Add AMReX as a git submodule

[maximumcats]

PR summary

With #760, this completes #651 by adding AMReX as a git submodule of Castro.

PR checklist

• test suite needs to be run on this PR
• this PR will change answers in the test suite
• all functions have docstrings as per the coding conventions
• the CHANGES file has been updated
• if appropriate, this change is described in the docs

[adam-m-jcbs]

Need any help with this? I've used submodules (and subtrees) pretty extensively in my repos.

[maximumcats]

Fortunately this change is fairly simple, though if you want to test it out to make sure I didn't miss anything, that's appreciated.

A question though -- in the interests of long term stability, should I create a subdirectory where we start putting dependencies (for now, just AMReX and Microphysics, but later potentially other things like pynucastro, Hypre, etc.)? If so what should it be called? "external", perhaps?

[zingale]

I like external/

[maximumcats]

Also, is it correct that once you have downloaded the submodule(s), git pull --recurse-submodules is all that is needed to keep the full repo (and submodules) up to date? Or is there some additional step needed to actually update the submodules to the latest commit after the pull?

[adam-m-jcbs]

external/ is not bad. My preference would be submodules/, but that may be less clear to new users. It may become inaccurate, too, if we root things there other than submodules eventually.

[adam-m-jcbs]

@maxpkatz apologies for the delay in answering, but re: git pull --recurse-submodules

Both git clone --recurse-submodules and git pull --recurse-submodules I believe can achieve what you want. Ultimately, what we care about is what happens when you do git submodule update. The behavior for this should be configured by us in .gitmodules in the superproject (Castro).

The main relevant documentation is man git-submodules and man gitmodules (for the .gitmodules config file). Changing .gitmodules will impact what happens when we do git pull --recurse-submodules. By default, a checkout is performed. This can be nice for stability, because it checks out the specific commit registered in the superproject. However, this means it will not pull the current head of development or similar. Instead, submodules using the checkout update strategy will ALWAYS point to the specific commit referenced in the superproject (when you cd into the submodule, you'll find it in a detached head state). Until you update the superproject, it will keep going back to that commit.

We may want to instead use the rebase strategy. In this case, the current branch of the submodule will be rebased onto the commit recorded in the superproject. The nice part of this is that it keeps AMReX even with the current version of development or whichever branch the submodule is on. The bad part is it may rebase things that break within the superproject but didn't break when they ran tests on AMReX. This is a theoretical possibility, but maybe our development and merging practices are good enough this isn't a worry?

Ultimately, we should encourage people to use a "pull" model with submodules. It is WAY easier to manage only pulling in the latest tested release of submodules into a superproject than trying to let people push changes to submodules from within the superproject. Technically, yes, you could modify AMReX within Castro and push those changes to AMReX. In practice, this is dangerous and error-prone. It shouldn't be done by people that aren't at least intermediate experts in git and probably even in git submodules.

I hope that helps.

[adam-m-jcbs]

I did a quick check of our .gitmodules. To the best of my knowledge, it implies we're currently using the checkout submodule update strategy, as I think this is the default and we do not specify an update strategy for our submodules.