Use zstd from stdlib/backport#2009
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zstandard is used in tests/io/test_file.py. It had been indirectly installed through xopen's zstd extra, but that extra is no longer provided as of xopen version 2.1.0.
Use the built-in zstd support in Python 3.14 and the equivalent backport for older versions.
The latest version uses the built-in zstd support in Python 3.14 and the equivalent backport for older versions.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
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Coverage 72.96% 72.96%
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Branches 2102 2102
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joverlee521
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joverlee521
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Thanks for the quick fix!
| extras_require = { | ||
| 'dev': [ | ||
| "cram >=0.7", | ||
| "backports.zstd; python_version < '3.14'", |
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Makes sense to include as dev dependency in augur, but we'll need to figure out downstream uses of the indirect dependency (e.g. pathogens in GH search).
I think the least disruptive is to add zstandard to the runtimes + ambient instructions
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OH zstandard is already included in conda-base, so just need to update docker-base and ambient instructions.
I'll make PRs.
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conda-base only includes zstd (command line tool), not zstandard (Python package). I think we can replace the former with the latter (depends on the former).
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Ah, thanks for pointing out the distinction. Will update conda-base.
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The first commit addresses test failures that came with release of xopen 2.1.0 (specifically pycompression/xopen@755210b).
The other two commits follow through with related improvements, but are not strictly necessary.
Checklist