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Merge branch 'master' into staging
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commit
4c1918db34
51 changed files with 4617 additions and 1129 deletions
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@ -166,14 +166,13 @@
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(define-public python-psutil
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(package
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(name "python-psutil")
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(version "5.6.2")
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(version "5.6.3")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "psutil" version))
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(sha256
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(base32
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"1v95vb5385qscfdvphv8l2w22bmir3d7yhpi02n58v3mlqy1r3l2"))))
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(base32 "1wv31zly44qj0rp2acg58xbnc7bf6ffyadasq093l455q30qafl6"))))
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(build-system python-build-system)
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(arguments
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;; FIXME: some tests does not return and times out.
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@ -1924,13 +1923,13 @@ files.")
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(define-public python-pyld
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(package
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(name "python-pyld")
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(version "1.0.3")
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(version "1.0.5")
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(source (origin
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(method url-fetch)
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(uri (pypi-uri "PyLD" version))
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(sha256
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(base32
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"12i2g6xdj30k7xxcibg3sc5y76snwq8l6n8fy9lyi577kgy0h2pm"))))
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"1ywbdbsrkg533qh8xn9ifjh2mvam6v5msrjyqq73jfpvcp89qvff"))))
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(build-system python-build-system)
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(home-page "https://github.com/digitalbazaar/pyld")
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(synopsis "Python implementation of the JSON-LD specification")
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@ -3000,14 +2999,13 @@ receive files via the SCP1 protocol, as implemented by the OpenSSH
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(define-public python-rst.linker
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(package
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(name "python-rst.linker")
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(version "1.10")
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(version "1.11")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "rst.linker" version))
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(sha256
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(base32
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"0iqaacp7pj1s8avs4kc0qg0r7dscywaq37y6l9j14glqdikk0wdj"))))
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(base32 "0pqsfqqx8h0pq21k8l3k62kznrgaj2ala93c64s4d9rpbr4mgkd2"))))
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(build-system python-build-system)
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(propagated-inputs
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`(("python-dateutil" ,python-dateutil)
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@ -6146,13 +6144,13 @@ Python.")
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(define-public snakemake
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(package
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(name "snakemake")
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(version "5.2.4")
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(version "5.7.1")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "snakemake" version))
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(sha256
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(base32 "0gj0xxgiq3mp9qyyrbfzldiaq1giliqw0in64nqiz7vx49myqj7z"))))
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(base32 "1pnpvvn8n2a78cg360wz3ldmpqrsm2wzi0c0dmvki9fnsw6fxdas"))))
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(build-system python-build-system)
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(arguments
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;; TODO: Package missing test dependencies.
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@ -6170,18 +6168,19 @@ Python.")
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"/bin/snakemake")))
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#t)))))
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(propagated-inputs
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`(("python-gitpython" ,python-gitpython)
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("python-wrapt" ,python-wrapt)
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("python-requests" ,python-requests)
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("python-appdirs" ,python-appdirs)
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`(("python-appdirs" ,python-appdirs)
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("python-configargparse" ,python-configargparse)
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("python-datrie" ,python-datrie)
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("python-docutils" ,python-docutils)
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("python-gitpython" ,python-gitpython)
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("python-jinja2" ,python-jinja2)
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("python-jsonschema" ,python-jsonschema)
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("python-networkx" ,python-networkx)
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("python-psutil" ,python-psutil)
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("python-pyyaml" ,python-pyyaml)
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("python-ratelimiter" ,python-ratelimiter)))
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("python-ratelimiter" ,python-ratelimiter)
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("python-requests" ,python-requests)
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("python-wrapt" ,python-wrapt)))
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(home-page "https://snakemake.readthedocs.io")
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(synopsis "Python-based execution environment for make-like workflows")
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(description
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@ -6190,24 +6189,6 @@ providing a clean and modern domain specific specification language (DSL) in
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Python style, together with a fast and comfortable execution environment.")
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(license license:expat)))
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;; This is currently needed for the pigx-* packages.
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(define-public snakemake-4
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(package (inherit snakemake)
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(version "4.4.0")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "snakemake" version))
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(sha256
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(base32 "0g0paia4z7w3srnqdmavq3hrb2x7qnpf81jx50njl0p7y4y0j8jv"))))
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(propagated-inputs
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`(("python-wrapt" ,python-wrapt)
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("python-requests" ,python-requests)
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("python-appdirs" ,python-appdirs)
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("python-configargparse" ,python-configargparse)
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("python-pyyaml" ,python-pyyaml)
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("python-ratelimiter" ,python-ratelimiter)))))
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(define-public python-pyqrcode
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(package
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(name "python-pyqrcode")
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@ -14854,14 +14835,13 @@ Included are implementations of:
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(define-public bpython
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(package
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(name "bpython")
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(version "0.17.1")
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(version "0.18")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "bpython" version))
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(sha256
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(base32
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"0bxhxi5zxdkrf8b4gwn0d363kdz3qnypjwhm1aydki53ph8ca1w9"))))
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(base32 "1hl6frgvr2lqaxqczl8amg9xih32b3gzv429vs0qrjb8wpdj1k2n"))))
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(build-system python-build-system)
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(arguments
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`(#:phases
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@ -14884,10 +14864,10 @@ Included are implementations of:
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(propagated-inputs
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`(("python-pygments" ,python-pygments)
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("python-requests" ,python-requests)
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("python-babel" ,python-babel) ; optional, for internationalization
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("python-babel" ,python-babel) ; optional, for internationalization
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("python-curtsies" ,python-curtsies) ; >= 0.1.18
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("python-greenlet" ,python-greenlet)
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("python-urwid" ,python-urwid) ; for bpython-urwid only
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("python-urwid" ,python-urwid) ; for bpython-urwid only
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("python-six" ,python-six)))
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(native-inputs
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`(("python-sphinx" ,python-sphinx)
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@ -16610,3 +16590,57 @@ It is the recommended replacement for Python's original
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@code{distro} also provides a command-line interface to output the platform
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information in various formats.")
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(license license:asl2.0)))
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(define-public python-cairosvg
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(package
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(name "python-cairosvg")
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(version "2.4.2")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "CairoSVG" version))
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(sha256
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(base32 "1bb7irxbaxxb9ahm3z5wsx1q96mm5gzskc7b6q07h9ikcnb8yrjf"))))
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(build-system python-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(replace 'check
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(lambda _ (invoke "pytest"))))))
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(propagated-inputs
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`(("python-cairocffi" ,python-cairocffi)
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("python-cssselect2" ,python-cssselect2)
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("python-defusedxml" ,python-defusedxml)
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("python-pillow" ,python-pillow)
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("python-tinycss2" ,python-tinycss2)))
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(native-inputs
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`(("python-pytest-flake8" ,python-pytest-flake8)
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("python-pytest-isort" ,python-pytest-isort)
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("python-pytest-runner" ,python-pytest-runner)))
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(home-page "https://cairosvg.org/")
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(synopsis "SVG to PDF/PS/PNG converter based on Cairo")
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(description "CairoSVG is a SVG converter based on Cairo. It can export
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SVG files to PDF, PostScript and PNG files. The main part of CairoSVG is a
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SVG parser, trying to follow the SVG 1.1 recommendation from the W3C. Once
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parsed, the result is drawn to a Cairo surface that can be exported to
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qvarious formats: PDF, PostScript, PNG and even SVG.")
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(license license:lgpl3+)))
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(define-public python-pyphen
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(package
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(name "python-pyphen")
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(version "0.9.5")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "Pyphen" version))
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(sha256
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(base32 "08c9y69ry9d6m4zalhnalg86lsp9v2j5n1ziw5vxfmiihx83lqrv"))))
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(build-system python-build-system)
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;; TODO: Use the Guix system hyphenation packages hyphen-* rather than the
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;; embedded set provided by upstream - like Debian does.
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(home-page "https://github.com/Kozea/Pyphen")
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(synopsis "Pure Python module to hyphenate text")
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(description "Pyphen is a pure Python module to hyphenate text using
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existing Hunspell hyphenation dictionaries.")
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(license (list license:gpl2 license:lgpl2.1 license:mpl1.1))))
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