[[!comment format=mdwn
 username="Ilya_Shlyakhter"
 avatar="http://cdn.libravatar.org/avatar/1647044369aa7747829c38b9dcc84df0"
 subject="git and submodule configs"
 date="2019-09-09T18:47:41Z"
 content="""
Here is the git config:
[[!format sh \"\"\"
(master_env_v156_py36) 14:35  [viral-ngs-benchmarks] $ git config -l | grep annex- | grep -v uuid
remote.origin.annex-ignore=true
remote.ilya-work.annex-speculate-present=true
remote.ilya-work.annex-readonly=true
remote.ilya-work.annex-sync=false
remote.dnanexus.annex-externaltype=dnanexus
remote.dnanexus.annex-cost=100.0
remote.dnanexus.annex-availability=GloballyAvailable
remote.dnanexus.annex-security-allow-unverified-downloads=ACKTHPPT
remote.dnanexus.annex-sync=false
remote.dnanexus.annex-ignore=false
remote.viral-ngs-benchmarks-s3.annex-s3=true
remote.my-ldir.annex-externaltype=ldir
remote.my-ldir.annex-cost=200.0
remote.my-ldir.annex-availability=LocallyAvailable
remote.from-ilya-work.annex-externaltype=canget
remote.from-ilya-work.annex-readonly=true
remote.from-ilya-work.annex-sync=false
remote.from-ilya-work.annex-ignore=true
remote.from-ilya-work-01.annex-externaltype=canget
remote.from-ilya-work-01.annex-ignore=true
remote.from-ilya-work-01.annex-cost=200.0
remote.from-ilya-work-01.annex-availability=LocallyAvailable
remote.from-ilya-work-01.annex-readonly=true
remote.from-ilya-work-01.annex-sync=false
remote.from-ilya-work-02.annex-externaltype=canget
remote.from-ilya-work-02.annex-readonly=true
remote.from-ilya-work-02.annex-sync=false
remote.from-ilya-work-02.annex-ignore=true
remote.from-ilya-work-03.annex-externaltype=canget
remote.from-ilya-work-03.annex-cost=200.0
remote.from-ilya-work-03.annex-availability=GloballyAvailable
remote.from-ilya-work-03.annex-speculate-present=true
remote.mygs.annex-externaltype=gs_uri
remote.mygs.annex-cost=400.0
remote.mygs.annex-availability=GloballyAvailable
remote.s3-viral-ngs-benchmarks-web.annex-s3=true
\"\"\"]]

\"stderr output is sometimes appearing before stdout output that actually comes first\" -- probably from running in an Emacs shell terminal.  But the `git-annex-sync` commands were entered by hand, not in a script, so earlier commands' output is earlier.

\"the second sync found one modified file to commit, so something must have modified that file in between the two sync runs\" -- could the first sync run have somehow modified it?

If relevant, this git-annex repo has one submodule, configured as

[[!format sh \"\"\"
[submodule \"viral-ngs\"]
        path = viral-ngs
        url = git@github.com:broadinstitute/viral-ngs.git
        branch = is-dx-benchmarks

\"\"\"]]

Maybe, add test cases for `git-annex-sync` on repos with submodules?
"""]]
