[PATCH] Add krona-tools.

This is a neat little visualisation tool that generates zoomable HTML5 charts from hierarchical data e.g. disk usage http://marbl.github.io/Krona/examples/du.krona.html It is mainly used for bioinformatics (specifically metagenomics) I believe, but is more generally applicable. Not sure if web.sc

[PATCH] gnu: Add krona-tools.

* gnu/packages/web.scm (krona-tools): New variable. --- gnu/packages/web.scm | 96 1 file changed, 96 insertions(+) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 58de65c..a6279c8 100644 --- a/gnu/packages/web.scm +++ b/gnu/pack

Re: [PATCH v3] gnu: Add python2-shedskin.

> My instinct is that we should make it refer directly to the libraries > (pcre and libgc) but that user-facing executables like make and g++ > should be installed by the user. Yeah, I did it like that in the existing patch. > The examples may not be 100% relevant; is shedskin totally useless > w

Re: pypi URL change

On 25/04/16 10:13, Cyril Roelandt wrote: On 04/25/2016 01:21 AM, Ben Woodcroft wrote: 2) The new URLs are even uglier than the old one and a working pypi-uri would hide them from our eyes. Yeah but it is my understanding that the new pattern will only be applied to new releases, so how will p

Re: GuixSD encrypted root?

Hi, > Or, as Leo suggests, it could be that shepherd starts the device-mapping > service, which runs “cryptsetup luksOpen”, which never completes because > you don’t know it’s waiting for you to enter a passphrase. I doubt that it's that. The only change I have to do for it to work just fine is

Re: [PATCH] gnu: Add ristretto.

Kei Yamashita writes: > XFCE's image viewer is packaged at last! Pushed, thanks!

Re: pypi URL change

On 04/25/2016 01:21 AM, Ben Woodcroft wrote: > 2) The new URLs are even uglier than the old one and a working pypi-uri > would hide them from our eyes. Yeah but it is my understanding that the new pattern will only be applied to new releases, so how will pypi-uri know what pattern to apply? Cyri

Re: [PATCH v2 03/10] gnu: Add python-pytest-pep8.

On 25/04/16 03:04, Efraim Flashner wrote: On Sun, Apr 24, 2016 at 11:06:17PM +1000, Ben Woodcroft wrote: [..] + ;; 'setup.py test' does not run tests + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (

Re: [PATCH v2 03/10] gnu: Add python-pytest-pep8.

On 25/04/16 03:04, Efraim Flashner wrote: On Sun, Apr 24, 2016 at 11:06:17PM +1000, Ben Woodcroft wrote: [..] + (let ((out (assoc-ref outputs "out"))) + (setenv "PYTHONPATH" + (string-append +(getenv "PYTHONPATH") +

[PATCH 0/1] Don't bootstrap ncmpcpp?

I wondered why we re-bootstrap ncmpcpp, so I tried to build without doing it. It works fine for me. Does anyone know why we started doing it? The mailing list thread where the patch was submitted doesn't address it [0]. I've attached a patch to stop doing it and remove the unused inputs. I'm not

[PATCH 1/1] gnu: ncmpcpp: Remove bootstrapping inputs.

* gnu/packages/mpd.scm (ncmpcpp)[arguments]: Remove 'autogen' phase. [native-inputs]: Remove autoconf, automake, and libtool. --- gnu/packages/mpd.scm | 14 ++ 1 file changed, 2 insertions(+), 12 deletions(-) diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index 63cb16f..4860

Re: pypi URL change

On 25/04/16 08:26, Cyril Roelandt wrote: On 04/24/2016 09:27 AM, Ben Woodcroft wrote: Hi, Today I tried using pypi-url to autogenerate a package that was only released today. Unfortunately, it seems that the URL scheme has changed and I was unable to download, though I believe this only affec

Re: pypi URL change

On 04/24/2016 09:27 AM, Ben Woodcroft wrote: > Hi, > > Today I tried using pypi-url to autogenerate a package that was only > released today. Unfortunately, it seems that the URL scheme has changed > and I was unable to download, though I believe this only affects newly > released package versi

Re: Proposal: Prefix language-name for language library packages

Am 24.04.2016 um 20:57 schrieb Leo Famulari: > What about C? Do we need c-linux-libre? ;) Oh, you hit the weak point of this proposal: I can not formulate a rule, why e.g. libsodium does not need to be prefixed by "c-". And what about c++ libraries? Maybe the main difference is that one can not (o

Re: Language library packages should require language package

Hartmut Goebel skribis: > But you are missing my main point: While `guix environment --ad-hoc > python-requests` installs some depended python packages, it does not > install `python`. This is asymmetric and quite different than users are > used from rpm and deb based systems. Indeed. I underst

Re: [PATCH] Remove extra .scm appended to guile-minikanren files

Erik Edrosa skribis: > Was looking to play around with minikanren so I installed > guile-minikanren on guix and noticed the scheme files had an extra .scm > appended to them when installed. So this patch removes them from the files. Indeed. > From ddc117f8c04406a4ddc6a1ccf3a7510182d8b678 Mon Se

Re: [PATCH 0/2] Update Python to current versions

Leo Famulari skribis: > On Fri, Apr 22, 2016 at 08:41:04AM +0200, Hartmut Goebel wrote: >> Am 22.04.2016 um 01:12 schrieb Cyril Roelandt: >> > I think the latest Python 3.x is Python 3.5.1 (see >> > https://www.python.org/). Maybe we should forget about 3.4.x, WDYT? >> >> Python 3.4.4 is the lat

Re: Branching based on Python version (was [PATCH 2/6] gnu: add python-sqlparse and python2-sqlparse)

Leo Famulari skribis: > On Thu, Apr 21, 2016 at 09:19:49PM +0200, Hartmut Goebel wrote: >> * gnu/packages/python.scm (python-sqlparse) (python2-sqlparse): >> New variables. > >> +(arguments >> + `(#:phases >> + (modify-phases %standard-phases >> + (replace 'check >> +

Re: [PATCH 3/6] gnu: add python-selenium and python2-selenium

Hartmut Goebel skribis: > +;; FIXME webdriver/firefox contains pre-build binaries. Build them in > +;; guix, but the source is not included. In addition to Leo’s reply, could you make sure the blobs are removed in a ‘snippet’? See ‘shogun’ in machine-learning.scm for an example of that.

Re: Adding a symlink to python-wrapper rebuilds python?

Hartmut Goebel skribis: > I'm curious: I added "python-config" to the symlinks in package > "python-wrapper". I thought, this would just use the "python" package > already in the store and augment it with he symlinks. > > Instead "guix build python-wrapper" tried to download the the *source* > fo

Re: GuixSD encrypted root?

l...@gnu.org (Ludovic Courtès) skribis: > Hey, > > Danny Milosavljevic skribis: > >> Yeah, but even using a non-required-for-boot encrypted filesystem (i.e. not >> an encrypted root, just encrypted home) doesn't work. As soon as I add >> "mount? #t" it hangs. >> >> I'm now using a workaround wh

Re: [PATCH 2/3] gnu: Add reposurgeon.

Hello! Mathieu Lirzin skribis: > l...@gnu.org (Ludovic Courtès) writes: [...] >>> + ;; xsltproc generates random ids when the source document >>> doesn't >>> + ;; provide them. This is making the build not reproducible. >>> + (substitute* "reposurgeon.xml"

[PATCH] gnu: Add ristretto.

XFCE's image viewer is packaged at last! 0001-gnu-Add-ristretto.patch Description: Binary data

Re: GuixSD encrypted root?

Hey, Danny Milosavljevic skribis: > Yeah, but even using a non-required-for-boot encrypted filesystem (i.e. not > an encrypted root, just encrypted home) doesn't work. As soon as I add > "mount? #t" it hangs. > > I'm now using a workaround where it's specified using "mount? #f" and I mount >

Re: [PATCH 1/6] gnu: Add python-tblib and python2-tblib

On Thu, Apr 21, 2016 at 09:19:48PM +0200, Hartmut Goebel wrote: > * packages/python.scm (python-tblib) (python2-tblib): New > variables. Thanks for the updated patch! > +(define-public python-tblib > + (package > +(name "python-tblib") > +(version "1.3.0") > +(source > + (origi

Branching based on Python version (was [PATCH 2/6] gnu: add python-sqlparse and python2-sqlparse)

On Thu, Apr 21, 2016 at 09:19:49PM +0200, Hartmut Goebel wrote: > * gnu/packages/python.scm (python-sqlparse) (python2-sqlparse): > New variables. > +(arguments > + `(#:phases > + (modify-phases %standard-phases > + (replace 'check > + (lambda* _ > + ;

Re: [PATCH 3/6] gnu: add python-selenium and python2-selenium

On Thu, Apr 21, 2016 at 09:19:50PM +0200, Hartmut Goebel wrote: > * gnu/packages/python.scm (python-selenium) (python2-selenium): > New variables. > --- > gnu/packages/python.scm | 29 + > 1 file changed, 29 insertions(+) > > diff --git a/gnu/packages/python.scm b/gn

Re: [PATCH] Add python-tables.

On Thu, Apr 21, 2016 at 05:28:58PM +0200, Ricardo Wurmus wrote: > Subject: [PATCH] gnu: Add python-tables. > +(arguments > + `(#:configure-flags > + (list (string-append "--hdf5=" > +(assoc-ref %build-inputs "hdf5"))) > + ;; FIXME: python-build-sys

Re: [PATCH 0/1] Update OpenLDAP, fixing CVE-2015-6908

On Thu, Apr 21, 2016 at 02:57:48PM -0400, Leo Famulari wrote: > There is a remote denial of service bug in OpenLDAP in version 2.4.42 > and earlier [0]. > > This patch updates OpenLDAP to the latest version. > > This change will require several hundred packages to be rebuilt. Should > it go on se

Re: Proposal: Prefix language-name for language library packages

On Sun, Apr 24, 2016 at 03:22:03PM +0200, Hartmut Goebel wrote: > Hi, > > I propose to generalizing the specification [1,2] as we already have for > Perl, Python and Java for most programming languages. In short: > > Package names should be prefixed with the name of the language and if > the pack

Re: GuixSD encrypted root?

On Sun, Apr 24, 2016 at 06:04:25PM +0200, Danny Milosavljevic wrote: > On Sun, 24 Apr 2016 16:22:16 +0200 > l...@gnu.org (Ludovic Courtès) wrote: > > > Encrypted root file systems are not supported yet (some people managed > > to work around the lack of support, but that’s somewhat fragile.) > >

Re: [PATCH 2/2] gnu: Add gnome-tweak-tool.

On Sun, Apr 24, 2016 at 01:19:35PM +0200, Jan Nieuwenhuizen wrote: > Leo Famulari writes: > > I think we need to wrap gnome-tweak-tool's executable, which the > > python-build-system normally does automatically. AIUI, that's why all of > > the python-build-system packages don't require Python itsel

Re: [PATCH v2 03/10] gnu: Add python-pytest-pep8.

On Sun, Apr 24, 2016 at 11:06:17PM +1000, Ben Woodcroft wrote: > * gnu/packages/python.scm (python-pytest-pep8, python2-pytest-pep8): New > variables. > --- > gnu/packages/python.scm | 60 > + > 1 file changed, 60 insertions(+) > > diff --git a/gnu

Re: GuixSD encrypted root?

On Sun, 24 Apr 2016 16:22:16 +0200 l...@gnu.org (Ludovic Courtès) wrote: > Encrypted root file systems are not supported yet (some people managed > to work around the lack of support, but that’s somewhat fragile.) > > Good news is we’re getting there! You can track progress at >

Re: Proposal: Prefix language-name for language library packages

Hi, I've always like the Gentoo approach most. Have a qualified package name like dev-java/ant and if you try to install "ant" and it's unique: good. If you try to install "ant" and there are multiple ones: you get a disambiguation error. If you try to install "dev-java/ant" there's no ambigu

4 projects accepted for GSoC!

Hello! I am pleased to announce that 4 students have been accepted to work on Guix for the Google Summer of Code! • Efraim Flashner will work on a Bourne-shell compiler front-end for Guile mentors: Eric Bavier, myself https://libreplanet.org/wiki/Group:Guix/GSoC-2016#Write_a_Bourne-she

Re: Import from Debian?

Hartmut Goebel skribis: > did anybody work on some "guix import debian"? We already have “guix import nix” but (1) the non-trivial parts cannot be automatically translated (because they’re written in Bash in Nixpkgs), and (2) meta-data, in particular licenses, needs to be double-checked and adju

Re: [PATCH] version bump libgcrypt -> 1.7

Leo Famulari skribis: > On Wed, Apr 20, 2016 at 07:03:40PM +0200, Ludovic Courtès wrote: >> Leo Famulari skribis: >> >> > On Sun, Apr 17, 2016 at 11:53:51AM +0200, ng0 wrote: >> >> Updated libgcrypt patch. >> > >> > Is there a consensus on upgrading from 1.6.5 and making the change on >> > core

Re: GuixSD encrypted root?

Hi! Encrypted root file systems are not supported yet (some people managed to work around the lack of support, but that’s somewhat fragile.) Good news is we’re getting there! You can track progress at . Thanks, Ludo’.

Re: Language library packages should require language package

Am 24.04.2016 um 15:09 schrieb Thompson, David: > That's not quite right. It will give you exactly what you asked for: > an environment with only python-requests used in it. python-requests > defines no search paths, so no environment variables are set. But where is `python-requests` then? > N

Proposal: Prefix language-name for language library packages

Hi, I propose to generalizing the specification [1,2] as we already have for Perl, Python and Java for most programming languages. In short: Package names should be prefixed with the name of the language and if the package name already contains the name of the language, it gets removed there. I

Re: [PATCH 03/10] gnu: Add python-pytest-pep8.

On 22/04/16 04:26, Hartmut Goebel wrote: Am 21.04.2016 um 15:21 schrieb Ben Woodcroft: + (add-after 'install 'post-install-check + ;; 'setup.py test' does not run tests + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs

Re: [PATCH 02/10] gnu: Add python-bz2file.

Hi Hartmut, Thanks for your comments. On 22/04/16 04:24, Hartmut Goebel wrote: Am 21.04.2016 um 15:21 schrieb Ben Woodcroft: +(arguments + `(#:phases + (modify-phases %standard-phases + ;; python setup.py test does not work as of 0.98 + ;; but there is only the on

Re: Language library packages should require language package

Sorry, I accidentally sent the previous email before I was finished writing. The rest of the response is below. On Sun, Apr 24, 2016 at 8:24 AM, Hartmut Goebel wrote: [...] > Now the weirdness analysis: > > $ cat echo_paths.sh > echo PATH=$PATH > echo PYTHONPATH=$PYTHONPATH > type python > > N

Re: [PATCH 08/10] gnu: python-ipython: Use 'python2-variant'.

On 22/04/16 01:14, Ricardo Wurmus wrote: Ben Woodcroft writes: * gnu/packages/python.scm (python-ipython)[properties]: New field. (python2-ipython): Use 'strip-python2-variant'. The commit message should mention the changes to the “inputs” and “propagated-input” fields because it isn’t obvi

Re: [PATCH 08/10] gnu: python-ipython: Use 'python2-variant'.

On 22/04/16 01:14, Ricardo Wurmus wrote: Ben Woodcroft writes: * gnu/packages/python.scm (python-ipython)[properties]: New field. (python2-ipython): Use 'strip-python2-variant'. The commit message should mention the changes to the “inputs” and “propagated-input” fields because it isn’t obvi

Re: Language library packages should require language package

On Sun, Apr 24, 2016 at 8:24 AM, Hartmut Goebel wrote: > Hi, > > playing around with guix environment, I stepped over some weirdness The > weirdest of is (e.g.): > > guix environment --ad-hoc python-requests > > will give you . . . . nothing. That's not quite right. It will give you exactly wha

[PATCH v2 08/10] gnu: python-ipython: Use 'python2-variant'.

* gnu/packages/python.scm (python-ipython)[properties]: New field. (python2-ipython): Use 'strip-python2-variant'. [inputs, propagated-inputs]: Do not redefine inherited values. --- gnu/packages/python.scm | 26 +- 1 file changed, 9 insertions(+), 17 deletions(-) diff --gi

[PATCH v2 10/10] gnu: Add python-scikit-bio.

* gnu/packages/python.scm (python-scikit-bio, python2-scikit-bio): New variables. --- gnu/packages/bioinformatics.scm | 84 + 1 file changed, 84 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 899ce1c..fa67

[PATCH v2 07/10] gnu: python-tornado: Use 'python2-variant'.

* gnu/packages/python.scm (python-tornado)[properties]: New field. (python2-tornado): Build with 'strip-python2-variant'. --- gnu/packages/python.scm | 6 -- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index ccd4a28..ee2cab8 1

[PATCH v2 09/10] gnu: Add python-natsort.

* gnu/packages/python.scm (python-natsort, python2-natsort): New variables. --- gnu/packages/python.scm | 41 + 1 file changed, 41 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 40d28b1..8ae7566 100644 --- a/gnu/packages/

[PATCH v2 02/10] gnu: Add python-bz2file.

* gnu/packages/python.scm (python-bz2file, python2-bz2file): New variables. --- gnu/packages/python.scm | 37 + 1 file changed, 37 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index ecd16c5..c07dae6 100644 --- a/gnu/packages/pyth

[PATCH v2 04/10] gnu: Add python-pytest-flakes.

* gnu/packages/python.scm (python-pytest-flakes, python2-pytest-flakes): New variables. --- gnu/packages/python.scm | 45 + 1 file changed, 45 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index b1a4969..4175fad 100644 ---

[PATCH v2 03/10] gnu: Add python-pytest-pep8.

* gnu/packages/python.scm (python-pytest-pep8, python2-pytest-pep8): New variables. --- gnu/packages/python.scm | 60 + 1 file changed, 60 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index c07dae6..b1a4969 100644 ---

[PATCH v2 05/10] gnu: Add python-future.

* gnu/packages/python.scm (python-future, python2-future): New variables. --- gnu/packages/python.scm | 32 +++- 1 file changed, 31 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 4175fad..28eebf1 100644 --- a/gnu/packa

[PATCH v2] Add python-scikit-bio.

Apologies, still trying to get used to git send-email; please ignore the 2 patches just sent separate to this iteration. Thanks, ben

[PATCH v2 06/10] gnu: Add python-cachecontrol.

* gnu/packages/python.scm (python-cachecontrol, python2-cachecontrol): New variables. --- gnu/packages/python.scm | 31 +++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 28eebf1..ccd4a28 100644 --- a/gnu/packages/

[PATCH v2 01/10] gnu: Add python2-pytest-cache.

* gnu/packages/python.scm (python-pytest-cache)[properties]: New field. (python2-pytest-cache): New variable. --- gnu/packages/python.scm | 14 -- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 0379352..ecd16c5 100

[PATCH 2/2] gnu: Add python-scikit-bio.

* gnu/packages/python.scm (python-scikit-bio, python2-scikit-bio): New variables. --- gnu/packages/bioinformatics.scm | 84 + 1 file changed, 84 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 899ce1c..fa67

Re: [PATCH 0/2]: Add biom-format.

On 24/04/16 22:27, Ben Woodcroft wrote: Thanks in advance. I'm not 100% on whether this should just be called 'biom' or 'biom-format'. I figured it'd be more consistent amongst Python 2 & 3 to be 'python-biom-format' and 'python2-biom-format', but I'm open to ideas. Ah, I realise now this

Import from Debian?

Hi, did anybody work on some "guix import debian"? If we'd had something like this, this could increase the speed for adding new packages a lot. I found a Python module `python-debian` which seams to allow analyzing .dsc files and control files quite easily. If it is of interest, I could implemen

[PATCH 2/2] gnu: Add python-biom-format.

* gnu/packages/bioinformatics.scm (python-biom-format, python2-biom-format): New variables. --- gnu/packages/bioinformatics.scm | 40 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fa67

[PATCH 1/2] gnu: Add python-pyqi.

* gnu/packages/python.scm (python-pyqi, python2-pyqi): New variables. --- gnu/packages/python.scm | 48 1 file changed, 48 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 8ae7566..2436a1f 100644 --- a/gnu/packages

[PATCH 0/2]: Add biom-format.

Thanks in advance. I'm not 100% on whether this should just be called 'biom' or 'biom-format'. I figured it'd be more consistent amongst Python 2 & 3 to be 'python-biom-format' and 'python2-biom-format', but I'm open to ideas. Thanks. ben

Language library packages should require language package

Hi, playing around with guix environment, I stepped over some weirdness The weirdest of is (e.g.): guix environment --ad-hoc python-requests will give you . . . . nothing. Since python-requests does not have python as input, the package is installed somewhere out of reach. This is even true wh

Re: [PATCH 2/2] gnu: Add gnome-tweak-tool.

Leo Famulari writes: >> Gnome-tweak-tool is written in python2: it won't run without it. How >> could loosening the python2 dependency be helpful? > > Ah, I didn't realize it was a Python program with an Autotools build > system. > > I think we need to wrap gnome-tweak-tool's executable, which th

pypi URL change

Hi, Today I tried using pypi-url to autogenerate a package that was only released today. Unfortunately, it seems that the URL scheme has changed and I was unable to download, though I believe this only affects newly released package versions. I found this on the nix mailing list: http://comme