From 42d6bffc2ff55406e75bf2f7096d4074c18cf382 Mon Sep 17 00:00:00 2001 From: Konrad Hinsen Date: Tue, 2 Jan 2018 20:04:53 +0100 Subject: gnu: Add python2-mmtk. * gnu/packages/python.scm (python2-mmtk): New public variable. --- gnu/packages/python.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 3dde9af340..d64c9bf850 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12249,3 +12249,44 @@ (define-public python2-scientific 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))) -- cgit v1.2.3 From 8f25c2e438f0f3bd39ea26ebfa6dcda189f050ea Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 5 Jan 2018 13:38:33 -0500 Subject: gnu: python-click-threading: Update to 0.4.4. * gnu/packages/python.scm (python-click-threading): Update to 0.4.4. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index d64c9bf850..79e2c1c672 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6808,13 +6808,13 @@ (define-public python2-atomicwrites (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))) -- cgit v1.2.3 From 8cbbea150d62b64fc041496b0a1b5b764c98d93c Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 5 Jan 2018 13:39:06 -0500 Subject: gnu: python-click-log: Update to 0.2.1. * gnu/packages/python.scm (python-click-log): Update to 0.2.1. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 79e2c1c672..29fa2809ab 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6827,13 +6827,13 @@ (define-public python-click-threading (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))) -- cgit v1.2.3 From 0215f94e69b133bf33f9bc54ea05df976dbfc9d8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 8 Jan 2018 15:32:00 +0100 Subject: gnu: snakemake: Update to 4.4.0. * gnu/packages/python.scm (snakemake): Update to 4.4.0. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 29fa2809ab..4e1fc0abf2 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4815,13 +4815,13 @@ (define-public python2-networkx2 (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. -- cgit v1.2.3 From 9e8401a539c2d6198f927c90862ffa3490e932ed Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 10 Jan 2018 04:39:40 +0100 Subject: gnu: python-ply, python2-ply: Update to 3.10. * gnu/packages/python.scm (python-ply): Update to 3.10. --- gnu/packages/python.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 4e1fc0abf2..69a034fd84 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -32,7 +32,7 @@ ;;; Copyright © 2016, 2017 Alex Vong ;;; Copyright © 2016, 2017 Arun Isaac ;;; Copyright © 2016, 2017 Julien Lepiller -;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice +;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2016, 2017 Thomas Danckaert ;;; Copyright © 2017 Carlo Zancanaro ;;; Copyright © 2017 Frederick M. Muriithi @@ -8553,14 +8553,14 @@ (define-public python2-pika (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") -- cgit v1.2.3 From b438d7cfa8154aaf0b7ea0d64bd45e2c33db455e Mon Sep 17 00:00:00 2001 From: Ben Sturmfels Date: Wed, 10 Jan 2018 12:23:08 +1100 Subject: gnu: pelican: Enable Markdown support. * gnu/packages/python.scm (pelican)[propagated-inputs]: Add python-markdown to support Markdown as mentioned in the package description. Signed-off-by: Leo Famulari --- gnu/packages/python.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 69a034fd84..2d2c3116c4 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2472,7 +2472,8 @@ (define-public pelican ("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 -- cgit v1.2.3 From 0ee12dc9f1606b80c26a9c39c28da99070d20b12 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 10 Jan 2018 19:18:56 +0100 Subject: gnu: python-idna: Update to 2.6. * gnu/packages/python.scm (python-idna): Update to 2.6. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 2d2c3116c4..0b582e6b73 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5973,14 +5973,14 @@ (define-public python2-ipaddr (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") -- cgit v1.2.3