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chore(repo): clear the 99 critical and high Dependabot alerts - #537
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VisCy had 10 critical and 89 high Dependabot alerts, all in uv.lock, and Biohub security needs them gone before the repo moves to the Biohub org. Upgrading every alerted package clears all of them. torch now needs 2.13 or later for a torch.jit.script memory corruption fix. Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
The 9 packages we publish to PyPI built wheels and sdists with no license text, because hatchling only looks for a license file in each package folder. Rename LICENSE to LICENSE.md, as in waveorder and iohub, and copy it into each package. Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
Match waveorder and iohub so reporters know to disclose vulnerabilities privately and contributors know which code of conduct applies. Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
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pymdown-extensions 12.3 made `md` a required argument of pymdownx.highlight.Highlight.__init__. mkdocstrings 1.0.4 subclasses it without passing `md`, so `zensical build` failed with "Highlight.__init__() missing 1 required positional argument: 'md'". mkdocstrings 1.0.8 builds cleanly.
srivarra
marked this pull request as ready for review
November 4, 2026 21:53
This was referenced Nov 5, 2026
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Related issue
#474. This gets VisCy ready to move to the Biohub GitHub org.
Summary
VisCy has 10 critical and 89 high Dependabot alerts, all in
uv.lock, and no security policy. This PR upgrades every alerted package, which clears all of them, and addsSECURITY.md, a code of conduct, and a PR template to match waveorder and iohub.torch now needs 2.13 or later. The lock moves torch from 2.12 to 2.15 and CUDA from 13.0 to 13.2. I tested it on an HPC GPU node (see Testing).
We can turn on secret scanning and CodeQL after the move to the Biohub org.
Testing
uv sync --all-packages --group doc && zensical build --cleanpasses.uv.lock.LICENSE.md.Checklist