Updated for 1.0

[mlhetland]

Updated to use new iteration protocol, if available. Importing done creates problems otherwise.

[coveralls]

Coverage decreased (-0.2%) to 78.687% when pulling fbfeca4 on mlhetland:1.0-fixes into b2f76ee on dcjones:master.

[mpastell]

Any change for merging this and tagging a new release soon? It would be great to get Weave.jl running on 1.0 and it depends on this package.

[mlhetland]

It'd be great for me to have this work by the end of the week; otherwise, I'll be using 0.7 in my course this semester :-}

[sglyon]

Thank you for submitting.

Will you please enable tests on julia 0.7 and 1.0? To do this we need to change these lines to also include - 0.7 and - 1.0

Once we see that this fix changes tests we will be good to merge.

[mlhetland]

It seems it's the test infrastructure itself that fails, as it uses Pkg in a pre-1.0 way?

[mlhetland]

That is, rather than julia -e 'Pkg.clone(pwd()), it should be julia -e 'using Pkg; Pkg.clone(pwd()), though only for Julia 1.0, so unless you can have different commands for different versions, I guess you need an if VERSION thing in there as well.

[mlhetland]

The following should work:

julia -e 'if VERSION >= v"0.7" using Pkg end; Pkg.clone(pwd())

[mpastell]

@mlhetland yes, that's what some other packages seem to use.

[mlhetland]

Maybe something @sglyon wants to address? (Or should I change it? Not sure where the Travis infrastructure is, ATM, but I’m sure it’s possible to find it :-))

[sglyon]

I think we should make that change -- it is what I would do myself so if you are willing to do it on this branch that'd be great!

[mlhetland]

Didn't notice that it was all just further down in the Travis-file xD Fixed.

[mlhetland]

Hm. I thought I tested it with 1.0, but it seems maybe I only tested with 0.7 for deprecation warnings. Still importing start and next, which don't exist in 1.0. Sorry about that! I'll do some bug-fixing an test properly in 1.0 :-)

[mlhetland]

Well, one problem is that we'll need Codecs#master. I guess they haven't tagged a release with the fixes there yet.

[mpastell]

Codecs has been tagged, but not merged JuliaLang/METADATA.jl#16489 .

[mlhetland]

Oh, OK.

[mlhetland]

Anyway: I've tested with Julia 0.6, 0.7 and 1.0, and the tests run fine locally for me. But then, of course, I use Compat for 0.6 and Compat#master for 0.7 and 1.0.

[mlhetland]

So I guess as soon as we get the right version of Codecs, the tests here should pass.

[sglyon]

Sounds great, thank you for all the work here. Please notify us on this thread when I should review and prepare to merge

[TransGirlCodes]

What is the status of this PR please? We need a 1.0 compatible version of YAML for BioJulia packages ASAP, but don't want to tread on toes of people already working on PRs :)

[TransGirlCodes]

Codecs.jl v0.5.0 has been release which works for julia v0.7 / v1.0, if this PR uses that version it should pass?

[mlhetland]

The holdup has been that Codecs 0.5 hasn't been merged into METADATA. If you can specify specific tags or branches in your requirements, you could always just use this PR and 0.5 of Codecs directly. I could add a tag, if that's useful (i.e., rather than checking out the branch). But using Codecs#v0.5.0 and https://github.com/mlhetland/YAML.jl#1.0-fixes currently works.

As soon as Codecs 0.5 is in METADATA, the checks here should pass, I guess, yes.

[sglyon]

Ok great, thank you for the update

[mlhetland]

I’m on my phone right now, so it’s a bit awkward to check, but I believe Codecs 0.5 should now be available. Can we manually re-run the checks? (It seems they’re stale at the moment?)

[TransGirlCodes]

@mlhetland Codec 0.5 is indeed available now. If you have access to the travis you re-run the CI checks.

[mlhetland]

Hm. If I do have access, I at least can’t figure out how. (Wouldn’t I need write access to this repo? Am I missing something?)

[mlhetland]

Just thought I'd push a change to trigger a new check – so I added a Project.toml file. :-)

[mlhetland]

Being too clever here, I guess – breaking stuff. (Tricky when I can't test the CI stuff locally…) The deprecation warning for clone said to use add, but that doesn't work with a path, it seems. (Maybe I'm just using it wrong.) And there was an issue with developing a package with the same UUID as the project (which I guess makes sense – though here it is the same project), so I just removed the Project.toml file, again. I think it's correct – it works fine with, say, instantiate; it's just that the Travis setup had issues with it. I guess it can be re-added later.

[mpastell]

See e.g Weave for travis config that works with project.toml https://github.com/mpastell/Weave.jl/blob/master/.travis.yml

[mlhetland]

Ah – yeah, I looked at Weave (since I assumed you were up to date, given the discussion earlier :-). I just didn't want to hack around too much, and wasn't sure which parts worked with Julia 0.6 (given that some parts of it don't). If you have a suggested edit for the YAML Travis file, I'd be happy to implement it :-)

[mlhetland]

I'm having a look at it now.

[mlhetland]

All done, and ready to merge! (cc @sglyon)

[mlhetland]

Now that YAML.jl is in BioJulia, maybe @benjward can merge this?

[sglyon]

Merged thank you!

[TransGirlCodes]

Thanks for merging @sglyon

[mlhetland]

Now getting a release would be great, so this becomes available without using YAML#master… :-> (BTW, my Project.toml already says version = 0.2.2.)

[TransGirlCodes]

I’m coming to this only now of course and I don’t know how the versioning has been done previously. I tried to release a v0.2.2 in line with your Project.toml, but attobot yelled at me - the metadata url is still set to the old repo, so I’ve submitted a PR to fix that and then v0.2.2 can get released without a hitch. Best, Ben.

…

On 16 Aug 2018, at 13:03, Magnus Lie Hetland ***@***.***> wrote: Now getting a release would be great, so this becomes available without using YAML#master… :-> (BTW, my Project.toml already says version = 0.2.2.) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#54 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADPejZgACaOVT1N-gVZS2NFPY9NLARqtks5uRV-lgaJpZM4V1T9H>.

[TransGirlCodes]

Actually the version number is going to be v0.3.0, since julia 0.5 support is dropped, and previous v0.2.x versions supported julia 0.5, METADATA CI is making me increment the minor version number (as it should to be fair!).

[mlhetland]

Ah, sure. You should edit Project.toml so it has version = "3.0.0", then :-)