Actions fix for releases

[marohrdanz]

This is a fix for the failed action during the release of 2.24.0.

Analysis showed the failure was due to the code trying to run on what appears to be a minified version of custom.js, and getting to the part for the cbioportal logo:

   logo: "https://www.cbioportal.org/images/cbioportal_logo.png",

This part includes the search string "images/", which is hard-coded into CompilerUtilities.java, therefore triggering an attempt to copy a file 'cbioportal_logo.png'. Of course that file does not exist in this repo, resulting in failure of the action.

For reasons I do not understand, changing the runner from macOS to ubuntu eliminates the problem (I tested in a personal fork of this repo).

In addition to this "fix", this pull request

• Adds workflow_dispatch to allow each workflow to be triggered manually
  • This allows us to create the artifacts w/o creating a new release or push if desired
• Specifies ubuntu 22.04 for the runner instead of just using the latest stable version
• Updates the GitHub actions "checkout" and "setup-java" from v2 -> v3
  • This eliminates the deprecation notice: Node.js 12 actions are deprecated. Please update the following actions to use Node.js 16: actions/checkout@v2, actions/setup-java@v2. For more information see: https://github.blog/changelog/2022-09-22-github-actions-all-actions-will-begin-running-on-node16-instead-of-node12/.
• Replaces the deprecated set-output command
  • This eliminates the deprecation notice: The set-output 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/

[ChrisWakefield]

@jmelott To what are you referring? "runs-on: ubuntu-latest" ?

[jmelott]

@ChrisWakefield Yes, I was referring to "runs-on: ubuntu-latest".

[ChrisWakefield]

For reasons I do not understand, changing the runner from macOS to ubuntu eliminates the problem

@marohrdanz Sorry Mary. Too mysterious. I also looked at the code and the contents of the custom.js file. Is it possible custom.js became different for your personal fork version? (and the past versions?). I see no good reason why changing "runs-on" should give any different result.

Beyond this, CompilerUtilities.java leaves much to be desired.

[marohrdanz]

@jmelott I had those same concerns about 'latest'. My logic for using it was

• It's just a runner, and we're not using anything particularly fancy installed in the operating system
• Using 'latest' might help with fewer updates because of deprecations and security updates.

I'm open to alternatives: https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners

[marohrdanz]

@ChrisWakefield My instinct was some cached info, but experimentation suggested otherwise.

[ChrisWakefield]

@jmelott

Yes, I was referring to "runs-on: ubuntu-latest".

I think we want it to fail so the surprise comes as early as possible. Ideally, the condition you're flagging gets noticed before a production release. (...Hence Mary's change to "Adds workflow_dispatch to allow the workflow to be triggered manually").

That designation ("ubuntu-latest") is what github actions calls them. According to them: "Before moving the-latest label to a new OS version we will announce the change and give sufficient lead time for users to update their workflows". (https://github.com/actions/runner-images)

To clarify, I’m for leaving -latest in place (for THIS).

[ChrisWakefield]

We decided to proceed with the runner in ubuntu. Later we will restore using "-latest" for the runs-on, or not. An issue should be opened about macos and windows runners give a failure.