[don't merge] Dummy PR raising pandas min version to v2 to test v2 in pathogen ci #1672
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…f cram tests Cram tests are perfect for parallelization. Each test is independend and we have 178 of them. The wrapper script allows to run tests in parallel. In my experiments, on an M1 Pro, total test time was reduced from 7m30s to 1m23s, a more than 5x speedup. I got best results with `-j8` (instead of all 10). The wrapper takes many of cram's options, one can still run tests of a single directory, for example `./parallel_cram.sh tests/functional/tree`. One caveat: it seems that iqtree creates files in the _input_ file directory. So we should copy the input files to a temporary directory before running.
…est's temp folder
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #1672 +/- ##
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+ Coverage 72.25% 72.28% +0.02%
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Files 79 79
Lines 8276 8276
Branches 1691 1691
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+ Hits 5980 5982 +2
+ Misses 2011 2009 -2
Partials 285 285 ☔ View full report in Codecov by Sentry. |
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Pathogen CI passes with v2.2.3 of pandas, nice!
https://github.com/nextstrain/augur/actions/runs/11768011018/job/32777345497?pr=1672#step:5:76 |
5 tasks
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This was really just to allow doing pathogen ci with pandas v2 @victorlin - and it passed 🎉 |
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parallel_cram.shfor parallel execution of cram testsDescription of proposed changes
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