toil icon indicating copy to clipboard operation
toil copied to clipboard

Issues/3819 python310

Open Hexotical opened this issue 3 years ago • 2 comments

Changelog Entry

To be copied to the draft changelog by merger:

python 3.10 testing

Reviewer Checklist

  • [ ] Make sure it is coming from issues/XXXX-fix-the-thing in the Toil repo, or from an external repo.
    • [ ] If it is coming from an external repo, make sure to pull it in for CI with:
      contrib/admin/test-pr otheruser theirbranchname issues/XXXX-fix-the-thing
      
    • [ ] If there is no associated issue, create one.
  • [ ] Read through the code changes. Make sure that it doesn't have:
    • [ ] Addition of trailing whitespace.
    • [ ] New variable or member names in camelCase that want to be in snake_case.
    • [ ] New functions without type hints.
    • [ ] New functions or classes without informative docstrings.
    • [ ] Changes to semantics not reflected in the relevant docstrings.
    • [ ] New or changed command line options for Toil workflows that are not reflected in docs/running/{cliOptions,cwl,wdl}.rst
    • [ ] New features without tests.
  • [ ] Comment on the lines of code where problems exist with a review comment. You can shift-click the line numbers in the diff to select multiple lines.
  • [ ] Finish the review with an overall description of your opinion.

Merger Checklist

  • [ ] Make sure the PR passes tests.
  • [ ] Make sure the PR has been reviewed since its last modification. If not, review it.
  • [ ] Merge with the Github "Squash and merge" feature.
    • [ ] If there are multiple authors' commits, add Co-authored-by to give credit to all contributing authors.
  • [ ] Copy its recommended changelog entry to the Draft Changelog.
  • [ ] Append the issue number in parentheses to the changelog entry.

Hexotical avatar Sep 14 '22 18:09 Hexotical

Rerunning tests with the updated CI/CD image.

DailyDreaming avatar Sep 21 '22 17:09 DailyDreaming

I think this looks good.

@DailyDreaming Do we actually want to drop the other Python versions from the main tests? Should we maybe keep 3.7 so we do the highest and lowest ostensibly supported versions?

Hmmm... maybe we could keep the old python tests, but reduce the time. These tests have been taking 100+ minutes each, unfortunately, and I think for older versions of python, we should run a much shorter set of tests, and keep the extensive testing to the main python version we've pinned. This limits the instances we can provision (and increases cost), for far too long per run I think.

Overall, we should probably re-organize the tests and try to reduce the time as they've gotten a little out of hand in runtime.

DailyDreaming avatar Sep 27 '22 19:09 DailyDreaming

It looks like one of the CWL conformance tests timed out on Kubernetes:

https://ucsc-ci.com/databiosphere/toil/-/jobs/24890

Test 287 timed out: toil-cwl-runner --clean=always --logDebug --statusWait=10 --setEnv=SINGULARITY_DOCKER_HUB_MIRROR --batchSystem=kubernetes --outdir=/tmp/tmpj9i3nalu tests/conditionals/cond-wf-003_nojs.cwl tests/conditionals/test-false.yml
Pass through pattern with pickValue: first_non_null; 'when' is false'; no javascript

I don't think this is related to the PR being tested.

adamnovak avatar Oct 14 '22 22:10 adamnovak