Submitting a module to cpan

jillrowe has asked for the wisdom of the Perl Monks concerning the following question:

Replies are listed 'Best First'.
Re: Submitting a module to cpan by Corion (Patriarch) on Jul 15, 2014 at 13:07 UTC
Usually, you get mail back from CPAN after your upload gets processed. If you are really certain that you uploaded Annovar::Wrapper, look at that mail whether there were indexing problems. Also, I note that you use a different name for your distribution than you use for the modules. Your distribution was uploaded as "master", which is a really bad distribution name. This suggests that your upload never succeeded, because CPAN will only ever allow one file to be uploaded with the same name. I suggest you use a traditional naming scheme such as ExtUtils::MakeMaker produces when you execute `make dist`. There also has been a bug report opened for your distribution a long time ago hinting at your problematic choice of distribution name. Please consider fixing your tooling so it does use a better filename. The defaults are fine, so why don't you use them?	[reply] [d/l]
Re: Submitting a module to cpan by hippo (Archbishop) on Jul 15, 2014 at 12:57 UTC
Does the missing module appear in your directory at pause.perl.org? Did you receive the email from PAUSE that it had been uploaded and/or indexed?	[reply]
Re: Submitting a module to cpan by kcott (Archbishop) on Jul 15, 2014 at 17:40 UTC
G'day Jillian, Welcome to the monastery. You may already be aware of this but, if not, you may find PAUSE: menu has useful information. -- Ken	[reply]
Re: Submitting a module to cpan (Annovar::Wrapper Runner::Init ) by Anonymous Monk on Jul 15, 2014 at 21:16 UTC
Hi, some notes for your consideration Well, http://pause.perl.org/incoming/ doesn't list any Annovar... or master anymore, I guess its been processed Also, `use lib "/home/guests/jir2004/perlmodule/Runner-Init/lib";` doesn't belong in modules Hard coded paths like that don't belong in stuff you upload to cpan at all In your programs, use FindBin or File::FindLib or some such to to add to @INC at runtime For your own personal machine you can also manage installed modules the INSTALL_BASE way ( local::lib way ) as demonstrated in Re^3: object version does not match bootstrap parameter ( cpanm --local-lib PERL5LIB) data such as "bin\slurmtest" generally is put in "t" directory not bin -- bin is for programs :) either "t" directory or a "share" dir OTOH, the names of your modules seem , unguided :) http://pause.perl.org/pause/query?ACTION=pause_namingmodules#NAMES_TO_AVOID Runner::Init introduces Runner which isn't a good top level namespace (its new), maybe IPC::Runner cause it exists? Annovar another toplevel namespace ... not sure how ANNOVAR works, but maybe it belong somewhere in Bio::Tools::Run::Annovar (not sure about this either as I don't Bio:: at all)? To complete the circle for others who might be interested in commenting on these things of yours PrePAN - Runner::Slurm, Runner::Threads, and Runner::MCE PrePAN - Annovar::Wrapper https://github.com/jerowe/Runner-Init https://github.com/jerowe/Annovar-Wrapper	[reply] [d/l]
Re: Submitting a module to cpan by Anonymous Monk on Jul 16, 2014 at 08:25 UTC
Hippo - I did get an email from Pause. It says this. The URL https://github.com/jerowe/Annovar-Wrapper/tree/Annovar-Wrapper-1.1 has entered CPAN as file: $CPAN/authors/id/J/JI/JILLROWE/Annovar-Wrapper-1.1 size: 1370 bytes md5: 8bce9b023a3dd8057a71bef931a11501 No action is required on your part Request entered by: JILLROWE (Jillian Rowe) Request entered on: Mon, 07 Jul 2014 10:55:50 GMT Request completed: Mon, 07 Jul 2014 10:56:53 GMT Thanks, Corion - I know master is a terrible name. I had to fiddle a bit with uploading things from github. I didn't see many resources out there. I have proper names now, promise. ;) I deleted the master from PAUSE just now. kCott - Thanks for the welcome! I'm a long time lurker, but first time poster. I've looked through the PAUSE menu, but probably not enough. Anonymous - Thanks for the tip about the File::FindLib. That clearly shouldn't have been in there. Lesson learned, will do it properly even in testing. I didn't want to make Annovar::Wrapper a part of the BioPerl distribution. I love bioperl, but its a pain to install and Annovar::Wrapper doesn't have a single bioperl dependency. Bio::Tools::Run also has a rather specific way of doing things that I didn't follow because I prefer to write my wrappers in Moose. It seems rather cruel to make users install both BioPerl and Moose. ;)	[reply]
Re^2: Submitting a module to cpan ( ...X::... modules BioX::Annovar) by Anonymous Monk on Jul 16, 2014 at 09:42 UTC
I didn't want to make Annovar::Wrapper a part of the BioPerl distribution. Great, you don't have to, but since annovar is somekindof bio related module ... If you look on CPAN for Wrapper you'll find lots of existing namespaces with a bunch of related modules and then a ::Wrapper module You should drop ::Wrapper from the module name, add it to the description `=head1 NAME Annovar - wrapper for bin/annovar` [download] There are no annovar things on cpan There are bioinformatics, gene reated modules There are things like BioX::CLPM - Perl Tools for Mass Spec Peptide Matching Which don't appear to depend on Bio::Perl I can't find guidlines about "...X::..." modules... And I'm not sure about Bio::Perl guidelines regarding BioX, but maybe BioX is like DBIx, where you can drop DBI/Bio adjacent modules So now for your consideration (with the caveats) BioX::Annovar - wrapper for openbioinformatics.org/annovar/ - functional annotation of genetic variants from high-throughput sequencing data	[reply] [d/l]
Re^3: Submitting a module to cpan ( ...X::... modules BioX::Annovar) by jillrowe (Initiate) on Jul 16, 2014 at 10:20 UTC
Thanks! I think this is the BioX way to go with my naming. ;)	[reply]
Re: Submitting a module to cpan by tobyink (Canon) on Jul 16, 2014 at 12:22 UTC
Yay! You did it! toby döt ink	[reply]
Re^2: Submitting a module to cpan by jillrowe (Initiate) on Jul 17, 2014 at 06:44 UTC
I did finally do it! I had a post describing how I did it, but it seems to be stuck somewhere or I didn't do it properly. I'll rewrite it if it doesn't come up soon. Can anyone shed some wisdom on why my pod is displaying the way it is? lib/Annovar -Examples.pod -Wrapper.pm When I look at the main Annovar::Wrapper page, I get the pod from Examples.pod instead of the inline pod from Annovar::Wrapper.pm. https://metacpan.org/pod/Annovar::Wrapper Any ideas for me?	[reply]
Re^3: Submitting a module to cpan by tobyink (Canon) on Jul 17, 2014 at 08:13 UTC
Check that the NAME sections of your pod match their module name. MetaCPAN places a lot of importance on the NAME section. For example Annovar/Examples.pod should contain the following NAME section: `=head1 NAME Annovar::Examples - blah blah blah blah blah` [download] toby döt ink	[reply] [d/l]
Re: Submitting a module to cpan by Anonymous Monk on Jul 16, 2014 at 08:41 UTC
Ok, so looking at my cpan page, http://search.cpan.org/~jillrowe/, I don't think I have this whole submission thing down. I have two modules I want to submit. I have the Runner-Init, which has a few modules within it, and Annovar-Wrapper. They are here https://github.com/jerowe/Annovar-Wrapper https://github.com/jerowe/Runner-Init Where can I find a resource on submitting a module using git? There was a blog post that is referenced all over the place, but its not there anymore. There are plenty of resources on making a module best practices, but not so much on the actual submission of a module. Help, please!	[reply]
Re^2: Submitting a module to cpan (releasing using git) by Anonymous Monk on Jul 16, 2014 at 09:54 UTC
Where can I find a resource on submitting a module using git? :) good question that should be in the FAQ I can't help, I've long given up the PAUSE, but I did find these which probably wont help much mentions git and pause :) Authoring CPAN modules paths stuff http://blogs.perl.org/users/john_mcnamara/2009/12/uploading-to-cpan-from-github.html ?? Perl modules on CPAN and github - oylenshpeegul's blog eww :) Dist::Zilla - Tutorial - Integrating Dist::Zilla with Git preparing for CPAN from github, Minilla::Tutorial says minil can push to CPAN from git repository	[reply]
Re^3: Submitting a module to cpan (releasing using git) by jillrowe (Initiate) on Jul 16, 2014 at 10:10 UTC
Everything for git and uploading a module references this blog post http://blog.usarundbrief.com/?p=36 Which clearly no longer exists. The milla tool looks very promising. I will look into that. I used the module-start to set up my skeleton and just went from there, but maybe I should have looked into the Dist::Zilla too. When I get this figured out I will definitely thoroughly document it someplace!	[reply]
Re^4: Submitting a module to cpan (releasing using git) by Anonymous Monk on Jul 16, 2014 at 11:11 UTC
Re^5: Submitting a module to cpan (releasing using git) by Anonymous Monk on Jul 16, 2014 at 11:13 UTC
Re^4: Submitting a module to cpan (releasing using git) by marto (Cardinal) on Jul 16, 2014 at 10:18 UTC
Re^4: Submitting a module to cpan (releasing using git) by jillrowe (Initiate) on Jul 16, 2014 at 12:21 UTC
Re^2: Submitting a module to cpan by hippo (Archbishop) on Jul 16, 2014 at 09:22 UTC
Most of the submission process is covered in the About PAUSE page. Have you read this? Specifically what more do you need to know than is covered in this document? The fact that you have chosen to use git as your version control system should not be relevant. Once you've built the distribution tarball and tested it yourself just follow the submission instructions which apply regardless of the repository. By the way, your last 2 posts have come in as Anonymous. It would probably help you to keep track of responses, etc. if you were to login.	[reply]