use-module (guix build-system cmake)
  #:use-module (gnu packages)
  #:use-module (gnu packages glib)
  #:use-module (gnu packages kde-frameworks)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages qt))

(define-public libqtxdg
  (package
    (name "libqtxdg")
    (version "1.2.0")
    (source
     (origin
       (method url-fetch)
       (uri
         (string-append "https://github.com/lxde/libqtxdg/releases/"
                        "download/" version "/" name "-" version ".tar.xz"))
       (sha256
        (base32
         "1ncqs0lcll5nx69hxfg33m3jfkryjqrjhr2kdci0b8pyaqdv1jc8"))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #f ; test fails with message "Exception"
       #:configure-flags '("-DBUILD_TESTS=ON")))
    (native-inputs
     `(("pkg-config" ,pkg-config)))
    (propagated-inputs
     `(("qtbase" ,qtbase))) ; according to Qt5Xdg.pc
    (home-page "https://github.com/lxde/libqtxdg")
    (synopsis "Qt implementation of freedesktop.org xdg specifications")
    (description "Libqtxdg implements the freedesktop.org xdg specifications
in Qt.")
    (license lgpl2.1+)))

(define-public liblxqt
  (package
    (name "liblxqt")
    (version "0.9.0")
    (source
     (origin
       (method url-fetch)
       (uri
         (string-append "https://github.com/lxde/" name
                        "/archive/" version ".tar.gz"))
       (file-name (string-append name "-" version ".tar.gz"))
       (sha256
        (base32
         "0mbl3qc0yfgfsndqrw8vg8k5irsy0pg2wrad8nwv0aphphd4n7rg"))
       (patches (search-patches "liblxqt-include.patch"))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #f))
    (native-inputs `(("pkg-config" ,pkg-config)))
    (inputs
     `(("kwindowsystem" ,kwindowsystem)
       ("libqtxdg" ,libqtxdg)
       ("qtbase" ,qtbase)
       ("qttools" ,qttools)
       ("qtx11extras" ,qtx11extras)))
    (home-page "http://lxqt.org/")
    (synopsis "Core utility library for all LXQt components")
    (description "liblxqt provides the basic libraries shared by the
components of the LXQt desktop environment.")
    (license lgpl2.1+)))

(define-public lxqt-session
  (package
    (name "lxqt-session")
    (version "0.9.0")
    (source
     (origin
       (method url-fetch)
       (uri
         (string-append "https://github.com/lxde/" name
                        "/archive/" version ".tar.gz"))
       (file-name (string-append name "-" version ".tar.gz"))
       (sha256
        (base32
         "1sdwcfrfqkg7ibrsncs1skdap9n8wm4rg6n9d0fgdz2q4d45h75a"))))
    (build-system cmake-build-system)
    (native-inputs `(("pkg-config" ,pkg-config)))
    (inputs
     `(("kwindowsystem" ,kwindowsystem)
       ("liblxqt" ,liblxqt)
       ("libqtxdg" ,libqtxdg)
       ("qtbase" ,qtbase)
       ("qttools" ,qttools)
       ("qtx11extras" ,qtx11extras)))
    (arguments
     `(#:tests? #f ; no check target
       #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'fix-installation-paths
           (lambda _
             ;; The variable LXQT_TRANSLATIONS_DIR is set in
             ;; liblxqt-0.9.0/share/cmake/lxqt/lxqt-config.cmake
             ;; to the liblxqt installation directory, followed by
             ;; "/share/lxqt/translations".
             ;; We need to have it point to the current installation
             ;; directory instead.
             (substitute* '("lxqt-session/CMakeLists.txt"
                            "lxqt-config-session/CMakeLists.txt")
               (("\\$\\{LXQT_TRANSLATIONS_DIR\\}")
                "${CMAKE_INSTALL_PREFIX}/share/lxqt/translations")))))))
    (home-page "http://lxqt.org/")
    (synopsis "Session manager for LXQt")
    (description "lxqt-session provides the standard session manager
for the LXQt desktop environment.")
    (license lgpl2.1+)))

(define-public lxqt-build-tools
  (package
    (name "lxqt-build-tools")
    (version "0.5.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://github.com/lxde/lxqt-build-tools/releases/"
                           "download/" version "/" name "-" version ".tar.xz"))
       (file-name (string-append name "-" version ".tar.xz"))
       (sha256
        (base32
         "13b5x26p6ycnwzlgg1cgvlc88wjrjmlb3snrrmzh0xgh9h6hhvd6"))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #f))                    ; no tests
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("glib" ,glib)))
    (inputs
     `(("qtbase" ,qtbase)))
    (synopsis "LXQt Build tools")
    (description
     "Lxqt-build-tools is providing several tools needed to build LXQt
itself as well as other components maintained by the LXQt project.")
    (home-page "http://lxqt.org")
    (license lgpl2.1+)))


code:
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012, 2013, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2018 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 m4)
  #:use-module (guix licenses)
  #:use-module (gnu packages)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix build-system gnu))

(define-public m4
  (package
   (name "m4")
   (version "1.4.18")
   (source (origin
            (method url-fetch)
            (uri (string-append "mirror://gnu/m4/m4-"
                                version ".tar.xz"))
            (sha256
             (base32
              "01sfjd5a4waqw83bibvmn522g69qfqvwig9i2qlgy154l1nfihgj"))))
   (build-system gnu-build-system)
   (arguments
    `(;; Explicitly disable tests when cross-compiling, otherwise 'make check'
      ;; proceeds and fails, unsurprisingly.
      #:tests? ,(not (%current-target-system))

      #:phases
      (modify-phases %standard-phases
        (add-before 'check 'pre-check
          (lambda* (#:key inputs #:allow-other-keys)
            ;; Fix references to /bin/sh.
            (let ((bash (assoc-ref inputs "bash")))
              (for-each patch-shebang
                        (find-files "tests" "\\.sh$"))
              (substitute* (find-files "tests"
                                       "posix_spawn")
                (("/bin/sh")
                 (format #f "~a/bin/sh" bash)))
              #t))))))
   (synopsis "Macro processor")
   (description
    "GNU M4 is an implementation of the M4 macro language, which features
some extensions over other implementations, some of which are required by GNU
Autoconf.  It is used as a macro processor, which means it processes text,
expanding macros as it encounters them.  It also has some built-in functions,
for example to run shell commands or to do arithmetic.")
   (license gpl3+)
   (home-page "https://www.gnu.org/software/m4/")))


code:
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
;;; Copyright © 2018 Mark Meyer <mark@ofosos.org>
;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.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 machine-learning)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix utils)
  #:use-module (guix download)
  #:use-module (guix svn-download)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system ocaml)
  #:use-module (guix build-system python)
  #:use-module (guix build-system r)
  #:use-module (guix git-download)
  #:use-module (gnu packages)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages cran)
  #:use-module (gnu packages dejagnu)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages image)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages ocaml)
  #:use-module (gnu packages onc-rpc)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
  #:use-module (gnu packages statistics)
  #:use-module (gnu packages swig)
  #:use-module (gnu packages xml)
  #:use-module (gnu packages xorg))

(define-public fann
  ;; The last release is >100 commits behind, so we package from git.
  (let ((commit "d71d54788bee56ba4cf7522801270152da5209d7"))
    (package
      (name "fann")
      (version (string-append "2.2.0-1." (string-take commit 8)))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/libfann/fann.git")
                      (commit commit)))
                (file-name (string-append name "-" version "-checkout"))
                (sha256
                 (base32
                  "0ibwpfrjs6q2lijs8slxjgzb2llcl6rk3v2ski4r6215g5jjhg3x"))))
      (build-system cmake-build-system)
      (arguments
       `(#:phases
         (modify-phases %standard-phases
           (replace 'check
             (lambda* (#:key outputs #:allow-other-keys)
               (let* ((out (assoc-ref outputs "out")))
                 (with-directory-excursion (string-append (getcwd) "/tests")
                   (invoke "./fann_tests"))))))))
      (home-page "http://leenissen.dk/fann/wp/")
      (synopsis "Fast Artificial Neural Network")
      (description
       "FANN is a free open source neural network library, which implements
multilayer artificial neural networks in C with support for both fully
connected and sparsely connected networks.")
      (license license:lgpl2.1))))

(define-public libsvm
  (package
    (name "libsvm")
    (version "3.22")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://www.csie.ntu.edu.tw/~cjlin/libsvm/"
                           name "-" version ".tar.gz"))
       (sha256
        (base32
         "0zd7s19y5vb7agczl6456bn45cj1y64739sslaskw1qk7dywd0bd"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ;no "check" target
       #:phases (modify-phases %standard-phases
                  (delete 'configure)
                  (replace
                   'install             ; no ‘install’ target
                   (lambda* (#:key outputs #:allow-other-keys)
                     (let* ((out (assoc-ref outputs "out"))
                            (bin (string-append out "/bin/")))
                       (mkdir-p bin)
                       (for-each (lambda (file)
                                   (copy-file file (string-append bin file)))
                                 '("svm-train"
                                   "svm-predict"
                                   "svm-scale")))
                     #t)))))
    (home-page "http://www.csie.ntu.edu.tw/~cjlin/libsvm/")
    (synopsis "Library for Support Vector Machines")
    (description
     "LIBSVM is a machine learning library for support vector
classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
distribution estimation (one-class SVM).  It supports multi-class
classification.")
    (license license:bsd-3)))

(define-public python-libsvm
  (package (inherit libsvm)
    (name "python-libsvm")
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ;no "check" target
       #:make-flags '("-C" "python")
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (replace
          'install                      ; no ‘install’ target
          (lambda* (#:key inputs outputs #:allow-other-keys)
            (let ((site (string-append (assoc-ref outputs "out")
                                       "/lib/python"
                                       (string-take
                                        (string-take-right
                                         (assoc-ref inputs "python") 5) 3)
                                       "/site-packages/")))
              (substitute* "python/svm.py"
                (("../libsvm.so.2") "libsvm.so.2"))
              (mkdir-p site)
              (for-each (lambda (file)
                          (copy-file file (string-append site (basename file))))
                        (find-files "python" "\\.py"))
              (copy-file "libsvm.so.2"
                         (string-append site "libsvm.so.2")))
            #t)))))
    (inputs
     `(("python" ,python)))
    (synopsis "Python bindings of libSVM")))

(define-public ghmm
  ;; The latest release candidate is several years and a couple of fixes have
  ;; been published since.  This is why we download the sources from the SVN
  ;; repository.
  (let ((svn-revision 2341))
    (package
      (name "ghmm")
      (version (string-append "0.9-rc3-0." (number->string svn-revision)))
      (source (origin
                (method svn-fetch)
                (uri (svn-reference
                      (url "http://svn.code.sf.net/p/ghmm/code/trunk")
                      (revision svn-revision)))
                (file-name (string-append name "-" version))
                (sha256
                 (base32
                  "0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
      (build-system gnu-build-system)
      (arguments
       `(#:imported-modules (,@%gnu-build-system-modules
                             (guix build python-build-system))
         #:phases
         (modify-phases %standard-phases
           (add-after 'unpack 'enter-dir
             (lambda _ (chdir "ghmm") #t))
           (delete 'check)
           (add-after 'install 'check
             (assoc-ref %standard-phases 'check))
           (add-before 'check 'fix-PYTHONPATH
             (lambda* (#:key inputs outputs #:allow-other-keys)
               (let ((python-version ((@@ (guix build python-build-system)
                                           get-python-version)
                                      (assoc-ref inputs "python"))))
                 (setenv "PYTHONPATH"
                         (string-append (getenv "PYTHONPATH")
                                        ":" (assoc-ref outputs "out")
                                        "/lib/python" python-version
                                        "/site-packages")))
               #t))
           (add-after 'enter-dir 'fix-runpath
             (lambda* (#:key outputs #:allow-other-keys)
               (substitute* "ghmmwrapper/setup.py"
                 (("^(.*)extra_compile_args = \\[" line indent)
                  (string-append indent
                                 "extra_link_args = [\"-Wl,-rpath="
                                 (assoc-ref outputs "out") "/lib\"],\n"
                                 line
                                 "\"-Wl,-rpath="
                                 (assoc-ref outputs "out")
                                 "/lib\", ")))
               #t))
           (add-after 'enter-dir 'disable-broken-tests
             (lambda _
               (substitute* "tests/Makefile.am"
                 ;; GHMM_SILENT_TESTS is assumed to be a command.
                 (("TESTS_ENVIRONMENT.*") "")
                 ;; Do not build broken tests.
                 (("chmm .*") "")
                 (("read_fa .*") "")
                 (("mcmc .*") "")
                 (("label_higher_order_test.*$")
                  "label_higher_order_test\n"))

               ;; These Python unittests are broken as there is no gato.
               ;; See https://sourceforge.net/p/ghmm/support-requests/3/
               (substitute* "ghmmwrapper/ghmmunittests.py"
                 (("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
                   line indent)
                  (string-append indent
                                 "@unittest.skip(\"Disabled by Guix\")\n"
                                 line)))
               #t))
           (add-after 'disable-broken-tests 'autogen
             (lambda _
               (invoke "bash" "autogen.sh"))))))
      (inputs
       `(("python" ,python-2) ; only Python 2 is supported
         ("libxml2" ,libxml2)))
      (native-inputs
       `(("pkg-config" ,pkg-config)
         ("dejagnu" ,dejagnu)
         ("swig" ,swig)
         ("autoconf" ,autoconf)
         ("automake" ,automake)
         ("libtool" ,libtool)))
      (home-page "http://ghmm.org")
      (synopsis "Hidden Markov Model library")
      (description
       "The General Hidden Markov Model library (GHMM) is a C library with
additional Python bindings implementing a wide range of types of @dfn{Hidden
Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
training, HMM clustering, HMM mixtures.")
      (license license:lgpl2.0+))))

(define-public mcl
  (package
    (name "mcl")
    (version "14.137")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "http://micans.org/mcl/src/mcl-"
                    (string-replace-substring version "." "-")
                    ".tar.gz"))
              (sha256
               (base32
                "15xlax3z31lsn62vlg94hkm75nm40q4679amnfg13jm8m2bnhy5m"))))
    (build-system gnu-build-system)
    (arguments
     `(#:configure-flags (list "--enable-blast")))
    (inputs
     `(("perl" ,perl)))
    (home-page "http://micans.org/mcl/")
    (synopsis "Clustering algorithm for graphs")
    (description
     "The MCL algorithm is short for the @dfn{Markov Cluster Algorithm}, a
fast and scalable unsupervised cluster algorithm for graphs (also known as
networks) based on simulation of (stochastic) flow in graphs.")
    ;; In the LICENCE file and web page it says "The software is licensed
    ;; under the GNU General Public License, version 3.", but in several of
    ;; the source code files it suggests GPL3 or later.
    ;; http://listserver.ebi.ac.uk/pipermail/mcl-users/2016/000376.html
    (license license:gpl3)))

(define-public ocaml-mcl
  (package
    (name "ocaml-mcl")
    (version "12-068oasis4")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://github.com/fhcrc/mcl/archive/"
             version ".tar.gz"))
       (file-name (string-append name "-" version ".tar.gz"))
       (sha256
        (base32
         "1l5jbhwjpsj38x8b9698hfpkv75h8hn3kj0gihjhn8ym2cwwv110"))))
    (build-system ocaml-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-before 'configure 'patch-paths
           (lambda _
             (substitute* "configure"
               (("SHELL = /bin/sh") (string-append "SHELL = "(which "sh"))))
             (substitute* "setup.ml"
               (("LDFLAGS=-fPIC")
                (string-append "LDFLAGS=-fPIC\"; \"SHELL=" (which "sh"))))
             #t)))))
    (home-page "https://github.com/fhcrc/mcl")
    (synopsis "OCaml wrappers around MCL")
    (description
     "This package provides OCaml bindings for the MCL graph clustering
algorithm.")
    (license license:gpl3)))

(define-public ocaml4.01-mcl
  (package-with-ocaml4.01 ocaml-mcl))

(define-public randomjungle
  (package
    (name "randomjungle")
    (version "2.1.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "http://www.imbs-luebeck.de/imbs/sites/default/files/u59/"
             "randomjungle-" version ".tar_.gz"))
       (sha256
        (base32
         "12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w"))))
    (build-system gnu-build-system)
    (arguments
     `(#:configure-flags
       (list (string-append "--with-boost="
                            (assoc-ref %build-inputs "boost")))
       #:phases
       (modify-phases %standard-phases
         (add-before
          'configure 'set-CXXFLAGS
          (lambda _
            (setenv "CXXFLAGS" "-fpermissive ")
            #t)))))
    (inputs
     `(("boost" ,boost)
       ("gsl" ,gsl)
       ("libxml2" ,libxml2)
       ("zlib" ,zlib)))
    (native-inputs
     `(("gfortran" ,gfortran)
       ("gfortran:lib" ,gfortran "lib")))
    ;; Non-portable assembly instructions are used so building fails on
    ;; platforms other than x86_64 or i686.
    (supported-systems '("x86_64-linux" "i686-linux"))
    (home-page "http://www.imbs-luebeck.de/imbs/de/node/227/")
    (synopsis "Implementation of the Random Forests machine learning method")
    (description
     "Random Jungle is an implementation of Random Forests.  It is supposed to
analyse high dimensional data.  In genetics, it can be used for analysing big
Genome Wide Association (GWA) data.  Random Forests is a powerful machine
learning method.  Most interesting features are variable selection, missing
value imputation, classifier creation, generalization error estimation and
sample proximities between pairs of cases.")
    (license license:gpl3+)))

(define-public shogun
  (package
    (name "shogun")
    (version "6.1.3")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "ftp://shogun-toolbox.org/shogun/releases/"
             (version-major+minor version)
             "/sources/shogun-" version ".tar.bz2"))
       (sha256
        (base32
         "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp"))
       (modules '((guix build utils)
                  (ice-9 rdelim)))
       (snippet
        '(begin
           ;; Remove non-free sources and files referencing them
           (for-each delete-file
                     (find-files "src/shogun/classifier/svm/"
                                 "SVMLight\\.(cpp|h)"))
           (for-each delete-file
                     (find-files "examples/undocumented/libshogun/"
                                 (string-append
                                  "(classifier_.*svmlight.*|"
                                  "evaluation_cross_validation_locked_comparison).cpp")))
           ;; Remove non-free functions.
           (define (delete-ifdefs file)
             (with-atomic-file-replacement file
               (lambda (in out)
                 (let loop ((line (read-line in 'concat))
                            (skipping? #f))
                   (if (eof-object? line)
                       #t
                       (let ((skip-next?
                              (or (and skipping?
                                       (not (string-prefix?
                                             "#endif //USE_SVMLIGHT" line)))
                                  (string-prefix?
                                   "#ifdef USE_SVMLIGHT" line))))
                         (when (or (not skipping?)
                                   (and skipping? (not skip-next?)))
                           (display line out))
                         (loop (read-line in 'concat) skip-next?)))))))
           (for-each delete-ifdefs
                     (append
                      (find-files "src/shogun/classifier/mkl"
                                  "^MKLClassification\\.cpp")
                      (find-files "src/shogun/classifier/svm"
                                  "^SVMLightOneClass\\.(cpp|h)")
                      (find-files "src/shogun/multiclass"
                                  "^ScatterSVM\\.(cpp|h)")
                      (find-files "src/shogun/kernel/"
                                  "^(Kernel|CombinedKernel|ProductKernel)\\.(cpp|h)")
                      (find-files "src/shogun/regression/svr"
                                  "^(MKLRegression|SVRLight)\\.(cpp|h)")
                      (find-files "src/shogun/transfer/domain_adaptation"
                                  "^DomainAdaptationSVM\\.(cpp|h)")))
           #t))))
    (build-system cmake-build-system)
    (arguments
     '(#:tests? #f ;no check target
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'delete-broken-symlinks
           (lambda _
             (for-each delete-file '("applications/arts/data"
                                     "applications/asp/data"
                                     "applications/easysvm/data"
                                     "applications/msplicer/data"
                                     "applications/ocr/data"
                                     "examples/meta/data"
                                     "examples/undocumented/data"))
             #t))
         (add-after 'unpack 'change-R-target-path
           (lambda* (#:key outputs #:allow-other-keys)
             (substitute* '("src/interfaces/r/CMakeLists.txt"
                            "examples/meta/r/CMakeLists.txt")
               (("\\$\\{R_COMPONENT_LIB_PATH\\}")
                (string-append (assoc-ref outputs "out")
                               "/lib/R/library/")))
             #t))
         (add-after 'unpack 'fix-octave-modules
           (lambda* (#:key outputs #:allow-other-keys)
             (substitute* "src/interfaces/octave/CMakeLists.txt"
               (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
                "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")
               ;; change target directory
               (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
                (string-append (assoc-ref outputs "out")
                               "/share/octave/packages")))
             (substitute* '("src/interfaces/octave/swig_typemaps.i"
                            "src/interfaces/octave/sg_print_functions.cpp")
               ;; "octave/config.h" and "octave/oct-obj.h" deprecated in Octave.
               (("octave/config\\.h") "octave/octave-config.h")
               (("octave/oct-obj.h") "octave/ovl.h"))
             #t))
         (add-after 'unpack 'move-rxcpp
           (lambda* (#:key inputs #:allow-other-keys)
             (let ((rxcpp-dir "shogun/third-party/rxcpp"))
               (mkdir-p rxcpp-dir)
               (install-file (assoc-ref inputs "rxcpp") rxcpp-dir)
               #t)))
         (add-before 'build 'set-HOME
           ;; $HOME needs to be set at some point during the build phase
           (lambda _ (setenv "HOME" "/tmp") #t)))
       #:configure-flags
       (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
             "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
             "-DBUILD_META_EXAMPLES=OFF" ;requires unpackaged ctags
             ;;"-DINTERFACE_JAVA=ON" ;requires unpackaged jblas
             ;;"-DINTERFACE_RUBY=ON" ;requires unpackaged ruby-narray
             ;;"-DINTERFACE_PERL=ON" ;"FindPerlLibs" does not exist
             ;;"-DINTERFACE_LUA=ON"  ;fails because lua doesn't build pkgconfig file
             "-DINTERFACE_OCTAVE=ON"
             "-DINTERFACE_PYTHON=ON"
             "-DINTERFACE_R=ON")))
    (inputs
     `(("python" ,python)
       ("numpy" ,python-numpy)
       ("r-minimal" ,r-minimal)
       ("octave" ,octave)
       ("swig" ,swig)
       ("eigen" ,eigen)
       ("hdf5" ,hdf5)
       ("atlas" ,atlas)
       ("arpack" ,arpack-ng)
       ("lapack" ,lapack)
       ("glpk" ,glpk)
       ("libxml2" ,libxml2)
       ("lzo" ,lzo)
       ("zlib" ,zlib)))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("rxcpp" ,rxcpp)))
    ;; Non-portable SSE instructions are used so building fails on platforms
    ;; other than x86_64.
    (supported-systems '("x86_64-linux"))
    (home-page "http://shogun-toolbox.org/")
    (synopsis "Machine learning toolbox")
    (description
     "The Shogun Machine learning toolbox provides a wide range of unified and
efficient Machine Learning (ML) methods.  The toolbox seamlessly allows to
combine multiple data representations, algorithm classes, and general purpose
tools.  This enables both rapid prototyping of data pipelines and extensibility
in terms of new algorithms.")
    (license license:gpl3+)))

(define-public rxcpp
  (package
    (name "rxcpp")
    (version "4.0.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://github.com/ReactiveX/RxCpp/archive/v"
                           version ".tar.gz"))
       (sha256
        (base32
         "0y2isr8dy2n1yjr9c5570kpc9lvdlch6jv0jvw000amwn5d3krsh"))
       (file-name (string-append name "-" version ".tar.gz"))))
    (build-system cmake-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'remove-werror
           (lambda _
             (substitute* (find-files ".")
               (("-Werror") ""))
             #t))
         (replace 'check
           (lambda _
             (invoke "ctest"))))))
    (native-inputs
     `(("catch" ,catch-framework)))
    (home-page "http://reactivex.io/")
    (synopsis "Reactive Extensions for C++")
    (description
     "The Reactive Extensions for C++ (RxCpp) is a library of algorithms for
values-distributed-in-time.  ReactiveX is a library for composing asynchronous
and event-based programs by using observable sequences.

It extends the observer pattern to support sequences of data and/or events and
adds operators that allow you to compose sequences together declaratively while
abstracting away concerns about things like low-level threading,
synchronization, thread-safety, concurrent data structures, and non-blocking
I/O.")
    (license license:asl2.0)))

(define-public r-adaptivesparsity
  (package
    (name "r-adaptivesparsity")
    (version "1.6")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "AdaptiveSparsity" version))
              (sha256
               (base32
                "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
    (properties
     `((upstream-name . "AdaptiveSparsity")))
    (build-system r-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'link-against-armadillo
           (lambda _
             (substitute* "src/Makevars"
               (("PKG_LIBS=" prefix)
                (string-append prefix "-larmadillo"))))))))
    (propagated-inputs
     `(("r-mass" ,r-mass)
       ("r-matrix" ,r-matrix)
       ("r-rcpp" ,r-rcpp)
       ("r-rcpparmadillo" ,r-rcpparmadillo)))
    (inputs
     `(("armadillo" ,armadillo)))
    (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
    (synopsis "Adaptive sparsity models")
    (description
     "This package implements the Figueiredo machine learning algorithm for
adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
geometric models.")
    (license license:lgpl3+)))

(define-public r-kernlab
  (package
    (name "r-kernlab")
    (version "0.9-27")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "kernlab" version))
       (sha256
        (base32
         "1m0xqf6gyvwayz7w3c83y32ayvnlz0jicj8ijk808zq9sh7dbbgn"))))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/kernlab")
    (synopsis "Kernel-based machine learning tools")
    (description
     "This package provides kernel-based machine learning methods for
classification, regression, clustering, novelty detection, quantile regression
and dimensionality reduction.  Among other methods @code{kernlab} includes
Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
and a QP solver.")
    (license license:gpl2)))

(define-public dlib
  (package
    (name "dlib")
    (version "19.7")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "http://dlib.net/files/dlib-" version ".tar.bz2"))
              (sha256
               (base32
                "1mljz02kwkrbggyncxv5fpnyjdybw2qihaacb3js8yfkw12vwpc2"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  ;; Delete ~13MB of bundled dependencies.
                  (delete-file-recursively "dlib/external")
                  (delete-file-recursively "docs/dlib/external")
                  #t))))
    (build-system cmake-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'disable-asserts
           (lambda _
             ;; config.h recommends explicitly enabling or disabling asserts
             ;; when building as a shared library. By default neither is set.
             (substitute* "dlib/config.h"
               (("^//#define DLIB_DISABLE_ASSERTS") "#define DLIB_DISABLE_ASSERTS"))
             #t))
         (add-after 'disable-asserts 'disable-failing-tests
           (lambda _
             ;; One test times out on MIPS, so we need to disable it.
             ;; Others are flaky on some platforms.
             (let* ((system ,(or (%current-target-system)
                                 (%current-system)))
                    (disabled-tests (cond
                                     ((string-prefix? "mips64" system)
                                      '("object_detector" ; timeout
                                        "data_io"))
                                     ((string-prefix? "armhf" system)
                                      '("learning_to_track"))
                                     ((string-prefix? "i686" system)
                                      '("optimization"))
                                     (else '()))))
               (for-each
                (lambda (test)
                  (substitute* "dlib/test/makefile"
                    (((string-append "SRC \\+= " test "\\.cpp")) "")))
                disabled-tests)
               #t)))
         (replace 'check
           (lambda _
             ;; No test target, so we build and run the unit tests here.
             (let ((test-dir (string-append "../dlib-" ,version "/dlib/test")))
               (with-directory-excursion test-dir
                 (invoke "make" "-j" (number->string (parallel-job-count)))
                 (invoke "./dtest" "--runall"))
               #t)))
         (add-after 'install 'delete-static-library
           (lambda* (#:key outputs #:allow-other-keys)
             (delete-file (string-append (assoc-ref outputs "out")
                                         "/lib/libdlib.a"))
             #t)))))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ;; For tests.
       ("libnsl" ,libnsl)))
    (inputs
     `(("giflib" ,giflib)
       ("lapack" ,lapack)
       ("libjpeg" ,libjpeg)
       ("libpng" ,libpng)
       ("libx11" ,libx11)
       ("openblas" ,openblas)
       ("zlib" ,zlib)))
    (synopsis
     "Toolkit for making machine learning and data analysis applications in C++")
    (description
     "Dlib is a modern C++ toolkit containing machine learning algorithms and
tools.  It is used in both industry and academia in a wide range of domains
including robotics, embedded devices, mobile phones, and large high performance
computing environments.")
    (home-page "http://dlib.net")
    (license license:boost1.0)))

(define-public python-scikit-learn
  (package
    (name "python-scikit-learn")
    (version "0.19.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/scikit-learn/scikit-learn.git")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "1dk9hdj01c0bny4ps78b7869fjw9gr6qklxf6wyql8h6nh4k19xm"))
       (patches (search-patches
                 "python-scikit-learn-fix-test-non-determinism.patch"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'build 'build-ext
           (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace") #t))
         (replace 'check
           (lambda _
             ;; Restrict OpenBLAS threads to prevent segfaults while testing!
             (setenv "OPENBLAS_NUM_THREADS" "1")
             ;; Disable tests that require network access
             (delete-file "sklearn/datasets/tests/test_mldata.py")
             (delete-file "sklearn/datasets/tests/test_rcv1.py")
             (invoke "pytest" "sklearn")
             #t))
         ;; FIXME: This fails with permission denied
         (delete 'reset-gzip-timestamps))))
    (inputs
     `(("openblas" ,openblas)))
    (native-inputs
     `(("python-pytest" ,python-pytest)
       ("python-pandas" ,python-pandas) ;for tests
       ("python-cython" ,python-cython)))
    (propagated-inputs
     `(("python-numpy" ,python-numpy)
       ("python-scipy" ,python-scipy)))
    (home-page "http://scikit-learn.org/")
    (synopsis "Machine Learning in Python")
    (description
     "Scikit-learn provides simple and efficient tools for data mining and
data analysis.")
    (license license:bsd-3)))

(define-public python2-scikit-learn
  (let ((parent (package-with-python2 python-scikit-learn)))
    (package (inherit parent)
      (arguments
       (substitute-keyword-arguments (package-arguments parent)
         ((#:phases phases)
          `(modify-phases ,phases
             (replace 'check
               (lambda _
                 ;; Restrict OpenBLAS threads to prevent segfaults while testing!
                 (setenv "OPENBLAS_NUM_THREADS" "1")
                 ;; Some tests expect to be able to write to HOME.
                 (setenv "HOME" "/tmp")
                 ;; Disable tests that require network access
                 (delete-file "sklearn/datasets/tests/test_kddcup99.py")
                 (delete-file "sklearn/datasets/tests/test_mldata.py")
                 (delete-file "sklearn/datasets/tests/test_rcv1.py")
                 (invoke "pytest" "sklearn")
                 #t)))))))))

(define-public python-autograd
  (let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
         (revision "0")
         (version (git-version "0.0.0" revision commit)))
    (package
      (name "python-autograd")
      (home-page "https://github.com/HIPS/autograd")
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url home-page)
                      (commit commit)))
                (sha256
                 (base32
                  "189sv2xb0mwnjawa9z7mrgdglc1miaq93pnck26r28fi1jdwg0z4"))
                (file-name (git-file-name name version))))
      (version version)
      (build-system python-build-system)
      (native-inputs
       `(("python-nose" ,python-nose)
         ("python-pytest" ,python-pytest)))
      (propagated-inputs
       `(("python-future" ,python-future)
         ("python-numpy" ,python-numpy)))
      (arguments
       `(#:phases (modify-phases %standard-phases
                    (replace 'check
                      (lambda _
                        (invoke "py.test" "-v"))))))
      (synopsis "Efficiently computes derivatives of NumPy code")
      (description "Autograd can automatically differentiate native Python and
NumPy code.  It can handle a large subset of Python's features, including loops,
ifs, recursion and closures, and it can even take derivatives of derivatives
of derivatives.  It supports reverse-mode differentiation
(a.k.a. backpropagation), which means it can efficiently take gradients of
scalar-valued functions with respect to array-valued arguments, as well as
forward-mode differentiation, and the two can be composed arbitrarily.  The
main intended application of Autograd is gradient-based optimization.")
      (license license:expat))))

(define-public python2-autograd
  (package-with-python2 python-autograd))

(define-public lightgbm
  (package
    (name "lightgbm")
    (version "2.0.12")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/Microsoft/LightGBM/archive/v"
                    version ".tar.gz"))
              (sha256
               (base32
                "132zf0yk0545mg72hyzxm102g3hpb6ixx9hnf8zd2k55gas6cjj1"))
              (file-name (string-append name "-" version ".tar.gz"))))
    (native-inputs
     `(("python-pytest" ,python-pytest)
       ("python-nose" ,python-nose)))
    (inputs
     `(("openmpi" ,openmpi)))
    (propagated-inputs
     `(("python-numpy" ,python-numpy)
       ("python-scipy" ,python-scipy)))
    (arguments
     `(#:configure-flags
       '("-DUSE_MPI=ON")
       #:phases
       (modify-phases %standard-phases
         (replace 'check
           (lambda* (#:key outputs #:allow-other-keys)
             (with-directory-excursion ,(string-append "../LightGBM-" version)
               (invoke "pytest" "tests/c_api_test/test_.py")))))))
    (build-system cmake-build-system)
    (home-page "https://github.com/Microsoft/LightGBM")
    (synopsis "Gradient boosting framework based on decision tree algorithms")
    (description "LightGBM is a gradient boosting framework that uses tree
based learning algorithms.  It is designed to be distributed and efficient with
the following advantages:

@itemize
@item Faster training speed and higher efficiency
@item Lower memory usage
@item Better accuracy
@item Parallel and GPU learning supported (not enabled in this package)
@item Capable of handling large-scale data
@end itemize\n")
    (license license:expat)))

(define-public vowpal-wabbit
  ;; Language bindings not included.
  (package
    (name "vowpal-wabbit")
    (version "8.5.0")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/JohnLangford/vowpal_wabbit/archive/"
                    version ".tar.gz"))
              (sha256
               (base32
                "0clp2kb7rk5sckhllxjr5a651awf4s8dgzg4659yh4hf5cqnf0gr"))
              (file-name (string-append name "-" version ".tar.gz"))))
    (inputs
     `(("boost" ,boost)
       ("zlib" ,zlib)))
    (arguments
     `(#:configure-flags
       (list (string-append "--with-boost="
                            (assoc-ref %build-inputs "boost")))))
    (build-system gnu-build-system)
    (home-page "https://github.com/JohnLangford/vowpal_wabbit")
    (synopsis "Fast machine learning library for online learning")
    (description "Vowpal Wabbit is a machine learning system with techniques
such as online, hashing, allreduce, reductions, learning2search, active, and
interactive learning.")
    (license license:bsd-3)))