Set up our pytest suite for the codecov integration

[pstjohn]

This will require @dorotat-nv to add the CODECOV_TOKEN secret to our blossom runners.

[trvachov]

any way we can make this work without sudo? I worry run_pytest.sh will be run in some CI environment where sudo isn't available.

[trvachov]

Thinking out loud, you might want to make this bash script with a command like arg to optionally disable codecov

[pstjohn]

hmm good catch, this was a snippet from the codecov CLI help I copied + pasted in.
For now I'm fairly sure that we have sudo in our base container; the other option would be to set this up during the container build

[pstjohn]

might be easier to just install codecov-cli in our requirements-test.txt. edit, well, that leads to a conflicting httpx version. So I think the options are

1. use sudo here for now (benefits being that codecov doesn't end up in our release container, but tests might take slightly longer to run, and we use sudo.)
2. install the codecov binary as part of the docker image. Might get cached more easily, but we'd end up shipping this as part of our release image.

if we had a bionemo-testing image, this might be a bit cleaner 🤷

[trvachov]

maybe I don't know how codecov works, but where is this being uploaded?

[pstjohn]

Yeah IIUC this will upload by default to the standard codecov cloud, using our CODECOV_TOKEN to identify / authenticate

[dorotat-nv]

I would set integration with codecov as optional, controlled by a flag --codecov to run_pytest.sh script

[pstjohn]

ok, added a --no-codecov option

[pstjohn]

/build-ci

[pstjohn]

/build-ci