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Add python 3.10 CI tests
Changelog Entry
To be copied to the draft changelog by merger:
Add CI tests for python 3.10 to address issue #3819
Reviewer Checklist
- [ ] Make sure it is coming from
issues/XXXX-fix-the-thingin 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.
- [ ] If it is coming from an external repo, make sure to pull it in for CI with:
- [ ] Read through the code changes. Make sure that it doesn't have:
- [ ] Addition of trailing whitespace.
- [ ] New variable or member names in
camelCasethat want to be insnake_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.
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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.
Looks like it's failing because it's pulling in a pyparsing that's too old to work on 3.10. I think pyparsing comes from packaging, which we depend on transitively from somewhere. But since at some point we import packaging ourselves anyway, we could just add a dependency on packaging>=21.1, which would have https://github.com/pypa/packaging/commit/286458816562e119f15ea075d18d87ef1eb55988 and support 3.10 (presumably along with its dependencies). Then we could fix https://github.com/DataBiosphere/toil/issues/3617 at the same time.