On Wed, Feb 24, 2016 at 4:54 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Hai,
>
> These are nice arguments for the advantage of GitHub. I think we should
> set aside a session at the developers meeting to discuss things further as
> a group.
>
> My main fear is that we could easily end up fragmenting things and lose
> the benefit we all gain from having Amber be recognized as a actual package
> rather than a collection of a bunch of individual software from lots of
> different places. We also have the complexity of multiple development areas
> etc. If Github does indeed have a lot of cool features the question we
> should ask is should we consider getting a professional GitHub account (so
> we can have both private and public development) to encompass the central
> project that is AMBER and move all the various AmberTools github efforts
> into that (and then do away with the current Amber git server).
>
> That way we avoid all these cross platform issues and we also avoid the
> issue of losing the concept of AMBER as an identity. My opinion is that we
> all benefit from being associated with the concept of AMBER as a product
> and therefore we should work to maintain this as much as possible and avoid
> unnecessarily diluting it.
>
> What would be the disadvantages of this - besides the obvious one which is
> cost (I don't actually know how much a professional account on GitHub would
> cost us). I assume it is flexible enough to have the necessary permissions
> we would need etc.
>
I think AMBER only needs to make pmemd private repo (or I know at least
pytraj, cpptraj, parmed, pymsmt are public repos). Here is the price
https://github.com/pricing
($25/month for organization with 10 private repos)
Hai
>
> All the best
> Ross
>
> > On Feb 24, 2016, at 1:42 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> > On Wed, Feb 24, 2016 at 3:53 PM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
> >
> >> Hi Hai,
> >>
> >> But this doesn't solve the problem I think? This will give us no logs
> no?
> >
> >
> > No it does not. I just want to explain why Gerald got incredibly long log
> > message for only two files.
> >
> >
> >
> >> What we ideally want is all of the various logs for all of the changes
> you
> >> made etc to various files but only associated with those files. So the
> >> problem is the squashed commit. How do we avoid this?
> >>
> >>
> > I have no problem with not squashing pytraj commits if others developes
> do
> > not feel that I am polluting amber log with thousands of pytraj's
> commits.
> >
> > I initially developed pytraj on github and make a subtree on amber repo
> > after joining Case group. So developing on github is unavoidable in my
> > case.
> >
> > Per github development issue: I myself prefer to develop here since there
> > are many benefits
> >
> > - .There are many other developers (outside amber community) on github.
> > Most of the time they only care about a single package in AMBER. So it's
> > much easier to perform git clone from github, edit, make pull request, do
> > code review. So AMBER package is benefit from wider contributions. For
> > example, ParmEd is not only developed by AMBER developer (mostly Jason),
> > but is also got code contribution from Pande, Chodera and other groups
> > (this is a typical workflow: https://github.com/ParmEd/ParmEd/issues/592
> ).
> > More example: cpptraj is not able to be installed in Windows (
> > https://github.com/Amber-MD/cpptraj/pull/197)
> >
> > Another example: The MDAnalysis package (similar to cpptraj but written
> in
> > Python) have drammatically contributions when they move their code base
> > from Google Code Project Hosting to github (please check the period
> between
> > 2015-2016: https://github.com/MDAnalysis/mdanalysis/graphs/contributors
> )
> >
> > - free continuous integration: we are using travis for continuously
> > compiling, testing, combining different environments for our code
> > (example from cpptraj: https://travis-ci.org/Amber-MD/cpptraj). The
> service
> > is free, reliable, well supported, widely used (by Google, Microsoft,
> > facebook, ...). Whenever submitting a single commit to github, travis
> will
> > automatically pull the new code, compile and perform the testing in a
> > completely fresh environment. This is much better than testing on my old
> > laptop.
> >
> > - code review: We care about the quality of the code, so if anyone wants
> to
> > contribute to, for example, ParmEd, he/she needs to fork the master
> branch,
> > make change and make a pull request. traivis will pull the code from
> > contributor, perform the testing to make sure new code does not break the
> > tests. This is an example: https://github.com/ParmEd/ParmEd/pull/585.
> You
> > can see that the new code is not always accepted, the committee needs to
> > make change until the test pass.
> >
> > Also, github interface is very good for code review:
> > https://github.com/ParmEd/ParmEd/pull/585/files
> >
> > - easier manage new tasks: I used to make my feature request, comments
> and
> > related stuff to cpptraj by gmail document with Dan. This is nightmare
> :D.
> > github uses issue tag to make those simple:
> > https://github.com/Amber-MD/cpptraj/issues,
> > https://github.com/Amber-MD/cpptraj/issues/93). We can open, close,
> refer
> > from one to another issue easily.
> >
> > By the way, I just want to express by idea about github. I agree that we
> > should bring this stuff to amber dev meeting next month.
> >
> > cheers
> >
> > Hai
> >
> > All the best
> >> Ross
> >>
> >>> On Feb 24, 2016, at 12:37 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >>>
> >>> Hi
> >>>
> >>> this is due to my fault in keeping very long git commit message for
> >>> squashing. But after realizing this, I made the message extremely
> >> shorter.
> >>>
> >>> For example
> >>>
> >>> $ git show --name-only 2f1951b0864c06409acdfe797416e20e29cfd0b6
> >>> commit 2f1951b0864c06409acdfe797416e20e29cfd0b6
> >>> Author: Hai Nguyen <hainm.comp.gmail.com>
> >>> Date: Fri Feb 19 16:38:04 2016 -0500
> >>>
> >>> Squashed commit of pytraj
> >>>
> >>> AmberTools/src/pytraj/.travis.yml
> >>> AmberTools/src/pytraj/devtools/travis-ci/coveralls
> >>> AmberTools/src/pytraj/pytraj/__init__.py
> >>> AmberTools/src/pytraj/pytraj/all_actions.py
> >>> AmberTools/src/pytraj/pytraj/io.py
> >>> AmberTools/src/pytraj/tests/test_checkoverlap.py
> >>>
> >>> cheers
> >>> Hai
> >>>
> >>> On Wed, Feb 24, 2016 at 3:24 PM, Gerald Monard <
> >>> Gerald.Monard.univ-lorraine.fr> wrote:
> >>>
> >>>> I do think that the following is a problem:
> >>>>
> >>>> $ git show --oneline --name-only acc59a3
> >>>> acc59a3 Squashed commit of the following:
> >>>> doc/Amber.lyx
> >>>> doc/amber.bib
> >>>>
> >>>> $ git show --name-only acc59a3 | wc -l
> >>>> 7428
> >>>>
> >>>>> 7000 lines of explanation for 2 files...
> >>>>
> >>>> G.
> >>>>
> >>>> On 02/24/2016 08:32 PM, Hai Nguyen wrote:
> >>>>> hi,
> >>>>>
> >>>>> We only squash commits for cpptraj, pytraj and parmed when pulling
> >>>> commits
> >>>>> from github repos. Last year pytraj has > 1000 commits, cpptraj >
> 1000
> >>>>> commits, parmed > 1000 commits . If not squashing to few big commits,
> >>>> amber
> >>>>> git log will be populated and even more difficult to debug other
> >>>> programs.
> >>>>>
> >>>>> So if anyone wants to 'git blame', ... any files in those packages,
> >>>> he/she
> >>>>> should check corresponding github repo https://github.com/Amber-MD
> >>>>>
> >>>>> For other programs, nothing change (I just tested '*git log --color
> >>>>> mkrelease_at*')
> >>>>>
> >>>>> Hai
> >>>>>
> >>>>> On Wed, Feb 24, 2016 at 2:12 PM, Gerald Monard <
> >>>>> Gerald.Monard.univ-lorraine.fr> wrote:
> >>>>>
> >>>>>> Hi,
> >>>>>>
> >>>>>> This problem was already raised a couple of weeks ago by Ross: by
> >> using
> >>>>>> squash commits, git sees only one total commit. If you run "git
> blame
> >>>>>> amber.bib", then you will see the commit md5sum of this squashed
> >> commit
> >>>>>> and not an individual one inside the squashed commit. This means
> that
> >>>>>> the change of one individual file is related to a sum of changes.
> Thus
> >>>>>> if one wants more details about that commit (with its title and
> log),
> >>>>>> then the only thing you get is a big log with potentially hundreds
> of
> >>>>>> changes and files involved. It's then difficult to understand what's
> >>>>>> going on there.
> >>>>>>
> >>>>>> Best,
> >>>>>>
> >>>>>> Gerald.
> >>>>>>
> >>>>>> On 02/24/2016 07:41 PM, Hai Nguyen wrote:
> >>>>>>> alternatively,
> >>>>>>>
> >>>>>>> you can try
> >>>>>>>
> >>>>>>> type*: git log --color -p amber.bib*
> >>>>>>> then search keyword amber.bib by typing:* /amber.bib*
> >>>>>>> to repeat the search, press* 'n'*
> >>>>>>> (similar to vim)
> >>>>>>>
> >>>>>>> tag "*-p*" will show the modified content
> >>>>>>>
> >>>>>>> Hai
> >>>>>>>
> >>>>>>> On Wed, Feb 24, 2016 at 12:31 PM, Timothy J Giese <
> >>>>>> timothyjgiese.gmail.com>
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>>> There is a gui called "gitk" that is sometimes useful.
> >>>>>>>>
> >>>>>>>> Open gitk, then
> >>>>>>>> next to "Find",
> >>>>>>>> select "touching paths:"
> >>>>>>>> and then enter the name of the file;
> >>>>>>>> e.g., AmberTools/src/sander/multisander.F90
> >>>>>>>>
> >>>>>>>> Then the arrow buttons next to "Find" will skip up and down
> through
> >>>>>>>> those commits that edit that file.
> >>>>>>>>
> >>>>>>>> -Tim
> >>>>>>>>
> >>>>>>>> On 02/24/2016 12:22 PM, David A Case wrote:
> >>>>>>>>> I'm pinging git experts about what (if anything) we can do with
> the
> >>>>>>>> following
> >>>>>>>>> problem:
> >>>>>>>>>
> >>>>>>>>> If I cd to the amber14/doc directory and type "git log amber.bib"
> >> (in
> >>>>>>>> order
> >>>>>>>>> to find recent changes to this file), I get the following:
> >>>>>>>>>
> >>>>>>>>> commit acc59a342da64bf949ac6828b45294b275970344
> >>>>>>>>> Author: Hai Nguyen <hainm.comp.gmail.com>
> >>>>>>>>> Date: Thu Feb 4 11:02:31 2016 -0500
> >>>>>>>>>
> >>>>>>>>> Squashed commit of the following:
> >>>>>>>>>
> >>>>>>>>> commit 689f1f003ea81f51a26f4791e46ed9fa18ee8b5e
> >>>>>>>>> Merge: 8a40ed6 9c3c6ef
> >>>>>>>>> Author: Hai Nguyen <hainm.users.noreply.github.com>
> >>>>>>>>> Date: Thu Feb 4 01:50:52 2016 -0500
> >>>>>>>>>
> >>>>>>>>> Merge pull request #1136 from hainm/master
> >>>>>>>>>
> >>>>>>>>> add ref_mask for rmsd
> >>>>>>>>>
> >>>>>>>>> commit 9c3c6ef39bd1c4a45308733b54439dde4d7f3edf
> >>>>>>>>> Author: Hai Nguyen <hainm.comp.gmail.com>
> >>>>>>>>> Date: Thu Feb 4 01:40:16 2016 -0500
> >>>>>>>>>
> >>>>>>>>> fix
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> ...etc...etc for hundreds of commit logs, (7500 lines of text)
> >> almost
> >>>>>>>> none
> >>>>>>>>> of which actually did anything to amber.bib itself.
> >>>>>>>>>
> >>>>>>>>> I can redirect the output to a file, and use a text editor to try
> >> to
> >>>>>> find
> >>>>>>>>> what I'm looking for, but I wonder if there is not a better way.
> >> Do
> >>>> we
> >>>>>>>> really
> >>>>>>>>> need commits that are thousands of lines long? Is there a better
> >> way
> >>>>>> to
> >>>>>>>>> maintain a useful history? Some fancy option to the "git log"
> >>>> command
> >>>>>>>> that
> >>>>>>>>> alleviates this?
> >>>>>>>>>
> >>>>>>>>> ...thx...dac
> >>>>>>>>>
> >>>>>>>>> _______________________________________________
> >>>>>>>>> AMBER-Developers mailing list
> >>>>>>>>> AMBER-Developers.ambermd.org
> >>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> AMBER-Developers mailing list
> >>>>>>>> AMBER-Developers.ambermd.org
> >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> AMBER-Developers mailing list
> >>>>>>> AMBER-Developers.ambermd.org
> >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>>>>>>
> >>>>>>
> >>>>>> --
> >>>>>>
> >>>>>>
> >>>>
> >>
> ____________________________________________________________________________
> >>>>>>
> >>>>>> Prof. Gerald MONARD
> >>>>>> SRSMC, Université de Lorraine, CNRS
> >>>>>> Boulevard des Aiguillettes B.P. 70239
> >>>>>> F-54506 Vandoeuvre-les-Nancy, FRANCE
> >>>>>>
> >>>>>> e-mail : Gerald.Monard.univ-lorraine.fr
> >>>>>> tel. : +33 (0)383.684.381
> >>>>>> fax : +33 (0)383.684.371
> >>>>>> web : http://www.monard.info
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>
> >>
> ____________________________________________________________________________
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> AMBER-Developers mailing list
> >>>>>> AMBER-Developers.ambermd.org
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>>>>>
> >>>>> _______________________________________________
> >>>>> AMBER-Developers mailing list
> >>>>> AMBER-Developers.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>>>>
> >>>>
> >>>> --
> >>>>
> >>>>
> >>
> ____________________________________________________________________________
> >>>>
> >>>> Prof. Gerald MONARD
> >>>> SRSMC, Université de Lorraine, CNRS
> >>>> Boulevard des Aiguillettes B.P. 70239
> >>>> F-54506 Vandoeuvre-les-Nancy, FRANCE
> >>>>
> >>>> e-mail : Gerald.Monard.univ-lorraine.fr
> >>>> tel. : +33 (0)383.684.381
> >>>> fax : +33 (0)383.684.371
> >>>> web : http://www.monard.info
> >>>>
> >>>>
> >>>>
> >>
> ____________________________________________________________________________
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER-Developers mailing list
> >>>> AMBER-Developers.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>>>
> >>> _______________________________________________
> >>> AMBER-Developers mailing list
> >>> AMBER-Developers.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>
> >>
> >> _______________________________________________
> >> AMBER-Developers mailing list
> >> AMBER-Developers.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>
>
> _______________________________________________
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Received on Wed Feb 24 2016 - 14:30:05 PST
