Ben Woodcroft <b.woodcr...@uq.edu.au> 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.
>From 0a6220a664ecf3aa967211db5bf9e9b9e539220d Mon Sep 17 00:00:00 2001
From: Marius Bakke <mba...@fastmail.com>
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
>From 6a8ddd17d7f11e0687217c8649a452a1a56c596c Mon Sep 17 00:00:00 2001
From: Marius Bakke <mba...@fastmail.com>
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 © 2016 Jan Nieuwenhuizen <jann...@gnu.org>
;;; Copyright © 2016 ng0 <n...@we.make.ritual.n0.is>
;;; Copyright © 2016 Tobias Geerinckx-Rice <m...@tobias.gr>
+;;; Copyright © 2016 Marius Bakke <mba...@fastmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -729,6 +730,30 @@ different Unicode encodings which happen automatically during
parsing/saving.")
(license license:expat)))
+(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 source
+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/GPL2
+ license:psfl)))) ; pyxb/utils/activestate.py
+
+(define-public python2-pyxb
+ (package-with-python2 python-pyxb))
+
(define-public xmlto
(package
(name "xmlto")
--
2.10.0
>From 396cbcbfda24ce5cd1caecedf01407bf6a1f70a1 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mba...@fastmail.com>
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
