chore: updates to satisfy ruff and sprocket lint - #322
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The Sprocket lint appears to be failing for the new As for the image bumps, this PR doesn't actually change anything, so I'm inclined not to bump the images and re-release. I think we can just update the script formatting and let that change trickle out as we make substantive changes to the images. |
a-frantz
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a-frantz
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noting that this PR does not include any CHANGELOG entries, and I think that's fine. Just one question about a java flag, otherwise LGTM
| gatk \ | ||
| --java-options \ | ||
| "-XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xms3000m -Xmx~{java_heap_size}g" \ | ||
| "-XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xms3000m -Xmx~{java_heap_size}g -XX:-UseContainerSupport" \ |
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I shared this in Slack previously (while you were out): https://stjude.slack.com/archives/C025KBTS9JQ/p1778606767391569
Essentially, it looks like, by default, the JVM detects when it is running in a container and can override your heap space settings. This seems to only really be an issue when using small heap spaces, such as during our CI tests.
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It was previously buried in #282, but I promoted it to this PR since it resolves the CI test failures in gatk4.
a-frantz
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chore: python updates for ruff
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Updates to satisfy the new version of Ruff.
Adds
setto each command block to satisfysprocket lint.Before submitting this PR, please make sure:
scripts/ordocker/directories, please ensure any image versions have been incremented accordingly!