From mboxrd@z Thu Jan 1 00:00:00 1970 From: Marius Bakke Subject: Re: [PATCH 2/3] gnu: Add python-pyxb. Date: Wed, 21 Sep 2016 22:14:07 +0100 Message-ID: <87h999ymzk.fsf@ike.i-did-not-set--mail-host-address--so-tickle-me> References: <20160917101047.4597-1-mbakke@fastmail.com> <20160917101047.4597-3-mbakke@fastmail.com> <3bd16b58-b3d1-d47c-2433-c3a721681463@uq.edu.au> <39d81c47-a96d-1f1c-ad1d-a80e7b7f109d@uq.edu.au> <1a9d61d6-0ee2-1161-25b4-9ffd32396039@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:59584) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bmoqZ-0004Fo-R2 for guix-devel@gnu.org; Wed, 21 Sep 2016 17:14:29 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bmoqV-0005Et-Ga for guix-devel@gnu.org; Wed, 21 Sep 2016 17:14:26 -0400 Received: from out2-smtp.messagingengine.com ([66.111.4.26]:44697) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bmoqT-00059i-0s for guix-devel@gnu.org; Wed, 21 Sep 2016 17:14:23 -0400 In-Reply-To: <1a9d61d6-0ee2-1161-25b4-9ffd32396039@uq.edu.au> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: Ben Woodcroft , "guix-devel@gnu.org" --=-=-= Content-Type: text/plain Ben Woodcroft writes: > Hi again, > > > On 20/09/16 16:34, Ben Woodcroft wrote: >> Oops, forgot to cc the list. >> >> >> On 20/09/16 16:02, Ben Woodcroft wrote: >>> Hi Marius, >>> >>> Thanks for the patches. >>> >>> On 17/09/16 20:10, Marius Bakke wrote: >>>> [..] >>>> + (add-after 'unpack 'fix-tests >>>> + (lambda _ >>>> + ;; See https://github.com/pabigot/pyxb/issues/26 ... >>>> + (delete-file "tests/trac/test-trac-0091.py") >>> >>> The fix for that test failing seems straightforward enough, might be >>> better to include as a patch so those tests are run. >>> https://github.com/pabigot/pyxb/commit/d4bdd5a1c712cd70f96264ae13b55d015cbf3335 >>> > Actually, 1.2.5 just got released which has both of these fixes. Can you > send an updated patch please? Hi Ben, Thanks for the review. Updated patches attached. --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0001-gnu-python-pysam-Update-to-0.9.1.4.patch >From 0a6220a664ecf3aa967211db5bf9e9b9e539220d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Sep 2016 18:05:15 +0100 Subject: [PATCH 1/3] gnu: python-pysam: Update to 0.9.1.4. * gnu/packages/bioinformatics.scm (python-pysam, python2-pysam): Update to 0.9.1.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7a27e0b..47b884e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1290,13 +1290,13 @@ multiple sequence alignments.") (define-public python-pysam (package (name "python-pysam") - (version "0.8.4") + (version "0.9.1.4") (source (origin (method url-fetch) (uri (pypi-uri "pysam" version)) (sha256 (base32 - "1slx5mb94mzm5qzk52q270sab0sar95j67w1g1k452nz3s9j7krh")))) + "1i1djacqbr88y7w18b4aa78zxnsyr4sz7yqdq2spi7gs0y6pzvjn")))) (build-system python-build-system) (arguments `(#:tests? #f ; tests are excluded in the manifest -- 2.10.0 --=-=-= Content-Type: text/x-patch; charset=utf-8 Content-Disposition: attachment; filename=0002-gnu-Add-python-pyxb.patch Content-Transfer-Encoding: quoted-printable >From 6a8ddd17d7f11e0687217c8649a452a1a56c596c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 17 Sep 2016 10:33:28 +0100 Subject: [PATCH 2/3] gnu: Add python-pyxb. * gnu/packages/xml.scm (python-pyxb, python2-pyxb): New variables. --- gnu/packages/xml.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 7befad5..cd3426b 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -13,6 +13,7 @@ ;;; Copyright =C2=A9 2016 Jan Nieuwenhuizen ;;; Copyright =C2=A9 2016 ng0 ;;; Copyright =C2=A9 2016 Tobias Geerinckx-Rice +;;; Copyright =C2=A9 2016 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -729,6 +730,30 @@ different Unicode encodings which happen automatically= during parsing/saving.") (license license:expat))) =20 +(define-public python-pyxb + (package + (name "python-pyxb") + (version "1.2.5") + (source (origin + (method url-fetch) + (uri (pypi-uri "PyXB" version)) + (sha256 + (base32 + "0rzzwibfqa28gxgcxx4cybx1qcg0g6fand06ykj3gz7z5kp653sf")))) + (build-system python-build-system) + (home-page "http://pyxb.sourceforge.net/") + (synopsis "Python XML Schema Bindings") + (description + "PyXB (\"pixbee\") is a pure Python package that generates Python sou= rce +code for classes that correspond to data structures defined by XMLSchema.") + (license (list license:asl2.0 ; Most files. + license:expat ; pyxb/utils/six.py + license:gpl2 ; bundled jquery in doc is dual MIT/G= PL2 + license:psfl)))) ; pyxb/utils/activestate.py + +(define-public python2-pyxb + (package-with-python2 python-pyxb)) + (define-public xmlto (package (name "xmlto") --=20 2.10.0 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0003-gnu-python2-pbcore-Update-to-1.2.10.patch >From 396cbcbfda24ce5cd1caecedf01407bf6a1f70a1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 17 Sep 2016 10:42:56 +0100 Subject: [PATCH 3/3] gnu: python2-pbcore: Update to 1.2.10. * gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.10. [propagated-inputs]: New field. Add python2-pyxb. --- gnu/packages/bioinformatics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 47b884e..a598351 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3376,13 +3376,13 @@ interrupted by stop codons. OrfM finds and prints these ORFs.") (define-public python2-pbcore (package (name "python2-pbcore") - (version "1.2.8") + (version "1.2.10") (source (origin (method url-fetch) (uri (pypi-uri "pbcore" version)) (sha256 (base32 - "02pfn5raa3zf739672bg0dkx7z3j2c4nx7vmpfjqy5b12jrqpymk")))) + "1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i")))) (build-system python-build-system) (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7 (inputs @@ -3395,6 +3395,8 @@ interrupted by stop codons. OrfM finds and prints these ORFs.") ("python-nose" ,python2-nose) ("python-setuptools" ,python2-setuptools) ("python-sphinx" ,python2-sphinx))) + (propagated-inputs + `(("python-pyxb" ,python2-pyxb))) (home-page "http://pacificbiosciences.github.io/pbcore/") (synopsis "Library for reading and writing PacBio data files") (description -- 2.10.0 --=-=-=--