Thank you, Jason! I've learned my lesson. It seems Wes' changes are still there. I don't get it how it's fixed.
Qin
On Mar 22, 2013, at 8:52 PM, Jason Swails wrote:
> As Dan mentioned, the current HEAD seems to be in pretty good shape.
>
> git-related advice for manual updates follows:
>
> Merging a Lyx file is less stable than merging source files. A good
> strategy in my experience, if git reports a conflict, is *not* to try to
> resolve it by hand, but rather to copy the LyX file to some other location,
> get a copy of the 'current' origin git manual, open both your version and
> the 'official', and copy your changes over to the 'official' manual from
> your backed up copy. I can envision 2 scenarios where you'll run into this:
>
> 1) You have already made local commits and a "git pull" reports a conflict:
>
> If you have already created a commit to the manual locally but haven't
> pushed, you should copy your version of the LyX file somewhere safe, do a
> "git fetch origin" to update your repo's knowledge of what is on the
> remote, then do a
>
> git checkout origin/master doc/AmberTools12.lyx
>
> to replace the LyX file in your repository with the most up-to-date one in
> the main repository. Commit this change and then do your git pull, which
> should not report a merge failure (at least in the LyX file). Then follow
> the above copy-and-paste instructions to apply your changes to the latest
> version (and commit your changes quickly! ;)).
>
> 2) You have local changes, but you have not made any commits:
>
> If you have NOT committed any changes to the manual, and instead get an
> error like "cannot pull because you have local changes", then you should
> first copy your lyx version somewhere outside the git repository then stash
> your changes:
>
> git stash
>
> do your pull (git pull), then try to put your changes back:
>
> git stash pop
>
> If this reports a conflict, don't try to resolve it. Just do a "git reset
> HEAD" followed by a
>
> git checkout doc/AmberTools12.lyx
>
> to reset the manual back to the current state in the git tree. Then, open
> your backup in LyX alongside the 'official' manual and copy your changes
> over.
>
> I hope this is helpful to some,
> Jason
>
> On Fri, Mar 22, 2013 at 11:27 PM, Qin Cai <qcai.uci.edu> wrote:
>
>> I think the problem is I cherry-pick Wes's commit from pbsa-dev in which
>> the revisions were made to an old version of AmberTools12.lyx.
>>
>> Now that we have rolled it back, let me ask Wes if he can make his
>> revisions to the latest version of AmberTools12.lyx.
>>
>> Qin
>> On Mar 22, 2013, at 7:49 PM, Daniel Roe wrote:
>>
>>> Hi,
>>>
>>> For what it's worth, the manual seems OK now (as of 4583f5678f56...).
>>>
>>> -Dan
>>>
>>> On Fri, Mar 22, 2013 at 8:39 PM, David A Case <case.biomaps.rutgers.edu>
>> wrote:
>>>> On Sat, Mar 23, 2013, Benjamin D Madej wrote:
>>>>>
>>>>> Is it safe to edit the AmberTools12.lyx file from the current
>>>>> version? I'd like to make a few last minute changes to a section I
>> added
>>>>> a few weeks ago.
>>>>
>>>> Please realize that notions like the "current version" are not useful
>> in a
>>>> situation where the file is changing hourly.
>>>>
>>>> You can work from commit 4823946ec1b61f5009. Please work carefully,
>> and do a
>>>> "git diff" before pushing any commits, to make sure that the changes in
>> the
>>>> file are the ones you want to make.
>>>>
>>>> If git reports conflicts, they can be very hard to resolve manually
>> (since
>>>> the lyx format has many repeated lines that tend to fool the automatic
>>>> merging). If you get conflicts, you often will need to get a clean
>> version,
>>>> and re-introduce your changes.
>>>>
>>>> [As I mentioned, going forward we will split the manual into separate
>> files
>>>> for each chapter, which should greatly reduce these problems.]
>>>>
>>>> ...thx...dac
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER-Developers mailing list
>>>> AMBER-Developers.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>
>>>
>>>
>>> --
>>> -------------------------
>>> Daniel R. Roe, PhD
>>> Department of Medicinal Chemistry
>>> University of Utah
>>> 30 South 2000 East, Room 201
>>> Salt Lake City, UT 84112-5820
>>> http://home.chpc.utah.edu/~cheatham/
>>> (801) 587-9652
>>> (801) 585-9119 (Fax)
>>>
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
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Received on Fri Mar 22 2013 - 22:00:04 PDT
