cclib-devel

Re: [cclib-devel] github fork

[Noel O'B. <bao...@gm...>]

(ccing to the list)

Hi Clyde,

Thanks for letting me know. You're free to do this of course - might
be good to make it clear that this is an "unofficial" fork though.
Just to save people contacting us asking about ASE.

Naturally for us we would prefer if you contribute any fixes directly
to cclib. In this case, if any of our units are incorrect we would
like to fix our source.

This might be the push we need to consider moving to Github. Git on
Windows though is a joke. The interface is not a lot better than the
old CVS one (you probably don't remember this) which also used to call
out to the command line. If only Github ran mercurial...:-/

- Noel



On 7 November 2013 15:05, Clyde Fare <cly...@gm...> wrote:
> Hi Noel
>
> I've got a git repository with cclib in it because I am faffing about trying
> to put together a bunch of python of tools associated with quantum chemistry
> to use with the ipython notebook. In my version I've changed the units that
> cclib uses in it's conversions because I want the various parsers I use to
> all use the same units.
>
> As I wanted an easy way of loading the package into Anaconda I've put the
> result on github here:
> https://github.com/Clyde-fare/cclib
>
> Github  have a very fork-me friendly mentality but it occurred to me that
> you might not be so happy that I'd done this so just wanted to check in with
> you - I could write a version that means the units used are chosen based on
> some flag (and your initial units are the default) which would mean I could
> keep my version synced with yours if that's something you would prefer.
>
> Cheers
>
> Clyde
>

Re: [cclib-devel] github fork

[Clyde F. <cly...@gm...>]

Hi Noel,

I've changed the readme to specifically state it's an unofficial fork and
for those who wish to contribute to follow your link.

I'm trying to construct, submit to the server, collect from the server,
extract data from the subsequent files and analyse them entirely from
within an IPython notebook.Consequently I'm using several different python
quantum chemistry wrappers. Part of the reason I've put cclib into a git is
because I'd like to have all the codes I'm modifying in one code management
system and partly it's because I assumed some of the modifications that
would be useful to me would not necessarily be useful to the majority of
the package users.

In terms of cclib i've modified the units not because I think they are
wrong but simply because I want the three parsers I use to produce
consistent results. For my Gaussian calculations I use cclib to extract
data from the main body of the log file, I use ASE's gaussian reader (
https://trac.fysik.dtu.dk/projects/ase/browser/trunk/ase/io/gaussian_reader.py)
to extract data from the machine readable content at the end of the
logfile, and I use molmod's fchk reader (
https://github.com/molmod/molmod/blob/master/molmod/io/fchk.py) to extract
data from the .fchk point files.

At the moment ASE's gaussian_reader and cclib use a different set of units
(and gaussian itself uses a third set of units).

Of course I would be thrilled if I could convince cclib and ase to
standardize their units. In terms of any changes I make, I'm happy to push
them back to the official version if it's thought suitable. (Of course if
you were on github that would be easier :D)

Cheers

Clyde


On 8 November 2013 09:47, Noel O'Boyle <bao...@gm...> wrote:

> (ccing to the list)
>
> Hi Clyde,
>
> Thanks for letting me know. You're free to do this of course - might
> be good to make it clear that this is an "unofficial" fork though.
> Just to save people contacting us asking about ASE.
>
> Naturally for us we would prefer if you contribute any fixes directly
> to cclib. In this case, if any of our units are incorrect we would
> like to fix our source.
>
> This might be the push we need to consider moving to Github. Git on
> Windows though is a joke. The interface is not a lot better than the
> old CVS one (you probably don't remember this) which also used to call
> out to the command line. If only Github ran mercurial...:-/
>
> - Noel
>
>
>
> On 7 November 2013 15:05, Clyde Fare <cly...@gm...> wrote:
> > Hi Noel
> >
> > I've got a git repository with cclib in it because I am faffing about
> trying
> > to put together a bunch of python of tools associated with quantum
> chemistry
> > to use with the ipython notebook. In my version I've changed the units
> that
> > cclib uses in it's conversions because I want the various parsers I use
> to
> > all use the same units.
> >
> > As I wanted an easy way of loading the package into Anaconda I've put the
> > result on github here:
> > https://github.com/Clyde-fare/cclib
> >
> > Github  have a very fork-me friendly mentality but it occurred to me that
> > you might not be so happy that I'd done this so just wanted to check in
> with
> > you - I could write a version that means the units used are chosen based
> on
> > some flag (and your initial units are the default) which would mean I
> could
> > keep my version synced with yours if that's something you would prefer.
> >
> > Cheers
> >
> > Clyde
> >
>

Re: [cclib-devel] github fork

[Karol M. L. <kar...@gm...>]

Hi guys,

Nice to see this. And Clyde -- nice project!

Noel, how recently have you looked at the github interface for Windows? If I rememeber
correctly, several weeks ago they made some significant improvements.

I don't know about mercurial, but they do support svn now.

Before moving to github, however, we could set up an "official" fork -- I'd be happy to do it,
and try to suck in Clyde's contribution via that. BTW, I'm +1 on moving to git. I always struggle
with the sourceforge svn tools.

- Karol

On Nov 08 2013, Noel O'Boyle wrote:
> (ccing to the list)
> 
> Hi Clyde,
> 
> Thanks for letting me know. You're free to do this of course - might
> be good to make it clear that this is an "unofficial" fork though.
> Just to save people contacting us asking about ASE.
> 
> Naturally for us we would prefer if you contribute any fixes directly
> to cclib. In this case, if any of our units are incorrect we would
> like to fix our source.
> 
> This might be the push we need to consider moving to Github. Git on
> Windows though is a joke. The interface is not a lot better than the
> old CVS one (you probably don't remember this) which also used to call
> out to the command line. If only Github ran mercurial...:-/
> 
> - Noel
> 
> 
> 
> On 7 November 2013 15:05, Clyde Fare <cly...@gm...> wrote:
> > Hi Noel
> >
> > I've got a git repository with cclib in it because I am faffing about trying
> > to put together a bunch of python of tools associated with quantum chemistry
> > to use with the ipython notebook. In my version I've changed the units that
> > cclib uses in it's conversions because I want the various parsers I use to
> > all use the same units.
> >
> > As I wanted an easy way of loading the package into Anaconda I've put the
> > result on github here:
> > https://github.com/Clyde-fare/cclib
> >
> > Github  have a very fork-me friendly mentality but it occurred to me that
> > you might not be so happy that I'd done this so just wanted to check in with
> > you - I could write a version that means the units used are chosen based on
> > some flag (and your initial units are the default) which would mean I could
> > keep my version synced with yours if that's something you would prefer.
> >
> > Cheers
> >
> > Clyde
> >
> 
> ------------------------------------------------------------------------------
> November Webinars for C, C++, Fortran Developers
> Accelerate application performance with scalable programming models. Explore
> techniques for threading, error checking, porting, and tuning. Get the most 
> from the latest Intel processors and coprocessors. See abstracts and register
> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel

-- 
written by Karol M. Langner
Fri Nov  8 15:32:34 EST 2013

Re: [cclib-devel] github fork

[Karol M. L. <kar...@gm...>]

Hi Noel,

It seems that Sourceforge actually now supports git repositories, if we wanted to convert and stay there.
The way to do it is to 'add' a git repository by adding the appropriate 'app' in the admin panel,
which creates an empty repository. The svn tree can then be converted to git and pushed to that.

I don't think we could resaonably use both repositories for development, so one would need to be
read-only, and I think we should keep the svn repo online for users that have that set up.

Meanwhile, to start off I pushed the trunk to a repostiory on github: https://github.com/langner/cclib
I will keep this up to date and would be in favor of moving mostly to github in the future.
If we went that route, I suppose the sf repo would be read-only. Additional things things to consider:
- what to do with current wiki / web page
- what to do with current branches
- what to do with previous releases/tags
- what to do with current and old issues in the tracker
- what to do with mailing lists

What do you think? I believe you did something similar for OpenBabel at some point. How did that work?

Cheers,
Karol

On Nov 08 2013, Karol M. Langner wrote:
> Hi guys,
> 
> Nice to see this. And Clyde -- nice project!
> 
> Noel, how recently have you looked at the github interface for Windows? If I rememeber
> correctly, several weeks ago they made some significant improvements.
> 
> I don't know about mercurial, but they do support svn now.
> 
> Before moving to github, however, we could set up an "official" fork -- I'd be happy to do it,
> and try to suck in Clyde's contribution via that. BTW, I'm +1 on moving to git. I always struggle
> with the sourceforge svn tools.
> 
> - Karol
> 
> On Nov 08 2013, Noel O'Boyle wrote:
> > (ccing to the list)
> > 
> > Hi Clyde,
> > 
> > Thanks for letting me know. You're free to do this of course - might
> > be good to make it clear that this is an "unofficial" fork though.
> > Just to save people contacting us asking about ASE.
> > 
> > Naturally for us we would prefer if you contribute any fixes directly
> > to cclib. In this case, if any of our units are incorrect we would
> > like to fix our source.
> > 
> > This might be the push we need to consider moving to Github. Git on
> > Windows though is a joke. The interface is not a lot better than the
> > old CVS one (you probably don't remember this) which also used to call
> > out to the command line. If only Github ran mercurial...:-/
> > 
> > - Noel
> > 
> > 
> > 
> > On 7 November 2013 15:05, Clyde Fare <cly...@gm...> wrote:
> > > Hi Noel
> > >
> > > I've got a git repository with cclib in it because I am faffing about trying
> > > to put together a bunch of python of tools associated with quantum chemistry
> > > to use with the ipython notebook. In my version I've changed the units that
> > > cclib uses in it's conversions because I want the various parsers I use to
> > > all use the same units.
> > >
> > > As I wanted an easy way of loading the package into Anaconda I've put the
> > > result on github here:
> > > https://github.com/Clyde-fare/cclib
> > >
> > > Github  have a very fork-me friendly mentality but it occurred to me that
> > > you might not be so happy that I'd done this so just wanted to check in with
> > > you - I could write a version that means the units used are chosen based on
> > > some flag (and your initial units are the default) which would mean I could
> > > keep my version synced with yours if that's something you would prefer.
> > >
> > > Cheers
> > >
> > > Clyde
> > >
> > 
> > ------------------------------------------------------------------------------
> > November Webinars for C, C++, Fortran Developers
> > Accelerate application performance with scalable programming models. Explore
> > techniques for threading, error checking, porting, and tuning. Get the most 
> > from the latest Intel processors and coprocessors. See abstracts and register
> > http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
> > _______________________________________________
> > cclib-devel mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-devel
> 
> -- 
> written by Karol M. Langner
> Fri Nov  8 15:32:34 EST 2013

-- 
written by Karol M. Langner
Sun Dec 29 00:39:40 EST 2013

Re: [cclib-devel] github fork

[Karol M. L. <kar...@gm...>]

Hi Clyde,

You might be interested to know cclib is now on github: https://github.com/cclib/cclib

Cheers,
Karol

On Nov 08 2013, Clyde Fare wrote:
> Hi Noel,
> 
> I've changed the readme to specifically state it's an unofficial fork and
> for those who wish to contribute to follow your link.
> 
> I'm trying to construct, submit to the server, collect from the server,
> extract data from the subsequent files and analyse them entirely from
> within an IPython notebook.Consequently I'm using several different python
> quantum chemistry wrappers. Part of the reason I've put cclib into a git is
> because I'd like to have all the codes I'm modifying in one code management
> system and partly it's because I assumed some of the modifications that
> would be useful to me would not necessarily be useful to the majority of
> the package users.
> 
> In terms of cclib i've modified the units not because I think they are
> wrong but simply because I want the three parsers I use to produce
> consistent results. For my Gaussian calculations I use cclib to extract
> data from the main body of the log file, I use ASE's gaussian reader (
> https://trac.fysik.dtu.dk/projects/ase/browser/trunk/ase/io/gaussian_reader.py)
> to extract data from the machine readable content at the end of the
> logfile, and I use molmod's fchk reader (
> https://github.com/molmod/molmod/blob/master/molmod/io/fchk.py) to extract
> data from the .fchk point files.
> 
> At the moment ASE's gaussian_reader and cclib use a different set of units
> (and gaussian itself uses a third set of units).
> 
> Of course I would be thrilled if I could convince cclib and ase to
> standardize their units. In terms of any changes I make, I'm happy to push
> them back to the official version if it's thought suitable. (Of course if
> you were on github that would be easier :D)
> 
> Cheers
> 
> Clyde
> 
> 
> On 8 November 2013 09:47, Noel O'Boyle <bao...@gm...> wrote:
> 
> > (ccing to the list)
> >
> > Hi Clyde,
> >
> > Thanks for letting me know. You're free to do this of course - might
> > be good to make it clear that this is an "unofficial" fork though.
> > Just to save people contacting us asking about ASE.
> >
> > Naturally for us we would prefer if you contribute any fixes directly
> > to cclib. In this case, if any of our units are incorrect we would
> > like to fix our source.
> >
> > This might be the push we need to consider moving to Github. Git on
> > Windows though is a joke. The interface is not a lot better than the
> > old CVS one (you probably don't remember this) which also used to call
> > out to the command line. If only Github ran mercurial...:-/
> >
> > - Noel
> >
> >
> >
> > On 7 November 2013 15:05, Clyde Fare <cly...@gm...> wrote:
> > > Hi Noel
> > >
> > > I've got a git repository with cclib in it because I am faffing about
> > trying
> > > to put together a bunch of python of tools associated with quantum
> > chemistry
> > > to use with the ipython notebook. In my version I've changed the units
> > that
> > > cclib uses in it's conversions because I want the various parsers I use
> > to
> > > all use the same units.
> > >
> > > As I wanted an easy way of loading the package into Anaconda I've put the
> > > result on github here:
> > > https://github.com/Clyde-fare/cclib
> > >
> > > Github  have a very fork-me friendly mentality but it occurred to me that
> > > you might not be so happy that I'd done this so just wanted to check in
> > with
> > > you - I could write a version that means the units used are chosen based
> > on
> > > some flag (and your initial units are the default) which would mean I
> > could
> > > keep my version synced with yours if that's something you would prefer.
> > >
> > > Cheers
> > >
> > > Clyde
> > >
> >

> ------------------------------------------------------------------------------
> November Webinars for C, C++, Fortran Developers
> Accelerate application performance with scalable programming models. Explore
> techniques for threading, error checking, porting, and tuning. Get the most 
> from the latest Intel processors and coprocessors. See abstracts and register
> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk

> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel


-- 
written by Karol M. Langner
Mon Dec 30 18:18:55 EST 2013

Re: [cclib-devel] github fork

[Clyde F. <cly...@gm...>]

 Hi,

Thanks for the update, great to see cclib on github!

Happy New Year

Clyde


On 30 December 2013 23:19, Karol M. Langner <kar...@gm...> wrote:

> Hi Clyde,
>
> You might be interested to know cclib is now on github:
> https://github.com/cclib/cclib
>
> Cheers,
> Karol
>
> On Nov 08 2013, Clyde Fare wrote:
> > Hi Noel,
> >
> > I've changed the readme to specifically state it's an unofficial fork and
> > for those who wish to contribute to follow your link.
> >
> > I'm trying to construct, submit to the server, collect from the server,
> > extract data from the subsequent files and analyse them entirely from
> > within an IPython notebook.Consequently I'm using several different
> python
> > quantum chemistry wrappers. Part of the reason I've put cclib into a git
> is
> > because I'd like to have all the codes I'm modifying in one code
> management
> > system and partly it's because I assumed some of the modifications that
> > would be useful to me would not necessarily be useful to the majority of
> > the package users.
> >
> > In terms of cclib i've modified the units not because I think they are
> > wrong but simply because I want the three parsers I use to produce
> > consistent results. For my Gaussian calculations I use cclib to extract
> > data from the main body of the log file, I use ASE's gaussian reader (
> >
> https://trac.fysik.dtu.dk/projects/ase/browser/trunk/ase/io/gaussian_reader.py
> )
> > to extract data from the machine readable content at the end of the
> > logfile, and I use molmod's fchk reader (
> > https://github.com/molmod/molmod/blob/master/molmod/io/fchk.py) to
> extract
> > data from the .fchk point files.
> >
> > At the moment ASE's gaussian_reader and cclib use a different set of
> units
> > (and gaussian itself uses a third set of units).
> >
> > Of course I would be thrilled if I could convince cclib and ase to
> > standardize their units. In terms of any changes I make, I'm happy to
> push
> > them back to the official version if it's thought suitable. (Of course if
> > you were on github that would be easier :D)
> >
> > Cheers
> >
> > Clyde
> >
> >
> > On 8 November 2013 09:47, Noel O'Boyle <bao...@gm...> wrote:
> >
> > > (ccing to the list)
> > >
> > > Hi Clyde,
> > >
> > > Thanks for letting me know. You're free to do this of course - might
> > > be good to make it clear that this is an "unofficial" fork though.
> > > Just to save people contacting us asking about ASE.
> > >
> > > Naturally for us we would prefer if you contribute any fixes directly
> > > to cclib. In this case, if any of our units are incorrect we would
> > > like to fix our source.
> > >
> > > This might be the push we need to consider moving to Github. Git on
> > > Windows though is a joke. The interface is not a lot better than the
> > > old CVS one (you probably don't remember this) which also used to call
> > > out to the command line. If only Github ran mercurial...:-/
> > >
> > > - Noel
> > >
> > >
> > >
> > > On 7 November 2013 15:05, Clyde Fare <cly...@gm...> wrote:
> > > > Hi Noel
> > > >
> > > > I've got a git repository with cclib in it because I am faffing about
> > > trying
> > > > to put together a bunch of python of tools associated with quantum
> > > chemistry
> > > > to use with the ipython notebook. In my version I've changed the
> units
> > > that
> > > > cclib uses in it's conversions because I want the various parsers I
> use
> > > to
> > > > all use the same units.
> > > >
> > > > As I wanted an easy way of loading the package into Anaconda I've
> put the
> > > > result on github here:
> > > > https://github.com/Clyde-fare/cclib
> > > >
> > > > Github  have a very fork-me friendly mentality but it occurred to me
> that
> > > > you might not be so happy that I'd done this so just wanted to check
> in
> > > with
> > > > you - I could write a version that means the units used are chosen
> based
> > > on
> > > > some flag (and your initial units are the default) which would mean I
> > > could
> > > > keep my version synced with yours if that's something you would
> prefer.
> > > >
> > > > Cheers
> > > >
> > > > Clyde
> > > >
> > >
>
> >
> ------------------------------------------------------------------------------
> > November Webinars for C, C++, Fortran Developers
> > Accelerate application performance with scalable programming models.
> Explore
> > techniques for threading, error checking, porting, and tuning. Get the
> most
> > from the latest Intel processors and coprocessors. See abstracts and
> register
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
>
> > _______________________________________________
> > cclib-devel mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-devel
>
>
> --
> written by Karol M. Langner
> Mon Dec 30 18:18:55 EST 2013
>