Internal API changes due to 10525

[mbauman]

There were a few internal APIs that I changed in JuliaLang/julia#10525. This is a start at fixing some of your uses of them. I think I got everything except a few assumptions about how Base.checkbounds will work with NAType, so this fails in a few places where you expect checkbounds to throw an NAException -- it is now a MethodError.

There is a lot more that you could do to adjust to a post-10525 world. Let me know if you have any questions along the way.

[mbauman]

Actually, these should be accompanied with a Compat entry to allow things to continue to work on 0.3.

[mbauman]

Ah, got it. Now the only remaining question is how to support these usages in 0.3. (Tsk tsk for using internal APIs). :)

[coveralls]

Coverage decreased (-0.02%) to 80.76% when pulling 36a5611 on mbauman:mb/10525 into b5d39c3 on JuliaStats:master.

[mbauman]

I'm not sure that there's a sensible way to use Compat here since these aren't exported methods. And there were only two other packages that got tripped up on this (that weren't cascading failures).

CC: @davidanthoff for ExcelReaders.jl, @kbarbary for FITSIO.jl (FITSIO might be just the change to checkbounds)

This PR has the information you'll need to get your packages up and running again after JuliaLang/julia#10525 changed some internal APIs regarding indexing.

[kbarbary]

@mbauman Thanks for the heads up, glad to see 10525 merged!

[alyst]

Oh, good that I have found this PR! I was almost desperate because of the cryptic failure in DataFrames (JuliaData/DataFrames.jl#810). It would be nice to see this merged soon.

[axsk]

Indeed #10525 broke my use of DataFrames completely. Thank you for this PR 👍, hope it will be merged soon

[nalimilan]

Any reason not to merge? The reduction in coverage appears to be due to the parts conditional on the Julia version (as expected).

[simonster]

Thanks! Sorry for the slow merge.