Replace boutdata and boututils directories with submodules

[johnomotani]

Get boutdata and boututils from the separate git repos (github.com/boutproject/boutdata and github.com/boutproject/boututils), including them as submodules.

I did check that the current versions of boututils and boutdata in next are identical to the versions in the separate git repos.

[johnomotani]

I added symlinks tools/pylib/boutdata -> externalpackages/boutdata/boutdata and tools/pylib/boututils -> externalpackages/boututils/boututils so the changes should be totally backward-compatible, as long as the submodules have been checked out.

[bendudson]

Thanks @johnomotani removing this duplication is good.

[johnomotani]

I think there's a problem with the automatic version numbering, that was recently added to boututils and boutdata, possibly related to the way I used symlinks. Investigating now...

[johnomotani]

When boutproject/boututils#16 and boutproject/boutdata#26 are merged, we can update the submodules and then the tests will pass.

[johnomotani]

The Fedora builds are failing. I need to add the Python setuptools_scm package, but I'm not sure how to do that for Fedora. It looks like there is a Fedora package https://src.fedoraproject.org/rpms/python-setuptools_scm. @dschwoerer @ZedThree where/how can I add it? Thanks!

[ZedThree]

I think you should just be able to add it here:

BOUT-dev/.travis_fedora.sh

Line 40 in 1407713

time dnf -y install dnf-plugins-core {petsc,hdf5}-${mpi}-devel /usr/lib/rpm/redhat/redhat-hardened-cc1 python3-h5py

@dschwoerer maintains the bout++ rpm which will bring in other dependencies, so it could be added there too -- that's external and I don't have access to do that.

Another option would be to pip install the packages in that script, after L40. We might actually want to do this for all the CI builds, as it will means less changes when the packages get updated.

Is setuptools_scm now a hard dependency to use the boutdata/boututils submodules in this repo?

[johnomotani]

Is setuptools_scm now a hard dependency to use the boutdata/boututils submodules in this repo?

Yes. It's not required when boutdata/boututils are installed, but since we use them straight from the git repos in the the submodules it is required.

[johnomotani]

I added python-setuptools_scm to the Fedora build as @ZedThree suggested, and setuptools_scm is now there. Now it complains that git isn't there, and therefore setuptools_scm can't get the version number for boututils. I'm a bit lost now. @dschwoerer what should we be doing with submodules in Fedora?

[ZedThree]

Just adding git to the same line should be sufficient I think? The Fedora build creates a docker image and copies the checked-out source into it, so the image doesn't actually use git.

[johnomotani]

The Fedora build creates a docker image and copies the checked-out source into it, so the image doesn't actually use git.

If it does the same for the submodules then I guess git wouldn't actually help, but if we go with the suggestion in #2198 (comment) to avoid a hard requirement on setuptools_scm then we'd get around this issue anyway.