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Merge branch 'master' into core-updates

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Leo Famulari 2018-01-11 14:22:50 -08:00
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@ -32,7 +32,7 @@
;;; Copyright © 2016, 2017 Alex Vong <alexvong1995@gmail.com>
;;; Copyright © 2016, 2017 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2016, 2017 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
;;; Copyright © 2017 Carlo Zancanaro <carlo@zancanaro.id.au>
;;; Copyright © 2017 Frederick M. Muriithi <fredmanglis@gmail.com>
@ -2534,7 +2534,8 @@ interested parties to subscribe to events, or \"signals\".")
("python-blinker" ,python-blinker)
("python-unidecode" ,python-unidecode)
("python-six" ,python-six)
("python-dateutil" ,python-dateutil)))
("python-dateutil" ,python-dateutil)
("python-markdown" ,python-markdown)))
(home-page "http://getpelican.com/")
(arguments
`(;; XXX Requires a lot more packages to do unit tests :P
@ -4857,13 +4858,13 @@ of the structure, dynamics, and functions of complex networks.")
(define-public snakemake
(package
(name "snakemake")
(version "4.2.0")
(version "4.4.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "snakemake" version))
(sha256
(base32 "0mgl44q152ws40zj2vicqark5szyd73vqy9pf26g6hk6dk0y0c79"))))
(base32 "0g0paia4z7w3srnqdmavq3hrb2x7qnpf81jx50njl0p7y4y0j8jv"))))
(build-system python-build-system)
(arguments
;; TODO: Package missing test dependencies.
@ -6023,14 +6024,14 @@ versions of Python.")
(define-public python-idna
(package
(name "python-idna")
(version "2.5")
(version "2.6")
(source
(origin
(method url-fetch)
(uri (pypi-uri "idna" version))
(sha256
(base32
"1ara12a7k2zc69msa0arrvw00gn61a6i6by01xb3lkkc0h4cxd9w"))))
"13qaab6d0s15gknz8v3zbcfmbj6v86hn9pjxgkdf62ch13imssic"))))
(build-system python-build-system)
(home-page "https://github.com/kjd/idna")
(synopsis "Internationalized domain names in applications")
@ -6859,13 +6860,13 @@ for atomic file system operations.")
(define-public python-click-threading
(package
(name "python-click-threading")
(version "0.4.3")
(version "0.4.4")
(source (origin
(method url-fetch)
(uri (pypi-uri "click-threading" version))
(sha256
(base32
"0xs4bg2ws0zgyiplk312l049hi23c2zqf1g771rjhh5vr2msk4cg"))))
"1rsxc2fbkxlhwhlmxsdjzq3spn284l6rvjfcz9mbb17ibgdgmc5j"))))
(build-system python-build-system)
(propagated-inputs
`(("python-click" ,python-click)))
@ -6878,13 +6879,13 @@ applications.")
(define-public python-click-log
(package
(name "python-click-log")
(version "0.2.0")
(version "0.2.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "click-log" version))
(sha256
(base32
"1bjrfxji1yv4fj0g78ri2yfgn2wbivn8g69fxfinxvxpmighhshp"))))
"1r1x85023cslb2pwldd089jjk573mk3w78cnashs77wrx7yz8fj9"))))
(build-system python-build-system)
(propagated-inputs
`(("python-click" ,python-click)))
@ -8600,14 +8601,14 @@ network support library.")
(define-public python-ply
(package
(name "python-ply")
(version "3.9")
(version "3.10")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ply" version))
(sha256
(base32
"0gpl0yli3w03ipyqfrp3w5nf0iawhsq65anf5wwm2wf5p502jzhd"))))
"1jxsr1d2f732r6ljhvm827113dckwl6qwakfvpbdhcbhvpvlmscn"))))
(build-system python-build-system)
(home-page "http://www.dabeaz.com/ply/")
(synopsis "Python Lex & Yacc")
@ -12296,3 +12297,44 @@ physical units, automatic derivatives, ...) whereas others are more
domain-specific (e.g. netCDF and PDB support). The library is currently
not actively maintained and works only with Python 2 and NumPy < 1.9.")
(license license:cecill-c)))
(define-public python2-mmtk
(package
(name "python2-mmtk")
(version "2.7.10")
(source
(origin
(method url-fetch)
(uri (string-append "https://bitbucket.org/khinsen/"
"mmtk/downloads/MMTK-" version ".tar.gz"))
(file-name (string-append "MMTK-" version ".tar.gz"))
(sha256
(base32
"1k4gsd50zja89dbzgy3aji7h4zpvbvdfrds7rxr3whqrsgcffnir"))))
(build-system python-build-system)
(native-inputs
`(("netcdf" ,netcdf)))
(propagated-inputs
`(("python-scientific" ,python2-scientific)
("python-tkinter" ,python-2 "tk")))
(arguments
`(#:python ,python-2
#:tests? #f
#:phases
(modify-phases %standard-phases
(add-before 'build 'includes-from-scientific
(lambda* (#:key inputs #:allow-other-keys)
(mkdir-p "Include/Scientific")
(copy-recursively
(string-append
(assoc-ref inputs "python-scientific")
"/include/python2.7/Scientific")
"Include/Scientific"))))))
(home-page "http://dirac.cnrs-orleans.fr/MMTK")
(synopsis "Python library for molecular simulation")
(description "MMTK is a library for molecular simulations with an emphasis
on biomolecules. It provides widely used methods such as Molecular Dynamics
and normal mode analysis, but also basic routines for implementing new methods
for simulation and analysis. The library is currently not actively maintained
and works only with Python 2 and NumPy < 1.9.")
(license license:cecill-c)))