mirror of
https://https.git.savannah.gnu.org/git/guix.git/
synced 2025-07-14 19:10:49 +02:00
Merge branch 'master' into staging
This commit is contained in:
commit
1af575f04d
181 changed files with 7425 additions and 3498 deletions
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@ -14,7 +14,7 @@
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;;; Copyright © 2015, 2016, 2017 Leo Famulari <leo@famulari.name>
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;;; Copyright © 2015, 2017 Ben Woodcroft <donttrustben@gmail.com>
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;;; Copyright © 2015, 2016 Erik Edrosa <erik.edrosa@gmail.com>
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;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
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;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
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;;; Copyright © 2015, 2017 Kyle Meyer <kyle@kyleam.com>
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;;; Copyright © 2015, 2016 Chris Marusich <cmmarusich@gmail.com>
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;;; Copyright © 2016 Danny Milosavljevic <dannym+a@scratchpost.org>
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@ -782,14 +782,14 @@ NetCDF files can also be read and modified. Python-HDF4 is a fork of
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(define-public python-h5py
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(package
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(name "python-h5py")
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(version "2.7.0")
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(version "2.8.0")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "h5py" version))
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(sha256
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(base32
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"0433sdv6xc9p7v1xs1gvbxp7p152ywi3nplgjb258q9fvw9469br"))))
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"0mdr6wrq02ac93m1aqx9kad0ppfzmm4imlxqgyy1x4l7hmdcc9p6"))))
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(build-system python-build-system)
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(arguments
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`(#:tests? #f ; no test target
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@ -2218,14 +2218,14 @@ environments and back.")
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(define-public python-pyyaml
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(package
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(name "python-pyyaml")
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(version "3.12")
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(version "3.13")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "PyYAML" version))
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(sha256
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(base32
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"1aqjl8dk9amd4zr99n8v2qxzgmr2hdvqfma4zh7a41rj6336c9sr"))))
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"1gx603g484z46cb74j9rzr6sjlh2vndxayicvlyhxdz98lhhkwry"))))
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(build-system python-build-system)
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(inputs
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`(("libyaml" ,libyaml)))
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@ -4210,23 +4210,53 @@ support for Python 3 and PyPy. It is based on cffi.")
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(file-name (string-append name "-" version ".tar.gz"))
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(sha256
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(base32
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"1rk2dvy3fxrga6bvvxc2fi5lbaynm5h4a0w0aaxyn3bc77rszjg9"))))
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"1rk2dvy3fxrga6bvvxc2fi5lbaynm5h4a0w0aaxyn3bc77rszjg9"))
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(patches (search-patches "python-cairocffi-dlopen-path.patch"))))
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(build-system python-build-system)
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(outputs '("out" "doc"))
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(inputs
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`(("gdk-pixbuf" ,gdk-pixbuf)
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("cairo" ,cairo)))
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`(("glib" ,glib)
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("gtk+" ,gtk+)
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("gdk-pixbuf" ,gdk-pixbuf)
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("cairo" ,cairo)
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("pango" ,pango)))
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(native-inputs
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`(("pkg-config" ,pkg-config)
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("python-pytest" ,python-pytest)
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("python-sphinx" ,python-sphinx)
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("python-docutils" ,python-docutils)))
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(propagated-inputs
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`(("python-xcffib" ,python-xcffib))) ; used at run time
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(arguments
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`(;; FIXME: Tests cannot find 'libcairo.so.2'.
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#:tests? #f
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#:tests? #t
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'patch-paths
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(substitute* (find-files "." "\\.py$")
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(("dlopen\\(ffi, 'cairo'")
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(string-append "dlopen(ffi, '" (assoc-ref inputs "cairo")
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"/lib/libcairo.so.2'"))
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(("dlopen\\(ffi, 'gdk-3'")
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(string-append "dlopen(ffi, '" (assoc-ref inputs "gtk+")
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"/lib/libgtk-3.so.0'"))
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(("dlopen\\(ffi, 'gdk_pixbuf-2.0'")
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(string-append "dlopen(ffi, '" (assoc-ref inputs "gdk-pixbuf")
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"/lib/libgdk_pixbuf-2.0.so.0'"))
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(("dlopen\\(ffi, 'glib-2.0'")
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(string-append "dlopen(ffi, '" (assoc-ref inputs "glib")
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"/lib/libglib-2.0.so.0'"))
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(("dlopen\\(ffi, 'gobject-2.0'")
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(string-append "dlopen(ffi, '" (assoc-ref inputs "glib")
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"/lib/libgobject-2.0.so.0'"))
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(("dlopen\\(ffi, 'pangocairo-1.0'")
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(string-append "dlopen(ffi, '" (assoc-ref inputs "pango")
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"/lib/libpangocairo-1.0.so.0'"))
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(("dlopen\\(ffi, 'pango-1.0'")
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(string-append "dlopen(ffi, '" (assoc-ref inputs "pango")
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"/lib/libpango-1.0.so.0'")))
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#t))
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(add-after 'install 'install-doc
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let* ((data (string-append (assoc-ref outputs "doc") "/share"))
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@ -5106,16 +5136,40 @@ of the structure, dynamics, and functions of complex networks.")
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(define-public python2-networkx2
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(package-with-python2 python-networkx2))
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(define-public python-datrie
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(package
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(name "python-datrie")
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(version "0.7.1")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "datrie" version))
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(sha256
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(base32
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"08r0if7dry2q7p34gf7ffyrlnf4bdvnprxgydlfxgfnvq8f3f4bs"))))
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(build-system python-build-system)
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(native-inputs
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`(("python-cython" ,python-cython)
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("python-hypothesis" ,python-hypothesis)
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("python-pytest" ,python-pytest)
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("python-pytest-runner" ,python-pytest-runner)))
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(home-page "https://github.com/kmike/datrie")
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(synopsis "Fast, efficiently stored trie for Python")
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(description
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"This package provides a fast, efficiently stored trie implementation for
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Python.")
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(license license:lgpl2.1+)))
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(define-public snakemake
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(package
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(name "snakemake")
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(version "4.4.0")
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(version "5.2.0")
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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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(base32 "0a1i5v5qxbmmpznp7my9nva8y7pxp8pjrwk2gxgisdskg35sq8s1"))))
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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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@ -5137,6 +5191,11 @@ of the structure, dynamics, and functions of complex networks.")
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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-datrie" ,python-datrie)
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("python-docutils" ,python-docutils)
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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-pyyaml" ,python-pyyaml)
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("python-ratelimiter" ,python-ratelimiter)))
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(home-page "https://bitbucket.org/snakemake/snakemake/wiki/Home")
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@ -5147,6 +5206,24 @@ 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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@ -6284,14 +6361,14 @@ designed to efficiently cope with extremely large amounts of data.")
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(define-public python-pyasn1
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(package
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(name "python-pyasn1")
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(version "0.4.2")
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(version "0.4.3")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "pyasn1" version))
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(sha256
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(base32
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"05bxnr4wmrg62m4qr1pg1p3z7bhwrv74jll3k42pgxwl36kv0n6j"))))
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"1z5h38anjzzrxpraa9iq9llffyx2zs8gx0q6dc1g029miwnn50gv"))))
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(build-system python-build-system)
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(home-page "http://pyasn1.sourceforge.net/")
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(synopsis "ASN.1 types and codecs")
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@ -6306,14 +6383,14 @@ suitable for a wide range of protocols based on the ASN.1 specification.")
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(define-public python-pyasn1-modules
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(package
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(name "python-pyasn1-modules")
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(version "0.0.8")
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(version "0.2.2")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "pyasn1-modules" version))
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(sha256
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(base32
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"0drqgw81xd3fxdlg89kgd79zzrabvfncvkbybi2wr6w2y4s1jmhh"))))
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"0ivm850yi7ajjbi8j115qpsj95bgxdsx48nbjzg0zip788c3xkx0"))))
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(build-system python-build-system)
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(propagated-inputs
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`(("python-pyasn1" ,python-pyasn1)))
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@ -12242,14 +12319,14 @@ pure Python module.")
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(define-public python-xenon
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(package
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(name "python-xenon")
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(version "0.5.1")
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(version "0.5.4")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "xenon" version))
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(sha256
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(base32
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"14kby2y48vp3sgwxqlm5d5789yibqwb1qli5fwcmdqg3iayrbklc"))))
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"029cbhysg2vr5n4jz8gpg2793f8wkwnqpr1qgv6c1dn685vy31mc"))))
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(build-system python-build-system)
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(native-inputs
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`(("python-pyyaml" ,python-pyyaml)
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@ -12261,12 +12338,7 @@ pure Python module.")
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`(#:phases
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(modify-phases %standard-phases
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(add-before 'build 'patch-test-requirements
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(lambda* (#:key inputs #:allow-other-keys)
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;; Update requirements from dependency==version to
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;; dependency>=version.
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(substitute* "requirements.txt"
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(("==") ">=")
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((",<1.5.0") ""))
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(lambda _
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;; Remove httpretty dependency for tests.
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(substitute* "setup.py"
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(("httpretty") ""))
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|
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