From mboxrd@z Thu Jan 1 00:00:00 1970 From: "Asfaw, Nardos" Subject: New outreachy participant introduction Date: Thu, 3 Oct 2019 16:11:58 +0000 Message-ID: <1570119118548.1674@iu.edu> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="_000_15701191185481674iuedu_" Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:51876) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iG3j3-0002qi-0p for guix-devel@gnu.org; Thu, 03 Oct 2019 12:13:10 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iG3j1-0001mW-2T for guix-devel@gnu.org; Thu, 03 Oct 2019 12:13:08 -0400 Received: from farley.uits.iu.edu ([134.68.220.39]:59723 helo=robin.uits.iu.edu) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iG3j0-0001mG-QO for guix-devel@gnu.org; Thu, 03 Oct 2019 12:13:07 -0400 Content-Language: en-US List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: "guix-devel@gnu.org" Cc: "outreachy@lepiller.eu" --_000_15701191185481674iuedu_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello Guix! My name is Nardos, and I am an Outreachy participant from Indiana Universit= y, Bloomington. I am a first time open source contributor hopeful. I am exc= ite to be here, but I will admit I am also a little nervous. I welcome feed= back as I am here to learn from all of you. I can be reached at nasfaw@iu.e= du or www.nardos.dev I also have a few questions: 1. I am opting to run Guix in a virtual machine on a kali linux. I have fo= und this resource: https://guix.gnu.org/manual/en/html_node/Running-Guix-in= -a-VM.html#Running-Guix-in-a-VM. Given your experience, would this cause a = problem down the line? Any recommendation on running Guix in a virtual mach= ine vs on my PC? 2. Upon making contributions, where is it posted? and how do I see feedback= s? I have seen lists of open projects and discussion treads such as this (h= ttps://issues.guix.gnu.org/issue/22138) on the Guix patch tracker. Are the= se the issues we currently working on? 3. Any beginner tips? and a good place to start? I look forward to working with you all. Thanks, Nardos --_000_15701191185481674iuedu_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hello Guix!


My name is Nardos, and I am an Outreachy participant from Indiana Univ= ersity, Bloomington. I am a first time open source contributor ho= peful. I am excite to be here, but I will admit I a= m also a little nervous. I welcome feedback as I am here to lea= rn from all of you. I can be reached at nasfaw@iu.edu or www.nardos.dev 

I also have a few questions:

1. I am opting to run Guix in a virtual machine on a kali linux.&= nbsp; I have found this resource: https://gui= x.gnu.org/manual/en/html_node/Running-Guix-in-a-VM.html#Running-Guix-in-a-V= M. Given your experience, would this cause a problem down the line? Any recom= mendation on running Guix in a virtual machine vs on my PC?

2. Upon making contributions, where is it posted? and how do I see fee= dbacks? I have seen lists of open projects and discussion treads such as th= is (https://issues.guix= .gnu.org/issue/22138)  on the Guix patch tracker. Are these the issues we currently working on? 


3. Any beginner tips? and a good place to start? 


I look forward to working with you all. 


Thanks,

Nardos

--_000_15701191185481674iuedu_-- From mboxrd@z Thu Jan 1 00:00:00 1970 From: Christopher Baines Subject: Re: New outreachy participant introduction Date: Thu, 03 Oct 2019 18:29:23 +0100 Message-ID: <878sq1pwjw.fsf@cbaines.net> References: <1570119118548.1674@iu.edu> Mime-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:34774) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iG4uw-00032i-Io for guix-devel@gnu.org; Thu, 03 Oct 2019 13:29:32 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iG4uv-00054R-50 for guix-devel@gnu.org; Thu, 03 Oct 2019 13:29:30 -0400 Received: from mira.cbaines.net ([2a01:7e00::f03c:91ff:fe69:8da9]:59714) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1iG4uu-000545-Up for guix-devel@gnu.org; Thu, 03 Oct 2019 13:29:29 -0400 In-reply-to: <1570119118548.1674@iu.edu> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: nasfaw@iu.edu Cc: guix-devel@gnu.org --=-=-= Content-Type: text/plain Asfaw, Nardos writes: > My name is Nardos, and I am an Outreachy participant from Indiana > University, Bloomington. I am a first time open source contributor > hopeful. I am excite to be here, but I will admit I am also a little > nervous. I welcome feedback as I am here to learn from all of you. I > can be reached at nasfaw@iu.edu or www.nardos.dev Hello Nardos, > I also have a few questions: > > 1. I am opting to run Guix in a virtual machine on a kali linux. I > have found this resource: > https://guix.gnu.org/manual/en/html_node/Running-Guix-in-a-VM.html#Running-Guix-in-a-VM. Given > your experience, would this cause a problem down the line? Any > recommendation on running Guix in a virtual machine vs on my PC? If you're happy installing Guix as a package manager within Kali, that might be easier than using a virtual machine. Both approaches should work though, and when you have an idea of what contributions you want to make, then you can work out which approach will be easier. > 2. Upon making contributions, where is it posted? and how do I see > feedbacks? I have seen lists of open projects and discussion treads > such as this (https://issues.guix.gnu.org/issue/22138) on the Guix > patch tracker. Are these the issues we currently working on? It depends on the contribution, but in general patches are sent to the guix-patches@gnu.org email address, and then appear on the https://issues.guix.info/ site. There's some relevant guidance here: https://guix.gnu.org/manual/en/html_node/Submitting-Patches.html#Submitting-Patches > 3. Any beginner tips? and a good place to start? I believe there are two Outreachy projects for Guix, so if you have a particular one in mind, let us know. If you're looking for where to begin contributing, it could be something to do with one of the Outreachy projects, working on packages for Guix, working on the documentation, fixing bugs, or something else. But from your first question above, it looks like you've started in the right place, getting Guix up and running on your machine is a prerequisite to everything. Chris --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQKTBAEBCgB9FiEEPonu50WOcg2XVOCyXiijOwuE9XcFAl2WL/NfFIAAAAAALgAo aXNzdWVyLWZwckBub3RhdGlvbnMub3BlbnBncC5maWZ0aGhvcnNlbWFuLm5ldDNF ODlFRUU3NDU4RTcyMEQ5NzU0RTBCMjVFMjhBMzNCMEI4NEY1NzcACgkQXiijOwuE 9XfyLw/+KwqMHfXQiQDBVXG67vlx1tQ+Zr3wLeZwCc3mXuP7zbUTTWEAtk2ipW7O LQUw2tCxq4r/kJibV0mRKBR55/LJ7HpMBAeaRipX3oRLE5x4/g26Fr3gRMZtqXBi DHt/ZyGGtw93C8gb8XPuPWovQJfsrNsxCKnlYUf6AG3RzLIkuXnlEMzeXU7SUyuU xG6/7l/aRxfVkPTv2xOqxw0UpOasv76fr7LFVjvJvI3leDGXrAOwFHrK3i7GmDZf kA/mi3bWDWhmFkr/gCyGqh1ctpImRFcT+fOt9ez8RjcAX02E2AnjkU63jhWJVK23 rS4jaOUZ86gL2/qrryIvW6frXH2Pw7+7MLBdyzLN9JvfG1wIZNXXaYMfxXO0n1Iu psyDcRG6t8l/25LEcT2vkSZgC2rLqLj3S4t4lVzu0l9VGxYQvDTeMi1TYUYodPf+ 0siQ6di4zByflEYL3JrtTIDJxeASrOgM5bbxM7lbWRSW8XPlZG+ayKCSlHmnxrL3 e/bb5B7XGVRr7FncXvr/m5bWfUDM4uuQMiqmoLBHl/QswC1KVVHZA/mhNgLvuzGu sbwFlpRmUuV2tPjjkTXU9uu3uaM7Q5vT2j778FuE49gE/QnlWXTy7qBJjZfo71XF sJORt5q1KDuiZf9tn2U8F/XMOJnYbSBEzqsXMvDZoXGeOrUaizE= =7qNt -----END PGP SIGNATURE----- --=-=-=-- From mboxrd@z Thu Jan 1 00:00:00 1970 From: =?UTF-8?Q?G=C3=A1bor_Boskovits?= Subject: Re: New outreachy participant introduction Date: Thu, 3 Oct 2019 21:18:18 +0200 Message-ID: References: <1570119118548.1674@iu.edu> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="00000000000060b2150594067365" Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:49230) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iG6cT-0001Z5-O7 for guix-devel@gnu.org; Thu, 03 Oct 2019 15:18:35 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iG6cS-0006lk-7h for guix-devel@gnu.org; Thu, 03 Oct 2019 15:18:33 -0400 Received: from mail-ed1-x530.google.com ([2a00:1450:4864:20::530]:44600) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iG6cR-0006lL-Sl for guix-devel@gnu.org; Thu, 03 Oct 2019 15:18:32 -0400 Received: by mail-ed1-x530.google.com with SMTP id r16so3607981edq.11 for ; Thu, 03 Oct 2019 12:18:31 -0700 (PDT) In-Reply-To: <1570119118548.1674@iu.edu> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: "Asfaw, Nardos" Cc: "guix-devel@gnu.org" , "outreachy@lepiller.eu" --00000000000060b2150594067365 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hello Nardos, Asfaw, Nardos ezt =C3=ADrta (id=C5=91pont: 2019. okt. 3., C= s, 18:13): > Hello Guix! > > My name is Nardos, and I am an Outreachy participant from Indiana > University, Bloomington. I am a first time open > source contributor hopeful. I am excite to be here, but I will admit I am > also a little nervous. I welcome feedback as I am here to learn from all > of you. I can be reached at nasfaw@iu.edu or www.nardos.dev > Happy to see you here. > I also have a few questions: > > 1. I am opting to run Guix in a virtual machine on a kali linux. I have > found this resource: > https://guix.gnu.org/manual/en/html_node/Running-Guix-in-a-VM.html#Runnin= g-Guix-in-a-VM. > Given your experience, would this cause a problem down the line? Any > recommendation on running Guix in a virtual machine vs on my PC? > This should work fine, but as Chris metioned, it might be easier to install Guix as a package manager. One trick with the vm image is that it barely contains enough space to be useful as is, so you will have to resize it. > 2. Upon making contributions, where is it posted? and how do I see > feedbacks? I have seen lists of open projects and discussion treads such = as > this (https://issues.guix.gnu.org/issue/22138) on the Guix patch > tracker. Are these the issues we currently working on? > To open a new issue you can send a mail to either guix-patches or bug-guix mailing list. Then the debbugs instance behind these lists creat a new issue number for your request. Further mails should be sent to issue-number@debbugs.gnu.org, where the issue number is in the acknowledgement e-mail. You can see that later in an url like you posted at issues.guix.gnu.org. > > 3. Any beginner tips? and a good place to start? > You could do some packaging, or go for an easy bug. In earlier rounds we recommended to try to package some R stuff first, as R has a well working importer. It is important to notice that there is a quite short deadline for initial contribution, and having something in is strictly needed for proceeding further. Therefore I would go for something really easy. Once you have one contribution registered, we can find something that is nearer to the project you are really interested in. Another aspect is that doing a simple packaging will get you familiar with the workflow and helps to check if everything is ok with the installation. Also, if you have a particular project in mind please let us know. > > I look forward to working with you all. > I am also looking forward to working with you. > > Thanks, > > Nardos > Best regards, g_bor --=20 OpenPGP Key Fingerprint: 7988:3B9F:7D6A:4DBF:3719:0367:2506:A96C:CF63:0B21 --00000000000060b2150594067365 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello Nardos,

Asfaw, Nardos <nasfaw@iu.edu>= ezt =C3=ADrta (id=C5=91pont: 2019. okt. 3., Cs, 18:13):

Hello Guix!


My name is Nardos, and I am an Outreachy participant from Indiana Univ= ersity, Bloomington. I am a first time open source=C2=A0contributor=C2=A0ho= peful.=C2=A0I am excite to be here,=C2=A0but=C2=A0I will admit=C2=A0I am also a li= ttle nervous.=C2=A0I welcome feedback as I am here to learn from all= of you.=C2=A0I can be reached at nasfaw@iu.edu or www.nardos.dev= =C2=A0

Happy to see you her= e.

<= div dir=3D"ltr" style=3D"font-size:12pt;color:rgb(0,0,0);background-color:r= gb(255,255,255);font-family:Calibri,Arial,Helvetica,sans-serif">

I also=C2=A0have a few questions:

1. I am opting to run Guix=C2=A0in a virtual machine on a kali linux.= =C2=A0 I have found this resource:=C2=A0https://guix.gnu.org/manual/en/html_node/Running-Guix-in-a-VM.html#= Running-Guix-in-a-VM. Given your experience, would this cause a problem down the line? Any recom= mendation on running Guix in a virtual machine vs on my PC?

This should work fine, but as Chris metioned, = it might be easier to install Guix as a package manager. One trick with the= vm image is that it barely contains enough space to be useful as is, so yo= u will have to resize it.


2. Upon making contributions, where is it posted? and how do I see fee= dbacks? I have seen lists of open projects and discussion treads such as th= is (h= ttps://issues.guix.gnu.org/issue/22138)=C2=A0 on the=C2=A0Guix patch tracker. Are these the issues we currently working on?=C2=A0

To open a new issue you can send a= mail to either guix-patches or bug-guix mailing list. Then the debbugs ins= tance behind these lists creat a new issue number for your request. Further= mails should be sent to is= sue-number@debbugs.gnu.org, where the issue number is in the acknowledg= ement e-mail. You can see that later in an url like you posted at issues.guix.gnu.org.


3. Any beginner tips? and a good place to start?=C2=A0

You could do some packaging, or go for an easy bug. In earlie= r rounds we recommended to try to package some R stuff first, as R has a we= ll working importer. It is important to notice that there is a quite short = deadline for initial contribution, and having something in is strictly need= ed for proceeding further. Therefore I would go for something really easy. = Once you have one contribution registered, we can find something that is ne= arer to the project you are really interested in.

= Another aspect is that doing a simple packaging will get you familiar with = the workflow and helps to check if everything is ok with the installation.<= /div>

Also, if you have a particular project in mind ple= ase let us know.


I look forward to working with you all.=C2=A0

=

I am also looking forward to working with you.


Thanks,

Nardos

Best regards,
g_bor

-- =
OpenPGP Key= Fingerprint: 7988:3B9F:7D6A:4DBF:3719:0367:2506:A96C:CF63:0B21
--00000000000060b2150594067365-- From mboxrd@z Thu Jan 1 00:00:00 1970 From: Julien Lepiller Subject: Re: New outreachy participant introduction Date: Fri, 04 Oct 2019 20:50:48 +0200 Message-ID: <5E2F10D1-6728-475C-84E0-B6B018EB74D1@lepiller.eu> References: <1570119118548.1674@iu.edu> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----TFYL13LBYYH9FA5CTSQPZVFIGI1CM6" Content-Transfer-Encoding: 7bit Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:36774) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iGSgT-00087d-FL for guix-devel@gnu.org; Fri, 04 Oct 2019 14:52:14 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iGSgQ-000087-Bc for guix-devel@gnu.org; Fri, 04 Oct 2019 14:52:08 -0400 Received: from lepiller.eu ([89.234.186.109]:41794) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1iGSgO-0007Ss-1R for guix-devel@gnu.org; Fri, 04 Oct 2019 14:52:06 -0400 In-Reply-To: <1570119118548.1674@iu.edu> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: "Asfaw, Nardos" , "guix-devel@gnu.org" Cc: "outreachy@lepiller.eu" ------TFYL13LBYYH9FA5CTSQPZVFIGI1CM6 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi Nardos, nice to meet you! Sorry I couldn't answer sooner=2E My server wa= s having a bit of troubles and I only received your mail now=2E It should b= e fine from now on=2E I think G=C3=A1bor already answered your questions nicely, and I have noth= ing to add=2E I'd like to encourage you to join our irc at #guix on freenod= e to meet everyone=2E If you have any question regarding the process of pac= kaging or about the proposed internships, do not hesitate to ask them here = or on IRC=2E Even if when mentors are not available, others may have answer= s for you ;)=20 Thank you, Julien Le 3 octobre 2019 18:11:58 GMT+02:00, "Asfaw, Nardos" a = =C3=A9crit : >Hello Guix! > >My name is Nardos, and I am an Outreachy participant from Indiana >University, Bloomington=2E I am a first time open source contributor >hopeful=2E I am excite to be here, but I will admit I am also a little >nervous=2E I welcome feedback as I am here to learn from all of you=2E I >can be reached at nasfaw@iu=2Eedu or www=2Enardos=2Edev > >I also have a few questions: > >1=2E I am opting to run Guix in a virtual machine on a kali linux=2E I >have found this resource: >https://guix=2Egnu=2Eorg/manual/en/html_node/Running-Guix-in-a-VM=2Ehtml#= Running-Guix-in-a-VM=2E >Given your experience, would this cause a problem down the line? Any >recommendation on running Guix in a virtual machine vs on my PC? > >2=2E Upon making contributions, where is it posted? and how do I see >feedbacks? I have seen lists of open projects and discussion treads >such as this (https://issues=2Eguix=2Egnu=2Eorg/issue/22138) on the Guix >patch tracker=2E Are these the issues we currently working on? > > >3=2E Any beginner tips? and a good place to start? > > >I look forward to working with you all=2E > > >Thanks, > >Nardos ------TFYL13LBYYH9FA5CTSQPZVFIGI1CM6 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi Nardos, nice to = meet you! Sorry I couldn't answer sooner=2E My server was having a bit of t= roubles and I only received your mail now=2E It should be fine from now on= =2E

I think G=C3=A1bor already answered your questions nicely, and I= have nothing to add=2E I'd like to encourage you to join our irc at #guix = on freenode to meet everyone=2E If you have any question regarding the proc= ess of packaging or about the proposed internships, do not hesitate to ask = them here or on IRC=2E Even if when mentors are not available, others may h= ave answers for you ;)

Thank you,
Julien

Le 3 octobre 2019 18:11:58 GMT+02:00, "Asfaw, Nardos" <nasfaw= @iu=2Eedu> a =C3=A9crit :

Hello Guix!


My name is Nardos, and I am an Outreachy participant from Indiana Uni= versity, Bloomington=2E I am a first time open source contributor = ;hopeful=2E I am excite to be here, but I will admit I = am also a little nervous=2E I welcome feedback as I am here to = learn from all of you=2E I can be reached at nasfaw@iu=2Eedu or www=2Enardos=2Edev 

I also have a few questions:

1=2E I am opting to run Guix in a virtual machine on a kali linu= x=2E  I have found this resource: https://guix=2Egnu=2Eorg/manual/en/html_node/Running-Guix-in-a-VM=2Ehtml#= Running-Guix-in-a-VM=2E Given your experience, would this cause a problem down the line? Any reco= mmendation on running Guix in a virtual machine vs on my PC?

2=2E Upon making contributions, where is it posted? and how do I see = feedbacks? I have seen lists of open projects and discussion treads such as= this (https://is= sues=2Eguix=2Egnu=2Eorg/issue/22138)  on the Guix patch tracker=2E Are these the issues we currently working on? 


3=2E Any beginner tips? and a good place to start? 


I look forward to working with you all=2E 


Thanks,

Nardos

------TFYL13LBYYH9FA5CTSQPZVFIGI1CM6-- From mboxrd@z Thu Jan 1 00:00:00 1970 From: =?UTF-8?Q?G=C3=A1bor_Boskovits?= Subject: Re: New outreachy participant introduction Date: Sat, 5 Oct 2019 11:28:54 +0200 Message-ID: References: <1570119118548.1674@iu.edu> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="00000000000044e00705942673c9" Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:36120) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iGgNB-0008MG-Jx for guix-devel@gnu.org; Sat, 05 Oct 2019 05:29:10 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iGgNA-0007rN-NS for guix-devel@gnu.org; Sat, 05 Oct 2019 05:29:09 -0400 Received: from mail-ed1-x534.google.com ([2a00:1450:4864:20::534]:41749) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iGgNA-0007r8-HK for guix-devel@gnu.org; Sat, 05 Oct 2019 05:29:08 -0400 Received: by mail-ed1-x534.google.com with SMTP id f20so8123858edv.8 for ; Sat, 05 Oct 2019 02:29:08 -0700 (PDT) In-Reply-To: List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: "Asfaw, Nardos" Cc: Guix-devel --00000000000044e00705942673c9 Content-Type: text/plain; charset="UTF-8" > > Hello Nardos, How did the installation go? Should you have any questions, please don't hesitate to contact us. We are here to help. >> Best regards, > g_bor > > -- > OpenPGP Key Fingerprint: 7988:3B9F:7D6A:4DBF:3719:0367:2506:A96C:CF63:0B21 > --00000000000044e00705942673c9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello Nardos,

<= div dir=3D"auto">How did the installation go?

Should you have any questions, please don't hesit= ate to contact us. We are here to help.


Best regards,
g_b= or

--
OpenPGP Key F= ingerprint: 7988:3B9F:7D6A:4DBF:3719:0367:2506:A96C:CF63:0B21
--00000000000044e00705942673c9-- From mboxrd@z Thu Jan 1 00:00:00 1970 From: "Asfaw, Nardos" Subject: Re: [External] Re: New outreachy participant introduction Date: Tue, 8 Oct 2019 03:23:08 +0000 Message-ID: <1570504991415.84097@iu.edu> References: <1570119118548.1674@iu.edu> , Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="_000_157050499141584097iuedu_" Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:55862) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iHg5h-0001Nn-IW for guix-devel@gnu.org; Mon, 07 Oct 2019 23:23:14 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iHg5f-0002XZ-RD for guix-devel@gnu.org; Mon, 07 Oct 2019 23:23:13 -0400 Received: from belushi.uits.indiana.edu ([129.79.1.188]:30839 helo=hartman.uits.indiana.edu) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iHg5f-0002XL-Ij for guix-devel@gnu.org; Mon, 07 Oct 2019 23:23:11 -0400 In-Reply-To: Content-Language: en-US List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: =?iso-8859-1?Q?G=E1bor_Boskovits?= Cc: Guix-devel --_000_157050499141584097iuedu_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Gabor, I apologize for the late reply. > How did the installation go? Based on your suggestion I was able to install it as a package manager on k= ali (I had help from the IRC chat group). > Should you have any questions, please don't hesitate to contact us. We ar= e here to help. I am going through the packaging guide (https://guix.gnu.org/blog/2018/a-p= ackaging-tutorial-for-guix/). Are there more documentations on packaging? = starting with packaging sounds interesting. Thanks again. Nardos ________________________________ From: G=E1bor Boskovits Sent: Saturday, October 5, 2019 5:28 AM To: Asfaw, Nardos Cc: Guix-devel Subject: [External] Re: New outreachy participant introduction This message was sent from a non-IU address. Please exercise caution when c= licking links or opening attachments from external sources. Hello Nardos, How did the installation go? Should you have any questions, please don't hesitate to contact us. We are = here to help. Best regards, g_bor -- OpenPGP Key Fingerprint: 7988:3B9F:7D6A:4DBF:3719:0367:2506:A96C:CF63:0B21 --_000_157050499141584097iuedu_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable


Hi Gabor,

I apologize for the late reply. 

> How did the installation go?

Based on your suggestion I was able to install it as a package manager on k= ali (I had help from the IRC chat group). 

> Should you have any questions, please don't hesitate to contact us. = We are here to help.

 I am going through the packaging guide (https://guix.gnu.org/blog/2018/a-packaging-tutorial-for-guix/).&= nbsp; Are there more documentations on packaging? starting with packag= ing sounds interesting. 

Tha= nks again.

Nardos


From: G=E1bor Boskovits <= ;boskovits@gmail.com>
Sent: Saturday, October 5, 2019 5:28 AM
To: Asfaw, Nardos
Cc: Guix-devel
Subject: [External] Re: New outreachy participant introduction
 
This message was sent from a non-IU address. Please exercise caution when c= licking links or opening attachments from external sources.

Hello Nardos,

How did the installation go?

Should you have any questions, please don't hesitate to c= ontact us. We are here to help.


Best regards,
g_bor

--
OpenPGP Key Fingerprint: 7988:3B9F:7D6A:4DBF:3719:0367:250= 6:A96C:CF63:0B21
--_000_157050499141584097iuedu_-- From mboxrd@z Thu Jan 1 00:00:00 1970 From: Christopher Baines Subject: Re: [External] Re: New outreachy participant introduction Date: Tue, 08 Oct 2019 07:48:24 +0100 Message-ID: <87a7abag1z.fsf@cbaines.net> References: <1570119118548.1674@iu.edu> <1570504991415.84097@iu.edu> Mime-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:44936) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iHjIN-0007CZ-9h for guix-devel@gnu.org; Tue, 08 Oct 2019 02:48:32 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iHjIM-0005ji-0o for guix-devel@gnu.org; Tue, 08 Oct 2019 02:48:31 -0400 Received: from mira.cbaines.net ([2a01:7e00::f03c:91ff:fe69:8da9]:34308) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1iHjIL-0005jU-Rb for guix-devel@gnu.org; Tue, 08 Oct 2019 02:48:29 -0400 In-reply-to: <1570504991415.84097@iu.edu> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: Asfaw@localhost, Nardos Cc: guix-devel@gnu.org --=-=-= Content-Type: text/plain Asfaw, Nardos writes: > Hi Gabor, > > I apologize for the late reply. > >> How did the installation go? > > Based on your suggestion I was able to install it as a package manager > on kali (I had help from the IRC chat group). Great, good stuff :) >> Should you have any questions, please don't hesitate to contact >> us. We are here to help. > > I am going through the packaging guide > (https://guix.gnu.org/blog/2018/a-packaging-tutorial-for-guix/). Are > there more documentations on packaging? starting with packaging sounds > interesting. That guide is a really good place to start, there's also the reference documentation in the manual [1], and the packages already within Guix itself. It's really useful to look at how existing packages work, to work out how to make new ones work in a similar way. 1: https://guix.gnu.org/manual/en/html_node/package-Reference.html#package-Reference The next challenge is finding something to package, it needs to be something not already packaged for Guix, but ideally where most or all of the dependencies are already packaged for Guix. If you have ideas, let us know and we can help work out how feasible they are. One good starting point would be an importer, there are a set of importers included in Guix that take a package definition from somewhere else (like the Python package index, or Rubygems) and try to generate a Guix package definition. If you're familiar with some packages from one of the collections with a corresponding importer, that might be a good place to start. Let us know how you get on, Chris --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQKTBAEBCgB9FiEEPonu50WOcg2XVOCyXiijOwuE9XcFAl2cMThfFIAAAAAALgAo aXNzdWVyLWZwckBub3RhdGlvbnMub3BlbnBncC5maWZ0aGhvcnNlbWFuLm5ldDNF ODlFRUU3NDU4RTcyMEQ5NzU0RTBCMjVFMjhBMzNCMEI4NEY1NzcACgkQXiijOwuE 9Xc/aw//ewzH5Dt47hwp+WFR5Dh5uiILxyfRO/X8soFLJubXOGo8GOSL3ZUbMzDY uzUzwX/kcxpzMFb6UKUbmWFHRVhxOuKBHvdBcgLhKcYoWICo9rEOtiKjR3ae2OGH 5hn5ELQjTvJ70jFvBSMPn9rJmAbJQ4/BKvRBLpMLS5jTDvqzDd2oOdj1FmfEryL8 tKU0mVKEPN4UEngR2geHXgiUfbrREkJH4ZEGbagxjwdpyDMPPtitLGMPeVR669Gf bHsxFw5mR/N/ZXV9y++GDBmRnC6irD+B6sa4l4Rcz97WmDN/FNEkwSHxifnEJiFP TSG2aL1IBwXf0RB+6/a4XRSLSahgHTqhU0M5YBNyElcAdiqO55PPpiZNDRNGbTmE o1O/PStDFVWjAhNYzpyUqZTScVFo9mZBKOwqgLATKZjgEDA8czZhnYSycno8beuQ smCKbwhtvFpkQiFgA9W3rPYzy1dqvM9beiMEkEp73BpWqAk/+tCqFG/lmX2j6qgY OE5LbOEO0DHs+8tWAAtd9t5ggM8zHFzlmj3xkHcePXi1H+g/11Yrur2uWlLVeBEo bH1ZsYGvmeUUik7MYvqBIEpwFG9+9uGB1Ls4Yy10iwYBCmFoysYfA5D3aC+Y9rFl LTMuCwx9B+iwo6e/yo7RlTF4CG05iXL3oYHkUk5CtPG/ajJIucA= =uZKj -----END PGP SIGNATURE----- --=-=-=-- From mboxrd@z Thu Jan 1 00:00:00 1970 From: zimoun Subject: Re: [External] Re: New outreachy participant introduction Date: Tue, 8 Oct 2019 15:24:19 +0200 Message-ID: References: <1570119118548.1674@iu.edu> <1570504991415.84097@iu.edu> <87a7abag1z.fsf@cbaines.net> Mime-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:41576) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iHpTh-0007ad-Fk for guix-devel@gnu.org; Tue, 08 Oct 2019 09:24:39 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iHpTb-00074B-VB for guix-devel@gnu.org; Tue, 08 Oct 2019 09:24:37 -0400 Received: from mail-qk1-x72a.google.com ([2607:f8b0:4864:20::72a]:37169) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iHpTb-00073C-QN for guix-devel@gnu.org; Tue, 08 Oct 2019 09:24:31 -0400 Received: by mail-qk1-x72a.google.com with SMTP id u184so16707991qkd.4 for ; Tue, 08 Oct 2019 06:24:31 -0700 (PDT) In-Reply-To: <87a7abag1z.fsf@cbaines.net> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: Christopher Baines Cc: Guix Devel Hi Nardos, Welcome ! :-) On Tue, 8 Oct 2019 at 08:48, Christopher Baines wrote: > One good starting point would be an importer, there are a set of > importers included in Guix that take a package definition from somewhere > else (like the Python package index, or Rubygems) and try to generate a > Guix package definition. If you're familiar with some packages from one > of the collections with a corresponding importer, that might be a good > place to start. As an example, let consider packages from BioConductor [1] (mainly R packages used in bioinformatics field). If I have right, then 2002 packages are still missing in Guix, so there is materials. ;-) Well, let's pick one which is not packaged yet: zinbwave [2]. Then it is easy: guix import cran -r -a bioconductor zinbwave This will download TAR archives and automatically compute the hash. It corresponds to the manual: guix download https://bioconductor.org/packages/release/bioc/src/contrib/zinbwave_1.6.0.tar.gz [1] https://bioconductor.org/ [2] https://bioconductor.org/packages/release/bioc/html/zinbwave.html Moreover, the importer provides the definition of the package: --8<---------------cut here---------------start------------->8--- (define-public r-zinbwave (package (name "r-zinbwave") (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zinbwave" version)) (sha256 (base32 "187r7l9jf2q74qaqx63df5zx6iphmvl817448balvfv9vqyhrp2j")))) (properties `((upstream-name . "zinbwave"))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) ("r-copula" ,r-copula) ("r-edger" ,r-edger) ("r-genefilter" ,r-genefilter) ("r-glmnet" ,r-glmnet) ("r-matrix" ,r-matrix) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-softimpute" ,r-softimpute) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://bioconductor.org/packages/zinbwave") (synopsis "Zero-Inflated Negative Binomial Model for RNA-Seq Data") (description " Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.") (license artistic2.0))) --8<---------------cut here---------------end--------------->8--- In the propagated input, you can see the package `r-copula` which is not yet packaged neither. But, the nice option --recursive does the job for you and it also gives you the package definition. Now, let add them to the Guix source. Clone the repo and go in the folder. The command: guix environment guix will download the dependencies to build Guix and setup all the variables correctly. Well, refer to the documentation to compile Guix from source. Basically: ./bootstrap ./configure --localstatedir=/var make Now, you can run this version with ./pre-inst-env, for example: ./pre-inst-env guix describe Well, ready to add one package! For example, add `r-copula` to the file gnu/package/cran.scm then recompile with make. Check if it is ok: ./pre-inst-env guile show r-copula Ouch! `r-psline` is missing so let also add it (the definition was provided by the importer), run make again. Now "./pre-inst-env guix show r-copula" should work. Add the package definition of zinbwave to the file gnu/package/bioconductor.scm. Let build them: ./pre-inst-env guix build r-zinbwave and time to breath. ;-) If something fails, try to investigate by yourself and do not hesitate to ask advices or help. If everything is ok, the package still needs some polishing: synopsis, description, indentation, etc and really important: check the license field. The next step is to commit the changes. In this case, three commits (one per package) seem nice. Give a look to previous commits as example of commit message (ChangeLog format, etc.). Now, it is time to prepare the submission: git format-patch --cover-letter - o patches master this will create the 3 patches in the folder patches/ and one cover letter. Edit the cover letter to describe what the patches are about then submit it to the bug tracker: git send-email --to=guix-patches@gnu.org patches/0000-cover-letter.patch Wait the answer to the bug tracker. You should receive an email (if your .gitconfig is ok) with the bug number. Last submit the patches: git send-email --to=ABCDEF@debbugs.gnu.org patches/000{1,2,3}-* where ABCDEF is the bug number. Well, if you need some inspiration to find unpackaged tools from BioConductor: wget https://git.bioconductor.org -qO - | sed -ne '/packages\/[a-zA-Z]/{s,^.*R.*packages/,,p}' > bioc_manifest ./pre-inst-env guile --no-auto-compile missing-bioconductor.scm bioc_manifest where the file `missing-bioconductor.scm` is given by: --8<---------------cut here---------------start------------->8--- (use-modules ((guix import utils) #:select (guix-name)) (gnu packages) (srfi srfi-1) ;lists (ice-9 textual-ports)) (define (fetch-names manifest) "Return a list of strings, each corresponding to a name from the input file MANIFEST." (call-with-input-file manifest (lambda (port) (let loop ((lines '()) (line (get-line port))) (if (eof-object? line) (reverse lines) (loop (cons line lines) (get-line port))))))) ;;; Start! (map (lambda (name) (when (null? (find-packages-by-name (guix-name "r-" name))) (begin (display name) (newline)))) (fetch-names (cadr (command-line)))) ;; wget https://git.bioconductor.org -qO - | sed -ne '/packages\/[a-zA-Z]/{s,^.*R.*packages/,,p}' > bioc_manifest ;; ./pre-inst-env guile --no-auto-compile missing-bioconductor.scm bioc_manifest --8<---------------cut here---------------end--------------->8--- Hope that help. All the best, simon From mboxrd@z Thu Jan 1 00:00:00 1970 From: "Asfaw, Nardos" Subject: Re: [External] Re: New outreachy participant introduction Date: Sun, 13 Oct 2019 00:41:15 +0000 Message-ID: <1570927278147.77440@iu.edu> References: <1570119118548.1674@iu.edu> <1570504991415.84097@iu.edu> <87a7abag1z.fsf@cbaines.net>, Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:51406) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iJRwp-0003yz-OW for guix-devel@gnu.org; Sat, 12 Oct 2019 20:41:25 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iJRwn-0001I4-Dh for guix-devel@gnu.org; Sat, 12 Oct 2019 20:41:23 -0400 Received: from robin.uits.iu.edu ([134.68.220.32]:26814) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iJRwn-00017G-0T for guix-devel@gnu.org; Sat, 12 Oct 2019 20:41:21 -0400 In-Reply-To: Content-Language: en-US List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: zimoun , Christopher Baines Cc: Guix Devel Thank you Zimon. =0A= =0A= This has been very helpful. =0A= ________________________________________=0A= From: zimoun =0A= Sent: Tuesday, October 8, 2019 9:24 AM=0A= To: Christopher Baines=0A= Cc: Asfaw, Nardos; Guix Devel=0A= Subject: Re: [External] Re: New outreachy participant introduction=0A= =0A= Hi Nardos,=0A= =0A= Welcome ! :-)=0A= =0A= =0A= On Tue, 8 Oct 2019 at 08:48, Christopher Baines wrote:= =0A= =0A= > One good starting point would be an importer, there are a set of=0A= > importers included in Guix that take a package definition from somewhere= =0A= > else (like the Python package index, or Rubygems) and try to generate a= =0A= > Guix package definition. If you're familiar with some packages from one= =0A= > of the collections with a corresponding importer, that might be a good=0A= > place to start.=0A= =0A= As an example, let consider packages from BioConductor [1] (mainly R=0A= packages used in bioinformatics field). If I have right, then 2002=0A= packages are still missing in Guix, so there is materials. ;-)=0A= =0A= Well, let's pick one which is not packaged yet: zinbwave [2]. Then it is ea= sy:=0A= =0A= guix import cran -r -a bioconductor zinbwave=0A= =0A= This will download TAR archives and automatically compute the hash. It=0A= corresponds to the manual:=0A= =0A= guix download=0A= https://bioconductor.org/packages/release/bioc/src/contrib/zinbwave_1.6.0.t= ar.gz=0A= =0A= =0A= [1] https://bioconductor.org/=0A= [2] https://bioconductor.org/packages/release/bioc/html/zinbwave.html=0A= =0A= =0A= Moreover, the importer provides the definition of the package:=0A= =0A= --8<---------------cut here---------------start------------->8---=0A= (define-public r-zinbwave=0A= (package=0A= (name "r-zinbwave")=0A= (version "1.6.0")=0A= (source=0A= (origin=0A= (method url-fetch)=0A= (uri (bioconductor-uri "zinbwave" version))=0A= (sha256=0A= (base32=0A= "187r7l9jf2q74qaqx63df5zx6iphmvl817448balvfv9vqyhrp2j"))))=0A= (properties `((upstream-name . "zinbwave")))=0A= (build-system r-build-system)=0A= (propagated-inputs=0A= `(("r-biocparallel" ,r-biocparallel)=0A= ("r-copula" ,r-copula)=0A= ("r-edger" ,r-edger)=0A= ("r-genefilter" ,r-genefilter)=0A= ("r-glmnet" ,r-glmnet)=0A= ("r-matrix" ,r-matrix)=0A= ("r-singlecellexperiment"=0A= ,r-singlecellexperiment)=0A= ("r-softimpute" ,r-softimpute)=0A= ("r-summarizedexperiment"=0A= ,r-summarizedexperiment)))=0A= (home-page=0A= "https://bioconductor.org/packages/zinbwave")=0A= (synopsis=0A= "Zero-Inflated Negative Binomial Model for RNA-Seq Data")=0A= (description=0A= " Implements a general and flexible zero-inflated negative=0A= binomial model that can be used to provide a low-dimensional=0A= representations of single-cell RNA-seq data. The model accounts for=0A= zero inflation (dropouts), over-dispersion, and the count nature of=0A= the data. The model also accounts for the difference in library sizes=0A= and optionally for batch effects and/or other covariates, avoiding the=0A= need for pre-normalize the data.")=0A= (license artistic2.0)))=0A= --8<---------------cut here---------------end--------------->8---=0A= =0A= In the propagated input, you can see the package `r-copula` which is=0A= not yet packaged neither. But, the nice option --recursive does the=0A= job for you and it also gives you the package definition.=0A= =0A= Now, let add them to the Guix source. Clone the repo and go in the=0A= folder. The command:=0A= =0A= guix environment guix=0A= =0A= will download the dependencies to build Guix and setup all the=0A= variables correctly. Well, refer to the documentation to compile Guix=0A= from source. Basically:=0A= =0A= ./bootstrap=0A= ./configure --localstatedir=3D/var=0A= make=0A= =0A= Now, you can run this version with ./pre-inst-env, for example:=0A= =0A= ./pre-inst-env guix describe=0A= =0A= =0A= Well, ready to add one package! For example, add `r-copula` to the=0A= file gnu/package/cran.scm then recompile with make. Check if it is ok:=0A= =0A= ./pre-inst-env guile show r-copula=0A= =0A= Ouch! `r-psline` is missing so let also add it (the definition was=0A= provided by the importer), run make again. Now "./pre-inst-env guix=0A= show r-copula" should work.=0A= Add the package definition of zinbwave to the file gnu/package/bioconductor= .scm.=0A= =0A= Let build them:=0A= =0A= ./pre-inst-env guix build r-zinbwave=0A= =0A= and time to breath. ;-)=0A= =0A= =0A= If something fails, try to investigate by yourself and do not hesitate=0A= to ask advices or help.=0A= If everything is ok, the package still needs some polishing: synopsis,=0A= description, indentation, etc and really important: check the license=0A= field.=0A= =0A= The next step is to commit the changes. In this case, three commits=0A= (one per package) seem nice. Give a look to previous commits as=0A= example of commit message (ChangeLog format, etc.). Now, it is time to=0A= prepare the submission:=0A= =0A= git format-patch --cover-letter - o patches master=0A= =0A= this will create the 3 patches in the folder patches/ and one cover=0A= letter. Edit the cover letter to describe what the patches are about=0A= then submit it to the bug tracker:=0A= =0A= git send-email --to=3Dguix-patches@gnu.org patches/0000-cover-letter.patc= h=0A= =0A= Wait the answer to the bug tracker.=0A= You should receive an email (if your .gitconfig is ok) with the bug=0A= number. Last submit the patches:=0A= =0A= git send-email --to=3DABCDEF@debbugs.gnu.org patches/000{1,2,3}-*=0A= =0A= where ABCDEF is the bug number.=0A= =0A= =0A= =0A= Well, if you need some inspiration to find unpackaged tools from BioConduct= or:=0A= =0A= wget https://git.bioconductor.org -qO - | sed -ne=0A= '/packages\/[a-zA-Z]/{s,^.*R.*packages/,,p}' > bioc_manifest=0A= ./pre-inst-env guile --no-auto-compile missing-bioconductor.scm bioc_mani= fest=0A= =0A= where the file `missing-bioconductor.scm` is given by:=0A= =0A= --8<---------------cut here---------------start------------->8---=0A= (use-modules ((guix import utils) #:select (guix-name))=0A= (gnu packages)=0A= (srfi srfi-1) ;lists=0A= (ice-9 textual-ports))=0A= =0A= (define (fetch-names manifest)=0A= "Return a list of strings, each corresponding to a name from the=0A= input file MANIFEST."=0A= (call-with-input-file manifest=0A= (lambda (port)=0A= (let loop ((lines '())=0A= (line (get-line port)))=0A= (if (eof-object? line)=0A= (reverse lines)=0A= (loop (cons line lines)=0A= (get-line port)))))))=0A= =0A= ;;; Start!=0A= =0A= (map (lambda (name)=0A= (when (null? (find-packages-by-name (guix-name "r-" name)))=0A= (begin=0A= (display name)=0A= (newline))))=0A= (fetch-names (cadr (command-line))))=0A= =0A= ;; wget https://git.bioconductor.org -qO - | sed -ne=0A= '/packages\/[a-zA-Z]/{s,^.*R.*packages/,,p}' > bioc_manifest=0A= ;; ./pre-inst-env guile --no-auto-compile missing-bioconductor.scm bioc_man= ifest=0A= --8<---------------cut here---------------end--------------->8---=0A= =0A= =0A= Hope that help.=0A= =0A= All the best,=0A= simon=0A= From mboxrd@z Thu Jan 1 00:00:00 1970 From: =?UTF-8?Q?G=C3=A1bor_Boskovits?= Subject: Re: [External] Re: New outreachy participant introduction Date: Wed, 16 Oct 2019 10:00:14 +0200 Message-ID: References: <1570119118548.1674@iu.edu> <1570504991415.84097@iu.edu> <87a7abag1z.fsf@cbaines.net> <1570927278147.77440@iu.edu> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="0000000000008f19fd0595027e5a" Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:42314) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iKeEU-0008Ax-4N for guix-devel@gnu.org; Wed, 16 Oct 2019 04:00:37 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iKeER-0006qE-J2 for guix-devel@gnu.org; Wed, 16 Oct 2019 04:00:34 -0400 Received: from mail-ed1-x52d.google.com ([2a00:1450:4864:20::52d]:37112) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iKeER-0006o5-68 for guix-devel@gnu.org; Wed, 16 Oct 2019 04:00:31 -0400 Received: by mail-ed1-x52d.google.com with SMTP id r4so20552970edy.4 for ; Wed, 16 Oct 2019 01:00:30 -0700 (PDT) In-Reply-To: <1570927278147.77440@iu.edu> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: "Asfaw, Nardos" Cc: Guix Devel --0000000000008f19fd0595027e5a Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hello Nardos, We have not heard from you for a while. Should you need any help, please feel free to reach out to us. Asfaw, Nardos ezt =C3=ADrta (id=C5=91pont: 2019. okt. 13., = Vas 2:41): > Thank you Zimon. > > This has been very helpful. > ________________________________________ > From: zimoun > Sent: Tuesday, October 8, 2019 9:24 AM > To: Christopher Baines > Cc: Asfaw, Nardos; Guix Devel > Subject: Re: [External] Re: New outreachy participant introduction > > Hi Nardos, > > Welcome ! :-) > > > On Tue, 8 Oct 2019 at 08:48, Christopher Baines wrote: > > > One good starting point would be an importer, there are a set of > > importers included in Guix that take a package definition from somewher= e > > else (like the Python package index, or Rubygems) and try to generate a > > Guix package definition. If you're familiar with some packages from one > > of the collections with a corresponding importer, that might be a good > > place to start. > > As an example, let consider packages from BioConductor [1] (mainly R > packages used in bioinformatics field). If I have right, then 2002 > packages are still missing in Guix, so there is materials. ;-) > > Well, let's pick one which is not packaged yet: zinbwave [2]. Then it is > easy: > > guix import cran -r -a bioconductor zinbwave > > This will download TAR archives and automatically compute the hash. It > corresponds to the manual: > > guix download > > https://bioconductor.org/packages/release/bioc/src/contrib/zinbwave_1.6.0= .tar.gz > > > [1] https://bioconductor.org/ > [2] https://bioconductor.org/packages/release/bioc/html/zinbwave.html > > > Moreover, the importer provides the definition of the package: > > --8<---------------cut here---------------start------------->8--- > (define-public r-zinbwave > (package > (name "r-zinbwave") > (version "1.6.0") > (source > (origin > (method url-fetch) > (uri (bioconductor-uri "zinbwave" version)) > (sha256 > (base32 > "187r7l9jf2q74qaqx63df5zx6iphmvl817448balvfv9vqyhrp2j")))) > (properties `((upstream-name . "zinbwave"))) > (build-system r-build-system) > (propagated-inputs > `(("r-biocparallel" ,r-biocparallel) > ("r-copula" ,r-copula) > ("r-edger" ,r-edger) > ("r-genefilter" ,r-genefilter) > ("r-glmnet" ,r-glmnet) > ("r-matrix" ,r-matrix) > ("r-singlecellexperiment" > ,r-singlecellexperiment) > ("r-softimpute" ,r-softimpute) > ("r-summarizedexperiment" > ,r-summarizedexperiment))) > (home-page > "https://bioconductor.org/packages/zinbwave") > (synopsis > "Zero-Inflated Negative Binomial Model for RNA-Seq Data") > (description > " Implements a general and flexible zero-inflated negative > binomial model that can be used to provide a low-dimensional > representations of single-cell RNA-seq data. The model accounts for > zero inflation (dropouts), over-dispersion, and the count nature of > the data. The model also accounts for the difference in library sizes > and optionally for batch effects and/or other covariates, avoiding the > need for pre-normalize the data.") > (license artistic2.0))) > --8<---------------cut here---------------end--------------->8--- > > In the propagated input, you can see the package `r-copula` which is > not yet packaged neither. But, the nice option --recursive does the > job for you and it also gives you the package definition. > > Now, let add them to the Guix source. Clone the repo and go in the > folder. The command: > > guix environment guix > > will download the dependencies to build Guix and setup all the > variables correctly. Well, refer to the documentation to compile Guix > from source. Basically: > > ./bootstrap > ./configure --localstatedir=3D/var > make > > Now, you can run this version with ./pre-inst-env, for example: > > ./pre-inst-env guix describe > > > Well, ready to add one package! For example, add `r-copula` to the > file gnu/package/cran.scm then recompile with make. Check if it is ok: > > ./pre-inst-env guile show r-copula > > Ouch! `r-psline` is missing so let also add it (the definition was > provided by the importer), run make again. Now "./pre-inst-env guix > show r-copula" should work. > Add the package definition of zinbwave to the file > gnu/package/bioconductor.scm. > > Let build them: > > ./pre-inst-env guix build r-zinbwave > > and time to breath. ;-) > > > If something fails, try to investigate by yourself and do not hesitate > to ask advices or help. > If everything is ok, the package still needs some polishing: synopsis, > description, indentation, etc and really important: check the license > field. > > The next step is to commit the changes. In this case, three commits > (one per package) seem nice. Give a look to previous commits as > example of commit message (ChangeLog format, etc.). Now, it is time to > prepare the submission: > > git format-patch --cover-letter - o patches master > > this will create the 3 patches in the folder patches/ and one cover > letter. Edit the cover letter to describe what the patches are about > then submit it to the bug tracker: > > git send-email --to=3Dguix-patches@gnu.org patches/0000-cover-letter.pa= tch > > Wait the answer to the bug tracker. > You should receive an email (if your .gitconfig is ok) with the bug > number. Last submit the patches: > > git send-email --to=3DABCDEF@debbugs.gnu.org patches/000{1,2,3}-* > > where ABCDEF is the bug number. > > > > Well, if you need some inspiration to find unpackaged tools from > BioConductor: > > wget https://git.bioconductor.org -qO - | sed -ne > '/packages\/[a-zA-Z]/{s,^.*R.*packages/,,p}' > bioc_manifest > ./pre-inst-env guile --no-auto-compile missing-bioconductor.scm > bioc_manifest > > where the file `missing-bioconductor.scm` is given by: > > --8<---------------cut here---------------start------------->8--- > (use-modules ((guix import utils) #:select (guix-name)) > (gnu packages) > (srfi srfi-1) ;lists > (ice-9 textual-ports)) > > (define (fetch-names manifest) > "Return a list of strings, each corresponding to a name from the > input file MANIFEST." > (call-with-input-file manifest > (lambda (port) > (let loop ((lines '()) > (line (get-line port))) > (if (eof-object? line) > (reverse lines) > (loop (cons line lines) > (get-line port))))))) > > ;;; Start! > > (map (lambda (name) > (when (null? (find-packages-by-name (guix-name "r-" name))) > (begin > (display name) > (newline)))) > (fetch-names (cadr (command-line)))) > > ;; wget https://git.bioconductor.org -qO - | sed -ne > '/packages\/[a-zA-Z]/{s,^.*R.*packages/,,p}' > bioc_manifest > ;; ./pre-inst-env guile --no-auto-compile missing-bioconductor.scm > bioc_manifest > --8<---------------cut here---------------end--------------->8--- > > > Hope that help. > > All the best, > simon > > --0000000000008f19fd0595027e5a Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello Nardos,

We have not heard from you for a while. Should you need any help, please = feel free to reach out to us.

Asfaw, Nardos <nasfaw@iu.edu> ezt =C3=ADrta (id=C5=91pont: 2019. okt. 13= ., Vas 2:41):
Thank you Zimon.

This has been very helpful.
________________________________________
From: zimoun <zimon.toutoune@gmail.com>
Sent: Tuesday, October 8, 2019 9:24 AM
To: Christopher Baines
Cc: Asfaw, Nardos; Guix Devel
Subject: Re: [External] Re: New outreachy participant introduction

Hi Nardos,

Welcome ! :-)


On Tue, 8 Oct 2019 at 08:48, Christopher Baines <mail@cbaines.net> = wrote:

> One good starting point would be an importer, there are a set of
> importers included in Guix that take a package definition from somewhe= re
> else (like the Python package index, or Rubygems) and try to generate = a
> Guix package definition. If you're familiar with some packages fro= m one
> of the collections with a corresponding importer, that might be a good=
> place to start.

As an example, let consider packages from BioConductor [1] (mainly R
packages used in bioinformatics field). If I have right, then 2002
packages are still missing in Guix, so there is materials. ;-)

Well, let's pick one which is not packaged yet: zinbwave [2]. Then it i= s easy:

=C2=A0 guix import cran -r -a bioconductor zinbwave

This will download TAR archives and automatically compute the hash. It
corresponds to the manual:

=C2=A0 guix download
https://b= ioconductor.org/packages/release/bioc/src/contrib/zinbwave_1.6.0.tar.gz=


[1] https://bioconductor.org/
[2] https://bioconductor= .org/packages/release/bioc/html/zinbwave.html


Moreover, the importer provides the definition of the package:

--8<---------------cut here---------------start------------->8---
(define-public r-zinbwave
=C2=A0 (package
=C2=A0 =C2=A0 (name "r-zinbwave")
=C2=A0 =C2=A0 (version "1.6.0")
=C2=A0 =C2=A0 (source
=C2=A0 =C2=A0 =C2=A0 (origin
=C2=A0 =C2=A0 =C2=A0 =C2=A0 (method url-fetch)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 (uri (bioconductor-uri "zinbwave" ver= sion))
=C2=A0 =C2=A0 =C2=A0 =C2=A0 (sha256
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (base32
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 "187r7l9jf2q74qaqx63df5zx6ip= hmvl817448balvfv9vqyhrp2j"))))
=C2=A0 =C2=A0 (properties `((upstream-name . "zinbwave")))
=C2=A0 =C2=A0 (build-system r-build-system)
=C2=A0 =C2=A0 (propagated-inputs
=C2=A0 =C2=A0 =C2=A0 `(("r-biocparallel" ,r-biocparallel)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 ("r-copula" ,r-copula)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 ("r-edger" ,r-edger)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 ("r-genefilter" ,r-genefilter)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 ("r-glmnet" ,r-glmnet)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 ("r-matrix" ,r-matrix)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 ("r-singlecellexperiment"
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0,r-singlecellexperiment)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 ("r-softimpute" ,r-softimpute)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 ("r-summarizedexperiment"
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0,r-summarizedexperiment)))
=C2=A0 =C2=A0 (home-page
=C2=A0 =C2=A0 =C2=A0 "https://bioconductor= .org/packages/zinbwave")
=C2=A0 =C2=A0 (synopsis
=C2=A0 =C2=A0 =C2=A0 "Zero-Inflated Negative Binomial Model for RNA-Se= q Data")
=C2=A0 =C2=A0 (description
=C2=A0 =C2=A0 =C2=A0 " Implements a general and flexible zero-inflated= negative
binomial model that can be used to provide a low-dimensional
representations of single-cell RNA-seq data.=C2=A0 The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of
the data.=C2=A0 The model also accounts for the difference in library sizes=
and optionally for batch effects and/or other covariates, avoiding the
need for pre-normalize the data.")
=C2=A0 =C2=A0 (license artistic2.0)))
--8<---------------cut here---------------end--------------->8---

In the propagated input, you can see the package `r-copula` which is
not yet packaged neither. But, the nice option --recursive does the
job for you and it also gives you the package definition.

Now, let add them to the Guix source. Clone the repo and go in the
folder. The command:

=C2=A0 guix environment guix

will download the dependencies to build Guix and setup all the
variables correctly. Well, refer to the documentation to compile Guix
from source. Basically:

=C2=A0 ./bootstrap
=C2=A0 ./configure --localstatedir=3D/var
=C2=A0 make

Now, you can run this version with ./pre-inst-env, for example:

=C2=A0 =C2=A0./pre-inst-env guix describe


Well, ready to add one package! For example, add `r-copula` to the
file gnu/package/cran.scm then recompile with make. Check if it is ok:

=C2=A0 ./pre-inst-env guile show r-copula

Ouch! `r-psline` is missing so let also add it (the definition was
provided by the importer), run make again. Now "./pre-inst-env guix show r-copula" should work.
Add the package definition of zinbwave to the file gnu/package/bioconductor= .scm.

Let build them:

=C2=A0 ./pre-inst-env guix build r-zinbwave

and time to breath. ;-)


If something fails, try to investigate by yourself and do not hesitate
to ask advices or help.
If everything is ok, the package still needs some polishing: synopsis,
description, indentation, etc and really important: check the license
field.

The next step is to commit the changes. In this case, three commits
(one per package) seem nice. Give a look to previous commits as
example of commit message (ChangeLog format, etc.). Now, it is time to
prepare the submission:

=C2=A0 git format-patch --cover-letter - o patches master

this will create the 3 patches in the folder patches/ and one cover
letter. Edit the cover letter to describe what the patches are about
then submit it to the bug tracker:

=C2=A0 git send-email --to=3Dguix-patches@gnu.org patches/0000-cover-= letter.patch

Wait the answer to the bug tracker.
You should receive an email (if your .gitconfig is ok) with the bug
number. Last submit the patches:

=C2=A0 git send-email --to=3DABCDEF@debbugs.gnu.org patches/000{1,2= ,3}-*

where ABCDEF is the bug number.



Well, if you need some inspiration to find unpackaged tools from BioConduct= or:

=C2=A0 wget https://git.bioconductor.org -qO - | sed -ne<= br> '/packages\/[a-zA-Z]/{s,^.*R.*packages/,,p}' > bioc_manifest
=C2=A0 ./pre-inst-env guile --no-auto-compile missing-bioconductor.scm bioc= _manifest

where the file `missing-bioconductor.scm` is given by:

--8<---------------cut here---------------start------------->8---
(use-modules ((guix import utils) #:select (guix-name))
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(gnu packages)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(srfi srfi-1)=C2=A0 ;lists<= br> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(ice-9 textual-ports))

(define (fetch-names manifest)
=C2=A0 "Return a list of strings, each corresponding to a name from th= e
input file MANIFEST."
=C2=A0 (call-with-input-file manifest
=C2=A0 =C2=A0 (lambda (port)
=C2=A0 =C2=A0 =C2=A0 (let loop ((lines '())
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(line (get-li= ne port)))
=C2=A0 =C2=A0 =C2=A0 =C2=A0 (if (eof-object? line)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (reverse lines)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (loop (cons line lines)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (get-line po= rt)))))))

;;; Start!

(map (lambda (name)
=C2=A0 =C2=A0 =C2=A0 =C2=A0(when (null? (find-packages-by-name (guix-name &= quot;r-" name)))
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(begin
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(display name)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(newline))))
=C2=A0 =C2=A0 =C2=A0(fetch-names (cadr (command-line))))

;; wget https://git.bioconductor.org -qO - | sed -ne
'/packages\/[a-zA-Z]/{s,^.*R.*packages/,,p}' > bioc_manifest
;; ./pre-inst-env guile --no-auto-compile missing-bioconductor.scm bioc_man= ifest
--8<---------------cut here---------------end--------------->8---


Hope that help.

All the best,
simon

--0000000000008f19fd0595027e5a-- From mboxrd@z Thu Jan 1 00:00:00 1970 From: "Asfaw, Nardos" Subject: Re: [External] Re: New outreachy participant introduction Date: Wed, 16 Oct 2019 14:16:19 +0000 Message-ID: <1571235380174.94278@iu.edu> References: <1570119118548.1674@iu.edu> <1570504991415.84097@iu.edu> <87a7abag1z.fsf@cbaines.net> <1570927278147.77440@iu.edu>, Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="_000_157123538017494278iuedu_" Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:38479) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iKk6m-0008F0-FM for guix-devel@gnu.org; Wed, 16 Oct 2019 10:17:03 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iKk6h-0001kO-DP for guix-devel@gnu.org; Wed, 16 Oct 2019 10:16:58 -0400 Received: from reubens.uits.indiana.edu ([129.79.1.193]:17088 helo=hartman.uits.indiana.edu) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iKk6g-0001jC-Px for guix-devel@gnu.org; Wed, 16 Oct 2019 10:16:55 -0400 In-Reply-To: Content-Language: en-US List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: =?iso-8859-2?Q?G=E1bor_Boskovits?= Cc: Guix Devel --_000_157123538017494278iuedu_ Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: quoted-printable Hi Gabor, Thanks for reaching out. I am still hanging. I am learning a lot on what it= means to be a developer outside of university courses. I am going through = the documentation (and examples provided in the email by simon) and the cha= t logs to sees if my questions have been asked before I come with questions= and solutions I have tried. Thanks, Nardos ________________________________ From: G=E1bor Boskovits Sent: Wednesday, October 16, 2019 4:00 AM To: Asfaw, Nardos Cc: zimoun; Christopher Baines; Guix Devel Subject: Re: [External] Re: New outreachy participant introduction Hello Nardos, We have not heard from you for a while. Should you need any help, please fe= el free to reach out to us. Asfaw, Nardos > ezt =EDrta (id=F5pont: = 2019. okt. 13., Vas 2:41): Thank you Zimon. This has been very helpful. ________________________________________ From: zimoun > Sent: Tuesday, October 8, 2019 9:24 AM To: Christopher Baines Cc: Asfaw, Nardos; Guix Devel Subject: Re: [External] Re: New outreachy participant introduction Hi Nardos, Welcome ! :-) On Tue, 8 Oct 2019 at 08:48, Christopher Baines > wrote: > One good starting point would be an importer, there are a set of > importers included in Guix that take a package definition from somewhere > else (like the Python package index, or Rubygems) and try to generate a > Guix package definition. If you're familiar with some packages from one > of the collections with a corresponding importer, that might be a good > place to start. As an example, let consider packages from BioConductor [1] (mainly R packages used in bioinformatics field). If I have right, then 2002 packages are still missing in Guix, so there is materials. ;-) Well, let's pick one which is not packaged yet: zinbwave [2]. Then it is ea= sy: guix import cran -r -a bioconductor zinbwave This will download TAR archives and automatically compute the hash. It corresponds to the manual: guix download https://bioconductor.org/packages/release/bioc/src/contrib/zinbwave_1.6.0.t= ar.gz [1] https://bioconductor.org/ [2] https://bioconductor.org/packages/release/bioc/html/zinbwave.html Moreover, the importer provides the definition of the package: --8<---------------cut here---------------start------------->8--- (define-public r-zinbwave (package (name "r-zinbwave") (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zinbwave" version)) (sha256 (base32 "187r7l9jf2q74qaqx63df5zx6iphmvl817448balvfv9vqyhrp2j")))) (properties `((upstream-name . "zinbwave"))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) ("r-copula" ,r-copula) ("r-edger" ,r-edger) ("r-genefilter" ,r-genefilter) ("r-glmnet" ,r-glmnet) ("r-matrix" ,r-matrix) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-softimpute" ,r-softimpute) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://bioconductor.org/packages/zinbwave") (synopsis "Zero-Inflated Negative Binomial Model for RNA-Seq Data") (description " Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.") (license artistic2.0))) --8<---------------cut here---------------end--------------->8--- In the propagated input, you can see the package `r-copula` which is not yet packaged neither. But, the nice option --recursive does the job for you and it also gives you the package definition. Now, let add them to the Guix source. Clone the repo and go in the folder. The command: guix environment guix will download the dependencies to build Guix and setup all the variables correctly. Well, refer to the documentation to compile Guix from source. Basically: ./bootstrap ./configure --localstatedir=3D/var make Now, you can run this version with ./pre-inst-env, for example: ./pre-inst-env guix describe Well, ready to add one package! For example, add `r-copula` to the file gnu/package/cran.scm then recompile with make. Check if it is ok: ./pre-inst-env guile show r-copula Ouch! `r-psline` is missing so let also add it (the definition was provided by the importer), run make again. Now "./pre-inst-env guix show r-copula" should work. Add the package definition of zinbwave to the file gnu/package/bioconductor= .scm. Let build them: ./pre-inst-env guix build r-zinbwave and time to breath. ;-) If something fails, try to investigate by yourself and do not hesitate to ask advices or help. If everything is ok, the package still needs some polishing: synopsis, description, indentation, etc and really important: check the license field. The next step is to commit the changes. In this case, three commits (one per package) seem nice. Give a look to previous commits as example of commit message (ChangeLog format, etc.). Now, it is time to prepare the submission: git format-patch --cover-letter - o patches master this will create the 3 patches in the folder patches/ and one cover letter. Edit the cover letter to describe what the patches are about then submit it to the bug tracker: git send-email --to=3Dguix-patches@gnu.org p= atches/0000-cover-letter.patch Wait the answer to the bug tracker. You should receive an email (if your .gitconfig is ok) with the bug number. Last submit the patches: git send-email --to=3DABCDEF@debbugs.gnu.org patches/000{1,2,3}-* where ABCDEF is the bug number. Well, if you need some inspiration to find unpackaged tools from BioConduct= or: wget https://git.bioconductor.org -qO - | sed -ne '/packages\/[a-zA-Z]/{s,^.*R.*packages/,,p}' > bioc_manifest ./pre-inst-env guile --no-auto-compile missing-bioconductor.scm bioc_mani= fest where the file `missing-bioconductor.scm` is given by: --8<---------------cut here---------------start------------->8--- (use-modules ((guix import utils) #:select (guix-name)) (gnu packages) (srfi srfi-1) ;lists (ice-9 textual-ports)) (define (fetch-names manifest) "Return a list of strings, each corresponding to a name from the input file MANIFEST." (call-with-input-file manifest (lambda (port) (let loop ((lines '()) (line (get-line port))) (if (eof-object? line) (reverse lines) (loop (cons line lines) (get-line port))))))) ;;; Start! (map (lambda (name) (when (null? (find-packages-by-name (guix-name "r-" name))) (begin (display name) (newline)))) (fetch-names (cadr (command-line)))) ;; wget https://git.bioconductor.org -qO - | sed -ne '/packages\/[a-zA-Z]/{s,^.*R.*packages/,,p}' > bioc_manifest ;; ./pre-inst-env guile --no-auto-compile missing-bioconductor.scm bioc_man= ifest --8<---------------cut here---------------end--------------->8--- Hope that help. All the best, simon --_000_157123538017494278iuedu_ Content-Type: text/html; charset="iso-8859-2" Content-Transfer-Encoding: quoted-printable

Hi Gabor,


Thanks for reaching out. I am still hanging. I am learning a l= ot on what it means to be a developer outside of university courses.&n= bsp;I am going through the documentation (and examples provided in the emai= l by simon) and the chat logs to sees if my questions have been asked before I come with questions and solutions I have tri= ed. 


Thanks,

Nardos

From: G=E1bor Boskovits <= ;boskovits@gmail.com>
Sent: Wednesday, October 16, 2019 4:00 AM
To: Asfaw, Nardos
Cc: zimoun; Christopher Baines; Guix Devel
Subject: Re: [External] Re: New outreachy participant introduction
 
Hello Nardos,

We have not heard from you for a while. Should you need a= ny help, please feel free to reach out to us.

Asfaw, Nardos <nasfaw@iu.edu> ezt =EDrta (id=F5pont: 2019. okt. 13., = Vas 2:41):
Thank you Zimon.

This has been very helpful.
________________________________________
From: zimoun <zimon.toutoune@gmail.com>
Sent: Tuesday, October 8, 2019 9:24 AM
To: Christopher Baines
Cc: Asfaw, Nardos; Guix Devel
Subject: Re: [External] Re: New outreachy participant introduction

Hi Nardos,

Welcome ! :-)


On Tue, 8 Oct 2019 at 08:48, Christopher Baines <mail@cbaines.net> = wrote:

> One good starting point would be an importer, there are a set of
> importers included in Guix that take a package definition from somewhe= re
> else (like the Python package index, or Rubygems) and try to generate = a
> Guix package definition. If you're familiar with some packages from on= e
> of the collections with a corresponding importer, that might be a good=
> place to start.

As an example, let consider packages from BioConductor [1] (mainly R
packages used in bioinformatics field). If I have right, then 2002
packages are still missing in Guix, so there is materials. ;-)

Well, let's pick one which is not packaged yet: zinbwave [2]. Then it is ea= sy:

  guix import cran -r -a bioconductor zinbwave

This will download TAR archives and automatically compute the hash. It
corresponds to the manual:

  guix download
https://b= ioconductor.org/packages/release/bioc/src/contrib/zinbwave_1.6.0.tar.gz=


[1] https://bioconductor.org/
[2] https://bioconductor.org/packages/release/bioc/html/zinbwave.html


Moreover, the importer provides the definition of the package:

--8<---------------cut here---------------start------------->8---
(define-public r-zinbwave
  (package
    (name "r-zinbwave")
    (version "1.6.0")
    (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zinbwave" ver= sion))
        (sha256
          (base32
            "187r7l9jf2q74qaqx63df5zx6ip= hmvl817448balvfv9vqyhrp2j"))))
    (properties `((upstream-name . "zinbwave")))
    (build-system r-build-system)
    (propagated-inputs
      `(("r-biocparallel" ,r-biocparallel)
        ("r-copula" ,r-copula)
        ("r-edger" ,r-edger)
        ("r-genefilter" ,r-genefilter)
        ("r-glmnet" ,r-glmnet)
        ("r-matrix" ,r-matrix)
        ("r-singlecellexperiment"
         ,r-singlecellexperiment)
        ("r-softimpute" ,r-softimpute)
        ("r-summarizedexperiment"
         ,r-summarizedexperiment)))
    (home-page
      "https://bioconductor= .org/packages/zinbwave")
    (synopsis
      "Zero-Inflated Negative Binomial Model for RNA-Se= q Data")
    (description
      " Implements a general and flexible zero-inflated= negative
binomial model that can be used to provide a low-dimensional
representations of single-cell RNA-seq data.  The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of
the data.  The model also accounts for the difference in library sizes=
and optionally for batch effects and/or other covariates, avoiding the
need for pre-normalize the data.")
    (license artistic2.0)))
--8<---------------cut here---------------end--------------->8---

In the propagated input, you can see the package `r-copula` which is
not yet packaged neither. But, the nice option --recursive does the
job for you and it also gives you the package definition.

Now, let add them to the Guix source. Clone the repo and go in the
folder. The command:

  guix environment guix

will download the dependencies to build Guix and setup all the
variables correctly. Well, refer to the documentation to compile Guix
from source. Basically:

  ./bootstrap
  ./configure --localstatedir=3D/var
  make

Now, you can run this version with ./pre-inst-env, for example:

   ./pre-inst-env guix describe


Well, ready to add one package! For example, add `r-copula` to the
file gnu/package/cran.scm then recompile with make. Check if it is ok:

  ./pre-inst-env guile show r-copula

Ouch! `r-psline` is missing so let also add it (the definition was
provided by the importer), run make again. Now "./pre-inst-env guix show r-copula" should work.
Add the package definition of zinbwave to the file gnu/package/bioconductor= .scm.

Let build them:

  ./pre-inst-env guix build r-zinbwave

and time to breath. ;-)


If something fails, try to investigate by yourself and do not hesitate
to ask advices or help.
If everything is ok, the package still needs some polishing: synopsis,
description, indentation, etc and really important: check the license
field.

The next step is to commit the changes. In this case, three commits
(one per package) seem nice. Give a look to previous commits as
example of commit message (ChangeLog format, etc.). Now, it is time to
prepare the submission:

  git format-patch --cover-letter - o patches master

this will create the 3 patches in the folder patches/ and one cover
letter. Edit the cover letter to describe what the patches are about
then submit it to the bug tracker:

  git send-email --to=3Dguix-patches@gnu.org patches/0000-cover-= letter.patch

Wait the answer to the bug tracker.
You should receive an email (if your .gitconfig is ok) with the bug
number. Last submit the patches:

  git send-email --to=3DABCDEF@debbugs.gnu.org patches/000{1,2= ,3}-*

where ABCDEF is the bug number.



Well, if you need some inspiration to find unpackaged tools from BioConduct= or:

  wget https://git.bioconductor.org -qO - | sed -ne
'/packages\/[a-zA-Z]/{s,^.*R.*packages/,,p}' > bioc_manifest
  ./pre-inst-env guile --no-auto-compile missing-bioconductor.scm bioc= _manifest

where the file `missing-bioconductor.scm` is given by:

--8<---------------cut here---------------start------------->8---
(use-modules ((guix import utils) #:select (guix-name))
             (gnu packages)
             (srfi srfi-1)  ;lists<= br>              (ice-9 textual-ports))

(define (fetch-names manifest)
  "Return a list of strings, each corresponding to a name from th= e
input file MANIFEST."
  (call-with-input-file manifest
    (lambda (port)
      (let loop ((lines '())
                 (line (get-li= ne port)))
        (if (eof-object? line)
            (reverse lines)
            (loop (cons line lines)
                  (get-line po= rt)))))))

;;; Start!

(map (lambda (name)
       (when (null? (find-packages-by-name (guix-name &= quot;r-" name)))
         (begin
           (display name)
           (newline))))
     (fetch-names (cadr (command-line))))

;; wget https://git.bioconductor.org -qO - | sed -ne
'/packages\/[a-zA-Z]/{s,^.*R.*packages/,,p}' > bioc_manifest
;; ./pre-inst-env guile --no-auto-compile missing-bioconductor.scm bioc_man= ifest
--8<---------------cut here---------------end--------------->8---


Hope that help.

All the best,
simon

--_000_157123538017494278iuedu_-- From mboxrd@z Thu Jan 1 00:00:00 1970 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= Subject: Re: [External] Re: New outreachy participant introduction Date: Sat, 19 Oct 2019 22:33:51 +0200 Message-ID: <874l04tqz4.fsf@gnu.org> References: <1570119118548.1674@iu.edu> <1570504991415.84097@iu.edu> <87a7abag1z.fsf@cbaines.net> <1570927278147.77440@iu.edu> <1571235380174.94278@iu.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:51372) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iLvQ9-0003RU-DP for guix-devel@gnu.org; Sat, 19 Oct 2019 16:33:54 -0400 In-Reply-To: <1571235380174.94278@iu.edu> (Nardos Asfaw's message of "Wed, 16 Oct 2019 14:16:19 +0000") List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: "Asfaw, Nardos" Cc: Guix Devel Hi Nardos, "Asfaw, Nardos" skribis: > Thanks for reaching out. I am still hanging. I am learning a lot on what = it means to be a developer outside of university courses. I am going throug= h the documentation (and examples provided in the email by simon) and the c= hat logs to sees if my questions have been asked before I come with questio= ns and solutions I have tried. At any rate, don=E2=80=99t hesitate to ask questions here or on #guix on IR= C! It=E2=80=99s surely tricky to get started with a development project so ask= ing questions can be helpful and we=E2=80=99ll be happy to provide guidance. Thanks, Ludo=E2=80=99. From mboxrd@z Thu Jan 1 00:00:00 1970 From: =?UTF-8?Q?G=C3=A1bor_Boskovits?= Subject: Re: [External] Re: New outreachy participant introduction Date: Thu, 24 Oct 2019 14:51:49 +0200 Message-ID: References: <1570119118548.1674@iu.edu> <1570504991415.84097@iu.edu> <87a7abag1z.fsf@cbaines.net> <1570927278147.77440@iu.edu> <1571235380174.94278@iu.edu> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="000000000000fedded0595a77fd1" Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:50072) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iNcaz-00083z-Lb for guix-devel@gnu.org; Thu, 24 Oct 2019 08:52:06 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iNcay-0005sO-9k for guix-devel@gnu.org; Thu, 24 Oct 2019 08:52:05 -0400 Received: from mail-ed1-x52e.google.com ([2a00:1450:4864:20::52e]:33873) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iNcay-0005rz-30 for guix-devel@gnu.org; Thu, 24 Oct 2019 08:52:04 -0400 Received: by mail-ed1-x52e.google.com with SMTP id b72so9583902edf.1 for ; Thu, 24 Oct 2019 05:52:04 -0700 (PDT) In-Reply-To: <1571235380174.94278@iu.edu> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: "Asfaw, Nardos" Cc: Guix Devel --000000000000fedded0595a77fd1 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hello, We have not heard from you for a while. Should you need any help, please let us know. Asfaw, Nardos ezt =C3=ADrta (id=C5=91pont: 2019. okt. 16., = Sze, 16:16): > Hi Gabor, > > > Thanks for reaching out. I am still hanging. I am learning a lot on what > it means to be a developer outside of university courses. I am going > through the documentation (and examples provided in the email by simon) a= nd > the chat logs to sees if my questions have been asked before I come with > questions and solutions I have tried. > > > Thanks, > > Nardos > ------------------------------ > Best regards, g_bor --=20 OpenPGP Key Fingerprint: 7988:3B9F:7D6A:4DBF:3719:0367:2506:A96C:CF63:0B21 --000000000000fedded0595a77fd1 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello,

We have not heard from you for a while. Should you need any help, please= let us know.

Asfaw, Nardos <nasfaw@= iu.edu> ezt =C3=ADrta (id=C5=91pont: 2019. okt. 16., Sze, 16:16):

Hi Gabor,


Thanks for reaching out.=C2=A0I=C2=A0am still hanging. I am learning a l= ot on what it means to be=C2=A0a developer outside of university courses.= =C2=A0I am going through the documentation (and examples provided in the em= ail=C2=A0by simon)=C2=A0and the chat logs to sees if my questions have been asked before=C2=A0I come with questions and solutions I have tri= ed.=C2=A0


Thanks,

Nardos


Best regards,
g_bor
--
<= div dir=3D"ltr">OpenPGP Key Fingerprint: 7988:3B9F:7D6A:4DBF:3719:0367:2506= :A96C:CF63:0B21
--000000000000fedded0595a77fd1--