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ci: drop pytest in favor of Sprocket test#263

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a-frantz wants to merge 73 commits intomainfrom
demonstration/sprocket-test
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ci: drop pytest in favor of Sprocket test#263
a-frantz wants to merge 73 commits intomainfrom
demonstration/sprocket-test

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@a-frantz a-frantz commented Sep 3, 2025

This PR is for demonstration purposes of the RFC document here

this PR has morphed from a demonstration into a real PR for swapping our test infra from pytest to Sprocket. Still a WIP as not all the tests are written yet and it has not been hooked into CI yet

@a-frantz a-frantz force-pushed the demonstration/sprocket-test branch from 535b997 to 7bc1e3a Compare October 8, 2025 13:13
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@a-frantz a-frantz changed the title DEMO: sprocket test example ci: drop pytest in favor of Sprocket test Dec 29, 2025
@a-frantz a-frantz requested a review from adthrasher April 15, 2026 16:08
@a-frantz a-frantz marked this pull request as ready for review April 15, 2026 16:08
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all tests passing 🎉
@adthrasher for local testing, I picard::mark_duplicates uses more memory than available on my MPB, so I've annotated that test with high_mem. Running sprocket dev test -f high_mem at the root of this branch should be all green. I'm seeing all green on the cluster as well. For executing tests there, try a parallelism = 300 to get a good balance of speed and resource utilization. See stjude-rust-labs/sprocket#821 for why just lifting the parallelism throttle completely doesn't work

Comment thread .github/workflows/build-and-test.yaml
Comment thread .github/workflows/sprocket-lint.yaml
Comment thread tools/picard.wdl
Comment on lines -203 to -205
String stringency_arg = if index_validation_stringency_less_exhaustive
then "--INDEX_VALIDATION_STRINGENCY LESS_EXHAUSTIVE"
else ""
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I don't recall what this parameter does. Why are we removing the argument?

adthrasher added a commit that referenced this pull request Apr 24, 2026
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Note to self: GATK4 tests work locally

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4 participants