Deprecate Bonsai.Onix Library

[cjsha]

• Add deprecation-notice.rst to every page in the Bonsai.ONIX directory
• Modify TOC to put Bonsai.ONIX as last entry, mark it as deprecated, and replace with OpenEphys.Onix1
• Add page for OpenEphys.Onix1 with example workflow for easy navigation

I name the "OpenEphys.Onix1" TOC entry "Onix Bonsai Library" because otherwise there is no indication that OpenEphys.Onix1 is for Bonsai.
I would even consider the Bonsa.ONIX entry in the TOC under its another dropdown named "Deprecated", "Deprecated Libraries" or something like that.
I figure the Neuropixels2 is a good workflow example to put on the onix1.rst page

[ChucklesOnGitHub]

I suggest the top level Bonsai section in the Software Guide is changed to Bonsai OpenEphys.Onix1 so that further referencing to that section makes more sense. It could also include a section to the new docs so the linkout is more immediate (in the menu).

Make the sections like this:

So that it is referenced in text like this:

[cjsha]

For some reason I can't comment directly on Ceci's post. I think it's not clear that OpenEphys.Onix1 is what people are looking for if they want to use Bonsai with ONIX. Under the presumption that people are looking for something related to Bonsai when navigating the software TOC, I understand why Jon would want to put an entry in the TOC that's just "Bonsai" or something like that. But we can still change the hyperlink so that it says:

which has been superseded by OpenEphys.Onix1

instead of

which has been superseded by Bonsai

[ChucklesOnGitHub]

to be clear: my suggestion was "Bonsai OpenEphys.Onix1" - refer to the language plus library, since it is not a standalone application like the GUI. And this would bring it closer hierarchically/visually-wise to the old "Bonsai.ONIX"

[cjsha]

I'll push the commit to fix my comments on this PR.

[jonnew]

@ChucklesOnGitHub With respect to renaming the software landing page from Bonsai -> OpenEphys.Onix1, I see your point but I think I disagree. The idea of the software page is a page for directing users to various software options for ONIX.

There are a couple :ref:s to this page in the docs and you are right that we will need to override their link text

:ref:Bonsai ONIX library <openephys_onix1ref>

I think @cjsha is doing that now.

[ChucklesOnGitHub]

Just to clarify, my suggestion is changing the software landing page from Bonsai -> Bonsai OpenEphys.Onix1 since this software option is not independent of the library.
And I mean it mostly to give people a menu item to click and immediately get redirected to the OpenEphys.Onix1 software docs page from the menu so that they don't have to navigate through the Bonsai page to get to software docs. It's a bit buried as it is now. It's ok if you want to go in a different direction, just my observation is that bonsai.onix is readily clickable but the new actual sofware doc page we want users to go to is an image inside another page.

[cjsha]

What I understand @ChucklesOnGitHub is that OpenEphys.Onix1 isn't enough of a first-class citizen like Bonsai.Onix was.
Calling it "Bonsai Open.Ephys.Onix1" also doesn't sit right with me (or Jon I think) though.

I made the subheader as you mentioned which I think helps, and created some direct references to that header. I think this at least starts to alleviate some of your concerns.

I've committed and pushed those changes I described (along with some typo fixes). This isn't a perfect solution, but I feel like it does the job. So, if there is urgency to getting these deprecation notices up, I can merge these changes to main so they deploy, as well as raise an issue if we want to continue discussing.

[cjsha]

Ceci said I could merge. I've raised an issue #64 to continue discussing these details if we want to.