Re: [ART] Website mockup rev2

[Ricardo Wurmus]

Luis Felipe López Acevedo writes:

> Here is a revision of the last mockup for the website [1]. This time
> aimed at a techie audience.
>
> http://sirgazil.bitbucket.org/static/temp/img/guixsd/home-view-rev2.jpg

I like this a lot better than the previous mockups (which would have
been great for something targetted at a different audience).

Just one comment: I know that the screenshots are just placeholders, but
there is no GNOME in the system distribution, yet all but one of the
screenshots show the GNOME Shell.

I even wonder if screenshots are necessary at all or if it wouldn't be
better to show some diagrams of e.g. how the store works instead.  The
diagrams were used in the slides but they are not in the official docs,
yet I found them immensely helpful in understanding the system.

~~ Ricardo

[ART] Website mockup rev2

[Luis Felipe López Acevedo]

Hi,

Here is a revision of the last mockup for the website [1]. This time
aimed at a techie audience.

http://sirgazil.bitbucket.org/static/temp/img/guixsd/home-view-rev2.jpg

Note that some sections that are currently available in
 are not present in this mockup. I'm
not suggesting to remove them, though. In the image I have of the future
website, I think these sections could be located in appropriate pages.
For example:

- Status and Downloading. These could be in the Download page.
- Getting involved. This would go in Contribute. And I'd suggest to use
a simple layout such as the one used in the GNOME website
.
- Maintainer and Licensing. These could be in the About page.

What do you think?


[1] https://lists.gnu.org/archive/html/guix-devel/2015-02/msg00500.html


-- 
Luis Felipe López Acevedo
http://sirgazil.bitbucket.org/

[PATCH] gnu: Add pumpa.

[David Thompson]

Here's our first pump.io client!  I created a new "pumpio" module
because there are other clients and libraries out there that could be
added in the future.

>From 6bdff480ca5d4a2ea017cb72471ede2ea13ed3d0 Mon Sep 17 00:00:00 2001
From: David Thompson 
Date: Fri, 20 Feb 2015 19:53:27 -0500
Subject: [PATCH] gnu: Add pumpa.

* gnu/packages/pumpio.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
---
 gnu-system.am   |  1 +
 gnu/packages/pumpio.scm | 68 +
 2 files changed, 69 insertions(+)
 create mode 100644 gnu/packages/pumpio.scm

diff --git a/gnu-system.am b/gnu-system.am
index eeadd8f..c1948b2 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -233,6 +233,7 @@ GNU_SYSTEM_MODULES =\
   gnu/packages/popt.scm\
   gnu/packages/pth.scm\
   gnu/packages/pulseaudio.scm			\
+  gnu/packages/pumpio.scm			\
   gnu/packages/pretty-print.scm			\
   gnu/packages/protobuf.scm			\
   gnu/packages/python.scm			\
diff --git a/gnu/packages/pumpio.scm b/gnu/packages/pumpio.scm
new file mode 100644
index 000..4a6375f
--- /dev/null
+++ b/gnu/packages/pumpio.scm
@@ -0,0 +1,68 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2015 David Thompson 
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see .
+
+(define-module (gnu packages pumpio)
+  #:use-module (guix licenses)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix build-system gnu)
+  #:use-module (gnu packages aspell)
+  #:use-module (gnu packages kde)
+  #:use-module (gnu packages qt)
+  #:use-module (gnu packages web))
+
+(define-public pumpa
+  (package
+(name "pumpa")
+(version "0.9")
+(source (origin
+  (method git-fetch) ; no source tarballs
+  (uri (git-reference
+(url "https://gitorious.org/pumpa/pumpa.git";)
+(commit (string-append "v" version
+  (sha256
+   (base32
+"0v55xq17wnc9mvpmrm5r3rjrsg9npnjv1lznbz8ppk77ba8pwimy"
+(build-system gnu-build-system)
+(arguments
+ '(#:phases (alist-replace
+ 'configure
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+   ;; Fix dependency tests.
+   (substitute* "pumpa.pro"
+ (("/usr/include/tidy\\.h")
+  (string-append (assoc-ref inputs "tidy")
+ "/include/tidy.h"))
+ (("/usr/include/aspell.h")
+  (string-append (assoc-ref inputs "aspell")
+ "/include/aspell.h")))
+   ;; Run qmake with proper installation prefix.
+   (let ((prefix (string-append "PREFIX="
+(assoc-ref outputs "out"
+ (zero? (system* "qmake" prefix
+ %standard-phases)))
+(inputs
+ `(("aspell" ,aspell)
+   ("qt" ,qt)
+   ("qjson" ,qjson)
+   ("tidy" ,tidy)))
+(synopsis "Qt-based pump.io client")
+(description "Pumpa is a simple pump.io client written in C++ and Qt.")
+(home-page "https://pumpa.branchable.com/";)
+(license gpl3+)))
-- 
2.1.4


-- 
David Thompson
Web Developer - Free Software Foundation - http://fsf.org
GPG Key: 0FF1D807
Support the FSF: https://fsf.org/donate

Re: Test failure cpan

[Andreas Enge]

On Fri, Feb 20, 2015 at 04:31:26PM -0500, David Thompson wrote:
> Mark just pushed a patch that fixes a 'guix pull' issue caused by the
> CPAN importer.  Perhaps the tests will pass now?

Unfortunately, it does not.

Andreas

Re: Test failure cpan

[Eric Bavier]

On Fri, 20 Feb 2015 16:31:26 -0500
David Thompson  wrote:

> Andreas Enge  writes:
> 
> > Hello,
> >
> > I just ran a "make check", and got a failure in the cpan test. Here is the
> > cpan.log:
> >
> > accepted connection from pid 9095, uid 1000
> > spurious SIGPOLL
> > 415 operations
> > accepted connection from pid 9095, uid 1000
> > 1 operations
> >  Starting test cpan  (Writing full log to "cpan.log")
> > tests/cpan.scm:63: FAIL cpan->guix-package
> > # of unexpected failures  1
> > ;;; note: source file ./srfi/srfi-64.scm
> > ;;;   newer than compiled 
> > /gnu/store/zjhaqhfbwkh5n4cbsrk8h7bg8yqrimls-guile-2.0.11/lib/guile/2.0/ccache/srfi/srfi-64.go
> > FAIL tests/cpan.scm (exit status: 1)
> >
> > I suppose it is related to the recent changes by Eric on the perl
> > import.
> 
> Mark just pushed a patch that fixes a 'guix pull' issue caused by the
> CPAN importer.  Perhaps the tests will pass now?
> 

I hope it fixes the 'guix pull' issue, but I don't think it will fix
the test failure.  I'm updating the test and will push a fix soon.  My
last commits changed the behavior of how module dependencies are
handled, and I failed to update the results that the test expects. 

Sorry about the mess.

`~Eric

Re: Test failure cpan

[David Thompson]

Andreas Enge  writes:

> Hello,
>
> I just ran a "make check", and got a failure in the cpan test. Here is the
> cpan.log:
>
> accepted connection from pid 9095, uid 1000
> spurious SIGPOLL
> 415 operations
> accepted connection from pid 9095, uid 1000
> 1 operations
>  Starting test cpan  (Writing full log to "cpan.log")
> tests/cpan.scm:63: FAIL cpan->guix-package
> # of unexpected failures  1
> ;;; note: source file ./srfi/srfi-64.scm
> ;;;   newer than compiled 
> /gnu/store/zjhaqhfbwkh5n4cbsrk8h7bg8yqrimls-guile-2.0.11/lib/guile/2.0/ccache/srfi/srfi-64.go
> FAIL tests/cpan.scm (exit status: 1)
>
> I suppose it is related to the recent changes by Eric on the perl
> import.

Mark just pushed a patch that fixes a 'guix pull' issue caused by the
CPAN importer.  Perhaps the tests will pass now?

-- 
David Thompson
Web Developer - Free Software Foundation - http://fsf.org
GPG Key: 0FF1D807
Support the FSF: https://fsf.org/donate

Re: [PATCH]: gnu: Add jalv.

[Andreas Enge]

I did not try to compile it, but the recipe looks good to me, so please
push.

Andreas

Re: [PATCH]: gnu: lilv: propagate inputs serd, sord and sratom.

[Andreas Enge]

On Fri, Feb 20, 2015 at 10:04:30PM +0100, Ricardo Wurmus wrote:
> lilv-0.pc requires the packages serd, sord and sratom to be present or
> else pkg-config fails when looking for the flags for lilv.

Okay, please push!

Andreas

[PATCH]: gnu: Add jalv.

[Ricardo Wurmus]

>From e253f67cd387dbad5629e53d113a717b41ca96af Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus 
Date: Fri, 20 Feb 2015 22:05:37 +0100
Subject: [PATCH] gnu: Add jalv.

* gnu/packages/audio.scm (jalv): New variable.
---
 gnu/packages/audio.scm | 31 +++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index abd6f32..b57085b 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -299,6 +299,37 @@ synchronous execution of all clients, and low latency operation.")
 ;; Most files are under GPLv2+, but some headers are under LGPLv2.1+
 (license (list license:gpl2+ license:lgpl2.1+
 
+(define-public jalv
+  (package
+(name "jalv")
+(version "1.4.6")
+(source (origin
+  (method url-fetch)
+  (uri (string-append "http://download.drobilla.net/jalv-";
+  version ".tar.bz2"))
+  (sha256
+   (base32
+"1f1hcq74n3ziw8bk97mn5a1vgw028dxikv3fchaxd430pbbhqgl9"
+(build-system waf-build-system)
+(arguments `(#:tests? #f)) ; no check target
+(inputs
+ `(("lv2" ,lv2)
+   ("lilv" ,lilv)
+   ("suil" ,suil)
+   ("gtk" ,gtk+-2)
+   ("gtkmm" ,gtkmm-2)
+   ("qt" ,qt-4)
+   ("jack" ,jack-1)))
+(native-inputs
+ `(("pkg-config" ,pkg-config)))
+(home-page "http://drobilla.net/software/jalv/";)
+(synopsis "Simple LV2 host for JACK")
+(description
+ "Jalv is a simple but fully featured LV2 host for JACK.  It runs LV2
+plugins and exposes their ports as JACK ports, essentially making any LV2
+plugin function as a JACK application.")
+(license license:isc)))
+
 (define-public ladspa
   (package
 (name "ladspa")
-- 
2.1.0

[PATCH]: gnu: lilv: propagate inputs serd, sord and sratom.

[Ricardo Wurmus]

lilv-0.pc requires the packages serd, sord and sratom to be present or
else pkg-config fails when looking for the flags for lilv.

The attached patch moves serd, sord and sratom from lilv's inputs to the
propagated-inputs field.

~~ Ricardo

>From a253ab3b2ed89148211275938b5e574a594d8526 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus 
Date: Fri, 20 Feb 2015 21:56:51 +0100
Subject: [PATCH] gnu: lilv: propagate inputs serd, sord and sratom.

* gnu/packages/audio.scm (lilv): move serd, sord and sratom to propagated
  inputs.
---
 gnu/packages/audio.scm | 8 +---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 40969ce..abd6f32 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -415,11 +415,13 @@ implementation of the Open Sound Control (OSC) protocol.")
"0aj2plkx56iar8vzjbq2l7hi7sp0ml99m0h44rgwai2x4vqkk2j2"
 (build-system waf-build-system)
 (arguments `(#:tests? #f)) ; no check target
-(inputs
- `(("lv2" ,lv2)
-   ("serd" ,serd)
+;; required by lilv-0.pc
+(propagated-inputs
+ `(("serd" ,serd)
("sord" ,sord)
("sratom" ,sratom)))
+(inputs
+ `(("lv2" ,lv2)))
 (native-inputs
  `(("pkg-config" ,pkg-config)))
 (home-page "http://drobilla.net/software/lilv/";)
-- 
2.1.0

Bugs in parsing build options

[Alex Kost]

Ludovic Courtès (2014-12-06 18:04 +0300) wrote:

> Deck Pickard  skribis:
>
>> From 9c27d995e1a622de8457209d40031b392538e0f8 Mon Sep 17 00:00:00 2001
>> From: nebuli 
>> Date: Fri, 5 Dec 2014 01:28:12 +0100
>> Subject: [PATCH] guix: scripts: Fix GUIX_BUILD_OPTIONS handling.
>>
>> Appending to "raw" args broke optional parameters in 'guix package -I'
>> and 'guix package -A', and possibly other places.  Therefore, switch to
>> parsing each set of options on its own and append resulting alists
>> together afterwards.
>>
>> * guix/scripts/archive.scm (parse-options-from): Rename from
>>   (parse-options) and add explicit argument.  New form of (parse-options)
>>   using its old algorithm via -from function.
>> * guix/scripts/build.scm: Ditto.
>> * guix/scripts/environment.scm: Ditto.
>> * guix/scripts/package.scm: Ditto.
>> * guix/scripts/system.scm: Ditto.
>
> Good catch.  I’ve applied it along with a test case that reproduces the
> problem and a clarification in the doc.

Hello, I think I found a problem with this commit.

I noticed that "--no-grub" option has no effect.  For example,
"guix system --no-grub reconfigure" installs GRUB anyway.

Further investigation showed that there is a problem in parsing build
options.  After that commit (847391f) we have the following code:

(append (parse-options-from args)
(parse-options-from (environment-build-options)))

in several places.  But 'parse-options-from' returns default values for
unspecified options, e.g. if you didn't set GUIX_BUILD_OPTIONS, then
(parse-options-from '()) will return an alist of default options
(including ‘(install-grub? . #t)’).

So build commands will just ignore such options as "--no-grub" or
"--no-substitutes" if a user didn't tweak GUIX_BUILD_OPTIONS.

-- 
Alex

Re: [PATCH 2/3]: Add pyyaml.

[Andreas Enge]

On Fri, Feb 20, 2015 at 05:48:04PM +0100, Ricardo Wurmus wrote:
> +(propagated-inputs
> + `(("libyaml" ,libyaml)))

Is it really needed to propagate the input? The _yaml.cpython-33m.so library
is automatically linked with libyaml-0.so.2 thanks to our ld. If it is needed,
could you add a quick explanation?

> +(description
> + " PyYAML is a YAML parser and emitter for Python.  PyYAML features a
 ↑ a space too much
Andreas

Test failure cpan

[Andreas Enge]

Hello,

I just ran a "make check", and got a failure in the cpan test. Here is the
cpan.log:

accepted connection from pid 9095, uid 1000
spurious SIGPOLL
415 operations
accepted connection from pid 9095, uid 1000
1 operations
 Starting test cpan  (Writing full log to "cpan.log")
tests/cpan.scm:63: FAIL cpan->guix-package
# of unexpected failures  1
;;; note: source file ./srfi/srfi-64.scm
;;;   newer than compiled 
/gnu/store/zjhaqhfbwkh5n4cbsrk8h7bg8yqrimls-guile-2.0.11/lib/guile/2.0/ccache/srfi/srfi-64.go
FAIL tests/cpan.scm (exit status: 1)

I suppose it is related to the recent changes by Eric on the perl import.

Andreas

Re: [PATCH]: Add HTSeq.

[Andreas Enge]

Looks good, please push! It is a bit unfortunate that the sources themselves
do not mention the license (PKG-INFO states that the license is unknown), but
the web page is clear. So maybe you could make the suggestion for the next
release to update the PKG-INFO file, and to maybe add a COPYING to the tarball.

Andreas

[PATCH 1/3]: Add libyaml

[Ricardo Wurmus]

>From c52c742aaa90fb68e496ef83b1763125a514e606 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus 
Date: Fri, 20 Feb 2015 17:35:09 +0100
Subject: [PATCH 1/3] gnu: Add libyaml.

* gnu/packages/web.scm (libyaml): New variable.
---
 gnu/packages/web.scm | 20 
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 308434f..5296c43 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -799,3 +799,23 @@ select or poll.")
 server).  It was primarily designed to be used by one person or a small group
 of people.")
 (license l:expat)))
+
+(define-public libyaml
+  (package
+(name "libyaml")
+(version "0.1.5")
+(source
+ (origin
+   (method url-fetch)
+   (uri (string-append
+ "http://pyyaml.org/download/libyaml/yaml-";
+ version ".tar.gz"))
+   (sha256
+(base32
+ "1vrv5ly58bkmcyc049ad180f2m8iav6l9h3v8l2fqdmrny7yx1zs"
+(build-system gnu-build-system)
+(home-page "http://pyyaml.org/wiki/LibYAML";)
+(synopsis "YAML 1.1 parser and emitter written in C")
+(description
+ "LibYAML is a YAML 1.1 parser and emitter written in C.")
+(license l:expat)))
-- 
2.1.0

[PATCH 0/3]: Add libyaml, pyyaml, pybedtools.

[Ricardo Wurmus]

Attached is a series of patches adding libyaml, the Python bindings to
libyaml, and pybedtools (Python bindings to bedtools), which depends on
the former two.

~~ Ricardo

[PATCH 3/3]: Add pybedtools.

[Ricardo Wurmus]

>From 26054dc29fa3132e58b2a71e20f37cfc3446a68d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus 
Date: Fri, 20 Feb 2015 17:43:08 +0100
Subject: [PATCH 3/3] gnu: Add pybedtools.

* gnu/packages/bioinformatics.scm (python2-pybedtools): New variable.
---
 gnu/packages/bioinformatics.scm | 34 ++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b64dab7..092a6e3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -33,6 +33,7 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages tbb)
   #:use-module (gnu packages vim)
+  #:use-module (gnu packages web)
   #:use-module (gnu packages zip))
 
 (define-public bedops
@@ -141,6 +142,39 @@ intervals from multiple files in widely-used genomic file formats such as BAM,
 BED, GFF/GTF, VCF.")
 (license license:gpl2)))
 
+(define-public python2-pybedtools
+  (package
+(name "python2-pybedtools")
+(version "0.6.9")
+(source (origin
+  (method url-fetch)
+  (uri (string-append
+"https://pypi.python.org/packages/source/p/pybedtools/pybedtools-";
+version ".tar.gz"))
+  (sha256
+   (base32
+"1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an"
+(build-system python-build-system)
+(arguments `(#:python ,python-2)) ; no Python 3 support
+(inputs
+ `(("python-cython" ,python2-cython)
+   ("python-matplotlib" ,python2-matplotlib)
+   ("python-setuptools" ,python2-setuptools)))
+(propagated-inputs
+ `(("bedtools" ,bedtools)
+   ("samtools" ,samtools)))
+(native-inputs
+ `(("python-pyyaml" ,python2-pyyaml)
+   ("python-nose" ,python2-nose)))
+(home-page "https://pythonhosted.org/pybedtools/";)
+(synopsis "Python wrapper for BEDtools programs")
+(description
+ "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs,
+which are widely used for genomic interval manipulation or \"genome algebra\".
+pybedtools extends BEDTools by offering feature-level manipulations from with
+Python.")
+(license license:gpl2+)))
+
 (define-public bowtie
   (package
 (name "bowtie")
-- 
2.1.0

[PATCH 2/3]: Add pyyaml.

[Ricardo Wurmus]

>From 4b8d6f7a10bc4c20c267a4c26be4e5678ce96382 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus 
Date: Fri, 20 Feb 2015 17:38:17 +0100
Subject: [PATCH 2/3] gnu: Add pyyaml.

* gnu/packages/python.scm (python-pyyaml, python2-pyyaml): New variables.
---
 gnu/packages/python.scm | 32 
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index cb25419..e19d707 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -53,6 +53,7 @@
   #:use-module (gnu packages readline)
   #:use-module (gnu packages texlive)
   #:use-module (gnu packages texinfo)
+  #:use-module (gnu packages web)
   #:use-module (gnu packages which)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
@@ -1730,6 +1731,37 @@ environments and back.")
 (define-public python2-itsdangerous
   (package-with-python2 python-itsdangerous))
 
+(define-public python-pyyaml
+  (package
+(name "python-pyyaml")
+(version "3.11")
+(source
+ (origin
+   (method url-fetch)
+   (uri (string-append
+ "https://pypi.python.org/packages/source/P/PyYAML/PyYAML-";
+ version ".tar.gz"))
+   (sha256
+(base32
+ "1s26125vfnskng58ym37xhwv8v0mm95b2cwbjfag8prfhy596v63"
+(build-system python-build-system)
+(propagated-inputs
+ `(("libyaml" ,libyaml)))
+(native-inputs
+ `(("python-setuptools" ,python-setuptools)))
+(home-page "http://pyyaml.org/wiki/PyYAML";)
+(synopsis "YAML parser and emitter for Python")
+(description
+ " PyYAML is a YAML parser and emitter for Python.  PyYAML features a
+complete YAML 1.1 parser, Unicode support, pickle support, capable extension
+API, and sensible error messages.  PyYAML supports standard YAML tags and
+provides Python-specific tags that allow to represent an arbitrary Python
+object.")
+(license license:expat)))
+
+(define-public python2-pyyaml
+  (package-with-python2 python-pyyaml))
+
 (define-public python-virtualenv
   (package
 (name "python-virtualenv")
-- 
2.1.0

[PATCH]: Add HTSeq.

[Ricardo Wurmus]

>From 3b812ce1c3458f832aa6eaac0d15502832bae8d5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus 
Date: Fri, 20 Feb 2015 16:41:50 +0100
Subject: [PATCH] gnu: Add HTSeq.

* gnu/packages/bioinformatics.scm (htseq): New variable.
---
 gnu/packages/bioinformatics.scm | 24 
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c13e649..b64dab7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -311,6 +311,30 @@ several alignment strategies enable effective alignment of RNA-seq reads, in
 particular, reads spanning multiple exons.")
 (license license:gpl3+)))
 
+(define-public htseq
+  (package
+(name "htseq")
+(version "0.6.1")
+(source (origin
+  (method url-fetch)
+  (uri (string-append
+"https://pypi.python.org/packages/source/H/HTSeq/HTSeq-";
+version ".tar.gz"))
+  (sha256
+   (base32
+"1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv"
+(build-system python-build-system)
+(arguments `(#:python ,python-2)) ; only Python 2 is supported
+(inputs
+ `(("python-numpy" ,python2-numpy)
+   ("python-setuptools" ,python2-setuptools)))
+(home-page "http://www-huber.embl.de/users/anders/HTSeq/";)
+(synopsis "Analysing high-throughput sequencing data with Python")
+(description
+ "HTSeq is a Python package that provides infrastructure to process data
+from high-throughput sequencing assays.")
+(license license:gpl3+)))
+
 (define-public rseqc
   (package
 (name "rseqc")
-- 
2.1.0

Re: [PATCH]: fix scipy build

[Andreas Enge]

On Fri, Feb 20, 2015 at 12:35:19PM +0100, Ricardo Wurmus wrote:
> just like matplotlib also python-scipy needs to first install the UTF-8
> locale before setting it.  The attached patch is virtually identical to
> the matplotlib patch[1].

Please push for now, and please revert if at some point in time we switch
to a utf-8 build environment.

Andreas

[PATCH]: fix scipy build

[Ricardo Wurmus]

Hi Guix,

just like matplotlib also python-scipy needs to first install the UTF-8
locale before setting it.  The attached patch is virtually identical to
the matplotlib patch[1].

~~ Ricardo

[1]: http://lists.gnu.org/archive/html/guix-devel/2015-02/msg00506.html

>From d6b6d8c52d71519385ca16e89f5140d2563041e8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus 
Date: Fri, 20 Feb 2015 12:19:38 +0100
Subject: [PATCH] gnu: python-scipy: install UTF-8 locale.

* gnu/packages/python.scm (python-scipy): Install en_US.UTF-8 locale in
  install-doc phase to avoid encoding error.
---
 gnu/packages/python.scm | 6 +-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 7dc7435..cb25419 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -2357,7 +2357,11 @@ toolkits.")
   (html (string-append doc "/html"))
   (pyver ,(string-append "PYVER=")))
  (with-directory-excursion "doc"
-   ;; Without setting this variable we get an encoding error.
+   ;; Install and set UTF-8 locale to avoid an encoding error.
+   (setenv "LOCPATH" (getcwd))
+   (system* "localedef" "--no-archive"
+"--prefix" (getcwd) "-i" "en_US"
+"-f" "UTF-8" "./en_US.UTF-8")
(setenv "LANG" "en_US.UTF-8")
;; Fix generation of images for mathematical expressions.
(substitute* (find-files "source" "conf\\.py")
-- 
2.1.0

Re: Gnupg update

[Andreas Enge]

On Thu, Feb 19, 2015 at 06:44:16PM -0500, Mark H Weaver wrote:
> Minor nit: According to our conventions, instead of listing the same
> file twice, write this:
> * gnu/packages/gnupg.scm (gnupg): Update to 2.1.2.
>   (gnupg-2.0): Copy of previous package for version 2.0.26.

Good point, I amended this.

> One more note of caution: I notice that you added 'npth' to core-updates
> instead of master, so I guess this needs to go to core-updates also.  In
> retrospect, they both could have gone to master.

Indeed. I started work on updating the packages in gnupg.scm on core-updates,
since I overestimated the impact it would have on package rebuilds ("guix
refresh -l gnupg" shows that in fact only a few packages depend on gnupg).
So to facilitate merging, I continued in core-updates.

Andreas