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-rw-r--r--gnu/packages/python.scm66
1 files changed, 54 insertions, 12 deletions
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 5d87c7486e..99e5bd9e0b 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -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)))