[Bioperl-l] git help

[Dave Messina]

Hey thanks so much, Duke! Very helpful!


Dave



On Fri, Apr 1, 2011 at 18:17, Jonathan "Duke" Leto <jonathan at leto.net>wrote:

> Howdy,
>
> Here are some PROTIPs that I think will be of use to many people:
>
> 1) Beware of "git commit -a". You can use "git show" to look at your most
> recent
> commit before you push it. Always make sure it contains what you think
> it should.
>
> 2) As a general rule, you shouldn't do a "git pull" when you have
> uncommitted
> changes. You shouldn't merge branches when you have uncommitted changes,
> either. Another way to get around this is to use the git "stash". Think of
> it
> as a cubby hole to put stuff to the side until you need it again.
>
> You could have typed
>
>    git stash
>    git pull --rebase
>    git stash pop
>
> As you can see, the stash is stack that you can "push" and "pop".
>
> 3) Updating the index and updating the actual files in your directory
> (called
> the working copy) can be done independently.
>
> The command:
>    git pull --rebase
>
> is equivalent to
>
>    git fetch                   # sync remote index to local index
>    git rebase origin/master    # update working copy with local index
>
> The second way which splits it up is useful when you want to do something
> in between, such as:
>
>    git fetch
>    git diff master...origin/master # what am I going to pull in?
>    git rebase origin/master
>
> I hope this arms BioPerl hackers with a better understanding of Git. If you
> have more Git questions, feel free to ask.
>
> Duke
>
>
> On Thu, Mar 31, 2011 at 4:13 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
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>
>
> --
> Jonathan "Duke" Leto
> jonathan at leto.net
> http://leto.net
>
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