[Bioperl-l] git help

[Chris Fields]

Also, forgot to mention but we've moved FeatureIO out to it's own repo to reorganize it somewhat, so I'll likely migrate your changes over there.  We're eschewing Bio::SeqFeature::Annotated for simpler features and a few other bits that should allow for more flexibility in the future.  

chris

On Mar 31, 2011, at 7:19 PM, Scott Cain wrote:

> I just went a head and:
> 
>  git commit -a
>  git pull --rebase
>  git push
> 
> as suggested by rbuels.  That appeared to work.
> 
> Scott
> 
> 
> On Thu, Mar 31, 2011 at 7:13 PM, Scott Cain <scott at scottcain.net> wrote:
>> Hi all,
>> 
>> I just want to know if it is safe for me to commit.  Here is what git
>> said to me:
>> 
>> scott-cains-macbook-pro:bioperl-live cain$ git commit
>> # On branch master
>> # Your branch is behind 'origin/master' by 47 commits, and can be
>> fast-forwarded.
>> #
>> # Changed but not updated:
>> #   (use "git add <file>..." to update what will be committed)
>> #   (use "git checkout -- <file>..." to discard changes in working directory)
>> #
>> #       modified:   Bio/DB/GFF.pm
>> #       modified:   Bio/FeatureIO/gff.pm
>> #       modified:   scripts/Bio-DB-GFF/bulk_load_gff.PLS
>> #       modified:   scripts/Bio-DB-GFF/fast_load_gff.PLS
>> #       modified:   t/SeqFeature/FeatureIO.t
>> #       modified:   t/data/knownGene.gff3
>> #
>> # Untracked files:
>> #   (use "git add <file>..." to include in what will be committed)
>> #
>> #       scripts/Bio-DB-GFF/genbank2gff3.diff
>> no changes added to commit (use "git add" and/or "git commit -a")
>> ----------------------
>> 
>> so should I do a git commit -a?
>> 
>> Also, when I try a git pull, this is what it tells me:
>> 
>> scott-cains-macbook-pro:bioperl-live cain$ git pull
>> Updating 1c2cf24..d5de022
>> error: Your local changes to 'Bio/FeatureIO/gff.pm' would be
>> overwritten by merge.  Aborting.
>> Please, commit your changes or stash them before you can merge.
>> 
>> Thanks,
>> Scott
>> 
>> 
>> 
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> 
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