Atlas packaging template

[PolarBean]

Following on from the discussion at #399 I have created a functional version of the template script and updated example mouse to follow the new template.

[alessandrofelder]

Thanks a lot for this @PolarBean - looking good.

I've made many comments, but most of them are small. I've tried to reduce duplicate info by making the example script doc-strings cater to people that like concrete examples, and make the template script doc-strings more instructions about what one needs to do.

I still kind of think we could do with just one and not the other, but happy to keep both for now. We can think more about this as we refactor the API and head towards version 2.

As always, I am open to counter-arguments to my suggestions 🙂

(I've made some suggestions to make the linter happier with the template script, but it's unlikely to have covered all of it. That also needs to be addressed before we merge this.)

Some questions I have:

• should we explain somewhere how to include additional references or is that considered out-of-scope here?
• should we point to mesh helper functions somewhere?

[adamltyson]

should we explain somewhere how to include additional references or is that considered out-of-scope here?

Should we have an explicit section like:

# **** OPTIONAL *****
additional reference stuff

[PolarBean]

should we explain somewhere how to include additional references or is that considered out-of-scope here?

Should we have an explicit section like:

# **** OPTIONAL *****
additional reference stuff

this seems like a good solution but i cant see any instances of an atlas that has multiple citable documents (if this is what you're referring to). How should this be implemented?

[PolarBean]

@alessandrofelder I've addressed your comments and am ready for this to be re-reviewed once you have the time :)

[adamltyson]

this seems like a good solution but i cant see any instances of multiple an atlas that has multiple citable documents (if this is what you're referring to). How should this be implemented?

Here we mean multiple reference images (i.e. templates, we should rename this!). I think the AZBA has 2 reference images.

[alessandrofelder]

Thanks a lot @PolarBean - looking good!
Two more tiny comments, then we can merge this.

[alessandrofelder]

I am tempted to merge this at some point this week, and open a new issue for moving it away from AllenSDK - any objections @PolarBean @adamltyson ?

[adamltyson]

No argument from me.

[PolarBean]

Works for me!