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

Message ID 87h999ymzk.fsf@ike.i-did-not-set--mail-host-address--so-tickle-me
State New
Headers show

Commit Message

Marius Bakke Sept. 21, 2016, 9:14 p.m. UTC
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.

Comments

Ben Woodcroft Sept. 22, 2016, 12:46 a.m. UTC | #1
On 22/09/16 07:14, Marius Bakke wrote:
> [..]
> Hi Ben,
>
> Thanks for the review. Updated patches attached.
>
Hi,

> Subject: [PATCH 1/3] gnu: python-pysam: Update to 0.9.1.4.
I'm not sure whether this is a product of the upgrade or not, but I 
notice this in the build log. I think it is harmless though, WDYT?

starting phase `validate-runpath'
validating RUNPATH of 10 binaries in 
"/gnu/store/bpiq3lm6b1kpf54i1vj2dl09ff293wic-python-pysam-0.9.1.4/lib"...
/gnu/store/bpiq3lm6b1kpf54i1vj2dl09ff293wic-python-pysam-0.9.1.4/lib/python3.4/site-packages/pysam-0.9.1.4-py3.4-linux-x86_64.egg/pysam/libchtslib.cpython-34m.so: 
warning: RUNPATH contains bogus entries: ("pysam" "." 
"build/lib.linux-x86_64-3.4/pysam")

Also, I notice that pysam bundles htslib, bcftools and samtools C code. 
Hopefully it should be straightforward enough to remove htslib as there 
are install instructions, I'm not sure about the other two. This 
shouldn't block the patch here, but would you mind taking a look?
http://pysam.readthedocs.io/en/latest/installation.html#installation

The other two patches LGTM.
ben
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Patch

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