Is Cypress the new preferred E2E tool?

With the vNext team focused on using Cypress, may I assume that Protractor will no longer be supported by Aurelia CLI and documentation?

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On the contrary. vNext won’t even need any special kind of support in order to work with protractor et al. This is an important driver in the design of vNext: to leverage natives and stick to standards as much as possible, so a well-designed tool should not require special work to integrate. Looking at the numerous bundlers and testing frameworks we’ve already experimented with, this appears to be coming along quite well.

Regarding protractor, that’s just a wrapper to make testing Angular easier and nowadays offers little to nothing for frameworks which are not Angular (it used to bring async to the table, but that’s been built in the upstream libraries for a while now)
I would recommend simply using selenium-webdriver / wdio, that’ll give you fewer dependencies and a cleaner setup overall.

More importantly, I would recommend not to look at the vNext CI / testing infrastructure as an indicator of what we will or won’t support.
We are simply using the things that make our job easier and an important factor there is speed, as we have lots and lots of tests. Cypress is the fastest thing out there for e2e, low-level, perfect for us. We will also be using selenium for some cross-browser testing.

Of course end users use a bigger variety of tools than we do, and you can definitely count on something as common as protractor to just work.