Include coverage from code executed remotely

[davidwaroquiers]

In integration tests, part of the jobflow-remote code is executed in docker containers (jf execution command line within slurm/sge/pbs submission scripts). This PR activates coverage in the docker containers and copies back the coverage files locally. These are then combined with the local coverage file to give a proper coverage.

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 72.06%. Comparing base (cd38086) to head (12455c3).
Report is 7 commits behind head on develop.

❌ Your project status has failed because the head coverage (27.12%) is below the target coverage (50.00%). You can increase the head coverage or adjust the target coverage.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #255      +/-   ##
===========================================
+ Coverage    71.35%   72.06%   +0.70%     
===========================================
  Files           50       50              
  Lines         6749     6758       +9     
  Branches      1083     1084       +1     
===========================================
+ Hits          4816     4870      +54     
+ Misses        1568     1514      -54     
- Partials       365      374       +9     

Flag	Coverage Δ
all_tests	27.12% <ø> (-44.24%)	⬇️
db_tests	66.91% <ø> (-0.01%)	⬇️
integration_tests	45.62% <ø> (+0.04%)	⬆️
unit_tests	27.12% <ø> (+13.74%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

see 6 files with indirect coverage changes

[ml-evs]

Looks nice, thanks @davidwaroquiers!

My only general comment is that perhaps the "remote" coverage could be flagged as such -- i.e., take the coverage file from docker as a separate xml and upload it to codecov with a separate flag before combining it with the rest. Might help some future debugging, though can definitely be done in a different PR! Otherwise happy to approve pending the conflict fix and discussion of Python versions.

[davidwaroquiers]

Looks nice, thanks @davidwaroquiers!

My only general comment is that perhaps the "remote" coverage could be flagged as such -- i.e., take the coverage file from docker as a separate xml and upload it to codecov with a separate flag before combining it with the rest. Might help some future debugging, though can definitely be done in a different PR! Otherwise happy to approve pending the conflict fix and discussion of Python versions.

Thanks for your review!

This can be done and we can discuss it. My only "concern" is that in any case, this will only ever cover a "small" part of the code as the "remote" coverage is only about the "jf execution" command (hidden command from the user btw, it doesn't appear in the help as it is only meant to be used "internally" within the submitted script). Where would you see this to help debugging ?