Updating finding new dockerfiles and building them to test

[erinyoung]

EDIT : NOW READY FOR REVIEW!!!

This is not a new docker container. There are some depreciation warnings to our github actions for new dockerfiles in PR. I need to test these, but this is what it may look like.

[erinyoung]

For future reference (if it takes me forever to come back to this), this is how github actions is getting variables from actions: https://hynek.me/til/set-output-deprecation-github-actions/

[erinyoung]

Also, https://github.com/ewels/MultiQC/blob/a8cbadef13bbc2201b54da072fd00be0c061f273/.github/workflows/multiqc_linux.yml has an awesome way to put a variable in the action name. This is helpful when looking for specific actions.

[erinyoung]

Also, I want to test out run-name https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions

[erinyoung]

Alright : this is now ready for review.

This is phase 1/n of the facelift of StaPH-B/docker-builds.

What this does :

• adds more information to "manual deploy"
• brings "manual deploy" up to date to remove all depreciation warnings
• brings "manual test" up to date to remove all depreciation warnings
• brings the current "find_dockerfiles" github actions workflow up-to-date to remove all depreciation warnings
  • looks for the following in either the dockerfile or built image:
  • labels
  • app and test layers
  • WORKDIR

What this PR does NOT do :

• use a workflow in parallel (still not supported by github actions - even with version 3)

[erinyoung]

The build-to-test changes seem to work great (https://github.com/StaPH-B/docker-builds/actions/runs/3622848226/jobs/6108036499)

[erinyoung]

I've updated all the "manual deploy" steps, as well. There are still warnings, but they aren't something I can do something about unless we want to go with some other command than docker/build-push-action. https://github.com/StaPH-B/docker-builds/actions/runs/3622937452

Run docker/build-push-action@v2
Warning: The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
Docker info
Warning: The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

[kapsakcj]

Apologies for the delay in reviewing, I'll review this PR ASAP

[kapsakcj]

Love this addition, it makes the names of GH Action workflow much more descriptive than "Manual Deploy"

[erinyoung]

I know! I saw it in multiqc's repo. I feel like it's going to make deploy better.

[kapsakcj]

OK, so here's what testing I've done:

First - I ran the workflow .github/workflows/manual-deploy.yml using SPAdes 3.15.4 as the guinea pig dockerfile. I did not ask it to overwrite the :latest image tag, just update the dockerhub and quay tags for :3.15.4

It failed due to the cab.spbu.ru server failling to properly serve up the files requested. SO I opted to edit the dockerfile on this PR to download from GitHub instead of the Russian server (9a7787a) and watch the GHActions cascade occur.

Second - The workflows (find_new_dockerfiles and build_to_test) passed as expected after I edited the spades 3.15.4 dockerfile ✔️ , so....

Third I ran the manual-deploy.yml workflow again to test now that it's switched to downloading from Github. log here: https://github.com/StaPH-B/docker-builds/actions/runs/3741894625

The deploy workflow ran as expected this time. The new checks for ps and ca-certificates worked as expected as well as the checks for app and test layers of dockerfiles. Also the check for WORKDIR label was successful

Lastly - I pushed a commit to update to docker/build-push-action@v3 for build-to-deploy.yml workflow (78d3abd)

^ After making this commit, I re-ran manual-deploy.yml with the same spades 3.15.4 dockerfile as a test, just to make sure things go as expected. They did 🎉 . Log here: https://github.com/StaPH-B/docker-builds/actions/runs/3742167477/jobs/6352761688

I'm good with merging this PR

[kapsakcj]

And lastly, regarding the save-state warning associated with docker/build-push-action: I did not see the warning after upgrading to the docker/build-push-action@v3. I believe the maintainers of that workflow resolved the issue docker/build-push-action#703 (comment)

[erinyoung]

Yay!

[kapsakcj]

I'll let you delete the dev branch if you're finished with it