Re: [PATCH 2/3] gnu: Add python-pyxb.

[Marius Bakke <mbakke@fastmail.com>]

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Ben Woodcroft <b.woodcroft@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.


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From 0a6220a664ecf3aa967211db5bf9e9b9e539220d Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@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


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From 6a8ddd17d7f11e0687217c8649a452a1a56c596c Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@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 <janneke@gnu.org>
 ;;; Copyright © 2016 ng0 <ng0@we.make.ritual.n0.is>
 ;;; Copyright © 2016 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2016 Marius Bakke <mbakke@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


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From 396cbcbfda24ce5cd1caecedf01407bf6a1f70a1 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@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