Merge branch 'master' into staging

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Marius Bakke 2019-10-23 20:48:55 +02:00
commit 4c1918db34
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51 changed files with 4617 additions and 1129 deletions

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@ -166,14 +166,13 @@
(define-public python-psutil
(package
(name "python-psutil")
(version "5.6.2")
(version "5.6.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "psutil" version))
(sha256
(base32
"1v95vb5385qscfdvphv8l2w22bmir3d7yhpi02n58v3mlqy1r3l2"))))
(base32 "1wv31zly44qj0rp2acg58xbnc7bf6ffyadasq093l455q30qafl6"))))
(build-system python-build-system)
(arguments
;; FIXME: some tests does not return and times out.
@ -1924,13 +1923,13 @@ files.")
(define-public python-pyld
(package
(name "python-pyld")
(version "1.0.3")
(version "1.0.5")
(source (origin
(method url-fetch)
(uri (pypi-uri "PyLD" version))
(sha256
(base32
"12i2g6xdj30k7xxcibg3sc5y76snwq8l6n8fy9lyi577kgy0h2pm"))))
"1ywbdbsrkg533qh8xn9ifjh2mvam6v5msrjyqq73jfpvcp89qvff"))))
(build-system python-build-system)
(home-page "https://github.com/digitalbazaar/pyld")
(synopsis "Python implementation of the JSON-LD specification")
@ -3000,14 +2999,13 @@ receive files via the SCP1 protocol, as implemented by the OpenSSH
(define-public python-rst.linker
(package
(name "python-rst.linker")
(version "1.10")
(version "1.11")
(source
(origin
(method url-fetch)
(uri (pypi-uri "rst.linker" version))
(sha256
(base32
"0iqaacp7pj1s8avs4kc0qg0r7dscywaq37y6l9j14glqdikk0wdj"))))
(base32 "0pqsfqqx8h0pq21k8l3k62kznrgaj2ala93c64s4d9rpbr4mgkd2"))))
(build-system python-build-system)
(propagated-inputs
`(("python-dateutil" ,python-dateutil)
@ -6146,13 +6144,13 @@ Python.")
(define-public snakemake
(package
(name "snakemake")
(version "5.2.4")
(version "5.7.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "snakemake" version))
(sha256
(base32 "0gj0xxgiq3mp9qyyrbfzldiaq1giliqw0in64nqiz7vx49myqj7z"))))
(base32 "1pnpvvn8n2a78cg360wz3ldmpqrsm2wzi0c0dmvki9fnsw6fxdas"))))
(build-system python-build-system)
(arguments
;; TODO: Package missing test dependencies.
@ -6170,18 +6168,19 @@ Python.")
"/bin/snakemake")))
#t)))))
(propagated-inputs
`(("python-gitpython" ,python-gitpython)
("python-wrapt" ,python-wrapt)
("python-requests" ,python-requests)
("python-appdirs" ,python-appdirs)
`(("python-appdirs" ,python-appdirs)
("python-configargparse" ,python-configargparse)
("python-datrie" ,python-datrie)
("python-docutils" ,python-docutils)
("python-gitpython" ,python-gitpython)
("python-jinja2" ,python-jinja2)
("python-jsonschema" ,python-jsonschema)
("python-networkx" ,python-networkx)
("python-psutil" ,python-psutil)
("python-pyyaml" ,python-pyyaml)
("python-ratelimiter" ,python-ratelimiter)))
("python-ratelimiter" ,python-ratelimiter)
("python-requests" ,python-requests)
("python-wrapt" ,python-wrapt)))
(home-page "https://snakemake.readthedocs.io")
(synopsis "Python-based execution environment for make-like workflows")
(description
@ -6190,24 +6189,6 @@ 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")
@ -14854,14 +14835,13 @@ Included are implementations of:
(define-public bpython
(package
(name "bpython")
(version "0.17.1")
(version "0.18")
(source
(origin
(method url-fetch)
(uri (pypi-uri "bpython" version))
(sha256
(base32
"0bxhxi5zxdkrf8b4gwn0d363kdz3qnypjwhm1aydki53ph8ca1w9"))))
(base32 "1hl6frgvr2lqaxqczl8amg9xih32b3gzv429vs0qrjb8wpdj1k2n"))))
(build-system python-build-system)
(arguments
`(#:phases
@ -14884,10 +14864,10 @@ Included are implementations of:
(propagated-inputs
`(("python-pygments" ,python-pygments)
("python-requests" ,python-requests)
("python-babel" ,python-babel) ; optional, for internationalization
("python-babel" ,python-babel) ; optional, for internationalization
("python-curtsies" ,python-curtsies) ; >= 0.1.18
("python-greenlet" ,python-greenlet)
("python-urwid" ,python-urwid) ; for bpython-urwid only
("python-urwid" ,python-urwid) ; for bpython-urwid only
("python-six" ,python-six)))
(native-inputs
`(("python-sphinx" ,python-sphinx)
@ -16610,3 +16590,57 @@ It is the recommended replacement for Python's original
@code{distro} also provides a command-line interface to output the platform
information in various formats.")
(license license:asl2.0)))
(define-public python-cairosvg
(package
(name "python-cairosvg")
(version "2.4.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "CairoSVG" version))
(sha256
(base32 "1bb7irxbaxxb9ahm3z5wsx1q96mm5gzskc7b6q07h9ikcnb8yrjf"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _ (invoke "pytest"))))))
(propagated-inputs
`(("python-cairocffi" ,python-cairocffi)
("python-cssselect2" ,python-cssselect2)
("python-defusedxml" ,python-defusedxml)
("python-pillow" ,python-pillow)
("python-tinycss2" ,python-tinycss2)))
(native-inputs
`(("python-pytest-flake8" ,python-pytest-flake8)
("python-pytest-isort" ,python-pytest-isort)
("python-pytest-runner" ,python-pytest-runner)))
(home-page "https://cairosvg.org/")
(synopsis "SVG to PDF/PS/PNG converter based on Cairo")
(description "CairoSVG is a SVG converter based on Cairo. It can export
SVG files to PDF, PostScript and PNG files. The main part of CairoSVG is a
SVG parser, trying to follow the SVG 1.1 recommendation from the W3C. Once
parsed, the result is drawn to a Cairo surface that can be exported to
qvarious formats: PDF, PostScript, PNG and even SVG.")
(license license:lgpl3+)))
(define-public python-pyphen
(package
(name "python-pyphen")
(version "0.9.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "Pyphen" version))
(sha256
(base32 "08c9y69ry9d6m4zalhnalg86lsp9v2j5n1ziw5vxfmiihx83lqrv"))))
(build-system python-build-system)
;; TODO: Use the Guix system hyphenation packages hyphen-* rather than the
;; embedded set provided by upstream - like Debian does.
(home-page "https://github.com/Kozea/Pyphen")
(synopsis "Pure Python module to hyphenate text")
(description "Pyphen is a pure Python module to hyphenate text using
existing Hunspell hyphenation dictionaries.")
(license (list license:gpl2 license:lgpl2.1 license:mpl1.1))))