Move MDAnalysis to GitHub due to Google Code closure

[GoogleCodeExporter]

Google announced that they will shutdown Googlecode 
http://google-opensource.blogspot.com/2015/03/farewell-to-google-code.html (as 
also reported on Ars Technica [1]). The service including all code will be gone 
by 2016:

* August 24, 2015 - The site goes read-only. You can still checkout/view 
project source, issues, and wikis.

* January 25, 2016 - The project hosting service is closed. You will be able to 
download a tarball of project source, issues, and wikis. These tarballs will be 
available throughout the rest of 2016.

Today, "Export to GitHub" buttons appeared on Google Code. I suggest, we make 
the 0.9.0 release from Google Code and then migrate to GitHub. GitHub is a 
nicer platform for collaborative coding but it's hugely annoying that the Issue 
tracker will be lost and we have to think about what to do about that.

Oliver

[1] 
http://arstechnica.com/information-technology/2015/03/google-to-close-google-cod
e-open-source-project-hosting/

Original issue reported on code.google.com by orbeckst on 12 Mar 2015 at 5:05

• Blocking: #134, #235, #236
• Blocked on: #231, #232, #233, #234

[GoogleCodeExporter]

From reading the google link above, it looks like Issues will get ported to 
Github with the provided tool too, unless you've tried this and it failed?

Otherwise moving to Github post 0.9 sounds good.

Richard

Original comment by richardjgowers on 12 Mar 2015 at 5:59

[GoogleCodeExporter]

No haven't tried it yet; just was a bit sceptical, but it seems that there are 
other people out there who also thought about these things, so I think we'll 
manage in the end.

I also wonder how the wiki will get moved, and how we can continue serving the 
sphinx docs of the development branchs etc � but I suppose we'll see. It will 
be an opportunity for some "spring cleaning"... 

I just set up https://github.com/MDAnalysis so that we will have a proper place 
to go to. We can discuss post 0.9.0 how to organize things.

Original comment by orbeckst on 12 Mar 2015 at 6:54

[GoogleCodeExporter]

For future reference:

FAQ: https://code.google.com/p/support-tools/wiki/GitHubExporterFAQ

Notes:
- one can also do a manual export (see FAQ)
- must export to a user GitHub account (which will then transfer to the GitHub 
Organization MDAnalysis https://github.com/MDAnalysis). The procedure is 
described at https://help.github.com/articles/transferring-a-repository/
- using the redirect makes the Google Code project front page inaccessible so 
make sure to copy all text BEFORE setting the "project moved" flag

According to the FAQ, Issues will be exported. The wiki will become a branch 
'wiki' and the pages converted to MarkDown format.

Original comment by orbeckst on 12 Mar 2015 at 9:31

[GoogleCodeExporter]

There are a couple of options for documentation hosting. My favorite is 
readthedocs (https://readthedocs.org/), which can handle generating sphinx 
autodoc elements that rely on C modules by mocking the imports 
(http://docs.readthedocs.org/en/latest/faq.html#i-get-import-errors-on-libraries
-that-depend-on-c-modules). The advantage of this service as that the docs are 
generated and hosted for any number of branches, and each commit to a branch 
triggers regeneration automatically.

Another reasonable option is manually generating the docs and then hosting them 
as static pages on github (https://pages.github.com/) for the project. Of 
course we could host these things wherever we want, but github provides the 
static hosting for free. :D

Original comment by dot...@gmail.com on 17 Mar 2015 at 4:35

[GoogleCodeExporter]

David,

if you can get the MDAnalysis docs to build on ReadTheDocs then that would be 
great but Tyler and I gave up in frustration, see Issue 183. (There's also a 
branch in which Tyler tried some mocking but he might be able to say more.) If 
you want to give it a short, I'll reopen Issue 183 and make you the owner, 
unless Tyler (with his documentation manager-hat on) has any other ideas.

I'll also cross-reference Issue 134 for the broader context.

GitHub pages work well although I haven't got a good workflow to use them – 
look at the horrible mess at 
https://github.com/orbeckst/GromacsWrapper/wiki/Preparing-online-docs ... any 
suggestions more than welcome!!!

Oliver

Original comment by orbeckst on 17 Mar 2015 at 5:20

[GoogleCodeExporter]

Yeah, I started working on Readthedocs functionality again after we gave up as 
I'm a fair bit better at that now that I use Readthedocs for my own open-source 
github project documentation (i.e., 
http://py-sphere-voronoi.readthedocs.org/en/latest/voronoi_utility.html).

But then I gave up again because of various build problems with MDAnalysis. I 
think it may be possible to do with the proper mocking of modules, and is 
definitely a very clean solution from a convenience standpoint for the reasons 
mentioned (automatic update to reflect source, looks great, etc.). 

There's a few tricky things with creating a 'virtual environment' for 
installing MDA when it builds on RTD I think, and if we really want this to 
work we might have to be willing to change the directory structure used for 
installing or building in a fundamental way--I think Oli thought that might be 
too extreme last time?!  

Maybe make David the owner and he could continue working on the branch I 
started, or start a new one, and if there's something I can do to help we can 
communicate and work on that branch? A fresh set of eyes on the challenge can't 
hurt.

Tyler  

Original comment by tyler.je.reddy@gmail.com on 17 Mar 2015 at 5:56

[GoogleCodeExporter]

I'll be happy to take the issue over. I had to do some munging about with 
readthedocs to handle building docs for my own project as well 
(http://mdsynthesis.readthedocs.org/en/latest/), and I'm willing to try it with 
MDAnalysis.

I'll likely consult with you, Tyler, as I work on it.

Original comment by dot...@gmail.com on 17 Mar 2015 at 11:36

[GoogleCodeExporter]

Do we want to put a version of the main repo in the new space on github so I 
can start setting up the readthedocs elements? Otherwise I could do it myself 
from my own account and then move the urls over later.

Original comment by dot...@gmail.com on 19 Mar 2015 at 11:02

[GoogleCodeExporter]

I was just working directly off the google code repo for my testing purposes: 
https://readthedocs.org/projects/mda-test/

Actually, I did at least get to a point where you could load the index of the 
docs: http://mda-test.readthedocs.org/en/test_readthedocs/

The 'official' MDAnalysis page for readthedocs is here: 
https://readthedocs.org/projects/mdanalysis/
But I was just doing most of the testing on the docs branch on my own page so I 
didn't make a huge mess on the regular one.

Your own github repo + your own readthedocs webhook for testing, and then 
merging back the working sphinx adjustments, etc., sounds smart to me. I can 
always pull request off your page is there's something I can do to help.

Original comment by tyler.je.reddy@gmail.com on 20 Mar 2015 at 12:05

[GoogleCodeExporter]

@David re: docs: From reading the issues for export 
https://code.google.com/p/support-tools/issues/list our best hope appears to be 
to use the export wizard (instead of manual tools) but this might take a while 
and it cannot update an existing repo. Therefore, I'd like to try a clean 
transition where we stop using google code and then start using GitHub. 
However, you can already push a clone to your own github space and work on 
that. Eventually this can be merged/rebased as usual – as Tyler suggests.

I'd like to move further discussions of docs-related things to Issue 183.

Original comment by orbeckst on 22 Mar 2015 at 5:09

[GoogleCodeExporter]

I started a wiki page MoveToGitHub [1] to list considerations for the move. 
Please have a look so that we can have a discussion on how to do this the best 
way.

As a timeline I suggest we first do the quick 0.9.1 release (Séb will sort out 
the details) and then do the move in the week following the release.

Please already have a look at the various feature branches [2] (use the 
"Branch" selection menu) and decide if the branch is still necessary or can be 
deleted. I'd like to avoid transferring branches that we don't need.

More TODOs to come... but I am waiting for comments (in this thread) on how to 
do the move in the best way.

Oliver

[1] https://code.google.com/p/mdanalysis/wiki/MoveToGitHub
[2] https://code.google.com/p/mdanalysis/source/browse/package

Original comment by orbeckst on 22 Mar 2015 at 6:41

[GoogleCodeExporter]

Original comment by orbeckst on 27 Mar 2015 at 5:19

• Now blocking: #134

[GoogleCodeExporter]

Original comment by orbeckst on 28 Mar 2015 at 1:28

• Now blocked on: #231

[GoogleCodeExporter]

Original comment by orbeckst on 28 Mar 2015 at 1:33

• Now blocked on: #232

[GoogleCodeExporter]

Original comment by orbeckst on 28 Mar 2015 at 1:35

• Now blocked on: #233

[GoogleCodeExporter]

Original comment by orbeckst on 28 Mar 2015 at 1:38

• Now blocked on: #234

[GoogleCodeExporter]

Original comment by orbeckst on 28 Mar 2015 at 1:42

• Now blocking: #235

[GoogleCodeExporter]

Original comment by orbeckst on 29 Mar 2015 at 5:48

• Now blocking: #236

[GoogleCodeExporter]

In principle the move from Google Code to GitHub is complete. There are lots of 
things to iron out (such as wiki, docs and homepage and how to do attachments 
with the issue tracker, uploading old downloads to pypi, splitting of tools 
("applications") into own repos, ...) but the code is up and all the 
infrastructure is in place.

@Developers: please start using https://github.com/MDAnalysis/mdanalysis and 
provide feedback if anything is not working properly.

New clones:

   git clone git@github.com:MDAnalysis/mdanalysis.git

Changing existing repositories (assuming that the google code repo was named 
"origin"):

   git remote rename origin googlecode
   git remote add origin git@github.com:MDAnalysis/mdanalysis.git

This should be sufficient to use the new repository, for instance, update your 
develop branch:

   git pull origin develop

Thanks to everyone for their patience and support!
Oliver

Original comment by orbeckst on 5 Apr 2015 at 5:57

• Changed state: Done