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Merge branch 'master' into staging

This commit is contained in:
Marius Bakke 2018-07-28 18:34:59 +02:00
commit 1af575f04d
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181 changed files with 7425 additions and 3498 deletions

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@ -14,7 +14,7 @@
;;; Copyright © 2015, 2016, 2017 Leo Famulari <leo@famulari.name>
;;; Copyright © 2015, 2017 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2015, 2016 Erik Edrosa <erik.edrosa@gmail.com>
;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015, 2017 Kyle Meyer <kyle@kyleam.com>
;;; Copyright © 2015, 2016 Chris Marusich <cmmarusich@gmail.com>
;;; Copyright © 2016 Danny Milosavljevic <dannym+a@scratchpost.org>
@ -782,14 +782,14 @@ NetCDF files can also be read and modified. Python-HDF4 is a fork of
(define-public python-h5py
(package
(name "python-h5py")
(version "2.7.0")
(version "2.8.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "h5py" version))
(sha256
(base32
"0433sdv6xc9p7v1xs1gvbxp7p152ywi3nplgjb258q9fvw9469br"))))
"0mdr6wrq02ac93m1aqx9kad0ppfzmm4imlxqgyy1x4l7hmdcc9p6"))))
(build-system python-build-system)
(arguments
`(#:tests? #f ; no test target
@ -2218,14 +2218,14 @@ environments and back.")
(define-public python-pyyaml
(package
(name "python-pyyaml")
(version "3.12")
(version "3.13")
(source
(origin
(method url-fetch)
(uri (pypi-uri "PyYAML" version))
(sha256
(base32
"1aqjl8dk9amd4zr99n8v2qxzgmr2hdvqfma4zh7a41rj6336c9sr"))))
"1gx603g484z46cb74j9rzr6sjlh2vndxayicvlyhxdz98lhhkwry"))))
(build-system python-build-system)
(inputs
`(("libyaml" ,libyaml)))
@ -4210,23 +4210,53 @@ support for Python 3 and PyPy. It is based on cffi.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1rk2dvy3fxrga6bvvxc2fi5lbaynm5h4a0w0aaxyn3bc77rszjg9"))))
"1rk2dvy3fxrga6bvvxc2fi5lbaynm5h4a0w0aaxyn3bc77rszjg9"))
(patches (search-patches "python-cairocffi-dlopen-path.patch"))))
(build-system python-build-system)
(outputs '("out" "doc"))
(inputs
`(("gdk-pixbuf" ,gdk-pixbuf)
("cairo" ,cairo)))
`(("glib" ,glib)
("gtk+" ,gtk+)
("gdk-pixbuf" ,gdk-pixbuf)
("cairo" ,cairo)
("pango" ,pango)))
(native-inputs
`(("pkg-config" ,pkg-config)
("python-pytest" ,python-pytest)
("python-sphinx" ,python-sphinx)
("python-docutils" ,python-docutils)))
(propagated-inputs
`(("python-xcffib" ,python-xcffib))) ; used at run time
(arguments
`(;; FIXME: Tests cannot find 'libcairo.so.2'.
#:tests? #f
#:tests? #t
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-paths
(lambda* (#:key inputs outputs #:allow-other-keys)
(substitute* (find-files "." "\\.py$")
(("dlopen\\(ffi, 'cairo'")
(string-append "dlopen(ffi, '" (assoc-ref inputs "cairo")
"/lib/libcairo.so.2'"))
(("dlopen\\(ffi, 'gdk-3'")
(string-append "dlopen(ffi, '" (assoc-ref inputs "gtk+")
"/lib/libgtk-3.so.0'"))
(("dlopen\\(ffi, 'gdk_pixbuf-2.0'")
(string-append "dlopen(ffi, '" (assoc-ref inputs "gdk-pixbuf")
"/lib/libgdk_pixbuf-2.0.so.0'"))
(("dlopen\\(ffi, 'glib-2.0'")
(string-append "dlopen(ffi, '" (assoc-ref inputs "glib")
"/lib/libglib-2.0.so.0'"))
(("dlopen\\(ffi, 'gobject-2.0'")
(string-append "dlopen(ffi, '" (assoc-ref inputs "glib")
"/lib/libgobject-2.0.so.0'"))
(("dlopen\\(ffi, 'pangocairo-1.0'")
(string-append "dlopen(ffi, '" (assoc-ref inputs "pango")
"/lib/libpangocairo-1.0.so.0'"))
(("dlopen\\(ffi, 'pango-1.0'")
(string-append "dlopen(ffi, '" (assoc-ref inputs "pango")
"/lib/libpango-1.0.so.0'")))
#t))
(add-after 'install 'install-doc
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((data (string-append (assoc-ref outputs "doc") "/share"))
@ -5106,16 +5136,40 @@ of the structure, dynamics, and functions of complex networks.")
(define-public python2-networkx2
(package-with-python2 python-networkx2))
(define-public python-datrie
(package
(name "python-datrie")
(version "0.7.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "datrie" version))
(sha256
(base32
"08r0if7dry2q7p34gf7ffyrlnf4bdvnprxgydlfxgfnvq8f3f4bs"))))
(build-system python-build-system)
(native-inputs
`(("python-cython" ,python-cython)
("python-hypothesis" ,python-hypothesis)
("python-pytest" ,python-pytest)
("python-pytest-runner" ,python-pytest-runner)))
(home-page "https://github.com/kmike/datrie")
(synopsis "Fast, efficiently stored trie for Python")
(description
"This package provides a fast, efficiently stored trie implementation for
Python.")
(license license:lgpl2.1+)))
(define-public snakemake
(package
(name "snakemake")
(version "4.4.0")
(version "5.2.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "snakemake" version))
(sha256
(base32 "0g0paia4z7w3srnqdmavq3hrb2x7qnpf81jx50njl0p7y4y0j8jv"))))
(base32 "0a1i5v5qxbmmpznp7my9nva8y7pxp8pjrwk2gxgisdskg35sq8s1"))))
(build-system python-build-system)
(arguments
;; TODO: Package missing test dependencies.
@ -5137,6 +5191,11 @@ of the structure, dynamics, and functions of complex networks.")
("python-requests" ,python-requests)
("python-appdirs" ,python-appdirs)
("python-configargparse" ,python-configargparse)
("python-datrie" ,python-datrie)
("python-docutils" ,python-docutils)
("python-jinja2" ,python-jinja2)
("python-jsonschema" ,python-jsonschema)
("python-networkx" ,python-networkx)
("python-pyyaml" ,python-pyyaml)
("python-ratelimiter" ,python-ratelimiter)))
(home-page "https://bitbucket.org/snakemake/snakemake/wiki/Home")
@ -5147,6 +5206,24 @@ providing a clean and modern domain specific specification language (DSL) in
Python style, together with a fast and comfortable execution environment.")
(license license:expat)))
;; This is currently needed for the pigx-* packages.
(define-public snakemake-4
(package (inherit snakemake)
(version "4.4.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "snakemake" version))
(sha256
(base32 "0g0paia4z7w3srnqdmavq3hrb2x7qnpf81jx50njl0p7y4y0j8jv"))))
(propagated-inputs
`(("python-wrapt" ,python-wrapt)
("python-requests" ,python-requests)
("python-appdirs" ,python-appdirs)
("python-configargparse" ,python-configargparse)
("python-pyyaml" ,python-pyyaml)
("python-ratelimiter" ,python-ratelimiter)))))
(define-public python-pyqrcode
(package
(name "python-pyqrcode")
@ -6284,14 +6361,14 @@ designed to efficiently cope with extremely large amounts of data.")
(define-public python-pyasn1
(package
(name "python-pyasn1")
(version "0.4.2")
(version "0.4.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyasn1" version))
(sha256
(base32
"05bxnr4wmrg62m4qr1pg1p3z7bhwrv74jll3k42pgxwl36kv0n6j"))))
"1z5h38anjzzrxpraa9iq9llffyx2zs8gx0q6dc1g029miwnn50gv"))))
(build-system python-build-system)
(home-page "http://pyasn1.sourceforge.net/")
(synopsis "ASN.1 types and codecs")
@ -6306,14 +6383,14 @@ suitable for a wide range of protocols based on the ASN.1 specification.")
(define-public python-pyasn1-modules
(package
(name "python-pyasn1-modules")
(version "0.0.8")
(version "0.2.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyasn1-modules" version))
(sha256
(base32
"0drqgw81xd3fxdlg89kgd79zzrabvfncvkbybi2wr6w2y4s1jmhh"))))
"0ivm850yi7ajjbi8j115qpsj95bgxdsx48nbjzg0zip788c3xkx0"))))
(build-system python-build-system)
(propagated-inputs
`(("python-pyasn1" ,python-pyasn1)))
@ -12242,14 +12319,14 @@ pure Python module.")
(define-public python-xenon
(package
(name "python-xenon")
(version "0.5.1")
(version "0.5.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "xenon" version))
(sha256
(base32
"14kby2y48vp3sgwxqlm5d5789yibqwb1qli5fwcmdqg3iayrbklc"))))
"029cbhysg2vr5n4jz8gpg2793f8wkwnqpr1qgv6c1dn685vy31mc"))))
(build-system python-build-system)
(native-inputs
`(("python-pyyaml" ,python-pyyaml)
@ -12261,12 +12338,7 @@ pure Python module.")
`(#:phases
(modify-phases %standard-phases
(add-before 'build 'patch-test-requirements
(lambda* (#:key inputs #:allow-other-keys)
;; Update requirements from dependency==version to
;; dependency>=version.
(substitute* "requirements.txt"
(("==") ">=")
((",<1.5.0") ""))
(lambda _
;; Remove httpretty dependency for tests.
(substitute* "setup.py"
(("httpretty") ""))