Comments (5)
pandas release notes indicate 0.18 had breaking changes, and I did not audit 0.18's changes, or the breaking changes of even newer releases, against augur's usage of pandas. This may be me being over-conservative. It would be less conservative, but still reasonable, to set minimums that are known good and accept the possibility of breakage from new versions we haven't tried.
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on various systems I had 0.19, 0.20, 0.21 installed. haven't run into any problems. I think minimum req are fine. If we are incompatible with latest numpy, scipy, pandas, we better find out about it sooner rather than later.
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Nod. My previous flurry of changes to deps were all based around the previous requirements.txt
files that were kept manually pinned to exact versions. This change will be a further departure from those, but I think that's ok. @trvrb?
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I would say to upgrade pandas version across the board. Keep it the same for fauna/requirements.txt
, augur/requirement.txt
and augur/setup.py
. And quickly confirm nothing breaking with upgrades. Would be nice to keep dependency versions consistent across components. Certainly makes pip
installs easier.
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I removed the upper bound in augur. we only use it to read csv....
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Related Issues (20)
- [export] format confidence values to save bytes
- augur curate format-dates should mask empty date fields
- augur curate I/O: verify NDJSON records have the same fields HOT 2
- augur curate parse-genbank-location: Remove `database` check
- Improve typing experience with CI HOT 4
- Update docs for new augur curate subcommands HOT 2
- Improve help output for augur curate subcommands
- Branch length units in augur refine output HOT 1
- Generate CLI documentation files? HOT 4
- augur curate rename: Add option to drop fields/columns HOT 3
- augur curate parse-genbank-location with an empty location field causes inconsistent field errors
- Update pinned dependencies HOT 2
- Officially support python 3.12: test for it and add trove classifier
- Update .mailmap HOT 3
- `augur curate` could have a more helpful error message
- update build docs to mention checking `conda-base` build summary
- augur curate: improve metadata header parsing HOT 1
- [traits] cmd should warn when metadata is completely missing for a given node HOT 3
- No standard test environment HOT 7
- tree: Update Cram tests
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