--allow-unrelated-histories failed

[alecristia]

I've been working on a yoda repo from three machines, and had some childproject installation issues in one of them a couple of weeks ago. I now fixed that but when I try datalad update --merge I get:

[INFO ] Fetching updates for Dataset(/Users/acristia/Documents/gitrepos/RELIVAL)
merge(error): . (dataset) [CommandError(CommandError: 'git -c diff.ignoreSubmodules=none merge --allow-unrelated-histories origin/master' failed with exitcode 1)]
update(error): . (dataset) [Update of origin/master failed]
action summary:
merge (error: 1)
update (error: 1)

A google search for this error returns nothing.

[alecristia]

this cryptic message means that the local version and the version that we are trying to pull from have diverged in ways that cannot be automatically resolved. When I run git status I get a list of things that are problematic, as follows:

On branch master
Your branch and 'origin/master' have diverged,
and have 7 and 10 different commits each, respectively.
(use "git pull" to merge the remote branch into yours)
You have unmerged paths.
(fix conflicts and run "git commit")
(use "git merge --abort" to abort the merge)

followed by a list of not-offending changes in green, and a list of offending changes in red.

The solution is to deal with each of the offending issues and then run git commit or the datalad equivalent to make the two version align.

[alecristia]

for me, what that looked like was that both had modified .gitmodules. I figured I may have something wrong locally, so did: git reset HEAD .gitmodules.

I also got two things that were deleted in the GIN version but not my local version, which were embedded datasets. So to fix those cleanly, I first uninstalled the two nested datasets:

datalad uninstall -r DATASETS/el1000-metrics/
datalad uninstall -r DATASETS/laac-metrics/

This resulted in an error:

to-be-dropped dataset has revisions that are not available at any known sibling

I was quite certain that I hadn't done any intelligent in my local versions, so tried:
datalad uninstall -r --nocheck DATASETS/laac-metrics/
so that they were removed even though they had local changes not reflected on GIN.

This led to another error:

CommandError: 'git -c diff.ignoreSubmodules=none config -z -l --file .gitmodules' failed with exitcode 128
fatal: bad config line 1 in file .gitmodules

which led me to revise my initial decision: perhaps my local gitmodules was not so bad after all. So I tried to undo my reset with:
git reset 'HEAD@{1}' .gitmodules
but got:

CommandError: 'git -c diff.ignoreSubmodules=none config -z -l --file .gitmodules' failed with exitcode 128
fatal: bad config line 1 in file .gitmodules