According to this page, git-annex should automatically convert the .git file of submodules into a symlink. However, I have a repository where on some machines, this doesn't happen.
$ file .git
.git: ASCII text
$ git-annex info
git-annex: First run: git-annex init
$ file .git
.git: ASCII text
Even more mysteriously, it works on some other checkouts of the repository on the same machine.
Ignore the remark about different behaviour on the same machine; I was looking at the wrong thing.
It does appear that GitHub Actions does not correctly fetch the
annexdirectory for submodules, which must be the source of the error.The conversion is made when you run
git annex init, which you have apparently not done..If the git-annex branch were available, it would automatically initialize and convert, so you may be on to something if you meant to say it did not fetch the git-annex branch.
It appears the
checkoutaction on GitHub Actions mangles submodules that usegit-annex. The solution is to ask the checkout action to do a deep clone: