natverse / nat

NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

https://natverse.org/nat/

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GitHub actions with coveralls #475

Closed dokato closed 3 years ago

dokato commented 3 years ago

Related to #450.

I had a quick try on github actions, I can't quite figure out why Windows CMTK installation fails... I also temporarily switched of ubuntu release as it was taking forever to pull down dependencies. This should work no problem though. If we want to get unblock for now, I suggest testing on mac/ubuntu now and figure the rest later?

dokato commented 3 years ago

Also @jefferis I need a bit more info on what travisbuildchildren.sh supposed to do?

codecov[bot] commented 3 years ago

Codecov Report

:exclamation: No coverage uploaded for pull request base (master@a155984). Click here to learn what that means. The diff coverage is n/a.

:exclamation: Current head 6ae8c70 differs from pull request most recent head 0bd9463. Consider uploading reports for the commit 0bd9463 to get more accurate results

@@            Coverage Diff            @@
##             master     #475   +/-   ##
=========================================
  Coverage          ?   76.89%           
=========================================
  Files             ?       47           
  Lines             ?     5856           
  Branches          ?        0           
=========================================
  Hits              ?     4503           
  Misses            ?     1353           
  Partials          ?        0

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update a155984...0bd9463. Read the comment docs.

jefferis commented 3 years ago

Thanks so much @dokato. I would like to merge quickly, but just wanted to check re coverage. I have been using coveralls for status (there is a badge) but not as a CI check. Were you suggesting a codecov CI check? This might be good.

Also could you summarise the windows issues? I did not have a Windows build in the past, but it might be nice to add one.

dokato commented 3 years ago

Were you suggesting a codecov CI check? This might be good.

Ah, force of habit. I used in previous projects codecov mainly. I can change to coveralls, no problem.

With windows the error comes from installing CMTK. The excerpt from logs is below.

CMake Error at Utilities/numdiff-5.2.1/CMakeLists.txt:155 (MESSAGE):
  Declaration of vsprintf() not present!

You can see the whole logs here. I wasn't sure if there's an easy way to install from exe using windows command line.

BTW I checked also curls from travisbuildchildren.sh, they seem not to work now. Do we need some replacement here too?

dokato commented 3 years ago

@jefferis I had a first go with coveralls, looks like we need to have COVERALLS_TOKEN set up: https://github.com/r-lib/covr#coveralls. It probably wasn't needed for travis.

Now it failed:

Error in covr::coveralls() : 
  Failed to upload coverage data. Reply by Coveralls: Couldn't find a repository matching this job.

jefferis commented 3 years ago

@dokato, I added the COVERALLS_TOKEN as a secret and reran the jobs, but that still failed. I forgot, but I think it needs to be exposed explicitly in the workflow doc.

jefferis commented 3 years ago

This is really frustrating re coveralls. The best lead I have found is here. But I think we should already be fulfilling everything that he says.

dokato commented 3 years ago

Thanks @jefferis, actually just before lunch I found this thread with your comments from April ;) I'm testing 2 more things from this user advice. If that doesn't work, are you happy to migrate to codecov?

jefferis commented 3 years ago

If that doesn't work, are you happy to migrate to codecov?

Sure. I do have a lot of coverage history but the end of the day we're mostly interested in current state and the next delta.

dokato commented 3 years ago

Before I do that, are you sure @jefferis that the coveralls repo token is correctly set up as secret? I tested on my repo (todor) locally and with GA and it worked just fine: https://github.com/dokato/todor/runs/3036482539?check_suite_focus=true#step:12:14 I.e.

> Rscript -e 'covr::coveralls(service_name="jenkins")' 
$message
[1] "Job ##3.1"

$url
[1] "https://coveralls.io/jobs/83379076"

Could you share with me this token through some vault? I don't have privilidges for nat to see it here.

jefferis commented 3 years ago

Thanks for all of this @dokato. As you can see I have just gone with your codecov branch – not worth going against the current for something not mission critical!