NML2/LEMS export

[dokato]

Currently without documentation because I didn't know how to integrate it with the rest.

I also changed the name of exporter from brian2lems to nmlexport.

[dokato]

It fails tests because there is no requirement for pylems module in setup.py. I wanted to add it, but - as I have made a lot of changes during GSOC there- I'm not sure whether the most recent version is available on PIP. Is there any way to install it from GIT automatically?

[mstimberg]

It fails tests because there is no requirement for pylems module in setup.py. I wanted to add it, but - as I have made a lot of changes during GSOC there- I'm not sure whether the most recent version is available on PIP. Is there any way to install it from GIT automatically?

This is a bit tricky, since as you say I think there's no released version with your changes yet. Also, the tests are based on a conda package, so we'd need a conda package for pylems as well. I'll think about a solution.

About the documentation: the following two steps should be all that is needed:

1. Add your exporter_*.rst files to the docs_sphinx/user directory
2. Add the lines exporter_user and exporter_developer to the table of contents in docs_sphinx/user/index.rst

This should take care of everything, you can run make html in the docs_sphinx directory to create the documentation locally and check whether it looks alright. A somewhat nicer alternative to what I explained above would probably to create a new directory in docs_sphinx/user, say neuroml2 and add the two files there. Then in that newly created directory you'd add a new index.rst file with a table of contents similar to the index.rst in docs_sphinx/user, referring to exporter_user and exporter_developer. Finally you'd have to mention that index file as neuroml2/index in docs_sphinx/user/index.rst. Hope that's somewhat clear :)

[dokato]

Ok, I updated documentation with new files and modified user/index, but unfortunately I didn't have a chance to test it as I got some strange error when running make: Could not import extension sphinxcontrib.issuetracker even after updating my Sphinx to the most recent version. In my other projects make html works fine.

[mstimberg]

Ok, I updated documentation with new files and modified user/index, but unfortunately I didn't have a chance to test it as I got some strange error when running make: Could not import extension sphinxcontrib.issuetracker even after updating my Sphinx to the most recent version. In my other projects make html works fine.

Thanks, I'll have a look at it soon. We use a non-standard extension that allows to easily link to bugs in github's bug-tracker. You have to manually install the sphinxcontrib-issuetracker extension (e.g. with pip) to make it work. It is listed as a requirement for brian2tools, but only as an optional requirement, you'll have to install with the [docs] option to have the dependency taken into account.

[dokato]

Thanks for your hint on how to use sphinx in brian2tools. Now as it works fine, after building the docs I realized that exporter's developer guide should be rather in developer folder so I just moved that file there in the most recent commit.

[mstimberg]

Sorry, I have been quite busy lately with other stuff and did not really have time yet to look into this.

I still don't have a clear plan what to do about the pylems dependency. @pgleeson: would you say that there is a plan to release a new version of pylemsanytime soon? It does not change very much for us: since we recommend installing brian2tools via its conda package, we'll have to provide a conda package for pylems, anyway. If the pylems's next release is quite far in the future, we'd do a 0.48+git20160909 package of it ourselves, but of course an official version number would lead to less potential confusion.

[mstimberg]

Um, we still have not merged this... @dokato : could you allow me to add changes to your branch (as explained here: https://help.github.com/articles/allowing-changes-to-a-pull-request-branch-created-from-a-fork/)? I'd then fix up the testing, etc.

@pgleeson: Do you have plans to do a pylems release any time soon? Otherwise we might just tell users to install it from github for now.

[dokato]

@mstimberg, of course, just updated.

[pgleeson]

@mstimberg The changes which were part of PRs had all been incorporated in master & the latest version v0.4.9 is on PYPI (I just now updated it with some minor changes).

[mstimberg]

Great, many thanks @pgleeson and @dokato, I'll try to polish and merge the PR soon.

[mstimberg]

Ok, I'll finally merge this -- it's about time :) I'll do some more polishing in the master branch directly (documentation, release notes, ...) and will do a 0.2 release of brian2tools soon.