Fix CI

[maxkfranz]

General information

This PR fixes CI so that everything is green.

Associated issues:

• 140

• 118

• 139

Checklist

Author:

• [x] One or more reviewers have been assigned.
• [x] Automated tests have been included in this pull request, if possible, for the new feature(s) or bug fix.
• [x] The associated GitHub issues are included (above).
• [x] Notes have been included (below).

Reviewers:

• [x] All automated checks are passing (green check next to latest commit).
• [x] At least one reviewer has signed off on the pull request. Reviewers have two business days to review the pull request, after which the author may merge in the pull request unilaterally.

Notes

Broad summary (details in commits)

• Fixes CI w.r.t.
  • tests
  • installation
• Remove support for TravisCI in favour of GitHub Actions. Travis doesn't look like a good longterm solution going forward.

[maxkfranz]

@d2fong, a good test to verify that this PR is sufficient would be to merge in fix/no-red into your PR's branch. If your PR is green after that, then it's probably good.

[d2fong]

One of the tests fails for me still:

  1) History (Snapshots)
       creates thumbnails:
     Error: Timeout of 15000ms exceeded. For async tests and hooks, ensure "done()" is called; if returning a Promise, ensure it resolves. (/Users/dylan/src/idekerlab/cytoscape-explore/test/history-test.js)
      at listOnTimeout (node:internal/timers:557:17)
      at processTimers (node:internal/timers:500:7)

[d2fong]

But I ran it again and it passes. Maybe the time limit should be increased?

[maxkfranz]

15s is too long. If it takes that long, the user is going to be left hanging. Ultimately still a test failure in my opinion. It’s hard to get puppeteer setups just right

We could comment out that test and make an issue for the problem if we want to move forward quickly

On Mar 3, 2022, at 19:21, Dylan Fong @.***> wrote:

 But I ran it again and it passes. Maybe the time limit should be increased?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.

[maxkfranz]

The test is commented out in 608f827. #145 needs to be fixed before dockerised CI instances will run correctly

[maxkfranz]

@d2fong, do you want to put the patch for #145 in this PR? It looks like GH Actions was able to reproduce the checksum error affecting docker: https://github.com/cytoscape/cytoscape-explore/runs/5452877547?check_suite_focus=true

[d2fong]

Ok I pushed a fix. We were working on refactoring the monorepo stuff so the dependency broke. Sorry.

[d2fong]

@keiono, how would I update the ndex-client dependency using the new monorepo?

[d2fong]

@maxkfranz I think there is an issue with installing a git repo branch as a dependency when running the dockerized CI instance. Is this by design or is it ok to use branches from a git repo as a dependency?

[maxkfranz]

I think you can use a git repo as a dependency, but the package manager is strict with the lock files now (for security etc.). It looks like there's a hash check that's failing. So, we need the hash to be the same as what's installed when npm install was used to add to package.json.

How we make the hash consistent is up to you guys. Here are some possibilities:

(1) Use a stable branch in your repo that's not changing. Every time you change it, you have to update the lock file here in CE. I'm not crazy about this option, since it's easy to get things out of sync and the failures can be non-obvious.

(2) Point to a specific commit in the git address instead of a branch.

(3) Publish to npm so version numbers can be used. Maybe a beta version like 1.0.0-beta1?

Maybe you've got a better/simpler suggestion to get the hash right than these three? Whatever works

[d2fong]

I think the issue might be related to docker and git not having the right permissions.

npm ERR! /usr/bin/git ls-remote -h -t ssh://git@github.com/ndexbio/ndex-js-client.git
npm ERR! 
npm ERR! No user exists for uid 1001
npm ERR! fatal: Could not read from remote repository.
npm ERR! 
npm ERR! Please make sure you have the correct access rights
npm ERR! and the repository exists.
npm ERR! 
npm ERR! exited with error code: 12[8](https://github.com/cytoscape/cytoscape-explore/runs/5453467076?check_suite_focus=true#step:6:8)

[maxkfranz]

Could we use a public https address instead of a private ssh one? Is ssh needed if we're only cloning?

[d2fong]

Thats weird because I specified it as git+https://github.com/ndexbio/ndex-js-client.git#develop

[d2fong]

Ok Kei and Jing updated the proper version/monorepo

[maxkfranz]

@jingjingbic, @d2fong, @chrtannus -- you can merge dev into your branches for your PRs now to help make your PRs green

[chrtannus]

Great! I've just merged dev into feature/recent-networks and the PR and it's all green now.