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Merge branch 'master' into core-updates

This commit is contained in:
Leo Famulari 2017-07-23 03:42:12 -04:00
commit 6c1a317e29
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@ -43,6 +43,7 @@
;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017 Kei Kebreau <kei@openmailbox.org>
;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2017 Muriithi Frederick Muriuki <fredmanglis@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -100,6 +101,7 @@
#:use-module (gnu packages qt)
#:use-module (gnu packages readline)
#:use-module (gnu packages sdl)
#:use-module (gnu packages search)
#:use-module (gnu packages shells)
#:use-module (gnu packages ssh)
#:use-module (gnu packages statistics)
@ -655,26 +657,50 @@ on localhost.")
(define-public python-pytz
(package
(name "python-pytz")
(version "2016.10")
(version "2017.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pytz" version ".tar.bz2"))
(uri (pypi-uri "pytz" version ".zip"))
(sha256
(base32
"0az099cyp6p5xbsvfcdacj4hvxncbwm2ayn3h55mcp07zb2b45kh"))))
"12cmd3j46d2gcw08bspvp6s9icfcvx88zjz52n1bli9dyvl5dh7m"))))
(build-system python-build-system)
(arguments `(#:tests? #f)) ; no test target
(native-inputs
`(("unzip" ,unzip)))
(home-page "http://pythonhosted.org/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.")
(description "This library brings the Olson tz database into Python. It
allows accurate and cross platform timezone calculations using Python 2.4 or
higher. It also solves the issue of ambiguous times at the end of daylight
saving time. Almost all of the Olson timezones are supported.")
(license license:expat)))
(define-public python2-pytz
(package-with-python2 python-pytz))
(define-public python-clyent
(package
(name "python-clyent")
(version "1.2.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "clyent" version))
(sha256
(base32
"1r9987qmy1pz3hq54160bapqsywpq14waw4w9x3ly8hmq7kpgfbj"))))
(build-system python-build-system)
(native-inputs
`(("python-mock" ,python-mock)))
(home-page "https://github.com/binstar/clyent")
(synopsis "Command line client library")
(description "Clyent is a Python command line utiliy library. It is used
by @code{binstar}, @code{binstar-build} and @code{chalmers}.")
(license license:bsd-3)))
(define-public python2-clyent
(package-with-python2 python-clyent))
(define-public python-babel
(package
@ -2715,6 +2741,46 @@ version numbers.")
(propagated-inputs
`(("python2-functools32" ,python2-functools32))))))
(define-public python-schema
(package
(name "python-schema")
(version "0.6.6")
(source
(origin
(method url-fetch)
(uri (pypi-uri "schema" version))
(sha256
(base32
"1lw28j9w9vxyigg7vkfkvi6ic9lgjkdnfvnxdr7pklslqvzmk2vm"))))
(build-system python-build-system)
(native-inputs
`(("python-pytest" ,python-pytest)))
(home-page "https://github.com/keleshev/schema")
(synopsis "Simple data validation library")
(description
"@code{python-schema} is a library for validating Python data
structures, such as those obtained from config-files, forms, external
services or command-line parsing, converted from JSON/YAML (or
something else) to Python data-types.")
(license license:psfl)))
(define-public python2-schema
(package-with-python2 python-schema))
(define-public python-schema-0.5
(package (inherit python-schema)
(version "0.5.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "schema" version))
(sha256
(base32
"10zqvpaky51kgb8nd42bk7jwl8cn2zvayxjpdc1wwmpybj92x67s"))))))
(define-public python2-schema-0.5
(package-with-python2 python-schema-0.5))
(define-public python-kitchen
(package
(name "python-kitchen")
@ -3125,6 +3191,36 @@ reStructuredText.")
(define-public python2-pygments
(package-with-python2 python-pygments))
(define-public python-sphinxcontrib-websupport
(package
(name "python-sphinxcontrib-websupport")
(version "1.0.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "sphinxcontrib-websupport" version))
(sha256
(base32
"1f9f0wjpi9nhikbyaz6d19s7qvzdf1nq2g5dsh640fma4q9rd1bs"))))
(build-system python-build-system)
(propagated-inputs
`(("python-mock" ,python-mock)
("python-pytest" ,python-pytest)
("python-xapian-bindings" ,python-xapian-bindings)))
;; Needed for running the test suite
(native-inputs
`(("python-six" ,python-six)
("python-jinja2" ,python-jinja2)
("python-docutils" ,python-docutils)
("python-sphinx" ,python-sphinx)
("python-sqlalchemy" ,python-sqlalchemy)
("python-whoosh" ,python-whoosh)))
(home-page "http://sphinx-doc.org/")
(synopsis "Sphinx API for web applications")
(description "This package provides a Python API to easily integrate
Sphinx documentation into your web application. It provides tools to
integrate Sphinx documents in web templates and to handle searches.")
(license license:bsd-3)))
(define-public python-sphinx
(package
(name "python-sphinx")
@ -3169,6 +3265,36 @@ sources.")
(license license:bsd-3)
(properties `((python2-variant . ,(delay python2-sphinx))))))
(define-public python-sphinx-1.6
(package (inherit python-sphinx)
(name "python-sphinx")
(version "1.6.3")
(source (origin
(method url-fetch)
(uri (pypi-uri "Sphinx" version))
(sha256
(base32
"1rj6f3i8hmrx2qlkshi5kp5xcy98dlynwlyl05yvflj5f66dp2xg"))))
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _
;; Requires Internet access.
(delete-file "tests/test_build_linkcheck.py")
(substitute* "tests/test_build_latex.py"
(("@pytest.mark.sphinx\\('latex', testroot='images'\\)")
"@pytest.mark.skip()"))
(zero? (system* "make" "test")))))))
(propagated-inputs
`(("python-sphinxcontrib-websupport" ,python-sphinxcontrib-websupport)
,@(package-propagated-inputs python-sphinx)))
(native-inputs
`(("python-pytest" ,python-pytest-3.0)
("imagemagick" ,imagemagick) ; for "convert"
,@(package-native-inputs python-sphinx)))
(properties '())))
(define-public python-sphinx-1.5.3
(package
(inherit python-sphinx)
@ -3684,7 +3810,39 @@ association studies (GWAS) on extremely large data sets.")
("pkg-config" ,pkg-config)
("python-sphinx" ,python-sphinx)
("python-numpydoc" ,python-numpydoc)
("texlive" ,texlive)
("texlive" ,(texlive-union (list texlive-fonts-amsfonts
texlive-fonts-ec
texlive-generic-ifxetex
texlive-generic-pdftex
texlive-latex-amsfonts
texlive-latex-capt-of
texlive-latex-cmap
texlive-latex-environ
texlive-latex-eqparbox
texlive-latex-etoolbox
texlive-latex-expdlist
texlive-latex-fancyhdr
texlive-latex-fancyvrb
texlive-latex-fncychap
texlive-latex-float
texlive-latex-framed
texlive-latex-geometry
texlive-latex-graphics
texlive-latex-hyperref
texlive-latex-mdwtools
texlive-latex-multirow
texlive-latex-oberdiek
texlive-latex-parskip
texlive-latex-preview
texlive-latex-tabulary
texlive-latex-threeparttable
texlive-latex-titlesec
texlive-latex-trimspaces
texlive-latex-ucs
texlive-latex-upquote
texlive-latex-url
texlive-latex-varwidth
texlive-latex-wrapfig)))
("texinfo" ,texinfo)
("perl" ,perl)
("scipy-sphinx-theme"
@ -3713,6 +3871,11 @@ association studies (GWAS) on extremely large data sets.")
(scipy-sphinx-theme "scipy-sphinx-theme")
(sphinx-theme-checkout (assoc-ref inputs scipy-sphinx-theme))
(pyver ,(string-append "PYVER=")))
;; FIXME: this is needed to for texlive-union to generate
;; fonts, which are not found.
(setenv "HOME" "/tmp")
(with-directory-excursion "doc"
(copy-recursively sphinx-theme-checkout scipy-sphinx-theme)
(mkdir-p html)
@ -4480,6 +4643,35 @@ multivalue dictionary that retains the order of insertions and deletions.")
(define-public python2-furl
(package-with-python2 python-furl))
(define-public python-flaky
(package
(name "python-flaky")
(version "3.4.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "flaky" version))
(sha256
(base32
"18pkmf79rfkfpy1d2rrx3v55nxj762ilyk9rvd6s6dccxw58imsa"))))
(build-system python-build-system)
(arguments
;; TODO: Tests require 'coveralls' and 'genty' which are not in Guix yet.
'(#:tests? #f))
(home-page "https://github.com/box/flaky")
(synopsis "Automatically rerun flaky tests")
(description
"Flaky is a plugin for @code{nose} or @code{py.test} that automatically
reruns flaky tests.
Ideally, tests reliably pass or fail, but sometimes test fixtures must rely
on components that aren't 100% reliable. With flaky, instead of removing
those tests or marking them to @code{@skip}, they can be automatically
retried.")
(license license:asl2.0)))
(define-public python2-flaky
(package-with-python2 python-flaky))
(define-public python-flask-babel
(package
(name "python-flask-babel")
@ -5429,7 +5621,40 @@ tools for mocking system commands and recording calls to those.")
("python-nose" ,python-nose)
("python-sphinx" ,python-sphinx)
("python-shpinx-rtd-theme" ,python-sphinx-rtd-theme)
("texlive" ,texlive)
;; FIXME: It's possible that a smaller union would work just as well.
("texlive" ,(texlive-union (list texlive-fonts-amsfonts
texlive-fonts-ec
texlive-generic-ifxetex
texlive-generic-pdftex
texlive-latex-amsfonts
texlive-latex-capt-of
texlive-latex-cmap
texlive-latex-environ
texlive-latex-eqparbox
texlive-latex-etoolbox
texlive-latex-expdlist
texlive-latex-fancyhdr
texlive-latex-fancyvrb
texlive-latex-fncychap
texlive-latex-float
texlive-latex-framed
texlive-latex-geometry
texlive-latex-graphics
texlive-latex-hyperref
texlive-latex-mdwtools
texlive-latex-multirow
texlive-latex-oberdiek
texlive-latex-parskip
texlive-latex-preview
texlive-latex-tabulary
texlive-latex-threeparttable
texlive-latex-titlesec
texlive-latex-trimspaces
texlive-latex-ucs
texlive-latex-upquote
texlive-latex-url
texlive-latex-varwidth
texlive-latex-wrapfig)))
("texinfo" ,texinfo)))
(arguments
`(#:phases
@ -6049,13 +6274,13 @@ of the structure, dynamics, and functions of complex networks.")
(define-public snakemake
(package
(name "snakemake")
(version "3.11.2")
(version "3.13.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "snakemake" version))
(sha256
(base32 "0qcp7y9csvanyzh08jppryhd5di8r1z7p0d4wkfg5591pj3bb8zp"))))
(base32 "1nixb944r4hlskwkzc4wjs34b40xpxpw9gmhhm5p09gvmm22ap5d"))))
(build-system python-build-system)
(arguments
;; TODO: Package missing test dependencies.
@ -6337,6 +6562,31 @@ connection to each user.")
(define-public python2-backports-abc
(package-with-python2 python-backports-abc))
(define-public python-backports-csv
(package
(name "python-backports-csv")
(version "1.0.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "backports.csv" version))
(sha256
(base32
"1imzbrradkfn8s2m1qcimyn74dn1mz2p3j381jljn166rf2i6hlc"))))
(build-system python-build-system)
(home-page "https://github.com/ryanhiebert/backports.csv")
(synopsis "Backport of Python 3's csv module for Python 2")
(description
"Provides a backport of Python 3's @code{csv} module for parsing
comma separated values. The API of the @code{csv} module in Python 2
is drastically different from the @code{csv} module in Python 3.
This is due, for the most part, to the difference between str in
Python 2 and Python 3.")
(license license:psfl)))
(define-public python2-backports-csv
(package-with-python2 python-backports-csv))
(define-public python2-backports-shutil-get-terminal-size
(package
(name "python2-backports-shutil-get-terminal-size")
@ -7392,14 +7642,14 @@ responses, rather than doing any computation.")
(define-public python-cryptography-vectors
(package
(name "python-cryptography-vectors")
(version "1.9")
(version "2.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cryptography_vectors" version))
(sha256
(base32
"1wvq1p1viam1diz9x6d61x1bsy6cninv7cjgd35x9ffig9r6gxxv"))))
"0qadys01517k5wy0rifxip02p08kzrqxm5j0lmmlp0kr07h9jc7h"))))
(build-system python-build-system)
(home-page "https://github.com/pyca/cryptography")
(synopsis "Test vectors for the cryptography package")
@ -7414,14 +7664,14 @@ responses, rather than doing any computation.")
(define-public python-cryptography
(package
(name "python-cryptography")
(version "1.9")
(version "2.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cryptography" version))
(sha256
(base32
"10j8r1s29f4h59kp3mla14g588rm7qpn90nrczijk03i49q3662m"))))
"1c40qlxyn1jgg99f3pqi7146d3561rn9zdqc7w8f7kwr9ysm696k"))))
(build-system python-build-system)
(inputs
`(("openssl" ,openssl)))
@ -7463,16 +7713,14 @@ message digests and key derivation functions.")
(define-public python-pyopenssl
(package
(name "python-pyopenssl")
(version "17.1.0")
(version "17.2.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyOpenSSL" version))
(patches
(search-patches "python-pyopenssl-17.1.0-test-overflow.patch"))
(sha256
(base32
"0qwmqhfsq84ydir9dz273ypmlcvs7v71m1jns0sd4k0h6lfsa82s"))))
"0d283g4zi0hr9papd24mjl70mi15gyzq6fx618rizi87dgipqqax"))))
(build-system python-build-system)
(arguments
'(#:phases
@ -7496,7 +7744,8 @@ message digests and key derivation functions.")
(inputs
`(("openssl" ,openssl)))
(native-inputs
`(("python-pretend" ,python-pretend)
`(("python-flaky" ,python-flaky)
("python-pretend" ,python-pretend)
("python-pytest" ,python-pytest-3.0)))
(home-page "https://github.com/pyca/pyopenssl")
(synopsis "Python wrapper module around the OpenSSL library")
@ -11641,53 +11890,6 @@ addresses, and phone numbers.")
`(("python2-ipaddress" ,python2-ipaddress)
,@(package-propagated-inputs base))))))
(define-public python-fake-factory
(package
(name "python-fake-factory")
(version "0.7.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "fake-factory" version))
(sha256
(base32
"0vs0dkmg0dlaxf8w6q2i3k0i03gmp56ablldv7ci9x3nbadkn71g"))
(patches
(search-patches
"python-fake-factory-fix-build-32bit.patch"))))
(build-system python-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _
(zero? (system* "python" "-m" "unittest" "-v" "faker.tests")))))))
(native-inputs
`(;; For testing
("python-email-validator" ,python-email-validator)
("python-mock" ,python-mock)
("python-ukpostcodeparser" ,python-ukpostcodeparser)))
(propagated-inputs
`(("python-dateutil" ,python-dateutil)
("python-six" ,python-six)))
(home-page "https://github.com/joke2k/faker")
(synopsis "Python package that generates fake data")
(description
"Faker is a Python package that generates fake data such as names,
addresses, and phone numbers.")
(license license:expat)
(properties `((python2-variant . ,(delay python2-fake-factory))
(superseded . ,python-faker)))))
(define-public python2-fake-factory
(let ((base (package-with-python2 (strip-python2-variant
python-fake-factory))))
(package
(inherit base)
(properties `((superseded . ,python2-faker)))
(propagated-inputs
`(("python2-ipaddress" ,python2-ipaddress)
,@(package-propagated-inputs base))))))
(define-public python-pyaml
(package
(name "python-pyaml")
@ -14297,6 +14499,29 @@ pytest report.")
(define-public python2-pytest-warnings
(package-with-python2 python-pytest-warnings))
(define-public python-pytest-capturelog
(package
(name "python-pytest-capturelog")
(version "0.7")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pytest-capturelog" version ".tar.gz"))
(sha256
(base32
"038049nyjl7di59ycnxvc9nydivc5m8np3hqq84j2iirkccdbs5n"))))
(build-system python-build-system)
(propagated-inputs
`(("pytest" ,python-pytest-3.0)))
(home-page "http://bitbucket.org/memedough/pytest-capturelog/overview")
(synopsis "Pytest plugin to catch log messages")
(description
"Python-pytest-catchlog is a pytest plugin to catch log messages.")
(license license:expat)))
(define-public python2-pytest-capturelog
(package-with-python2 python-pytest-capturelog))
(define-public python-pytest-catchlog
(package
(name "python-pytest-catchlog")
@ -15173,6 +15398,49 @@ by path in a JSON document (see RFC 6901).")
(define-public python2-jsonpointer
(package-with-python2 python-jsonpointer))
(define-public python-jsonpatch
(package
(name "python-jsonpatch")
(version "1.16")
(source
(origin
(method url-fetch)
;; pypi version lacks tests.js
(uri (string-append "https://github.com/stefankoegl/python-json-patch/"
"archive/v" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"085ykisl8v7mv9h7hvhdy3l2fjzs4214gx32r5k6nx4f76hbv6y5"))))
(build-system python-build-system)
(native-inputs
`(("python-jsonpointer" ,python-jsonpointer)))
(home-page "https://github.com/stefankoegl/python-json-patch")
(synopsis "Applying JSON Patches in Python 2.6+ and 3.x")
(description "@code{jsonpatch} is a library and program that allows
applying JSON Patches according to RFC 6902.")
(license license:bsd-3)))
(define-public python2-jsonpatch
(package-with-python2 python-jsonpatch))
(define-public python-jsonpatch-0.4
(package (inherit python-jsonpatch)
(name "python-jsonpatch")
(version "0.4")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/stefankoegl/python-json-patch/"
"archive/v" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0j0cd9z9zyp8kppp464jxrfgrnbgkzl1yi10i5gsv8yz6d95929d"))))))
(define-public python2-jsonpatch-0.4
(package-with-python2 python-jsonpatch-0.4))
(define-public python-rfc3987
(package
(name "python-rfc3987")