Merge branch 'master' into core-updates

This commit is contained in:
Leo Famulari 2016-03-21 12:22:31 -04:00
commit 09ec508a4c
184 changed files with 27612 additions and 1722 deletions

View file

@ -1029,44 +1029,6 @@ 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")
@ -1160,10 +1122,10 @@ Python 3.3+.")
(package-with-python2 python-simplejson))
(define-public python2-pyicu
(define-public python-pyicu
(package
(name "python2-pyicu")
(version "1.8")
(name "python-pyicu")
(version "1.9.2")
(source
(origin
(method url-fetch)
@ -1171,19 +1133,22 @@ Python 3.3+.")
version ".tar.gz"))
(sha256
(base32
"1y361x82lnh9k9srmdx3q92z5iag112z7r5fxm0n1sfwb349yjdw"))))
"1diba0g8md614fvm9yf50paiwdkhj6rd7xwf1rg9mc0pxc0hhn4v"))))
(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)))
(license x11)
(properties `((python2-variant . ,(delay python2-pyicu))))))
(define-public python2-pyicu
(package
(inherit (package-with-python2
(strip-python2-variant python-pyicu)))
(native-inputs `(("python2-setuptools" ,python2-setuptools)))))
(define-public python2-dogtail
;; Python 2 only, as it leads to "TabError: inconsistent use of tabs and
@ -4585,67 +4550,6 @@ converts incoming documents to Unicode and outgoing documents to UTF-8.")
(strip-python2-variant python-beautifulsoup4)))
(native-inputs `(("python2-setuptools" ,python2-setuptools)))))
(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")
@ -4947,20 +4851,19 @@ It is written entirely in Python.")
(define-public python-tornado
(package
(name "python-tornado")
(version "4.1")
(version "4.3")
(source
(origin
(method url-fetch)
(uri (string-append
"https://pypi.python.org/packages/source/t/tornado/"
"tornado-" version ".tar.gz"))
(uri (pypi-uri "tornado" version))
(sha256
(base32 "0a12f00h277zbifibnj46wf14801f573irvf6hwkgja5vspd7awr"))))
(base32 "1gzgwayl6hmc9jfcl88bni4jcsk2jcca9dn1rvrfsvnijcjx7hn9"))))
(build-system python-build-system)
(inputs
`(("python-certifi" ,python-certifi)))
(native-inputs
`(("python-setuptools" ,python-setuptools)))
`(("python-backports-abc" ,python-backports-abc)
("python-setuptools" ,python-setuptools)))
(home-page "http://www.tornadoweb.org/")
(synopsis "Python web framework and asynchronous networking library")
(description
@ -4977,8 +4880,34 @@ connection to each user.")
(inputs
`(("python2-backport-ssl-match-hostname"
,python2-backport-ssl-match-hostname)
("python2-singledispatch", python2-singledispatch)
,@(package-inputs tornado))))))
;; the python- version can be removed with python-3.5
(define-public python-backports-abc
(package
(name "python-backports-abc")
(version "0.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "backports_abc" version))
(sha256
(base32
"19fh75lni9pb673n2fn505m1rckm0af0szcv5xx1qm1xpa940glb"))))
(build-system python-build-system)
(inputs
`(("python-setuptools" ,python-setuptools)))
(home-page "https://github.com/cython/backports_abc")
(synopsis "Backport of additions to the 'collections.abc' module.")
(description
"Python-backports-abc provides a backport of additions to the
'collections.abc' module in Python-3.5.")
(license psfl)))
(define-public python2-backports-abc
(package-with-python2 python-backports-abc))
(define-public python-waf
(package
(name "python-waf")
@ -5831,7 +5760,7 @@ responses, rather than doing any computation.")
(define-public python-cryptography-vectors
(package
(name "python-cryptography-vectors")
(version "1.2.2")
(version "1.2.3")
(source
(origin
(method url-fetch)
@ -5840,7 +5769,7 @@ responses, rather than doing any computation.")
version ".tar.gz"))
(sha256
(base32
"1zg47fzzn30mgkkbwrxqqcfq9crgabcmxyiy106n9404wbhfjkkl"))))
"0shawgpax79gvjrj0a313sll9gaqys7q1hxngn6j4k24lmz7bwki"))))
(build-system python-build-system)
(native-inputs
`(("python-setuptools" ,python-setuptools)))
@ -5857,14 +5786,14 @@ responses, rather than doing any computation.")
(define-public python-cryptography
(package
(name "python-cryptography")
(version "1.2.2")
(version "1.2.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cryptography" version))
(sha256
(base32
"0rvaha7ymgbqkzbxk7xmj67k5b3hbp8w8cn3m5z776vd22wrq89z"))))
"0kj511z4g21fhcr649pyzpl0zzkkc7hsgxxjys6z8wwfvmvirccf"))))
(build-system python-build-system)
(inputs
`(("openssl" ,openssl)))
@ -6819,7 +6748,14 @@ WebSocket usage in Python programs.")
(description "Library for atomic file writes using platform dependent tools
for atomic filesystem operations.")
(home-page "https://github.com/untitaker/python-atomicwrites")
(license license:expat)))
(license license:expat)
(properties `((python2-variant . ,(delay python2-atomicwrites))))))
(define-public python2-atomicwrites
(package (inherit (package-with-python2
(strip-python2-variant python-atomicwrites)))
(native-inputs
`(("python2-setuptools" ,python2-setuptools)))))
(define-public python-requests-toolbelt
(package
@ -7520,13 +7456,13 @@ Amazon Web Services (AWS) API.")
(define-public python-hypothesis
(package
(name "python-hypothesis")
(version "3.0.4")
(version "3.1.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "hypothesis" version))
(sha256
(base32
"0bh6pqyc56cqlbpg0ffzjs6466blyylix4nsw11qrqwf01cg9gdq"))))
"0qyqq9akm4vshhn8cngjc1qykcvsn7cz6dlm6njfsgpbraqrmbbw"))))
(build-system python-build-system)
(propagated-inputs
`(("python-flake8" ,python-flake8)
@ -8256,3 +8192,270 @@ introspection of @code{zope.interface} instances in code.")
(inherit (package-with-python2
(strip-python2-variant python-psycopg2)))
(native-inputs `(("python2-setuptools" ,python2-setuptools)))))
(define-public python-vobject
(package
(name "python-vobject")
(version "0.9.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "vobject" version))
(sha256
(base32
"1cwzjnrdr9yg2x21wbf3kf59ibnchvj33mygd69yzi178a9gs9gz"))))
(build-system python-build-system)
(inputs
`(("python-dateutil-2" ,python-dateutil-2)
("python-pyicu" ,python-pyicu)))
(synopsis "Parse and generate vCard and vCalendar files")
(description "Vobject is intended to be a full featured Python package for
parsing and generating vCard and vCalendar files. Currently, iCalendar files
are supported and well tested. vCard 3.0 files are supported, and all data
should be imported, but only a few components are understood in a sophisticated
way.")
(home-page "http://eventable.github.io/vobject/")
(license asl2.0)
(properties `((python2-variant . ,(delay python2-vobject))))))
(define-public python2-vobject
(package
(inherit (package-with-python2
(strip-python2-variant python-vobject)))
(native-inputs `(("python2-setuptools" ,python2-setuptools)))))
(define-public python-munkres
(package
(name "python-munkres")
(version "1.0.7")
(source (origin
(method url-fetch)
(uri (pypi-uri "munkres" version))
(sha256
(base32
"1i6nf45i0kkzdx6k70giybsqxz4dxsjbrkrfqgjd7znfkf25sjik"))))
(build-system python-build-system)
(arguments
'(#:tests? #f)) ; no test suite
(home-page "http://software.clapper.org/munkres/")
(synopsis "Implementation of the Munkres algorithm")
(description "The Munkres module provides an implementation of the Munkres
algorithm (also called the Hungarian algorithm or the Kuhn-Munkres algorithm),
useful for solving the Assignment Problem.")
(license bsd-3)))
(define-public python2-munkres
(package-with-python2 python-munkres))
(define-public python-flask
(package
(name "python-flask")
(version "0.10.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "Flask" version))
(sha256
(base32
"0wrkavjdjndknhp8ya8j850jq7a1cli4g5a93mg8nh1xz2gq50sc"))))
(build-system python-build-system)
(propagated-inputs
`(("python-itsdangerous" ,python-itsdangerous)
("python-jinja2" ,python-jinja2)
("python-werkzeug" ,python-werkzeug)))
(home-page "https://github.com/mitsuhiko/flask/")
(synopsis "Microframework based on Werkzeug, Jinja2 and good intentions")
(description "Flask is a micro web framework based on the Werkzeug toolkit
and Jinja2 template engine. It is called a micro framework because it does not
presume or force a developer to use a particular tool or library.")
(license bsd-3)
(properties `((python2-variant . ,(delay python2-flask))))))
(define-public python2-flask
(package (inherit (package-with-python2
(strip-python2-variant python-flask)))
(native-inputs `(("python2-setuptools" ,python2-setuptools)))))
(define-public python-cookies
(package
(name "python-cookies")
(version "2.2.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "cookies" version))
(sha256
(base32
"13pfndz8vbk4p2a44cfbjsypjarkrall71pgc97glk5fiiw9idnn"))))
(build-system python-build-system)
(arguments
`(;; test are broken: https://gitlab.com/sashahart/cookies/issues/3
#:tests? #f))
(native-inputs
`(("python-pytest" ,python2-pytest)))
(synopsis "HTTP cookie parser and renderer")
(description "A RFC 6265-compliant HTTP cookie parser and renderer in
Python.")
(home-page "https://gitlab.com/sashahart/cookies")
(license license:expat)
(properties `((python2-variant . ,(delay python2-cookies))))))
(define-public python2-cookies
(let ((cookies (package-with-python2
(strip-python2-variant python-cookies))))
(package (inherit cookies)
(native-inputs `(("python2-setuptools" ,python2-setuptools)
,@(package-native-inputs cookies))))))
(define-public python-responses
(package
(name "python-responses")
(version "0.5.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "responses" version))
(sha256
(base32
"1spcfxixyk9k7pk82jm6zqkwk031s95lh8q0mz7539jrb7269bcc"))))
(build-system python-build-system)
(arguments
`(;; Test suite is not distributed:
;; https://github.com/getsentry/responses/issues/38
#:tests? #f))
(native-inputs
`(("python-cookies" ,python-cookies)
("python-mock" ,python-mock)))
(propagated-inputs
`(("python-requests" ,python-requests)
("python-six" ,python-six)))
(home-page "https://github.com/getsentry/responses")
(synopsis "Utility for mocking out the `requests` Python library")
(description "A utility library for mocking out the `requests` Python
library.")
(license asl2.0)
(properties `((python2-variant . ,(delay python2-responses))))))
(define-public python2-responses
(let ((responses (package-with-python2
(strip-python2-variant python-responses))))
(package (inherit responses)
(native-inputs `(("python2-setuptools" ,python2-setuptools)
,@(package-native-inputs responses))))))
(define-public python-pathlib
(package
(name "python-pathlib")
(version "1.0.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "pathlib" version))
(sha256
(base32
"17zajiw4mjbkkv6ahp3xf025qglkj0805m9s41c45zryzj6p2h39"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _ (zero? (system* "python" "./test_pathlib.py")))))))
(home-page "https://pathlib.readthedocs.org/")
(synopsis "Object-oriented filesystem paths")
(description "Pathlib offers a set of classes to handle filesystem paths.
It offers the following advantages over using string objects:
@enumerate
@item No more cumbersome use of os and os.path functions. Everything can
be done easily through operators, attribute accesses, and method calls.
@item Embodies the semantics of different path types. For example,
comparing Windows paths ignores casing.
@item Well-defined semantics, eliminating any inconsistencies or
ambiguities (forward vs. backward slashes, etc.).
@end enumerate\n")
(license license:expat)))
(define-public python2-pathlib
(package-with-python2 python-pathlib))
(define-public python-jellyfish
(package
(name "python-jellyfish")
(version "0.5.3")
(source (origin
(method url-fetch)
(uri (pypi-uri "jellyfish" version))
(sha256
(base32
"12bxh8cy9xmvyrjz7aw159nd5pyvb645rkvw4r6bvm4xbvs8gd07"))))
(build-system python-build-system)
(native-inputs
`(("python-pytest" ,python-pytest)))
(home-page "https://github.com/jamesturk/jellyfish")
(synopsis "Approximate and phonetic matching of strings")
(description "Jellyfish uses a variety of string comparison and phonetic
encoding algorithms to do fuzzy string matching.")
(license bsd-2)
(properties `((python2-variant . ,(delay python2-jellyfish))))))
(define-public python2-jellyfish
(let ((jellyfish (package-with-python2
(strip-python2-variant python-jellyfish))))
(package (inherit jellyfish)
(native-inputs `(("python2-setuptools" ,python2-setuptools)
("python2-unicodecsv" ,python2-unicodecsv)
,@(package-native-inputs jellyfish))))))
(define-public python2-unicodecsv
(package
(name "python2-unicodecsv")
(version "0.14.1")
(source (origin
(method url-fetch)
;; The test suite is not included in the PyPi release.
;; https://github.com/jdunck/python-unicodecsv/issues/19
(uri (string-append "https://github.com/jdunck/python-unicodecsv/"
"archive/" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"087nqanfcyp6mlfbbr5lva5f3w6iz1bybls9xlrb8icmc474wh4w"))))
(build-system python-build-system)
(arguments
`(;; It supports Python 3, but Python 3 can already do Unicode CSV.
#:python ,python-2))
(native-inputs
`(("python2-setuptools" ,python2-setuptools)
("python2-unittest2" ,python2-unittest2)))
(home-page "https://github.com/jdunck/python-unicodecsv")
(synopsis "Unicode CSV module for Python 2")
(description "Unicodecsv is a drop-in replacement for Python 2.7's CSV
module, adding support for Unicode strings.")
(license bsd-2)))
(define-public python-rarfile
(package
(name "python-rarfile")
(version "2.7")
(source (origin
(method url-fetch)
(uri (pypi-uri "rarfile" version))
(sha256
(base32
"0d8n1dlpiz7av8dmbp0vclrwl9cnxizr4f2c9xvj1h5nvn480527"))
;; https://github.com/markokr/rarfile/pull/17/
(patches (list (search-patch "python-rarfile-fix-tests.patch")))))
(build-system python-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(replace 'check
;; Many tests fail, but the installation proceeds.
(lambda _ (zero? (system* "make" "-C" "test" "test")))))))
(native-inputs
`(("which" ,which))) ; required for tests
(propagated-inputs
`(("libarchive" ,libarchive)))
(home-page "https://github.com/markokr/rarfile")
(synopsis "RAR archive reader for Python")
(description "This is Python module for RAR archive reading. The interface
is made as zipfile like as possible.")
(license isc)))
(define-public python2-rarfile
(package-with-python2 python-rarfile))