;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2014, 2015 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2015 Omar Radwan <toxemicsquire4@gmail.com>
;;; Copyright © 2015 Pierre-Antoine Rault <par@rigelk.eu>
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; 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 python)
  #:use-module ((guix licenses)
                #:select (asl2.0 bsd-3 bsd-2 non-copyleft cc0 x11 x11-style
                          gpl2 gpl2+ gpl3+ lgpl2.0+ lgpl2.1 lgpl2.1+ lgpl3+
                          psfl public-domain x11-style))
  #:use-module ((guix licenses) #:select (expat zlib) #:prefix license:)
  #:use-module (gnu packages)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages databases)
  #:use-module (gnu packages elf)
  #:use-module (gnu packages fontutils)
  #:use-module (gnu packages gdbm)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages ghostscript)
  #:use-module (gnu packages glib)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages icu4c)
  #:use-module (gnu packages image)
  #:use-module (gnu packages imagemagick)
  #:use-module (gnu packages libffi)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages openssl)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages readline)
  #:use-module (gnu packages texlive)
  #:use-module (gnu packages texinfo)
  #:use-module (gnu packages web)
  #:use-module (gnu packages base)
  #:use-module (gnu packages xml)
  #:use-module (gnu packages xorg)
  #:use-module (gnu packages zip)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix utils)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system python)
  #:use-module (guix build-system trivial)
  #:use-module (srfi srfi-1))

(define-public python-2
  (package
    (name "python")
    (version "2.7.6")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://www.python.org/ftp/python/"
                          version "/Python-" version ".tar.xz"))
      (patches (list (search-patch "python-libffi-mips-n32-fix.patch")
                     (search-patch "python2-sqlite-3.8.4-test-fix.patch")))
      (patch-flags '("-p0"))
      (sha256
       (base32
        "18gnpyh071dxa0rv3silrz92jw9qpblswzwv4gzqcwxzz20qxmhz"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f
;;       258 tests OK.
;;       103 tests failed:
;;          test_bz2 test_distutils test_file test_file2k test_popen2
;;          test_shutil test_signal test_site test_slice test_smtplib
;;          test_smtpnet test_socket test_socketserver test_softspace
;;          test_sort test_sqlite test_ssl test_startfile test_str
;;          test_strftime test_string test_stringprep test_strop test_strptime
;;          test_strtod test_struct test_structmembers test_structseq
;;          test_subprocess test_sunaudiodev test_sundry test_symtable
;;          test_syntax test_sys test_sys_setprofile test_sys_settrace
;;          test_sysconfig test_tarfile test_tcl test_telnetlib test_tempfile
;;          test_textwrap test_thread test_threaded_import
;;          test_threadedtempfile test_threading test_threading_local
;;          test_threadsignals test_time test_timeout test_tk test_tokenize
;;          test_tools test_trace test_traceback test_transformer
;;          test_ttk_guionly test_ttk_textonly test_tuple test_typechecks
;;          test_ucn test_unary test_undocumented_details test_unicode
;;          test_unicode_file test_unicodedata test_univnewlines
;;          test_univnewlines2k test_unpack test_urllib test_urllib2
;;          test_urllib2_localnet test_urllib2net test_urllibnet test_urlparse
;;          test_userdict test_userlist test_userstring test_uu test_uuid
;;          test_wait3 test_wait4 test_warnings test_wave test_weakref
;;          test_weakset test_whichdb test_winreg test_winsound test_with
;;          test_wsgiref test_xdrlib test_xml_etree test_xml_etree_c
;;          test_xmllib test_xmlrpc test_xpickle test_xrange test_zipfile
;;          test_zipfile64 test_zipimport test_zipimport_support test_zlib
;;       31 tests skipped:
;;          test_aepack test_al test_applesingle test_ascii_formatd test_bsddb
;;          test_bsddb185 test_bsddb3 test_cd test_cl test_codecmaps_cn
;;          test_codecmaps_hk test_codecmaps_jp test_codecmaps_kr
;;          test_codecmaps_tw test_ctypes test_curses test_dl test_gdb test_gl
;;          test_imageop test_imgfile test_ioctl test_kqueue
;;          test_linuxaudiodev test_macos test_macostools test_msilib
;;          test_multiprocessing test_ossaudiodev test_pep277
;;          test_scriptpackages
;;       7 skips unexpected on linux2:
;;          test_ascii_formatd test_bsddb test_bsddb3 test_ctypes test_gdb
;;          test_ioctl test_multiprocessing
;;    One of the typical errors:
;;    test_unicode
;;    test test_unicode crashed -- <type 'exceptions.OSError'>: [Errno 2] No such file or directory
       #:test-target "test"
       #:configure-flags
        (let ((bz2 (assoc-ref %build-inputs "bzip2"))
              (gdbm (assoc-ref %build-inputs "gdbm"))
              (libffi (assoc-ref %build-inputs "libffi"))
              (sqlite (assoc-ref %build-inputs "sqlite"))
              (openssl (assoc-ref %build-inputs "openssl"))
              (readline (assoc-ref %build-inputs "readline"))
              (zlib (assoc-ref %build-inputs "zlib")))
         (list "--enable-shared"                  ; allow embedding
               "--with-system-ffi"                ; build ctypes
               (string-append "CPPFLAGS="
                "-I" bz2 "/include "
                "-I" gdbm "/include "
                "-I" sqlite "/include "
                "-I" openssl "/include "
                "-I" readline "/include "
                "-I" zlib "/include")
               (string-append "LDFLAGS="
                "-L" bz2 "/lib "
                "-L" gdbm "/lib "
                "-L" libffi "/lib "
                "-L" sqlite "/lib "
                "-L" openssl "/lib "
                "-L" readline "/lib "
                "-L" zlib "/lib")))

        #:modules ((guix build gnu-build-system)
                   (guix build utils)
                   (guix build rpath)
                   (srfi srfi-26))
        #:imported-modules ((guix build gnu-build-system)
                            (guix build utils)
                            (guix build rpath))

        #:phases
        (alist-cons-after
         'strip 'add-lib-to-runpath
         (lambda* (#:key outputs #:allow-other-keys)
           (let* ((out (assoc-ref outputs "out"))
                  (lib (string-append out "/lib")))
             ;; Add LIB to the RUNPATH of all the executables.
             (with-directory-excursion out
               (for-each (cut augment-rpath <> lib)
                         (find-files "bin" ".*")))))
         (alist-cons-before
          'configure 'patch-lib-shells
          (lambda _
            ;; Filter for existing files, since some may not exist in all
            ;; versions of python that are built with this recipe.
            (substitute* (filter file-exists?
                                 '("Lib/subprocess.py"
                                   "Lib/popen2.py"
                                   "Lib/distutils/tests/test_spawn.py"
                                   "Lib/test/test_subprocess.py"))
              (("/bin/sh") (which "sh"))))
          (alist-cons-before
           'check 'pre-check
           (lambda _
             ;; 'Lib/test/test_site.py' needs a valid $HOME
             (setenv "HOME" (getcwd)))
           %standard-phases)))))
    (inputs
     `(("bzip2" ,bzip2)
       ("gdbm" ,gdbm)
       ("libffi" ,libffi)                         ; for ctypes
       ("sqlite" ,sqlite)                         ; for sqlite extension
       ("openssl" ,openssl)
       ("readline" ,readline)
       ("zlib" ,zlib)
       ("patchelf" ,patchelf)))                   ; for (guix build rpath)
    (native-inputs
     `(("pkg-config" ,pkg-config)))
    (native-search-paths
     (list (search-path-specification
            (variable "PYTHONPATH")
            (files '("lib/python2.7/site-packages")))))
    (home-page "http://python.org")
    (synopsis
     "High-level, dynamically-typed programming language")
    (description
     "Python is a remarkably powerful dynamic programming language that
is used in a wide variety of application domains.  Some of its key
distinguishing features include: clear, readable syntax; strong
introspection capabilities; intuitive object orientation; natural
expression of procedural code; full modularity, supporting hierarchical
packages; exception-based error handling; and very high level dynamic
data types.")
    (license psfl)))

(define-public python
  (package (inherit python-2)
    (version "3.3.5")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://www.python.org/ftp/python/"
                                  version "/Python-" version ".tar.xz"))
              (patches (list (search-patch "python-fix-tests.patch")
                             (search-patch "python-sqlite-3.8.4-test-fix.patch")
                             (search-patch "python-libffi-mips-n32-fix.patch")))
              (patch-flags '("-p0"))
              (sha256
               (base32
                "1rdncc7g8g6f3lfdg33rli1yffbiq8z283xy4f5ksl1l8i49psdb"))))
    (arguments
     (let ((args `(#:modules ((guix build gnu-build-system)
                              (guix build utils)
                             (srfi srfi-1)
                              (srfi srfi-26))
                   ,@(package-arguments python-2))))
       (substitute-keyword-arguments args
         ((#:tests? _) #t))))
    (native-search-paths
     (list (search-path-specification
            (variable "PYTHONPATH")
            (files '("lib/python3.3/site-packages")))))))

(define-public python-wrapper
  (package (inherit python)
    (name "python-wrapper")
    (source #f)
    (build-system trivial-build-system)
    (propagated-inputs `(("python" ,python)))
    (arguments
     `(#:modules ((guix build utils))
       #:builder
         (begin
           (use-modules (guix build utils))
           (let ((bin (string-append (assoc-ref %outputs "out") "/bin"))
                 (python (string-append (assoc-ref %build-inputs "python") "/bin/")))
                (mkdir-p bin)
                (for-each
                  (lambda (old new)
                    (symlink (string-append python old)
                             (string-append bin "/" new)))
                  `("python3", "pydoc3", "idle3")
                  `("python",  "pydoc",  "idle"))))))
    (description (string-append (package-description python)
     "\n\nThis wrapper package provides symbolic links to the python binaries
      without version suffix."))))


(define-public python-pytz
  (package
    (name "python-pytz")
    (version "2013b")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://launchpad.net/pytz/main/" version
                          "/+download/pytz-" version ".tar.bz2"))
      (sha256
       (base32
        "19giwgfcrg0nr1gdv49qnmf2jb2ilkcfc7qyqvfpz4dp0p64ksv5"))))
    (build-system python-build-system)
    (arguments `(#:tests? #f)) ; no test target
    (home-page "https://launchpad.net/pytz")
    (synopsis "Python timezone library")
    (description
     "This library allows accurate and cross platform timezone calculations
using Python 2.4 or higher and provides access to the Olson timezone database.")
    (license x11)))

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


(define-public python-babel
  (package
    (name "python-babel")
    (version "1.3")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/B/Babel/Babel-"
                          version ".tar.gz"))
      (sha256
       (base32
        "0bnin777lc53nxd1hp3apq410jj5wx92n08h7h4izpl4f4sx00lz"))))
    (build-system python-build-system)
    (inputs
     `(("python-pytz" ,python-pytz)
       ("python-setuptools" ,python-setuptools)))
    (arguments `(#:tests? #f)) ; no test target
    (home-page "http://babel.pocoo.org/")
    (synopsis
     "Tools for internationalizing Python applications")
    (description
     "Babel is composed of two major parts:
- tools to build and work with gettext message catalogs
- a Python interface to the CLDR (Common Locale Data Repository), providing
access to various locale display names, localized number and date formatting,
etc. ")
    (license bsd-3)))

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

(define-public python-h5py
  (package
    (name "python-h5py")
    (version "2.4.0")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/h/h5py/h5py-"
                          version ".tar.gz"))
      (sha256
       (base32
        "0q4f9l8grf6pwp64xbv8bmyxx416s7h4522nnxac056ap3savbps"))))
    (build-system python-build-system)
    (inputs
     `(("python-cython" ,python-cython)
       ("python-numpy" ,python-numpy)
       ("hdf5" ,hdf5)))
    (native-inputs
     `(("python-setuptools" ,python-setuptools)))
    (arguments `(#:tests? #f)) ; no test target
    (home-page "http://www.h5py.org/")
    (synopsis "Read and write HDF5 files from Python")
    (description
     "The h5py package provides both a high- and low-level interface to the
HDF5 library from Python.  The low-level interface is intended to be a
complete wrapping of the HDF5 API, while the high-level component supports
access to HDF5 files, datasets and groups using established Python and NumPy
concepts.")
    (license bsd-3)))

(define-public python2-h5py
  (let ((h5py (package-with-python2 python-h5py)))
    (package (inherit h5py)
      (inputs
       `(("python2-numpy" ,python2-numpy)
         ,@(alist-delete
            "python-numpy"
            (package-inputs h5py)))))))

(define-public python-lockfile
  (package
    (name "python-lockfile")
    (version "0.9.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://pypi.python.org/packages/source/l/lockfile/"
                           "lockfile-" version ".tar.gz"))
       (sha256
        (base32
         "0iwif7i84gwpvrnpv4brshdk8j6l77smvknm8k3bg77mj6f5ini3"))))
    (build-system python-build-system)
    (arguments '(#:test-target "check"))
    (home-page "http://code.google.com/p/pylockfile/")
    (synopsis "Platform-independent file locking module")
    (description
     "The lockfile package exports a LockFile class which provides a simple
API for locking files.")
    (license license:expat)))

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

(define-public python-mock
  (package
    (name "python-mock")
    (version "1.0.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://pypi.python.org/packages/source/m/mock/"
                           "mock-" version ".tar.gz"))
       (sha256
        (base32
         "0kzlsbki6q0awf89rc287f3aj8x431lrajf160a70z0ikhnxsfdq"))))
    (build-system python-build-system)
    (arguments '(#:test-target "check"))
    (home-page "http://code.google.com/p/mock/")
    (synopsis "Python mocking and patching library for testing")
    (description
     "Mock is a library for testing in Python.  It allows you to replace parts
of your system under test with mock objects and make assertions about how they
have been used.")
    (license license:expat)))

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


(define-public python-setuptools
  (package
    (name "python-setuptools")
    (version "12.1")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/s/setuptools/setuptools-"
                          version ".tar.gz"))
      (sha256
       (base32
        "04bfk7si1pwj3b5k2b1x9b1zkiclybmzpw6alrs5bciri56lg9zs"))))
    (build-system python-build-system)
    ;; FIXME: Tests require pytest, which itself relies on setuptools.
    ;; One could bootstrap with an internal untested setuptools.
    (arguments
     `(#:tests? #f))
    (home-page "https://pypi.python.org/pypi/setuptools")
    (synopsis
     "Library designed to facilitate packaging Python projects")
    (description
     "Setuptools is a fully-featured, stable library designed to facilitate
packaging Python projects, where packaging includes:
Python package and module definitions,
distribution package metadata,
test hooks,
project installation,
platform-specific details,
Python 3 support.")
    (license psfl)))

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


(define-public python-pycrypto
  (package
    (name "python-pycrypto")
    (version "2.6.1")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/p/"
                          "pycrypto/pycrypto-" version ".tar.gz"))
      (sha256
       (base32
        "0g0ayql5b9mkjam8hym6zyg6bv77lbh66rv1fyvgqb17kfc1xkpj"))))
    (build-system python-build-system)
    (native-inputs
     `(("python-setuptools" ,python-setuptools)))
    (inputs
     `(("python" ,python)
       ("gmp" ,gmp)))
    (arguments
     `(#:phases
       (alist-cons-before
        'build 'set-build-env
        ;; pycrypto runs an autoconf configure script behind the scenes
        (lambda _
          (setenv "CONFIG_SHELL" (which "bash")))
        %standard-phases)))
    (home-page "http://www.pycrypto.org/")
    (synopsis "Cryptographic modules for Python")
    (description
     "Pycrypto is a collection of both secure hash functions (such as SHA256
and RIPEMD160), and various encryption algorithms (AES, DES, RSA, ElGamal,
etc.).  The package is structured to make adding new modules easy.")
    (license public-domain)))

(define-public python-keyring
  (package
    (name "python-keyring")
    (version "3.8")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/k/"
                          "keyring/keyring-" version ".zip"))
      (sha256
       (base32
        "1vxazfbcwggyfyramh55shkxs08skhpqrkm6lrrjnygnm8c1l2zg"))))
    (build-system python-build-system)
    (native-inputs
     `(("unzip" ,unzip)
       ("python-setuptools" ,python-setuptools)
       ("python-mock" ,python-mock)))
    (inputs
     `(("python-pycrypto" ,python-pycrypto)))
    (arguments
     `(#:tests? #f                      ;TODO: tests require pytest
       #:phases
       (alist-replace
        'unpack
        (lambda _
          (let ((unzip (string-append (assoc-ref %build-inputs "unzip")
                                      "/bin/unzip"))
                (source (assoc-ref %build-inputs "source")))
            (and (zero? (system* unzip source))
                 (chdir (string-append "keyring-" ,version)))))
        %standard-phases)))
    (home-page "http://bitbucket.org/kang/python-keyring-lib")
    (synopsis "Store and access your passwords safely")
    (description
     "The Python keyring lib provides a easy way to access the system keyring
service from python.  It can be used in any application that needs safe
password storage.")
    ;; "MIT" and PSF dual license
    (license x11)))

(define-public python-six
  (package
    (name "python-six")
    (version "1.7.2")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/s/"
                          "six/six-" version ".tar.gz"))
      (sha256
       (base32
        "164rns26aqfqx2hwi0qq3scl50s69japn0fvgvrjsbyg7r1mxf67"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (home-page "http://pypi.python.org/pypi/six/")
    (synopsis "Python 2 and 3 compatibility utilities")
    (description
     "Six is a Python 2 and 3 compatibility library.  It provides utility
functions for smoothing over the differences between the Python versions with
the goal of writing Python code that is compatible on both Python versions.
Six supports every Python version since 2.5.  It is contained in only one
Python file, so it can be easily copied into your project.")
    (license x11)))

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

(define-public python-dateutil-2
  (package
    (name "python-dateutil")
    (version "2.2")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/p/"
                          name "/" name "-" version ".tar.gz"))
      (sha256
       (base32
        "0s74ad6r789810s10dxgvaf48ni6adac2icrdad34zxygqq6bj7f"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)
       ("python-six" ,python-six)))
    (home-page "http://labix.org/python-dateutil")
    (synopsis "Extensions to the standard datetime module")
    (description
     "The dateutil module provides powerful extensions to the standard
datetime module, available in Python 2.3+.")
    (license bsd-3)))

(define-public python2-dateutil-2
  (package-with-python2 python-dateutil-2))

(define-public python-dateutil
  (package
    (name "python-dateutil")
    (version "1.5") ; last version for python < 3
    (source
     (origin
      (method url-fetch)
      (uri (string-append "http://labix.org/download/python-dateutil/"
                          "python-dateutil-" version ".tar.gz"))
      (sha256
       (base32
        "0fqfglhy5khbvsipr3x7m6bcaqljh8xl5cw33vbfxy7qhmywm2n0"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (home-page "http://labix.org/python-dateutil")
    (synopsis "Extensions to the standard datetime module")
    (description
     "The dateutil module provides powerful extensions to the standard
datetime module, available in Python 2.3+.")
    (license psfl)))

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

(define-public python-parsedatetime
  (package
    (name "python-parsedatetime")
    (version "1.2")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/p/"
                          "parsedatetime/parsedatetime-" version ".tar.gz"))
      (sha256
       (base32
        "1zcj0pzxvpl4j2ma9awmpkfxldybi2kjaahjjpmgfbg5cxwcjsqv"))))
    (build-system python-build-system)
    (native-inputs
     `(("python-setuptools" ,python-setuptools)))
    (arguments `(#:tests? #f))          ;no test target
    (home-page "http://github.com/bear/parsedatetime/")
    (synopsis
     "Parse human-readable date/time text")
    (description
     "Parse human-readable date/time text")
    (license asl2.0)))

(define-public python-tzlocal
  (package
    (name "python-tzlocal")
    (version "1.1.1")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/t/"
                          "tzlocal/tzlocal-" version ".zip"))
      (sha256
       (base32
        "1m3y918c3chf41fwg2bx4w42bqsjzn3dyvvcmwwy13c8gj6zssv9"))))
    (build-system python-build-system)
    (native-inputs
     `(("unzip" ,unzip)
       ("python-setuptools" ,python-setuptools)))
    (inputs `(("python-pytz" ,python-pytz)))
    (arguments
     `(#:phases
       (alist-replace
        'unpack
        (lambda _
          (let ((unzip (string-append (assoc-ref %build-inputs "unzip")
                                      "/bin/unzip"))
                (source (assoc-ref %build-inputs "source")))
            (and (zero? (system* unzip source))
                 (chdir (string-append "tzlocal-" ,version)))))
        %standard-phases)))
    (home-page "https://github.com/regebro/tzlocal")
    (synopsis
     "Local timezone information for Python")
    (description
     "Tzlocal returns a tzinfo object with the local timezone information.
This module attempts to fix a glaring hole in pytz, that there is no way to
get the local timezone information, unless you know the zoneinfo name, and
under several distributions that's hard or impossible to figure out.")
    (license cc0)))

(define-public python-pysam
  (package
    (name "python-pysam")
    (version "0.8.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://pypi.python.org/packages/source/p/pysam/pysam-"
                           version ".tar.gz"))
       (sha256
        (base32
         "1fb6i6hbpzxaxb62kyyp5alaidwhj40f7c6gwbhr6njzlqd5l459"))))
    (build-system python-build-system)
    (arguments
     `(#:tests? #f ; tests are excluded in the manifest
       #:phases
       (alist-cons-before
        'build 'set-flags
        (lambda _
          (setenv "LDFLAGS" "-lncurses")
          (setenv "CFLAGS" "-D_CURSES_LIB=1"))
        %standard-phases)))
    (inputs
     `(("python-cython"     ,python-cython)
       ("python-setuptools" ,python-setuptools)
       ("ncurses"           ,ncurses)
       ("zlib"              ,zlib)))
    (home-page "https://github.com/pysam-developers/pysam")
    (synopsis "Python bindings to the SAMtools C API")
    (description
     "Pysam is a Python module for reading and manipulating files in the
SAM/BAM format.  Pysam is a lightweight wrapper of the SAMtools C API.  It
also includes an interface for tabix.")
    (license license:expat)))

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

(define-public python2-pysqlite
  (package
    (name "python2-pysqlite")
    (version "2.6.3a")                            ; see below
    (source
     (origin
      (method url-fetch)
      ;; During the switch from code.google.com to pypi.python.org, the 2.6.3
      ;; tarball was modified, but the version number was kept:
      ;; <https://lists.gnu.org/archive/html/guix-devel/2014-02/msg00077.html>.
      ;; Here we want to refer to the pypi-hosted 2.6.3 tarball.
      (uri (string-append
            "https://pypi.python.org/packages/source/p/pysqlite/pysqlite-"
            "2.6.3" ".tar.gz"))
      (sha256
       (base32
        "13djzgnbi71znjjyaw4nybg6smilgszcid646j5qav7mdchkb77y"))))
    (build-system python-build-system)
    (inputs
     `(("sqlite" ,sqlite)))
    (arguments
     `(#:python ,python-2 ; incompatible with Python 3
       #:tests? #f)) ; no test target
    (home-page "https://pypi.python.org/pypi/pysqlite")
    (synopsis "SQLite bindings for Python")
    (description
     "Pysqlite provides SQLite bindings for Python that comply to the
Database API 2.0T.")
    (license license:zlib)))


(define-public python2-mechanize
  (package
    (name "python2-mechanize")
    (version "0.2.5")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/m/mechanize/mechanize-"
                          version ".tar.gz"))
      (sha256
       (base32
        "0rj7r166i1dyrq0ihm5rijfmvhs8a04im28lv05c0c3v206v4rrf"))))
    (build-system python-build-system)
    (inputs
     `(("python2-setuptools" ,python2-setuptools)))
    (arguments
     `(#:python ,python-2 ; apparently incompatible with Python 3
       #:tests? #f))
         ;; test fails with message
         ;; AttributeError: 'module' object has no attribute 'test_pullparser'
         ;; (python-3.3.2) or
         ;; AttributeError: 'module' object has no attribute 'test_urllib2_localnet'
         ;; (python-2.7.5).
         ;; The source code is from March 2011 and probably not up-to-date
         ;; with respect to python unit tests.
    (home-page "http://wwwsearch.sourceforge.net/mechanize/")
    (synopsis
     "Stateful programmatic web browsing in Python")
    (description
     "Mechanize implements stateful programmatic web browsing in Python,
after Andy Lester’s Perl module WWW::Mechanize.")
    (license (non-copyleft "file://COPYING"
                        "See COPYING in the distribution."))))


(define-public python-simplejson
  (package
    (name "python-simplejson")
    (version "3.3.0")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/s/simplejson/simplejson-"
                          version ".tar.gz"))
      (sha256
       (base32
        "07wsry5j44l5zzm74l4j2bvasiq8n5m32f31n2p7c68i5vc6p2ks"))))
    (build-system python-build-system)
    (home-page "http://simplejson.readthedocs.org/en/latest/")
    (synopsis
     "Json library for Python")
    (description
     "JSON (JavaScript Object Notation) is a subset of JavaScript syntax
 (ECMA-262 3rd edition) used as a lightweight data interchange format.

Simplejson exposes an API familiar to users of the standard library marshal
and pickle modules.  It is the externally maintained version of the json
library contained in Python 2.6, but maintains compatibility with Python 2.5
and (currently) has significant performance advantages, even without using
the optional C extension for speedups.  Simplejson is also supported on
Python 3.3+.")
    (license x11)))

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


(define-public python2-pyicu
  (package
    (name "python2-pyicu")
    (version "1.8")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/P/PyICU/PyICU-"
                          version ".tar.gz"))
      (sha256
       (base32
        "1y361x82lnh9k9srmdx3q92z5iag112z7r5fxm0n1sfwb349yjdw"))))
    (build-system python-build-system)
    (inputs
     `(("icu4c" ,icu4c)))
    (arguments
     `(#:python ,python-2 ; Python 3 works also, but needs special care for
                          ; linking with libpython3.3m
       #:tests? #f)) ; no check target
    (home-page "http://pyicu.osafoundation.org/")
    (synopsis "Python extension wrapping the ICU C++ API")
    (description
     "PyICU is a python extension wrapping the ICU C++ API.")
    (license x11)))

(define-public python2-dogtail
  ;; Python 2 only, as it leads to "TabError: inconsistent use of tabs and
  ;; spaces in indentation" with Python 3.
  (package
    (name "python2-dogtail")
    (version "0.8.2")
    (source (origin
             (method url-fetch)
             (uri (string-append
                   "https://fedorahosted.org/released/dogtail/dogtail-"
                   version ".tar.gz"))
             (sha256
              (base32
               "1yc4cg7ip87z15gyd4wy2vzbywrjc52a3m8r8gqy2b50d65llcg1"))))
    (build-system python-build-system)
    (arguments `(#:python ,python-2
                 #:tests? #f))                    ; invalid command "test"
    (home-page "https://fedorahosted.org/dogtail/")
    (synopsis "GUI test tool and automation framework written in ​Python")
    (description
     "Dogtail is a GUI test tool and automation framework written in Python.
It uses Accessibility (a11y) technologies to communicate with desktop
applications. dogtail scripts are written in Python and executed like any
other Python program.")
    (license gpl2+)))

(define-public python2-empy
  (package
    (name "python2-empy")
    (version "3.3")
    (source (origin
             (method url-fetch)
             (uri (string-append "http://www.alcyone.com/software/empy/empy-"
                                 version ".tar.gz"))
             (sha256
              (base32
               "01g8mmkfnvjdmlhsihwyx56lrg7r5m5d2fg6mnxsvy6g0dnl69f6"))))
    (build-system python-build-system)
    (arguments
     `(#:python ,python-2
       #:phases (alist-replace
                 'check
                 (lambda _
                   (zero? (system* "./test.sh")))
                 %standard-phases)))
    (home-page "http://www.alcyone.com/software/empy/")
    (synopsis "Templating system for Python")
    (description
     "EmPy is a system for embedding Python expressions and statements in
template text; it takes an EmPy source file, processes it, and produces
output.  This is accomplished via expansions, which are special signals to the
EmPy system and are set off by a special prefix (by default the at sign, @).
EmPy can expand arbitrary Python expressions and statements in this way, as
well as a variety of special forms.  Textual data not explicitly delimited in
this way is sent unaffected to the output, allowing Python to be used in
effect as a markup language.  Also supported are callbacks via hooks,
recording and playback via diversions, and dynamic, chainable filters.  The
system is highly configurable via command line options and embedded
commands.")
    (license lgpl2.1+)))

(define-public python2-element-tree
  (package
    (name "python2-element-tree")
    (version "1.2.6")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "http://effbot.org/media/downloads/elementtree-"
                    version "-20050316.tar.gz"))
              (sha256
               (base32
                "016bphqnlg0l4vslahhw4r0aanw95bpypy65r1i1acyb2wj5z7dj"))))
    (build-system python-build-system)
    (arguments
     `(#:python ,python-2                       ; seems to be part of Python 3
       #:tests? #f))                            ; no 'test' sub-command
    (synopsis "Toolkit for XML processing in Python")
    (description
     "ElementTree is a Python library supporting lightweight XML processing.")
    (home-page "http://effbot.org/zone/element-index.htm")
    (license (x11-style "http://docs.python.org/2/license.html"
                        "Like \"CWI LICENSE AGREEMENT FOR PYTHON \
0.9.0 THROUGH 1.2\"."))))

(define-public python2-pybugz
  (package
    (name "python2-pybugz")
    (version "0.6.11")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "http://bits.liquidx.net/projects/pybugz/pybugz-"
                    version ".tar.gz"))
              (sha256
               (base32
                "17ni00p08gp5lkxlrrcnvi3x09fmajnlbz4da03qcgl9q21ym4jd"))
              (patches (map search-patch
                            (list "pybugz-stty.patch"
                                  "pybugz-encode-error.patch")))))
    (build-system python-build-system)
    (arguments
     `(#:python ,python-2                         ; SyntaxError with Python 3
       #:tests? #f))                              ; no 'test' sub-command
    (inputs `(("element-tree" ,python2-element-tree)))
    (synopsis "Python and command-line interface to Bugzilla")
    (description
     "PyBugz is a Python library and command-line tool to query the Bugzilla
bug tracking system.  It is meant as an aid to speed up interaction with the
bug tracker.")
    (home-page "http://www.liquidx.net/pybugz/")
    (license gpl2)))

(define-public python-enum34
  (package
    (name "python-enum34")
    (version "1.0")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/e/"
                          "enum34/enum34-" version ".tar.gz"))
      (sha256
       (base32
        "0dg6mpg9n4g9diyrbnbb5vd9d1qw9f265zwhknqy0mxh0cvmjjrq"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (arguments
     `(#:phases
       (alist-replace
        'check
        (lambda _ (zero? (system* "python" "enum/test_enum.py")))
        %standard-phases)))
    (home-page "https://pypi.python.org/pypi/enum34")
    (synopsis "Backported Python 3.4 Enum")
    (description
     "Enum34 is the new Python stdlib enum module available in Python 3.4
backported for previous versions of Python from 2.4 to 3.3.")
    (license bsd-3)))

(define-public python-parse-type
  (package
    (name "python-parse-type")
    (version "0.3.4")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/p/"
                          "parse_type/parse_type-" version ".tar.gz"))
      (sha256
       (base32
        "0iv1c34npr4iynwpgv1vkjx9rjd18a85ir8c01gc5f7wp8iv7l1x"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)
       ("python-six" ,python-six)
       ("python-parse" ,python-parse)
       ("python-enum34" ,python-enum34))) ;required for python<3.4
    (arguments '(#:tests? #f))            ;TODO: tests require pytest
    (home-page "https://github.com/jenisys/parse_type")
    (synopsis "Extended parse module")
    (description
     "Parse_type extends the python parse module.")
    (license bsd-3)))

(define-public python-parse
  (package
    (name "python-parse")
    (version "1.6.4")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/p/"
                          "parse/parse-" version ".tar.gz"))
      (sha256
       (base32
        "0m30q64l6szl7s9mhvqy64w2fdhdn8lb91fmacjiwbv3479cmk57"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (alist-replace
        'check
        (lambda _ (zero? (system* "python" "test_parse.py")))
        %standard-phases)))
    (home-page "https://github.com/r1chardj0n3s/parse")
    (synopsis "Parse strings")
    (description
     "Parse strings using a specification based on the Python format()
syntax.")
    (license x11)))


(define-public scons
  (package
    (name "scons")
    (version "2.1.0")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://sourceforge/scons/scons-"
                                 version ".tar.gz"))
             (sha256
              (base32
               "07cjn4afb2cljjrd3cr7xf062qq58z8q96f58z6yplhdyqafsfa1"))))
    (build-system python-build-system)
    (arguments
     ;; With Python 3.x, fails to build with a syntax error.
     `(#:python ,python-2
       #:tests? #f))                       ; no 'python setup.py test' command
    (home-page "http://scons.org/")
    (synopsis "Software construction tool written in Python")
    (description
     "SCons is a software construction tool.  Think of SCons as an improved,
cross-platform substitute for the classic Make utility with integrated
functionality similar to autoconf/automake and compiler caches such as ccache.
In short, SCons is an easier, more reliable and faster way to build
software.")
    (license x11)))

(define-public python-extras
  (package
    (name "python-extras")
    (version "0.0.3")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/e/extras/extras-"
             version ".tar.gz"))
       (sha256
        (base32
         "1h7zx4dfyclalg0fqnfjijpn0f793a9mx8sy3b27gd31nr6dhq3s"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (arguments
     ;; error in setup.cfg: command 'test' has no such option 'buffer'
     '(#:tests? #f))
    (home-page "https://github.com/testing-cabal/extras")
    (synopsis "Useful extensions to the Python standard library")
    (description
     "Extras is a set of extensions to the Python standard library.")
    (license license:expat)))

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

(define-public python-mimeparse
  (package
    (name "python-mimeparse")
    (version "0.1.4")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/p/python-mimeparse/python-mimeparse-"
             version ".tar.gz"))
       (sha256
        (base32
         "1hyxg09kaj02ri0rmwjqi86wk4nd1akvv7n0dx77azz76wga4s9w"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (arguments
     '(#:tests? #f)) ; no setup.py test command
    (home-page
     "https://github.com/dbtsai/python-mimeparse")
    (synopsis "Python library for parsing MIME types")
    (description
     "Mimeparse provides basic functions for parsing MIME type names and
matching them against a list of media-ranges.")
    (license license:expat)))

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

(define-public python-nose
  (package
    (name "python-nose")
    (version "1.3.4")
    (source
      (origin
        (method url-fetch)
        (uri (string-append
               "https://pypi.python.org/packages/source/n/nose/nose-"
               version ".tar.gz"))
        (sha256
          (base32
            "00qymfgwg4iam4xi0w9bnv7lcb3fypq1hzfafzgs1rfmwaj67g3n"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (arguments
     '(#:tests? #f)) ; FIXME: test suite fails
    (home-page "http://readthedocs.org/docs/nose/")
    (synopsis "Python testing library")
    (description
     "Nose extends the unittest library to make testing easier.")
    (license lgpl2.0+)))

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

(define-public python-unittest2
  (package
    (name "python-unittest2")
    (version "0.5.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/u/unittest2py3k/unittest2py3k-"
             version ".tar.gz"))
       (sha256
        (base32
         "00yl6lskygcrddx5zspkhr0ibgvpknl4678kkm6s626539grq93q"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (home-page "http://pypi.python.org/pypi/unittest2")
    (synopsis "Python unit testing library")
    (description
     "Unittest2 is a replacement for the unittest module in the Python
standard library.")
    (license psfl)))

(define-public python2-unittest2
  (package (inherit python-unittest2)
    (name "python2-unittest2")
    (version "0.5.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/u/unittest2/unittest2-"
             version ".tar.gz"))
       (sha256
        (base32
         "0wbs4i4x3x7klr3v35ss6p9mcqz883i1xgcpkhvl7n2lyv6yhpda"))))
    (inputs
     `(("python2-setuptools" ,python-setuptools)))
    (arguments
     `(#:python ,python-2
       #:tests? #f)))) ; no setup.py test command

(define-public python-py
  (package
    (name "python-py")
    (version "1.4.23")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/p/py/py-"
             version ".tar.gz"))
       (sha256
        (base32
         "1jkhffpai419v5rickm2vz86p9bkg3b3kcm2k4bi5wfajhw2m3xs"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (home-page "http://pylib.readthedocs.org/")
    (synopsis "Python library for parsing, I/O, instrospection, and logging")
    (description
     "Py is a Python library for file name parsing, .ini file parsing, I/O,
code introspection, and logging.")
    (license license:expat)))

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

(define-public python-pytest
  (package
    (name "python-pytest")
    (version "2.6.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/p/pytest/pytest-"
             version ".tar.gz"))
       (sha256
        (base32
         "0g2w4p0n42wvz8rq4k6gnzpkakgz3g8sfanxk8jrsra9675snkcr"))
       (modules '((guix build utils)))
       (snippet
        ;; One of the tests involves the /usr directory, so it fails.
        '(substitute* "testing/test_argcomplete.py"
           (("def test_remove_dir_prefix\\(self\\):")
            "@pytest.mark.xfail\n    def test_remove_dir_prefix(self):")))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)
       ("python-py" ,python-py)
       ("python-nose" ,python-nose)
       ("python-mock" ,python-mock)))
    (home-page "http://pytest.org")
    (synopsis "Python testing library")
    (description
     "Pytest is a testing tool that provides auto-discovery of test modules
and functions, detailed info on failing assert statements, modular fixtures,
and many external plugins.")
    (license license:expat)))

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

(define-public python-scripttest
  (package
    (name "python-scripttest")
    (version "1.3")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/s/scripttest/scripttest-"
             version ".tar.gz"))
       (sha256
        (base32
         "0f4w84k8ck82syys7yg9maz93mqzc8p5ymis941x034v44jzq74m"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)
       ("python-pytest" ,python-pytest)))
    (home-page "http://pythonpaste.org/scripttest/")
    (synopsis "Python library to test command-line scripts")
    (description "Scripttest is a Python helper library for testing
interactive command-line applications.  With it you can run a script in a
subprocess and see the output as well as any file modifications.")
    (license license:expat)))

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

(define-public python-testtools
  (package
    (name "python-testtools")
    (version "1.0.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/t/testtools/testtools-"
             version ".tar.gz"))
       (sha256
        (base32
         "1dyml28ykpl5jb9khdmcdvhy1cxqingys6qvj2k04fzlaj6z3bbx"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)
       ("python-mimeparse" ,python-mimeparse)
       ("python-extras" ,python-extras)))
    (home-page "https://github.com/testing-cabal/testtools")
    (synopsis
     "Extensions to the Python standard library unit testing framework")
    (description
     "Testtools extends the Python standard library unit testing framework to
provide matchers, more debugging information, and cross-Python
compatibility.")
    (license psfl)))

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

(define-public python-testscenarios
  (package
    (name "python-testscenarios")
    (version "0.4")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/t/testscenarios/testscenarios-"
             version ".tar.gz"))
       (sha256
        (base32
         "1671jvrvqlmbnc42j7pc5y6vc37q44aiwrq0zic652pxyy2fxvjg"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)
       ("python-testtools" ,python-testtools)
       ("python-mimeparse" ,python-mimeparse)))
    (home-page "https://launchpad.net/testscenarios")
    (synopsis "Pyunit extension for dependency injection")
    (description
     "Testscenarios provides clean dependency injection for Python unittest
style tests.")
    (license (list bsd-3 asl2.0)))) ; at the user's option

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

(define-public python-testresources
  (package
    (name "python-testresources")
    (version "0.2.7")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/t/testresources/testresources-"
             version ".tar.gz"))
       (sha256
        (base32
         "0cbj3plbllyz42c4b5xxgwaa7mml54lakslrn4kkhinxhdri22md"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (home-page "https://launchpad.net/testresources")
    (synopsis
     "Pyunit extension for managing test resources")
    (description
     "Testresources is an extension to Python's unittest to allow declarative
use of resources by test cases.")
    (license (list bsd-3 asl2.0)))) ; at the user's option

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

(define-public python-subunit
  (package
    (name "python-subunit")
    (version "0.0.21")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/p/python-subunit/python-subunit-"
             version ".tar.gz"))
       (sha256
        (base32
         "1nkw9wfbvizmpajbj3in8ns07g7lwkiv8hip14jjlwk3cacls6jv"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)
       ("python-testtools" ,python-testtools)
       ("python-mimeparse" ,python-mimeparse)
       ("python-testscenarios" ,python-testscenarios)))
    (home-page "http://launchpad.net/subunit")
    (synopsis "Python implementation of the subunit protocol")
    (description
     "Python-subunit is a Python implementation of the subunit test streaming
protocol.")
    (license (list bsd-3 asl2.0)))) ; at the user's option

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

(define-public python-fixtures
  (package
    (name "python-fixtures")
    (version "0.3.16")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/f/fixtures/fixtures-"
             version ".tar.gz"))
       (sha256
        (base32
         "0x9r2gwilcig5g54k60bxzg96zabizq1855lrprlb4zckalp9asc"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (arguments
     '(#:tests? #f)) ; no setup.py test command
    (home-page "https://launchpad.net/python-fixtures")
    (synopsis "Python test fixture library")
    (description
     "Fixtures provides a way to create reusable state, useful when writing
Python tests.")
    (license (list bsd-3 asl2.0)))) ; at user's option

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

(define-public python-testrepository
  (package
    (name "python-testrepository")
    (version "0.0.20")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/t/testrepository/testrepository-"
             version ".tar.gz"))
       (sha256
        (base32
         "1ssqb07c277010i6gzzkbdd46gd9mrj0bi0i8vn560n2k2y4j93m"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)
       ("python-testtools" ,python-testtools)
       ("python-subunit" ,python-subunit)
       ("python-fixtures" ,python-fixtures)
       ("python-mimeparse" ,python-mimeparse)))
    (home-page "https://launchpad.net/testrepository")
    (synopsis "Database for Python test results")
    (description "Testrepository provides a database of test results which can
be used as part of a developer's workflow to check things such as what tests
have failed since the last commit or what tests are currently failing.")
    (license (list bsd-3 asl2.0)))) ; at user's option

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

(define-public python-coverage
  (package
    (name "python-coverage")
    (version "3.7.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/c/coverage/coverage-"
             version ".tar.gz"))
       (sha256
        (base32
         "0knlbq79g2ww6xzsyknj9rirrgrgc983dpa2d9nkdf31mb2a3bni"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (home-page "http://nedbatchelder.com/code/coverage")
    (synopsis "Code coverage measurement for Python")
    (description
     "Coverage measures code coverage, typically during test execution.  It
uses the code analysis tools and tracing hooks provided in the Python standard
library to determine which lines are executable, and which have been
executed.")
    (license bsd-3)))

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

(define-public python-discover
  (package
    (name "python-discover")
    (version "0.4.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/d/discover/discover-"
             version ".tar.gz"))
       (sha256
        (base32
         "0y8d0zwiqar51kxj8lzmkvwc3b8kazb04gk5zcb4nzg5k68zmhq5"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (home-page "http://pypi.python.org/pypi/discover/")
    (synopsis
     "Python test discovery for unittest")
    (description
     "Discover provides test discovery for unittest, a feature that has been
backported from Python 2.7 for Python 2.4+")
    (license bsd-3)))

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

(define-public behave
  (package
    (name "behave")
    (version "1.2.4")
    (source (origin
             (method url-fetch)
             (uri (string-append "https://pypi.python.org/packages/source/b/"
                                 name "/" name "-" version ".tar.gz"))
             (sha256
              (base32
               "1v2rfy8xnf0rk7cj4cgr7lam4015d458i7bg0xqs9czfv6njlm14"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)
       ("python-six" ,python-six)
       ("python-enum43" ,python-enum34)
       ("python-parse" ,python-parse)
       ("python-parse-type" ,python-parse-type)))
    (arguments `(#:tests? #f))          ;TODO: tests require nose>=1.3 and
                                        ;PyHamcrest>=1.8
    (home-page "http://github.com/behave/behave")
    (synopsis "Python behavior-driven development")
    (description
     "Behave is a tool for behavior-driven development in python.
Behavior-driven development (or BDD) is an agile software development
technique that encourages collaboration between developers, QA and
non-technical or business participants in a software project.  Behave uses
tests written in a natural language style, backed up by Python code.")
    (license x11)))

(define-public python-exif-read
  (package
    (name "python-exif-read")
    (version "1.4.2")
    (source (origin
              (method url-fetch)
              (uri
               (string-append
                "https://pypi.python.org/packages/source/E/ExifRead/ExifRead-"
                version ".tar.gz"))
              (sha256
               (base32
                "17c627gcdmyc05hz4zk8qs4pjgw6rc68qzjzgz8gh1cmpsd7acf1"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (arguments `(#:tests? #f)) ; no tests
    (home-page "https://github.com/ianare/exif-py")
    (synopsis "Python library to extract EXIF data from image files")
    (description
     "ExifRead is a Python library to extract EXIF data from tiff and jpeg
files.")
    (license bsd-3)))

(define-public python2-exif-read
  (package-with-python2 python-exif-read))

(define-public python-pyld
  (package
    (name "python-pyld")
    (version "0.6.0")
    (source (origin
              (method url-fetch)
              (uri
               (string-append
                "https://pypi.python.org/packages/source/P/PyLD/PyLD-"
                version ".tar.gz"))
              (sha256
               (base32
                "1l9ymj85fsvayqplinzpk0kyiq6m74ps9xd3a9fhlxfn1rldf8x8"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (arguments `(#:tests? #f)) ; no tests
    (home-page "http://github.com/digitalbazaar/pyld")
    (synopsis "Python implementation of the JSON-LD specification")
    (description
     "PyLD is an implementation of the JSON-LD specification.")
    (license bsd-3)))

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

(define-public python-certifi
  (package
    (name "python-certifi")
    (version "14.05.14")
    (source (origin
              (method url-fetch)
              (uri
               (string-append
                "https://pypi.python.org/packages/source/c/certifi/certifi-"
                version ".tar.gz"))
              (sha256
               (base32
                "0s8vxzfz6s4m6fvxc7z25k9j35w0rh6jkw3wwcd1az1mssncn6qy"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (arguments `(#:tests? #f)) ; no tests
    (home-page "http://python-requests.org/")
    (synopsis "Python CA certificate bundle")
    (description
     "Certifi is a Python library that contains a CA certificate bundle, which
is used by the Requests library to verify HTTPS requests.")
    (license asl2.0)))

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

(define-public python2-requests
  (package
    (name "python2-requests")
    (version "2.4.0")
    (source (origin
             (method url-fetch)
             (uri
              (string-append
               "https://pypi.python.org/packages/source/r/requests/requests-"
               version ".tar.gz"))
             (sha256
              (base32
               "0gknlfx1wakrrm1zi8gi03x2lzj4dsns0vjw0nsmgqvkphyf01vh"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)
       ("python-certifi" ,python-certifi)))
    (arguments `(#:tests? #f ; no tests
                 #:python ,python-2))
    (home-page "http://python-requests.org/")
    (synopsis "Python HTTP library")
    (description
     "Requests is a Python HTTP client library.  It aims to be easier to use
than Python’s urllib2 library.")
    (license asl2.0)))

(define-public python-jsonschema
  (package
    (name "python-jsonschema")
    (version "2.4.0")
    (source (origin
             (method url-fetch)
             (uri
              (string-append
               "https://pypi.python.org/packages/source/j/jsonschema/jsonschema-"
               version ".tar.gz"))
             (sha256
              (base32
               "1yik3031ziygvq66rj3mzfqdgxj29sg1bkfc46wsgi7lnbqs560j"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (home-page "http://github.com/Julian/jsonschema")
    (synopsis "Implementation of JSON Schema for Python")
    (description
     "Jsonschema is an implementation of JSON Schema for Python.")
    (license license:expat)))

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

(define-public python-unidecode
  (package
    (name "python-unidecode")
    (version "0.04.16")
    (source (origin
             (method url-fetch)
             (uri
              (string-append
               "https://pypi.python.org/packages/source/U/Unidecode/Unidecode-"
               version ".tar.gz"))
             (sha256
              (base32
               "0yv56vc49rvippyxgxvcyz7jklc07ky38rcspax7p00sgmriiljc"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (home-page "https://pypi.python.org/pypi/Unidecode")
    (synopsis "ASCII transliterations of Unicode text")
    (description
     "Unidecode provides ASCII transliterations of Unicode text.  Unidecode is
useful when integrating with legacy code that doesn't support Unicode, or for
ease of entry of non-Roman names on a US keyboard, or when constructing ASCII
machine identifiers from human-readable Unicode strings that should still be
somewhat intelligeble.")
    (license gpl2+)))

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

(define-public python-pyjwt
  (package
    (name "python-pyjwt")
    (version "0.2.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/P/PyJWT/PyJWT-"
             version ".tar.gz"))
       (sha256
        (base32
         "1ahqblfy2sj3xz34wsa48cn9rp0dspzq56p54i5znmws3b8gml6g"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (arguments
     '(#:tests? #f)) ; test suite doesn't work
    (home-page "http://github.com/progrium/pyjwt")
    (synopsis "JSON Web Token implementation in Python")
    (description
     "PyJWT is a JSON Web Token implementation written in Python.")
    (license license:expat)))

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

(define-public python-oauthlib
  (package
    (name "python-oauthlib")
    (version "0.6.3")
    (source (origin
              (method url-fetch)
              (uri
               (string-append
                "https://pypi.python.org/packages/source/o/oauthlib/oauthlib-"
                version ".tar.gz"))
              (sha256
               (base32
                "1yaj3j64la4arwsbhbfmpnickzh3jpg9nlpyg409v8pp24isn48a"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)
       ("python-pyjwt" ,python-pyjwt)
       ("python-pycrypto" ,python-pycrypto)
       ("python-nose" ,python-nose)
       ("python-mock" ,python-mock)))
    (home-page "https://github.com/idan/oauthlib")
    (synopsis "OAuth implementation for Python")
    (description
     "Oauthlib is a generic, spec-compliant, thorough implementation of the
OAuth request-signing logic.")
    (license bsd-3)))

(define-public python2-oauthlib
  (let ((base (package-with-python2 python-oauthlib)))
    (package
      (inherit base)
      (inputs
       (append (package-inputs base)
               `(("python2-unittest2" ,python2-unittest2)))))))

(define-public python-itsdangerous
  (package
    (name "python-itsdangerous")
    (version "0.24")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/i/itsdangerous/itsdangerous-"
             version ".tar.gz"))
       (sha256
        (base32
         "06856q6x675ly542ig0plbqcyab6ksfzijlyf1hzhgg3sgwgrcyb"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (home-page "http://github.com/mitsuhiko/itsdangerous")
    (synopsis "Python library for passing data to/from untrusted environments")
    (description
     "Itsdangerous provides various helpers to pass trusted data to untrusted
environments and back.")
    (license bsd-3)))

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

(define-public python-pyyaml
  (package
    (name "python-pyyaml")
    (version "3.11")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/P/PyYAML/PyYAML-"
             version ".tar.gz"))
       (sha256
        (base32
         "1s26125vfnskng58ym37xhwv8v0mm95b2cwbjfag8prfhy596v63"))))
    (build-system python-build-system)
    (inputs
     `(("libyaml" ,libyaml)))
    (native-inputs
     `(("python-setuptools" ,python-setuptools)))
    (home-page "http://pyyaml.org/wiki/PyYAML")
    (synopsis "YAML parser and emitter for Python")
    (description
     "PyYAML is a YAML parser and emitter for Python.  PyYAML features a
complete YAML 1.1 parser, Unicode support, pickle support, capable extension
API, and sensible error messages.  PyYAML supports standard YAML tags and
provides Python-specific tags that allow to represent an arbitrary Python
object.")
    (license license:expat)))

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

(define-public python-virtualenv
  (package
    (name "python-virtualenv")
    (version "1.11.6")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/v/virtualenv/virtualenv-"
             version ".tar.gz"))
       (sha256
        (base32
         "1xq4prmg25n9cz5zcvbqx68lmc3kl39by582vd8pzs9f3qalqyiy"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)
       ("python-mock" ,python-mock)
       ("python-nose" ,python-nose)))
    (home-page "https://virtualenv.pypa.io/")
    (synopsis "Virtual Python environment builder")
    (description
     "Virtualenv is a tool to create isolated Python environments.")
    (license license:expat)))

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

(define-public python-markupsafe
  (package
    (name "python-markupsafe")
    (version "0.23")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/M/MarkupSafe/MarkupSafe-"
             version ".tar.gz"))
       (sha256
        (base32
         "1hvip33wva3fnmvfp9x5klqri7hpl1hkgqmjbss18nmrb7zimv54"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (home-page "http://github.com/mitsuhiko/markupsafe")
    (synopsis "XML/HTML/XHTML markup safe string implementation for Python")
    (description
     "Markupsafe provides an XML/HTML/XHTML markup safe string implementation
for Python.")
    (license bsd-3)))

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

(define-public python-jinja2
  (package
    (name "python-jinja2")
    (version "2.7.3")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/J/Jinja2/Jinja2-"
             version ".tar.gz"))
       (sha256
        (base32
         "1nwg9yfqgy421lncnm63k1zf9xkd1klc0jm0fr4p3dad01fsq91f"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)
       ("python-markupsafe" ,python-markupsafe)))
    (home-page "http://jinja.pocoo.org/")
    (synopsis "Python template engine")
    (description
     "Jinja2 is a small but fast and easy to use stand-alone template engine
written in pure Python.")
    (license bsd-3)))

(define-public python2-jinja2
  (package-with-python2 python-jinja2))

(define-public python-docutils
  (package
    (name "python-docutils")
    (version "0.12")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/d/docutils/docutils-"
             version ".tar.gz"))
       (sha256
        (base32
         "1ylnjnw1x4b2y7blr6x35ncdzn69k253kw4cdkv6asdb21w73ny7"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (arguments
     '(#:tests? #f)) ; no setup.py test command
    (home-page "http://docutils.sourceforge.net/")
    (synopsis "Python Documentation Utilities")
    (description
     "Docutils is a modular system for processing documentation into useful
formats, such as HTML, XML, and LaTeX.  For input Docutils supports
reStructuredText.")
    ;; Most of the source code is public domain, but some source files are
    ;; licensed under the PFSL, BSD 2-clause, and GPLv3+ licenses.
    (license (list public-domain psfl bsd-2 gpl3+))))

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

(define-public python-pygments
  (package
    (name "python-pygments")
    (version "1.6")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/P/Pygments/Pygments-"
             version ".tar.gz"))
       (sha256
        (base32
         "1h11r6ss8waih51vcksfvzghfxiav2f8svc0812fa5kmyz5d97kr"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (home-page "http://pygments.org/")
    (synopsis "Syntax highlighting")
    (description
     "Pygments is a syntax highlighting package written in Python.")
    (license bsd-2)))

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

(define-public python-sphinx
  (package
    (name "python-sphinx")
    (version "1.2.3")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/S/Sphinx/Sphinx-"
             version ".tar.gz"))
       (sha256
        (base32
         "011xizm3jnmf4cvs5i6kgf6c5nn046h79i8j0vd0f27yw9j3p4wl"))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)
       ("python-jinja2" ,python-jinja2)
       ("python-docutils" ,python-docutils)
       ("python-pygments" ,python-pygments)))
    (home-page "http://sphinx-doc.org/")
    (synopsis "Python documentation generator")
    (description "Sphinx is a tool that makes it easy to create documentation
for Python projects or other documents consisting of multiple reStructuredText
sources.")
    (license bsd-3)))

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

(define-public python-sphinx-rtd-theme
  (package
    (name "python-sphinx-rtd-theme")
    (version "0.1.6")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://pypi.python.org/packages/source/s/"
                           "sphinx_rtd_theme/sphinx_rtd_theme-"
                           version ".tar.gz"))
       (sha256
        (base32
         "19nw3rn7awplcdrz63kg1njqwkbymfg9lwn7l2grhdyhyr2gaa8g"))))
    (build-system python-build-system)
    (arguments
     `(;; With standard flags, the install phase attempts to create a zip'd
       ;; egg file, and fails with an error: 'ZIP does not support timestamps
       ;; before 1980'
       #:configure-flags '("--single-version-externally-managed"
                           "--record=sphinx-rtd-theme.txt")))
    (native-inputs
     `(("python-setuptools" ,python-setuptools)))
    (inputs
     `(("python-docutils" ,python-docutils)
       ("python-sphinx" ,python-sphinx)))
    (home-page "https://github.com/snide/sphinx_rtd_theme/")
    (synopsis "ReadTheDocs.org theme for Sphinx")
    (description "A theme for Sphinx used by ReadTheDocs.org.")
    (license license:expat)))

(define-public python2-sphinx-rtd-theme
  (package-with-python2 python-sphinx-rtd-theme))

(define-public python-scikit-learn
  (package
    (name "python-scikit-learn")
    (version "0.15.2")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://github.com/scikit-learn/scikit-learn/archive/"
             version ".tar.gz"))
       (sha256
        (base32
         "1rb93h2q15f219sz60sczjb65rg70xjmnp0q4pkkaairx5s05q55"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (alist-cons-before
        'build 'set-environment-variables
        (lambda* (#:key inputs #:allow-other-keys)
          (let* ((atlas-threaded
                  (string-append (assoc-ref inputs "atlas")
                                 "/lib/libtatlas.so"))
                 ;; On single core CPUs only the serial library is created.
                 (atlas-lib
                  (if (file-exists? atlas-threaded)
                      atlas-threaded
                      (string-append (assoc-ref inputs "atlas")
                                     "/lib/libsatlas.so"))))
            (setenv "ATLAS" atlas-lib)))
        (alist-cons-before
         'check 'set-HOME
         ;; some tests require access to "$HOME"
         (lambda _ (setenv "HOME" "/tmp"))
         ;; Tests can only be run after the library has been installed and not
         ;; within the source directory.
         (alist-cons-after
          'install 'check
          (lambda _
            (with-directory-excursion "/tmp"
              ;; With Python 3 one test of 3334 fails
              ;; (sklearn.tests.test_common.test_transformers); see
              ;; https://github.com/scikit-learn/scikit-learn/issues/3693
              (system* "nosetests" "-v" "sklearn")))
          (alist-delete 'check %standard-phases))))))
    (inputs
     `(("atlas" ,atlas)
       ("python-nose" ,python-nose)))
    (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 bsd-3)))

(define-public python2-scikit-learn
  (let ((scikit (package-with-python2 python-scikit-learn)))
    (package (inherit scikit)
      (propagated-inputs
       `(("python2-numpy" ,python2-numpy)
         ("python2-scipy" ,python2-scipy)
         ,@(alist-delete
            "python-numpy"
            (alist-delete
             "python-scipy" (package-propagated-inputs scikit))))))))

(define-public python-cython
  (package
    (name "python-cython")
    (version "0.21.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "http://cython.org/release/Cython-"
                           version ".tar.gz"))
       (sha256
        (base32
         "0ddz2l2dvcy5hdkxx4xlfiwpccvwia7ixgcy4h0pdv46a4i4vxj3"))))
    (build-system python-build-system)
    ;; we need the full python package and not just the python-wrapper
    ;; because we need libpython3.3m.so
    (inputs
     `(("python" ,python)))
    (arguments
     `(#:phases
       (alist-cons-before
        'check 'set-HOME
        ;; some tests require access to "$HOME/.cython"
        (lambda* _ (setenv "HOME" "/tmp"))
        (alist-replace
         'check
         (lambda _ (zero? (system* "python" "runtests.py" "-vv")))
         %standard-phases))))
    (home-page "http://cython.org/")
    (synopsis "C extensions for Python")
    (description "Cython is an optimising static compiler for both the Python
programming language and the extended Cython programming language.  It makes
writing C extensions for Python as easy as Python itself.")
    (license asl2.0)))

(define-public python2-cython
  (package (inherit (package-with-python2 python-cython))
    (name "python2-cython")
    (inputs
     `(("python-2" ,python-2))))) ; this is not automatically changed

;; This version of numpy is missing the documentation and is only used to
;; build matplotlib which is required to build numpy's documentation.
(define python-numpy-bootstrap
  (package
    (name "python-numpy-bootstrap")
    (version "1.9.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://sourceforge/numpy"
                           "/numpy-" version ".tar.gz"))
       (sha256
        (base32
         "070ybfvpgfmiz2hs94x445hvkh9dh52nyi0m8jp5kdihgvhbnx80"))))
    (build-system python-build-system)
    (inputs
     `(("python-nose" ,python-nose)
       ("atlas" ,atlas)))
    (native-inputs
     `(("gfortran" ,gfortran-4.8)))
    (arguments
     `(#:phases
       (alist-cons-before
        'build 'set-environment-variables
        (lambda* (#:key inputs #:allow-other-keys)
          (let* ((atlas-threaded
                  (string-append (assoc-ref inputs "atlas")
                                 "/lib/libtatlas.so"))
                 ;; On single core CPUs only the serial library is created.
                 (atlas-lib
                  (if (file-exists? atlas-threaded)
                      atlas-threaded
                      (string-append (assoc-ref inputs "atlas")
                                     "/lib/libsatlas.so"))))
            (setenv "ATLAS" atlas-lib)))
        ;; Tests can only be run after the library has been installed and not
        ;; within the source directory.
        (alist-cons-after
         'install 'check
         (lambda _
           (with-directory-excursion "/tmp"
             (zero? (system* "python" "-c"
                             "import numpy; numpy.test(verbose=2)"))))
         (alist-delete
          'check
          %standard-phases)))))
    (home-page "http://www.numpy.org/")
    (synopsis "Fundamental package for scientific computing with Python")
    (description "NumPy is the fundamental package for scientific computing
with Python. It contains among other things: a powerful N-dimensional array
object, sophisticated (broadcasting) functions, tools for integrating C/C++
and Fortran code, useful linear algebra, Fourier transform, and random number
capabilities.")
    (license bsd-3)))

(define python2-numpy-bootstrap
  (package-with-python2 python-numpy-bootstrap))

(define-public python-numpy
  (package (inherit python-numpy-bootstrap)
    (name "python-numpy")
    (outputs '("out" "doc"))
    (inputs
     `(("which" ,which)
       ("python-setuptools" ,python-setuptools)
       ("python-matplotlib" ,python-matplotlib)
       ("python-sphinx" ,python-sphinx)
       ("python-pyparsing" ,python-pyparsing)
       ("python-numpydoc" ,python-numpydoc)
       ,@(package-inputs python-numpy-bootstrap)))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("texlive" ,texlive)
       ("texinfo" ,texinfo)
       ("perl" ,perl)
       ,@(package-native-inputs python-numpy-bootstrap)))
    (arguments
     `(,@(substitute-keyword-arguments
             (package-arguments python-numpy-bootstrap)
           ((#:phases phases)
            `(alist-cons-after
              'install 'install-doc
              (lambda* (#:key outputs #:allow-other-keys)
                (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
                       (doc (string-append
                             data "/doc/" ,name "-"
                             ,(package-version python-numpy-bootstrap)))
                       (info (string-append data "/info"))
                       (html (string-append doc "/html"))
                       (pyver ,(string-append "PYVER=")))
                  (with-directory-excursion "doc"
                    (mkdir-p html)
                    (system* "make" "html" pyver)
                    (system* "make" "latex" "PAPER=a4" pyver)
                    (system* "make" "-C" "build/latex"
                             "all-pdf" "PAPER=a4" pyver)
                    ;; FIXME: Generation of the info file fails.
                    ;; (system* "make" "info" pyver)
                    ;; (mkdir-p info)
                    ;; (copy-file "build/texinfo/numpy.info"
                    ;;            (string-append info "/numpy.info"))
                    (for-each (lambda (file)
                                (copy-file (string-append "build/latex" file)
                                           (string-append doc file)))
                              '("/numpy-ref.pdf" "/numpy-user.pdf"))
                    (with-directory-excursion "build/html"
                      (for-each (lambda (file)
                                  (let* ((dir (dirname file))
                                         (tgt-dir (string-append html "/" dir)))
                                    (unless (equal? "." dir)
                                      (mkdir-p tgt-dir))
                                    (copy-file file (string-append html "/" file))))
                                (find-files "." ".*"))))))
              ,phases)))))))

(define-public python2-numpy
  (let ((numpy (package-with-python2 python-numpy)))
    (package (inherit numpy)
      ;; Make sure we use exactly PYTHON2-MATPLOTLIB, which is customized for
      ;; Python 2.
      (inputs `(("python2-matplotlib" ,python2-matplotlib)
                ,@(alist-delete "python-matplotlib"
                                (package-inputs numpy)))))))

(define-public python-pyparsing
  (package
    (name "python-pyparsing")
    (version "2.0.3")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://sourceforge/pyparsing"
                           "/pyparsing-" version ".tar.gz"))
       (sha256
        (base32
         "0kw4py7gn45j93q8r7bzajfrjdc3xlsn2yzln41lf9zmrghjkrq6"))))
    (build-system python-build-system)
    (outputs '("out" "doc"))
    (arguments
     `(#:tests? #f ; no test target
       #:modules ((guix build python-build-system)
                  (guix build utils))
       #:phases
       (alist-cons-after
        'install 'install-doc
        (lambda* (#:key outputs #:allow-other-keys)
          (let* ((doc (string-append (assoc-ref outputs "doc")
                                     "/share/doc/" ,name "-" ,version))
                 (html-doc (string-append doc "/html"))
                 (examples (string-append doc "/examples")))
            (mkdir-p html-doc)
            (mkdir-p examples)
            (for-each
             (lambda (dir tgt)
               (map (lambda (file)
                      (copy-file file (string-append tgt "/" (basename file))))
                    (find-files dir ".*")))
             (list "docs" "htmldoc" "examples")
             (list doc html-doc examples))))
        %standard-phases)))
    (home-page "http://pyparsing.wikispaces.com")
    (synopsis "Python parsing class library")
    (description
     "The pyparsing module is an alternative approach to creating and
executing simple grammars, vs. the traditional lex/yacc approach, or the use
of regular expressions.  The pyparsing module provides a library of classes
that client code uses to construct the grammar directly in Python code.")
    (license license:expat)))

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

(define-public python-numpydoc
  (package
    (name "python-numpydoc")
    (version "0.5")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/n/numpydoc/numpydoc-"
             version ".tar.gz"))
       (sha256
        (base32
         "0d4dnifaxkll50jx6czj05y8cb4ny60njd2wz299sj2jxfy51w4k"))
       (modules '((guix build utils)))
       (snippet
        '(begin
           ;; Drop a test requiring matplotlib, which we cannot add as an
           ;; input since it would create a circular dependency: Extend the
           ;; test for Python 3, where it is already dropped, to Python 2.
           (substitute* "numpydoc/tests/test_plot_directive.py"
             (("3") "2"))))))
    (build-system python-build-system)
    (inputs
     `(("python-setuptools" ,python-setuptools)
       ("python-docutils" ,python-docutils)
       ("python-sphinx" ,python-sphinx)
       ("python-nose" ,python-nose)))
    (home-page "https://pypi.python.org/pypi/numpydoc")
    (synopsis
     "Numpy's Sphinx extensions")
    (description
     "Sphinx extension to support docstrings in Numpy format.")
    (license bsd-2)))

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

(define-public python-matplotlib
  (package
    (name "python-matplotlib")
    (version "1.4.2")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://sourceforge/matplotlib"
                           "/matplotlib-" version ".tar.gz"))
       (sha256
        (base32
         "0m6v9nwdldlwk22gcd339zg6mny5m301fxgks7z8sb8m9wawg8qp"))))
    (build-system python-build-system)
    (outputs '("out" "doc"))
    (propagated-inputs ; the following packages are all needed at run time
     `(("python-pyparsing" ,python-pyparsing)
       ("python-pygobject" ,python-pygobject)
       ("gobject-introspection" ,gobject-introspection)
       ;; The 'gtk+' package (and 'gdk-pixbuf', 'atk' and 'pango' propagated
       ;; from 'gtk+') provides the required 'typelib' files used by
       ;; 'gobject-introspection'. The location of these files is set with the
       ;; help of the environment variable GI_TYPELIB_PATH. At build time this
       ;; is done automatically by a 'native-search-path' procedure. However,
       ;; at run-time the user must set this variable as follows:
       ;;
       ;; export GI_TYPELIB_PATH=~/.guix-profile/lib/girepository-1.0
       ("gtk+" ,gtk+)
       ;; From version 1.4.0 'matplotlib' makes use of 'cairocffi' instead of
       ;; 'pycairo'. However, 'pygobject' makes use of a 'pycairo' 'context'
       ;; object. For this reason we need to import both libraries.
       ;; https://pythonhosted.org/cairocffi/cffi_api.html#converting-pycairo
       ("python-pycairo" ,python-pycairo)
       ("python-cairocffi" ,python-cairocffi)))
    (inputs
     `(("python-setuptools" ,python-setuptools)
       ("python-dateutil" ,python-dateutil-2)
       ("python-six" ,python-six)
       ("python-pytz" ,python-pytz)
       ("python-numpy" ,python-numpy-bootstrap)
       ("python-sphinx" ,python-sphinx)
       ("python-numpydoc" ,python-numpydoc)
       ("python-nose" ,python-nose)
       ("python-mock" ,python-mock)
       ("libpng" ,libpng)
       ("imagemagick" ,imagemagick)
       ("freetype" ,freetype)
       ("cairo" ,cairo)
       ("glib" ,glib)
       ("python-pillow" ,python-pillow)
       ;; FIXME: Add backends when available.
       ;("python-wxpython" ,python-wxpython)
       ;("python-pyqt" ,python-pyqt)
       ))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("texlive" ,texlive)
       ("texinfo" ,texinfo)))
    (arguments
     `(#:phases
       (alist-cons-before
        'build 'configure-environment
        (lambda* (#:key outputs inputs #:allow-other-keys)
          (let ((cairo (assoc-ref inputs "cairo"))
                (gtk+ (assoc-ref inputs "gtk+")))
            ;; Setting these directories in the 'basedirlist' of 'setup.cfg'
            ;; has not effect.
            (setenv "LD_LIBRARY_PATH"
                    (string-append cairo "/lib:" gtk+ "/lib"))
            (setenv "HOME" (getcwd))
            (call-with-output-file "setup.cfg"
              (lambda (port)
                (format port "[rc_options]~%
backend = GTK3Agg~%")))))
        (alist-cons-after
         'install 'install-doc
         (lambda* (#:key outputs #:allow-other-keys)
           (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
                  (doc (string-append data "/doc/" ,name "-" ,version))
                  (info (string-append data "/info"))
                  (html (string-append doc "/html")))
             (with-directory-excursion "doc"
               ;; Produce pdf in 'A4' format.
               (substitute* (find-files "." "conf\\.py")
                 (("latex_paper_size = 'letter'")
                  "latex_paper_size = 'a4'"))
               (mkdir-p html)
               (mkdir-p info)
               ;; The doc recommends to run the 'html' target twice.
               (system* "python" "make.py" "html")
               (system* "python" "make.py" "html")
               (system* "python" "make.py" "latex")
               (system* "python" "make.py" "texinfo")
               (copy-file "build/texinfo/matplotlib.info"
                          (string-append info "/matplotlib.info"))
               (copy-file "build/latex/Matplotlib.pdf"
                          (string-append doc "/Matplotlib.pdf"))
               (copy-recursively "build/html" html))))
        %standard-phases))))
    (home-page "http://matplotlib.org")
    (synopsis "2D plotting library for Python")
    (description
     "Matplotlib is a Python 2D plotting library which produces publication
quality figures in a variety of hardcopy formats and interactive environments
across platforms.  Matplotlib can be used in Python scripts, the python and
ipython shell, web application servers, and six graphical user interface
toolkits.")
    (license psfl)))

(define-public python2-matplotlib
  (let ((matplotlib (package-with-python2 python-matplotlib)))
    (package (inherit matplotlib)
      ;; Make sure to use special packages for Python 2 instead
      ;; of those automatically rewritten by package-with-python2.
      (propagated-inputs
       `(("python2-pycairo" ,python2-pycairo)
         ("python2-pygobject-2" ,python2-pygobject-2)
         ,@(alist-delete "python-pycairo"
                         (alist-delete "python-pygobject"
                                       (package-propagated-inputs
                                        matplotlib))))))))

(define-public python-scipy
  (package
    (name "python-scipy")
    (version "0.15.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://sourceforge/scipy"
                           "/scipy-" version ".tar.xz"))
       (sha256
        (base32
         "0fsqi05s035d7p6s8h3h2pvk1axias16chy17rw9l1bxvrfhmncf"))))
    (build-system python-build-system)
    (inputs
     `(("python-numpy" ,python-numpy)
       ("python-matplotlib" ,python-matplotlib)
       ("python-pyparsing" ,python-pyparsing)
       ("python-nose" ,python-nose)
       ("python-sphinx" ,python-sphinx)
       ("atlas" ,atlas)))
    (native-inputs
     `(("gfortran" ,gfortran-4.8)
       ("texlive" ,texlive)
       ("perl" ,perl)))
    (outputs '("out" "doc"))
    (arguments
     `(#:phases
       (alist-cons-before
        'build 'set-environment-variables
        (lambda* (#:key inputs #:allow-other-keys)
          (let* ((atlas-threaded
                  (string-append (assoc-ref inputs "atlas")
                                 "/lib/libtatlas.so"))
                 ;; On single core CPUs only the serial library is created.
                 (atlas-lib
                  (if (file-exists? atlas-threaded)
                      atlas-threaded
                      (string-append (assoc-ref inputs "atlas")
                                     "/lib/libsatlas.so"))))
            (setenv "ATLAS" atlas-lib)))
        (alist-cons-after
         'install 'install-doc
         (lambda* (#:key outputs #:allow-other-keys)
           (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
                  (doc (string-append data "/doc/" ,name "-" ,version))
                  (html (string-append doc "/html"))
                  (pyver ,(string-append "PYVER=")))
             (with-directory-excursion "doc"
               ;; Fix generation of images for mathematical expressions.
               (substitute* (find-files "source" "conf\\.py")
                 (("pngmath_use_preview = True")
                  "pngmath_use_preview = False"))
               (mkdir-p html)
               (system* "make" "html" pyver)
               (system* "make" "latex" "PAPER=a4" pyver)
               (system* "make" "-C" "build/latex" "all-pdf" "PAPER=a4" pyver)
               (copy-file "build/latex/scipy-ref.pdf"
                          (string-append doc "/scipy-ref.pdf"))
               (with-directory-excursion "build/html"
                 (for-each (lambda (file)
                             (let* ((dir (dirname file))
                                    (tgt-dir (string-append html "/" dir)))
                               (unless (equal? "." dir)
                                 (mkdir-p tgt-dir))
                               (copy-file file (string-append html "/" file))))
                           (find-files "." ".*"))))))
         ;; Tests can only be run after the library has been installed and not
         ;; within the source directory.
         (alist-cons-after
          'install 'check
          (lambda _
            (with-directory-excursion "/tmp"
              (zero? (system* "python" "-c" "import scipy; scipy.test()"))))
          (alist-delete
           'check
           %standard-phases))))))
    (home-page "http://www.scipy.org/")
    (synopsis "The Scipy library provides efficient numerical routines")
    (description "The SciPy library is one of the core packages that make up
the SciPy stack.  It provides many user-friendly and efficient numerical
routines such as routines for numerical integration and optimization.")
    (license bsd-3)))

(define-public python2-scipy
  (let ((scipy (package-with-python2 python-scipy)))
    (package (inherit scipy)
      ;; Use packages customized for python-2.
      (inputs `(("python2-matplotlib" ,python2-matplotlib)
                ("python2-numpy" ,python2-numpy)
                ,@(alist-delete "python-matplotlib"
                                (alist-delete "python-numpy"
                                              (package-inputs scipy))))))))

(define-public python-sqlalchemy
  (package
    (name "python-sqlalchemy")
    (version "0.9.7")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/S/"
                          "SQLAlchemy/SQLAlchemy-" version ".tar.gz"))
      (sha256
       (base32
        "059ayifj5l08v6vv56anhyibyllscn10dlzr2fcw68gz1hfjdzsz"))))
    (build-system python-build-system)
    (native-inputs
     `(("python-cython" ,python-cython) ;for c extensions
       ("python-pytest" ,python-pytest)
       ("python-mock"   ,python-mock))) ;for tests
    (arguments
     `(#:phases (alist-replace
                 'check
                 (lambda _ (zero? (system* "py.test")))
                 %standard-phases)))
    (home-page "http://www.sqlalchemy.org")
    (synopsis "Database abstraction library")
    (description
     "SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that
gives application developers the full power and flexibility of SQL.  It
provides a full suite of well known enterprise-level persistence patterns,
designed for efficient and high-performing database access, adapted into a
simple and Pythonic domain language.")
    (license x11)))

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

(define-public python-distutils-extra
  (package
    (name "python-distutils-extra")
    (version "2.38")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://launchpad.net/python-distutils-extra/trunk/"
                          version "/+download/python-distutils-extra-"
                          version ".tar.gz"))
      (sha256
       (base32
        "0lx15kcbby9zisx33p2h5hgakgwh2bvh0ibag8z0px4j6ifhs41x"))))
    (build-system python-build-system)
    (native-inputs
     `(("python-setuptools" ,python-setuptools)))
    (home-page "https://launchpad.net/python-distutils-extra/")
    (synopsis "Enhancements to Python's distutils")
    (description
     "The python-distutils-extra module enables you to easily integrate
gettext support, themed icons, and scrollkeeper-based documentation into
Python's distutils.")
    (license gpl2)))

(define-public python2-distutils-extra
  (package-with-python2 python-distutils-extra))

(define-public python2-elib.intl
  (package
    (name "python2-elib.intl")
    (version "0.0.3")
    (source
     (origin
       ;; This project doesn't tag releases or publish tarballs, so we take
       ;; source from a (semi-arbitrary, i.e. latest as of now) git commit.
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/dieterv/elib.intl.git")
             (commit "d09997cfef")))
       (sha256
        (base32
         "0y7vzff9xgbnaay7m0va1arl6g68ncwrvbgwl7jqlclsahzzb09d"))))
    (build-system python-build-system)
    (native-inputs
     `(("python2-setuptools" ,python2-setuptools)))
    (arguments
     ;; incompatible with Python 3 (exception syntax)
     `(#:python ,python-2
       #:tests? #f
       ;; With standard flags, the install phase attempts to create a zip'd
       ;; egg file, and fails with an error: 'ZIP does not support timestamps
       ;; before 1980'
       #:configure-flags '("--single-version-externally-managed"
                           "--record=elib.txt")))
    (home-page "https://github.com/dieterv/elib.intl")
    (synopsis "Enhanced internationalization for Python")
    (description
     "The elib.intl module provides enhanced internationalization (I18N)
services for your Python modules and applications.")
    (license lgpl3+)))

(define-public python-pillow
  (package
    (name "python-pillow")
    (version "2.6.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://pypi.python.org/packages/source/P/"
                           "Pillow/Pillow-" version ".tar.gz"))
       (sha256
        (base32
         "0iw36c73wkhz88wa78v6l43llsb080ihw8yq7adhfqxdib7l4hzr"))))
    (build-system python-build-system)
    (native-inputs
     `(("python-setuptools" ,python-setuptools)
       ("python-nose"       ,python-nose)))
    (inputs
     `(("lcms"     ,lcms)
       ("zlib"     ,zlib)
       ("libjpeg"  ,libjpeg)
       ("openjpeg" ,openjpeg)
       ("libtiff"  ,libtiff)))
    (propagated-inputs
     `(;; Used at runtime for pkg_resources
       ("python-setuptools" ,python-setuptools)))
    (arguments
     `(#:phases (alist-cons-after
                 'install 'check-installed
                 (lambda _
                   (begin
                     (setenv "HOME" (getcwd))
                     (and (zero? (system* "python" "selftest.py" "--installed"))
                          (zero? (system* "python" "test-installed.py")))))
                 (alist-delete 'check %standard-phases))))
    (home-page "https://pypi.python.org/pypi/Pillow")
    (synopsis "Fork of the Python Imaging Library")
    (description
     "The Python Imaging Library adds image processing capabilities to your
Python interpreter.  This library provides extensive file format support, an
efficient internal representation, and fairly powerful image processing
capabilities.  The core image library is designed for fast access to data
stored in a few basic pixel formats.  It should provide a solid foundation for
a general image processing tool.")
    (license (x11-style
              "http://www.pythonware.com/products/pil/license.htm"
              "The PIL Software License"))))

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

(define-public python-pycparser
  (package
    (name "python-pycparser")
    (version "2.10")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/p/"
                          "pycparser/pycparser-" version ".tar.gz"))
      (sha256
       (base32
        "0v5qfq03yvd1pi0dwlgfai0p3dh9bq94pydn19c4pdn0c6v9hzcm"))))
    (outputs '("out" "doc"))
    (build-system python-build-system)
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("python-setuptools" ,python-setuptools)))
    (arguments
     `(#:phases
       (alist-replace
        'check
        (lambda _
          (with-directory-excursion "tests"
            (zero? (system* "python" "all_tests.py"))))
        (alist-cons-after
         'install 'install-doc
         (lambda* (#:key outputs #:allow-other-keys)
           (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
                  (doc (string-append data "/doc/" ,name "-" ,version))
                  (examples (string-append doc "/examples")))
             (mkdir-p examples)
             (for-each (lambda (file)
                         (copy-file (string-append "." file)
                                    (string-append doc file)))
                       '("/README.rst" "/CHANGES" "/LICENSE"))
             (copy-recursively "examples" examples)))
         %standard-phases))))
    (home-page "https://github.com/eliben/pycparser")
    (synopsis "C parser in Python")
    (description
     "Pycparser is a complete parser of the C language, written in pure Python
using the PLY parsing library.  It parses C code into an AST and can serve as
a front-end for C compilers or analysis tools.")
    (license bsd-3)))

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

(define-public python-cffi
  (package
    (name "python-cffi")
    (version "0.8.6")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/c/"
                          "cffi/cffi-" version ".tar.gz"))
      (sha256
       (base32 "0406j3sgndmx88idv5zxkkrwfqxmjl18pj8gf47nsg4ymzixjci5"))))
    (build-system python-build-system)
    (outputs '("out" "doc"))
    (inputs
     `(("libffi" ,libffi)))
    (propagated-inputs ; required at run-time
     `(("python-pycparser" ,python-pycparser)))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("python-sphinx" ,python-sphinx)
       ("python-setuptools" ,python-setuptools)))
    (arguments
     `(#:tests? #f ; FIXME: requires pytest
       #:phases
       (alist-cons-after
        'install 'install-doc
        (lambda* (#:key outputs #:allow-other-keys)
          (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
                 (doc (string-append data "/doc/" ,name "-" ,version))
                 (html (string-append doc "/html")))
            (with-directory-excursion "doc"
              (system* "make" "html")
              (mkdir-p html)
              (copy-recursively "build/html" html))
            (copy-file "LICENSE" (string-append doc "/LICENSE"))))
        %standard-phases)))
    (home-page "http://cffi.readthedocs.org")
    (synopsis "Foreign function interface for Python")
    (description
     "Foreign Function Interface for Python calling C code.")
    (license license:expat)))

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

(define-public python-xcffib
  (package
    (name "python-xcffib")
    (version "0.1.9")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/x/"
                          "xcffib/xcffib-" version ".tar.gz"))
      (sha256
       (base32
        "0655hzxv57h1a9ja9kwp0ichbkhf3djw32k33d66xp0q37dq2y81"))))
    (build-system python-build-system)
    (inputs
     `(("libxcb" ,libxcb)
       ("python-six" ,python-six)))
    (native-inputs
     `(("python-setuptools" ,python-setuptools)))
    (propagated-inputs
     `(("python-cffi" ,python-cffi))) ; used at run time
    (arguments
     `(#:phases
       (alist-cons-after
        'install 'install-doc
        (lambda* (#:key outputs #:allow-other-keys)
          (let ((doc (string-append (assoc-ref outputs "out") "/share"
                                    "/doc/" ,name "-" ,version)))
            (mkdir-p doc)
            (copy-file "README.md"
                       (string-append doc "/README.md"))))
        %standard-phases)))
    (home-page "https://github.com/tych0/xcffib")
    (synopsis "XCB Python bindings")
    (description
     "Xcffib is a replacement for xpyb, an XCB Python bindings.  It adds
support for Python 3 and PyPy.  It is based on cffi.")
    (license license:expat)))

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

(define-public python-cairocffi
  (package
    (name "python-cairocffi")
    (version "0.6")
    (source
     (origin
      (method url-fetch)
      ;; The archive on pypi is missing the 'utils' directory!
      (uri (string-append "https://github.com/SimonSapin/cairocffi/archive/v"
                          version ".tar.gz"))
      (file-name (string-append name "-" version ".tar.gz"))
      (sha256
       (base32
        "03w5p62sp3nqiccx864sbq0jvh7946277jqx3rcc3dch5xwfvv51"))))
    (build-system python-build-system)
    (outputs '("out" "doc"))
    (inputs
     `(("gdk-pixbuf" ,gdk-pixbuf)
       ("cairo" ,cairo)))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("python-sphinx" ,python-sphinx)
       ("python-docutils" ,python-docutils)
       ("python-setuptools" ,python-setuptools)))
    (propagated-inputs
     `(("python-xcffib" ,python-xcffib))) ; used at run time
    (arguments
     `(#:phases
       (alist-cons-after
        'install 'install-doc
        (lambda* (#:key inputs outputs #:allow-other-keys)
          (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
                 (doc (string-append data "/doc/" ,name "-" ,version))
                 (html (string-append doc "/html")))
            (setenv "LD_LIBRARY_PATH"
                    (string-append (assoc-ref inputs "cairo") "/lib" ":"
                                   (assoc-ref inputs "gdk-pixbuf") "/lib"))
            (setenv "LANG" "en_US.UTF-8")
            (mkdir-p html)
            (for-each (lambda (file)
                        (copy-file (string-append "." file)
                                   (string-append doc file)))
                      '("/README.rst" "/CHANGES" "/LICENSE"))
            (system* "python" "setup.py" "build_sphinx")
            (copy-recursively "docs/_build/html" html)))
        %standard-phases)))
    (home-page "https://github.com/SimonSapin/cairocffi")
    (synopsis "Python bindings and object-oriented API for Cairo")
    (description
     "Cairocffi is a CFFI-based drop-in replacement for Pycairo, a set of
Python bindings and object-oriented API for cairo.  Cairo is a 2D vector
graphics library with support for multiple backends including image buffers,
PNG, PostScript, PDF, and SVG file output.")
    (license bsd-3)))

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

(define-public python-ipython
  (package
    (name "python-ipython")
    (version "2.3.1")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://pypi.python.org/packages/source/i/"
                          "ipython/ipython-" version ".tar.gz"))
      (sha256
       (base32 "1764gi5m3ff481rjk336cw6i2h4zlc0nxam9rc5m8m7yl9m4d61y"))))
    (build-system python-build-system)
    (outputs '("out" "doc"))
    ;; FIXME: add optional dependencies when available: pyzmq, tornado, ...
    (inputs
     `(("readline" ,readline)
       ("python-matplotlib" ,python-matplotlib)
       ("python-numpy" ,python-numpy-bootstrap)
       ("python-numpydoc" ,python-numpydoc)
       ("python-nose" ,python-nose)))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("python-sphinx" ,python-sphinx)
       ("texlive" ,texlive)
       ("texinfo" ,texinfo)
       ("python-setuptools" ,python-setuptools)))
    (arguments
     `(#:phases
       (alist-cons-after
        'install 'install-doc
        (lambda* (#:key inputs outputs #:allow-other-keys)
          (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
                 (doc (string-append data "/doc/" ,name "-" ,version))
                 (html (string-append doc "/html"))
                 (man1 (string-append data "/man/man1"))
                 (info (string-append data "/info"))
                 (examples (string-append doc "/examples")))
            (setenv "LANG" "en_US.UTF-8")
            (with-directory-excursion "docs"
              ;; FIXME: html and pdf fail to build without optional pyzmq
              ;(system* "make" "html")
              ;(system* "make" "pdf" "PAPER=a4")
              (system* "make" "info"))
            (copy-recursively "docs/man" man1)
            (copy-recursively "examples" examples)
            ;; (copy-recursively "docs/build/html" html)
            ;; (copy-file "docs/build/latex/ipython.pdf"
            ;;            (string-append doc "/ipython.pdf"))
            (mkdir-p info)
            (copy-file "docs/build/texinfo/ipython.info"
                       (string-append info "/ipython.info"))
            (copy-file "COPYING.rst" (string-append doc "/COPYING.rst"))))
        ;; Tests can only be run after the library has been installed and not
        ;; within the source directory.
        (alist-cons-after
         'install 'check
         (lambda* (#:key outputs #:allow-other-keys)
           ;; The test procedure appears to miss the fact that some optional
           ;; dependencies are missing.
           ;; (with-directory-excursion "/tmp"
           ;;   (zero? (system* (string-append (assoc-ref outputs "out")
           ;;                                  "/bin/iptest"))))
           #t)
         (alist-delete
          'check
          %standard-phases)))))
    (home-page "http://ipython.org")
    (synopsis "IPython is a tool for interactive computing in Python")
    (description
     "IPython provides a rich architecture for interactive computing with:
Powerful interactive shells, a browser-based notebook, support for interactive
data visualization, embeddable interpreters and tools for parallel
computing.")
    (license bsd-3)))

(define-public python2-ipython
  (let ((ipython (package-with-python2 python-ipython)))
    (package (inherit ipython)
      ;; Make sure we use custom python2-NAME packages.
      (inputs
       `(("python2-matplotlib" ,python2-matplotlib)
         ,@(alist-delete "python-matplotlib"
                         (package-inputs ipython)))))))

(define-public python-isodate
  (package
    (name "python-isodate")
    (version "0.5.1")
    (source
      (origin
        (method url-fetch)
        (uri (string-append
              "https://pypi.python.org/packages/source/i/isodate/isodate-"
              version
              ".tar.gz"))
        (sha256
          (base32
            "1yqjn0is0p64cmk9xhq4hc6q06jk86d60kg2jws58d78q0qysami"))))
    (build-system python-build-system)
    (inputs
      `(("python-setuptools" ,python-setuptools)))
    (home-page
      "http://cheeseshop.python.org/pypi/isodate")
    (synopsis
      "Python date parser and formatter")
    (description
      "Python-isodate is a python module for parsing and formatting
ISO 8601 dates, time and duration.")
    (license bsd-3)))

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

(define-public python-html5lib
  (package
    (name "python-html5lib")
    (version "1.0b3")
    (source
      (origin
        (method url-fetch)
        (uri (string-append
              "https://pypi.python.org/packages/source/h/html5lib/html5lib-"
              version
              ".tar.gz"))
        (sha256
          (base32
            "1l5i6xzckzx4hnh9qzv9q3kyhkgjx2hsi2k9srgci3qizjmvp6ln"))))
    (build-system python-build-system)
    (propagated-inputs
      `(("python-six" ,python-six))) ; required to "import html5lib"
    (inputs
      `(("python-setuptools" ,python-setuptools)))
    (arguments
     `(#:test-target "check"))
    (home-page
      "https://github.com/html5lib/html5lib-python")
    (synopsis
      "Python HTML parser based on the WHATWG HTML specifcation")
    (description
      "Html5lib is an HTML parser based on the WHATWG HTML specifcation
and written in Python.")
    (license license:expat)))

(define-public python2-html5lib
  (package-with-python2 python-html5lib))

(define-public python-urwid
  (package
    (name "python-urwid")
    (version "1.3.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/u/urwid/urwid-"
             version ".tar.gz"))
       (sha256
        (base32
         "18mb0yy94sjc434rd61m2sfnw27sa0nyrszpj5a9r9zh7fnlzw19"))))
    (build-system python-build-system)
    (native-inputs `(("python-setuptools" ,python-setuptools)))
    (home-page "http://urwid.org")
    (synopsis "Console user interface library for Python")
    (description
     "Urwid is a curses-based UI/widget library for Python.  It includes many
features useful for text console applications.")
    (license lgpl2.1+)))

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

(define-public python-dbus
  (package
    (name "python-dbus")
    (version "1.2.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "http://dbus.freedesktop.org/releases/dbus-python/dbus-python-"
             version ".tar.gz"))
       (sha256
        (base32 "1py62qir966lvdkngg0v8k1khsqxwk5m4s8nflpk1agk5f5nqb71"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("pkg-config" ,pkg-config)))
    (inputs
     `(("python" ,python)
       ("dbus" ,dbus)
       ("dbus-glib" ,dbus-glib)
       ("glib" ,glib)))
    (synopsis "Python bindings for D-bus")
    (description "python-dbus provides bindings for libdbus, the reference
implementation of D-Bus.")
    (home-page "http://www.freedesktop.org/wiki/Software/DBusBindings/")
    (license license:expat)))

(define-public python2-dbus
  (package (inherit python-dbus)
    (name "python2-dbus")
    (inputs `(("python" ,python-2)
              ,@(alist-delete "python"
                              (package-inputs python-dbus)
                              equal?)))
    ;; FIXME: on Python 2, the test_utf8 fails with:
    ;; "ValueError: unichr() arg not in range(0x10000) (narrow Python build)"
    (arguments `(#:tests? #f))))

(define-public python-apsw
  (package
    (name "python-apsw")
    (version "3.8.7.3-r1")
    (source
      (origin
        (method url-fetch)
        (uri (string-append
              "https://pypi.python.org/packages/source/a/apsw/apsw-"
              version
              ".tar.gz"))
        (sha256
          (base32
            "1rgxdypg7hym0qny15rx5khrghx9fkppfgsfa2s8lg917924mv7l"))))
    (build-system python-build-system)
    (inputs
      `(("python-setuptools" ,python-setuptools)
        ("sqlite" ,sqlite)))
    (arguments
     `(#:phases
        ;; swap check and install phases
        (alist-cons-after
         'install 'check
         (assoc-ref %standard-phases 'check)
         (alist-delete
          'check
          %standard-phases))))
    (home-page "https://github.com/rogerbinns/apsw/")
    (synopsis "Another Python SQLite Wrapper")
    (description "APSW is a Python wrapper for the SQLite
embedded relational database engine.  In contrast to other wrappers such as
pysqlite it focuses on being a minimal layer over SQLite attempting just to
translate the complete SQLite API into Python.")
    (license license:zlib)))

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

(define-public python-lxml
  (package
    (name "python-lxml")
    (version "3.4.2")
    (source
      (origin
        (method url-fetch)
        (uri (string-append
              "https://pypi.python.org/packages/source/l/lxml/lxml-"
              version
              ".tar.gz"))
        (sha256
          (base32
            "0pd23qz8vms1mgm41p96h4vac5y91igs4wr9640gnvxgk019kmf7"))))
    (build-system python-build-system)
    (inputs
      `(("libxml2" ,libxml2)
        ("libxslt" ,libxslt)
        ("python-setuptools" ,python-setuptools)))
    (home-page "http://lxml.de/")
    (synopsis
      "Python XML processing library")
    (description
      "The lxml XML toolkit is a Pythonic binding for the C libraries
libxml2 and libxslt.")
    (license bsd-3))) ; and a few more, see LICENSES.txt

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

(define-public python-pillow
  (package
    (name "python-pillow")
    (version "2.7.0")
    (source
      (origin
        (method url-fetch)
        (uri (string-append
              "https://pypi.python.org/packages/source/P/Pillow/Pillow-"
              version
              ".tar.gz"))
        (sha256
          (base32
            "1y0rysgd7vqpl5lh0lsra7j2k30azwxqlh5jnqk1i0pmfc735s96"))))
    (build-system python-build-system)
    (inputs
      `(("freetype" ,freetype)
        ("lcms" ,lcms)
        ("libjpeg" ,libjpeg)
        ("libtiff" ,libtiff)
        ("openjpeg" ,openjpeg)
        ("python-setuptools" ,python-setuptools)
        ("zlib" ,zlib)))
    (arguments
     `(#:tests? #f)) ; no check target
    (home-page "http://python-pillow.github.io/")
    (synopsis "Pillow fork of Python Imaging Library")
    (description "Pillow is a fork of the Python Imaging Library (PIL).")
    ;; PIL license, see
    ;; http://www.pythonware.com/products/pil/license.htm
    (license (x11-style
               "file://PKG-INFO"
               "See http://www.pythonware.com/products/pil/license.htm"))))

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

(define-public python2-pil
  (package
    (name "python2-pil")
    (version "1.1.7")
    (source
      (origin
        (method url-fetch)
        (uri (string-append
              "http://effbot.org/downloads/Imaging-"
              version ".tar.gz"))
        (sha256
          (base32
            "04aj80jhfbmxqzvmq40zfi4z3cw6vi01m3wkk6diz3lc971cfnw9"))
       (modules '((guix build utils)))
       (snippet
        ;; Adapt to newer freetype. As the package is unmaintained upstream,
        ;; there is no use in creating a patch and reporting it.
        '(substitute* "_imagingft.c"
           (("freetype/")
            "freetype2/")))))
    (build-system python-build-system)
    (inputs
      `(("freetype" ,freetype)
        ("libjpeg" ,libjpeg)
        ("libtiff" ,libtiff)
        ("python-setuptools" ,python-setuptools)
        ("zlib" ,zlib)))
    (arguments
     ;; Only the fork python-pillow works with Python 3.
     `(#:python ,python-2
       #:tests? #f ; no check target
       #:phases
         (alist-cons-before
          'build 'configure
          ;; According to README and setup.py, manual configuration is
          ;; the preferred way of "searching" for inputs.
          ;; lcms is not found, TCL_ROOT refers to the unavailable tkinter.
          (lambda* (#:key inputs #:allow-other-keys)
            (let ((jpeg (assoc-ref inputs "libjpeg"))
                  (zlib (assoc-ref inputs "zlib"))
                  (tiff (assoc-ref inputs "libtiff"))
                  (freetype (assoc-ref inputs "freetype")))
              (substitute* "setup.py"
                (("JPEG_ROOT = None")
                 (string-append "JPEG_ROOT = libinclude(\"" jpeg "\")"))
                (("ZLIB_ROOT = None")
                 (string-append "ZLIB_ROOT = libinclude(\"" zlib "\")"))
                (("TIFF_ROOT = None")
                 (string-append "TIFF_ROOT = libinclude(\"" tiff "\")"))
                (("FREETYPE_ROOT = None")
                 (string-append "FREETYPE_ROOT = libinclude(\""
                                freetype "\")")))))
          %standard-phases)))
    (home-page "http://www.pythonware.com/products/pil/")
    (synopsis "Python Imaging Library")
    (description "The Python Imaging Library (PIL) adds image processing
capabilities to the Python interpreter.")
    (license (x11-style
               "file://README"
               "See 'README' in the distribution."))))

(define-public python2-cssutils
  (package
    (name "python2-cssutils")
    (version "1.0")
    (source
      (origin
        (method url-fetch)
        (uri (string-append
              "https://pypi.python.org/packages/source/c/cssutils/cssutils-"
              version
              ".zip"))
        (sha256
          (base32
            "1bwim1353r4hqiir73sn4sc43y7ymh09qx0kly7vj048blppc125"))))
    (build-system python-build-system)
    (native-inputs
      `(("python2-mock" ,python2-mock) ; for the tests
        ("unzip" ,unzip))) ; for unpacking the source
    (inputs
      `(("python2-setuptools" ,python2-setuptools)))
    (arguments
     `(#:python ,python-2 ; Otherwise tests fail with a syntax error.
       #:tests? #f ; The tests apparently download an external URL.
       ))
    (home-page "http://cthedot.de/cssutils/")
    (synopsis
      "CSS Cascading Style Sheets library for Python")
    (description
      "Cssutils is a Python package for parsing and building CSS
Cascading Style Sheets.  Currently it provides a DOM only and no rendering
options.")
    (license lgpl3+)))

(define-public python-cssselect
  (package
    (name "python-cssselect")
    (version "0.9.1")
    (source
      (origin
        (method url-fetch)
        (uri (string-append
              "https://pypi.python.org/packages/source/c/cssselect/cssselect-"
              version
              ".tar.gz"))
        (sha256
          (base32
            "10h623qnp6dp1191jri7lvgmnd4yfkl36k9smqklp1qlf3iafd85"))))
    (build-system python-build-system)
    (inputs
      `(("python-setuptools" ,python-setuptools)))
    (arguments
     ;; tests fail with message
     ;; AttributeError: 'module' object has no attribute 'tests'
     `(#:tests? #f))
    (home-page
      "https://pythonhosted.org/cssselect/")
    (synopsis
      "CSS3 selector parser and translator to XPath 1.0")
    (description
      "Cssselect ia a Python module that parses CSS3 Selectors and translates
them to XPath 1.0 expressions.  Such expressions can be used in lxml or
another XPath engine to find the matching elements in an XML or HTML document.")
    (license bsd-3)))

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

(define-public python-netifaces
  (package
    (name "python-netifaces")
    (version "0.10.4")
    (source
      (origin
        (method url-fetch)
        (uri (string-append
              "https://pypi.python.org/packages/source/n/netifaces/netifaces-"
              version
              ".tar.gz"))
        (sha256
          (base32
            "1plw237a4zib4z8s62g0mrs8gm3kjfrp5sxh6bbk9nl3rdls2mln"))))
    (build-system python-build-system)
    (inputs
      `(("python-setuptools" ,python-setuptools)))
    (home-page
      "https://bitbucket.org/al45tair/netifaces")
    (synopsis
      "Python module for portable network interface information")
    (description
      "Netifaces is a Python module providing information on network
interfaces in an easy and portable manner.")
    (license license:expat)))

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

(define-public snakemake
  (package
    (name "snakemake")
    (version "3.2.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/s/snakemake/snakemake-"
             version ".tar.gz"))
       (sha256
        (base32 "0fi4b63sj60hvi7rfydvmz2icl4wj74djw5sn2gl8hxd02qw4b91"))))
    (build-system python-build-system)
    (inputs `(("python-setuptools" ,python-setuptools)))
    (home-page "https://bitbucket.org/johanneskoester/snakemake")
    (synopsis "Python-based execution environment for make-like workflows")
    (description
      "Snakemake aims to reduce the complexity of creating workflows by
providing a clean and modern domain specific specification language (DSL) in
Python style, together with a fast and comfortable execution environment.")
    (license license:expat)))

(define-public python-testlib
  (package
    (name "python-testlib")
    (version "0.6.5")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/t/testlib/testlib-"
             version ".zip"))
       (sha256
        (base32 "1mz26cxn4x8bbgv0rn0mvj2z05y31rkc8009nvdlb3lam5b4mj3y"))))
    (build-system python-build-system)
    (inputs
      `(("python-setuptools" ,python-setuptools)))
    (native-inputs
     `(("unzip" ,unzip)))
    (arguments
     `(#:phases
       (alist-replace
        'unpack
        (lambda* (#:key inputs outputs #:allow-other-keys)
          (let ((unzip (string-append (assoc-ref inputs "unzip")
                                      "/bin/unzip"))
                (source (assoc-ref inputs "source")))
            (and (zero? (system* unzip source))
                 (chdir (string-append "testlib-" ,version)))))
        %standard-phases)))
    (synopsis "Python micro test suite harness")
    (description "A micro unittest suite harness for Python.")
    (home-page "https://github.com/trentm/testlib")
    (license license:expat)))

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

(define-public python2-xlib
  (package
    (name "python2-xlib")
    (version "0.14")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/python-xlib/"
                                  "python-xlib-" version ".tar.gz"))
              (sha256
               (base32
                "1sv0447j0rx8cgs3jhjl695p5pv13ihglcjlrrz1kq05lsvb0wa7"))))
    (build-system python-build-system)
    (arguments
     `(#:python ,python-2                         ;Python 2 only
       #:tests? #f))                              ;no tests
    (inputs
     `(("python-setuptools" ,python-setuptools)))
    (home-page "http://python-xlib.sourceforge.net/")
    (synopsis "Python X11 client library")
    (description
     "The Python X Library is intended to be a fully functional X client
library for Python programs.  It is useful to implement low-level X clients.
It is written entirely in Python.")
    (license gpl2+)))