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docs(repo): meet CZI open source requirements and clear all Dependabot alerts - #594
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All 140 open Dependabot alerts on waveorder came from packages pinned in uv.lock, 53 of them high or critical. Upgrade each alerted package to its newest compatible release, and require torch>=2.13.0, the first release with the torch.jit.script memory corruption fix (GHSA-rrmf-rvhw-rf47). PyPI's Linux torch wheels have used CUDA 13 since 2.11. Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
Add a security policy, the Contributor Covenant code of conduct, and a pull request template, rename LICENSE to LICENSE.md, and point the README and contributing guide at them. Matches what iohub adopted for the same requirements. Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
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Nov 2, 2026
srivarra
marked this pull request as ready for review
November 2, 2026 22:11
talonchandler
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Nov 2, 2026
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Thanks for handling @srivarra
This was referenced Nov 5, 2026
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Related issue
N/A. Gets waveorder ready for the move to the Biohub GitHub org.
Summary
waveorder fell short of the CZI open source requirements. It had 140 open Dependabot alerts, 53 of them high or critical, and it had no security policy or code of conduct. This PR fixes both the same way iohub did.
It upgrades every alerted package in
uv.lockand addsSECURITY.md, the Contributor Covenant, a PR template, and a project status line.LICENSEbecomesLICENSE.md.torch now requires 2.13.0 or later for a
torch.jit.scriptmemory corruption fix. Its PyPI Linux wheels use CUDA 13, so GPU nodes need a CUDA 13 driver.We still need secret scanning to confirm the git history has no secrets in it. We can turn it on after the repo moves to the Biohub org.
Testing
uv run pyteston Python 3.13: 721 passed, 2 skipped, 2 xfailed.uv.lock, and I think it's good to go.LICENSE.mdas its license file.Checklist